hooke/main.tex: Rework lead-in paragraph to avoid 'uninteresting'

[thesis.git] / src / root.bib

@string{AAPT = "AAPT"}
@string{AcP = "Academic Press"}
@string{CoRR = "arXiv Computing Research Repository"}.
@string{ACM = "Association for Computing Machinery"}
@string{KAstrom = "{\AA}str{\"o}m, K.~J."}
@string{ACM:SIGCSE = "ACM Special Interest Group on Computer Science Education Bulletin"}
@string{ACM:CSur = "ACM Computing Surveys"}
@string{ACS:ChemBiol = "ACS Chem Biol"}
@string{AIP = "AIP"}
@string{APL = "Applied Physics Letters"}
@string{DAbramavicius = "Abramavicius, Darius"}
@string{JFAbril = "Abril, J. F."}
@string{JAbu-Threideh = "Abu-Threideh, J."}
@string{KAdachi = "Adachi, Kengo"}
@string{MDAdams = "Adams, M. D."}
@string{AW = "Addison-Wesley Longman Publishing Co., Inc."}
@string{AdvExpMedBiol = "Advances in Experimental Medicine and Biology"}
@string{SAinavarapu = "Ainavarapu, Sri Rama Koti"}
@string{DAioanei = "Aioanei, Daniel"}
@string{TRAlbrecht = "Albreacht, T.~R."}
@string{AMB = "Algorithms for molecular biology: AMB"}
@string{FAli = "Ali, F."}
@string{JFAllemand = "Allemand, Jean-Fran\c{c}ois"}
@string{DAllen = "Allen, D."}
@string{MAllen = "Allen, Mark D."}
@string{RAlon = "Alon, Ronen"}
@string{PAmanatides = "Amanatides, P."}
@string{NMAmer = "Amer, Nabil M."}
@string{AJP = "American Journal of Physics"}
@string{APS = "American Physical Society"}
@string{AS = "American Scientist"}
@string{ASA = "American Statistical Association"}
@string{HAn = "An, H."}
@string{KNAn = "An, Kai-Nan"}
@string{ABioChem = "Analytical biochemistry"}
@string{BAndreopoulos = "Andreopoulos, Bill"}
@string{IAndricioaei = "Andricioaei, Ioan"}
@string{ACIEE = "Angew. Chem. Int. Ed. Engl."}
@string{ARBBS = "Annu Rev Biophys Biomol Struct"}
@string{ARBC = "Annual Review of Biochemistry"}
@string{DAnselmetti = "Anselmetti, Dario"}
@string{AAntoniadis = "Antoniadis, Anestis"}
@string{AMC = "Applied Mathematics and Computation"}
@string{SArcidiacono = "Arcidiacono, S"}
@string{CArciola = "Arciola, Carla Renata"}
@string{ABArtyukhin = "Artyukhin, Alexander B."}
@string{DAruliah = "Aruliah, Dhavide A."}
@string{SAsakawa = "Asakawa, S."}
@string{AAwe = "Awe, A."}
@string{SBedard = "B\'edard, Sabrina"}
@string{WBaase = "Baase, Walter A."}
@string{YBaba = "Baba, Y."}
@string{HBaden = "Baden, H."}
@string{CBadilla = "Badilla, Carmen L."}
@string{VBafna = "Bafna, V."}
@string{BBagchi = "Bagchi, B."}
@string{MBalamurali = "Balamurali, M. M."}
@string{DBaldwin = "Baldwin, D."}
@string{ABaljon = "Baljon, Arlette R. C."}
@string{RBallerini = "Ballerini, R."}
@string{RMBallew = "Ballew, R. M."}
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@string{GBaneyx = "Baneyx, Gretchen"}
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@string{WBBarbazuk = "Barbazuk, W. B."}
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@string{IBarrow = "Barrow, I."}
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@string{FBenedetti = "Benedetti, Fabrizio"}
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@string{DRBentley = "Bentley, D. R."}
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@string{DBerk = "Berk, D."}
@string{FBerkemeier = "Berkemeier, Felix"}
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@string{RBest = "Best, Robert B."}
@string{GBethel = "Bethel, G."}
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@string{KBiddick = "Biddick, K."}
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@string{BIOINFO = "Bioinformatics (Oxford, England)"}
@string{Biomet = "Biometrika"}
@string{BPJ = "Biophysical Journal"}
%string{BPJ = "Biophys. J."}
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@string{EBranscomb = "Branscomb, E."}
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@string{SBroedel = "Broedel, Sheldon E."}
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@string{BrooksCole = "Brooks/Cole"}
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@string{GBussi = "Bussi, Giovanni"}
@string{CBustamante = "Bustamante, Carlos"}
@string{YBustanji = "Bustanji, Yasser"}
@string{HJButt = {Butt, Hans-J\"urgen}}
@string{CUP = "Cambridge University Press"}
@string{MCaminha = "Caminha, M."}
@string{ICampbell = "Campbell, Iain D."}
@string{MJCampbell = "Campbell, M. J."}
@string{DSCannell = "Cannell, D.~S."}
@string{YCao = "Cao, Yi"}
@string{MCapitanio = "Capitanio, M."}
@string{MCargill = "Cargill, M."}
@string{PCarl = "Carl, Philippe"}
@string{BACarnes = "Carnes, B. A."}
@string{JCarnes-Stine = "Carnes-Stine, J."}
@string{MCarrionVazquez = "Carrion-Vazquez, Mariano"}
@string{CCarter = "Carter, C."}
@string{ACarver = "Carver, A."}
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@string{PCaulk = "Caulk, P."}
@string{CCecconi = "Cecconi, Ciro"}
@string{ACenter = "Center, A."}
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@string{HSChan = "Chan, H.~S."}
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@string{CHChang = "Chang, Chung-Hung"}
@string{EChapman = "Chapman, Edwin R."}
@string{RCharlab = "Charlab, R."}
@string{KChaturvedi = "Chaturvedi, K."}
@string{AChauhan = "Chauhan, A."}
@string{VPChauhan = "Chauhan, V.~P."}
@string{CChauzy = "Chauzy, C."}
@string{SChe = "Che, Shunai"}
@string{CEC = "Chemical Engineering Communications"}
@string{CHEMREV = "Chemical reviews"}
@string{CHEM = "Chemistry (Weinheim an der Bergstrasse, Germany)"}
@string{CPC = "Chemphyschem"}
@string{HCChen = "Chen, H. C."}
@string{LChen = "Chen, L."}
@string{XNChen = "Chen, X. N."}
@string{XiChen = "Chen, Xinyong"}
@string{XuChen = "Chen, Xuming"}
@string{JFCheng = "Cheng, J. F."}
@string{MLCheng = "Cheng, M. L."}
@string{VGCheung = "Cheung, V. G."}
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@string{AChinwalla = "Chinwalla, A."}
@string{FChow = "Chow, Flora"}
@string{JChoy = "Choy, Jason"}
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@string{XChu = "Chu, Xueying"}
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@string{CEP = "Control Engineering Practice"}
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@string{YCui = "Cui, Y."}
@string{COSB = "Current Opinion in Structural Biology"}
@string{COCB = "Current Opinion in Chemical Biology"}
@string{LCurry = "Curry, L."}
@string{CDahlke = "Dahlke, C."}
@string{FDahlquist = "Dahlquist, Frederick W."}
@string{PDalhaimer = "Dalhaimer, Paul"}
@string{SDanaher = "Danaher, S."}
@string{LDavenport = "Davenport, L."}
@string{MCDavies = "Davies, M.~C."}
@string{MDavis = "Davis, Matt"}
@string{SDecatur = "Decatur, Sean M."}
@string{WDeGrado = "DeGrado, William F."}
@string{PDebrunner = "Debrunner, P."}
@string{ADelcher = "Delcher, A."}
@string{WDeLorbe = "DeLorbe, William J."}
@string{BDelpech = "Delpech, B."}
@string{Demography = "Demography"}
@string{ZDeng = "Deng, Z."}
@string{RDesilets = "Desilets, R."}
@string{IDew = "Dew, I."}
@string{CDewhurst = "Dewhurst, Charles"}
@string{VDiFrancesco = "Di Francesco, V."}
@string{KDiemer = "Diemer, K."}
@string{GDietler = "Dietler, Giovanni"}
@string{HDietz = "Dietz, Hendrik"}
@string{SDietz = "Dietz, S."}
@string{EDijkstra = "Dijkstra, Edsger Wybe"}
@string{KADill = "Dill, K. A."}
@string{RDima = "Dima, Ruxandra I."}
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@string{KDodson = "Dodson, K."}
@string{NDoggett = "Doggett, N."}
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@string{LDoup = "Doup, L."}
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@string{TDrobek = "Drobek, T."}
@string{Drexel = "Drexel University"}
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@string{YFDufrene = "Dufr{\^e}ne, Yves F."}
@string{ADunham = "Dunham, A."}
@string{DDunlap = "Dunlap, D."}
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@string{VDupres = "Dupres, Vincent"}
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@string{EMBO = "EMBO Rep."}
@string{REckel = "Eckel, R."}
@string{KEilbeck = "Eilbeck, K."}
@string{MElbaum = "Elbaum, Michael"}
@string{E:NHPL = "Elsevier, North-Holland Personal Library"}
@string{DEly = "Ely, D."}
@string{SEmerling = "Emerling, S."}
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@string{MEsaki = "Esaki, Masatoshi"}
@string{SEsparham = "Esparham, S."}
@string{EBJ = "European biophysics journal: EBJ"}
@string{EJP = "European Journal of Physics"}
@string{EPL = "Europhysics Letters"}
@string{CEvangelista = "Evangelista, C."}
@string{CAEvans = "Evans, C. A."}
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@string{JFernandez = "Fernandez, Julio M."}
@string{SFerriera = "Ferriera, S."}
@string{AEFilippov = "Filippov, A. E."}
@string{LFinzi = "Finzi, L."}
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@string{MFlanigan = "Flanigan, M."}
@string{BFlannery = "Flannery, B."}
@string{LFlorea = "Florea, L."}
@string{ELFlorin = "Florin, Ernst-Ludwig"}
@string{FoldDes = "Fold Des"}
@string{NRForde = "Forde, Nancy R."}
@string{CFosler = "Fosler, C."}
@string{SFossey = "Fossey, S. A."}
@string{SFowler = "Fowler, Susan B."}
@string{GFranzen = "Franzen, Gereon"}
@string{SFreitag = "Freitag, S."}
@string{LFrench = "French, L."}
@string{RWFriddle = "Friddle, Raymond W."}
@string{CFriedman = "Friedman, C."}
@string{RFriedman = "Friedman, Ran"}
@string{MFritz = "Fritz, M."}
@string{HFuchs = "Fuchs, Harald"}
@string{TFujii = "Fujii, Tadashi"}
@string{HFujita = "Fujita, Hideaki"}
@string{AFujiyama = "Fujiyama, A."}
@string{RFulton = "Fulton, R."}
@string{TFunck = "Funck, Theodor"}
@string{TFurey = "Furey, T."}
@string{SFuruike = "Furuike, Shou"}
@string{GLGaborMiklos = "Gabor Miklos, G. L."}
@string{AEGabrielian = "Gabrielian, A. E."}
@string{WGan = "Gan, W."}
@string{DNGanchev = "Ganchev, Dragomir N."}
@string{MGao = "Gao, Mu"}
@string{DGarcia = "Garcia, D."}
@string{TGarcia = "Garcia, Tzintzuni"}
@string{NGarg = "Garg, N."}
@string{HEGaub = "Gaub, Hermann E."}
@string{MGautel = "Gautel, Mathias"}
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@string{NSGavrilova = "Gavrilova, N. S."}
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@string{UGeisler = "Geisler, Ulrich"}
@string{GENE = "Gene"}
@string{CGerber = "Gerber, Christoph"}
@string{CGergely = "Gergely, C."}
@string{RGibbs = "Gibbs, R."}
@string{DGilbert = "Gilbert, D."}
@string{HGire = "Gire, H."}
@string{MGiuntini = "Giuntini, M."}
@string{SGlanowski = "Glanowski, S."}
@string{JGlaser = "Glaser, Jens"}
@string{KGlasser = "Glasser, K."}
@string{AGlodek = "Glodek, A."}
@string{GGloeckner = "Gloeckner, G."}
@string{AGluecksmann = "Gluecksmann, A."}
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@string{AGomezCasado = "Gomez-Casado, Alberto"}
@string{BGompertz = "Gompertz, Benjamin"}
@string{FGong = "Gong, F."}
@string{GordonBreach = "Gordon Breach Scientific Publishing Ltd."}
@string{MGorokhov = "Gorokhov, M."}
@string{JHGorrell = "Gorrell, J. H."}
@string{SAGould = "Gould, S.~A."}
@string{KGraham = "Graham, K."}
@string{HLGranzier = "Granzier, Henk L."}
@string{FGrater = "Gr{\"a}ter, Frauke"}
@string{EDGreen = "Green, E. D."}
@string{SGGregory = "Gregory, S. G."}
@string{BGropman = "Gropman, B."}
@string{CGrossman = "Grossman, C."}
@string{HGrubmuller = {Grubm\"uller, Helmut}}
@string{AGrutzner = {Gr\"utzner, Anika}}
@string{ZGu = "Gu, Z."}
@string{PGuan = "Guan, P."}
@string{RGuigo = "Guig\'o, R."}
@string{EJGumbel = "Gumbel, Emil Julius"}
@string{HJGuntherodt = "Guntherodt, Hans-Joachim"}
@string{NGuo = "Guo, N."}
@string{YGuo = "Guo, Yi"}
@string{MGutman = "Gutman, Menachem"}
@string{RTGuy = "Guy, Richard T."}
@string{PHanggi = {H\"anggi, Peter}}
@string{THa = "Ha, Taekjip"}
@string{JHaack = "Haack, Julie A."}
@string{SHaddock = "Haddock, Steven H.~D."}
@string{GHager = "Hager, Gabriele"}
@string{THagglund = "H{\"a}gglund, T."}
@string{RHajjar = "Hajjar, Roger J."}
@string{AHalpern = "Halpern, A."}
@string{KHalvorsen = "Halvorsen, Ken"}
@string{FHan = "Han, Fangpu"}
@string{CCHang = "Hang, C.~C."}
@string{SHannenhalli = "Hannenhalli, S."}
@string{HHansma = "Hansma, H. G."}
@string{PHansma = "Hansma, Paul K."}
@string{DHarbrecht = "Harbrecht, Douglas"}
@string{SHarper = "Harper, Sandy"}
@string{MHarris = "Harris, M."}
@string{BHart = "Hart, B."}
@string{DPHart = "Hart, D.P."}
@string{JWHatfield = "Hatfield, John William"}
@string{THatton = "Hatton, T."}
@string{MHattori = "Hattori, M."}
@string{DHaussler = "Haussler, D."}
@string{THawkins = "Hawkins, T."}
@string{CHaynes = "Haynes, C."}
@string{JHaynes = "Haynes, J."}
@string{WHeckl = "Heckl, W. M."}
@string{CVHeer = "Heer, C.~V."}
@string{JHeil = "Heil, J."}
@string{RHeilig = "Heilig, R."}
@string{TJHeiman = "Heiman, T. J."}
@string{CHeiner = "Heiner, C."}
@string{MHelmes = "Helmes, M."}
@string{JHemmerle = "Hemmerle, J."}
@string{SHenderson = "Henderson, S."}
@string{BHeymann = "Heymann, Berthold"}
@string{NHiaro = "Hiaro, N."}
@string{MEHiggins = "Higgins, M. E."}
@string{THilburn = "Hilburn, Thomas B."}
@string{LHillier = "Hillier, L."}
@string{HHinssen = "Hinssen, Horst"}
@string{PHinterdorfer = "Hinterdorfer, Peter"}
@string{HistochemJ = "Histochem J"}
@string{SHladun = "Hladun, S."}
@string{WKHo = "Ho, W.~K."}
@string{RHochstrasser = "Hochstrasser, Robin M."}
@string{CSHodges = "Hodges, C.~S."}
@string{CHoff = "Hoff, C."}
@string{WHoff = "Hoff, Wouter D."}
@string{JLHolden = "Holden, J. L."}
@string{RAHolt = "Holt, R. A."}
@string{GHofmann = "Hofmann, Gerd"}
@string{MHonda = "Honda, M."}
@string{NPCHong = "Hong, Neil P. Chue"}
@string{XHong = "Hong, Xia"}
@string{LHood = "Hood, L."}
@string{JHoover = "Hoover, J."}
@string{JHorber = "Horber, J. K. H."}
@string{HHosser = "Hosser, H."}
@string{DHostin = "Hostin, D."}
@string{JHouck = "Houck, J."}
@string{AHoumeida = "Houmeida, Ahmed"}
@string{JHoward = "Howard, J."}
@string{THowland = "Howland, T."}
@string{BHsiao = "Hsiao, Benjamin S."}
@string{CKHu = "Hu, Chin-Kun"}
@string{DLHu = "Hu, David L."}
@string{BHuang = "Huang, Baiqu"}
@string{HHuang = "Huang, Hector Han-Li"}
@string{MHubain = "Hubain, Maurice"}
@string{AJHudspeth = "Hudspeth, A.~J."}
@string{KHuff = "Huff, Katy"}
@string{JHughes = "Hughes, John"}
@string{GHummer = "Hummer, Gerhard"}
@string{SJHumphray = "Humphray, S. J."}
@string{WLHung = "Hung, Wen-Liang"}
@string{MHunkapiller = "Hunkapiller, M."}
@string{DHHuson = "Huson, D. H."}
@string{JHutter = "Hutter, Jeffrey L."}
@string{CHyeon = "Hyeon, Changbong"}
@string{IEEE:TIT = "IEEE Transactions on Information Theory"}
@string{IEEE:SPM = "IEEE Signal Processing Magazine"}
@string{CIbegwam = "Ibegwam, C."}
@string{JRIdol = "Idol, J. R."}
@string{SImprota = "Improta, S."}
@string{TInoue = "Inoue, Tadashi"}
@string{IJBMM = "International Journal of Biological Macromolecules"}
@string{IJCIS = "International Journal of Computer \& Information Sciences"}
@string{AItkin = "Itkin, Anna"}
@string{HItoh = "Itoh, Hiroyasu"}
@string{AIrback = "Irback, Anders"}
@string{AMIsaacs = "Isaacs, Adrian M."}
@string{BIsralewitz = "Isralewitz, B."}
@string{SIstrail = "Istrail, S."}
@string{MIvemeyer = "Ivemeyer, M."}
@string{DIzhaky = "Izhaky, David"}
@string{SIzrailev = "Izrailev, S."}
@string{TJahnke = "J{\"a}hnke, Torsten"}
@string{WJang = "Jang, W."}
@string{HJanovjak = "Janovjak, Harald"}
@string{LJanosi = "Janosi, Lorant"}
@string{AJanshoff = "Janshoff, Andreas"}
@string{JJAP = "Japanese Journal of Applied Physics"}
@string{MJaschke = "Jaschke, Manfred"}
@string{DJennings = "Jennings, D."}
@string{HFJi = "Ji, Hai-Feng"}
@string{RRJi = "Ji, R. R."}
@string{YJia = "Jia, Yiwei"}
@string{SJiang = "Jiang, Shaoyi"}
@string{XJiang = "Jiang, Xingqun"}
@string{DJohannsmann = "Johannsmann, Diethelm"}
@string{CJohnson = "Johnson, Colin P."}
@string{JJohnson = "Johnson, J."}
@string{AJollymore = "Jollymore, Ashlee"}
@string{REJones = "Jones, R.E."}
@string{SJones = "Jones, S."}
@string{CJordan = "Jordan, C."}
@string{JJordan = "Jordan, J."}
%string{JACS = "J Am Chem Soc"}
@string{JACS = "Journal of the American Chemical Society"}
@string{JASA = "Journal of the American Statistical Association"}
@string{JAP = "Journal of Applied Physics"}
@string{JBM = "J Biomech"}
@string{JBT = "J Biotechnol"}
@string{JCPPCB = "Journal de Chimie Physique et de Physico-Chimie Biologique"}
@string{JCS = "Journal of Cell Science"}
@string{JCompP = "Journal of Computational Physics"}
@string{JEChem = "Journal of Electroanalytical Chemistry"}
@string{JMathBiol = "J Math Biol"}
@string{JMicro = "Journal of Microscopy"}
@string{JPhysio = "Journal of Physiology"}
@string{JStructBiol = "Journal of Structural Biology"}
@string{JTB = "J Theor Biol"}
@string{JMB = "Journal of Molecular Biology"}
@string{JP:CM = "Journal of Physics: Condensed Matter"}
@string{JP:CON = "Journal of Physics: Conference Series"}
@string{JRNBS:C = "Journal of Research of the National Bureau of Standards.  Section C: Engineering and Instrumentation"}
@string{WSJuang = "Juang, F.~S."}
@string{DAJuckett = "Juckett, D. A."}
@string{SRJun = "Jun, Se-Ran"}
@string{DKaftan = "Kaftan, David"}
@string{LKagan = "Kagan, L."}
@string{FKalush = "Kalush, F."}
@string{ELKaplan = "Kaplan, E. L."}
@string{RKapon = "Kapon, Ruti"}
@string{AKardinal = "Kardinal, Angelika"}
@string{BKarlak = "Karlak, B."}
@string{MKarplus = "Karplus, Martin"}
@string{MKarrenbach = "Karrenbach, Martin"}
@string{JKasha = "Kasha, J."}
@string{KKawasaki = "Kawasaki, K."}
@string{ZKe = "Ke, Z."}
@string{AKejariwal = "Kejariwal, A."}
@string{MSKellermayer = "Kellermayer, Mikl\'os S. Z."}
@string{TKempe = "Kempe, Thomas"}
@string{SKennedy = "Kennedy, S."}
@string{SBHKent = "Kent, Stephen B. H."}
@string{WJKent = "Kent, W. J."}
@string{KAKetchum = "Ketchum, K. A."}
@string{FKienberger = "Kienberger, Ferry"}
@string{SHKim = "Kim, Sung-Hou"}
@string{WKing = "King, William Trevor"}
@string{KKinosita = "{Kinosita Jr.}, Kazuhiko"}
@string{IRKirsch = "Kirsch, I. R."}
@string{JKlafter = "Klafter, J."}
@string{AKleiner = "Kleiner, Ariel"}
@string{DKlimov = "Klimov, Dmitri K."}
@string{LKline = "Kline, L."}
@string{LKlumb = "Klumb, L."}
@string{KAPPP = "Kluwer Academic Publishers--Plenum Publishers"}
@string{CDKodira = "Kodira, C. D."}
@string{SKoduru = "Koduru, S."}
@string{PKoehl = "Koehl, Patrice"}
@string{BKolmerer = "Kolmerer, B."}
@string{JKorenberg = "Korenberg, J."}
@string{IKosztin = "Kosztin, Ioan"}
@string{JKovacevic = "Kovacevic, Jelena"}
@string{CKraft = "Kraft, C."}
@string{HAKramers = "Kramers, H. A."}
@string{AKrammer = "Krammer, Andre"}
@string{SKravitz = "Kravitz, S."}
@string{HJKreuzer = {Kreuzer, Hans J\"urgen}}
@string{MMGKrishna = "Krishna, Mallela M. G."}
@string{KKroy = "Kroy, Klaus"}
@string{HHKu = "Ku, H.~H."}
@string{TAKucaba = "Kucaba, T. A."}
@string{Kucherlapati = "Kucherlapati"}
@string{JKudoh = "Kudoh, J."}
@string{MKuhn = "Kuhn, Michael"}
@string{MKulke = "Kulke, Michael"}
@string{CKwok = "Kwok, Carol H."}
@string{RLevy = "L\'evy, R"}
@string{DLabeit = "Labeit, Dietmar"}
@string{SLabeit = "Labeit, Siegfried"}
@string{DLabudde = "Labudde, Dirk"}
@string{SLahmers = "Lahmers, Sunshine"}
@string{ZLai = "Lai, Z."}
@string{CLam = "Lam, Canaan"}
@string{JLamb = "Lamb, Jonathan C."}
@string{LANG = "Langmuir"}
% "Langmuir : the ACS journal of surfaces and colloids",
@string{WLau = "Lau, Wai Leung"}
@string{RLaw = "Law, Richard"}
@string{BLazareva = "Lazareva, B."}
@string{MLeake = "Leake, Mark C."}
@string{ELee = "Lee, E."}
@string{HLee = "Lee, Haeshin"}
@string{SLee = "Lee, Sunyoung"}
@string{HLehmann = "Lehmann, H."}
@string{HLehrach = "Lehrach, H."}
@string{YLei = "Lei, Y."}
@string{PLelkes = "Lelkes, Peter I."}
@string{OLequin = "Lequin, Olivier"}
@string{CLethias = "Lethias, Claire"}
@string{SLeuba = "Leuba, Sanford H."}
@string{ALeung = "Leung, A."}
@string{MLeuschner = "Leuschner, Mirko"}
@string{AJLevine = "Levine, A. J."}
@string{CLevinthal = "Levinthal, Cyrus"}
@string{ALevitsky = "Levitsky, A."}
@string{SLevy = "Levy, S."}
@string{MLewis = "Lewis, M."}
@string{JLItalien = "L'Italien, James J."}
@string{BLi = "Li, Bing"}
@string{CYLi = "Li, Christopher Y."}
@string{HLi = "Li, Hongbin"}
@string{JLi = "Li, J."}
@string{LeLi = "Li, Lewyn"}
@string{LiLi = "Li, Lingyu"}
@string{MSLi = "Li, Mai Suan"}
@string{PWLi = "Li, P. W."}
@string{YLi = "Li, Yajun"}
@string{ZLi = "Li, Z."}
@string{YLiang = "Liang, Y."}
@string{GLiao = "Liao, George"}
@string{FCLin = "Lin, Fan-Chi"}
@string{JLin = "Lin, Jianhua"}
@string{SHLin = "Lin, Sheng-Hsien"}
@string{XLin = "Lin, X."}
@string{JLindahl = "Lindahl, Joakim"}
@string{SLindsay = "Lindsay, Stuart M."}
@string{WALinke = "Linke, Wolfgang A."}
@string{RLippert = "Lippert, R."}
@string{JLis = "Lis, John T."}
@string{RLiu = "Liu, Runcong"}
@string{WLiu = "Liu, W."}
@string{XLiu = "Liu, X."}
@string{YLiu = "Liu, Yichun"}
@string{LLivadaru = "Livadaru, L."}
@string{YSLo = "Lo, Yu-Shiu"}
@string{GLois = "Lois, Gregg"}
@string{JLopez = "Lopez, J."}
@string{LANL = "Los Alamos National Laboratory"}
@string{LAS = "Los Alamos Science"}
@string{ALove = "Love, A."}
@string{FLu = "Lu, F."}
@string{HLu = "Lu, Hui"}
@string{QLu = "Lu, Qinghua"}
@string{MLudwig = "Ludwig, Markus"}
@string{ZPLuo = "Luo, Zong-Ping"}
@string{ZLuthey-Schulten = "Luthey-Schulten, Z."}
@string{EMunck = {M\"unck, E.}}
@string{DMa = "Ma, D."}
@string{LMa = "Ma, Liang"}
@string{MMaaloum = "Maaloum, Mounir"}
@string{Macromol = "Macromolecules"}
@string{AMadan = "Madan, A."}
@string{VVMaduro = "Maduro, V. V."}
@string{CMaingonnat = "Maingonnat, C."}
@string{SMajid = "Majid, Sophia"}
@string{WMajoros = "Majoros, W."}
@string{DEMakarov = "Makarov, Dmitrii E."}
@string{RMamdani = "Mamdani, Reneeta"}
@string{EMandello = "Mandello, Enrico"}
@string{GManderson = "Manderson, Gavin"}
@string{FMann = "Mann, F."}
@string{AMansson = "M{\aa}nsson, Alf"}
@string{ERMardis = "Mardis, E. R."}
@string{JMarion = "Marion, J."}
@string{JFMarko = "Marko, John F."}
@string{MMarra = "Marra, M."}
@string{PMarszalek = "Marszalek, Piotr E."}
@string{MMartin = "Martin, M. J."}
@string{YMartin = "Martin, Y."}
@string{HMassa = "Massa, H."}
@string{GAMatei = "Matei, G.~A."}
@string{DMaterassi = "Materassi, Donatello"}
@string{JMathe = "Math\'e, J\'er\^ome"}
@string{AMatouschek = "Matouschek, Andreas"}
@string{BMatthews = "Matthews, Brian W."}
@string{DMay = "May, D."}
@string{RMayer = "Mayer, Richard"}
@string{LMayne = "Mayne, Leland"}
@string{AMays = "Mays, A."}
@string{OTMcCann = "McCann, O. T."}
@string{SMcCawley = "McCawley, S."}
@string{JMcDaniel = "McDaniel, J."}
@string{JMcEntyre = "McEntyre, J."}
@string{McGraw-Hill = "McGraw-Hill"}
@string{TMcIntosh = "McIntosh, T."}
@string{VAMcKusick = "McKusick, V. A."}
@string{IMcMullen = "McMullen, I."}
@string{JDMcPherson = "McPherson, J. D."}
@string{TMeasey = "Measey, Thomas J."}
@string{MAD = "Mech Ageing Dev"}
@string{PMeier = "Meier, Paul"}
@string{AMeller = "Meller, Amit"}
@string{CCMello = "Mello, Cecilia C."}
@string{RMerkel = "Merkel, R."}
@string{GVMerkulov = "Merkulov, G. V."}
@string{FMerzel = "Merzel, Franci"}
@string{HMetiu = "Metiu, Horia"}
@string{NMetropolis = "Metropolis, Nicholas"}
@string{GMeyer = "Meyer, Gerhard"}
@string{HMi = "Mi, H."}
@string{LMiao = "Miao, Linlin"}
@string{CMicheletti = "Micheletti, Cristian"}
@string{MMickler = "Mickler, Moritz"}
@string{AMiller = "Miller, A."}
@string{NMilshina = "Milshina, N."}
@string{SMinoshima = "Minoshima, S."}
@string{IMitchell = "Mitchell, Ian"}
@string{SMitternacht = "Mitternacht, Simon"}
@string{NJMlot = "Mlot, Nathan J."}
@string{CMobarry = "Mobarry, C."}
@string{NMohandas = "Mohandas, N."}
@string{SMohanty = "Mohanty, Sandipan"}
@string{UMohideen = "Mohideen, U."}
@string{PJMohr = "Mohr, Peter J."}
@string{VMontana = "Montana, Vedrana"}
@string{LMontanaro = "Montanaro, Lucio"}
@string{LMontelius = "Montelius, Lars"}
@string{CMontemagno = "Montemagno, Carlo D."}
@string{KTMontgomery = "Montgomery, K. T."}
@string{HMMoore = "Moore, H. M."}
@string{MMorgan = "Morgan, Michael"}
@string{LMoy = "Moy, L."}
@string{MMoy = "Moy, M."}
@string{VMoy = "Moy, Vincent T."}
@string{SMukamel = "Mukamel, Shaul"}
@string{DJMuller = "M{\"u}ller, Daniel J."}
@string{PMundel = "Mundeol, P."}
@string{EMuneyuki = "Muneyuki, Eiro"}
@string{RJMural = "Mural, R. J."}
@string{BMurphy = "Murphy, B."}
@string{SMurphy = "Murphy, S."}
@string{AMuruganujan = "Muruganujan, A."}
@string{EWMyers = "Myers, E. W."}
@string{RMMyers = "Myers, R. M."}
@string{AMylonakis = "Mylonakis, Andreas"}
@string{ENachliel = "Nachliel, Esther"}
@string{JNadeau = "Nadeau, J."}
@string{AKNaik = "Naik, A. K."}
@string{NANO = "Nano letters"}
@string{NT = "Nanotechnology"}
@string{VANarayan = "Narayan, V. A."}
@string{ANarechania = "Narechania, A."}
@string{PNassoy = "Nassoy, P."}
@string{NBS = "National Bureau of Standards"}
@string{NAT = "Nature"}
@string{NSB = "Nature Structural Biology"}
@string{NSMB = "Nature Structural Molecular Biology"}
@string{NRMCB = "Nature Reviews Molecular Cell Biology"}
@string{SNaylor = "Naylor, S."}
@string{CNeagoe = "Neagoe, Ciprian"}
@string{BNeelam = "Neelam, B."}
@string{MNeitzert = "Neitzert, Marcus"}
@string{CNelson = "Nelson, C."}
@string{KNelson = "Nelson, K."}
@string{RRNetz = "Netz, R.~R."}
@string{NR = "Neurochemical research"}
@string{NEURON = "Neuron"}
@string{RNevo = "Nevo, Reinat"}
@string{NJP = "New Journal of Physics"}
@string{DBNewell = "Newell, David B."}
@string{MNewman = "Newman, M."}
@string{INewton = "Newton, Isaac"}
@string{SNg = "Ng, Sean P."}
@string{NNguyen = "Nguyen, N."}
@string{TNguyen = "Nguyen, T."}
@string{MNguyen-Duong = "Nguyen-Duong, M."}
@string{INicholls = "Nicholls, Ian A."}
@string{NNichols = "Nichols, N.~B."}
@string{SNie = "Nie, S."}
@string{MNodell = "Nodell, M."}
@string{AANoegel = "Noegel, Angelika A."}
@string{HNoji = "Noji, Hiroyuki"}
@string{RNome = "Nome, Rene A."}
@string{NNowak = "Nowak, N."}
@string{ANoy = "Noy, Aleksandr"}
@string{NAR = "Nucleic Acids Research"}
@string{JNummela = "Nummela, Jeremiah"}
@string{JNunes = "Nunes, Joao"}
@string{DNusskern = "Nusskern, D."}
@string{GNyakatura = "Nyakatura, G."}
@string{CSOHern = "O'Hern, Corey S."}
@string{YOberdorfer = {Oberd\"orfer, York}}
@string{AOberhauser = "Oberhauser, Andres F."}
@string{FOesterhelt = "Oesterhelt, Filipp"}
@string{TOhashi = "Ohashi, Tomoo"}
@string{BOhler = "Ohler, Benjamin"}
@string{PDOlmsted = "Olmsted, Peter D."}
@string{AOlsen = "Olsen, A."}
@string{SJOlshansky = "Olshansky, S. J."}
@string{POmling = {Omlink, P{\"a}r}}
@string{JNOnuchic = "Onuchic, J. N."}
@string{YOono = "Oono, Y."}
@string{GOppenheim = "Oppenheim, Georges"}
@string{COpitz = "Optiz, Christiane A."}
@string{KOroszlan = "Oroszlan, Krisztina"}
@string{EOroudjev = "Oroudjev, E."}
@string{KOsoegawa = "Osoegawa, K."}
@string{OUP = "Oxford University Press"}
@string{EPaci = "Paci, Emanuele"}
@string{SPan = "Pan, S."}
@string{HSPark = "Park, H. S."}
@string{VParpura = "Parpura, Vladimir"}
@string{APastore = "Pastore, A."}
@string{APatrinos = "Patrinos, Aristides"}
@string{FPavone = "Pavone, F. S."}
@string{SHPayne = "Payne, Stephen H."}
@string{JPeck = "Peck, J."}
@string{HPeng = "Peng, Haibo"}
@string{QPeng = "Peng, Qing"}
@string{RNPerham = "Perham, Richard N."}
@string{OPerisic = "Perisic, Ognjen"}
@string{CPeterson = "Peterson, Craig L."}
@string{MPeterson = "Peterson, M."}
@string{SMPeterson = "Peterson, Susan M."}
@string{CPfannkoch = "Pfannkoch, C."}
@string{PA = "Pfl{\"u}gers Archiv: European journal of physiology"}
@string{PTRSL = "Philosophical Transactions of the Royal Society of London"}
@string{PR:E = "Phys Rev E Stat Nonlin Soft Matter Phys"}
@string{PRL = "Physical Review Letters"}
%string{PRL = "Phys Rev Lett"}
@string{Physica = "Physica"}
@string{GPing = "Ping, Guanghui"}
@string{NPinotsis = "Pinotsis, Nikos"}
@string{MPlumbley = "Plumbley, Mark"}
@string{PLOS:ONE = "PLOS ONE"}
%string{PLOS:ONE = "Public Library of Science ONE"}
@string{DPlunkett = "Plunkett, David"}
@string{PPodsiadlo = "Podsiadlo, Paul"}
@string{ASPolitou = "Politou, A. S."}
@string{APoustka = "Poustka, A."}
@string{CBPrater = "Prater, C.~B."}
@string{GPratesi = "Pratesi, G."}
@string{EPratts = "Pratts, E."}
@string{WPress = "Press, W."}
@string{PNAS = "Proceedings of the National Academy of Sciences of the
  United States of America"}
@string{PBPMB = "Progress in Biophysics and Molecular Biology"}
@string{PS = "Protein Science"}
@string{PROT = "Proteins"}
@string{RSUP = "Published for the Royal Society at the University Press"}
@string{EPuchner = "Puchner, Elias M."}
@string{VPuri = "Puri, V."}
@string{WPyckhout-Hintzen = "Pyckhout-Hintzen, Wim"}
@string{HQin = "Qin, Haina"}
@string{SQin = "Qin, S."}
@string{SRQuake = "Quake, Stephen R."}
@string{CQuate = "Quate, Calvin F."}
@string{HQureshi = "Qureshi, H."}
@string{SERadford = "Radford, Sheena E."}
@string{MRadmacher = "Radmacher, M."}
@string{MRaible = "Raible, M."}
@string{LRamirez = "Ramirez, L."}
@string{JRamser = "Ramser, J."}
@string{LRandles = "Randles, Lucy G."}
@string{VRaussens = "Raussens, Vincent"}
@string{IRay = "Ray, I."}
@string{MReardon = "Reardon, M."}
@string{ALCReddin = "Reddin, Andrew L. C."}
@string{SRedick = "Redick, Sambra D."}
@string{ZReich = "Reich, Ziv"}
@string{TReid = "Reid, T."}
@string{PReimann = "Reimann, P."}
@string{KReinert = "Reinert, K."}
@string{RReinhardt = "Reinhardt, R."}
@string{KRemington = "Remington, K."}
@string{RMP = "Rev. Mod. Phys."}
@string{RSI = "Review of Scientific Instruments"}
@string{FRief = "Rief, Frederick"}
@string{MRief = "Rief, Matthias"}
@string{KRitchie = "Ritchie, K."}
@string{MRobbins = "Robbins, Mark O."}
@string{CJRoberts = "Roberts, C.~J."}
@string{RJRoberts = "Roberts, R. J."}
@string{RRobertson = "Robertson, Ragan B."}
@string{HRoder = "Roder, Heinrich"}
@string{RRodriguez = "Rodriguez, R."}
@string{YHRogers = "Rogers, Y. H."}
@string{SRogic = "Rogic, S."}
@string{MRoman = "Roman, Marisa B."}
@string{GRomano = "Romano, G."}
@string{DRomblad = "Romblad, D."}
@string{RRos = "Ros, Robert"}
@string{BRosenberg = "Rosenberg, B."}
@string{JRosengren = "Rosengren, Jenny P."}
@string{ARosenthal = "Rosenthal, A."}
@string{ARoters = "Roters, Andreas"}
@string{WRowe = "Rowe, W."}
@string{LRowen = "Rowen, L."}
@string{BRuhfel = "Ruhfel, B."}
@string{DBRusch = "Rusch, D. B."}
@string{JMRuysschaert = "Ruysschaert, Jean-Marie"}
@string{JPRyckaert = "Ryckaert, Jean-Paul"}
@string{NSakaki = "Sakaki, Naoyoshi"}
@string{YSakaki = "Sakaki, Y."}
@string{SSalzberg = "Salzberg, S."}
@string{BSamori = "Samor{\`i}, Bruno"}
@string{MSandal = "Sandal, Massimo"}
@string{RSanders = "Sanders, R."}
@string{ASarkar = "Sarkar, Atom"}
@string{TSasaki = "Sasaki, T."}
@string{SSato = "Sato, S."}
@string{TSato = "Sato, Takehiro"}
@string{PSchaaf = "Schaaf, P."}
@string{RSchafer = "Schafer, Rolf"}
@string{TESchafer = "Sch{\"a}fer, Tilman E."}
@string{NScherer = "Scherer, Norbert F."}
@string{SScherer = "Scherer, S."}
@string{MSchilhabel = "Schilhabel, M."}
@string{HSchillers = "Schillers, Hermann"}
@string{BSchlegelberger = "Schlegelberger, B."}
@string{MSchleicher = "Schleicher, Michael"}
@string{MSchlierf = "Schlierf, Michael"}
@string{JSchmidt = "Schmidt, Jacob J."}
@string{LSchmitt = "Schmitt, Lutz"}
@string{JSchmutz = "Schmutz, J."}
@string{GSchuler = "Schuler, G."}
@string{GDSchuler = "Schuler, G. D."}
@string{KSchulten = "Schulten, Klaus"}
@string{ZSchulten = "Schulten, Zan"}
@string{MSchwab = "Schwab, M."}
@string{ISchwaiger = "Schwaiger, Ingo"}
@string{RSchwartz = "Schwartz, R."}
@string{RSchweitzerStenner = "Scheitzer-Stenner, Reinhard"}
@string{SCI = "Science"}
@string{CEScott = "Scott, C. E."}
@string{JScott = "Scott, J."}
@string{RScott = "Scott, R."}
@string{USeifert = "Seifert, Udo"}
@string{SKSekatskii = "Sekatskii, Sergey K."}
@string{MSekhon = "Sekhon, M."}
@string{TSekiguchi = "Sekiguchi, T."}
@string{BSenger = "Senger, B."}
@string{DBSenn = "Senn, David B."}
@string{PSeranski = "Seranski, P."}
@string{RSesboue = {Sesbo\"u\'e, R.}}
@string{EShakhnovich = "Shakhnovich, Eugene"}
@string{GShan = "Shan, Guiye"}
@string{JShang = "Shang, J."}
@string{WShao = "Shao, W."}
@string{DSharma = "Sharma, Deepak"}
@string{YJSheng = "Sheng, Yu-Jane"}
@string{KShibuya = "Shibuya, K."}
@string{JShillcock = "Shillcock, Julian"}
@string{AShimizu = "Shimizu, A."}
@string{NShimizu = "Shimizu, N."}
@string{RShimoKon = "Shimo-Kon, Rieko"}
@string{JPShine = "Shine, James P."}
@string{AShintani = "Shintani, A."}
@string{BShneiderman = "Shneiderman, Ben"}
@string{BShue = "Shue, B."}
@string{RSiebert = "Siebert, R."}
@string{EDSiggia = "Siggia, Eric D."}
@string{MSimon = "Simon, M."}
@string{MSimpson = "Simpson, M."}
@string{GESims = "Sims, Gregory E."}
@string{CSitter = "Sitter, C."}
@string{KVSjolander = "Sjolander, K. V."}
@string{MSkupski = "Skupski, M."}
@string{CSlayman = "Slayman, C."}
@string{MSmallwood = "Smallwood, M."}
@string{CSmith = "Smith, Corey L."}
@string{DASmith = "Smith, D. Alastair"}
@string{HOSmith = "Smith, H. O."}
@string{KBSmith = "Smith, Kathryn B."}
@string{SSmith = "Smith, S."}
@string{SBSmith = "Smith, S. B."}
@string{TSmith = "Smith, T."}
@string{JSoares = "Soares, J."}
@string{NDSocci = "Socci, N. D."}
@string{SEG = "Society of Exploration Geophysicists"}
@string{ESodergren = "Sodergren, E."}
@string{CSoderlund = "Soderlund, C."}
@string{JSong = "Song, Jianxing"}
@string{JSpanier = "Spanier, Jonathan E."}
@string{DSpeicher = "Speicher, David W."}
@string{GSpier = "Spier, G."}
@string{ASprague = "Sprague, A."}
@string{SPRINGER = "Springer Science + Business Media, LLC"}
@string{DBStaple = "Staple, Douglas B."}
@string{RStark = "Stark, R. W."}
@string{PSStayton = "Stayton, P. S."}
@string{REStenkamp = "Stenkamp, R. E."}
@string{SStepaniants = "Stepaniants, S."}
@string{EStewart = "Stewart, E."}
@string{MRStockmeier = "Stockmeier, M. R."}
@string{TStockwell = "Stockwell, T."}
@string{NEStone = "Stone, N. E."}
@string{AStout = "Stout, A."}
@string{TRStrick = "Strick, T. R."}
@string{CStroh = "Stroh, Cordula"}
@string{RStrong = "Strong, R."}
@string{JStruckmeier = "Struckmeier, Jens"}
@string{STR = "Structure"}
@string{TStrunz = "Strunz, Torsten"}
@string{MSu = "Su, Meihong"}
@string{GSubramanian = "Subramanian, G."}
@string{ESuh = "Suh, E."}
@string{JSun = "Sun, J."}
@string{YLSun = "Sun, Yu-Long"}
@string{MSundberg = "Sundberg, Mark"}
@string{WSundquist = "Sundquist, Wesley I."}
@string{KSurewicz = "Surewicz, Krystyna"}
@string{WKSurewicz = "Surewicz, Witold K."}
@string{GGSutton = "Sutton, G. G."}
@string{ASzabo = "Szabo, Attila"}
@string{STagerud = "T{\aa}gerud, Sven"}
@string{PTabor = "Tabor, P."}
@string{ATakahashi = "Takahashi, Akiri"}
@string{DTalaga = "Talaga, David S."}
@string{PTalkner = "Talkner, Peter"}
@string{RTampe = "Tamp{\'e}, Robert"}
@string{JTang = "Tang, Jianyong"}
@string{PTavan = "Tavan, P."}
@string{BNTaylor = "Taylor, Barry N."}
@string{THEMath = "Technische Hogeschool Eindhoven, Nederland,
  Onderafdeling der Wiskunde"}
@string{SJBTendler = "Tendler, S.~J.~B."}
@string{STeukolsky = "Teukolsky, S."}
@string{CJ = "The Computer Journal"}
@string{JBC = "The Journal of Biological Chemistry"}
@string{JCP = "The Journal of Chemical Physics"}
@string{JPC:B = "The Journal of Physical Chemistry B"}
@string{JPC:C = "The Journal of Physical Chemistry C"}
@string{RS = "The Royal Society"}
@string{DThirumalai = "Thirumalai, Devarajan"}
@string{PDThomas = "Thomas, P. D."}
@string{RThomas = "Thomas, R."}
@string{JThompson = "Thompson, J. B."}
@string{EJThoreson = "Thoreson, E.~J."}
@string{SThornton = "Thornton, S."}
@string{RWTillmann = "Tillmann, R.~W."}
@string{NNTint = "Tint, N. N."}
@string{BTiribilli = "Tiribilli, Bruno"}
@string{TTlusty = "Tlusty, Tsvi"}
@string{PTobias = "Tobias, Paul"}
@string{JTocaHerrera = "Toca-Herrera, Jose L."}
@string{CATovey = "Tovey, Craig A."}
@string{AToyoda = "Toyoda, A."}
@string{TASME = "Transactions of the American Society of Mechanical Engineers"}
@string{BTrask = "Trask, B."}
@string{TBI = "Tribology International"}
@string{JTrinick = "Trinick, John"}
@string{KTrombitas = "Trombit\'as, K."}
@string{ILTrong = "Trong, I. Le"}
@string{CHTsai = "Tsai, Chih-Hui"}
@string{HKTsao = "Tsao, Heng-Kwong"}
@string{STse = "Tse, S."}
@string{ZTshiprut = "Tshiprut, Z."}
@string{JCMTsibris = "Tsibris, J.C.M."}
@string{LTskhovrebova = "Tskhovrebova, Larissa"}
@string{HWTurnbull = "Turnbull, Herbert Westren"}
@string{RTurner = "Turner, R."}
@string{AUlman = "Ulman, Abraham"}
@string{UltraMic = "Ultramicroscopy"}
@string{UIP:Urbana = "University of Illinois Press, Urbana"}
@string{UTMB = "University of Texas Medical Branch"}
@string{MUrbakh = "Urbakh, M."}
@string{KJVanVliet = "Van Vliet, Krystyn J."}
@string{PVandewalle = "Vandewalle, Patrick"}
@string{CVech = "Vech, C."}
@string{OVelasquez = "Velasquez, O."}
@string{EVenter = "Venter, E."}
@string{JCVenter = "Venter, J. C."}
@string{PHVerdier = "Verdier, Peter H."}
@string{IVetter = "Vetter, Ingrid R."}
@string{MVetterli = "Vetterli, Martin"}
@string{WVetterling = "Vetterling, W."}
@string{MViani = "Viani, Mario B."}
@string{JCVoegel = "Voegel, J.-C."}
@string{VVogel = "Vogel, Viola"}
@string{CWagner-McPherson = "Wagner-McPherson, C."}
@string{RWahl = "Wahl, Reiner"}
@string{TAWaigh = "Waigh, Thomas A."}
@string{BWalenz = "Walenz, B."}
@string{JWallis = "Wallis, J."}
@string{KWalther = "Walther, Kirstin A."}
@string{AJWalton = "Walton, Alan J"}
@string{EBWalton = "Walton, Emily B."}
@string{AWang = "Wang, A."}
@string{FSWang = "Wang, F.~S."}
@string{GWang = "Wang, G."}
@string{JWang = "Wang, J."}
@string{MWang = "Wang, M."}
@string{MDWang = "Wang, Michelle D."}
@string{SWang = "Wang, Shuang"}
@string{XWang = "Wang, X."}
@string{ZWang = "Wang, Z."}
@string{HWatanabe = "Watanabe, Hiroshi"}
@string{KWatanabe = "Watanabe, Kaori"}
@string{RHWaterston = "Waterston, R. H."}
@string{BWaugh = "Waugh, Ben"}
@string{JWegiel = "Wegiel, J."}
@string{MWei = "Wei, M."}
@string{YWei = "Wei, Yen"}
@string{ALWeisenhorn = "Weisenhorn, A.~L."}
@string{JWeissenbach = "Weissenbach, J."}
@string{BLWelch = "Welch, Bernard Lewis"}
@string{GWen = "Wen, G."}
@string{MWen = "Wen, M."}
@string{JWetter = "Wetter, J."}
@string{EPWhite = "White, Ethan P."}
@string{ANWhitehead = "Whitehead, Alfred North"}
@string{AWhittaker = "Whittaker, A."}
@string{HKWickramasinghe = "Wickramasinghe, H. K."}
@string{RWides = "Wides, R."}
@string{AWiita = "Wiita, Arun P."}
@string{MWilchek = "Wilchek, Meir"}
@string{AWilcox = "Wilcox, Alexander J."}
@string{Williams = "Williams"}
@string{CCWilliams = "Williams, C. C."}
@string{MWilliams = "Williams, M."}
@string{SWilliams = "Williams, S."}
@string{WN = "Williams \& Norgate"}
@string{MWilmanns = "Wilmanns, Matthias"}
@string{GWilson = "Wilson, Greg"}
@string{PWilson = "Wilson, Paul"}
@string{RKWilson = "Wilson, R. K."}
@string{SWilson = "Wilson, Scott"}
@string{SWindsor = "Windsor, S."}
@string{EWinn-Deen = "Winn-Deen, E."}
@string{NWirth = "Wirth, Niklaus"}
@string{HMWisniewski = "Wisniewski, H.~M."}
@string{CWitt = "Witt, Christian"}
@string{KWolfe = "Wolfe, K."}
@string{TGWolfsberg = "Wolfsberg, T. G."}
@string{PGWolynes = "Wolynes, P. G."}
@string{WPWong = "Wong, Wesley P."}
@string{TWoodage = "Woodage, T."}
@string{GRWoodcock = "Woodcock, Glenna R."}
@string{JRWortman = "Wortman, J. R."}
@string{PEWright = "Wright, Peter E."}
@string{DWu = "Wu, D."}
@string{GAWu = "Wu, Guohong A."}
@string{JWWu = "Wu, Jong-Wuu"}
@string{MWu = "Wu, M."}
@string{YWu = "Wu, Yiming"}
@string{GJLWuite = "Wuite, Gijs J. L."}
@string{KWylie = "Wylie, K."}
@string{JXi = "Xi, Jun"}
@string{AXia = "Xia, A."}
@string{CXiao = "Xiao, C."}
@string{SXiao = "Xiao, Senbo"}
@string{TYada = "Yada, T."}
@string{CYan = "Yan, C."}
@string{MYandell = "Yandell, M."}
@string{GYang = "Yang, Guoliang"}
@string{YYang = "Yang, Yao"}
@string{BAYankner = "Yankner, Bruce A."}
@string{AYao = "Yao, A."}
@string{RYasuda = "Yaduso, Ryohei"}
@string{JYe = "Ye, J."}
@string{RYeh = "Yeh, Richard C."}
@string{RYonescu = "Yonescu, R."}
@string{SYooseph = "Yooseph, S."}
@string{MYoshida = "Yoshida, Masasuke"}
@string{WYu = "Yu, Weichang"}
@string{JMYuan = "Yuan, Jian-Min"}
@string{MYuan = "Yuan, Menglan"}
@string{AZandieh = "Zandieh, A."}
@string{JZaveri = "Zaveri, J."}
@string{KZaveri = "Zaveri, K."}
@string{MZhan = "Zhan, M."}
@string{HZhang = "Zhang, H."}
@string{JZhang = "Zhang, J."}
@string{QZhang = "Zhang, Q."}
@string{WZhang = "Zhang, W."}
@string{YZhang = "Zhang, Yanjie"}
@string{ZZhang = "Zhang, Zongtao"}
@string{JZhao = "Zhao, Jason Ming"}
@string{LZhao = "Zhao, Liming"}
@string{QZhao = "Zhao, Q."}
@string{SZhao = "Zhao, S."}
@string{LZheng = "Zheng, L."}
@string{XHZheng = "Zheng, X. H."}
@string{FZhong = "Zhong, F."}
@string{MZhong = "Zhong, Mingya"}
@string{WZhong = "Zhong, W."}
@string{HXZhou = "Zhou, Huan-Xiang"}
@string{SZhu = "Zhu, S."}
@string{XZhu = "Zhu, X."}
@string{YJZhu = "Zhu, Ying-Jie"}
@string{WZhuang = "Zhuang, Wei"}
@string{JZidar = "Zidar, Jernej"}
@string{JZiegler = "Ziegler, J.G."}
@string{NZinder = "Zinder, N."}
@string{RCZinober = "Zinober, Rebecca C."}
@string{JZlatanova = "Zlatanova, Jordanka"}
@string{PZou = "Zou, Peng"}
@string{GZuccheri = "Zuccheri, Giampaolo"}
@string{RZwanzig = "Zwanzig, R."}
@string{arXiv = "arXiv"}
@string{PGdeGennes = "de Gennes, P. G."}
@string{PJdeJong = "de Jong, P. J."}
@string{NGvanKampen = "van Kampen, N.G."}
@string{NIST:SEMATECH = "{NIST/SEMATECH}"}
@string{EDCola = "{\uppercase{d}}i Cola, Emanuela"}

@inbook{ NIST:chi-square,
  crossref = {NIST:ESH},
  chapter = {1.3.5.15: Chi-Square Goodness-of-Fit Test},
  year = 2013,
  month = may,
  day = 15,
  url = {http://www.itl.nist.gov/div898/handbook/eda/section3/eda35f.htm},
}

@inbook{ NIST:gumbel,
  crossref = {NIST:ESH},
  chapter = {1.3.6.6.16: Extreme Value Type {I} Distribution},
  year = 2009,
  month = oct,
  day = 9,
  url = {http://www.itl.nist.gov/div898/handbook/eda/section3/eda366g.htm},
}

@book{ NIST:ESH,
  editor = CCroarkin #" and "# PTobias,
  author = NIST:SEMATECH,
  title = {e-{H}andbook of Statistical Methods},
  year = 2013,
  month = may,
  publisher = NIST:SEMATECH,
  address = {Boulder, Colorado},
  url = {http://www.itl.nist.gov/div898/handbook/},
  note = {This manual was developed from seed material produced by
    Mary Natrella.},
}

@misc{ wikipedia:gumbel,
  author = "Wikipedia",
  title = "Gumbel distribution --- {W}ikipedia{,} The Free Encyclopedia",
  year = 2012,
  url = "http://en.wikipedia.org/wiki/Gumbel_distribution",
}

@book { gumbel58,
    author = EJGumbel,
    title = "Statistics of Extremes",
    year = 1958,
    publisher = CUP,
    address = "New York",
    note = "TODO: read",
}

@misc{ wikipedia:GEV,
  author = "Wikipedia",
  title = "Generalized extreme value distribution --- {W}ikipedia{,}
    The Free Encyclopedia",
  year = 2012,
  url = "http://en.wikipedia.org/wiki/Generalized_extreme_value_distribution",
}

@misc{ wikipedia:gompertz,
  author = "Wikipedia",
  title = "Gompertz distribution --- {W}ikipedia{,} The Free Encyclopedia",
  year = 2012,
  url = "http://en.wikipedia.org/wiki/Gompertz_distribution",
}

@misc{ wikipedia:gumbel-t1,
  author = "Wikipedia",
  title = "Type-1 Gumbel distribution --- {W}ikipedia{,} The Free
    Encyclopedia",
  year = 2012,
  url = "http://en.wikipedia.org/wiki/Type-1_Gumbel_distribution",
}

@misc{ wikipedia:gumbel-t2,
  author = "Wikipedia",
  title = "Type-2 Gumbel distribution --- {W}ikipedia{,} The Free
    Encyclopedia",
  year = 2012,
  url = "http://en.wikipedia.org/wiki/Type-2_Gumbel_distribution",
}

@article { allemand03,
    author = JFAllemand #" and "# DBensimon #" and "# VCroquette,
    title = "Stretching {DNA} and {RNA} to probe their interactions with
        proteins",
    year = 2003,
    month = jun,
    journal = COSB,
    volume = 13,
    number = 3,
    pages = "266--274",
    issn = "0959-440X",
    keywords = "DNA;DNA-Binding
        Proteins;Isomerases;Micromanipulation;Microscopy, Atomic Force;Nucleic
        Acid Conformation;Nucleotidyltransferases",
    abstract = "When interacting with a single stretched DNA, many proteins
        modify its end-to-end distance. This distance can be monitored in real
        time using various micromanipulation techniques that were initially
        used to determine the elastic properties of bare nucleic acids and
        their mechanically induced structural transitions. These methods are
        currently being applied to the study of DNA enzymes such as DNA and RNA
        polymerases, topoisomerases and structural proteins such as RecA. They
        permit the measurement of the probability distributions of the rate,
        processivity, on-time, affinity and efficiency for a large variety of
        DNA-based molecular motors."
}

@article { alon90,
    author = RAlon #" and "# EABayer #" and "# MWilchek,
    title = "Streptavidin contains an {RYD} sequence which mimics the {RGD}
        receptor domain of fibronectin",
    year = 1990,
    month = aug,
    day = 16,
    journal = BCBPRC,
    volume = 170,
    number = 3,
    pages = "1236--1241",
    issn = "0006-291X",
    doi = "DOI: 10.1016/0006-291X(90)90526-S",
    url = "http://www.sciencedirect.com/science/article/B6WBK-
        4F5M7K3-3C/2/c94b612e06efc8534ee24bb1da889811",
    keywords = "Amino Acid Sequence;Animals;Bacterial Proteins;Binding
        Sites;Cell Line;Cell Membrane;Cricetinae;Fibronectins;Molecular
        Sequence Data;Streptavidin",
    abstract = "Streptavidin binds at low levels and high affinity to cell
        surfaces, the cause of which can be traced to the occurrence of a
        sequence containing RYD (Arg-Tyr-Asp) in the protein molecule. This
        binding is enhanced in the presence of biotin. Cell-bound streptavidin
        can be displaced by fibronectin, as well as by RGD- and RYD-containing
        peptides. In addition, streptavidin can displace fibronectin from cell
        surfaces. The RYD sequence of streptavidin thus mimics RGD (Arg-Gly-
        Asp), the universal recognition domain present in fibronectin and other
        adhesion-related molecules. The observed adhesion to cells has no
        relevance to biotin-binding since the RYD sequence is not part of the
        biotin-binding site of streptavidin. Since the use of streptavidin in
        avidin-biotin technology is based on its biotin-binding properties,
        researchers are hereby warned against its indiscriminate use in
        histochemical and cytochemical studies.",
    note = "Biological role of streptavidin."
}

@article { balsera97,
    author = MBalsera #" and "# SStepaniants #" and "# SIzrailev #" and "#
        YOono #" and "# KSchulten,
    title = "Reconstructing potential energy functions from simulated force-
        induced unbinding processes",
    year = 1997,
    month = sep,
    journal = BPJ,
    volume = 73,
    number = 3,
    pages = "1281--1287",
    issn = "0006-3495",
    eprint = "http://www.biophysj.org/cgi/reprint/73/3/1281.pdf",
    url = "http://www.biophysj.org/cgi/content/abstract/73/3/1281",
    keywords = "Binding Sites;Biopolymers;Kinetics;Ligands;Microscopy, Atomic
        Force;Models, Chemical;Molecular Conformation;Protein
        Conformation;Proteins;Reproducibility of Results;Stochastic
        Processes;Thermodynamics",
    abstract = "One-dimensional stochastic models demonstrate that molecular
        dynamics simulations of a few nanoseconds can be used to reconstruct
        the essential features of the binding potential of macromolecules. This
        can be accomplished by inducing the unbinding with the help of external
        forces applied to the molecules, and discounting the irreversible work
        performed on the system by these forces. The fluctuation-dissipation
        theorem sets a fundamental limit on the precision with which the
        binding potential can be reconstructed by this method. The uncertainty
        in the resulting potential is linearly proportional to the irreversible
        component of work performed on the system during the simulation. These
        results provide an a priori estimate of the energy barriers observable
        in molecular dynamics simulations."
}

@article { baneyx02,
    author = GBaneyx #" and "# LBaugh #" and "# VVogel,
    title = "Supramolecular Chemistry And Self-assembly Special Feature:
        Fibronectin extension and unfolding within cell matrix fibrils
        controlled by cytoskeletal tension",
    year = 2002,
    journal = PNAS,
    volume = 99,
    number = 8,
    pages = "5139--5143",
    doi = "10.1073/pnas.072650799",
    eprint = "http://www.pnas.org/cgi/reprint/99/8/5139.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/99/8/5139",
    abstract = "Evidence is emerging that mechanical stretching can alter the
        functional states of proteins. Fibronectin (Fn) is a large,
        extracellular matrix protein that is assembled by cells into elastic
        fibrils and subjected to contractile forces. Assembly into fibrils
        coincides with expression of biological recognition sites that are
        buried in Fn's soluble state. To investigate how supramolecular
        assembly of Fn into fibrillar matrix enables cells to mechanically
        regulate its structure, we used fluorescence resonance energy transfer
        (FRET) as an indicator of Fn conformation in the fibrillar matrix of
        NIH 3T3 fibroblasts. Fn was randomly labeled on amine residues with
        donor fluorophores and site-specifically labeled on cysteine residues
        in modules FnIII7 and FnIII15 with acceptor fluorophores.
        Intramolecular FRET was correlated with known structural changes of Fn
        in denaturing solution, then applied in cell culture as an indicator of
        Fn conformation within the matrix fibrils of NIH 3T3 fibroblasts. Based
        on the level of FRET, Fn in many fibrils was stretched by cells so that
        its dimer arms were extended and at least one FnIII module unfolded.
        When cytoskeletal tension was disrupted using cytochalasin D, FRET
        increased, indicating refolding of Fn within fibrils. These results
        suggest that cell-generated force is required to maintain Fn in
        partially unfolded conformations. The results support a model of Fn
        fibril elasticity based on unraveling and refolding of FnIII modules.
        We also observed variation of FRET between and along single fibrils,
        indicating variation in the degree of unfolding of Fn in fibrils.
        Molecular mechanisms by which mechanical force can alter the structure
        of Fn, converting tensile forces into biochemical cues, are discussed."
}

@article { basche01,
    author = TBasche #" and "# SNie #" and "# JFernandez,
    title = "Single molecules",
    year = 2001,
    journal = PNAS,
    volume = 98,
    number = 19,
    pages = "10527--10528",
    doi = "10.1073/pnas.191365898",
    eprint = "http://www.pnas.org/cgi/reprint/98/19/10527.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/98/19/10527",
    note = "Mini summary of single-molecule techniques and look to future.
        Focuses on AFM, but mentions others."
}

@article { bechhoefer02,
    author = JBechhoefer #" and "# SWilson,
    title = "Faster, cheaper, safer optical tweezers for the undergraduate
        laboratory",
    collaboration = "",
    year = 2002,
    journal = AJP,
    volume = 70,
    number = 4,
    pages = "393--400",
    publisher = AAPT,
    doi = "10.1119/1.1445403",
    url = "http://link.aip.org/link/?AJP/70/393/1",
    keywords = "student experiments; safety; radiation pressure; laser beam
        applications",
    note = {Good discussion of the effect of correlation time on
      calibration.  References work on deconvolving thermal noise from
      other noise\citep{cowan98}.  Excellent detail on power spectrum
      derivation and thermal noise for extremely overdamped
      oscillators in Appendix A (references \citet{rief65}), except
      that their equation A12 is missing a factor of $1/\pi$.  I
      pointed this out to John Bechhoefer and he confirmed the
      error.},
    project = "Cantilever Calibration"
}

@article{ berg-sorensen05,
  author = KBergSorensen #" and "# HFlyvbjerg,
  title = {The colour of thermal noise in classical Brownian motion: a
    feasibility study of direct experimental observation},
  year = 2005,
  month = feb,
  day = 1,
  journal = NJP,
  volume = 7,
  number = {1},
  pages = {38},
  doi = {10.1088/1367-2630/7/1/038},
  url = {http://stacks.iop.org/1367-2630/7/i=1/a=038},
  eprint = {http://iopscience.iop.org/1367-2630/7/1/038/pdf/1367-2630_7_1_038.pdf},
  abstract = {One hundred years after Einstein modelled Brownian
    motion, a central aspect of this motion in incompressible fluids
    has not been verified experimentally: the thermal noise that
    drives the Brownian particle, is not white, as in Einstein's
    simple theory. It is slightly coloured, due to hydrodynamics and
    the fluctuation--dissipation theorem. This theoretical result from
    the 1970s was prompted by computer simulation results in apparent
    violation of Einstein's theory. We discuss how a direct
    experimental observation of this colour might be carried out by
    using optical tweezers to separate the thermal noise from the
    particle's dynamic response to it. Since the thermal noise is
    almost white, very good statistics is necessary to resolve its
    colour. That requires stable equipment and long recording times,
    possibly making this experiment one for the future only. We give
    results for experimental requirements and for stochastic errors as
    functions of experimental window and measurement time, and discuss
    some potential sources of systematic errors.},
}

@article { bedard08,
    author = SBedard #" and "# MMGKrishna #" and "# LMayne #" and "#
        SWEnglander,
    title = "Protein folding: Independent unrelated pathways or predetermined
        pathway with optional errors.",
    year = 2008,
    month = may,
    day = 20,
    journal = PNAS,
    volume = 105,
    number = 20,
    pages = "7182--7187",
    issn = "1091-6490",
    doi = "10.1073/pnas.0801864105",
    eprint = "http://www.pnas.org/content/105/20/7182.full.pdf",
    url = "http://www.pnas.org/content/105/20/7182.full",
    keywords = "Biochemistry;Guanidine;Kinetics;Micrococcal Nuclease;Models,
        Biological;Models, Chemical;Models, Theoretical;Protein
        Conformation;Protein Denaturation;Protein Folding;Protein Structure,
        Secondary;Proteins;Proteomics;Reproducibility of
        Results;Thermodynamics",
    abstract = "The observation of heterogeneous protein folding kinetics has
        been widely interpreted in terms of multiple independent unrelated
        pathways (IUP model), both experimentally and in theoretical
        calculations. However, direct structural information on folding
        intermediates and their properties now indicates that all of a protein
        population folds through essentially the same stepwise pathway,
        determined by cooperative native-like foldon units and the way that the
        foldons fit together in the native protein. It is essential to decide
        between these fundamentally different folding mechanisms. This article
        shows, contrary to previous supposition, that the heterogeneous folding
        kinetics observed for the staphylococcal nuclease protein (SNase) does
        not require alternative parallel pathways. SNase folding kinetics can
        be fit equally well by a single predetermined pathway that allows for
        optional misfolding errors, which are known to occur ubiquitously in
        protein folding. Structural, kinetic, and thermodynamic information for
        the folding intermediates and pathways of many proteins is consistent
        with the predetermined pathway-optional error (PPOE) model but contrary
        to the properties implied in IUP models."
}

@article { bell78,
    author = GIBell,
    title = "Models for the specific adhesion of cells to cells",
    year = 1978,
    month = may,
    day = 12,
    journal = SCI,
    volume = 200,
    number = 4342,
    pages = "618--627",
    issn = "0036-8075",
    url = "http://www.jstor.org/stable/1746930",
    keywords = "Antigen-Antibody Reactions; Cell Adhesion; Cell Membrane;
        Chemistry, Physical; Electrophysiology; Enzymes; Glycoproteins;
        Kinetics; Ligands; Membrane Proteins; Models, Biological; Receptors,
        Drug",
    abstract = "A theoretical framework is proposed for the analysis of
        adhesion between cells or of cells to surfaces when the adhesion is
        mediated by reversible bonds between specific molecules such as antigen
        and antibody, lectin and carbohydrate, or enzyme and substrate. From a
        knowledge of the reaction rates for reactants in solution and of their
        diffusion constants both in solution and on membranes, it is possible
        to estimate reaction rates for membrane-bound reactants. Two models are
        developed for predicting the rate of bond formation between cells and
        are compared with experiments. The force required to separate two cells
        is shown to be greater than the expected electrical forces between
        cells, and of the same order of magnitude as the forces required to
        pull gangliosides and perhaps some integral membrane proteins out of
        the cell membrane.",
    note = "The Bell model and a fair bit of cell bonding background.",
    project = "sawtooth simulation"
}

@article { berk91,
    author = DBerk #" and "# EEvans,
    title = "Detachment of agglutinin-bonded red blood cells. {III}. Mechanical
        analysis for large contact areas",
    year = 1991,
    month = apr,
    journal = BPJ,
    volume = 59,
    number = 4,
    pages = "861--872",
    issn = "0006-3495",
    keywords = "Cell Adhesion;Erythrocyte Membrane;Erythrocytes;Hemagglutinatio
        n;Hemagglutinins;Humans;Kinetics;Mathematics;Models,
        Biological;Pressure",
    abstract = "An experimental method and analysis are introduced which
        provide direct quantitation of the strength of adhesive contact for
        large agglutinin-bonded regions between macroscopically smooth membrane
        capsules (e.g., red blood cells). The approach yields intrinsic
        properties for separation of adherent regions independent of mechanical
        deformation of the membrane capsules during detachment. Conceptually,
        the micromechanical method involves one rigid test-capsule surface (in
        the form of a perfect sphere) held fixed by a micropipette and a second
        deformable capsule maneuvered with another micropipette to force
        contact with the test capsule. Only the test capsule is bound with
        agglutinin so that the maximum number of cross-bridges can be formed
        without steric interference. Following formation of a large adhesion
        region by mechanical impingement, the deformable capsule is detached
        from the rigid capsule surface by progressive aspiration into the
        micropipette. For the particular case modeled here, the deformable
        capsule is assumed to be a red blood cell which is preswollen by slight
        osmotic hydration before the test. The caliber of the detachment
        pipette is chosen so that the capsule will form a smooth cylindrical
        ``piston'' inside the pipette as it is aspirated. Because of the high
        flexibility of the membrane, the capsule naturally seals against the
        tube wall by pressurization even though it does not adhere to the
        glass. This arrangement maintains perfect axial symmetry and prevents
        the membrane from folding or buckling. Hence, it is possible to
        rigorously analyze the mechanics of deformation of the cell body to
        obtain the crucial ``transducer'' relation between pipette suction
        force and the membrane tension applied directly at the perimeter of the
        adhesive contact. Further, the geometry of the cell throughout the
        detachment process is predicted which provides accurate specification
        of the contact angle theta c between surfaces at the perimeter of the
        contact. A full analysis of red cell capsules during detachment has
        been carried out; however, it is shown that the shear rigidity of the
        red cell membrane can often be neglected so that the red cell can be
        treated as if it were an underfilled lipid bilayer vesicle. From the
        analysis, the mechanical leverage factor (1-cos theta c) and the
        membrane tension at the contact perimeter are determined to provide a
        complete description of the local mechanics of membrane separation as
        functions of large-scale experimental variables (e.g., suction force,
        contact diameter, overall cell length).(ABSTRACT TRUNCATED AT 400
        WORDS)"
}

@article { best02,
    author = RBest #" and "# SFowler #" and "# JTocaHerrera #" and "# JClarke,
    title = "A simple method for probing the mechanical unfolding pathway of
        proteins in detail",
    year = 2002,
    journal = PNAS,
    volume = 99,
    number = 19,
    pages = "12143--12148",
    doi = "10.1073/pnas.192351899",
    eprint = "http://www.pnas.org/cgi/reprint/99/19/12143.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/99/19/12143",
    abstract = "Atomic force microscopy is an exciting new single-molecule
        technique to add to the toolbox of protein (un)folding methods.
        However, detailed analysis of the unfolding of proteins on application
        of force has, to date, relied on protein molecular dynamics simulations
        or a qualitative interpretation of mutant data. Here we describe how
        protein engineering {Phi} value analysis can be adapted to characterize
        the transition states for mechanical unfolding of proteins. Single-
        molecule studies also have an advantage over bulk experiments, in that
        partial {Phi} values arising from partial structure in the transition
        state can be clearly distinguished from those averaged over alternate
        pathways. We show that unfolding rate constants derived in the standard
        way by using Monte Carlo simulations are not reliable because of the
        errors involved. However, it is possible to circumvent these problems,
        providing the unfolding mechanism is not changed by mutation, either by
        a modification of the Monte Carlo procedure or by comparing mutant and
        wild-type data directly. The applicability of the method is tested on
        simulated data sets and experimental data for mutants of titin I27.",
    note = "Points out order-of-magnitude errors in $k_{u0}$ estimation from
        fitting Monte Carlo simulations."
}

@article { best08a,
    author = RBest #" and "# GHummer,
    title = "Protein folding kinetics under force from molecular simulation.",
    year = 2008,
    month = mar,
    day = 26,
    journal = JACS,
    volume = 130,
    number = 12,
    pages = "3706--3707",
    issn = "1520-5126",
    doi = "10.1021/ja0762691",
    keywords = "Computer Simulation;Kinetics;Models, Chemical;Protein
        Folding;Stress, Mechanical;Ubiquitin",
    abstract = "Despite a large number of studies on the mechanical unfolding
        of proteins, there are still relatively few successful attempts to
        refold proteins in the presence of a stretching force. We explore
        refolding kinetics under force using simulations of a coarse-grained
        model of ubiquitin. The effects of force on the folding kinetics can be
        fitted by a one-dimensional Kramers theory of diffusive barrier
        crossing, resulting in physically meaningful parameters for the height
        and location of the folding activation barrier. By comparing parameters
        obtained from pulling in different directions, we find that the
        unfolded state plays a dominant role in the refolding kinetics. Our
        findings explain why refolding becomes very slow at even moderate
        pulling forces and suggest how it could be practically observed in
        experiments at higher forces."
}

@article { best08b,
    author = RBest #" and "# EPaci #" and "# GHummer #" and "# OKDudko,
    title = "Pulling direction as a reaction coordinate for the mechanical
        unfolding of single molecules.",
    year = 2008,
    month = may,
    day = 15,
    journal = JPC:B,
    volume = 112,
    number = 19,
    pages = "5968--5976",
    issn = "1520-6106",
    doi = "10.1021/jp075955j",
    keywords = "Computer Simulation;Kinetics;Models, Molecular;Protein
        Folding;Protein Structure, Tertiary;Time Factors;Ubiquitin",
    abstract = "The folding and unfolding kinetics of single molecules, such as
        proteins or nucleic acids, can be explored by mechanical pulling
        experiments. Determining intrinsic kinetic information, at zero
        stretching force, usually requires an extrapolation by fitting a
        theoretical model. Here, we apply a recent theoretical approach
        describing molecular rupture in the presence of force to unfolding
        kinetic data obtained from coarse-grained simulations of ubiquitin.
        Unfolding rates calculated from simulations over a broad range of
        stretching forces, for different pulling directions, reveal a
        remarkable ``turnover'' from a force-independent process at low force
        to a force-dependent process at high force, akin to the ``roll-over''
        in unfolding rates sometimes seen in studies using chemical denaturant.
        While such a turnover in rates is unexpected in one dimension, we
        demonstrate that it can occur for dynamics in just two dimensions. We
        relate the turnover to the quality of the pulling direction as a
        reaction coordinate for the intrinsic folding mechanism. A novel
        pulling direction, designed to be the most relevant to the intrinsic
        folding pathway, results in the smallest turnover. Our results are in
        accord with protein engineering experiments and simulations which
        indicate that the unfolding mechanism at high force can differ from the
        intrinsic mechanism. The apparent similarity between extrapolated and
        intrinsic rates in experiments, unexpected for different unfolding
        barriers, can be explained if the turnover occurs at low forces."
}

@article { borgia08,
    author = Borgia #" and "# Williams #" and "# Clarke,
    title = "Single-Molecule Studies of Protein Folding",
    year = 2008,
    month = jul,
    day = 07,
    journal = ARBC,
    volume = 77,
    pages = "101--125",
    issn = "0066-4154",
    doi = "10.1146/annurev.biochem.77.060706.093102",
    eprint = "http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.bioch
        em.77.060706.093102",
    url = "http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.biochem.
        77.060706.093102",
    abstract = "Although protein-folding studies began several decades ago, it
        is only recently that the tools to analyze protein folding at the
        single-molecule level have been developed. Advances in single-molecule
        fluorescence and force spectroscopy techniques allow investigation of
        the folding and dynamics of single protein molecules, both at
        equilibrium and as they fold and unfold. The experiments are far from
        simple, however, both in execution and in interpretation of the
        results. In this review, we discuss some of the highlights of the work
        so far and concentrate on cases where comparisons with the classical
        experiments can be made. We conclude that, although there have been
        relatively few startling insights from single-molecule studies, the
        rapid progress that has been made suggests that these experiments have
        significant potential to advance our understanding of protein folding.
        In particular, new techniques offer the possibility to explore regions
        of the energy landscape that are inaccessible to classical ensemble
        measurements and, perhaps, to observe rare events undetectable by other
        means."
}

@article { braverman08,
    author = EBraverman #" and "# RMamdani,
    title = "Continuous versus pulse harvesting for population models in
        constant and variable environment",
    year = 2008,
    month = sep,
    day = 18,
    journal = JMathBiol,
    volume = 57,
    number = 3,
    pages = "413--434",
    issn = "0303-6812",
    doi = "10.1007/s00285-008-0169-z",
    eprint =
        "http://www.springerlink.com/content/a1m23v50201m2401/fulltext.pdf",
    url = "http://www.springerlink.com/content/a1m23v50201m2401/",
    abstract = "We consider both autonomous and nonautonomous population models
        subject to either impulsive or continuous harvesting. It is
        demonstrated in the paper that the impulsive strategy can be as good as
        the continuous one, but cannot outperform it. We introduce a model,
        where certain harm to the population is incorporated in each harvesting
        event, and study it for the logistic and the Gompertz laws of growth.
        In this case, impulsive harvesting is not only the optimal strategy but
        is the only possible one.",
    note = "An example of non-exponential Gomperz law."
}

@article { brochard-wyart99,
    author = FBrochard-Wyart #" and "# ABuguin #" and "# PGdeGennes,
    title = "Dynamics of taut {DNA} chains",
    year = 1999,
    journal = EPL,
    volume = 47,
    number = 2,
    pages = "171--174",
    eprint =
        "http://www.iop.org/EJ/article/0295-5075/47/2/171/epl_47_2_171.pdf",
    url = "http://stacks.iop.org/0295-5075/47/171",
    abstract = {We discuss the dynamics of stretched DNA chains, subjected to a
        tension force f, in a "taut" regime where ph = flp0/kBT $>$ 1 (lp0
        being the unperturbed persistence length). We deal with two variables:
        the local transverse displacements u, and the longitudinal position of
        a monomer u[?]. The variables u and u[?] follow two distinct Rouse
        equations, with diffusion coefficients D[?] = f/e (where e is the
        solvent viscosity) and D[?] = 4ph1/2D[?]. We apply these ideas to a
        discussion of various transient regimes.},
    note = "Theory for weakly bending relaxation modes in WLCs and FJCs."
}

@article { brockwell02,
    author = DJBrockwell #" and "# GSBeddard #" and "# JClarkson #" and "#
        RCZinober #" and "# AWBlake #" and "# JTrinick #" and "# PDOlmsted #"
        and "# DASmith #" and "# SERadford,
    title = "The effect of core destabilization on the mechanical resistance of
        {I27}",
    year = 2002,
    month = jul,
    journal = BPJ,
    volume = 83,
    number = 1,
    pages = "458--472",
    issn = "0006-3495",
    doi = "10.1016/S0006-3495(02)75182-5",
    eprint = "http://www.biophysj.org/cgi/reprint/83/1/458.pdf",
    url = "http://www.biophysj.org/cgi/content/abstract/83/1/458",
    keywords = "Amino Acid Sequence; Dose-Response Relationship, Drug;
        Kinetics; Magnetic Resonance Spectroscopy; Models, Molecular; Molecular
        Sequence Data; Monte Carlo Method; Muscle Proteins; Mutation; Peptide
        Fragments; Protein Denaturation; Protein Folding; Protein Kinases;
        Protein Structure, Secondary; Protein Structure, Tertiary; Proteins;
        Thermodynamics",
    abstract = "It is still unclear whether mechanical unfolding probes the
        same pathways as chemical denaturation. To address this point, we have
        constructed a concatamer of five mutant I27 domains (denoted (I27)(5)*)
        and used it for mechanical unfolding studies. This protein consists of
        four copies of the mutant C47S, C63S I27 and a single copy of C63S I27.
        These mutations severely destabilize I27 (DeltaDeltaG(UN) = 8.7 and
        17.9 kJ mol(-1) for C63S I27 and C47S, C63S I27, respectively). Both
        mutations maintain the hydrogen bond network between the A' and G
        strands postulated to be the major region of mechanical resistance for
        I27. Measuring the speed dependence of the force required to unfold
        (I27)(5)* in triplicate using the atomic force microscope allowed a
        reliable assessment of the intrinsic unfolding rate constant of the
        protein to be obtained (2.0 x 10(-3) s(-1)). The rate constant of
        unfolding measured by chemical denaturation is over fivefold faster
        (1.1 x 10(-2) s(-1)), suggesting that these techniques probe different
        unfolding pathways. Also, by comparing the parameters obtained from the
        mechanical unfolding of a wild-type I27 concatamer with that of
        (I27)(5)*, we show that although the observed forces are considerably
        lower, core destabilization has little effect on determining the
        mechanical sensitivity of this domain."
}

@article { brockwell03,
    author = DJBrockwell #" and "# EPaci #" and "# RCZinober #" and "#
        GSBeddard #" and "# PDOlmsted #" and "# DASmith #" and "# RNPerham #"
        and "# SERadford,
    title = "Pulling geometry defines the mechanical resistance of a beta-sheet
        protein",
    year = 2003,
    month = sep,
    day = 17,
    journal = NSB,
    volume = 10,
    number = 9,
    pages = "731--737",
    issn = "1072-8368",
    doi = "10.1038/nsb968",
    eprint = "http://www.nature.com/nsmb/journal/v10/n9/pdf/nsb968.pdf",
    url = "http://www.nature.com/nsmb/journal/v10/n9/abs/nsb968.html",
    keywords = "Anisotropy;Escherichia coli;Kinetics;Models, Molecular;Monte
        Carlo Method;Protein Folding;Protein Structure, Secondary;Protein
        Structure, Tertiary;Proteins;Software;Temperature;Thermodynamics",
    abstract = "Proteins show diverse responses when placed under mechanical
        stress. The molecular origins of their differing mechanical resistance
        are still unclear, although the orientation of secondary structural
        elements relative to the applied force vector is thought to have an
        important function. Here, by using a method of protein immobilization
        that allows force to be applied to the same all-beta protein, E2lip3,
        in two different directions, we show that the energy landscape for
        mechanical unfolding is markedly anisotropic. These results, in
        combination with molecular dynamics (MD) simulations, reveal that the
        unfolding pathway depends on the pulling geometry and is associated
        with unfolding forces that differ by an order of magnitude. Thus, the
        mechanical resistance of a protein is not dictated solely by amino acid
        sequence, topology or unfolding rate constant, but depends critically
        on the direction of the applied extension.",
    note = "Another scaffold effect paper. TODO: details"
}

@article { brower-toland02,
    author = BDBrowerToland #" and "# CSmith #" and "# RYeh #" and "# JLis #"
        and "# CPeterson #" and "# MDWang,
    title = "From the Cover: Mechanical disruption of individual nucleosomes
        reveals a reversible multistage release of {DNA}",
    year = 2002,
    journal = PNAS,
    volume = 99,
    number = 4,
    pages = "1960--1965",
    doi = "10.1073/pnas.022638399",
    eprint = "http://www.pnas.org/cgi/reprint/99/4/1960.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/99/4/1960",
    abstract = "The dynamic structure of individual nucleosomes was examined by
        stretching nucleosomal arrays with a feedback-enhanced optical trap.
        Forced disassembly of each nucleosome occurred in three stages.
        Analysis of the data using a simple worm-like chain model yields 76 bp
        of DNA released from the histone core at low stretching force.
        Subsequently, 80 bp are released at higher forces in two stages: full
        extension of DNA with histones bound, followed by detachment of
        histones. When arrays were relaxed before the dissociated state was
        reached, nucleosomes were able to reassemble and to repeat the
        disassembly process. The kinetic parameters for nucleosome disassembly
        also have been determined."
}

@article { bryngelson87,
    author = JDBryngelson #" and "# PGWolynes,
    title = "Spin glasses and the statistical mechanics of protein folding",
    year = 1987,
    month = nov,
    journal = PNAS,
    volume = 84,
    number = 21,
    pages = "7524--7528",
    issn = "0027-8424",
    keywords = "Kinetics; Mathematics; Models, Theoretical; Protein
        Conformation; Proteins; Stochastic Processes",
    abstract = "The theory of spin glasses was used to study a simple model of
        protein folding. The phase diagram of the model was calculated, and the
        results of dynamics calculations are briefly reported. The relation of
        these results to folding experiments, the relation of these hypotheses
        to previous protein folding theories, and the implication of these
        hypotheses for protein folding prediction schemes are discussed.",
    note = "Seminal protein folding via energy landscape paper."
}

@article { bryngelson95,
    author = JDBryngelson #" and "# JNOnuchic #" and "# NDSocci #" and "#
        PGWolynes,
    title = "Funnels, pathways, and the energy landscape of protein folding: a
        synthesis",
    year = 1995,
    month = mar,
    journal = PROT,
    volume = 21,
    number = 3,
    pages = "167--195",
    issn = "0887-3585",
    doi = "10.1002/prot.340210302",
    keywords = "Amino Acid Sequence; Chemistry, Physical; Computer Simulation;
        Data Interpretation, Statistical; Kinetics; Models, Chemical; Molecular
        Sequence Data; Protein Biosynthesis; Protein Conformation; Protein
        Folding; Proteins; Thermodynamics",
    abstract = "The understanding, and even the description of protein folding
        is impeded by the complexity of the process. Much of this complexity
        can be described and understood by taking a statistical approach to the
        energetics of protein conformation, that is, to the energy landscape.
        The statistical energy landscape approach explains when and why unique
        behaviors, such as specific folding pathways, occur in some proteins
        and more generally explains the distinction between folding processes
        common to all sequences and those peculiar to individual sequences.
        This approach also gives new, quantitative insights into the
        interpretation of experiments and simulations of protein folding
        thermodynamics and kinetics. Specifically, the picture provides simple
        explanations for folding as a two-state first-order phase transition,
        for the origin of metastable collapsed unfolded states and for the
        curved Arrhenius plots observed in both laboratory experiments and
        discrete lattice simulations. The relation of these quantitative ideas
        to folding pathways, to uniexponential vs. multiexponential behavior in
        protein folding experiments and to the effect of mutations on folding
        is also discussed. The success of energy landscape ideas in protein
        structure prediction is also described. The use of the energy landscape
        approach for analyzing data is illustrated with a quantitative analysis
        of some recent simulations, and a qualitative analysis of experiments
        on the folding of three proteins. The work unifies several previously
        proposed ideas concerning the mechanism protein folding and delimits
        the regions of validity of these ideas under different thermodynamic
        conditions."
}

@article { bullard06,
    author = BBullard #" and "# TGarcia #" and "# VBenes #" and "# MLeake #"
        and "# WALinke #" and "# AOberhauser,
    title = "The molecular elasticity of the insect flight muscle proteins
        projectin and kettin",
    year = 2006,
    journal = PNAS,
    volume = 103,
    number = 12,
    pages = "4451--4456",
    doi = "10.1073/pnas.0509016103",
    eprint = "http://www.pnas.org/cgi/reprint/103/12/4451.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/103/12/4451",
    abstract = "Projectin and kettin are titin-like proteins mainly responsible
        for the high passive stiffness of insect indirect flight muscles, which
        is needed to generate oscillatory work during flight. Here we report
        the mechanical properties of kettin and projectin by single-molecule
        force spectroscopy. Force-extension and force-clamp curves obtained
        from Lethocerus projectin and Drosophila recombinant projectin or
        kettin fragments revealed that fibronectin type III domains in
        projectin are mechanically weaker (unfolding force, Fu {approx} 50-150
        pN) than Ig-domains (Fu {approx} 150-250 pN). Among Ig domains in
        Sls/kettin, the domains near the N terminus are less stable than those
        near the C terminus. Projectin domains refolded very fast [85% at 15
        s-1 (25{degrees}C)] and even under high forces (15-30 pN). Temperature
        affected the unfolding forces with a Q10 of 1.3, whereas the refolding
        speed had a Q10 of 2-3, probably reflecting the cooperative nature of
        the folding mechanism. High bending rigidities of projectin and kettin
        indicated that straightening the proteins requires low forces. Our
        results suggest that titin-like proteins in indirect flight muscles
        could function according to a folding-based-spring mechanism."
}

@article { bustamante08,
    author = CBustamante,
    title = "In singulo Biochemistry: When Less Is More",
    year = 2008,
    journal = ARBC,
    volume = 77,
    pages = "45--50",
    issn = "0066-4154",
    doi = "10.1146/annurev.biochem.012108.120952",
    eprint = "http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.bioch
        em.012108.120952",
    url = "http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.biochem.
        012108.120952",
    abstract = "It has been over one-and-a-half decades since methods of
        single-molecule detection and manipulation were first introduced in
        biochemical research. Since then, the application of these methods to
        an expanding variety of problems has grown at a vertiginous pace. While
        initially many of these experiments led more to confirmatory results
        than to new discoveries, today single-molecule methods are often the
        methods of choice to establish new mechanism-based results in
        biochemical research. Throughout this process, improvements in the
        sensitivity, versatility, and both spatial and temporal resolution of
        these techniques has occurred hand in hand with their applications. We
        discuss here some of the advantages of single-molecule methods over
        their bulk counterparts and argue that these advantages should help
        establish them as essential tools in the technical arsenal of the
        modern biochemist."
}

@article { bustamante94,
    author = CBustamante #" and "# JFMarko #" and "# EDSiggia #" and "# SSmith,
    title = "Entropic elasticity of lambda-phage {DNA}",
    year = 1994,
    month = sep,
    day = 09,
    journal = SCI,
    volume = 265,
    number = 5178,
    pages = "1599--1600",
    issn = "0036-8075",
    doi = "10.1126/science.8079175",
    eprint = "http://www.sciencemag.org/cgi/reprint/265/5178/1599.pdf",
    url = "http://www.sciencemag.org/cgi/content/abstract/265/5178/1599",
    keywords = "Bacteriophage lambda; DNA, Viral; Least-Squares Analysis;
        Thermodynamics",
    note = "WLC interpolation formula."
}

@article { bustanji03,
    author = YBustanji #" and "# CArciola #" and "# MConti #" and "# EMandello
        #" and "# LMontanaro #" and "# BSamori,
    title = "Dynamics of the interaction between a fibronectin molecule and a
        living bacterium under mechanical force",
    year = 2003,
    journal = PNAS,
    volume = 100,
    number = 23,
    pages = "13292--13297",
    doi = "10.1073/pnas.1735343100",
    eprint = "http://www.pnas.org/cgi/reprint/100/23/13292.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/100/23/13292",
    abstract = "Fibronectin (Fn) is an important mediator of bacterial
        invasions and of persistent infections like that of Staphylococcus
        epidermis. Similar to many other types of cell-protein adhesion, the
        binding between Fn and S. epidermidis takes place under physiological
        shear rates. We investigated the dynamics of the interaction between
        individual living S. epidermidis cells and single Fn molecules under
        mechanical force by using the scanning force microscope. The mechanical
        strength of this interaction and the binding site in the Fn molecule
        were determined. The energy landscape of the binding/unbinding process
        was mapped, and the force spectrum and the association and dissociation
        rate constants of the binding pair were measured. The interaction
        between S. epidermidis cells and Fn molecules is compared with those of
        two other protein/ligand pairs known to mediate different dynamic
        states of adhesion of cells under a hydrodynamic flow: the firm
        adhesion mediated by biotin/avidin interactions, and the rolling
        adhesion, mediated by L-selectin/P-selectin glycoprotein ligand-1
        interactions. The inner barrier in the energy landscape of the Fn case
        characterizes a high-energy binding mode that can sustain larger
        deformations and for significantly longer times than the correspondent
        high-strength L-selectin/P-selectin glycoprotein ligand-1 binding mode.
        The association kinetics of the former interaction is much slower to
        settle than the latter. On this basis, the observations made at the
        macroscopic scale by other authors of a strong lability of the
        bacterial adhesions mediated by Fn under high turbulent flow are
        rationalized at the molecular level."
}

@article{ martin87,
  author = YMartin #" and "# CCWilliams #" and "# HKWickramasinghe,
  title = {Atomic force microscope---force mapping and profiling on a
    sub 100-\AA scale},
  year = 1987,
  month = may,
  day = 15,
  journal = JAP,
  volume = 61,
  number = 10,
  pages = {4723--4729},
  issn = "0021-8979",
  issn_online = "1089-7550",
  doi = {10.1063/1.338807},
  url = {http://jap.aip.org/resource/1/japiau/v61/i10/p4723_s1},
  language = "eng",
  abstract = {A modified version of the atomic force microscope is
    introduced that enables a precise measurement of the force between
    a tip and a sample over a tip-sample distance range of 30--150
    \AA. As an application, the force signal is used to maintain the
    tip-sample spacing constant, so that profiling can be achieved
    with a spatial resolution of 50 \AA. A second scheme allows the
    simultaneous measurement of force and surface profile; this scheme
    has been used to obtain material-dependent information from
    surfaces of electronic materials.},
}

@article { butt95,
    author = HJButt #" and "# MJaschke,
    title = "Calculation of thermal noise in atomic force microscopy",
    year = 1995,
    journal = NT,
    volume = 6,
    number = 1,
    pages = "1--7",
    doi = "10.1088/0957-4484/6/1/001",
    url = "http://stacks.iop.org/0957-4484/6/1",
    abstract = "Thermal fluctuations of the cantilever are a fundamental source
        of noise in atomic force microscopy. We calculated thermal noise using
        the equipartition theorem and considering all possible vibration modes
        of the cantilever. The measurable amplitude of thermal noise depends on
        the temperature, the spring constant K of the cantilever and on the
        method by which the cantilever defletion is detected. If the deflection
        is measured directly, e.g. with an interferometer or a scanning
        tunneling microscope, the thermal noise of a cantilever with a free end
        can be calculated from square root kT/K. If the end of the cantilever
        is supported by a hard surface no thermal fluctuations of the
        deflection are possible. If the optical lever technique is applied to
        measure the deflection, the thermal noise of a cantilever with a free
        end is square root 4kT/3K. When the cantilever is supported thermal
        noise decreases to square root kT/3K, but it does not vanish.",
    note = "Corrections to basic $kx^2 = kB T$ due to higher order modes in
        rectangular cantilevers.",
    project = "Cantilever Calibration"
}

@article { cao07,
    author = YCao #" and "# MBalamurali #" and "# DSharma #" and "# HLi,
    title = "A functional single-molecule binding assay via force spectroscopy",
    year = 2007,
    journal = PNAS,
    volume = 104,
    number = 40,
    pages = "15677--15681",
    doi = "10.1073/pnas.0705367104",
    eprint = "http://www.pnas.org/cgi/reprint/104/40/15677.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/104/40/15677",
    abstract = "Protein-ligand interactions, including protein-protein
        interactions, are ubiquitously essential in biological processes and
        also have important applications in biotechnology. A wide range of
        methodologies have been developed for quantitative analysis of protein-
        ligand interactions. However, most of them do not report direct
        functional/structural consequence of ligand binding. Instead they only
        detect the change of physical properties, such as fluorescence and
        refractive index, because of the colocalization of protein and ligand,
        and are susceptible to false positives. Thus, important information
        about the functional state of proteinligand complexes cannot be
        obtained directly. Here we report a functional single-molecule binding
        assay that uses force spectroscopy to directly probe the functional
        consequence of ligand binding and report the functional state of
        protein-ligand complexes. As a proof of principle, we used protein G
        and the Fc fragment of IgG as a model system in this study. Binding of
        Fc to protein G does not induce major structural changes in protein G
        but results in significant enhancement of its mechanical stability.
        Using mechanical stability of protein G as an intrinsic functional
        reporter, we directly distinguished and quantified Fc-bound and Fc-free
        forms of protein G on a single-molecule basis and accurately determined
        their dissociation constant. This single-molecule functional binding
        assay is label-free, nearly background-free, and can detect functional
        heterogeneity, if any, among proteinligand interactions. This
        methodology opens up avenues for studying protein-ligand interactions
        in a functional context, and we anticipate that it will find broad
        application in diverse protein-ligand systems."
}

@article { carl01,
    author = PCarl #" and "# CKwok #" and "# GManderson #" and "# DSpeicher #"
        and "# DDischer,
    title = "Forced unfolding modulated by disulfide bonds in the Ig domains of
        a cell adhesion molecule",
    year = 2001,
    journal = PNAS,
    volume = 98,
    number = 4,
    pages = "1565--1570",
    doi = "10.1073/pnas.031409698",
    eprint = "http://www.pnas.org/cgi/reprint/98/4/1565.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/98/4/1565",
    abstract = ""
}

@article { carrion-vazquez00,
    author = MCarrionVazquez #" and "# AOberhauser #" and "# TEFisher #" and "#
        PMarszalek #" and "# HLi #" and "# JFernandez,
    title = "Mechanical design of proteins studied by single-molecule force
        spectroscopy and protein engineering",
    year = 2000,
    journal = PBPMB,
    volume = 74,
    number = "1-2",
    pages = "63--91",
    doi = "10.1016/S0079-6107(00)00017-1",
    issn = "0079-6107",
    eprint = "http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1302160&blo
        btype=pdf",
    url = "http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1302160",
    keywords = "Elasticity;Hydrogen Bonding;Microscopy, Atomic Force;Protein
        Denaturation;Protein Engineering;Protein Folding;Recombinant
        Proteins;Signal Processing, Computer-Assisted",
    abstract = "Mechanical unfolding and refolding may regulate the molecular
        elasticity of modular proteins with mechanical functions. The
        development of the atomic force microscopy (AFM) has recently enabled
        the dynamic measurement of these processes at the single-molecule
        level. Protein engineering techniques allow the construction of
        homomeric polyproteins for the precise analysis of the mechanical
        unfolding of single domains. alpha-Helical domains are mechanically
        compliant, whereas beta-sandwich domains, particularly those that
        resist unfolding with backbone hydrogen bonds between strands
        perpendicular to the applied force, are more stable and appear
        frequently in proteins subject to mechanical forces. The mechanical
        stability of a domain seems to be determined by its hydrogen bonding
        pattern and is correlated with its kinetic stability rather than its
        thermodynamic stability. Force spectroscopy using AFM promises to
        elucidate the dynamic mechanical properties of a wide variety of
        proteins at the single molecule level and provide an important
        complement to other structural and dynamic techniques (e.g., X-ray
        crystallography, NMR spectroscopy, patch-clamp).",
  note = {Surface contact \fref{figure}{2} is a modified version of
    \xref{baljon96}{figure}{1}.  They are both good pictures for
    explaining that the tip's radius of curvature ($\sim 20\U{nm}$) is
    larger than the I27 domains\citet{improta96} ($\sim 2\U{nm}$).},
}

@article { carrion-vazquez03,
    author = MCarrionVazquez #" and "# HLi #" and "# HLu #" and "# PMarszalek
        #" and "# AOberhauser #" and "# JFernandez,
    title = "The mechanical stability of ubiquitin is linkage dependent",
    year = 2003,
    month = sep,
    day = 17,
    journal = NSB,
    volume = 10,
    number = 9,
    pages = "738--743",
    issn = "1072-8368",
    doi = "10.1038/nsb965",
    eprint = "http://www.nature.com/nsmb/journal/v10/n9/pdf/nsb965.pdf",
    url = "http://www.nature.com/nsmb/journal/v10/n9/abs/nsb965.html",
    keywords = "Humans;Hydrogen Bonding;Kinetics;Lysine;Microscopy, Atomic
        Force;Models, Molecular;Polyubiquitin;Protein Binding;Protein
        Folding;Protein Structure, Tertiary;Ubiquitin",
    abstract = "Ubiquitin chains are formed through the action of a set of
        enzymes that covalently link ubiquitin either through peptide bonds or
        through isopeptide bonds between their C terminus and any of four
        lysine residues. These naturally occurring polyproteins allow one to
        study the mechanical stability of a protein, when force is applied
        through different linkages. Here we used single-molecule force
        spectroscopy techniques to examine the mechanical stability of
        N-C-linked and Lys48-C-linked ubiquitin chains. We combined these
        experiments with steered molecular dynamics (SMD) simulations and found
        that the mechanical stability and unfolding pathway of ubiquitin
        strongly depend on the linkage through which the mechanical force is
        applied to the protein. Hence, a protein that is otherwise very stable
        may be easily unfolded by a relatively weak mechanical force applied
        through the right linkage. This may be a widespread mechanism in
        biological systems."
}

@article { carrion-vazquez99a,
    author = MCarrionVazquez #" and "# PMarszalek #" and "# AOberhauser #" and
        "# JFernandez,
    title = "Atomic force microscopy captures length phenotypes in single
        proteins",
    year = 1999,
    journal = PNAS,
    volume = 96,
    number = 20,
    pages = "11288--11292",
    doi = "10.1073/pnas.96.20.11288",
    eprint = "http://www.pnas.org/cgi/reprint/96/20/11288.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/96/20/11288",
    abstract = ""
}

@article { carrion-vazquez99b,
    author = MCarrionVazquez #" and "# AOberhauser #" and "# SFowler #" and "#
        PMarszalek #" and "# SBroedel #" and "# JClarke #" and "# JFernandez,
    title = "Mechanical and chemical unfolding of a single protein: A
        comparison",
    year = 1999,
    journal = PNAS,
    volume = 96,
    number = 7,
    pages = "3694--3699",
    doi = "10.1073/pnas.96.7.3694",
    eprint = "http://www.pnas.org/cgi/reprint/96/7/3694.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/96/7/3694"
}

@article { chyan04,
    author = CLChyan #" and "# FCLin #" and "# HPeng #" and "# JMYuan #" and "#
        CHChang #" and "# SHLin #" and "# GYang,
    title = "Reversible mechanical unfolding of single ubiquitin molecules",
    year = 2004,
    month = dec,
    day = 10,
    address = "Department of Chemistry, National Dong Hwa University,
        Hualien, Taiwan.",
    journal = BPJ,
    volume = 87,
    number = 6,
    pages = "3995--4006",
    issn = "0006-3495",
    doi = "10.1529/biophysj.104.042754",
    eprint = "http://download.cell.com/biophysj/pdf/PIIS0006349504738643.pdf",
    url = "http://www.cell.com/biophysj/abstract/S0006-3495(04)73864-3",
    language = "eng",
    keywords = "Computer
        Simulation;Elasticity;Mechanics;Micromanipulation;Microscopy, Atomic
        Force;Models, Chemical;Models, Molecular;Protein Conformation;Protein
        Denaturation;Protein Folding;Stress, Mechanical;Structure-Activity
        Relationship;Ubiquitin",
    abstract = "Single-molecule manipulation techniques have enabled the
        characterization of the unfolding and refolding process of individual
        protein molecules, using mechanical forces to initiate the unfolding
        transition. Experimental and computational results following this
        approach have shed new light on the mechanisms of the mechanical
        functions of proteins involved in several cellular processes, as well
        as revealed new information on the protein folding/unfolding free-
        energy landscapes. To investigate how protein molecules of different
        folds respond to a stretching force, and to elucidate the effects of
        solution conditions on the mechanical stability of a protein, we
        synthesized polymers of the protein ubiquitin and characterized the
        force-induced unfolding and refolding of individual ubiquitin molecules
        using an atomic-force-microscope-based single-molecule manipulation
        technique. The ubiquitin molecule was highly resistant to a stretching
        force, and the mechanical unfolding process was reversible. A model
        calculation based on the hydrogen-bonding pattern in the native
        structure was performed to explain the origin of this high mechanical
        stability. Furthermore, pH effects were studied and it was found that
        the forces required to unfold the protein remained constant within a pH
        range around the neutral value, and forces decreased as the solution pH
        was lowered to more acidic values.",
    note = "includes pH effects",
}

@article { ciccotti86,
    author = GCiccotti #" and "# JPRyckaert,
    title = "Molecular dynamics simulation of rigid molecules",
    year = 1986,
    journal = CPR,
    volume = 4,
    number = 6,
    pages = "346--392",
    issn = "0167-7977",
    doi = "10.1016/0167-7977(86)90022-5",
    url = "http://dx.doi.org/10.1016/0167-7977(86)90022-5",
    note = "I haven't read this, but it looks like a nice review of MD with
        constraints."
}

@article { claverie01,
    author = JMClaverie,
    title = "Gene number. What if there are only 30,000 human genes?",
    year = 2001,
    month = feb,
    day = 16,
    journal = SCI,
    volume = 291,
    number = 5507,
    pages = "1255--1257",
    issn = "0036-8075",
    url = "http://www.sciencemag.org/cgi/content/full/291/5507/1255",
    keywords = "Animals;Computational Biology;Drug Industry;Expressed Sequence
        Tags;Gene Expression;Gene Expression Regulation;Genes;Genetic
        Techniques;Genome, Human;Genomics;Human Genome Project;Humans;Models,
        Genetic;Polymorphism, Single Nucleotide;Proteins;RNA, Messenger"
}

@misc { codata-boltzmann,
    key = "codata-boltzmann",
    crossref = "codata06",
    url = "http://physics.nist.gov/cgi-bin/cuu/Value?k"
}

@article { codata06,
    author = PJMohr #" and "# BNTaylor #" and "# DBNewell,
    key = "codata06",
    title = "{CODATA} recommended values of the fundamental physical constants:
        2006",
    year = 2008,
    month = jun,
    journal = RMP,
    volume = 80,
    number = 2,
    pages = "633--730",
    numpages = 97,
    publisher = APS,
    doi = "10.1103/RevModPhys.80.633"
}

@article { collins03,
    author = FSCollins #" and "# MMorgan #" and "# APatrinos,
    title = "The Human Genome Project: Lessons from large-scale biology.",
    year = 2003,
    month = apr,
    day = 11,
    journal = SCI,
    volume = 300,
    number = 5617,
    pages = "286--290",
    issn = "1095-9203",
    doi = "10.1126/science.1084564",
    eprint = "http://www.sciencemag.org/cgi/reprint/300/5617/286.pdf",
    url = "http://www.sciencemag.org/cgi/content/summary/300/5617/277",
    keywords = "Access to Information;Computational Biology;Databases, Nucleic
        Acid;Genome, Human;Genomics;Government Agencies;History, 20th
        Century;Human Genome Project;Humans;International Cooperation;National
        Institutes of Health (U.S.);Private Sector;Public Policy;Public
        Sector;Publishing;Quality Control;Sequence Analysis, DNA;United States",
    note = "See also: \href{http://www.ornl.gov/sci/techresources/Human_Genome/
        project/journals/journals.shtml}{Landmark HPG Papers}"
}

@article { cornish07,
    author = PVCornish #" and "# THa,
    title = "A survey of single-molecule techniques in chemical biology",
    year = 2007,
    month = jan,
    day = 23,
    journal = ACS:ChemBiol,
    volume = 2,
    number = 1,
    pages = "53--61",
    issn = "1554-8937",
    doi = "10.1021/cb600342a",
    keywords = "Animals;Data Collection;Humans;Microscopy, Atomic
        Force;Microscopy, Fluorescence;Molecular Biology",
    abstract = "Single-molecule methods have revolutionized scientific research
        by rendering the investigation of once-inaccessible biological
        processes amenable to scientific inquiry. Several of the more
        established techniques will be emphasized in this Review, including
        single-molecule fluorescence microscopy, optical tweezers, and atomic
        force microscopy, which have been applied to many diverse biological
        processes. Serving as a taste of all the exciting research currently
        underway, recent examples will be discussed of translocation of RNA
        polymerase, myosin VI walking, protein folding, and enzyme activity. We
        will end by providing an assessment of what the future holds, including
        techniques that are currently in development."
}

@book { cowan98,
    author = GCowan,
    title = "Statistical Data Analysis",
    year = 1998,
    publisher = OUP,
    address = "New York",
    note = "Noise deconvolution in Chapter 11",
    project = "Cantilever Calibration"
}

@article { craig01,
    author = DCraig #" and "# AKrammer #" and "# KSchulten #" and "# VVogel,
    title = "Comparison of the early stages of forced unfolding for fibronectin
        type {III} modules",
    year = 2001,
    journal = PNAS,
    volume = 98,
    number = 10,
    pages = "5590--5595",
    doi = "10.1073/pnas.101582198",
    eprint = "http://www.pnas.org/cgi/reprint/98/10/5590.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/98/10/5590",
    abstract = ""
}

@article { delpech01,
    author = BDelpech #" and "# MNCourel #" and "# CMaingonnat #" and "#
        CChauzy #" and "# RSesboue #" and "# GPratesi,
    title = "Hyaluronan digestion and synthesis in an experimental model of
        metastatic tumour",
    year = 2001,
    month = "September/October",
    journal = HistochemJ,
    volume = 33,
    number = "9-10",
    pages = "553--558",
    issn = "0018-2214",
    keywords = "Animals;Culture Media;Humans;Hyaluronic
        Acid;Hyaluronoglucosaminidase;Mice;Mice, Nude;Neoplasm
        Metastasis;Neoplasm Transplantation;Neoplasms, Experimental;Tumor
        Cells, Cultured",
    abstract = "To approach the question of hyaluronan catabolism in tumours,
        we have selected the cancer cell line H460M, a highly metastatic cell
        line in the nude mouse. H460M cells release hyaluronidase in culture
        media at a high rate of 57 pU/cell/h, without producing hyaluronan.
        Hyaluronidase was measured in the H460M cell culture medium at the
        optimum pH 3.8, and was not found above pH 4.5, with the enzyme-linked
        sorbent assay technique and zymography. Tritiated hyaluronan was
        digested at pH 3.8 by cells or cell membranes as shown by gel
        permeation chromatography, but no activity was recorded at pH 7 with
        this technique. Hyaluronan was digested in culture medium by tumour
        slices, prepared from tumours developed in nude mice grafted with H460M
        cells, showing that hyaluronan could be digested in complex tissue at
        physiological pH. Culture of tumour slices with tritiated acetate
        resulted in the accumulation within 2 days of radioactive
        macromolecules in the culture medium. The radioactive macromolecular
        material was mostly digested by Streptomyces hyaluronidase, showing
        that hyaluronan was its main component and that hyaluronan synthesis
        occurred together with its digestion. These results demonstrate that
        the membrane-associated hyaluronidase of H460M cells can act in vivo,
        and that hyaluronan, which is synthesised by the tumour stroma, can be
        made soluble and reduced to a smaller size by tumour cells before being
        internalised and further digested."
}

@article { diCola05,
    author = EDCola #" and "# TAWaigh #" and "# JTrinick #" and "#
        LTskhovrebova #" and "# AHoumeida #" and "# WPyckhout-Hintzen #" and "#
        CDewhurst,
    key = "diCola05",
    title = "Persistence length of titin from rabbit skeletal muscles measured
        with scattering and microrheology techniques",
    year = 2005,
    month = jun,
    day = 25,
    journal = BPJ,
    volume = 88,
    number = 6,
    pages = "4095--4106",
    issn = "0006-3495",
    doi = "10.1529/biophysj.104.054908",
    eprint = "http://download.cell.com/biophysj/pdf/PIIS0006349505734603.pdf",
    url = "http://www.cell.com/biophysj/retrieve/pii/S0006349505734603",
    keywords = "Animals;Biophysics;Elasticity;Light;Muscle Proteins;Muscle,
        Skeletal;Neutrons;Protein Conformation;Protein
        Kinases;Rabbits;Rheology;Scattering, Radiation;Temperature",
    abstract = "The persistence length of titin from rabbit skeletal muscles
        was measured using a combination of static and dynamic light
        scattering, and neutron small angle scattering. Values of persistence
        length in the range 9-16 nm were found for titin-II, which corresponds
        to mainly physiologically inelastic A-band part of the protein, and for
        a proteolytic fragment with 100-nm contour length from the
        physiologically elastic I-band part. The ratio of the hydrodynamic
        radius to the static radius of gyration indicates that the proteins
        obey Gaussian statistics typical of a flexible polymer in a -solvent.
        Furthermore, measurements of the flexibility as a function of
        temperature demonstrate that titin-II and the I-band titin fragment
        experience a similar denaturation process; unfolding begins at 318 K
        and proceeds in two stages: an initial gradual 50\% change in
        persistence length is followed by a sharp unwinding transition at 338
        K. Complementary microrheology (video particle tracking) measurements
        indicate that the viscoelasticity in dilute solution behaves according
        to the Flory/Fox model, providing a value of the radius of gyration for
        titin-II (63 +/- 1 nm) in agreement with static light scattering and
        small angle neutron scattering results."
}

@article { dietz04,
    author = HDietz #" and "# MRief,
    title = "Exploring the energy landscape of {GFP} by single-molecule
        mechanical experiments",
    year = 2004,
    journal = PNAS,
    volume = 101,
    number = 46,
    pages = "16192--16197",
    doi = "10.1073/pnas.0404549101",
    eprint = "http://www.pnas.org/cgi/reprint/101/46/16192.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/101/46/16192",
    abstract = "We use single-molecule force spectroscopy to drive
        single GFP molecules from the native state through their
        complex energy landscape into the completely unfolded
        state. Unlike many smaller proteins, mechanical GFP unfolding
        proceeds by means of two subsequent intermediate states. The
        transition from the native state to the first intermediate
        state occurs near thermal equilibrium at $\approx35\U{pN}$ and
        is characterized by detachment of a seven-residue N-terminal
        $\alpha$-helix from the beta barrel. We measure the
        equilibrium free energy cost associated with this transition
        as 22 kBT. Detachment of this small $\alpha$-helix completely
        destabilizes GFP thermodynamically even though the
        $\beta$-barrel is still intact and can bear load.  Mechanical
        stability of the protein on the millisecond timescale,
        however, is determined by the activation barrier of unfolding
        the $\beta$-barrel out of this thermodynamically unstable
        intermediate state. High bandwidth, time-resolved measurements
        of the cantilever relaxation phase upon unfolding of the
        $\beta$-barrel revealed a second metastable mechanical
        intermediate with one complete $\beta$-strand detached from
        the barrel. Quantitative analysis of force distributions and
        lifetimes lead to a detailed picture of the complex mechanical
        unfolding pathway through a rough energy landscape.",
    note = "Towards use of Green Flourescent Protein (GFP) as an
        embedded force probe.  Nice energy-landscape-to-one-dimension
        compression graphic.",
    project = "Energy landscape roughness"
}

@article { dietz06a,
    author = HDietz #" and "# MRief,
    title = "Protein structure by mechanical triangulation",
    year = 2006,
    month = jan,
    day = 31,
    journal = PNAS,
    volume = 103,
    number = 5,
    pages = "1244--1247",
    doi = "10.1073/pnas.0509217103",
    eprint = "http://www.pnas.org/cgi/reprint/103/5/1244.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/103/5/1244",
    abstract = "Knowledge of protein structure is essential to understand
        protein function. High-resolution protein structure has so far been the
        domain of ensemble methods. Here, we develop a simple single-molecule
        technique to measure spatial position of selected residues within a
        folded and functional protein structure in solution. Construction and
        mechanical unfolding of cysteine-engineered polyproteins with
        controlled linkage topology allows measuring intramolecular distance
        with angstrom precision. We demonstrate the potential of this technique
        by determining the position of three residues in the structure of green
        fluorescent protein (GFP). Our results perfectly agree with the GFP
        crystal structure. Mechanical triangulation can find many applications
        where current bulk structural methods fail."
}

@article { dietz06b,
    author = HDietz #" and "# FBerkemeier #" and "# MBertz #" and "# MRief,
    title = "Anisotropic deformation response of single protein molecules",
    year = 2006,
    month = aug,
    day = 22,
    journal = PNAS,
    volume = 103,
    number = 34,
    pages = "12724--12728",
    doi = "10.1073/pnas.0602995103",
    eprint = "http://www.pnas.org/cgi/reprint/103/34/12724.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/103/34/12724",
    abstract = "Single-molecule methods have given experimental access to the
        mechanical properties of single protein molecules. So far, access has
        been limited to mostly one spatial direction of force application.
        Here, we report single-molecule experiments that explore the mechanical
        properties of a folded protein structure in precisely controlled
        directions by applying force to selected amino acid pairs. We
        investigated the deformation response of GFP in five selected
        directions. We found fracture forces widely varying from 100 pN up to
        600 pN. We show that straining the GFP structure in one of the five
        directions induces partial fracture of the protein into a half-folded
        intermediate structure. From potential widths we estimated directional
        spring constants of the GFP structure and found values ranging from 1
        N/m up to 17 N/m. Our results show that classical continuum mechanics
        and simple mechanistic models fail to describe the complex mechanics of
        the GFP protein structure and offer insights into the mechanical design
        of protein materials."
}

@article { dietz07,
    author = HDietz #" and "# MRief,
    title = "Detecting Molecular Fingerprints in Single Molecule Force
        Spectroscopy Using Pattern Recognition",
    year = 2007,
    journal = JJAP,
    volume = 46,
    number = "8B",
    pages = "5540--5542",
    issn = "0021-4922",
    doi = "10.1143/JJAP.46.5540",
    url = "http://jjap.ipap.jp/link?JJAP/46/5540/",
    keywords = "single molecule, protein mechanics, force spectroscopy, AFM,
        pattern recognition, GFP",
    abstract = "Single molecule force spectroscopy has given experimental
        access to the mechanical properties of protein molecules. Typically,
        less than 1% of the experimental recordings reflect true single
        molecule events due to abundant surface and multiple-molecule
        interactions. A key issue in single molecule force spectroscopy is thus
        to identify the characteristic mechanical `fingerprint' of a specific
        protein in noisy data sets. Here, we present an objective pattern
        recognition algorithm that is able to identify fingerprints in such
        noisy data sets.",
    note = "Automatic force curve selection. Seems a bit shoddy. Details
        later."
}

@article{ berkemeier11,
  author = FBerkemeier #" and "# MBertz #" and "# SXiao #" and "#
    NPinotsis #" and "# MWilmanns #" and "# FGrater #" and "# MRief,
  title = "Fast-folding $\alpha$-helices as reversible strain absorbers
    in the muscle protein myomesin.",
  journal = PNAS,
  year = 2011,
  month = aug,
  day = 23,
  address = "Physik Department E22, Technische Universit{\"a}t
    M{\"u}nchen, James-Franck-Stra{\ss}e, 85748 Garching, Germany.",
  volume = 108,
  number = 34,
  pages = "14139--14144",
  keywords = "Biomechanics",
  keywords = "Kinetics",
  keywords = "Microscopy, Atomic Force",
  keywords = "Molecular Dynamics Simulation",
  keywords = "Muscle Proteins",
  keywords = "Protein Folding",
  keywords = "Protein Multimerization",
  keywords = "Protein Stability",
  keywords = "Protein Structure, Secondary",
  keywords = "Protein Structure, Tertiary",
  keywords = "Protein Unfolding",
  abstract = "The highly oriented filamentous protein network of
    muscle constantly experiences significant mechanical load during
    muscle operation. The dimeric protein myomesin has been identified
    as an important M-band component supporting the mechanical
    integrity of the entire sarcomere. Recent structural studies have
    revealed a long $\alpha$-helical linker between the C-terminal
    immunoglobulin (Ig) domains My12 and My13 of myomesin. In this
    paper, we have used single-molecule force spectroscopy in
    combination with molecular dynamics simulations to characterize
    the mechanics of the myomesin dimer comprising immunoglobulin
    domains My12-My13. We find that at forces of approximately 30?pN
    the $\alpha$-helical linker reversibly elongates allowing the
    molecule to extend by more than the folded extension of a full
    domain. High-resolution measurements directly reveal the
    equilibrium folding/unfolding kinetics of the individual helix. We
    show that $\alpha$-helix unfolding mechanically protects the
    molecule homodimerization from dissociation at physiologically
    relevant forces. As fast and reversible molecular springs the
    myomesin $\alpha$-helical linkers are an essential component for
    the structural integrity of the M band.",
  ISSN = "1091-6490",
  doi = "10.1073/pnas.1105734108",
  URL = "http://www.ncbi.nlm.nih.gov/pubmed/21825161",
  language = "eng",
}

@article { dill97,
    author = KADill #" and "# HSChan,
    title = "From Levinthal to pathways to funnels.",
    year = 1997,
    month = jan,
    journal = NSB,
    volume = 4,
    number = 1,
    pages = "10--19",
    issn = "1072-8368",
    doi = "10.1038/nsb0197-10",
    eprint = "http://www.nature.com/nsmb/journal/v4/n1/pdf/nsb0197-10.pdf",
    url = "http://www.nature.com/nsmb/journal/v4/n1/abs/nsb0197-10.html",
    keywords = "Kinetics;Models, Chemical;Protein Folding",
    abstract = "While the classical view of protein folding kinetics relies on
        phenomenological models, and regards folding intermediates in a
        structural way, the new view emphasizes the ensemble nature of protein
        conformations. Although folding has sometimes been regarded as a linear
        sequence of events, the new view sees folding as parallel microscopic
        multi-pathway diffusion-like processes. While the classical view
        invoked pathways to solve the problem of searching for the needle in
        the haystack, the pathway idea was then seen as conflicting with
        Anfinsen's experiments showing that folding is pathway-independent
        (Levinthal's paradox). In contrast, the new view sees no inherent
        paradox because it eliminates the pathway idea: folding can funnel to a
        single stable state by multiple routes in conformational space. The
        general energy landscape picture provides a conceptual framework for
        understanding both two-state and multi-state folding kinetics. Better
        tests of these ideas will come when new experiments become available
        for measuring not just averages of structural observables, but also
        correlations among their fluctuations. At that point we hope to learn
        much more about the real shapes of protein folding landscapes.",
    note = "Pretty folding funnel figures."
}

@article { discher06,
    author = DDischer #" and "# NBhasin #" and "# CJohnson,
    title = "Covalent chemistry on distended proteins",
    year = 2006,
    journal = PNAS,
    volume = 103,
    number = 20,
    pages = "7533--7534",
    doi = "10.1073/pnas.0602388103",
    eprint = "http://www.pnas.org/cgi/reprint/103/20/7533.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/103/20/7533.pdf"
}

@article { dudko03,
    author = OKDudko #" and "# AEFilippov #" and "# JKlafter #" and "# MUrbakh,
    title = "Beyond the conventional description of dynamic force spectroscopy
        of adhesion bonds",
    year = 2003,
    month = sep,
    day = 30,
    journal = PNAS,
    volume = 100,
    number = 20,
    pages = "11378--11381",
    issn = "0027-8424",
    doi = "10.1073/pnas.1534554100",
    eprint = "http://www.pnas.org/content/100/20/11378.full.pdf",
    url = "http://www.pnas.org/content/100/20/11378.abstract",
    keywords = "Spectrum Analysis;Temperature",
    abstract = "Dynamic force spectroscopy of single molecules is described by
        a model that predicts a distribution of rupture forces, the
        corresponding mean rupture force, and variance, which are all amenable
        to experimental tests. The distribution has a pronounced asymmetry,
        which has recently been observed experimentally. The mean rupture force
        follows a (lnV)2/3 dependence on the pulling velocity, V, and differs
        from earlier predictions. Interestingly, at low pulling velocities, a
        rebinding process is obtained whose signature is an intermittent
        behavior of the spring force, which delays the rupture. An extension to
        include conformational changes of the adhesion complex is proposed,
        which leads to the possibility of bimodal distributions of rupture
        forces."
}

@article { dudko06,
    author = OKDudko #" and "# GHummer #" and "# ASzabo,
    title = "Intrinsic rates and activation free energies from single-molecule
        pulling experiments",
    year = 2006,
    month = mar,
    day = 17,
    journal = PRL,
    volume = 96,
    number = 10,
    pages = 108101,
    issn = "0031-9007",
    doi = "10.1103/PhysRevLett.96.108101",
    keywords = "Biophysics;Computer Simulation;Data Interpretation,
        Statistical;Kinetics;Micromanipulation;Models, Chemical;Models,
        Molecular;Molecular Conformation;Muscle Proteins;Nucleic Acid
        Conformation;Protein Binding;Protein Denaturation;Protein
        Folding;Protein Kinases;RNA;Stress, Mechanical;Thermodynamics;Time
        Factors",
    abstract = "We present a unified framework for extracting kinetic
        information from single-molecule pulling experiments at constant force
        or constant pulling speed. Our procedure provides estimates of not only
        (i) the intrinsic rate coefficient and (ii) the location of the
        transition state but also (iii) the free energy of activation. By
        analyzing simulated data, we show that the resulting rates of force-
        induced rupture are significantly more reliable than those obtained by
        the widely used approach based on Bell's formula. We consider the
        uniqueness of the extracted kinetic information and suggest guidelines
        to avoid over-interpretation of experiments."
}

@article { dudko07,
    author = OKDudko #" and "# JMathe #" and "# ASzabo #" and "# AMeller #" and
        "# GHummer,
    title = "Extracting kinetics from single-molecule force spectroscopy:
        Nanopore unzipping of {DNA} hairpins",
    year = 2007,
    month = jun,
    day = 15,
    journal = BPJ,
    volume = 92,
    number = 12,
    pages = "4188--4195",
    issn = "0006-3495",
    doi = "10.1529/biophysj.106.102855",
    eprint = "http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1877759&blo
        btype=pdf",
    keywords = "Computer
        Simulation;DNA;Elasticity;Mechanics;Micromanipulation;Microscopy,
        Atomic Force;Models, Chemical;Models, Molecular;Nanostructures;Nucleic
        Acid Conformation;Porosity;Stress, Mechanical",
    abstract = "Single-molecule force experiments provide powerful new tools to
        explore biomolecular interactions. Here, we describe a systematic
        procedure for extracting kinetic information from force-spectroscopy
        experiments, and apply it to nanopore unzipping of individual DNA
        hairpins. Two types of measurements are considered: unzipping at
        constant voltage, and unzipping at constant voltage-ramp speeds. We
        perform a global maximum-likelihood analysis of the experimental data
        at low-to-intermediate ramp speeds. To validate the theoretical models,
        we compare their predictions with two independent sets of data,
        collected at high ramp speeds and at constant voltage, by using a
        quantitative relation between the two types of measurements.
        Microscopic approaches based on Kramers theory of diffusive barrier
        crossing allow us to estimate not only intrinsic rates and transition
        state locations, as in the widely used phenomenological approach based
        on Bell's formula, but also free energies of activation. The problem of
        extracting unique and accurate kinetic parameters of a molecular
        transition is discussed in light of the apparent success of the
        microscopic theories in reproducing the experimental data."
}

@article{ dudko08,
  author = OKDudko #" and "# GHummer #" and "# ASzabo,
  title = "Theory, analysis, and interpretation of single-molecule
    force spectroscopy experiments.",
  journal = PNAS,
  year = 2008,
  month = oct,
  day = 14,
  address = "Department of Physics and Center for Theoretical
    Biological Physics, University of California at San Diego, La
    Jolla, CA 92093, USA.
    dudko@physics.ucsd.edu",
  volume = 105,
  number = 41,
  pages = "15755--15760",
  keywords = "DNA",
  keywords = "Half-Life",
  keywords = "Kinetics",
  keywords = "Microscopy, Atomic Force",
  keywords = "Motion",
  keywords = "Nucleic Acid Conformation",
  keywords = "Nucleic Acid Denaturation",
  keywords = "Protein Folding",
  keywords = "Thermodynamics",
  abstract = "Dynamic force spectroscopy probes the kinetic and
    thermodynamic properties of single molecules and molecular
    assemblies. Here, we propose a simple procedure to extract kinetic
    information from such experiments. The cornerstone of our method
    is a transformation of the rupture-force histograms obtained at
    different force-loading rates into the force-dependent lifetimes
    measurable in constant-force experiments. To interpret the
    force-dependent lifetimes, we derive a generalization of Bell's
    formula that is formally exact within the framework of Kramers
    theory. This result complements the analytical expression for the
    lifetime that we derived previously for a class of model
    potentials. We illustrate our procedure by analyzing the nanopore
    unzipping of DNA hairpins and the unfolding of a protein attached
    by flexible linkers to an atomic force microscope. Our procedure
    to transform rupture-force histograms into the force-dependent
    lifetimes remains valid even when the molecular extension is a
    poor reaction coordinate and higher-dimensional free-energy
    surfaces must be considered. In this case the microscopic
    interpretation of the lifetimes becomes more challenging because
    the lifetimes can reveal richer, and even nonmonotonic, dependence
    on the force.",
  ISSN = "1091-6490",
  doi = "10.1073/pnas.0806085105",
  URL = "http://www.ncbi.nlm.nih.gov/pubmed/18852468",
  language = "eng",
}

@article { evans01,
    author = EEvans,
    title = "Probing the relation between force--lifetime--and chemistry in
        single molecular bonds",
    year = 2001,
    journal = ARBBS,
    volume = 30,
    pages = "105--128",
    issn = "1056-8700",
    doi = "10.1146/annurev.biophys.30.1.105",
    url = "http://arjournals.annualreviews.org/doi/abs/10.1146%2Fannurev.biophys.30.1.105",
    keywords = "Biophysics;Kinetics;Microscopy, Atomic Force;Models,
        Chemical;Protein Binding;Spectrum Analysis;Time Factors",
    abstract = "On laboratory time scales, the energy landscape of a weak bond
        along a dissociation pathway is fully explored through Brownian-thermal
        excitations, and energy barriers become encoded in a dissociation time
        that varies with applied force. Probed with ramps of force over an
        enormous range of rates (force/time), this kinetic profile is
        transformed into a dynamic spectrum of bond rupture force as a function
        of loading rate. On a logarithmic scale in loading rate, the force
        spectrum provides an easy-to-read map of the prominent energy barriers
        traversed along the force-driven pathway and exposes the differences in
        energy between barriers. In this way, the method of dynamic force
        spectroscopy (DFS) is being used to probe the complex relation between
        force-lifetime-and chemistry in single molecular bonds. Most important,
        DFS probes the inner world of molecular interactions to reveal barriers
        that are difficult or impossible to detect in assays of near
        equilibrium dissociation but that determine bond lifetime and strength
        under rapid detachment. To use an ultrasensitive force probe as a
        spectroscopic tool, we need to understand the physics of bond
        dissociation under force, the impact of experimental technique on the
        measurement of detachment force (bond strength), the consequences of
        complex interactions in macromolecular bonds, and effects of multiply-
        bonded attachments."
}

@article { evans91a,
    author = EEvans #" and "# DBerk #" and "# ALeung,
    title = "Detachment of agglutinin-bonded red blood cells. {I}. Forces to
        rupture molecular-point attachments",
    year = 1991,
    month = apr,
    journal = BPJ,
    volume = 59,
    number = 4,
    pages = "838--848",
    issn = "0006-3495",
    keywords = "ABO Blood-Group System;Animals;Antibodies,
        Monoclonal;Erythrocyte Deformability;Erythrocyte
        Membrane;Erythrocytes;Glycophorin;Helix
        (Snails);Hemagglutinins;Humans;Immune Sera;Lectins;Mathematics;Models,
        Biological",
    abstract = "A simple micromechanical method has been developed to measure
        the rupture strength of a molecular-point attachment (focal bond)
        between two macroscopically smooth membrane capsules. In the procedure,
        one capsule is prepared with a low density coverage of adhesion
        molecules, formed as a stiff sphere, and held at fixed position by a
        micropipette. The second capsule without adhesion molecules is
        pressurized into a spherical shape with low suction by another pipette.
        This capsule is maneuvered to initiate point contact at the pole
        opposite the stiff capsule which leads to formation of a few (or even
        one) molecular attachments. Then, the deformable capsule is slowly
        withdrawn by displacement of the pipette. Analysis shows that the end-
        to-end extension of the capsule provides a direct measure of the force
        at the point contact and, therefore, the rupture strength when
        detachment occurs. The range for point forces accessible to this
        technique depends on the elastic moduli of the membrane, membrane
        tension, and the size of the capsule. For biological and synthetic
        vesicle membranes, the range of force lies between 10(-7)-10(-5) dyn
        (10(-12)-10(-10) N) which is 100-fold less than presently measurable by
        Atomic Force Microscopy! Here, the approach was used to study the
        forces required to rupture microscopic attachments between red blood
        cells formed by a monoclonal antibody to red cell membrane glycophorin,
        anti-A serum, and a lectin from the snail-helix pomatia. Failure of the
        attachments appeared to be a stochastic function of the magnitude and
        duration of the detachment force. We have correlated the statistical
        behavior observed for rupture with a random process model for failure
        of small numbers of molecular attachments. The surprising outcome of
        the measurements and analysis was that the forces deduced for short-
        time failure of 1-2 molecular attachments were nearly the same for all
        of the agglutinin, i.e., 1-2 x 10(-6) dyn. Hence, microfluorometric
        tests were carried out to determine if labeled agglutinins and/or
        labeled surface molecules were transferred between surfaces after
        separation of large areas of adhesive contact. The results showed that
        the attachments failed because receptors were extracted from the
        membrane."
}

@article { evans91b,
    author = EEvans #" and "# DBerk #" and "# ALeung #" and "# NMohandas,
    title = "Detachment of agglutinin-bonded red blood cells. {II}. Mechanical
        energies to separate large contact areas",
    year = 1991,
    month = apr,
    journal = BPJ,
    volume = 59,
    number = 4,
    pages = "849--860",
    issn = "0006-3495",
    keywords = "Animals;Antibodies, Monoclonal;Cell Adhesion;Erythrocyte
        Membrane;Erythrocytes;Helix
        (Snails);Hemagglutination;Hemagglutinins;Humans;Immune
        Sera;Kinetics;Lectins;Mathematics",
    abstract = "As detailed in a companion paper (Berk, D., and E. Evans. 1991.
        Biophys. J. 59:861-872), a method was developed to quantitate the
        strength of adhesion between agglutinin-bonded membranes without
        ambiguity due to mechanical compliance of the cell body. The
        experimental method and analysis were formulated around controlled
        assembly and detachment of a pair of macroscopically smooth red blood
        cell surfaces. The approach provides precise measurement of the
        membrane tension applied at the perimeter of an adhesive contact and
        the contact angle theta c between membrane surfaces which defines the
        mechanical leverage factor (1-cos theta c) important in the definition
        of the work to separate a unit area of contact. Here, the method was
        applied to adhesion and detachment of red cells bound together by
        different monoclonal antibodies to red cell membrane glycophorin and
        the snail-helix pomatia-lectin. For these tests, one of the two red
        cells was chemically prefixed in the form of a smooth sphere then
        equilibrated with the agglutinin before the adhesion-detachment
        procedure. The other cell was not exposed to the agglutinin until it
        was forced into contact with the rigid cell surface by mechanical
        impingement. Large regions of agglutinin bonding were produced by
        impingement but no spontaneous spreading was observed beyond the forced
        contact. Measurements of suction force to detach the deformable cell
        yielded consistent behavior for all of the agglutinins: i.e., the
        strength of adhesion increased progressively with reduction in contact
        diameter throughout detachment. This tension-contact diameter behavior
        was not altered over a ten-fold range of separation rates. In special
        cases, contacts separated smoothly after critical tensions were
        reached; these were the highest values attained for tension. Based on
        measurements reported in another paper (Evans et al. 1991. Biophys. J.
        59:838-848) of the forces required to rupture molecular-point
        attachments, the density of cross-bridges was estimated with the
        assumption that the tension was proportional to the discrete rupture
        force x the number of attachments per unit length. These estimates
        showed that only a small fraction of agglutinin formed cross-bridges at
        initial assembly and increased progressively with separation. When
        critical tension levels were reached, it appeared that nearly all local
        agglutinin was involved as cross-bridges. Because one cell surface was
        chemically fixed, receptor accumulation was unlikely; thus, microscopic
        ``roughness'' and steric repulsion probably modulated formation of
        cross-bridges on initial contact.(ABSTRACT TRUNCATED AT 400 WORDS)"
}

@article { evans97,
    author = EEvans #" and "# KRitchie,
    title = "Dynamic strength of molecular adhesion bonds",
    year = 1997,
    month = apr,
    journal = BPJ,
    volume = 72,
    number = 4,
    pages = "1541--1555",
    issn = "0006-3495",
    eprint = "http://www.biophysj.org/cgi/reprint/72/4/1541.pdf",
    url = "http://www.biophysj.org/cgi/content/abstract/72/4/1541",
    keywords = "Avidin; Biotin; Chemistry, Physical; Computer Simulation;
        Mathematics; Monte Carlo Method; Protein Binding",
    abstract = "In biology, molecular linkages at, within, and beneath cell
        interfaces arise mainly from weak noncovalent interactions. These bonds
        will fail under any level of pulling force if held for sufficient time.
        Thus, when tested with ultrasensitive force probes, we expect cohesive
        material strength and strength of adhesion at interfaces to be time-
        and loading rate-dependent properties. To examine what can be learned
        from measurements of bond strength, we have extended Kramers' theory
        for reaction kinetics in liquids to bond dissociation under force and
        tested the predictions by smart Monte Carlo (Brownian dynamics)
        simulations of bond rupture. By definition, bond strength is the force
        that produces the most frequent failure in repeated tests of breakage,
        i.e., the peak in the distribution of rupture forces. As verified by
        the simulations, theory shows that bond strength progresses through
        three dynamic regimes of loading rate. First, bond strength emerges at
        a critical rate of loading (> or = 0) at which spontaneous dissociation
        is just frequent enough to keep the distribution peak at zero force. In
        the slow-loading regime immediately above the critical rate, strength
        grows as a weak power of loading rate and reflects initial coupling of
        force to the bonding potential. At higher rates, there is crossover to
        a fast regime in which strength continues to increase as the logarithm
        of the loading rate over many decades independent of the type of
        attraction. Finally, at ultrafast loading rates approaching the domain
        of molecular dynamics simulations, the bonding potential is quickly
        overwhelmed by the rapidly increasing force, so that only naked
        frictional drag on the structure remains to retard separation. Hence,
        to expose the energy landscape that governs bond strength, molecular
        adhesion forces must be examined over an enormous span of time scales.
        However, a significant gap exists between the time domain of force
        measurements in the laboratory and the extremely fast scale of
        molecular motions. Using results from a simulation of biotin-avidin
        bonds (Izrailev, S., S. Stepaniants, M. Balsera, Y. Oono, and K.
        Schulten. 1997. Molecular dynamics study of unbinding of the avidin-
        biotin complex. Biophys. J., this issue), we describe how Brownian
        dynamics can help bridge the gap between molecular dynamics and probe
        tests.",
    project = "sawtooth simulation"
}

@article { evans99,
    author = EEvans #" and "# KRitchie,
    title = "Strength of a weak bond connecting flexible polymer chains",
    year = 1999,
    month = may,
    journal = BPJ,
    volume = 76,
    number = 5,
    pages = "2439--2447",
    issn = "0006-3495",
    eprint = "http://www.biophysj.org/cgi/reprint/76/5/2439.pdf",
    url = "http://www.biophysj.org/cgi/content/abstract/76/5/2439",
    keywords = "Animals; Biophysics; Biopolymers; Microscopy, Atomic Force;
        Models, Chemical; Muscle Proteins; Protein Folding; Protein Kinases;
        Stochastic Processes; Stress, Mechanical; Thermodynamics",
    abstract = "Bond dissociation under steadily rising force occurs most
        frequently at a time governed by the rate of loading (Evans and
        Ritchie, 1997 Biophys. J. 72:1541-1555). Multiplied by the loading
        rate, the breakage time specifies the force for most frequent failure
        (called bond strength) that obeys the same dependence on loading rate.
        The spectrum of bond strength versus log(loading rate) provides an
        image of the energy landscape traversed in the course of unbonding.
        However, when a weak bond is connected to very compliant elements like
        long polymers, the load applied to the bond does not rise steadily
        under constant pulling speed. Because of nonsteady loading, the most
        frequent breakage force can differ significantly from that of a bond
        loaded at constant rate through stiff linkages. Using generic models
        for wormlike and freely jointed chains, we have analyzed the kinetic
        process of failure for a bond loaded by pulling the polymer linkages at
        constant speed. We find that when linked by either type of polymer
        chain, a bond is likely to fail at lower force under steady separation
        than through stiff linkages. Quite unexpectedly, a discontinuous jump
        can occur in bond strength at slow separation speed in the case of long
        polymer linkages. We demonstrate that the predictions of strength
        versus log(loading rate) can rationalize conflicting results obtained
        recently for unfolding Ig domains along muscle titin with different
        force techniques.",
    note = "Develops Kramers improvement on Bell model for domain unfolding.
        Presents unfolding under variable loading rates. Often cited as the
        ``Bell--Evans'' model. They derive a unitless treatment, scaling force
        by $f_\beta$, TODO; time by $\tau_f$, TODO; elasiticity by compliance
        $c(f)$. The appendix has relaxation time formulas for WLC and FJC
        polymer models.",
    project = "sawtooth simulation"
}

@article { fernandez04,
    author = JFernandez #" and "# HLi,
    title = "Force-clamp spectroscopy monitors the folding trajectory of a
        single protein",
    year = 2004,
    month = mar,
    day = 12,
    journal = SCI,
    volume = 303,
    number = 5664,
    pages = "1674--1678",
    issn = "1095-9203",
    doi = "10.1126/science.1092497",
    eprint = "http://www.sciencemag.org/cgi/reprint/303/5664/1674.pdf",
    url = "http://www.sciencemag.org/cgi/content/abstract/303/5664/1674",
    keywords = "Chemistry, Physical;Microscopy, Atomic Force;Physicochemical
        Phenomena;Polyubiquitin;Protein Conformation;Protein
        Denaturation;Protein Folding;Protein Structure, Secondary;Time
        Factors;Ubiquitin",
    abstract = "We used force-clamp atomic force microscopy to measure the end-
        to-end length of the small protein ubiquitin during its folding
        reaction at the single-molecule level. Ubiquitin was first unfolded and
        extended at a high force, then the stretching force was quenched and
        protein folding was observed. The folding trajectories were continuous
        and marked by several distinct stages. The time taken to fold was
        dependent on the contour length of the unfolded protein and the
        stretching force applied during folding. The folding collapse was
        marked by large fluctuations in the end-to-end length of the protein,
        but these fluctuations vanished upon the final folding contraction.
        These direct observations of the complete folding trajectory of a
        protein provide a benchmark to determine the physical basis of the
        folding reaction."
}

@article{ howard87,
  author = JHoward #" and "# AJHudspeth,
  title = {Mechanical relaxation of the hair bundle mediates
    adaptation in mechanoelectrical transduction by the
    bullfrog's saccular hair cell.},
  journal = PNAS,
  year = 1987,
  month = may,
  volume = 84,
  number = 9,
  pages = {3064--3068},
  issn = {0027-8424},
  url = {http://www.ncbi.nlm.nih.gov/pubmed/3495007},
  keywords = {Acclimatization},
  keywords = {Animals},
  keywords = {Electric Conductivity},
  keywords = {Electric Stimulation},
  keywords = {Hair Cells, Auditory},
  keywords = {Membrane Potentials},
  keywords = {Microelectrodes},
  keywords = {Physical Stimulation},
  keywords = {Rana catesbeiana},
  keywords = {Saccule and Utricle},
  abstract = {Mechanoelectrical transduction by hair cells of the
    frog's internal ear displays adaptation: the electrical response
    to a maintained deflection of the hair bundle declines over a
    period of tens of milliseconds. We investigated the role of
    mechanics in adaptation by measuring changes in hair-bundle
    stiffness following the application of force stimuli. Following
    step stimulation with a glass fiber, the hair bundle of a saccular
    hair cell initially had a stiffness of approximately equal to
    $1\U{mN/m}$. The stiffness then declined to a steady-state level
    near $0.6\U{mN/m}$ with a time course comparable to that of
    adaptation in the receptor current. The hair bundle may be modeled
    as the parallel combination of a spring, which represents the
    rotational stiffness of the stereocilia, and a series spring and
    dashpot, which respectively, represent the elastic element
    responsible for channel gating and the apparatus for adaptation.},
  language = {eng},
}

@article{ howard88,
  author = JHoward #" and "# AJHudspeth,
  title = {Compliance of the Hair Bundle Associated with Gating of
    Mechanoelectrical Transduction Channels in the Bullfrog's Saccular
    Hair Cell},
  year = 1988,
  month = may,
  journal = NEURON,
  volume = 1,
  pages = {189--199},
  doi = {10.1016/0896-6273(88)90139-0},
  url = {http://www.cell.com/neuron/retrieve/pii/0896627388901390},
  eprint = {http://download.cell.com/neuron/pdf/PII0896627388901390.pdf},
  note = {Initial thermal calibration paper as cited by
    \citet{florin95}.  This is not an AFM paper, but it uses the
    equipartition theorem to calculate the spring constant of hair
    fibers by measuring their tip displacement variance.  The
    discussion occurs in the \emph{Manufacture and Calibration of
    Fibers} section on pages 197--198.  Actual details are scarce, but
    I believe this is the original source of the ``Lorentzian'' and
    ``10\% accuracy'' ideas that have haunted themal calibration ever
    since.},
}

@article{ florin94,
  author = ELFlorin #" and "# VMoy #" and "# HEGaub,
  title = {Adhesion forces between individual ligand-receptor pairs},
  year = 1994,
  month = apr,
  day = 15,
  journal = SCI,
  volume = 264,
  number = 5157,
  pages = {415--417},
  doi = {10.1126/science.8153628},
  url = {http://www.sciencemag.org/content/264/5157/415.abstract},
  eprint = {http://www.sciencemag.org/content/264/5157/415.full.pdf},
  abstract ={The adhesion force between the tip of an atomic force
    microscope cantilever derivatized with avidin and agarose beads
    functionalized with biotin, desthiobiotin, or iminobiotin was
    measured. Under conditions that allowed only a limited number of
    molecular pairs to interact, the force required to separate tip
    and bead was found to be quantized in integer multiples of
    $160\pm20$ piconewtons for biotin and $85\pm15$ piconewtons for
    iminobiotin. The measured force quanta are interpreted as the
    unbinding forces of individual molecular pairs.},
}

@article { florin95,
    author = ELFlorin #" and "# MRief #" and "# HLehmann #" and "# MLudwig #"
        and "# CDornmair #" and "# VMoy #" and "# HEGaub,
    title = "Sensing specific molecular interactions with the atomic force
        microscope",
    year = 1995,
    journal = BIOSENSE,
    volume = 10,
    number = "9--10",
    pages = "895--901",
    issn = "0956-5663",
    doi = "10.1016/0956-5663(95)99227-C",
    url = "http://www.sciencedirect.com/science/article/B6TFC-
        3XY2HK9-G/2/6f4e9f67e9a1e14c8bbcc478e5360682",
    abstract = "One of the unique features of the atomic force microscope (AFM)
        is its capacity to measure interactions between tip and sample with
        high sensitivity and unparal leled spatial resolution. Since the
        development of methods for the functionaliza tion of the tips, the
        versatility of the AFM has been expanded to experiments wh ere specific
        molecular interactions are measured. For illustration, we present m
        easurements of the interaction between complementary strands of DNA. A
        necessary prerequisite for the quantitative analysis of the interaction
        force is knowledg e of the spring constant of the cantilevers. Here, we
        compare different techniqu es that allow for the in situ measurement of
        the absolute value of the spring co nstant of cantilevers.",
    note = {Good review of calibration to 1995, with experimental
        comparison between resonance-shift, reference-spring, and
        thermal methods.  They incorrectly cite \citet{hutter93} as
        being published in 1994.},
    project = "Cantilever Calibration"
}

@article{ burnham03,
  author = NABurnham #" and "# XiChen #" and "# CSHodges #" and "#
    GAMatei #" and "# EJThoreson #" and "# CJRoberts #" and "#
    MCDavies #" and "# SJBTendler,
  title = {Comparison of calibration methods for atomic-force
    microscopy cantilevers},
  year = 2003,
  month = jan,
  journal = NT,
  volume= 14,
  number = 1,
  pages = {1--6},
  url = {http://stacks.iop.org/0957-4484/14/i=1/a=301},
  abstract = {The scientific community needs a rapid and reliable way
    of accurately determining the stiffness of atomic-force microscopy
    cantilevers. We have compared the experimentally determined values
    of stiffness for ten cantilever probes using four different
    methods. For rectangular silicon cantilever beams of well defined
    geometry, the approaches all yield values within 17\% of the
    manufacturer's nominal stiffness. One of the methods is new, based
    on the acquisition and analysis of thermal distribution functions
    of the oscillator's amplitude fluctuations. We evaluate this
    method in comparison to the three others and recommend it for its
    ease of use and broad applicability.},
  note = {Contains both the overdamped (\fref{equation}{6}) and
    general (\fref{equation}{8}) power spectral densities used in
    thermal cantilever calibration, but punts to textbooks for the
    derivation.},
}

@article { forde02,
    author = NRForde #" and "# DIzhaky #" and "# GRWoodcock #" and "# GJLWuite
        #" and "# CBustamante,
    title = "Using mechanical force to probe the mechanism of pausing and
        arrest during continuous elongation by Escherichia coli {RNA}
        polymerase",
    year = 2002,
    month = sep,
    day = 03,
    journal = PNAS,
    volume = 99,
    number = 18,
    pages = "11682--11687",
    issn = "0027-8424",
    doi = "10.1073/pnas.142417799",
    eprint = "http://www.pnas.org/cgi/reprint/99/18/11682.pdf",
    url = "http://www.pnas.org/content/99/18/11682",
    keywords = "DNA-Directed RNA Polymerases;Escherichia
        coli;Kinetics;Transcription, Genetic",
    abstract = "Escherichia coli RNA polymerase translocates along the DNA
        discontinuously during the elongation phase of transcription, spending
        proportionally more time at some template positions, known as pause and
        arrest sites, than at others. Current models of elongation suggest that
        the enzyme backtracks at these locations, but the dynamics are
        unresolved. Here, we study the role of lateral displacement in pausing
        and arrest by applying force to individually transcribing molecules. We
        find that an assisting mechanical force does not alter the
        translocation rate of the enzyme, but does reduce the efficiency of
        both pausing and arrest. Moreover, arrested molecules cannot be rescued
        by force, suggesting that arrest occurs by a bipartite mechanism: the
        enzyme backtracks along the DNA followed by a conformational change of
        the ternary complex (RNA polymerase, DNA and transcript), which cannot
        be reversed mechanically."
}

@article { freitag97,
    author = SFreitag #" and "# ILTrong #" and "# LKlumb #" and "# PSStayton #"
        and "# REStenkamp,
    title = "Structural studies of the streptavidin binding loop.",
    year = 1997,
    month = jun,
    journal = PS,
    volume = 6,
    number = 6,
    pages = "1157--1166",
    issn = "0961-8368",
    doi = "10.1002/pro.5560060604",
    keywords = "Allosteric Regulation;Bacterial Proteins;Binding
        Sites;Biotin;Crystallography, X-Ray;Hydrogen Bonding;Ligands;Models,
        Molecular;Molecular Conformation;Streptavidin;Tryptophan",
    abstract = "The streptavidin-biotin complex provides the basis for many
        important biotechnological applications and is an interesting model
        system for studying high-affinity protein-ligand interactions. We
        report here crystallographic studies elucidating the conformation of
        the flexible binding loop of streptavidin (residues 45 to 52) in the
        unbound and bound forms. The crystal structures of unbound streptavidin
        have been determined in two monoclinic crystal forms. The binding loop
        generally adopts an open conformation in the unbound species. In one
        subunit of one crystal form, the flexible loop adopts the closed
        conformation and an analysis of packing interactions suggests that
        protein-protein contacts stabilize the closed loop conformation. In the
        other crystal form all loops adopt an open conformation. Co-
        crystallization of streptavidin and biotin resulted in two additional,
        different crystal forms, with ligand bound in all four binding sites of
        the first crystal form and biotin bound in only two subunits in a
        second. The major change associated with binding of biotin is the
        closure of the surface loop incorporating residues 45 to 52. Residues
        49 to 52 display a 3(10) helical conformation in unbound subunits of
        our structures as opposed to the disordered loops observed in other
        structure determinations of streptavidin. In addition, the open
        conformation is stabilized by a beta-sheet hydrogen bond between
        residues 45 and 52, which cannot occur in the closed conformation. The
        3(10) helix is observed in nearly all unbound subunits of both the co-
        crystallized and ligand-free structures. An analysis of the temperature
        factors of the binding loop regions suggests that the mobility of the
        closed loops in the complexed structures is lower than in the open
        loops of the ligand-free structures. The two biotin bound subunits in
        the tetramer found in the MONO-b1 crystal form are those that
        contribute Trp 120 across their respective binding pockets, suggesting
        a structural link between these binding sites in the tetramer. However,
        there are no obvious signatures of binding site communication observed
        upon ligand binding, such as quaternary structure changes or shifts in
        the region of Trp 120. These studies demonstrate that while
        crystallographic packing interactions can stabilize both the open and
        closed forms of the flexible loop, in their absence the loop is open in
        the unbound state and closed in the presence of biotin. If present in
        solution, the helical structure in the open loop conformation could
        moderate the entropic penalty associated with biotin binding by
        contributing an order-to-disorder component to the loop closure.",
    note = "\href{http://www.rcsb.org/pdb/explore.do?structureId=1SWE}{PDB ID:
        1SWE}, DOI:
        \href{http://dx.doi.org/10.2210/pdb1swe/pdb}{10.2210/pdb1swe/pdb}."
}

@article { friddle08,
    author = RWFriddle #" and "# PPodsiadlo #" and "# ABArtyukhin #" and "#
        ANoy,
    title = "Near-Equilibrium Chemical Force Microscopy",
    year = 2008,
    journal = JPC:C,
    volume = 112,
    number = 13,
    pages = "4986--4990",
    doi = "10.1021/jp7095967",
    eprint = "http://pubs.acs.org/doi/pdf/10.1021/jp7095967",
    url = "http://pubs.acs.org/doi/abs/10.1021/jp7095967"
}

@article { fujii02,
    author = TFujii #" and "# YLSun #" and "# KNAn #" and "# ZPLuo,
    title = "Mechanical properties of single hyaluronan molecules",
    year = 2002,
    month = apr,
    journal = JBM,
    volume = 35,
    number = 4,
    pages = "527--531",
    issn = "0021-9290",
    keywords = "Biomechanics;Cross-Linking Reagents;Elasticity;Extracellular
        Matrix;Humans;Hyaluronic Acid;Lasers;Microspheres;Nanotechnology",
    abstract = "Hyaluronan (HA) is a major component of the extracellular
        matrix. It plays an important role in the mechanical functions of the
        extracellular matrix and stabilization of cells. Currently, its
        mechanical properties have been investigated only at the gross level.
        In this study, the mechanical properties of single HA molecules were
        directly measured with an optical tweezer technique, yielding a
        persistence length of 4.5 +/- 1.2 nm. This information may help us to
        understand the mechanical roles in the extracellular matrix
        infrastructure, cell attachment, and to design tissue engineering and
        drug delivery systems where the mechanical functions of HA are
        essential."
}

@article { ganchev08,
    author = DNGanchev #" and "# NJCobb #" and "# KSurewicz #" and "#
        WKSurewicz,
    title = "Nanomechanical properties of human prion protein amyloid as probed
        by force spectroscopy",
    year = 2008,
    month = sep,
    day = 15,
    journal = BPJ,
    volume = 95,
    number = 6,
    pages = "2909--2915",
    issn = "1542-0086",
    doi = "10.1529/biophysj.108.133108",
    abstract = "Amyloids are associated with a number of protein misfolding
        disorders, including prion diseases. In this study, we used single-
        molecule force spectroscopy to characterize the nanomechanical
        properties and molecular structure of amyloid fibrils formed by human
        prion protein PrP90-231. Force-extension curves obtained by specific
        attachment of a gold-covered atomic force microscope tip to engineered
        Cys residues could be described by the worm-like chain model for
        entropic elasticity of a polymer chain, with the size of the N-terminal
        segment that could be stretched entropically depending on the tip
        attachment site. The data presented here provide direct information
        about the forces required to extract an individual monomer from the
        core of the PrP90-231 amyloid, and indicate that the beta-sheet core of
        this amyloid starts at residue approximately 164-169. The latter
        finding has important implications for the ongoing debate regarding the
        structure of PrP amyloid."
}

@article { gao03,
    author = MGao #" and "# DCraig #" and "# OLequin #" and "# ICampbell #" and
        "# VVogel #" and "# KSchulten,
    title = "Structure and functional significance of mechanically unfolded
        fibronectin type {III1} intermediates",
    year = 2003,
    journal = PNAS,
    volume = 100,
    number = 25,
    pages = "14784--14789",
    doi = "10.1073/pnas.2334390100",
    eprint = "http://www.pnas.org/cgi/reprint/100/25/14784.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/100/25/14784",
    abstract = "Fibronectin (FN) forms fibrillar networks coupling cells to the
        extracellular matrix. The formation of FN fibrils, fibrillogenesis, is
        a tightly regulated process involving the exposure of cryptic binding
        sites in individual FN type III (FN-III) repeats presumably exposed by
        mechanical tension. The FN-III1 module has been previously proposed to
        contain such cryptic sites that promote the assembly of extracellular
        matrix FN fibrils. We have combined NMR and steered molecular dynamics
        simulations to study the structure and mechanical unfolding pathway of
        FN-III1. This study finds that FN-III1 consists of a {beta}-sandwich
        structure that unfolds to a mechanically stable intermediate about four
        times the length of the native folded state. Considering previous
        experimental findings, our studies provide a structural model by which
        mechanical stretching of FN-III1 may induce fibrillogenesis through
        this partially unfolded intermediate."
}

@article { gavrilov01,
    author = LAGavrilov #" and "# NSGavrilova,
    title = "The reliability theory of aging and longevity",
    year = 2001,
    month = dec,
    day = 21,
    journal = JTB,
    volume = 213,
    number = 4,
    pages = "527--545",
    issn = "0022-5193",
    doi = "10.1006/jtbi.2001.2430",
    keywords = "Adult;Aged;Aging;Animals;Humans;Longevity;Middle Aged;Models,
        Biological;Survival Rate;Systems Theory",
    abstract = "Reliability theory is a general theory about systems failure.
        It allows researchers to predict the age-related failure kinetics for a
        system of given architecture (reliability structure) and given
        reliability of its components. Reliability theory predicts that even
        those systems that are entirely composed of non-aging elements (with a
        constant failure rate) will nevertheless deteriorate (fail more often)
        with age, if these systems are redundant in irreplaceable elements.
        Aging, therefore, is a direct consequence of systems redundancy.
        Reliability theory also predicts the late-life mortality deceleration
        with subsequent leveling-off, as well as the late-life mortality
        plateaus, as an inevitable consequence of redundancy exhaustion at
        extreme old ages. The theory explains why mortality rates increase
        exponentially with age (the Gompertz law) in many species, by taking
        into account the initial flaws (defects) in newly formed systems. It
        also explains why organisms ``prefer'' to die according to the Gompertz
        law, while technical devices usually fail according to the Weibull
        (power) law. Theoretical conditions are specified when organisms die
        according to the Weibull law: organisms should be relatively free of
        initial flaws and defects. The theory makes it possible to find a
        general failure law applicable to all adult and extreme old ages, where
        the Gompertz and the Weibull laws are just special cases of this more
        general failure law. The theory explains why relative differences in
        mortality rates of compared populations (within a given species) vanish
        with age, and mortality convergence is observed due to the exhaustion
        of initial differences in redundancy levels. Overall, reliability
        theory has an amazing predictive and explanatory power with a few, very
        general and realistic assumptions. Therefore, reliability theory seems
        to be a promising approach for developing a comprehensive theory of
        aging and longevity integrating mathematical methods with specific
        biological knowledge.",
    note = "An example of exponential (standard) Gomperz law."
}

@article { gergely00,
    author = CGergely #" and "# JCVoegel #" and "# PSchaaf #" and "# BSenger #"
        and "# MMaaloum #" and "# JHorber #" and "# JHemmerle,
    title = "Unbinding process of adsorbed proteins under external stress
        studied by atomic force microscopy spectroscopy",
    year = 2000,
    journal = PNAS,
    volume = 97,
    number = 20,
    pages = "10802--10807",
    doi = "10.1073/pnas.180293097",
    eprint = "http://www.pnas.org/cgi/reprint/97/20/10802.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/97/20/10802"
}

@article { gompertz25,
    author = BGompertz,
    title = "On the Nature of the Function Expressive of the Law of Human
        Mortality, and on a New Mode of Determining the Value of Life
        Contingencies",
    year = 1825,
    journal = PTRSL,
    volume = 115,
    number = "",
    pages = "513--583",
    issn = 02610523,
    publisher = RS,
    copyright = "Copyright \copy\ 1825 The Royal Society",
    url = "http://www.jstor.org/stable/107756",
    abstract = "",
    jstor_articletype = "primary_article",
    jstor_formatteddate = 1825,
    jstor_issuetitle = ""
}

@article{ welch38,
  author = BLWelch,
  title = {The significance of the difference between two means when
    the population variances are unequal},
  year = 1938,
  month = feb,
  journal = Biomet,
  volume = 29,
  number = "3-4",
  pages = {350--362},
  keywords = "Population",
  issn = "0006-3444",
  url = "http://www.jstor.org/stable/2332010",
  language = "eng",
}

@article{ welch47,
  author = BLWelch,
  title = {The generalization of {Student's} problems when several
    different population variances are involved},
  year = 1947,
  month = jan,
  journal = Biomet,
  volume = 34,
  number = "1-2",
  pages = {28--35},
  keywords = "Population",
  issn = "0006-3444",
  url = "http://www.ncbi.nlm.nih.gov/pubmed/20287819",
  jstor_url = "http://www.jstor.org/stable/2332510",
  language = "eng",
}

@article { granzier97,
    author = HLGranzier #" and "# MSKellermayer #" and "# MHelmes #" and "#
        KTrombitas,
    title = "Titin elasticity and mechanism of passive force development in rat
        cardiac myocytes probed by thin-filament extraction",
    year = 1997,
    month = oct,
    journal = BPJ,
    volume = 73,
    number = 4,
    pages = "2043--2053",
    issn = "0006-3495",
    doi = "10.1016/S0006-3495(97)78234-1",
    url = "http://www.cell.com/biophysj/retrieve/pii/S0006349597782341",
    keywords = "Amino Acid Sequence;Animals;Biomechanics;Biophysical
        Phenomena;Biophysics;Cell Fractionation;Elasticity;Gelsolin;Microscopy,
        Immunoelectron;Models, Cardiovascular;Molecular Structure;Muscle
        Proteins;Myocardial Contraction;Myocardium;Protein
        Kinases;Rats;Sarcomeres",
    abstract = "Titin (also known as connectin) is a giant filamentous protein
        whose elastic properties greatly contribute to the passive force in
        muscle. In the sarcomere, the elastic I-band segment of titin may
        interact with the thin filaments, possibly affecting the molecule's
        elastic behavior. Indeed, several studies have indicated that
        interactions between titin and actin occur in vitro and may occur in
        the sarcomere as well. To explore the properties of titin alone, one
        must first eliminate the modulating effect of the thin filaments by
        selectively removing them. In the present work, thin filaments were
        selectively removed from the cardiac myocyte by using a gelsolin
        fragment. Partial extraction left behind approximately 100-nm-long thin
        filaments protruding from the Z-line, whereas the rest of the I-band
        became devoid of thin filaments, exposing titin. By applying a much
        more extensive gelsolin treatment, we also removed the remaining short
        thin filaments near the Z-line. After extraction, the extensibility of
        titin was studied by using immunoelectron microscopy, and the passive
        force-sarcomere length relation was determined by using mechanical
        techniques. Titin's regional extensibility was not detectably affected
        by partial thin-filament extraction. Passive force, on the other hand,
        was reduced at sarcomere lengths longer than approximately 2.1 microm,
        with a 33 +/- 9\% reduction at 2.6 microm. After a complete extraction,
        the slack sarcomere length was reduced to approximately 1.7 microm. The
        segment of titin near the Z-line, which is otherwise inextensible,
        collapsed toward the Z-line in sarcomeres shorter than approximately
        2.0 microm, but it was extended in sarcomeres longer than approximately
        2.3 microm. Passive force became elevated at sarcomere lengths between
        approximately 1.7 and approximately 2.1 microm, but was reduced at
        sarcomere lengths of >2.3 microm. These changes can be accounted for by
        modeling titin as two wormlike chains in series, one of which increases
        its contour length by recruitment of the titin segment near the Z-line
        into the elastic pool."
}

@article { grossman05,
    author = CGrossman #" and "# AStout,
    title = "Optical Tweezers Advanced Lab",
    year = 2005,
    season = "Fall",
    numpages = 12,
    eprint = "http://chirality.swarthmore.edu/PHYS81/OpticalTweezers.pdf",
    note = {Fairly complete overdamped PSD derivation in
        \fref{section}{4.3}.  Cites \citet{tlusty98} and
        \citet{bechhoefer02} for further details.  However, Tlusty
        (listed as reference 8) doesn't contain the thermal response
        fn.\ derivation it was cited for.  Also, the single sided PSD
        definition credited to reference 9 (listed as Bechhoefer)
        looks more like Press (listed as reference 10).  I imagine
        Grossman and Stout mixed up their references, and meant to
        refer to \citet{bechhoefer02} and \citet{press92} respectively
        instead.},
    project = "Cantilever Calibration"
}

@article { halvorsen09,
    author = KHalvorsen #" and "# WPWong,
    title = "Massively parallel single-molecule manipulation using centrifugal
        force",
    year = 2009,
    journal = arXiv,
    url = "http://arxiv.org/abs/0912.5370",
    abstract = {Precise manipulation of single molecules has already led to
        remarkable insights in physics, chemistry, biology and medicine.
        However, widespread adoption of single-molecule techniques has been
        impeded by equipment cost and the laborious nature of making
        measurements one molecule at a time. We have solved these issues with a
        new approach: massively parallel single-molecule force measurements
        using centrifugal force. This approach is realized in a novel
        instrument that we call the Centrifuge Force Microscope (CFM), in which
        objects in an orbiting sample are subjected to a calibration-free,
        macroscopically uniform force-field while their micro-to-nanoscopic
        motions are observed. We demonstrate high-throughput single-molecule
        force spectroscopy with this technique by performing thousands of
        rupture experiments in parallel, characterizing force-dependent
        unbinding kinetics of an antibody-antigen pair in minutes rather than
        days. Additionally, we verify the force accuracy of the instrument by
        measuring the well-established DNA overstretching transition at 66
        $\pm$ 3 pN. With significant benefits in efficiency, cost, simplicity,
        and versatility, "single-molecule centrifugation" has the potential to
        revolutionize single-molecule experimentation, and open access to a
        wider range of researchers and experimental systems.}
}

@article { hanggi90,
    author = PHanggi #" and "# PTalkner #" and "# MBorkovec,
    title = "Reaction-rate theory: Fifty years after {K}ramers",
    year = 1990,
    month = "Apr",
    journal = RMP,
    volume = 62,
    number = 2,
    pages = "251--341",
    numpages = 90,
    publisher = APS,
    doi = "10.1103/RevModPhys.62.251",
    eprint = "http://www.physik.uni-augsburg.de/theo1/hanggi/Papers/112.pdf",
    url = "http://prola.aps.org/abstract/RMP/v62/i2/p251_1",
    note = "\emph{The} Kramers' theory review article. See pages 268--279 for
        the Kramers-specific introduction.",
    project = "sawtooth simulation"
}

@article { hatfield99,
    author = JWHatfield #" and "# SRQuake,
    title = "Dynamic Properties of an Extended Polymer in Solution",
    year = 1999,
    month = "Apr",
    journal = PRL,
    volume = 82,
    number = 17,
    pages = "3548--3551",
    numpages = 3,
    publisher = APS,
    doi = "10.1103/PhysRevLett.82.3548",
    url = "http://link.aps.org/abstract/PRL/v82/p3548",
    note = "Defines WLC and FJC models, citing textbooks.",
    project = "sawtooth simulation"
}

@article { heymann00,
    author = BHeymann #" and "# HGrubmuller,
    title = "Dynamic force spectroscopy of molecular adhesion bonds",
    year = 2000,
    month = jun,
    day = 26,
    journal = PRL,
    volume = 84,
    number = "26 Pt 1",
    pages = "6126--6129",
    issn = "0031-9007",
    doi = "10.1103/PhysRevLett.84.6126",
    eprint = "http://prola.aps.org/pdf/PRL/v84/i26/p6126_1",
    url = "http://prola.aps.org/abstract/PRL/v84/p6126",
    abstract = "Recent advances in atomic force microscopy, biomembrane force
        probe experiments, and optical tweezers allow one to measure the
        response of single molecules to mechanical stress with high precision.
        Such experiments, due to limited spatial resolution, typically access
        only one single force value in a continuous force profile that
        characterizes the molecular response along a reaction coordinate. We
        develop a theory that allows one to reconstruct force profiles from
        force spectra obtained from measurements at varying loading rates,
        without requiring increased resolution. We show that spectra obtained
        from measurements with different spring constants contain complementary
        information."
}

@article { hummer01,
    author = GHummer #" and "# ASzabo,
    title = "From the Cover: Free energy reconstruction from nonequilibrium
        single-molecule pulling experiments",
    year = 2001,
    journal = PNAS,
    volume = 98,
    number = 7,
    pages = "3658--3661",
    doi = "10.1073/pnas.071034098",
    eprint = "http://www.pnas.org/cgi/reprint/98/7/3658.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/98/7/3658",
    note = "READ"
}

@article { hummer03,
    author = GHummer #" and "# ASzabo,
    title = "Kinetics from nonequilibrium single-molecule pulling experiments",
    year = 2003,
    month = jul,
    journal = BPJ,
    volume = 85,
    number = 1,
    pages = "5--15",
    issn = "0006-3495",
    eprint = "http://www.biophysj.org/cgi/reprint/85/1/5.pdf",
    url = "http://www.biophysj.org/cgi/content/abstract/85/1/5",
    keywords = "Computer Simulation; Crystallography; Energy Transfer;
        Kinetics; Lasers; Micromanipulation; Microscopy, Atomic Force; Models,
        Molecular; Molecular Conformation; Motion; Muscle Proteins;
        Nanotechnology; Physical Stimulation; Protein Conformation; Protein
        Denaturation; Protein Folding; Protein Kinases; Stress, Mechanical",
    abstract = "Mechanical forces exerted by laser tweezers or atomic force
        microscopes can be used to drive rare transitions in single molecules,
        such as unfolding of a protein or dissociation of a ligand. The
        phenomenological description of pulling experiments based on Bell's
        expression for the force-induced rupture rate is found to be inadequate
        when tested against computer simulations of a simple microscopic model
        of the dynamics. We introduce a new approach of comparable complexity
        to extract more accurate kinetic information about the molecular events
        from pulling experiments. Our procedure is based on the analysis of a
        simple stochastic model of pulling with a harmonic spring and
        encompasses the phenomenological approach, reducing to it in the
        appropriate limit. Our approach is tested against computer simulations
        of a multimodule titin model with anharmonic linkers and then an
        illustrative application is made to the forced unfolding of I27
        subunits of the protein titin. Our procedure to extract kinetic
        information from pulling experiments is simple to implement and should
        prove useful in the analysis of experiments on a variety of systems.",
    note = "READ",
    project = "sawtooth simulation"
}

@article { hutter05,
    author = JHutter,
    title = "Comment on tilt of atomic force microscope cantilevers: Effect on
        spring constant and adhesion measurements.",
    year = 2005,
    month = mar,
    day = 15,
    journal = LANG,
    volume = 21,
    number = 6,
    pages = "2630--2632",
    issn = "0743-7463",
    doi = "10.1021/la047670t",
    note = "Tilted cantilever corrections (not needed? see Ohler/VEECO note)",
    project = "Cantilever Calibration"
}

@article { hutter93,
    author = JHutter #" and "# JBechhoefer,
    title = "Calibration of atomic-force microscope tips",
    year = 1993,
    journal = RSI,
    volume = 64,
    number = 7,
    pages = "1868--1873",
    publisher = AIP,
    doi = "10.1063/1.1143970",
    url = "http://link.aip.org/link/?RSI/64/1868/1",
    keywords = {atomic force microscopy; calibration; quality factor; probes;
        resonance; silicon nitrides; mica; van der waals forces},
    note = {Original equipartition-based calibration method (thermal
        calibration), after the brief mention in \citet{howard88}.
        This is the first paper I've found that works out the theory
        in detail, although they punt to page 431 of \citet{heer72}
        instead of listing a formula for their ``Lorentzian''.  The
        experimental data uses high-$Q$ cantilevers in air, and their
        figure 2 shows clear water-layer snap-off.  There is a
        published erratum\citep{hutter93-erratum}.},
    project = "Cantilever Calibration"
}

@article{ hutter93-erratum,
  author = JHutter #" and "# JBechhoefer,
  title = "Erratum: Calibration of atomic-force microscope tips",
  year = 1993,
  month = nov,
  journal = RSI,
  volume = 64,
  number = 11,
  pages = 3342,
  publisher = AIP,
  doi = "10.1063/1.1144449",
  url = "http://rsi.aip.org/resource/1/rsinak/v64/i11/p3342_s1",
  note = {V.~Croquette pointed out that they should calibrate the
    response of their optical-detection electronics.},
  project = "Cantilever Calibration",
}

@book{ heer72,
  author = CVHeer,
  title = {Statistical mechanics, kinetic theory, and stochastic processes},
  year = 1972,
  publisher = AcP,
  address = {New York},
  numpages = 602,
  isbn = {0-123-36550-3},
  language = {English},
  keywords = {Statistical mechanics.; Kinetic theory of gases.; Stochastic processes.},
}

@article { hyeon03,
    author = CHyeon #" and "# DThirumalai,
    title = "Can energy landscape roughness of proteins and {RNA} be measured
        by using mechanical unfolding experiments?",
    year = 2003,
    month = sep,
    day = 02,
    journal = PNAS,
    volume = 100,
    number = 18,
    pages = "10249--10253",
    issn = "0027-8424",
    doi = "10.1073/pnas.1833310100",
    eprint = "http://www.pnas.org/cgi/reprint/100/18/10249.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/100/18/10249",
    keywords = "Protein Folding; Proteins; RNA; Temperature; Thermodynamics",
    abstract = "By considering temperature effects on the mechanical unfolding
        rates of proteins and RNA, whose energy landscape is rugged, the
        question posed in the title is answered in the affirmative. Adopting a
        theory by Zwanzig [Zwanzig, R. (1988) Proc. Natl. Acad. Sci. USA 85,
        2029-2030], we show that, because of roughness characterized by an
        energy scale epsilon, the unfolding rate at constant force is retarded.
        Similarly, in nonequilibrium experiments done at constant loading
        rates, the most probable unfolding force increases because of energy
        landscape roughness. The effects are dramatic at low temperatures. Our
        analysis suggests that, by using temperature as a variable in
        mechanical unfolding experiments of proteins and RNA, the ruggedness
        energy scale epsilon, can be directly measured.",
    note = "Derives the major theory behind my thesis. The Kramers rate
        equation is \xref{hanggi90}{equation}{4.56c} (page 275).",
    project = "Energy Landscape Roughness"
}

@article { improta96,
    author = SImprota #" and "# ASPolitou #" and "# APastore,
    title = "Immunoglobulin-like modules from titin {I}-band: Extensible
        components of muscle elasticity.",
    year = 1996,
    month = mar,
    day = 15,
    journal = STR,
    volume = 4,
    number = 3,
    pages = "323--337",
    issn = "0969-2126",
    doi = "10.1016/S0969-2126(96)00036-6",
    keywords = "Amino Acid Sequence;Immunoglobulins;Magnetic Resonance
        Spectroscopy;Models, Molecular;Molecular Sequence Data;Molecular
        Structure;Muscle Proteins;Protein Kinases;Protein Structure,
        Secondary;Protein Structure, Tertiary;Sequence Alignment",
    abstract = "BACKGROUND. The giant muscle protein titin forms a filament
        which spans half of the sarcomere and performs, along its length, quite
        diverse functions. The region of titin located in the sarcomere I-band
        is believed to play a major role in extensibility and passive
        elasticity of muscle. In the I-band, the titin sequence consists mostly
        of repetitive motifs of tandem immunoglobulin-like (Ig) modules
        intercalated by a potentially non-globular region. The highly
        repetitive titin architecture suggests that the molecular basis of its
        mechanical properties be approached through the characterization of the
        isolated components of the I-band and their interfaces. In the present
        paper, we report on the structure determination in solution of a
        representative Ig module from the I-band (I27) as solved by NMR
        techniques. RESULTS. The structure of I27 consists of a beta sandwich
        formed by two four-stranded sheets (named ABED and A'GFC). This fold
        belongs to the intermediate frame (I frame) of the immunoglobulin
        superfamily. Comparison of I27 with another titin module from the
        region located in the M-line (M5) shows that two loops (between the B
        and C and the F and G strands) are shorter in I27, conferring a less
        elongated appearance to this structure. Such a feature is specific to
        the Ig domains in the I-band and might therefore be related to the
        functions of the protein in this region. The structure of tandem Ig
        domains as modeled from I27 suggests the presence of hinge regions
        connecting contiguous modules. CONCLUSIONS. We suggest that titin Ig
        domains in the I-band function as extensible components of muscle
        elasticity by stretching the hinge regions.",
    note = "\href{http://www.rcsb.org/pdb/explore.do?structureId=1TIT}{PDB ID:
        1TIT}, DOI:
        \href{http://dx.doi.org/10.2210/pdb1tit/pdb}{10.2210/pdb1tit/pdb}."
}

@article { irback05,
    author = AIrback #" and "# SMitternacht #" and "# SMohanty,
    title = "Dissecting the mechanical unfolding of ubiquitin",
    year = 2005,
    journal = PNAS,
    volume = 102,
    number = 38,
    pages = "13427--13432",
    doi = "10.1073/pnas.0501581102",
    eprint = "http://www.pnas.org/cgi/reprint/102/38/13427.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/102/38/13427",
    abstract = "The unfolding behavior of ubiquitin under the influence of a
        stretching force recently was investigated experimentally by single-
        molecule constant-force methods. Many observed unfolding traces had a
        simple two-state character, whereas others showed clear evidence of
        intermediate states. Here, we use Monte Carlo simulations to
        investigate the force-induced unfolding of ubiquitin at the atomic
        level. In agreement with experimental data, we find that the unfolding
        process can occur either in a single step or through intermediate
        states. In addition to this randomness, we find that many quantities,
        such as the frequency of occurrence of intermediates, show a clear
        systematic dependence on the strength of the applied force. Despite
        this diversity, one common feature can be identified in the simulated
        unfolding events, which is the order in which the secondary-structure
        elements break. This order is the same in two- and three-state events
        and at the different forces studied. The observed order remains to be
        verified experimentally but appears physically reasonable."
}

@article{ grubmuller96,
  author = HGrubmuller #" and "# BHeymann #" and "# PTavan,
  title = {Ligand binding: molecular mechanics calculation of the
    streptavidin-biotin rupture force.},
  year = 1996,
  month = feb,
  day = 16,
  address = {Theoretische Biophysik, Institut f{\"u}r Medizinische
             Optik, Ludwig- Maximilians-Universit{\"a}t M{\"u}nchen,
             Germany. Helmut.Grubmueller@ Physik.uni-muenchen.de},
  journal = SCI,
  volume = 271,
  number = 5251,
  pages = {997--999},
  issn = {0036-8075},
  url = {http://www.ncbi.nlm.nih.gov/pubmed/8584939},
  eprint = {http://pubman.mpdl.mpg.de/pubman/item/escidoc:1690312:2/component/escidoc:1690313/1690312.pdf},
  language = {eng},
  keywords = {Bacterial Proteins},
  keywords = {Biotin},
  keywords = {Chemistry, Physical},
  keywords = {Computer Simulation},
  keywords = {Hydrogen Bonding},
  keywords = {Ligands},
  keywords = {Microscopy, Atomic Force},
  keywords = {Models, Chemical},
  keywords = {Molecular Conformation},
  keywords = {Physicochemical Phenomena},
  keywords = {Protein Conformation},
  keywords = {Streptavidin},
  keywords = {Thermodynamics},
  abstract = {The force required to rupture the streptavidin-biotin
                 complex was calculated here by computer simulations.
                 The computed force agrees well with that obtained by
                 recent single molecule atomic force microscope
                 experiments. These simulations suggest a detailed
                 multiple-pathway rupture mechanism involving five major
                 unbinding steps. Binding forces and specificity are
                 attributed to a hydrogen bond network between the
                 biotin ligand and residues within the binding pocket of
                 streptavidin. During rupture, additional water bridges
                 substantially enhance the stability of the complex and
                 even dominate the binding interactions. In contrast,
                 steric restraints do not appear to contribute to the
                 binding forces, although conformational motions were
                 observed.},
}


@article { izrailev97,
    author = SIzrailev #" and "# SStepaniants #" and "# MBalsera #" and "#
        YOono #" and "# KSchulten,
    title = "Molecular dynamics study of unbinding of the avidin-biotin
        complex",
    year = 1997,
    month = apr,
    journal = BPJ,
    volume = 72,
    number = 4,
    pages = "1568--1581",
    issn = "0006-3495",
    eprint = "http://www.biophysj.org/cgi/reprint/72/4/1568.pdf",
    url = "http://www.biophysj.org/cgi/content/abstract/72/4/1568",
    keywords = "Avidin;Binding Sites;Biotin;Computer Simulation;Hydrogen
        Bonding;Mathematics;Microscopy, Atomic Force;Microspheres;Models,
        Molecular;Molecular Structure;Protein Binding;Protein
        Conformation;Protein Folding;Sepharose",
    abstract = "We report molecular dynamics simulations that induce, over
        periods of 40-500 ps, the unbinding of biotin from avidin by means of
        external harmonic forces with force constants close to those of AFM
        cantilevers. The applied forces are sufficiently large to reduce the
        overall binding energy enough to yield unbinding within the measurement
        time. Our study complements earlier work on biotin-streptavidin that
        employed a much larger harmonic force constant. The simulations reveal
        a variety of unbinding pathways, the role of key residues contributing
        to adhesion as well as the spatial range over which avidin binds
        biotin. In contrast to the previous studies, the calculated rupture
        forces exceed by far those observed. We demonstrate, in the framework
        of models expressed in terms of one-dimensional Langevin equations with
        a schematic binding potential, the associated Smoluchowski equations,
        and the theory of first passage times, that picosecond to nanosecond
        simulation of ligand unbinding requires such strong forces that the
        resulting protein-ligand motion proceeds far from the thermally
        activated regime of millisecond AFM experiments, and that simulated
        unbinding cannot be readily extrapolated to the experimentally observed
        rupture."
}

@article { janshoff00,
    author = AJanshoff #" and "# MNeitzert #" and "# YOberdorfer #" and "#
        HFuchs,
    title = "Force Spectroscopy of Molecular Systems-Single Molecule
        Spectroscopy of Polymers and Biomolecules.",
    year = 2000,
    month = sep,
    day = 15,
    journal = ACIEE,
    volume = 39,
    number = 18,
    pages = "3212--3237",
    issn = "1521-3773",
    doi = "10.1002/1521-3773(20000915)39:18<3212::AID-ANIE3212>3.0.CO;2-X",
    eprint = "",
    url = "http://dx.doi.org/10.1002/1521-3773(20000915)39:18<3212::AID-ANIE3212>3.0.CO;2-X",
    abstract = "How do molecules interact with each other? What happens if a
        neurotransmitter binds to a ligand-operated ion channel? How do
        antibodies recognize their antigens? Molecular recognition events play
        a pivotal role in nature: in enzymatic catalysis and during the
        replication and transcription of the genome; it is also important for
        the cohesion of cellular structures and in numerous metabolic reactions
        that molecules interact with each other in a specific manner.
        Conventional methods such as calorimetry provide very precise values of
        binding enthalpies; these are, however, average values obtained from a
        large ensemble of molecules without knowledge of the dynamics of the
        molecular recognition event. Which forces occur when a single molecular
        couple meets and forms a bond? Since the development of the scanning
        force microscope and force spectroscopy a couple of years ago, tools
        have now become available for measuring the forces between interfaces
        with high precision-starting from colloidal forces to the interaction
        of single molecules. The manipulation of individual molecules using
        force spectroscopy is also possible. In this way, the mechanical
        properties on a molecular scale are measurable. The study of single
        molecules is not an exclusive domain of force spectroscopy; it can also
        be performed with a surface force apparatus, laser tweezers, or the
        micropipette technique. Regardless of these techniques, force
        spectroscopy has been proven as an extraordinary versatile tool. The
        intention of this review article is to present a critical evaluation of
        the actual development of static force spectroscopy. The article mainly
        focuses on experiments dealing with inter- and intramolecular forces-
        starting with ``simple'' electrostatic forces, then ligand-receptor
        systems, and finally the stretching of individual molecules."
}

@article { jollymore09,
    author = AJollymore #" and "# CLethias #" and "# QPeng #" and "# YCao #"
        and "# HLi,
    title = "Nanomechanical properties of tenascin-{X} revealed by single-
        molecule force spectroscopy",
    year = 2009,
    month = jan,
    day = 30,
    journal = JMB,
    volume = 385,
    number = 4,
    pages = "1277--1286",
    issn = "1089-8638",
    doi = "10.1016/j.jmb.2008.11.038",
    url = "http://dx.doi.org/10.1016/j.jmb.2008.11.038",
    keywords = "Animals;Biomechanics;Cattle;Fibronectins;Kinetics;Microscopy,
        Atomic Force;Protein Folding;Protein Structure, Tertiary;Spectrum
        Analysis;Tenascin",
    abstract = "Tenascin-X is an extracellular matrix protein and binds a
        variety of molecules in extracellular matrix and on cell membrane.
        Tenascin-X plays important roles in regulating the structure and
        mechanical properties of connective tissues. Using single-molecule
        atomic force microscopy, we have investigated the mechanical properties
        of bovine tenascin-X in detail. Our results indicated that tenascin-X
        is an elastic protein and the fibronectin type III (FnIII) domains can
        unfold under a stretching force and refold to regain their mechanical
        stability upon the removal of the stretching force. All the 30 FnIII
        domains of tenascin-X show similar mechanical stability, mechanical
        unfolding kinetics, and contour length increment upon domain unfolding,
        despite their large sequence diversity. In contrast to the homogeneity
        in their mechanical unfolding behaviors, FnIII domains fold at
        different rates. Using the 10th FnIII domain of tenascin-X (TNXfn10) as
        a model system, we constructed a polyprotein chimera composed of
        alternating TNXfn10 and GB1 domains and used atomic force microscopy to
        confirm that the mechanical properties of TNXfn10 are consistent with
        those of the FnIII domains of tenascin-X. These results lay the
        foundation to further study the mechanical properties of individual
        FnIII domains and establish the relationship between point mutations
        and mechanical phenotypic effect on tenascin-X. Moreover, our results
        provided the opportunity to compare the mechanical properties and
        design of different forms of tenascins. The comparison between
        tenascin-X and tenascin-C revealed interesting common as well as
        distinguishing features for mechanical unfolding and folding of
        tenascin-C and tenascin-X and will open up new avenues to investigate
        the mechanical functions and architectural design of different forms of
        tenascins."
}

@article { jones05,
    author = REJones #" and "# DPHart,
    title = "Force interactions between substrates and {SPM} cantilevers
        immersed in fluids",
    year = 2005,
    journal = TBI,
    volume = 38,
    number = 3,
    pages = "355--361",
    issn = "0301-679X",
    doi = "DOI: 10.1016/j.triboint.2004.08.016",
    url = "http://www.sciencedirect.com/science/article/B6V57-4DN9K7J-1/2/fef91
        ac022594c2c6a701376d83ecd31",
    keywords = "AFM;Liquid;Hydrodynamic;Lubrication",
    abstract = "With the availability of equipment used in Scanning Probe
        Microscopy (SPM), researchers have been able to probe the local fluid-
        substrate force interactions with resolutions of pN using a variety of
        SPM cantilevers. When using such methods, it is essential to
        differentiate between contributions to the net force on the cantilever.
        Specifically, the interaction between the cantilever, substrate and
        fluid, quantified while generating force curves, are discussed and
        compared with theoretical models for squeeze-film effects and drag on
        the SPM cantilevers. In addition we have demonstrated a simple method
        for utilizing the system as a micro-viscometer, independently measuring
        the viscosity of the lubricant for each test."
}

@article { juckett93,
    author = DAJuckett #" and "# BRosenberg,
    title = "Comparison of the {G}ompertz and {W}eibull functions as
        descriptors for human mortality distributions and their intersections",
    year = 1993,
    month = jun,
    journal = MAD,
    volume = 69,
    number = "1--2",
    pages = "1--31",
    issn = "0047-6374",
    doi = "10.1016/0047-6374(93)90068-3",
    keywords = "Adolescent;Adult;Aged;Aged, 80 and
        over;Aging;Biometry;Child;Child, Preschool;Data Interpretation,
        Statistical;Female;Humans;Infant;Infant, Newborn;Longitudinal
        Studies;Male;Middle Aged;Models, Biological;Models,
        Statistical;Mortality",
    abstract = "The Gompertz and Weibull functions are compared with respect to
        goodness-of-fit to human mortality distributions; ability to describe
        mortality curve intersections; and, parameter interpretation. The
        Gompertz function is shown to be a better descriptor for 'all-causes'
        of deaths and combined disease categories while the Weibull function is
        shown to be a better descriptor of purer, single causes-of-death. A
        modified form of the Weibull function maps directly to the inherent
        degrees of freedom of human mortality distributions while the Gompertz
        function does not. Intersections in the old-age tails of mortality are
        explored in the context of both functions and, in particular, the
        relationship between distribution intersections, and the Gompertz
        ln[R0] versus alpha regression is examined. Evidence is also presented
        that mortality intersections are fundamental to the survivorship form
        and not the rate (hazard) form. Finally, comparisons are made to the
        parameter estimates in recent longitudinal Gompertzian analyses and the
        probable errors in those analyses are discussed.",
    note = "Nice table of various functions associated with Gompertz and
        Weibull models."
}

@article { kaplan58,
    author = ELKaplan #" and "# PMeier,
    title = "Nonparametric Estimation from Incomplete Observations",
    year = 1958,
    month = "jun",
    journal = JASA,
    volume = 53,
    number = 282,
    pages = "457--481",
    issn = 01621459,
    publisher = ASA,
    copyright = "Copyright \copy\ 1958 American Statistical Association",
    url = "http://www.jstor.org/stable/2281868",
    abstract = ""
}

@article { kellermayer03,
    author = MSKellermayer #" and "# CBustamante #" and "# HLGranzier,
    title = "Mechanics and structure of titin oligomers explored with atomic
        force microscopy",
    year = 2003,
    journal = BBABE,
    volume = 1604,
    number = 2,
    pages = "105--114",
    issn = "0005-2728",
    doi = "10.1016/S0005-2728(03)00029-X",
    url = "http://dx.doi.org/10.1016/S0005-2728(03)00029-X",
    keywords = "Titin;Wormlike chain;Unfolding;Elasticity;AFM;Molecular force
        spectroscopy",
    abstract = "Titin is a giant polypeptide that spans half of the striated
        muscle sarcomere and generates passive force upon stretch. To explore
        the elastic response and structure of single molecules and oligomers of
        titin, we carried out molecular force spectroscopy and atomic force
        microscopy (AFM) on purified full-length skeletal-muscle titin. From
        the force data, apparent persistence lengths as long as ~1.5 nm were
        obtained for the single, unfolded titin molecule. Furthermore, data
        suggest that titin molecules may globally associate into oligomers
        which mechanically behave as independent wormlike chains (WLCs).
        Consistent with this, AFM of surface-adsorbed titin molecules revealed
        the presence of oligomers. Although oligomers may form globally via
        head-to-head association of titin, the constituent molecules otherwise
        appear independent from each other along their contour. Based on the
        global association but local independence of titin molecules, we
        discuss a mechanical model of the sarcomere in which titin molecules
        with different contour lengths, corresponding to different isoforms,
        are held in a lattice. The net force response of aligned titin
        molecules is determined by the persistence length of the tandemly
        arranged, different WLC components of the individual molecules, the
        ratio of their overall contour lengths, and by domain unfolding events.
        Biased domain unfolding in mechanically selected constituent molecules
        may serve as a compensatory mechanism for contour- and persistence-
        length differences. Variation in the ratio and contour length of the
        component chains may provide mechanisms for the fine-tuning of the
        sarcomeric passive force response.",
    note = ""
}

@article { kellermayer97,
    author = MSKellermayer #" and "# SBSmith #" and "# HLGranzier #" and "#
        CBustamante,
    title = "Folding-unfolding transitions in single titin molecules
        characterized with laser tweezers",
    year = 1997,
    month = may,
    day = 16,
    journal = SCI,
    volume = 276,
    number = 5315,
    pages = "1112--1116",
    issn = "0036-8075",
    keywords = "Amino Acid
        Sequence;Elasticity;Entropy;Immunoglobulins;Lasers;Models,
        Chemical;Muscle Contraction;Muscle Proteins;Muscle Relaxation;Muscle,
        Skeletal;Protein Denaturation;Protein Folding;Protein Kinases;Stress,
        Mechanical",
    abstract = "Titin, a giant filamentous polypeptide, is believed to play a
        fundamental role in maintaining sarcomeric structural integrity and
        developing what is known as passive force in muscle. Measurements of
        the force required to stretch a single molecule revealed that titin
        behaves as a highly nonlinear entropic spring. The molecule unfolds in
        a high-force transition beginning at 20 to 30 piconewtons and refolds
        in a low-force transition at approximately 2.5 piconewtons. A fraction
        of the molecule (5 to 40 percent) remains permanently unfolded,
        behaving as a wormlike chain with a persistence length (a measure of
        the chain's bending rigidity) of 20 angstroms. Force hysteresis arises
        from a difference between the unfolding and refolding kinetics of the
        molecule relative to the stretch and release rates in the experiments,
        respectively. Scaling the molecular data up to sarcomeric dimensions
        reproduced many features of the passive force versus extension curve of
        muscle fibers."
}

@article { king10,
    author = WKing #" and "# MSu #" and "# GYang,
    title = "{M}onte {C}arlo simulation of mechanical unfolding of proteins
        based on a simple two-state model",
    year = 2010,
    month = mar,
    day = 1,
    address =      "Department of Physics, Drexel University, 3141
                   Chestnut Street, Philadelphia, PA 19104, USA.",
    journal = IJBMM,
    volume = 46,
    number = 2,
    pages = "159--166",
    issn = "0141-8130",
    alternative_issn = "1879-0003",
    doi = "10.1016/j.ijbiomac.2009.12.001",
    url = "http://www.sciencedirect.com/science/article/B6T7J-
        4XWMND2-1/2/7ef768562b4157fc201d450553e5de5e",
    language = "eng",
    keywords = "Atomic force microscopy;Mechanical unfolding;Monte Carlo
        simulation;Worm-like chain;Single molecule methods",
    abstract = "Single molecule methods are becoming routine biophysical
        techniques for studying biological macromolecules. In mechanical
        unfolding of proteins, an externally applied force is used to induce
        the unfolding of individual protein molecules. Such experiments have
        revealed novel information that has significantly enhanced our
        understanding of the function and folding mechanisms of several types
        of proteins. To obtain information on the unfolding kinetics and the
        free energy landscape of the protein molecule from mechanical unfolding
        data, a Monte Carlo simulation based on a simple two-state kinetic
        model is often used. In this paper, we provide a detailed description
        of the procedure to perform such simulations and discuss the
        approximations and assumptions involved. We show that the appearance of
        the force versus extension curves from mechanical unfolding of proteins
        is affected by a variety of experimental parameters, such as the length
        of the protein polymer and the force constant of the cantilever. We
        also analyze the errors associated with different methods of data
        pooling and present a quantitative measure of how well the simulation
        results fit experimental data. These findings will be helpful in
        experimental design, artifact identification, and data analysis for
        single molecule studies of various proteins using the mechanical
        unfolding method."
}

@article { kleiner07,
    author = AKleiner #" and "# EShakhnovich,
    title = "The mechanical unfolding of ubiquitin through all-atom Monte Carlo
        simulation with a Go-type potential",
    year = 2007,
    month = mar,
    day = 15,
    journal = BPJ,
    volume = 92,
    number = 6,
    pages = "2054--2061",
    issn = "0006-3495",
    doi = "10.1529/biophysj.106.081257",
    eprint = "http://www.biophysj.org/cgi/reprint/92/6/2054",
    url = "http://www.biophysj.org/cgi/content/full/92/6/2054",
    keywords = "Computer Simulation; Models, Chemical; Models, Molecular;
        Models, Statistical; Monte Carlo Method; Motion; Protein Conformation;
        Protein Denaturation; Protein Folding; Ubiquitin",
    abstract = "The mechanical unfolding of proteins under a stretching force
        has an important role in living systems and is a logical extension of
        the more general protein folding problem. Recent advances in
        experimental methodology have allowed the stretching of single
        molecules, thus rendering this process ripe for computational study. We
        use all-atom Monte Carlo simulation with a G?-type potential to study
        the mechanical unfolding pathway of ubiquitin. A detailed, robust,
        well-defined pathway is found, confirming existing results in this vein
        though using a different model. Additionally, we identify the protein's
        fundamental stabilizing secondary structure interactions in the
        presence of a stretching force and show that this fundamental
        stabilizing role does not persist in the absence of mechanical stress.
        The apparent success of simulation methods in studying ubiquitin's
        mechanical unfolding pathway indicates their potential usefulness for
        future study of the stretching of other proteins and the relationship
        between protein structure and the response to mechanical deformation."
}

@article { klimov00,
    author = DKlimov #" and "# DThirumalai,
    title = "Native topology determines force-induced unfolding pathways in
        globular proteins",
    year = 2000,
    month = jun,
    day = 20,
    journal = PNAS,
    volume = 97,
    number = 13,
    pages = "7254--7259",
    issn = "0027-8424",
    doi = "10.1073/pnas.97.13.7254",
    eprint = "http://www.pnas.org/cgi/reprint/97/13/7254.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/97/13/7254",
    keywords = "Animals; Humans; Protein Folding; Proteins; Spectrin",
    abstract = "Single-molecule manipulation techniques reveal that stretching
        unravels individually folded domains in the muscle protein titin and
        the extracellular matrix protein tenascin. These elastic proteins
        contain tandem repeats of folded domains with beta-sandwich
        architecture. Herein, we propose by stretching two model sequences (S1
        and S2) with four-stranded beta-barrel topology that unfolding forces
        and pathways in folded domains can be predicted by using only the
        structure of the native state. Thermal refolding of S1 and S2 in the
        absence of force proceeds in an all-or-none fashion. In contrast, phase
        diagrams in the force-temperature (f,T) plane and steered Langevin
        dynamics studies of these sequences, which differ in the native
        registry of the strands, show that S1 unfolds in an allor-none fashion,
        whereas unfolding of S2 occurs via an obligatory intermediate. Force-
        induced unfolding is determined by the native topology. After proving
        that the simulation results for S1 and S2 can be calculated by using
        native topology alone, we predict the order of unfolding events in Ig
        domain (Ig27) and two fibronectin III type domains ((9)FnIII and
        (10)FnIII). The calculated unfolding pathways for these proteins, the
        location of the transition states, and the pulling speed dependence of
        the unfolding forces reflect the differences in the way the strands are
        arranged in the native states. We also predict the mechanisms of force-
        induced unfolding of the coiled-coil spectrin (a three-helix bundle
        protein) for all 20 structures deposited in the Protein Data Bank. Our
        approach suggests a natural way to measure the phase diagram in the
        (f,C) plane, where C is the concentration of denaturants.",
    note = {Simulated unfolding time scales for Ig27-like S1 and S2 domains.},
}

@article { klimov99,
    author = DKlimov #" and "# DThirumalai,
    title = "Stretching single-domain proteins: Phase diagram and kinetics of
        force-induced unfolding",
    year = 1999,
    month = may,
    day = 25,
    journal = PNAS,
    volume = 96,
    number = 11,
    pages = "6166--6170",
    issn = "0027-8424",
    keywords = "Amino Acid Sequence;Kinetics;Models, Chemical;Protein
        Denaturation;Protein Folding;Proteins;Thermodynamics;Time Factors",
    abstract = "Single-molecule force spectroscopy reveals unfolding of domains
        in titin on stretching. We provide a theoretical framework for these
        experiments by computing the phase diagrams for force-induced unfolding
        of single-domain proteins using lattice models. The results show that
        two-state folders (at zero force) unravel cooperatively, whereas
        stretching of non-two-state folders occurs through intermediates. The
        stretching rates of individual molecules show great variations
        reflecting the heterogeneity of force-induced unfolding pathways. The
        approach to the stretched state occurs in a stepwise ``quantized''
        manner. Unfolding dynamics and forces required to stretch proteins
        depend sensitively on topology. The unfolding rates increase
        exponentially with force f till an optimum value, which is determined
        by the barrier to unfolding when f = 0. A mapping of these results to
        proteins shows qualitative agreement with force-induced unfolding of
        Ig-like domains in titin. We show that single-molecule force
        spectroscopy can be used to map the folding free energy landscape of
        proteins in the absence of denaturants."
}

@article { kosztin06,
    author = IKosztin #" and "# BBarz #" and "# LJanosi,
    title = "Calculating potentials of mean force and diffusion coefficients
        from nonequilibrium processes without Jarzynski's equality",
    year = 2006,
    month = feb,
    day = 10,
    journal = JCP,
    volume = 124,
    pages = 064106,
    issn = "0031-9007",
    doi = "10.1063/1.2166379",
    url = "http://link.aip.org/link/?JCPSA6/124/064106/1"
}

@article { kramers40,
    author = HAKramers,
    title = "Brownian motion in a field of force and the diffusion model of
        chemical reactions",
    year = 1940,
    month = apr,
    journal = Physica,
    volume = 7,
    number = 4,
    pages = "284--304",
    issn = "0031-8914",
    doi = "10.1016/S0031-8914(40)90098-2",
    url = "http://dx.doi.org/10.1016/S0031-8914(40)90098-2",
    abstract = "A particle which is caught in a potential hole and which,
        through the shuttling action of Brownian motion, can escape over a
        potential barrier yields a suitable model for elucidating the
        applicability of the transition state method for calculating the rate
        of chemical reactions.",
    note = "Seminal paper on thermally activated barrier crossings."
}

@article { krammer99,
    author = AKrammer #" and "# HLu #" and "# BIsralewitz #" and "# KSchulten
        #" and "# VVogel,
    title = "Forced unfolding of the fibronectin type {III} module reveals a
        tensile molecular recognition switch",
    year = 1999,
    month = feb,
    day = 16,
    journal = PNAS,
    volume = 96,
    number = 4,
    pages = "1351--1356",
    issn = "0027-8424",
    keywords = "Amino Acid Sequence;Binding Sites;Computer
        Simulation;Crystallography, X-Ray;Disulfides;Fibronectins;Hydrogen
        Bonding;Integrins;Models, Molecular;Oligopeptides;Protein
        Conformation;Protein Denaturation;Protein Folding;Protein Structure,
        Secondary;Protein Structure, Tertiary;Software;Tensile Strength",
    abstract = "The 10th type III module of fibronectin possesses a beta-
        sandwich structure consisting of seven beta-strands (A-G) that are
        arranged in two antiparallel sheets. It mediates cell adhesion to
        surfaces via its integrin binding motif, Arg78, Gly79, and Asp80 (RGD),
        which is placed at the apex of the loop connecting beta-strands F and
        G. Steered molecular dynamics simulations in which tension is applied
        to the protein's terminal ends reveal that the beta-strand G is the
        first to break away from the module on forced unfolding whereas the
        remaining fold maintains its structural integrity. The separation of
        strand G from the remaining fold results in a gradual shortening of the
        distance between the apex of the RGD-containing loop and the module
        surface, which potentially reduces the loop's accessibility to surface-
        bound integrins. The shortening is followed by a straightening of the
        RGD-loop from a tight beta-turn into a linear conformation, which
        suggests a further decrease of affinity and selectivity to integrins.
        The RGD-loop therefore is located strategically to undergo strong
        conformational changes in the early stretching stages of the module and
        thus constitutes a mechanosensitive control of ligand recognition."
}

@article { kreuzer01,
    author = HJKreuzer #" and "# SHPayne,
    title = "Stretching a macromolecule in an atomic force microscope:
        statistical mechanical analysis",
    year = 2001,
    month = feb,
    day = 23,
    journal = PR:E,
    volume = 63,
    number = "2 Pt 1",
    pages = 021906,
    issn = "1539-3755",
    eprint = "http://www.biophysj.org/cgi/reprint/80/6/2505.pdf",
    url = "http://www.biophysj.org/cgi/content/abstract/80/6/2505",
    keywords = "Biophysics;Macromolecular Substances;Microscopy, Atomic
        Force;Models, Statistical;Models, Theoretical;Statistics as Topic",
    abstract = "We formulate the proper statistical mechanics to describe the
        stretching of a macromolecule under a force provided by the cantilever
        of an atomic force microscope. In the limit of a soft cantilever the
        generalized ensemble of the coupled molecule/cantilever system reduces
        to the Gibbs ensemble for an isolated molecule subject to a constant
        force in which the extension is fluctuating. For a stiff cantilever we
        obtain the Helmholtz ensemble for an isolated molecule held at a fixed
        extension with the force fluctuating. Numerical examples are given for
        poly (ethylene glycol) chains."
}

@article { kroy07,
    author = KKroy #" and "# JGlaser,
    title = "The glassy wormlike chain",
    year = 2007,
    journal = NJP,
    volume = 9,
    number = 11,
    pages = 416,
    doi = "10.1088/1367-2630/9/11/416",
    eprint = "http://www.iop.org/EJ/article/1367-2630/9/11/416/njp7_11_416.pdf",
    url = "http://stacks.iop.org/1367-2630/9/416",
    abstract = "We introduce a new model for the dynamics of a wormlike chain
        (WLC) in an environment that gives rise to a rough free energy
        landscape, which we name the glassy WLC. It is obtained from the common
        WLC by an exponential stretching of the relaxation spectrum of its
        long-wavelength eigenmodes, controlled by a single parameter
        \\boldsymbol{\\cal E} . Predictions for pertinent observables such as
        the dynamic structure factor and the microrheological susceptibility
        exhibit the characteristics of soft glassy rheology and compare
        favourably with experimental data for reconstituted cytoskeletal
        networks and live cells. We speculate about the possible microscopic
        origin of the stretching, implications for the nonlinear rheology, and
        the potential physiological significance of our results.",
    note = "Has short section on WLC relaxation time in the weakly bending
        limit."
}

@article { labeit03,
    author = DLabeit #" and "# KWatanabe #" and "# CWitt #" and "# HFujita #"
        and "# YWu #" and "# SLahmers #" and "# TFunck #" and "# SLabeit #" and
        "# HLGranzier,
    title = "Calcium-dependent molecular spring elements in the giant protein
        titin",
    year = 2003,
    journal = PNAS,
    volume = 100,
    number = 23,
    pages = "13716--13721",
    doi = "10.1073/pnas.2235652100",
    eprint = "http://www.pnas.org/cgi/reprint/100/23/13716.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/100/23/13716",
    abstract = "Titin (also known as connectin) is a giant protein with a wide
        range of cellular functions, including providing muscle cells with
        elasticity. Its physiological extension is largely derived from the
        PEVK segment, rich in proline (P), glutamate (E), valine (V), and
        lysine (K) residues. We studied recombinant PEVK molecules containing
        the two conserved elements: {approx}28-residue PEVK repeats and E-rich
        motifs. Single molecule experiments revealed that calcium-induced
        conformational changes reduce the bending rigidity of the PEVK
        fragments, and site-directed mutagenesis identified four glutamate
        residues in the E-rich motif that was studied (exon 129), as critical
        for this process. Experiments with muscle fibers showed that titin-
        based tension is calcium responsive. We propose that the PEVK segment
        contains E-rich motifs that render titin a calcium-dependent molecular
        spring that adapts to the physiological state of the cell."
}

@article{ labeit95,
  author = SLabeit #" and "# BKolmerer,
  title = "Titins: Giant proteins in charge of muscle ultrastructure
    and elasticity.",
  journal = SCI,
  year = 1995,
  month = oct,
  day = 13,
  address = "European Molecular Biology Laboratory, Heidelberg, Germany.",
  volume = 270,
  number = 5234,
  pages = "293--296",
  keywords = "Actin Cytoskeleton",
  keywords = "Amino Acid Sequence",
  keywords = "Animals",
  keywords = "DNA, Complementary",
  keywords = "Elasticity",
  keywords = "Fibronectins",
  keywords = "Humans",
  keywords = "Immunoglobulins",
  keywords = "Molecular Sequence Data",
  keywords = "Muscle Contraction",
  keywords = "Muscle Proteins",
  keywords = "Muscle, Skeletal",
  keywords = "Myocardium",
  keywords = "Protein Kinases",
  keywords = "Rabbits",
  keywords = "Repetitive Sequences, Nucleic Acid",
  keywords = "Sarcomeres",
  abstract = "In addition to thick and thin filaments, vertebrate
    striated muscle contains a third filament system formed by the
    giant protein titin. Single titin molecules extend from Z discs to
    M lines and are longer than 1 micrometer. The titin filament
    contributes to muscle assembly and resting tension, but more
    details are not known because of the large size of the
    protein. The complete complementary DNA sequence of human cardiac
    titin was determined. The 82-kilobase complementary DNA predicts a
    3-megadalton protein composed of 244 copies of immunoglobulin and
    fibronectin type III (FN3) domains. The architecture of sequences
    in the A band region of titin suggests why thick filament
    structure is conserved among vertebrates. In the I band region,
    comparison of titin sequences from muscles of different passive
    tension identifies two elements that correlate with tissue
    stiffness. This suggests that titin may act as two springs in
    series. The differential expression of the springs provides a
    molecular explanation for the diversity of sarcomere length and
    resting tension in vertebrate striated muscles.",
  ISSN = "0036-8075",
  URL = "http://www.ncbi.nlm.nih.gov/pubmed/7569978",
  language = "eng",
}

@article { law03,
    author = RLaw #" and "# GLiao #" and "# SHarper #" and "# GYang #" and "#
        DSpeicher #" and "# DDischer,
    title = "Pathway shifts and thermal softening in temperature-coupled forced
        unfolding of spectrin domains",
    address = "Biophysical Engineering Lab, Institute for Medicine and
        Engineering, and School of Engineering and Applied Science,
        University of Pennsylvania, Philadelphia, Pennsylvania
        19104-6315, USA.",
    year = 2003,
    month = nov,
    journal = BPJ,
    volume = 85,
    number = 5,
    pages = "3286--3293",
    issn = "0006-3495",
    keywords = "Circular Dichroism;Elasticity;Heat;Microscopy, Atomic
        Force;Physical Stimulation;Protein Conformation;Protein
        Denaturation;Protein Folding;Protein Structure,
        Tertiary;Spectrin;Stress, Mechanical;Temperature",
    abstract = "Pathways of unfolding a protein depend in principle on the
        perturbation-whether it is temperature, denaturant, or even forced
        extension. Widely-shared, helical-bundle spectrin repeats are known to
        melt at temperatures as low as 40-45 degrees C and are also known to
        unfold via multiple pathways as single molecules in atomic force
        microscopy. Given the varied roles of spectrin family proteins in cell
        deformability, we sought to determine the coupled effects of
        temperature on forced unfolding. Bimodal distributions of unfolding
        intervals are seen at all temperatures for the four-repeat beta(1-4)
        spectrin-an alpha-actinin homolog. The major unfolding length
        corresponds to unfolding of a single repeat, and a minor peak at twice
        the length corresponds to tandem repeats. Increasing temperature shows
        fewer tandem events but has no effect on unfolding intervals. As T
        approaches T(m), however, mean unfolding forces in atomic force
        microscopy also decrease; and circular dichroism studies demonstrate a
        nearly proportional decrease of helical content in solution. The
        results imply a thermal softening of a helical linker between repeats
        which otherwise propagates a helix-to-coil transition to adjacent
        repeats. In sum, structural changes with temperature correlate with
        both single-molecule unfolding forces and shifts in unfolding
        pathways.",
  doi =          "10.1016/S0006-3495(03)74747-X",
  URL =          "http://www.ncbi.nlm.nih.gov/pubmed/14581229",
  language =     "eng",
}

@article { levinthal68,
    author = CLevinthal,
    title = "Are there pathways for protein folding?",
    year = 1968,
    journal = JCPPCB,
    volume = 65,
    number = 1,
    pages = "44--45",
    eprint =
        "http://www.biochem.wisc.edu/courses/biochem704/Reading/Levinthal1968.p
        df",
    note = "\emph{Not} Levinthal's paradox."
}

@inproceedings { levinthal69,
    editor = PDebrunner #" and "# JCMTsibris #" and "# EMunck,
    author = CLevinthal,
    title = "How to Fold Graciously.",
    booktitle = "Mossbauer Spectroscopy in Biological Systems",
    year = 1969,
    pages = "22--24",
    publisher = UIP:Urbana,
    address = "Allerton House, Monticello, IL",
    url = "http://www-miller.ch.cam.ac.uk/levinthal/levinthal.html"
}

@article { levy02,
    author = RLevy #" and "# MMaaloum,
    title = "Measuring the spring constant of atomic force microscope
        cantilevers: Thermal fluctuations and other methods",
    year = 2002,
    journal = NT,
    volume = 13,
    number = 1,
    pages = "33--37",
    doi = "10.1088/0957-4484/13/1/307",
    url = "http://stacks.iop.org/0957-4484/13/33",
    abstract = "Knowledge of the interaction forces between surfaces gained
        using an atomic force microscope (AFM) is crucial in a variety of
        industrial and scientific applications and necessitates a precise
        knowledge of the cantilever spring constant. Many methods have been
        devised to experimentally determine the spring constants of AFM
        cantilevers. The thermal fluctuation method is elegant but requires a
        theoretical model of the bending modes. For a rectangular cantilever,
        this model is available (Butt and Jaschke). Detailed thermal
        fluctuation measurements of a series of AFM cantilever beams have been
        performed in order to test the validity and accuracy of the recent
        theoretical models. The spring constant of rectangular cantilevers can
        also be determined easily with the method of Sader and White. We found
        very good agreement between the two methods. In the case of the
        V-shaped cantilever, we have shown that the thermal fluctuation method
        is a valid and accurate approach to the evaluation of the spring
        constant. A comparison between this method and those of Sader-
        Neumeister and of Ducker has been established. In some cases, we found
        disagreement between these two methods; the effect of non-conservation
        of material properties over all cantilevers from a single chip is
        qualitatively invoked.",
    note = "Good review of thermal calibration to 2002, but not much on the
        derviation of the Lorentzian fit.",
    project = "Cantilever Calibration"
}

@article { li00,
    author = HLi #" and "# AOberhauser #" and "# SFowler #" and "# JClarke #"
        and "# JFernandez,
    title = "Atomic force microscopy reveals the mechanical design of a modular
        protein",
    year = 2000,
    journal = PNAS,
    volume = 97,
    number = 12,
    pages = "6527--6531",
    doi = "10.1073/pnas.120048697",
    eprint = "http://www.pnas.org/cgi/reprint/97/12/6527.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/97/12/6527",
    abstract = "",
    note = "Unfolding order not from protein-surface interactions. Mechanical
        unfolding of a chain of interleaved domains $ABABAB\ldots$ yielded a
        run of $A$ unfoldings followed by a run of $B$ unfoldings."
}

@article { li01,
    author = HLi #" and "# AOberhauser #" and "# SRedick #" and "#
        MCarrionVazquez #" and "# HErickson #" and "# JFernandez,
    title = "Multiple conformations of {PEVK} proteins detected by single-
        molecule techniques",
    year = 2001,
    journal = PNAS,
    volume = 98,
    number = 19,
    pages = "10682--10686",
    doi = "10.1073/pnas.191189098",
    eprint = "http://www.pnas.org/cgi/reprint/98/19/10682.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/98/19/10682",
    abstract = "An important component of muscle elasticity is the PEVK region
        of titin, so named because of the preponderance of these amino acids.
        However, the PEVK region, similar to other elastomeric proteins, is
        thought to form a random coil and therefore its structure cannot be
        determined by standard techniques. Here we combine single-molecule
        electron microscopy and atomic force microscopy to examine the
        conformations of the human cardiac titin PEVK region. In contrast to a
        simple random coil, we have found that cardiac PEVK shows a wide range
        of elastic conformations with end-to-end distances ranging from 9 to 24
        nm and persistence lengths from 0.4 to 2.5 nm. Individual PEVK
        molecules retained their distinctive elastic conformations through many
        stretch-relaxation cycles, consistent with the view that these PEVK
        conformers cannot be interconverted by force. The multiple elastic
        conformations of cardiac PEVK may result from varying degrees of
        proline isomerization. The single-molecule techniques demonstrated here
        may help elucidate the conformation of other proteins that lack a well-
        defined structure."
}

@article { li03,
    author = HLi #" and "# JFernandez,
    title = "Mechanical design of the first proximal Ig domain of human cardiac
        titin revealed by single molecule force spectroscopy",
    year = 2003,
    month = nov,
    day = 14,
    journal = JMB,
    volume = 334,
    number = 1,
    pages = "75--86",
    issn = "0022-2836",
    doi = "10.1016/j.jmb.2003.09.036",
    keywords = "Amino Acid Sequence;Disulfides;Humans;Immunoglobulins;Models,
        Molecular;Molecular Sequence Data;Muscle Proteins;Myocardium;Protein
        Denaturation;Protein Engineering;Protein Kinases;Protein Structure,
        Tertiary;Spectrum Analysis",
    abstract = "The elastic I-band part of muscle protein titin contains two
        tandem immunoglobulin (Ig) domain regions of distinct mechanical
        properties. Until recently, the only known structure was that of the
        I27 module of the distal region, whose mechanical properties have been
        reported in detail. Recently, the structure of the first proximal
        domain, I1, has been resolved at 2.1A. In addition to the
        characteristic beta-sandwich structure of all titin Ig domains, the
        crystal structure of I1 showed an internal disulfide bridge that was
        proposed to modulate its mechanical extensibility in vivo. Here, we use
        single molecule force spectroscopy and protein engineering to examine
        the mechanical architecture of this domain. In contrast to the
        predictions made from the X-ray crystal structure, we find that the
        formation of a disulfide bridge in I1 is a relatively rare event in
        solution, even under oxidative conditions. Furthermore, our studies of
        the mechanical stability of I1 modules engineered with point mutations
        reveal significant differences between the mechanical unfolding of the
        I1 and I27 modules. Our study illustrates the varying mechanical
        architectures of the titin Ig modules."
}

@article { li05,
    author = LeLi #" and "# HHuang #" and "# CBadilla #" and "# JFernandez,
    title = "Mechanical unfolding intermediates observed by single-molecule
        force spectroscopy in a fibronectin type {III} module",
    year = 2005,
    month = jan,
    day = 28,
    journal = JMB,
    volume = 345,
    number = 4,
    pages = "817--826",
    issn = "0022-2836",
    doi = "10.1016/j.jmb.2004.11.021",
    keywords = "Fibronectins;Kinetics;Microscopy, Atomic Force;Models,
        Molecular;Mutagenesis, Site-Directed;Protein Denaturation;Protein
        Folding;Protein Structure, Tertiary;Recombinant Fusion Proteins",
    abstract = "Domain 10 of type III fibronectin (10FNIII) is known to play a
        pivotal role in the mechanical interactions between cell surface
        integrins and the extracellular matrix. Recent molecular dynamics
        simulations have predicted that 10FNIII, when exposed to a stretching
        force, unfolds along two pathways, each with a distinct, mechanically
        stable intermediate. Here, we use single-molecule force spectroscopy
        combined with protein engineering to test these predictions by probing
        the mechanical unfolding pathway of 10FNIII. Stretching single
        polyproteins containing the 10FNIII module resulted in sawtooth
        patterns where 10FNIII was seen unfolding in two consecutive steps. The
        native state unfolded at 100(+/-20) pN, elongating (10)FNIII by
        12(+/-2) nm and reaching a clearly marked intermediate that unfolded at
        50(+/-20) pN. Unfolding of the intermediate completed the elongation of
        the molecule by extending another 19(+/-2) nm. Site-directed
        mutagenesis of residues in the A and B beta-strands (E9P and L19P)
        resulted in sawtooth patterns with all-or-none unfolding events that
        elongated the molecule by 19(+/-2) nm. In contrast, mutating residues
        in the G beta-strand gave results that were dependent on amino acid
        position. The mutation I88P in the middle of the G beta-strand resulted
        in native like unfolding sawtooth patterns showing an intact
        intermediate state. The mutation Y92P, which is near the end of G beta-
        strand, produced sawtooth patterns with all-or-none unfolding events
        that lengthened the molecule by 17(+/-2) nm. These results are
        consistent with the view that 10FNIII can unfold in two different ways.
        Along one pathway, the detachment of the A and B beta-strands from the
        body of the folded module constitute the first unfolding event,
        followed by the unfolding of the remaining beta-sandwich structure.
        Along the second pathway, the detachment of the G beta-strands is
        involved in the first unfolding event. These results are in excellent
        agreement with the sequence of events predicted by molecular dynamics
        simulations of the 10FNIII module."
}

@article { msli06,
    author = MSLi #" and "# CKHu #" and "# DKlimov #" and "# DThirumalai,
    title = "Multiple stepwise refolding of immunoglobulin domain {I27} upon
        force quench depends on initial conditions",
    year = 2006,
    journal = PNAS,
    volume = 103,
    number = 1,
    pages = "93--98",
    doi = "10.1073/pnas.0503758103",
    eprint = "http://www.pnas.org/cgi/reprint/103/1/93.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/103/1/93",
    abstract = "Mechanical folding trajectories for polyproteins starting from
        initially stretched conformations generated by single-molecule atomic
        force microscopy experiments [Fernandez, J. M. & Li, H. (2004) Science
        303, 1674-1678] show that refolding, monitored by the end-to-end
        distance, occurs in distinct multiple stages. To clarify the molecular
        nature of folding starting from stretched conformations, we have probed
        the folding dynamics, upon force quench, for the single I27 domain from
        the muscle protein titin by using a C{alpha}-Go model. Upon temperature
        quench, collapse and folding of I27 are synchronous. In contrast,
        refolding from stretched initial structures not only increases the
        folding and collapse time scales but also decouples the two kinetic
        processes. The increase in the folding times is associated primarily
        with the stretched state to compact random coil transition.
        Surprisingly, force quench does not alter the nature of the refolding
        kinetics, but merely increases the height of the free-energy folding
        barrier. Force quench refolding times scale as f1.gif, where {Delta}xf
        {approx} 0.6 nm is the location of the average transition state along
        the reaction coordinate given by end-to-end distance. We predict that
        {tau}F and the folding mechanism can be dramatically altered by the
        initial and/or final values of force. The implications of our results
        for design and analysis of experiments are discussed."
}

@article { lin91,
    author = JLin,
    title = "Divergence measures based on the {S}hannon entropy",
    year = 1991,
    month = jan,
    journal = IEEE:TIT,
    volume = 37,
    number = 1,
    pages = "145--151",
    issn = "0018-9448",
    doi = "10.1109/18.61115",
    url = "http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?isnumber=2227&arnumbe
        r=61115&count=35&index=9",
    keywords = "divergence;dissimilarity measure;discrimintation
        information;entropy;probability of error bounds",
    abstract = "A novel class of information-theoretic divergence measures
        based on the Shannon entropy is introduced. Unlike the well-known
        Kullback divergences, the new measures do not require the condition of
        absolute continuity to be satisfied by the probability distributions
        involved. More importantly, their close relationship with the
        variational distance and the probability of misclassification error are
        established in terms of bounds. These bounds are crucial in many
        applications of divergence measures. The measures are also well
        characterized by the properties of nonnegativity, finiteness,
        semiboundedness, and boundedness."
}

@article { linke08,
    author = WALinke #" and "# AGrutzner,
    title = "Pulling single molecules of titin by {AFM}--recent advances and
        physiological implications",
    year = 2008,
    month = apr,
    day = 06,
    journal = PA,
    volume = 456,
    number = 1,
    pages = "101--115",
    issn = "0031-6768",
    doi = "10.1007/s00424-007-0389-x",
    abstract = "Perturbation of a protein away from its native state by
        mechanical stress is a physiological process immanent to many cells.
        The mechanical stability and conformational diversity of proteins under
        force therefore are important parameters in nature. Molecular-level
        investigations of ``mechanical proteins'' have enjoyed major
        breakthroughs over the last decade, a development to which atomic force
        microscopy (AFM) force spectroscopy has been instrumental. The giant
        muscle protein titin continues to be a paradigm model in this field. In
        this paper, we review how single-molecule mechanical measurements of
        titin using AFM have served to elucidate key aspects of protein
        unfolding-refolding and mechanisms by which biomolecular elasticity is
        attained. We outline recent work combining protein engineering and AFM
        force spectroscopy to establish the mechanical behavior of titin
        domains using molecular ``fingerprinting.'' Furthermore, we summarize
        AFM force-extension data demonstrating different mechanical stabilities
        of distinct molecular-spring elements in titin, compare AFM force-
        extension to novel force-ramp/force-clamp studies, and elaborate on
        exciting new results showing that AFM force clamp captures the
        unfolding and refolding trajectory of single mechanical proteins. Along
        the way, we discuss the physiological implications of the findings, not
        least with respect to muscle mechanics. These studies help us
        understand how proteins respond to forces in cells and how
        mechanosensing and mechanosignaling events may proceed in vivo."
}

@article { linke98a,
    author = WALinke #" and "# MRStockmeier #" and "# MIvemeyer #" and "#
        HHosser #" and "# PMundel,
    title = "Characterizing titin's {I}-band {Ig} domain region as an entropic
        spring",
    year = 1998,
    month = jun,
    journal = JCS,
    volume = "111 (Pt 11)",
    pages = "1567--1574",
    issn = "0021-9533",
    doi = "",
    eprint = "http://jcs.biologists.org/cgi/reprint/111/11/1567",
    url = "http://jcs.biologists.org/cgi/content/abstract/111/11/1567",
    keywords = "Animals;Elasticity;Immunoglobulins;Male;Muscle Proteins;Muscle,
        Skeletal;Protein Kinases;Rats;Rats, Wistar;Structure-Activity
        Relationship",
    abstract = "The poly-immunoglobulin domain region of titin, located within
        the elastic section of this giant muscle protein, determines the
        extensibility of relaxed myofibrils mainly at shorter physiological
        lengths. To elucidate this region's contribution to titin elasticity,
        we measured the elastic properties of the N-terminal I-band Ig region
        by using immunofluorescence/immunoelectron microscopy and myofibril
        mechanics and tried to simulate the results with a model of entropic
        polymer elasticity. Rat psoas myofibrils were stained with titin-
        specific antibodies flanking the Ig region at the N terminus and C
        terminus, respectively, to record the extension behaviour of that titin
        segment. The segment's end-to-end length increased mainly at small
        stretch, reaching approximately 90\% of the native contour length of
        the Ig region at a sarcomere length of 2.8 microm. At this extension,
        the average force per single titin molecule, deduced from the steady-
        state passive length-tension relation of myofibrils, was approximately
        5 or 2.5 pN, depending on whether we assumed a number of 3 or 6 titins
        per half thick filament. When the force-extension curve constructed for
        the Ig region was simulated by the wormlike chain model, best fits were
        obtained for a persistence length, a measure of the chain's bending
        rigidity, of 21 or 42 nm (for 3 or 6 titins/half thick filament), which
        correctly reproduced the curve for sarcomere lengths up to 3.4 microm.
        Systematic deviations between data and fits above that length indicated
        that forces of >30 pN per titin strand may induce unfolding of Ig
        modules. We conclude that stretches of at least 5-6 Ig domains, perhaps
        coinciding with known super repeat patterns of these titin modules in
        the I-band, may represent the unitary lengths of the wormlike chain.
        The poly-Ig regions might thus act as compliant entropic springs that
        determine the minute levels of passive tension at low extensions of a
        muscle fiber."
}

@article { linke98b,
    author = WALinke #" and "# MIvemeyer #" and "# PMundel #" and "#
        MRStockmeier #" and "# BKolmerer,
    title = "Nature of {PEVK}-titin elasticity in skeletal muscle",
    year = 1998,
    month = jul,
    day = 07,
    journal = PNAS,
    volume = 95,
    number = 14,
    pages = "8052--8057",
    issn = "0027-8424",
    keywords = "Animals;Elasticity;Fluorescent Antibody
        Technique;Male;Microscopy, Immunoelectron;Muscle Proteins;Muscle,
        Skeletal;Protein Kinases;Rats;Rats, Wistar;Stress, Mechanical",
    abstract = "A unique sequence within the giant titin molecule, the PEVK
        domain, has been suggested to greatly contribute to passive force
        development of relaxed skeletal muscle during stretch. To explore the
        nature of PEVK elasticity, we used titin-specific antibodies to stain
        both ends of the PEVK region in rat psoas myofibrils and determined the
        region's force-extension relation by combining immunofluorescence and
        immunoelectron microscopy with isolated myofibril mechanics. We then
        tried to fit the results with recent models of polymer elasticity. The
        PEVK segment elongated substantially at sarcomere lengths above 2.4
        micro(m) and reached its estimated contour length at approximately 3.5
        micro(m). In immunofluorescently labeled sarcomeres stretched and
        released repeatedly above 3 micro(m), reversible PEVK lengthening could
        be readily visualized. At extensions near the contour length, the
        average force per titin molecule was calculated to be approximately 45
        pN. Attempts to fit the force-extension curve of the PEVK segment with
        a standard wormlike chain model of entropic elasticity were successful
        only for low to moderate extensions. In contrast, the experimental data
        also could be correctly fitted at high extensions with a modified
        wormlike chain model that incorporates enthalpic elasticity. Enthalpic
        contributions are likely to arise from electrostatic stiffening, as
        evidenced by the ionic-strength dependency of titin-based myofibril
        stiffness; at high stretch, hydrophobic effects also might become
        relevant. Thus, at physiological muscle lengths, the PEVK region does
        not function as a pure entropic spring. Rather, PEVK elasticity may
        have both entropic and enthalpic origins characterizable by a polymer
        persistence length and a stretch modulus."
}

@article { liu03,
    author = WLiu #" and "# VMontana #" and "# EChapman #" and "# UMohideen #"
        and "# VParpura,
    title = "Botulinum toxin type {B} micromechanosensor",
    year = 2003,
    journal = PNAS,
    volume = 100,
    number = 23,
    pages = "13621--13625",
    doi = "10.1073/pnas.2233819100",
    eprint = "http://www.pnas.org/cgi/reprint/100/23/13621.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/100/23/13621",
    abstract = "Botulinum neurotoxin (BoNT) types A, B, E, and F are toxic to
        humans; early and rapid detection is essential for adequate medical
        treatment. Presently available tests for detection of BoNTs, although
        sensitive, require hours to days. We report a BoNT-B sensor whose
        properties allow detection of BoNT-B within minutes. The technique
        relies on the detection of an agarose bead detachment from the tip of a
        micromachined cantilever resulting from BoNT-B action on its
        substratum, the synaptic protein synaptobrevin 2, attached to the
        beads. The mechanical resonance frequency of the cantilever is
        monitored for the detection. To suspend the bead off the cantilever we
        use synaptobrevin's molecular interaction with another synaptic
        protein, syntaxin 1A, that was deposited onto the cantilever tip.
        Additionally, this bead detachment technique is general and can be used
        in any displacement reaction, such as in receptor-ligand pairs, where
        the introduction of one chemical leads to the displacement of another.
        The technique is of broad interest and will find uses outside
        toxicology."
}

@article { lois08,
    author = GLois #" and "# JBlawzdziewicz #" and "# CSOHern,
    title = "Reliable protein folding on complex energy landscapes: the free
        energy reaction path",
    year = 2008,
    month = sep,
    day = 15,
    journal = BPJ,
    volume = 95,
    number = 6,
    pages = "2692--2701",
    issn = "1542-0086",
    doi = "10.1529/biophysj.108.133132",
    abstract = "A theoretical framework is developed to study the dynamics of
        protein folding. The key insight is that the search for the native
        protein conformation is influenced by the rate r at which external
        parameters, such as temperature, chemical denaturant, or pH, are
        adjusted to induce folding. A theory based on this insight predicts
        that 1), proteins with complex energy landscapes can fold reliably to
        their native state; 2), reliable folding can occur as an equilibrium or
        out-of-equilibrium process; and 3), reliable folding only occurs when
        the rate r is below a limiting value, which can be calculated from
        measurements of the free energy. We test these predictions against
        numerical simulations of model proteins with a single energy scale."
}

@article { lu00a,
    author = HLu #" and "# AKrammer #" and "# BIsralewitz #" and "# VVogel #"
        and "# KSchulten,
    title = "Computer modeling of force-induced titin domain unfolding",
    year = 2000,
    journal = AdvExpMedBiol,
    volume = 481,
    pages = "143--60",
    issn = "0065-2598",
    url = {http://www.ncbi.nlm.nih.gov/pubmed/10987071},
    keywords = "Amino Acid Sequence;Animals;Computer
        Simulation;Elasticity;Fibronectins;Humans;Hydrogen
        Bonding;Immunoglobulins;Models, Molecular;Muscle Proteins;Muscle,
        Skeletal;Myofibrils;Protein Conformation;Protein Denaturation;Protein
        Kinases;Software",
    abstract = "Titin, a 1 micron long protein found in striated muscle
        myofibrils, possesses unique elastic and extensibility properties, and
        is largely composed of a PEVK region and beta-sandwich immunoglobulin
        (Ig) and fibronectin type III (FnIII) domains. The extensibility
        behavior of titin has been shown in atomic force microscope and optical
        tweezer experiments to partially depend on the reversible unfolding of
        individual Ig and FnIII domains. We performed steered molecular
        dynamics simulations to stretch single titin Ig domains in solution
        with pulling speeds of 0.1-1.0 A/ps, and FnIII domains with a pulling
        speed of 0.5 A/ps. Resulting force-extension profiles exhibit a single
        dominant peak for each domain unfolding, consistent with the
        experimentally observed sequential, as opposed to concerted, unfolding
        of Ig and FnIII domains under external stretching forces. The force
        peaks can be attributed to an initial burst of a set of backbone
        hydrogen bonds connected to the domains' terminal beta-strands.
        Constant force stretching simulations, applying 500-1000 pN of force,
        were performed on Ig domains. The resulting domain extensions are
        halted at an initial extension of 10 A until the set of all six
        hydrogen bonds connecting terminal beta-strands break simultaneously.
        This behavior is accounted for by a barrier separating folded and
        unfolded states, the shape of which is consistent with AFM and chemical
        denaturation data.",
    note = "discussion in journal on pages 161--2"
}

@article { lu00b,
    author = HLu #" and "# KSchulten,
    title = "The key event in force-induced unfolding of Titin's immunoglobulin
        domains",
    year = 2000,
    month = jul,
    journal = BPJ,
    volume = 79,
    number = 1,
    pages = "51--65",
    issn = "0006-3495",
    doi = {10.1016/S0006-3495(00)76273-4},
    url = {http://www.cell.com/biophysj/abstract/S0006-3495%2800%2976273-4},
    eprint = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1300915/pdf/10866937.pdf},
    keywords = "Amino Acid Sequence;Computer Simulation;Double Bind
        Interaction;Hydrogen Bonding;Immunoglobulins;Microscopy, Atomic
        Force;Models, Chemical;Models, Molecular;Molecular Sequence Data;Muscle
        Proteins;Protein Folding;Protein Kinases;Protein Structure,
        Tertiary;Stress, Mechanical;Water",
    abstract = "Steered molecular dynamics simulation of force-induced titin
        immunoglobulin domain I27 unfolding led to the discovery of a
        significant potential energy barrier at an extension of approximately
        14 A on the unfolding pathway that protects the domain against
        stretching. Previous simulations showed that this barrier is due to the
        concurrent breaking of six interstrand hydrogen bonds (H-bonds) between
        beta-strands A' and G that is preceded by the breaking of two to three
        hydrogen bonds between strands A and B, the latter leading to an
        unfolding intermediate. The simulation results are supported by
        Angstrom-resolution atomic force microscopy data. Here we perform a
        structural and energetic analysis of the H-bonds breaking. It is
        confirmed that H-bonds between strands A and B break rapidly. However,
        the breaking of the H-bond between strands A' and G needs to be
        assisted by fluctuations of water molecules. In nanosecond simulations,
        water molecules are found to repeatedly interact with the protein
        backbone atoms, weakening individual interstrand H-bonds until all six
        A'-G H-bonds break simultaneously under the influence of external
        stretching forces. Only when those bonds are broken can the generic
        unfolding take place, which involves hydrophobic interactions of the
        protein core and exerts weaker resistance against stretching than the
        key event."
}

@article { lu98,
    author = HLu #" and "# BIsralewitz #" and "# AKrammer #" and "# VVogel #"
        and "# KSchulten,
    title = "Unfolding of titin immunoglobulin domains by steered molecular
        dynamics simulation",
    year = 1998,
    month = aug,
    journal = BPJ,
    volume = 75,
    number = 2,
    pages = "662--671",
    issn = "0006-3495",
    doi = "10.1016/S0006-3495(98)77556-3",
    eprint = "http://download.cell.com/biophysj/pdf/PIIS0006349598775563.pdf",
    url = "http://www.cell.com/biophysj/abstract/S0006-3495(98)77556-3",
    keywords = "Amino Acid Sequence;Animals;Computer Simulation;Glutamic
        Acid;Immunoglobulins;Lysine;Macromolecular Substances;Models,
        Molecular;Molecular Sequence Data;Muscle
        Proteins;Myocardium;Proline;Protein Denaturation;Protein
        Folding;Protein Kinases;Protein Structure, Secondary;Sequence
        Alignment;Sequence Homology, Amino Acid;Valine",
    abstract = "Titin, a 1-microm-long protein found in striated muscle
        myofibrils, possesses unique elastic and extensibility properties in
        its I-band region, which is largely composed of a PEVK region (70\%
        proline, glutamic acid, valine, and lysine residue) and seven-strand
        beta-sandwich immunoglobulin-like (Ig) domains. The behavior of titin
        as a multistage entropic spring has been shown in atomic force
        microscope and optical tweezer experiments to partially depend on the
        reversible unfolding of individual Ig domains. We performed steered
        molecular dynamics simulations to stretch single titin Ig domains in
        solution with pulling speeds of 0.5 and 1.0 A/ps. Resulting force-
        extension profiles exhibit a single dominant peak for each Ig domain
        unfolding, consistent with the experimentally observed sequential, as
        opposed to concerted, unfolding of Ig domains under external stretching
        forces. This force peak can be attributed to an initial burst of
        backbone hydrogen bonds, which takes place between antiparallel beta-
        strands A and B and between parallel beta-strands A' and G. Additional
        features of the simulations, including the position of the force peak
        and relative unfolding resistance of different Ig domains, can be
        related to experimental observations."
}

@article { lu99,
    author = HLu #" and "# KSchulten,
    title = "Steered molecular dynamics simulations of force-induced protein
        domain unfolding",
    year = 1999,
    month = jun,
    day = 01,
    journal = PROT,
    volume = 35,
    number = 4,
    pages = "453--463",
    issn = "0887-3585",
    doi = "10.1002/(SICI)1097-0134(19990601)35:4<453::AID-PROT9>3.0.CO;2-M",
    eprint = "http://www3.interscience.wiley.com/cgi-bin/fulltext/65000328/PDFSTART",
    url = "http://www3.interscience.wiley.com/journal/65000328/abstract",
    keywords = "Computer Simulation;Fibronectins;Hydrogen Bonding;Microscopy,
        Atomic Force;Models, Molecular;Protein Denaturation",
    abstract = "Steered molecular dynamics (SMD), a computer simulation method
        for studying force-induced reactions in biopolymers, has been applied
        to investigate the response of protein domains to stretching apart of
        their terminal ends. The simulations mimic atomic force microscopy and
        optical tweezer experiments, but proceed on much shorter time scales.
        The simulations on different domains for 0.6 nanosecond each reveal two
        types of protein responses: the first type, arising in certain beta-
        sandwich domains, exhibits nanosecond unfolding only after a force
        above 1,500 pN is applied; the second type, arising in a wider class of
        protein domain structures, requires significantly weaker forces for
        nanosecond unfolding. In the first case, strong forces are needed to
        concertedly break a set of interstrand hydrogen bonds which protect the
        domains against unfolding through stretching; in the second case,
        stretching breaks backbone hydrogen bonds one by one, and does not
        require strong forces for this purpose. Stretching of beta-sandwich
        (immunoglobulin) domains has been investigated further revealing a
        specific relationship between response to mechanical strain and the
        architecture of beta-sandwich domains."
}

@article { makarov01,
    author = DEMakarov #" and "# PHansma #" and "# HMetiu,
    title = "Kinetic Monte Carlo simulation of titin unfolding",
    collaboration = "",
    year = 2001,
    journal = JCP,
    volume = 114,
    number = 21,
    pages = "9663--9673",
    publisher = AIP,
    doi = "10.1063/1.1369622",
    eprint = "http://hansmalab.physics.ucsb.edu/pdf/297%20-%20Makarov,%20D.E._J
        .Chem.Phys._2001.pdf",
    url = "http://link.aip.org/link/?JCP/114/9663/1",
    keywords = "proteins; hydrogen bonds; digital simulation; Monte Carlo
        methods; molecular biophysics; intramolecular mechanics;
        macromolecules; atomic force microscopy"
}

@article { marko95,
    author = JFMarko #" and "# EDSiggia,
    title = "Stretching {DNA}",
    affiliation = "",
    year = 1995,
    journal = Macromol,
    volume = 28,
    number = 26,
    pages = "8759--8770",
    issn = "0024-9297",
    eprint = "http://pubs.acs.org/cgi-
        bin/archive.cgi/mamobx/1995/28/i26/pdf/ma00130a008.pdf",
    url =
        "http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/ma00130a008
        ",
    abstract = "",
    note = "Derivation of the Worm-like Chain interpolation function."
}

@article { marszalek02,
    author = PMarszalek #" and "# HLi #" and "# AOberhauser #" and "#
        JFernandez,
    title = "Chair-boat transitions in single polysaccharide molecules observed
        with force-ramp {AFM}",
    year = 2002,
    journal = PNAS,
    volume = 99,
    number = 7,
    pages = "4278--4283",
    doi = "10.1073/pnas.072435699",
    eprint = "http://www.pnas.org/cgi/reprint/99/7/4278.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/99/7/4278",
    abstract = "Under a stretching force, the sugar ring of polysaccharide
        molecules switches from the chair to the boat-like or inverted chair
        conformation. This conformational change can be observed by stretching
        single polysaccharide molecules with an atomic force microscope. In
        those early experiments, the molecules were stretched at a constant
        rate while the resulting force changed over wide ranges. However,
        because the rings undergo force-dependent transitions, an experimental
        arrangement where the force is the free variable introduces an
        undesirable level of complexity in the results. Here we demonstrate the
        use of force-ramp atomic force microscopy to capture the conformational
        changes in single polysaccharide molecules. Force-ramp atomic force
        microscopy readily captures the ring transitions under conditions where
        the entropic elasticity of the molecule is separated from its
        conformational transitions, enabling a quantitative analysis of the
        data with a simple two-state model. This analysis directly provides the
        physico-chemical characteristics of the ring transitions such as the
        width of the energy barrier, the relative energy of the conformers, and
        their enthalpic elasticity. Our experiments enhance the ability of
        single-molecule force spectroscopy to make high-resolution measurements
        of the conformations of single polysaccharide molecules under a
        stretching force, making an important addition to polysaccharide
        spectroscopy."
}

@article { marszalek99,
    author = PMarszalek #" and "# HLu #" and "# HLi #" and "# MCarrionVazquez
        #" and "# AOberhauser #" and "# KSchulten #" and "# JFernandez,
    title = "Mechanical unfolding intermediates in titin modules",
    year = 1999,
    month = nov,
    day = 04,
    journal = NAT,
    volume = 402,
    number = 6757,
    pages = "100--103",
    issn = "0028-0836",
    doi = "10.1038/47083",
    eprint = "http://www.nature.com/nature/journal/v402/n6757/pdf/402100a0.pdf",
    url = "http://www.nature.com/nature/journal/v402/n6757/abs/402100a0.html",
    keywords = "Biomechanics;Computer Simulation;Humans;Hydrogen
        Bonding;Microscopy, Atomic Force;Models, Molecular;Muscle
        Proteins;Myocardium;Protein Folding;Protein Kinases;Recombinant
        Proteins",
    abstract = "The modular protein titin, which is responsible for the passive
        elasticity of muscle, is subjected to stretching forces. Previous work
        on the experimental elongation of single titin molecules has suggested
        that force causes consecutive unfolding of each domain in an all-or-
        none fashion. To avoid problems associated with the heterogeneity of
        the modular, naturally occurring titin, we engineered single proteins
        to have multiple copies of single immunoglobulin domains of human
        cardiac titin. Here we report the elongation of these molecules using
        the atomic force microscope. We find an abrupt extension of each domain
        by approximately 7 A before the first unfolding event. This fast
        initial extension before a full unfolding event produces a reversible
        'unfolding intermediate' Steered molecular dynamics simulations show
        that the rupture of a pair of hydrogen bonds near the amino terminus of
        the protein domain causes an extension of about 6 A, which is in good
        agreement with our observations. Disruption of these hydrogen bonds by
        site-directed mutagenesis eliminates the unfolding intermediate. The
        unfolding intermediate extends titin domains by approximately 15\% of
        their slack length, and is therefore likely to be an important
        previously unrecognized component of titin elasticity."
}

@article { mcpherson01,
    author = JDMcPherson #" and "# MMarra #" and "# LHillier #" and "#
        RHWaterston #" and "# AChinwalla #" and "# JWallis #" and "# MSekhon #"
        and "# KWylie #" and "# ERMardis #" and "# RKWilson #" and "# RFulton
        #" and "# TAKucaba #" and "# CWagner-McPherson #" and "# WBBarbazuk #"
        and "# SGGregory #" and "# SJHumphray #" and "# LFrench #" and "#
        RSEvans #" and "# GBethel #" and "# AWhittaker #" and "# JLHolden #"
        and "# OTMcCann #" and "# ADunham #" and "# CSoderlund #" and "#
        CEScott #" and "# DRBentley #" and "# GSchuler #" and "# HCChen #" and
        "# WJang #" and "# EDGreen #" and "# JRIdol #" and "# VVMaduro #" and
        "# KTMontgomery #" and "# ELee #" and "# AMiller #" and "# SEmerling #"
        and "# Kucherlapati #" and "# RGibbs #" and "# SScherer #" and "#
        JHGorrell #" and "# ESodergren #" and "# KClerc-Blankenburg #" and "#
        PTabor #" and "# SNaylor #" and "# DGarcia #" and "# PJdeJong #" and "#
        JJCatanese #" and "# NNowak #" and "# KOsoegawa #" and "# SQin #" and
        "# LRowen #" and "# AMadan #" and "# MDors #" and "# LHood #" and "#
        BTrask #" and "# CFriedman #" and "# HMassa #" and "# VGCheung #" and
        "# IRKirsch #" and "# TReid #" and "# RYonescu #" and "# JWeissenbach
        #" and "# TBruls #" and "# RHeilig #" and "# EBranscomb #" and "#
        AOlsen #" and "# NDoggett #" and "# JFCheng #" and "# THawkins #" and
        "# RMMyers #" and "# JShang #" and "# LRamirez #" and "# JSchmutz #"
        and "# OVelasquez #" and "# KDixon #" and "# NEStone #" and "# DRCox #"
        and "# DHaussler #" and "# WJKent #" and "# TFurey #" and "# SRogic #"
        and "# SKennedy #" and "# SJones #" and "# ARosenthal #" and "# GWen #"
        and "# MSchilhabel #" and "# GGloeckner #" and "# GNyakatura #" and "#
        RSiebert #" and "# BSchlegelberger #" and "# JKorenberg #" and "#
        XNChen #" and "# AFujiyama #" and "# MHattori #" and "# AToyoda #" and
        "# TYada #" and "# HSPark #" and "# YSakaki #" and "# NShimizu #" and
        "# SAsakawa #" and "# KKawasaki #" and "# TSasaki #" and "# AShintani
        #" and "# AShimizu #" and "# KShibuya #" and "# JKudoh #" and "#
        SMinoshima #" and "# JRamser #" and "# PSeranski #" and "# CHoff #" and
        "# APoustka #" and "# RReinhardt #" and "# HLehrach,
    title = "A physical map of the human genome.",
    year = 2001,
    month = feb,
    day = 15,
    journal = NAT,
    volume = 409,
    number = 6822,
    pages = "934--941",
    issn = "0028-0836",
    doi = "10.1038/35057157",
    eprint = "http://www.nature.com/nature/journal/v409/n6822/pdf/409934a0.pdf",
    url = "http://www.nature.com/nature/journal/v409/n6822/full/409934a0.html",
    keywords = "Chromosomes, Artificial, Bacterial;Cloning, Molecular;Contig
        Mapping;DNA Fingerprinting;Gene Duplication;Genome, Human;Humans;In
        Situ Hybridization, Fluorescence;Repetitive Sequences, Nucleic Acid",
    abstract = "The human genome is by far the largest genome to be sequenced,
        and its size and complexity present many challenges for sequence
        assembly. The International Human Genome Sequencing Consortium
        constructed a map of the whole genome to enable the selection of clones
        for sequencing and for the accurate assembly of the genome sequence.
        Here we report the construction of the whole-genome bacterial
        artificial chromosome (BAC) map and its integration with previous
        landmark maps and information from mapping efforts focused on specific
        chromosomal regions. We also describe the integration of sequence data
        with the map."
}

@article { mello04,
    author = CCMello #" and "# DBarrick,
    title = "An experimentally determined protein folding energy landscape",
    year = 2004,
    month = sep,
    day = 28,
    journal = PNAS,
    volume = 101,
    number = 39,
    pages = "14102--14107",
    issn = "0027-8424",
    doi = "10.1073/pnas.0403386101",
    keywords = "Animals; Ankyrin Repeat; Circular Dichroism; Drosophila
        Proteins; Drosophila melanogaster; Gene Deletion; Models, Chemical;
        Models, Molecular; Protein Denaturation; Protein Folding; Protein
        Structure, Tertiary; Spectrometry, Fluorescence; Thermodynamics; Urea",
    abstract = "Energy landscapes have been used to conceptually describe and
        model protein folding but have been difficult to measure
        experimentally, in large part because of the myriad of partly folded
        protein conformations that cannot be isolated and thermodynamically
        characterized. Here we experimentally determine a detailed energy
        landscape for protein folding. We generated a series of overlapping
        constructs containing subsets of the seven ankyrin repeats of the
        Drosophila Notch receptor, a protein domain whose linear arrangement of
        modular structural units can be fragmented without disrupting
        structure. To a good approximation, stabilities of each construct can
        be described as a sum of energy terms associated with each repeat. The
        magnitude of each energy term indicates that each repeat is
        intrinsically unstable but is strongly stabilized by interactions with
        its nearest neighbors. These linear energy terms define an equilibrium
        free energy landscape, which shows an early free energy barrier and
        suggests preferred low-energy routes for folding."
}

@article { merkel99,
    author = RMerkel #" and "# PNassoy #" and "# ALeung #" and "# KRitchie #"
        and "# EEvans,
    title = "Energy landscapes of receptor-ligand bonds explored with dynamic
        force spectroscopy",
    year = 1999,
    month = jan,
    day = 07,
    journal = NAT,
    volume = 397,
    number = 6714,
    pages = "50--53",
    issn = "0028-0836",
    doi = "10.1038/16219",
    url = "http://www.nature.com/nature/journal/v397/n6714/full/397050a0.html",
    keywords = "Biotin;Microscopy, Atomic Force;Protein Binding;Streptavidin",
    abstract = "Atomic force microscopy (AFM) has been used to measure the
        strength of bonds between biological receptor molecules and their
        ligands. But for weak noncovalent bonds, a dynamic spectrum of bond
        strengths is predicted as the loading rate is altered, with the
        measured strength being governed by the prominent barriers traversed in
        the energy landscape along the force-driven bond-dissociation pathway.
        In other words, the pioneering early AFM measurements represent only a
        single point in a continuous spectrum of bond strengths, because theory
        predicts that these will depend on the rate at which the load is
        applied. Here we report the strength spectra for the bonds between
        streptavidin (or avidin) and biotins-the prototype of receptor-ligand
        interactions used in earlier AFM studies, and which have been modelled
        by molecular dynamics. We have probed bond formation over six orders of
        magnitude in loading rate, and find that the bond survival time
        diminished from about 1 min to 0.001 s with increasing loading rate
        over this range. The bond strength, meanwhile, increased from about 5
        pN to 170 pN. Thus, although they are among the strongest noncovalent
        linkages in biology (affinity of 10(13) to 10(15) M(-1)), these bonds
        in fact appear strong or weak depending on how fast they are loaded. We
        are also able to relate the activation barriers derived from our
        strength spectra to the shape of the energy landscape derived from
        simulations of the biotin-avidin complex."
}

@article { metropolis87,
    author = NMetropolis,
    title = "The Beginning of the {M}onte {C}arlo Method",
    year = 1987,
    journal = LAS,
    volume = 15,
    pages = "125--130",
    publisher = LANL,
    url = "http://library.lanl.gov/cgi-bin/getfile?15-12.pdf"
}

@article { mickler07,
    author = MMickler #" and "# RDima #" and "# HDietz #" and "# CHyeon #" and
        "# DThirumalai #" and "# MRief,
    title = "Revealing the bifurcation in the unfolding pathways of {GFP} by
        using single-molecule experiments and simulations",
    year = 2007,
    journal = PNAS,
    volume = 104,
    number = 51,
    pages = "20268--20273",
    doi = "10.1073/pnas.0705458104",
    eprint = "http://www.pnas.org/cgi/reprint/104/51/20268.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/104/51/20268",
    keywords = "AFM experiments, coarse-grained simulations, cross-link
        mutants, pathway bifurcation, plasticity of energy landscape",
    abstract = "Nanomanipulation of biomolecules by using single-molecule
        methods and computer simulations has made it possible to visualize the
        energy landscape of biomolecules and the structures that are sampled
        during the folding process. We use simulations and single-molecule
        force spectroscopy to map the complex energy landscape of GFP that is
        used as a marker in cell biology and biotechnology. By engineering
        internal disulfide bonds at selected positions in the GFP structure,
        mechanical unfolding routes are precisely controlled, thus allowing us
        to infer features of the energy landscape of the wild-type GFP. To
        elucidate the structures of the unfolding pathways and reveal the
        multiple unfolding routes, the experimental results are complemented
        with simulations of a self-organized polymer (SOP) model of GFP. The
        SOP representation of proteins, which is a coarse-grained description
        of biomolecules, allows us to perform forced-induced simulations at
        loading rates and time scales that closely match those used in atomic
        force microscopy experiments. By using the combined approach, we show
        that forced unfolding of GFP involves a bifurcation in the pathways to
        the stretched state. After detachment of an N-terminal {alpha}-helix,
        unfolding proceeds along two distinct pathways. In the dominant
        pathway, unfolding starts from the detachment of the primary N-terminal
        -strand, while in the minor pathway rupture of the last, C-terminal
        -strand initiates the unfolding process. The combined approach has
        allowed us to map the features of the complex energy landscape of GFP
        including a characterization of the structures, albeit at a coarse-
        grained level, of the three metastable intermediates.",
    note = {Hiccup in unfolding leg corresponds to unfolding
      intermediate (\fref{figure}{2}). The unfolding time scale in GFP
      is about $6\U{ms}$.},
}

@article { nevo03,
    author = RNevo #" and "# CStroh #" and "# FKienberger #" and "# DKaftan #"
        and "# VBrumfeld #" and "# MElbaum #" and "# ZReich #" and "#
        PHinterdorfer,
    title = "A molecular switch between alternative conformational states in
        the complex of {Ran} and importin beta1",
    year = 2003,
    month = jul,
    journal = NSB,
    volume = 10,
    number = 7,
    pages = "553--557",
    issn = "1072-8368",
    doi = "10.1038/nsb940",
    eprint = "http://www.nature.com/nsmb/journal/v10/n7/pdf/nsb940.pdf",
    url = "http://www.nature.com/nsmb/journal/v10/n7/abs/nsb940.html",
    keywords = "Guanosine Diphosphate; Guanosine Triphosphate; Microscopy,
        Atomic Force; Protein Binding; Protein Conformation; beta Karyopherins;
        ran GTP-Binding Protein",
    abstract = "Several million macromolecules are exchanged each minute
        between the nucleus and cytoplasm by receptor-mediated transport. Most
        of this traffic is controlled by the small GTPase Ran, which regulates
        assembly and disassembly of the receptor-cargo complexes in the
        appropriate cellular compartment. Here we applied dynamic force
        spectroscopy to study the interaction of Ran with the nuclear import
        receptor importin beta1 (impbeta) at the single-molecule level. We
        found that the complex alternates between two distinct conformational
        states of different adhesion strength. The application of an external
        mechanical force shifts equilibrium toward one of these states by
        decreasing the height of the interstate activation energy barrier. The
        other state can be stabilized by a functional Ran mutant that increases
        this barrier. These results support a model whereby functional control
        of Ran-impbeta is achieved by a population shift between pre-existing
        alternative conformations."
}

@article { nevo04,
    author = RNevo #" and "# VBrumfeld #" and "# MElbaum #" and "#
        PHinterdorfer #" and "# ZReich,
    title = "Direct discrimination between models of protein activation by
        single-molecule force measurements",
    year = 2004,
    month = oct,
    journal = BPJ,
    volume = 87,
    number = 4,
    pages = "2630--2634",
    issn = "0006-3495",
    doi = "10.1529/biophysj.104.041889",
    eprint = "http://www.biophysj.org/cgi/reprint/87/4/2630.pdf",
    url = "http://www.biophysj.org/cgi/content/abstract/87/4/2630",
    keywords = "Elasticity; Enzyme Activation; Micromanipulation; Microscopy,
        Atomic Force; Models, Chemical; Models, Molecular; Multiprotein
        Complexes; Nuclear Proteins; Physical Stimulation; Protein Binding;
        Stress, Mechanical; Structure-Activity Relationship; beta Karyopherins;
        ran GTP-Binding Protein",
    abstract = "The limitations imposed on the analyses of complex chemical and
        biological systems by ensemble averaging can be overcome by single-
        molecule experiments. Here, we used a single-molecule technique to
        discriminate between two generally accepted mechanisms of a key
        biological process--the activation of proteins by molecular effectors.
        The two mechanisms, namely induced-fit and population-shift, are
        normally difficult to discriminate by ensemble approaches. As a model,
        we focused on the interaction between the nuclear transport effector,
        RanBP1, and two related complexes consisting of the nuclear import
        receptor, importin beta, and the GDP- or GppNHp-bound forms of the
        small GTPase, Ran. We found that recognition by the effector proceeds
        through either an induced-fit or a population-shift mechanism,
        depending on the substrate, and that the two mechanisms can be
        differentiated by the data."
}

@article { nevo05,
    author = RNevo #" and "# VBrumfeld #" and "# RKapon #" and "# PHinterdorfer
        #" and "# ZReich,
    title = "Direct measurement of protein energy landscape roughness",
    year = 2005,
    month = may,
    journal = EMBO,
    volume = 6,
    number = 5,
    pages = "482--486",
    issn = "1469-221X",
    doi = "10.1038/sj.embor.7400403",
    eprint = "http://www.nature.com/embor/journal/v6/n5/pdf/7400403.pdf",
    url = "http://www.nature.com/embor/journal/v6/n5/abs/7400403.html",
    keywords = "Models, Molecular; Protein Binding; Protein Folding; Spectrum
        Analysis; Thermodynamics; beta Karyopherins; ran GTP-Binding Protein",
    abstract = "The energy landscape of proteins is thought to have an
        intricate, corrugated structure. Such roughness should have important
        consequences on the folding and binding kinetics of proteins, as well
        as on their equilibrium fluctuations. So far, no direct measurement of
        protein energy landscape roughness has been made. Here, we combined a
        recent theory with single-molecule dynamic force spectroscopy
        experiments to extract the overall energy scale of roughness epsilon
        for a complex consisting of the small GTPase Ran and the nuclear
        transport receptor importin-beta. The results gave epsilon > 5k(B)T,
        indicating a bumpy energy surface, which is consistent with the ability
        of importin-beta to accommodate multiple conformations and to interact
        with different, structurally distinct ligands.",
    note = "Applies \citet{hyeon03} to ligand-receptor binding.",
    project = "Energy Landscape Roughness"
}

@article { ng07a,
    author = SNg #" and "# KBillings #" and "# TOhashi #" and "# MAllen #" and
        "# RBest #" and "# LRandles #" and "# HErickson #" and "# JClarke,
    title = "Designing an extracellular matrix protein with enhanced mechanical
        stability",
    year = 2007,
    month = jun,
    day = 5,
    journal = PNAS,
    volume = 104,
    number = 23,
    pages = "9633--9637",
    doi = "10.1073/pnas.0609901104",
    eprint = "http://www.pnas.org/cgi/reprint/104/23/9633.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/104/23/9633",
    abstract = "The extracellular matrix proteins tenascin and fibronectin
        experience significant mechanical forces in vivo. Both contain a number
        of tandem repeating homologous fibronectin type III (fnIII) domains,
        and atomic force microscopy experiments have demonstrated that the
        mechanical strength of these domains can vary significantly. Previous
        work has shown that mutations in the core of an fnIII domain from human
        tenascin (TNfn3) reduce the unfolding force of that domain
        significantly: The composition of the core is apparently crucial to the
        mechanical stability of these proteins. Based on these results, we have
        used rational redesign to increase the mechanical stability of the 10th
        fnIII domain of human fibronectin, FNfn10, which is directly involved
        in integrin binding. The hydrophobic core of FNfn10 was replaced with
        that of the homologous, mechanically stronger TNfn3 domain. Despite the
        extensive substitution, FNoTNc retains both the three-dimensional
        structure and the cell adhesion activity of FNfn10. Atomic force
        microscopy experiments reveal that the unfolding forces of the
        engineered protein FNoTNc increase by {approx}20% to match those of
        TNfn3. Thus, we have specifically designed a protein with increased
        mechanical stability. Our results demonstrate that core engineering can
        be used to change the mechanical strength of proteins while retaining
        functional surface interactions."
}

@article { ng07b,
    author = SNg #" and "# JClarke,
    title = "Experiments Suggest that Simulations May Overestimate
        Electrostatic Contributions to the Mechanical Stability of a
        Fibronectin Type {III} Domain",
    journal = JMB,
    volume = 371,
    number = 4,
    pages = "851–854",
    year = 2007,
    month = aug,
    day = 24,
    issn = "0022-2836",
    doi = "10.1016/j.jmb.2007.06.015",
    url = "http://www.sciencedirect.com/science/article/pii/S0022283607007966",
    keywords = "AFM",
    keywords = "MD simulations",
    keywords = "titin",
    keywords = "forced unfolding",
    keywords = "extracellular matrix",
    abstract = "Steered molecular dynamics simulations have previously
        been used to investigate the mechanical properties of the
        extracellular matrix protein fibronectin. The simulations
        suggest that the mechanical stability of the tenth type III
        domain from fibronectin (FNfn10) is largely determined by a
        number of critical hydrogen bonds in the peripheral
        strands. Interestingly, the simulations predict that lowering
        the pH from 7 to ∼4.7 will increase the mechanical stability
        of FNfn10 significantly (by ∼33 %) due to the protonation of a
        few key acidic residues in the A and B strands. To test this
        simulation prediction, we used single-molecule atomic force
        microscopy (AFM) to investigate the mechanical stability of
        FNfn10 at neutral pH and at lower pH where these key residues
        have been shown to be protonated. Our AFM experimental results
        show no difference in the mechanical stability of FNfn10 at
        these different pH values. These results suggest that some
        simulations may overestimate the role played by electrostatic
        interactions in determining the mechanical stability of
        proteins."
}

@article { nome07,
    author = RNome #" and "# JZhao #" and "# WHoff #" and "# NScherer,
    title = "Axis-dependent anisotropy in protein unfolding from integrated
        nonequilibrium single-molecule experiments, analysis, and simulation",
    year = 2007,
    month = dec,
    day = 26,
    journal = PNAS,
    volume = 104,
    number = 52,
    pages = "20799--20804",
    issn = "1091-6490",
    doi = "10.1073/pnas.0701281105",
    eprint = "http://www.pnas.org/cgi/reprint/104/52/20799.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/104/52/20799",
    keywords = "Anisotropy; Bacterial Proteins; Biophysics; Computer
        Simulation; Cysteine; Halorhodospira halophila; Hydrogen Bonding;
        Kinetics; Luminescent Proteins; Microscopy, Atomic Force; Molecular
        Conformation; Protein Binding; Protein Conformation; Protein
        Denaturation; Protein Folding; Protein Structure, Secondary",
    abstract = "We present a comprehensive study that integrates experimental
        and theoretical nonequilibrium techniques to map energy landscapes
        along well defined pull-axis specific coordinates to elucidate
        mechanisms of protein unfolding. Single-molecule force-extension
        experiments along two different axes of photoactive yellow protein
        combined with nonequilibrium statistical mechanical analysis and
        atomistic simulation reveal energetic and mechanistic anisotropy.
        Steered molecular dynamics simulations and free-energy curves
        constructed from the experimental results reveal that unfolding along
        one axis exhibits a transition-state-like feature where six hydrogen
        bonds break simultaneously with weak interactions observed during
        further unfolding. The other axis exhibits a constant (unpeaked) force
        profile indicative of a noncooperative transition, with enthalpic
        (e.g., H-bond) interactions being broken throughout the unfolding
        process. Striking qualitative agreement was found between the force-
        extension curves derived from steered molecular dynamics calculations
        and the equilibrium free-energy curves obtained by JarzynskiHummerSzabo
        analysis of the nonequilibrium work data. The anisotropy persists
        beyond pulling distances of more than twice the initial dimensions of
        the folded protein, indicating a rich energy landscape to the
        mechanically fully unfolded state. Our findings challenge the notion
        that cooperative unfolding is a universal feature in protein
        stability."
}

@book { noy08,
    editor = ANoy,
    title = "Handbook of Molecular Force Spectroscopy",
    year = 2008,
    isbn = "978-0-387-49987-1",
    publisher = SPRINGER,
    note = "The first book about force spectroscopy. Discusses the scaffold
        effect in section 8.4.1."
}

@article { nummela07,
    author = JNummela #" and "# IAndricioaei,
    title = "{Exact Low-Force Kinetics from High-Force Single-Molecule
        Unfolding Events}",
    year = 2007,
    journal = BPJ,
    volume = 93,
    number = 10,
    pages = "3373--3381",
    doi = "10.1529/biophysj.107.111658",
    eprint = "http://www.biophysj.org/cgi/reprint/93/10/3373.pdf",
    url = "http://www.biophysj.org/cgi/content/abstract/93/10/3373",
    abstract = "Mechanical forces play a key role in crucial cellular processes
        involving force-bearing biomolecules, as well as in novel single-
        molecule pulling experiments. We present an exact method that enables
        one to extrapolate, to low (or zero) forces, entire time-correlation
        functions and kinetic rate constants from the conformational dynamics
        either simulated numerically or measured experimentally at a single,
        relatively higher, external force. The method has twofold relevance:
        1), to extrapolate the kinetics at physiological force conditions from
        molecular dynamics trajectories generated at higher forces that
        accelerate conformational transitions; and 2), to extrapolate unfolding
        rates from experimental force-extension single-molecule curves. The
        theoretical formalism, based on stochastic path integral weights of
        Langevin trajectories, is presented for the constant-force, constant
        loading rate, and constant-velocity modes of the pulling experiments.
        For the first relevance, applications are described for simulating the
        conformational isomerization of alanine dipeptide; and for the second
        relevance, the single-molecule pulling of RNA is considered. The
        ability to assign a weight to each trace in the single-molecule data
        also suggests a means to quantitatively compare unfolding pathways
        under different conditions."
}

@article { oberhauser01,
    author = AOberhauser #" and "# PHansma #" and "# MCarrionVazquez #" and "#
        JFernandez,
    title = "Stepwise unfolding of titin under force-clamp atomic force
        microscopy",
    year = 2001,
    journal = PNAS,
    volume = 98,
    number = 2,
    pages = "468--472",
    doi = "10.1073/pnas.021321798",
    eprint = "http://www.pnas.org/cgi/reprint/98/2/468.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/98/2/468",
    abstract = ""
}

@article { ohler07,
    author = BOhler,
    title = "Cantilever spring constant calibration using laser Doppler
        vibrometry",
    year = 2007,
    journal = RSI,
    volume = 78,
    number = 6,
    pages = 063701,
    numpages = 5,
    publisher = AIP,
    eid = 063701,
    doi = "10.1063/1.2743272",
    url = "http://link.aip.org/link/?RSI/78/063701/1",
    keywords = "calibration; vibration measurement; measurement by laser beam;
        Doppler measurement; measurement uncertainty; atomic force microscopy",
    note = "Excellent review of thermal calibration to 2007, but nothing in the
        way of derivations. Compares thermal tune and Sader method with laser
        Doppler vibrometry.",
    project = "Cantilever Calibration"
}

@article { olshansky97,
    author = SJOlshansky #" and "# BACarnes,
    title = "Ever since {G}ompertz",
    year = 1997,
    month = feb,
    journal = Demography,
    volume = 34,
    number = 1,
    pages = "1--15",
    issn = "0070-3370",
    url = "http://www.jstor.org/stable/2061656",
    keywords = "Aging;Biometry;History, 19th Century;History, 20th
        Century;Humans;Life Tables;Mortality;Sexual Maturation",
    abstract = "In 1825 British actuary Benjamin Gompertz made a simple but
        important observation that a law of geometrical progression pervades
        large portions of different tables of mortality for humans. The simple
        formula he derived describing the exponential rise in death rates
        between sexual maturity and old age is commonly, referred to as the
        Gompertz equation-a formula that remains a valuable tool in demography
        and in other scientific disciplines. Gompertz's observation of a
        mathematical regularity in the life table led him to believe in the
        presence of a low of mortality that explained why common age patterns
        of death exist. This law of mortality has captured the attention of
        scientists for the past 170 years because it was the first among what
        are now several reliable empirical tools for describing the dying-out
        process of many living organisms during a significant portion of their
        life spans. In this paper we review the literature on Gompertz's law of
        mortality and discuss the importance of his observations and insights
        in light of research on aging that has taken place since then.",
    note = "Hardly any actual math, but the references might be interesting.
        I'll look into them if I have the time. Available through several
        repositories."
}

@article { onuchic96,
    author = JNOnuchic #" and "# NDSocci #" and "# ZLuthey-Schulten #" and "#
        PGWolynes,
    title = "Protein folding funnels: the nature of the transition state
        ensemble",
    year = 1996,
    journal = FoldDes,
    volume = 1,
    number = 6,
    pages = "441--450",
    issn = "1359-0278",
    keywords = "Animals; Cytochrome c Group; Humans; Infant; Protein Folding",
    abstract = "BACKGROUND: Energy landscape theory predicts that the folding
        funnel for a small fast-folding alpha-helical protein will have a
        transition state half-way to the native state. Estimates of the
        position of the transition state along an appropriate reaction
        coordinate can be obtained from linear free energy relationships
        observed for folding and unfolding rate constants as a function of
        denaturant concentration. The experimental results of Huang and Oas for
        lambda repressor, Fersht and collaborators for C12, and Gray and
        collaborators for cytochrome c indicate a free energy barrier midway
        between the folded and unfolded regions. This barrier arises from an
        entropic bottleneck for the folding process. RESULTS: In keeping with
        the experimental results, lattice simulations based on the folding
        funnel description show that the transition state is not just a single
        conformation, but rather an ensemble of a relatively large number of
        configurations that can be described by specific values of one or a few
        order parameters (e.g. the fraction of native contacts). Analysis of
        this transition state or bottleneck region from our lattice simulations
        and from atomistic models for small alpha-helical proteins by Boczko
        and Brooks indicates a broad distribution for native contact
        participation in the transition state ensemble centered around 50\%.
        Importantly, however, the lattice-simulated transition state ensemble
        does include some particularly hot contacts, as seen in the
        experiments, which have been termed by others a folding nucleus.
        CONCLUSIONS: Linear free energy relations provide a crude spectroscopy
        of the transition state, allowing us to infer the values of a reaction
        coordinate based on the fraction of native contacts. This bottleneck
        may be thought of as a collection of delocalized nuclei where different
        native contacts will have different degrees of participation. The
        agreement between the experimental results and the theoretical
        predictions provides strong support for the landscape analysis."
}

@article { optiz03,
    author = COpitz #" and "# MKulke #" and "# MLeake #" and "# CNeagoe #" and
        "# HHinssen #" and "# RHajjar #" and "# WALinke,
    title = "Damped elastic recoil of the titin spring in myofibrils of human
        myocardium",
    year = 2003,
    journal = PNAS,
    volume = 100,
    number = 22,
    pages = "12688--12693",
    doi = "10.1073/pnas.2133733100",
    eprint = "http://www.pnas.org/cgi/reprint/100/22/12688.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/100/22/12688",
    abstract = "The giant protein titin functions as a molecular spring in
        muscle and is responsible for most of the passive tension of
        myocardium. Because the titin spring is extended during diastolic
        stretch, it will recoil elastically during systole and potentially may
        influence the overall shortening behavior of cardiac muscle. Here,
        titin elastic recoil was quantified in single human heart myofibrils by
        using a high-speed charge-coupled device-line camera and a
        nanonewtonrange force sensor. Application of a slack-test protocol
        revealed that the passive shortening velocity (Vp) of nonactivated
        cardiomyofibrils depends on: (i) initial sarcomere length, (ii)
        release-step amplitude, and (iii) temperature. Selective digestion of
        titin, with low doses of trypsin, decelerated myofibrillar passive
        recoil and eventually stopped it. Selective extraction of actin
        filaments with a Ca2+-independent gelsolin fragment greatly reduced the
        dependency of Vp on release-step size and temperature. These results
        are explained by the presence of viscous forces opposing myofibrillar
        passive recoil that are caused mainly by weak actin-titin interactions.
        Thus, Vp is determined by two distinct factors: titin elastic recoil
        and internal viscous drag forces. The recoil could be modeled as that
        of a damped entropic spring consisting of independent worm-like chains.
        The functional importance of myofibrillar elastic recoil was addressed
        by comparing instantaneous Vp to unloaded shortening velocity, which
        was measured in demembranated, fully Ca2+-activated, human cardiac
        fibers. Titin-driven passive recoil was much faster than active
        unloaded shortening velocity in early phases of isotonic contraction.
        Damped myofibrillar elastic recoil could help accelerate active
        contraction speed of human myocardium during early systolic
        shortening."
}

@article { oroudjev02,
    author = EOroudjev #" and "# JSoares #" and "# SArcidiacono #" and "#
        JThompson #" and "# SFossey #" and "# HHansma,
    title = "Segmented nanofibers of spider dragline silk: Atomic force
        microscopy and single-molecule force spectroscopy",
    year = 2002,
    journal = PNAS,
    volume = 99,
    number = 90002,
    pages = "6460--6465",
    doi = "10.1073/pnas.082526499",
    eprint = "http://www.pnas.org/cgi/reprint/99/suppl_2/6460.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/99/suppl_2/6460",
    abstract = "Despite its remarkable materials properties, the structure of
        spider dragline silk has remained unsolved. Results from two probe
        microscopy techniques provide new insights into the structure of spider
        dragline silk. A soluble synthetic protein from dragline silk
        spontaneously forms nanofibers, as observed by atomic force microscopy.
        These nanofibers have a segmented substructure. The segment length and
        amino acid sequence are consistent with a slab-like shape for
        individual silk protein molecules. The height and width of nanofiber
        segments suggest a stacking pattern of slab-like molecules in each
        nanofiber segment. This stacking pattern produces nano-crystals in an
        amorphous matrix, as observed previously by NMR and x-ray diffraction
        of spider dragline silk. The possible importance of nanofiber formation
        to native silk production is discussed. Force spectra for single
        molecules of the silk protein demonstrate that this protein unfolds
        through a number of rupture events, indicating a modular substructure
        within single silk protein molecules. A minimal unfolding module size
        is estimated to be around 14 nm, which corresponds to the extended
        length of a single repeated module, 38 amino acids long. The structure
        of this spider silk protein is distinctly different from the structures
        of other proteins that have been analyzed by single-molecule force
        spectroscopy, and the force spectra show correspondingly novel
        features."
}

@article { paci00,
    author = EPaci #" and "# MKarplus,
    title = "Unfolding proteins by external forces and temperature: The
        importance of topology and energetics",
    year = 2000,
    journal = PNAS,
    volume = 97,
    number = 12,
    pages = "6521--6526",
    doi = "10.1073/pnas.100124597",
    eprint = "http://www.pnas.org/cgi/reprint/97/12/6521.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/97/12/6521"
}

@article { paci99,
    author = EPaci #" and "# MKarplus,
    title = "Forced unfolding of fibronectin type 3 modules: an analysis by
        biased molecular dynamics simulations",
    year = 1999,
    month = may,
    day = 07,
    journal = JMB,
    volume = 288,
    number = 3,
    pages = "441--459",
    issn = "0022-2836",
    doi = "10.1006/jmbi.1999.2670",
    keywords = "Dimerization;Fibronectins;Humans;Hydrogen Bonding;Microscopy,
        Atomic Force;Protein Denaturation;Protein Folding",
    abstract = "Titin, an important constituent of vertebrate muscles, is a
        protein of the order of a micrometer in length in the folded state.
        Atomic force microscopy and laser tweezer experiments have been used to
        stretch titin molecules to more than ten times their folded lengths. To
        explain the observed relation between force and extension, it has been
        suggested that the immunoglobulin and fibronectin domains unfold one at
        a time in an all-or-none fashion. We use molecular dynamics simulations
        to study the forced unfolding of two different fibronectin type 3
        domains (the ninth, 9Fn3, and the tenth, 10Fn3, from human fibronectin)
        and of their heterodimer of known structure. An external biasing
        potential on the N to C distance is employed and the protein is treated
        in the polar hydrogen representation with an implicit solvation model.
        The latter provides an adiabatic solvent response, which is important
        for the nanosecond unfolding simulation method used here. A series of
        simulations is performed for each system to obtain meaningful results.
        The two different fibronectin domains are shown to unfold in the same
        way along two possible pathways. These involve the partial separation
        of the ``beta-sandwich'', an essential structural element, and the
        unfolding of the individual sheets in a stepwise fashion. The biasing
        potential results are confirmed by constant force unfolding
        simulations. For the two connected domains, there is complete unfolding
        of one domain (9Fn3) before major unfolding of the second domain
        (10Fn3). Comparison of different models for the potential energy
        function demonstrates that the dominant cohesive element in both
        proteins is due to the attractive van der Waals interactions;
        electrostatic interactions play a structural role but appear to make
        only a small contribution to the stabilization of the domains, in
        agreement with other studies of beta-sheet stability. The unfolding
        forces found in the simulations are of the order of those observed
        experimentally, even though the speed of the former is more than six
        orders of magnitude greater than that used in the latter."
}

@article { peng08,
    author = QPeng #" and "# HLi,
    title = "Atomic force microscopy reveals parallel mechanical unfolding
        pathways of T4 lysozyme: Evidence for a kinetic partitioning mechanism",
    year = 2008,
    journal = PNAS,
    volume = 105,
    number = 6,
    pages = "1885--1890",
    doi = "10.1073/pnas.0706775105",
    eprint = "http://www.pnas.org/cgi/reprint/105/6/1885.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/105/6/1885",
    abstract = "Kinetic partitioning is predicted to be a general mechanism for
        proteins to fold into their well defined native three-dimensional
        structure from unfolded states following multiple folding pathways.
        However, experimental evidence supporting this mechanism is still
        limited. By using single-molecule atomic force microscopy, here we
        report experimental evidence supporting the kinetic partitioning
        mechanism for mechanical unfolding of T4 lysozyme, a small protein
        composed of two subdomains. We observed that on stretching from its N
        and C termini, T4 lysozyme unfolds by multiple distinct unfolding
        pathways: the majority of T4 lysozymes unfold in an all-or-none fashion
        by overcoming a dominant unfolding kinetic barrier; and a small
        fraction of T4 lysozymes unfold in three-state fashion involving
        unfolding intermediate states. The three-state unfolding pathways do
        not follow well defined routes, instead they display variability and
        diversity in individual unfolding pathways. The unfolding intermediate
        states are local energy minima along the mechanical unfolding pathways
        and are likely to result from the residual structures present in the
        two subdomains after crossing the main unfolding barrier. These results
        provide direct evidence for the kinetic partitioning of the mechanical
        unfolding pathways of T4 lysozyme, and the complex unfolding behaviors
        reflect the stochastic nature of kinetic barrier rupture in mechanical
        unfolding processes. Our results demonstrate that single-molecule
        atomic force microscopy is an ideal tool to investigate the
        folding/unfolding dynamics of complex multimodule proteins that are
        otherwise difficult to study using traditional methods."
}

@book { press92,
    author = WPress #" and "# STeukolsky #" and "# WVetterling #" and "#
        BFlannery,
    title = "Numerical Recipies in {C}: The Art of Scientific Computing",
    year = 1992,
    edition = 2,
    publisher = CUP,
    address = "New York",
    eprint = "http://www.nrbook.com/a/bookcpdf.php",
    note = "See Sections 12.0, 12.1, 12.3, and 13.4 for a good introduction to
        Fourier transforms and power spectrum estimation.",
    project = "Cantilever Calibration"
}

@article { puchner08,
    author = EPuchner #" and "# GFranzen #" and "# MGautel #" and "# HEGaub,
    title = "Comparing proteins by their unfolding pattern.",
    year = 2008,
    month = jul,
    journal = BPJ,
    volume = 95,
    number = 1,
    pages = "426--434",
    issn = "1542-0086",
    doi = "10.1529/biophysj.108.129999",
    eprint = "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2426622/pdf/426.pdf",
    url = "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2426622/",
    keywords = "Algorithms;Computer Simulation;Microscopy, Atomic Force;Models,
        Chemical;Models, Molecular;Protein Denaturation;Protein
        Folding;Proteins",
    abstract = "Single molecule force spectroscopy has evolved into an
        important and extremely powerful technique for investigating the
        folding potentials of biomolecules. Mechanical tension is applied to
        individual molecules, and the subsequent, often stepwise unfolding is
        recorded in force extension traces. However, because the energy
        barriers of the folding potentials are often close to the thermal
        energy, both the extensions and the forces at which these barriers are
        overcome are subject to marked fluctuations. Therefore, force extension
        traces are an inadequate representation despite widespread use
        particularly when large populations of proteins need to be compared and
        analyzed. We show in this article that contour length, which is
        independent of fluctuations and alterable experimental parameters, is a
        more appropriate variable than extension. By transforming force
        extension traces into contour length space, histograms are obtained
        that directly represent the energy barriers. In contrast to force
        extension traces, such barrier position histograms can be averaged to
        investigate details of the unfolding potential. The cross-superposition
        of barrier position histograms allows us to detect and visualize the
        order of unfolding events. We show with this approach that in contrast
        to the sequential unfolding of bacteriorhodopsin, two main steps in the
        unfolding of the enzyme titin kinase are independent of each other. The
        potential of this new method for accurate and automated analysis of
        force spectroscopy data and for novel automated screening techniques is
        shown with bacteriorhodopsin and with protein constructs containing GFP
        and titin kinase.",
  note = {Contour length space and barrier position fingerprinting.
    There are errors in \fref{equation}{3}, propagated from
    \citet{livadaru03}.  I contacted Elias Puchner and pointed out the
    typos, and he revised his FRC fit parameters from $\gamma=22\dg$
    and $b=0.4\U{nm}$ to $\gamma=41\dg$ and $b=0.11\U{nm}$.  The
    combined effect on \fref{figure}{3} of fixing the equation typos
    and adjusting the fit parameters was small, so their conclusions
    are still sound.},
}

@article { raible04,
    author = MRaible #" and "# MEvstigneev #" and "# PReimann #" and "#
        FWBartels #" and "# RRos,
    title = "Theoretical analysis of dynamic force spectroscopy experiments on
        ligand-receptor complexes",
    year = 2004,
    month = aug,
    day = 26,
    journal = JBT,
    volume = 112,
    number = "1-2",
    pages = "13--23",
    issn = "0168-1656",
    doi = "10.1016/j.jbiotec.2004.04.017",
    keywords = "Binding Sites;Computer Simulation;DNA;DNA-Binding
        Proteins;Elasticity;Ligands;Macromolecular
        Substances;Micromanipulation;Microscopy, Atomic Force;Models,
        Chemical;Molecular Biology;Nucleic Acid Conformation;Physical
        Stimulation;Protein Binding;Protein Conformation;Stress, Mechanical",
    abstract = "The forced rupture of single chemical bonds in biomolecular
        compounds (e.g. ligand-receptor systems) as observed in dynamic force
        spectroscopy experiments is addressed. Under the assumption that the
        probability of bond rupture depends only on the instantaneously acting
        force, a data collapse onto a single master curve is predicted. For
        rupture data obtained experimentally by dynamic AFM force spectroscopy
        of a ligand-receptor bond between a DNA and a regulatory protein we do
        not find such a collapse. We conclude that the above mentioned,
        generally accepted assumption is not satisfied and we discuss possible
        explanations."
}

@article { raible06,
    author = MRaible #" and "# MEvstigneev #" and "# FWBartels #" and "# REckel
        #" and "# MNguyen-Duong #" and "# RMerkel #" and "# RRos #" and "#
        DAnselmetti #" and "# PReimann,
    title = "Theoretical analysis of single-molecule force spectroscopy
        experiments: heterogeneity of chemical bonds",
    year = 2006,
    month = jun,
    day = 01,
    journal = BPJ,
    volume = 90,
    number = 11,
    pages = "3851--3864",
    issn = "0006-3495",
    doi = "10.1529/biophysj.105.077099",
    eprint = "http://www.biophysj.org/cgi/reprint/90/11/3851.pdf",
    url = "http://www.biophysj.org/cgi/content/abstract/90/11/3851",
    keywords = "Biomechanics;Microscopy, Atomic Force;Models,
        Molecular;Statistical Distributions;Thermodynamics",
    abstract = "We show that the standard theoretical framework in single-
        molecule force spectroscopy has to be extended to consistently describe
        the experimental findings. The basic amendment is to take into account
        heterogeneity of the chemical bonds via random variations of the force-
        dependent dissociation rates. This results in a very good agreement
        between theory and rupture data from several different experiments."
}

@article{ bartels03,
  author = FWBartels #" and "# BBaumgarth #" and "# DAnselmetti
    #" and "# RRos #" and "# ABecker,
  title = "Specific binding of the regulatory protein Exp{G} to
    promoter regions of the galactoglucan biosynthesis gene cluster of
    Sinorhizobium meliloti--a combined molecular biology and force
    spectroscopy investigation.",
  journal = JStructBiol,
  year = 2003,
  month = aug,
  address = "Experimentelle Biophysik, Fakult{\"a}t f{\"u}r Physik,
    Universit{\"a}t Bielefeld, 33615 Bielefeld, Germany.",
  volume = 143,
  number = 2,
  pages = "145--152",
  keywords = "Base Sequence",
  keywords = "Binding Sites",
  keywords = "Conserved Sequence",
  keywords = "Fungal Proteins",
  keywords = "Galactans",
  keywords = "Glucans",
  keywords = "Kinetics",
  keywords = "Microscopy, Atomic Force",
  keywords = "Multigene Family",
  keywords = "Polysaccharides, Bacterial",
  keywords = "Promoter Regions, Genetic",
  keywords = "Protein Binding",
  keywords = "Sinorhizobium meliloti",
  keywords = "Trans-Activators",
  abstract = "Specific protein-DNA interaction is fundamental for all
    aspects of gene transcription. We focus on a regulatory
    DNA-binding protein in the Gram-negative soil bacterium
    Sinorhizobium meliloti 2011, which is capable of fixing molecular
    nitrogen in a symbiotic interaction with alfalfa plants. The ExpG
    protein plays a central role in regulation of the biosynthesis of
    the exopolysaccharide galactoglucan, which promotes the
    establishment of symbiosis. ExpG is a transcriptional activator of
    exp gene expression. We investigated the molecular mechanism of
    binding of ExpG to three associated target sequences in the exp
    gene cluster with standard biochemical methods and single molecule
    force spectroscopy based on the atomic force microscope
    (AFM). Binding of ExpG to expA1, expG-expD1, and expE1 promoter
    fragments in a sequence specific manner was demonstrated, and a 28
    bp conserved region was found.  AFM force spectroscopy experiments
    confirmed the specific binding of ExpG to the promoter regions,
    with unbinding forces ranging from 50 to 165 pN in a logarithmic
    dependence from the loading rates of 70-79000 pN/s. Two different
    regimes of loading rate-dependent behaviour were
    identified. Thermal off-rates in the range of k(off)=(1.2+/-1.0) x
    10(-3)s(-1) were derived from the lower loading rate regime for
    all promoter regions. In the upper loading rate regime, however,
    these fragments exhibited distinct differences which are
    attributed to the molecular binding mechanism.",
  ISSN = "1047-8477",
  URL = "http://www.ncbi.nlm.nih.gov/pubmed/12972351",
  language = "eng",
}

@article { rief02,
    author = MRief #" and "# HGrubmuller,
    title = "Force spectroscopy of single biomolecules",
    year = 2002,
    month = mar,
    day = 12,
    journal = CPC,
    volume = 3,
    number = 3,
    pages = "255--261",
    issn = "1439-4235",
    doi = "10.1002/1439-7641(20020315)3:3<255::AID-CPHC255>3.0.CO;2-M",
    url = "http://www3.interscience.wiley.com/journal/91016383/abstract",
    keywords = "Ligands;Microscopy, Atomic Force;Polysaccharides;Protein
        Denaturation;Proteins",
    abstract = "Many processes in the body are effected and regulated by highly
        specialized protein molecules: These molecules certainly deserve the
        name ``biochemical nanomachines''. Recent progress in single-molecule
        experiments and corresponding simulations with supercomputers enable us
        to watch these ``nanomachines'' at work, revealing a host of astounding
        mechanisms. Examples are the fine-tuned movements of the binding pocket
        of a receptor protein locking into its ligand molecule and the forced
        unfolding of titin, which acts as a molecular shock absorber to protect
        muscle cells. At present, we are not capable of designing such high
        precision machines, but we are beginning to understand their working
        principles and to simulate and predict their function.",
    note = "Nice, general review of force spectroscopy to 2002, but not much
        detail."
}

@book { rief65,
    author = FRief,
    title = "Fundamentals of Statistical and Thermal Physics",
    year = 1965,
    publisher = McGraw-Hill,
    address = "New York",
    note = "Thermal noise for simple harmonic oscillators, in Chapter
      15, Sections 6 and 10.",
    project = "Cantilever Calibration"
}

@article { rief97a,
    author = MRief #" and "# MGautel #" and "# FOesterhelt #" and "# JFernandez
        #" and "# HEGaub,
    title = "Reversible Unfolding of Individual Titin Immunoglobulin Domains by
        {AFM}",
    year = 1997,
    journal = SCI,
    volume = 276,
    number = 5315,
    pages = "1109--1112",
    doi = "10.1126/science.276.5315.1109",
    eprint = "http://www.sciencemag.org/cgi/reprint/276/5315/1109.pdf",
    url = "http://www.sciencemag.org/cgi/content/abstract/276/5315/1109",
    note = "Seminal paper for force spectroscopy on Titin. Cited by
        \citet{dietz04} (ref 9) as an example of how unfolding large proteins
        is easily interpreted (vs.\ confusing unfolding in bulk), but Titin is
        a rather simple example of that, because of its globular-chain
        structure.",
    project = "Energy Landscape Roughness"
}

@article { rief97b,
    author = MRief #" and "# FOesterhelt #" and "# BHeymann #" and "# HEGaub,
    title = "Single Molecule Force Spectroscopy on Polysaccharides by Atomic
        Force Microscopy",
    year = 1997,
    month = feb,
    day = 28,
    journal = SCI,
    volume = 275,
    number = 5304,
    pages = "1295--1297",
    issn = "1095-9203",
    doi = "10.1126/science.275.5304.1295",
    eprint = "http://www.sciencemag.org/cgi/reprint/275/5304/1295.pdf",
    url = "http://www.sciencemag.org/cgi/content/abstract/275/5304/1295",
    abstract = "Recent developments in piconewton instrumentation allow the
        manipulation of single molecules and measurements of intermolecular as
        well as intramolecular forces. Dextran filaments linked to a gold
        surface were probed with the atomic force microscope tip by vertical
        stretching. At low forces the deformation of dextran was found to be
        dominated by entropic forces and can be described by the Langevin
        function with a 6 angstrom Kuhn length. At elevated forces the strand
        elongation was governed by a twist of bond angles. At higher forces the
        dextran filaments underwent a distinct conformational change. The
        polymer stiffened and the segment elasticity was dominated by the
        bending of bond angles. The conformational change was found to be
        reversible and was corroborated by molecular dynamics calculations."
}

@article { rief98,
    author = MRief #" and "# JFernandez #" and "# HEGaub,
    title = "Elastically Coupled Two-Level Systems as a Model for Biopolymer
        Extensibility",
    year = 1998,
    month = nov,
    journal = PRL,
    volume = 81,
    number = 21,
    pages = "4764--4767",
    numpages = 3,
    publisher = APS,
    doi = "10.1103/PhysRevLett.81.4764",
    eprint = "http://prola.aps.org/pdf/PRL/v81/i21/p4764_1",
    url = "http://prola.aps.org/abstract/PRL/v81/i21/p4764_1",
    note = "Original details on mechanical unfolding analysis via Monte Carlo
        simulation."
}

@article { rief99,
    author = MRief #" and "# HClausen-Schaumann #" and "# HEGaub,
    title = "Sequence-dependent mechanics of single {DNA} molecules",
    year = 1999,
    month = apr,
    journal = NSB,
    volume = 6,
    number = 4,
    pages = "346--349",
    issn = "1072-8368",
    doi = "10.1038/7582",
    eprint = "http://www.nature.com/nsmb/journal/v6/n4/pdf/nsb0499_346.pdf",
    url = "http://www.nature.com/nsmb/journal/v6/n4/abs/nsb0499_346.html",
    keywords = "Bacteriophage lambda;Base Pairing;DNA;DNA, Single-Stranded;DNA,
        Viral;Gold;Mechanics;Microscopy, Atomic Force;Nucleotides;Spectrum
        Analysis;Thermodynamics",
    abstract = "Atomic force microscope-based single-molecule force
        spectroscopy was employed to measure sequence-dependent mechanical
        properties of DNA by stretching individual DNA double strands attached
        between a gold surface and an AFM tip. We discovered that in lambda-
        phage DNA the previously reported B-S transition, where 'S' represents
        an overstretched conformation, at 65 pN is followed by a nonequilibrium
        melting transition at 150 pN. During this transition the DNA is split
        into single strands that fully recombine upon relaxation. The sequence
        dependence was investigated in comparative studies with poly(dG-dC) and
        poly(dA-dT) DNA. Both the B-S and the melting transition occur at
        significantly lower forces in poly(dA-dT) compared to poly(dG-dC). We
        made use of the melting transition to prepare single poly(dG-dC) and
        poly(dA-dT) DNA strands that upon relaxation reannealed into hairpins
        as a result of their self-complementary sequence. The unzipping of
        these hairpins directly revealed the base pair-unbinding forces for G-C
        to be 20 +/- 3 pN and for A-T to be 9 +/- 3 pN."
}

@article{ schmitt00,
  author = LSchmitt #" and "# MLudwig #" and "# HEGaub #" and "# RTampe,
  title = "A metal-chelating microscopy tip as a new toolbox for
    single-molecule experiments by atomic force microscopy.",
  journal = BPJ,
  year = 2000,
  month = jun,
  address = "Institut f{\"u}r Physiologische Chemie,
    Philipps-Universit{\"a}t Marburg, 35033 Marburg,
    Germany. schmittl@mailer.uni-marburg.de",
  volume = 78,
  number = 6,
  pages = "3275--3285",
  keywords = "Chelating Agents",
  keywords = "Edetic Acid",
  keywords = "Histidine",
  keywords = "Metals",
  keywords = "Microscopy, Atomic Force",
  keywords = "Nitrilotriacetic Acid",
  keywords = "Peptides",
  keywords = "Recombinant Fusion Proteins",
  abstract = "In recent years, the atomic force microscope (AFM) has
    contributed much to our understanding of the molecular forces
    involved in various high-affinity receptor-ligand
    systems. However, a universal anchor system for such measurements
    is still required. This would open up new possibilities for the
    study of biological recognition processes and for the
    establishment of high-throughput screening applications. One such
    candidate is the N-nitrilo-triacetic acid (NTA)/His-tag system,
    which is widely used in molecular biology to isolate and purify
    histidine-tagged fusion proteins. Here the histidine tag acts as a
    high-affinity recognition site for the NTA chelator. Accordingly,
    we have investigated the possibility of using this approach in
    single-molecule force measurements. Using a histidine-peptide as a
    model system, we have determined the binding force for various
    metal ions. At a loading rate of 0.5 microm/s, the determined
    forces varied from 22 +/- 4 to 58 +/- 5 pN. Most importantly, no
    interaction was detected for Ca(2+) and Mg(2+) up to
    concentrations of 10 mM.  Furthermore, EDTA and a metal ion
    reloading step demonstrated the reversibility of the
    approach. Here the molecular interactions were turned off (EDTA)
    and on (metal reloading) in a switch-like fashion. Our results
    show that the NTA/His-tag system will expand the ``molecular
    toolboxes'' with which receptor-ligand systems can be investigated
    at the single-molecule level.",
  ISSN = "0006-3495",
  doi = "10.1016/S0006-3495(00)76863-9",
  URL = "http://www.ncbi.nlm.nih.gov/pubmed/10828003",
  language = "eng",
}

@article { roters96,
    author = ARoters #" and "# DJohannsmann,
    title = "Distance-dependent noise measurements in scanning force
        microscopy",
    year = 1996,
    journal = JP:CM,
    volume = 8,
    number = 41,
    pages = "7561-7577",
    doi = "10.1088/0953-8984",
    eprint = "http://www.iop.org/EJ/article/0953-8984/8/41/006/c64103.pdf",
    url = "http://stacks.iop.org/0953-8984/8/7561",
    abstract = "The changes in the thermal noise spectrum of a scanning-force-
        microscope cantilever upon approach of the tip to the sample were used
        to investigate the interactions between the cantilever and the sample.
        The investigation of thermal noise is the natural choice for dynamic
        measurements with little disturbance of the sample. In particular, the
        small amplitudes involved ensure linear dynamic response. It is
        possible to discriminate between viscous coupling, elastic coupling and
        changes in the effective mass. The technique is versatile in terms of
        substrates and environments. Hydrodynamic long-range interactions
        depending on the sample, the geometry and the ambient medium are
        observed. The dependence of hydrodynamic interaction on various
        parameters such as the viscosity and the density of the medium is
        described. For sufficiently soft surfaces, the method is sensitive to
        viscoelastic properties of the surface. For example, the viscous
        coupling to the surface is strongly increased when the surface is
        covered with a swollen `polymer brush'.",
    note = "They actually write down a Lagrangian formula and give a decent
        derivation of PSD, but don't show or work out the integrals.",
    project = "Cantilever Calibration"
}

@article { ryckaert77,
    author = JPRyckaert #" and "# GCiccotti #" and "# HJCBerendsen,
    title = "Numerical integration of the cartesian equations of motion of a
        system with constraints: molecular dynamics of n-alkanes",
    year = 1977,
    journal = JCompP,
    volume = 23,
    number = 3,
    pages = "327--341",
    issn = "0021-9991",
    doi = "10.1016/0021-9991(77)90098-5",
    url = "http://dx.doi.org/10.1016/0021-9991(77)90098-5",
    abstract = "A numerical algorithm integrating the 3N Cartesian equations of
        motion of a system of N points subject to holonomic constraints is
        formulated. The relations of constraint remain perfectly fulfilled at
        each step of the trajectory despite the approximate character of
        numerical integration. The method is applied to a molecular dynamics
        simulation of a liquid of 64 n-butane molecules and compared to a
        simulation using generalized coordinates. The method should be useful
        for molecular dynamics calculations on large molecules with internal
        degrees of freedom.",
    note = "Entry-level explaination of MD with rigid constraints. Explicit
        Verlet integrator example."
}

@article { sarkar04,
    author = ASarkar #" and "# RRobertson #" and "# JFernandez,
    title = "Simultaneous atomic force microscope and fluorescence measurements
        of protein unfolding using a calibrated evanescent wave",
    year = 2004,
    journal = PNAS,
    volume = 101,
    number = 35,
    pages = "12882--12886",
    doi = "10.1073/pnas.0403534101",
    eprint = "http://www.pnas.org/cgi/reprint/101/35/12882.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/101/35/12882",
    abstract = "Fluorescence techniques for monitoring single-molecule dynamics
        in the vertical dimension currently do not exist. Here we use an atomic
        force microscope to calibrate the distance-dependent intensity decay of
        an evanescent wave. The measured evanescent wave transfer function was
        then used to convert the vertical motions of a fluorescent particle
        into displacement ($SD =< 1$ nm). We demonstrate the use of the
        calibrated evanescent wave to resolve the 20.1 {+/-} 0.5-nm step
        increases in the length of the small protein ubiquitin during forced
        unfolding. The experiments that we report here make an important
        contribution to fluorescence microscopy by demonstrating the
        unambiguous optical tracking of a single molecule with a resolution
        comparable to that of an atomic force microscope."
}

@article { sato05,
    author = TSato #" and "# MEsaki #" and "# JFernandez #" and "# TEndo,
    title = "{Comparison of the protein-unfolding pathways between
        mitochondrial protein import and atomic-force microscopy measurements}",
    year = 2005,
    journal = PNAS,
    volume = 102,
    number = 50,
    pages = "17999--18004",
    doi = "10.1073/pnas.0504495102",
    eprint = "http://www.pnas.org/cgi/reprint/102/50/17999.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/102/50/17999",
    abstract = "Many newly synthesized proteins have to become unfolded during
        translocation across biological membranes. We have analyzed the effects
        of various stabilization/destabilization mutations in the Ig-like
        module of the muscle protein titin upon its import from the N terminus
        or C terminus into mitochondria. The effects of mutations on the import
        of the titin module from the C terminus correlate well with those on
        forced mechanical unfolding in atomic-force microscopy (AFM)
        measurements. On the other hand, as long as turnover of the
        mitochondrial Hsp70 system is not rate-limiting for the import, import
        of the titin module from the N terminus is sensitive to mutations in
        the N-terminal region but not the ones in the C-terminal region that
        affect resistance to global unfolding in AFM experiments. We propose
        that the mitochondrial-import system can catalyze precursor-unfolding
        by reducing the stability of unfolding intermediates."
}

@article { schlierf04,
    author = MSchlierf #" and "# HLi #" and "# JFernandez,
    title = "The unfolding kinetics of ubiquitin captured with single-molecule
        force-clamp techniques",
    year = 2004,
    month = may,
    day = 11,
    journal = PNAS,
    volume = 101,
    number = 19,
    pages = "7299--7304",
    issn = "0027-8424",
    doi = "10.1073/pnas.0400033101",
    eprint = "http://www.pnas.org/cgi/reprint/101/19/7299.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/101/19/7299",
    keywords = "Kinetics;Microscopy, Atomic Force;Probability;Ubiquitin",
    abstract = "We use single-molecule force spectroscopy to study the kinetics
        of unfolding of the small protein ubiquitin. Upon a step increase in
        the stretching force, a ubiquitin polyprotein extends in discrete steps
        of 20.3 +/- 0.9 nm marking each unfolding event. An average of the time
        course of these unfolding events was well described by a single
        exponential, which is a necessary condition for a memoryless Markovian
        process. Similar ensemble averages done at different forces showed that
        the unfolding rate was exponentially dependent on the stretching force.
        Stretching a ubiquitin polyprotein with a force that increased at a
        constant rate (force-ramp) directly measured the distribution of
        unfolding forces. This distribution was accurately reproduced by the
        simple kinetics of an all-or-none unfolding process. Our force-clamp
        experiments directly demonstrate that an ensemble average of ubiquitin
        unfolding events is well described by a two-state Markovian process
        that obeys the Arrhenius equation. However, at the single-molecule
        level, deviant behavior that is not well represented in the ensemble
        average is readily observed. Our experiments make an important addition
        to protein spectroscopy by demonstrating an unambiguous method of
        analysis of the kinetics of protein unfolding by a stretching force."
}

@article { schlierf06,
    author = MSchlierf #" and "# MRief,
    title = "Single-molecule unfolding force distributions reveal a funnel-
        shaped energy landscape",
    year = 2006,
    month = feb,
    day = 15,
    journal = BPJ,
    volume = 90,
    number = 4,
    pages = "L33--L35",
    issn = "0006-3495",
    doi = "10.1529/biophysj.105.077982",
    url = "http://www.biophysj.org/cgi/content/abstract/90/4/L33",
    keywords = "Models, Molecular; Protein Folding; Proteins; Thermodynamics",
    abstract = "The protein folding process is described as diffusion on a
        high-dimensional energy landscape. Experimental data showing details of
        the underlying energy surface are essential to understanding folding.
        So far in single-molecule mechanical unfolding experiments a simplified
        model assuming a force-independent transition state has been used to
        extract such information. Here we show that this so-called Bell model,
        although fitting well to force velocity data, fails to reproduce full
        unfolding force distributions. We show that by applying Kramers'
        diffusion model, we were able to reconstruct a detailed funnel-like
        curvature of the underlying energy landscape and establish full
        agreement with the data. We demonstrate that obtaining spatially
        resolved details of the unfolding energy landscape from mechanical
        single-molecule protein unfolding experiments requires models that go
        beyond the Bell model.",
  note = {The inspiration behind my sawtooth simulation.  Bell model
    fit to $f_{unfold}(v)$, but Kramers model fit to unfolding
    distribution for a given $v$.  \fref{equation}{3} in the
    supplement is \xref{evans99}{equation}{2}, but it is just
    $[\text{dying percent}] \cdot [\text{surviving population}]
       = [\text{deaths}]$.
    $\nu \equiv k$ is the force/time-dependent off rate.  The Kramers'
    rate equation (on page L34, the second equation in the paper) is
    \xref{hanggi90}{equation}{4.56b} (page 275) and
    \xref{socci96}{equation}{2} but \citet{schlierf06} gets the minus
    sign wrong in the exponent.  $U_F(x=0)\gg 0$ and
    $U_F(x_\text{max})\ll 0$ (\cf~\xref{schlierf06}{figure}{1}).
    Schlierf's integral (as written) contains
    $\exp{-U_F(x_\text{max})}\cdot\exp{U_F(0)}$, which is huge, when
    it should contain $\exp{U_F(x_\text{max})}\cdot\exp{-U_F(0)}$,
    which is tiny.  For more details and a picture of the peak that
    forms the bulk of the integrand, see
    \cref{eq:kramers,fig:kramers:integrand}.  I pointed out this
    problem to Michael Schlierf, but he was unconvinced.},
}

@article { schwaiger04,
    author = ISchwaiger #" and "# AKardinal #" and "# MSchleicher #" and "#
        AANoegel #" and "# MRief,
    title = "A mechanical unfolding intermediate in an actin-crosslinking
        protein",
    year = 2004,
    month = jan,
    day = 29,
    journal = NSMB,
    volume = 11,
    number = 1,
    pages = "81--85",
    issn = "1545-9993",
    doi = "10.1038/nsmb705",
    eprint = "http://www.nature.com/nsmb/journal/v11/n1/pdf/nsmb705.pdf",
    url = "http://www.nature.com/nsmb/journal/v11/n1/full/nsmb705.html",
    keywords = "Actins; Animals; Contractile Proteins; Cross-Linking Reagents;
        Dictyostelium; Dimerization; Microfilament Proteins; Microscopy, Atomic
        Force; Mutagenesis, Site-Directed; Protein Denaturation; Protein
        Folding; Protein Structure, Tertiary; Protozoan Proteins",
    abstract = "Many F-actin crosslinking proteins consist of two actin-binding
        domains separated by a rod domain that can vary considerably in length
        and structure. In this study, we used single-molecule force
        spectroscopy to investigate the mechanics of the immunoglobulin (Ig)
        rod domains of filamin from Dictyostelium discoideum (ddFLN). We find
        that one of the six Ig domains unfolds at lower forces than do those of
        all other domains and exhibits a stable unfolding intermediate on its
        mechanical unfolding pathway. Amino acid inserts into various loops of
        this domain lead to contour length changes in the single-molecule
        unfolding pattern. These changes allowed us to map the stable core of
        approximately 60 amino acids that constitutes the unfolding
        intermediate. Fast refolding in combination with low unfolding forces
        suggest a potential in vivo role for this domain as a mechanically
        extensible element within the ddFLN rod.",
    note = "ddFLN unfolding with WLC params for sacrificial domains. Gives
        persistence length $p = 0.5\mbox{ nm}$ in ``high force regime'', $p =
        0.9\mbox{ nm}$ in ``low force regime'', with a transition at $F =
        30\mbox{ pN}$.",
    project = "sawtooth simulation"
}

@article { schwaiger05,
    author = ISchwaiger #" and "# MSchleicher #" and "# AANoegel #" and "#
        MRief,
    title = "The folding pathway of a fast-folding immunoglobulin domain
        revealed by single-molecule mechanical experiments",
    year = 2005,
    month = jan,
    journal = EMBORep,
    volume = 6,
    number = 1,
    pages = "46--51",
    issn = "1469-221X",
    doi = "10.1038/sj.embor.7400317",
    eprint = "http://www.nature.com/embor/journal/v6/n1/pdf/7400317.pdf",
    url = "http://www.nature.com/embor/journal/v6/n1/index.html",
    keywords = "Animals; Contractile Proteins; Dictyostelium; Immunoglobulins;
        Kinetics; Microfilament Proteins; Models, Molecular; Protein Folding;
        Protein Structure, Tertiary",
    abstract = "The F-actin crosslinker filamin from Dictyostelium discoideum
        (ddFLN) has a rod domain consisting of six structurally similar
        immunoglobulin domains. When subjected to a stretching force, domain 4
        unfolds at a lower force than all the other domains in the chain.
        Moreover, this domain shows a stable intermediate along its mechanical
        unfolding pathway. We have developed a mechanical single-molecule
        analogue to a double-jump stopped-flow experiment to investigate the
        folding kinetics and pathway of this domain. We show that an obligatory
        and productive intermediate also occurs on the folding pathway of the
        domain. Identical mechanical properties suggest that the unfolding and
        refolding intermediates are closely related. The folding process can be
        divided into two consecutive steps: in the first step 60 C-terminal
        amino acids form an intermediate at the rate of 55 s(-1); and in the
        second step the remaining 40 amino acids are packed on this core at the
        rate of 179 s(-1). This division increases the overall folding rate of
        this domain by a factor of ten compared with all other homologous
        domains of ddFLN that lack the folding intermediate."
}

@article { sharma07,
    author = DSharma #" and "# OPerisic #" and "# QPeng #" and "# YCao #" and
        "# CLam #" and "# HLu #" and "# HLi,
    title = "Single-molecule force spectroscopy reveals a mechanically stable
        protein fold and the rational tuning of its mechanical stability",
    year = 2007,
    journal = PNAS,
    volume = 104,
    number = 22,
    pages = "9278--9283",
    doi = "10.1073/pnas.0700351104",
    eprint = "http://www.pnas.org/cgi/reprint/104/22/9278.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/104/22/9278",
    abstract = "It is recognized that shear topology of two directly connected
        force-bearing terminal [beta]-strands is a common feature among the
        vast majority of mechanically stable proteins known so far. However,
        these proteins belong to only two distinct protein folds, Ig-like
        [beta] sandwich fold and [beta]-grasp fold, significantly hindering
        delineating molecular determinants of mechanical stability and rational
        tuning of mechanical properties. Here we combine single-molecule atomic
        force microscopy and steered molecular dynamics simulation to reveal
        that the de novo designed Top7 fold [Kuhlman B, Dantas G, Ireton GC,
        Varani G, Stoddard BL, Baker D (2003) Science 302:13641368] represents
        a mechanically stable protein fold that is distinct from Ig-like [beta]
        sandwich and [beta]-grasp folds. Although the two force-bearing [beta]
        strands of Top7 are not directly connected, Top7 displays significant
        mechanical stability, demonstrating that the direct connectivity of
        force-bearing [beta] strands in shear topology is not mandatory for
        mechanical stability. This finding broadens our understanding of the
        design of mechanically stable proteins and expands the protein fold
        space where mechanically stable proteins can be screened. Moreover, our
        results revealed a substructure-sliding mechanism for the mechanical
        unfolding of Top7 and the existence of two possible unfolding pathways
        with different height of energy barrier. Such insights enabled us to
        rationally tune the mechanical stability of Top7 by redesigning its
        mechanical unfolding pathway. Our study demonstrates that computational
        biology methods (including de novo design) offer great potential for
        designing proteins of defined topology to achieve significant and
        tunable mechanical properties in a rational and systematic fashion."
}

@article { sheng05,
    author = YJSheng #" and "# SJiang #" and "# HKTsao,
    title = "Forced Kramers escape in single-molecule pulling experiments",
    collaboration = "",
    year = 2005,
    journal = JCP,
    volume = 123,
    number = 9,
    pages = 091102,
    numpages = 4,
    publisher = AIP,
    eid = 091102,
    doi = "10.1063/1.2046632",
    url = "http://link.aip.org/link/?JCP/123/091102/1",
    keywords = "molecular biophysics; bonds (chemical); proteins",
    note = "Gives appropriate Einstein-S... relation for diffusion to damping",
    project = "sawtooth simulation"
}

@article { shillcock98,
    author = JShillcock #" and "# USeifert,
    title = "Escape from a metastable well under a time-ramped force",
    year = 1998,
    month = "Jun",
    journal = PR:E,
    volume = 57,
    number = 6,
    pages = "7301--7304",
    numpages = 3,
    publisher = APS,
    doi = "10.1103/PhysRevE.57.7301",
    eprint = "http://prola.aps.org/pdf/PRE/v57/i6/p7301_1",
    url = "http://link.aps.org/abstract/PRE/v57/p7301",
    project = "sawtooth simulation"
}

@article { sims09,
    author = GESims #" and "# SRJun #" and "# GAWu #" and "# SHKim,
    title = "Alignment-free genome comparison with feature frequency profiles
        ({FFP}) and optimal resolutions",
    year = 2009,
    month = feb,
    day = 24,
    journal = PNAS,
    volume = 106,
    number = 8,
    pages = "2677--2682",
    issn = "1091-6490",
    doi = "10.1073/pnas.0813249106",
    eprint = "http://www.pnas.org/cgi/reprint/106/31/12826",
    url = "http://www.pnas.org/content/106/8/2677",
    keywords = "Genome;Introns;Phylogeny",
    abstract = "For comparison of whole-genome (genic + nongenic) sequences,
        multiple sequence alignment of a few selected genes is not appropriate.
        One approach is to use an alignment-free method in which feature (or
        l-mer) frequency profiles (FFP) of whole genomes are used for
        comparison-a variation of a text or book comparison method, using word
        frequency profiles. In this approach it is critical to identify the
        optimal resolution range of l-mers for the given set of genomes
        compared. The optimum FFP method is applicable for comparing whole
        genomes or large genomic regions even when there are no common genes
        with high homology. We outline the method in 3 stages: (i) We first
        show how the optimal resolution range can be determined with English
        books which have been transformed into long character strings by
        removing all punctuation and spaces. (ii) Next, we test the robustness
        of the optimized FFP method at the nucleotide level, using a mutation
        model with a wide range of base substitutions and rearrangements. (iii)
        Finally, to illustrate the utility of the method, phylogenies are
        reconstructed from concatenated mammalian intronic genomes; the FFP
        derived intronic genome topologies for each l within the optimal range
        are all very similar. The topology agrees with the established
        mammalian phylogeny revealing that intron regions contain a similar
        level of phylogenic signal as do coding regions."
}

@article { smith92,
    author = SBSmith #" and "# LFinzi #" and "# CBustamante,
    title = "Direct mechanical measurements of the elasticity of single {DNA}
        molecules by using magnetic beads",
    year = 1992,
    month = nov,
    day = 13,
    journal = SCI,
    volume = 258,
    number = 5085,
    pages = "1122--1126",
    issn = "0036-8075",
    doi = "10.1126/science.1439819",
    eprint = "http://www.sciencemag.org/cgi/reprint/258/5085/1122.pdf",
    url = "http://www.sciencemag.org/cgi/content/abstract/258/5085/1122",
    keywords = "Chemistry,
        Physical;Cisplatin;DNA;Elasticity;Ethidium;Glass;Indoles;Intercalating
        Agents;Magnetics;Mathematics;Microspheres",
    abstract = "Single DNA molecules were chemically attached by one end to a
        glass surface and by their other end to a magnetic bead. Equilibrium
        positions of the beads were observed in an optical microscope while the
        beads were acted on by known magnetic and hydrodynamic forces.
        Extension versus force curves were obtained for individual DNA
        molecules at three different salt concentrations with forces between
        10(-14) and 10(-11) newtons. Deviations from the force curves predicted
        by the freely jointed chain model suggest that DNA has significant
        local curvature in solution. Ethidium bromide and
        4',6-diamidino-2-phenylindole had little effect on the elastic response
        of the molecules, but their extent of intercalation was directly
        measured. Conversely, the effect of bend-inducing cis-
        diamminedichloroplatinum (II) was large and supports the hypothesis of
        natural curvature in DNA."
}

@article { smith96,
    author = SBSmith #" and "# YCui #" and "# CBustamante,
    title = "Overstretching {B}-{DNA}: the elastic response of individual
        double-stranded and single-stranded {DNA} molecules",
    year = 1996,
    month = feb,
    day = 09,
    journal = SCI,
    volume = 271,
    number = 5250,
    pages = "795--799",
    issn = "0036-8075",
    keywords = "Base Composition;Chemistry, Physical;DNA;DNA, Single-
        Stranded;Elasticity;Nucleic Acid Conformation;Osmolar
        Concentration;Thermodynamics",
    abstract = "Single molecules of double-stranded DNA (dsDNA) were stretched
        with force-measuring laser tweezers. Under a longitudinal stress of
        approximately 65 piconewtons (pN), dsDNA molecules in aqueous buffer
        undergo a highly cooperative transition into a stable form with 5.8
        angstroms rise per base pair, that is, 70\% longer than B form dsDNA.
        When the stress was relaxed below 65 pN, the molecules rapidly and
        reversibly contracted to their normal contour lengths. This transition
        was affected by changes in the ionic strength of the medium and the
        water activity or by cross-linking of the two strands of dsDNA.
        Individual molecules of single-stranded DNA were also stretched giving
        a persistence length of 7.5 angstroms and a stretch modulus of 800 pN.
        The overstretched form may play a significant role in the energetics of
        DNA recombination."
}

@article { socci96,
    author = NDSocci #" and "# JNOnuchic #" and "# PGWolynes,
    title = "Diffusive dynamics of the reaction coordinate for protein folding
        funnels",
    collaboration = "",
    year = 1996,
    journal = JCP,
    volume = 104,
    number = 15,
    pages = "5860--5868",
    publisher = AIP,
    doi = "10.1063/1.471317",
    eprint = "http://arxiv.org/pdf/cond-mat/9601091",
    url = "http://link.aip.org/link/?JCP/104/5860/1",
    keywords = "PROTEINS; FOLDS; DIFFUSION; MONTE CARLO METHOD; SIMULATION;
        FREE ENERGY",
    abstract = "The quantitative description of model protein folding kinetics
        using a diffusive collective reaction coordinate is examined. Direct
        folding kinetics, diffusional coefficients and free energy profiles are
        determined from Monte Carlo simulations of a 27-mer, 3 letter code
        lattice model, which corresponds roughly to a small helical protein.
        Analytic folding calculations, using simple diffusive rate theory,
        agree extremely well with the full simulation results. Folding in this
        system is best seen as a diffusive, funnel-like process.",
    note = "A nice introduction to some quantitative ramifications of the
        funnel energy landscape. There's also a bit of Kramers' theory and
        graph theory thrown in for good measure."
}

@article { socci99,
    author = NDSocci #" and "# JNOnuchic #" and "# PGWolynes,
    title = "Stretching lattice models of protein folding",
    year = 1999,
    month = mar,
    day = 02,
    journal = PNAS,
    volume = 96,
    number = 5,
    pages = "2031--2035",
    issn = "0027-8424",
    keywords = "Amino Acid Sequence;Drug Stability;Kinetics;Models,
        Theoretical;Molecular Sequence Data;Peptides;Protein
        Denaturation;Protein Folding",
    abstract = "A new class of experiments that probe folding of individual
        protein domains uses mechanical stretching to cause the transition. We
        show how stretching forces can be incorporated in lattice models of
        folding. For fast folding proteins, the analysis suggests a complex
        relation between the force dependence and the reaction coordinate for
        folding."
}

@article { staple08,
    author = DBStaple #" and "# SHPayne #" and "# ALCReddin #" and "# HJKreuzer,
    title = "Model for stretching and unfolding the giant multidomain muscle
        protein using single-molecule force spectroscopy.",
    year = 2008,
    month = dec,
    day = 12,
    journal = PRL,
    volume = 101,
    number = 24,
    pages = 248301,
    issn = "0031-9007",
    doi = "10.1103/PhysRevLett.101.248301",
    url = "http://dx.doi.org/10.1103/PhysRevLett.101.248301",
    keywords = "Kinetics;Microscopy, Atomic Force;Models, Chemical;Muscle
        Proteins;Protein Conformation;Protein Folding;Protein Kinases;Protein
        Structure, Tertiary;Thermodynamics",
    abstract = "Single-molecule manipulation has allowed the forced unfolding
        of multidomain proteins. Here we outline a theory that not only
        explains these experiments but also points out a number of difficulties
        in their interpretation and makes suggestions for further experiments.
        For titin we reproduce force-extension curves, the dependence of break
        force on pulling speed, and break-force distributions and also validate
        two common experimental views: Unfolding titin Ig domains can be
        explained as stepwise increases in contour length, and increasing force
        peaks in native Ig sequences represent a hierarchy of bond strengths.
        Our theory is valid for essentially any molecule that can be unfolded
        in atomic force microscopy; as a further example, we present force-
        extension curves for the unfolding of RNA hairpins."
}

@article { stark01,
    author = RStark #" and "# TDrobek #" and "# WHeckl,
    title = "Thermomechanical noise of a free v-shaped cantilever for atomic-
        force microscopy.",
    year = 2001,
    month = jan,
    journal = UltraMic,
    volume = 86,
    number = "1--2",
    pages = "207--215",
    issn = "0304-3991",
    doi = "http://dx.doi.org/10.1016/S0304-3991(00)00077-2",
    abstract = "We have calculated the thermal noise of a v-shaped AFM
        cantilever (Microlever, Type E, Thermomicroscopes) by means of a finite
        element analysis. The modal shapes of the first 10 eigenmodes are
        displayed as well as the numerical constants, which are needed for the
        calibration using the thermal noise method. In the first eigenmode,
        values for the thermomechanical noise of the z-displacement at 22
        degrees C temperature of square root of u2(1) = A/square root of
        c(cant) and the photodiode signal (normal-force) of S2(1) = A/square
        root of c(cant) were obtained. The results also indicate a systematic
        deviation ofthe spectral density of the thermomechanical noise of
        v-shaped cantilevers as compared to rectangular beam-shaped
        cantilevers.",
    note = "Higher mode adjustments for v-shaped cantilevers from simulation.",
    project = "Cantilever Calibration"
}

@article { strick96,
    author = TRStrick #" and "# JFAllemand #" and "# DBensimon #" and "#
        ABensimon #" and "# VCroquette,
    title = "The elasticity of a single supercoiled {DNA} molecule",
    year = 1996,
    month = mar,
    day = 29,
    journal = SCI,
    volume = 271,
    number = 5257,
    pages = "1835--1837",
    issn = "0036-8075",
    keywords = "Bacteriophage lambda;DNA, Superhelical;DNA,
        Viral;Elasticity;Magnetics;Nucleic Acid Conformation;Temperature",
    abstract = "Single linear DNA molecules were bound at multiple sites at one
        extremity to a treated glass cover slip and at the other to a magnetic
        bead. The DNA was therefore torsionally constrained. A magnetic field
        was used to rotate the beads and thus to coil and pull the DNA. The
        stretching force was determined by analysis of the Brownian
        fluctuations of the bead. Here the elastic behavior of individual
        lambda DNA molecules over- and underwound by up to 500 turns was
        studied. A sharp transition was discovered from a low to a high
        extension state at a force of approximately 0.45 piconewtons for
        underwound molecules and at a force of approximately 3 piconewtons for
        overwound ones. These transitions, probably reflecting the formation of
        alternative structures in stretched coiled DNA molecules, might be
        relevant for DNA transcription and replication."
}

@article { strunz99,
    author = TStrunz #" and "# KOroszlan #" and "# RSchafer #" and "#
        HJGuntherodt,
    title = "Dynamic force spectroscopy of single {DNA} molecules",
    year = 1999,
    journal = PNAS,
    volume = 96,
    number = 20,
    pages = "11277--11282",
    doi = "10.1073/pnas.96.20.11277",
    eprint = "http://www.pnas.org/cgi/reprint/96/20/11277.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/96/20/11277"
}

@article { szabo80,
    author = ASzabo #" and "# KSchulten #" and "# ZSchulten,
    title = "First passage time approach to diffusion controlled reactions",
    collaboration = "",
    year = 1980,
    journal = JCP,
    volume = 72,
    number = 8,
    pages = "4350--4357",
    publisher = AIP,
    doi = "10.1063/1.439715",
    url = "http://link.aip.org/link/?JCP/72/4350/1",
    keywords = "DIFFUSION; CHEMICAL REACTIONS; CHEMICAL REACTION KINETICS;
        PROBABILITY; DIFFERENTIAL EQUATIONS"
}

@article { talaga00,
    author = DTalaga #" and "# WLau #" and "# HRoder #" and "# JTang #" and "#
        YJia #" and "# WDeGrado #" and "# RHochstrasser,
    title = "Dynamics and folding of single two-stranded coiled-coil peptides
        studied by fluorescent energy transfer confocal microscopy",
    year = 2000,
    journal = PNAS,
    volume = 97,
    number = 24,
    pages = "13021--13026",
    doi = "10.1073/pnas.97.24.13021",
    eprint = "http://www.pnas.org/cgi/reprint/97/24/13021.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/97/24/13021"
}

@article { thirumalai05,
    author = DThirumalai #" and "# CHyeon,
    title = "{RNA} and Protein Folding: Common Themes and Variations",
    affiliation = "Biophysics Program, and Department of Chemistry and
        Biochemistry, Institute for Physical Science and Technology, University
        of Maryland, College Park, Maryland 20742",
    year = 2005,
    journal = Biochem,
    volume = 44,
    number = 13,
    pages = "4957--4970",
    issn = "0006-2960",
    url =
        "http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bi047314+",
    abstract = "Visualizing the navigation of an ensemble of unfolded molecules
        through the bumpy energy landscape in search of the native state gives
        a pictorial view of biomolecular folding. This picture, when combined
        with concepts in polymer theory, provides a unified theory of RNA and
        protein folding. Just as for proteins, the major folding free energy
        barrier for RNA scales sublinearly with the number of nucleotides,
        which allows us to extract the elusive prefactor for RNA folding.
        Several folding scenarios can be anticipated by considering variations
        in the energy landscape that depend on sequence, native topology, and
        external conditions. RNA and protein folding mechanism can be described
        by the kinetic partitioning mechanism (KPM) according to which a
        fraction () of molecules reaches the native state directly, whereas the
        remaining fraction gets kinetically trapped in metastable
        conformations. For two-state folders 1. Molecular chaperones are
        recruited to assist protein folding whenever is small. We show that the
        iterative annealing mechanism, introduced to describe chaperonin-
        mediated folding, can be generalized to understand protein-assisted RNA
        folding. The major differences between the folding of proteins and RNA
        arise in the early stages of folding. For RNA, folding can only begin
        after the polyelectrolyte problem is solved, whereas protein collapse
        requires burial of hydrophobic residues. Cross-fertilization of ideas
        between the two fields should lead to an understanding of how RNA and
        proteins solve their folding problems.",
    note = "unfolding-refolding"
}

@book { thornton04,
    author = SThornton #" and "# JMarion,
    title = "Classical Dynamics of Particles and Systems",
    year = 2004,
    edition = 5,
    isbn = "0-534-40896-6",
    publisher = BrooksCole,
    address = "Belmont, CA"
}

@article { tlusty98,
    author = TTlusty #" and "# AMeller #" and "# RBar-Ziv,
    title = "Optical Gradient Forces of Strongly Localized Fields",
    year = 1998,
    month = aug,
    journal = PRL,
    volume = 81,
    number = 8,
    pages = "1738--1741",
    numpages = 3,
    publisher = APS,
    doi = "10.1103/PhysRevLett.81.1738",
    eprint = "http://prola.aps.org/pdf/PRL/v81/i8/p1738_1",
    note = "also at
      \url{http://nanoscience.bu.edu/papers/p1738_1_Meller.pdf}.
      Cited by \citet{grossman05} for derivation of thermal response
      functions.  However, I only see a referenced thermal energy when
      they list the likelyhood of a small partical (radius $<R_c$)
      escaping due to thermal energy, where $R_c$ is roughly $R_c \sim
      (k_B T / \alpha I_0)^{1/3}$, $\alpha$ is a dielectric scaling
      term, and $I_0$ is the maximum beam energy density. I imagine
      Grossman and Stout mixed up this reference.",
    project = "Cantilever Calibration"
}

@article { tshiprut08,
    author = ZTshiprut #" and "# JKlafter #" and "# MUrbakh,
    title = "Single-molecule pulling experiments: when the stiffness of the
        pulling device matters",
    year = 2008,
    month = sep,
    day = 15,
    journal = BPJ,
    volume = 95,
    number = 6,
    pages = "L42--L44",
    issn = "1542-0086",
    doi = "10.1529/biophysj.108.141580",
    eprint = "http://www.biophysj.org/cgi/reprint/95/6/L42.pdf",
    abstract = "Using Langevin modeling, we investigate the role of the
        experimental setup on the unbinding forces measured in single-molecule
        pulling experiments. We demonstrate that the stiffness of the pulling
        device, K(eff), may influence the unbinding forces through its effect
        on the barrier heights for both unbinding and rebinding processes.
        Under realistic conditions the effect of K(eff) on the rebinding
        barrier is shown to play the most important role. This results in a
        significant increase of the mean unbinding force with the stiffness for
        a given loading rate. Thus, in contrast to the phenomenological Bell
        model, we find that the loading rate (the multiplicative value K(eff)V,
        V being the pulling velocity) is not the only control parameter that
        determines the mean unbinding force. If interested in intrinsic
        properties of a molecular system, we recommend probing the system in
        the parameter range corresponding to a weak spring and relatively high
        loading rates where rebinding is negligible.",
    note = "Cites \citet{dudko03} for Kramers' description of irreversible
        rupture, and claims it is required to explain the deviations in
        $\avg{F}$ at the same loading rate. Proposes Moese equation as an
        example potential. Cites \citet{walton08} for experimental evidence of
        $\avg{F}$ increasing with linker stiffness."
}

@article { uniprot10,
    author = UniProtConsort,
    key = "uniprot10",
    title = "The Universal Protein Resource (UniProt) in 2010.",
    year = 2010,
    month = jan,
    day = 20,
    journal = NAR,
    volume = 38,
    number = "Database issue",
    pages = "D142--D148",
    issn = "1362-4962",
    doi = "10.1093/nar/gkp846",
    url = "http://nar.oxfordjournals.org/cgi/content/abstract/38/suppl_1/D142",
    keywords = "Algorithms;Animals;Computational Biology;Databases, Nucleic
        Acid;Databases, Protein;Europe;Genome, Fungal;Genome,
        Viral;Humans;Information Storage and Retrieval;Internet;Protein
        Isoforms;Proteome;Proteomics;Software",
    abstract = "The primary mission of UniProt is to support biological
        research by maintaining a stable, comprehensive, fully classified,
        richly and accurately annotated protein sequence knowledgebase, with
        extensive cross-references and querying interfaces freely accessible to
        the scientific community. UniProt is produced by the UniProt Consortium
        which consists of groups from the European Bioinformatics Institute
        (EBI), the Swiss Institute of Bioinformatics (SIB) and the Protein
        Information Resource (PIR). UniProt is comprised of four major
        components, each optimized for different uses: the UniProt Archive, the
        UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt
        Metagenomic and Environmental Sequence Database. UniProt is updated and
        distributed every 3 weeks and can be accessed online for searches or
        download at http://www.uniprot.org."
}

@misc { uniprot:STRAV,
    key = "uniprot:STRAV",
    url = "http://www.uniprot.org/uniprot/P22629"
}

@book { vanKampen07,
    author = NGvanKampen,
    title = "Stochastic Processes in Physics and Chemistry",
    year = 2007,
    edition = 3,
    publisher = E:NHPL,
    address = "Amsterdam",
    note = "",
    project = "sawtooth simulation"
}

@article { venter01,
    author = JCVenter #" and "# MDAdams #" and "# EWMyers #" and "# PWLi #" and
        "# RJMural #" and "# GGSutton #" and "# HOSmith #" and "# MYandell #"
        and "# CAEvans #" and "# RAHolt #" and "# JDGocayne #" and "#
        PAmanatides #" and "# RMBallew #" and "# DHHuson #" and "# JRWortman #"
        and "# QZhang #" and "# CDKodira #" and "# XHZheng #" and "# LChen #"
        and "# MSkupski #" and "# GSubramanian #" and "# PDThomas #" and "#
        JZhang #" and "# GLGaborMiklos #" and "# CNelson #" and "# SBroder #"
        and "# AGClark #" and "# JNadeau #" and "# VAMcKusick #" and "# NZinder
        #" and "# AJLevine #" and "# RJRoberts #" and "# MSimon #" and "#
        CSlayman #" and "# MHunkapiller #" and "# RBolanos #" and "# ADelcher
        #" and "# IDew #" and "# DFasulo #" and "# MFlanigan #" and "# LFlorea
        #" and "# AHalpern #" and "# SHannenhalli #" and "# SKravitz #" and "#
        SLevy #" and "# CMobarry #" and "# KReinert #" and "# KRemington #" and
        "# JAbu-Threideh #" and "# EBeasley #" and "# KBiddick #" and "#
        VBonazzi #" and "# RBrandon #" and "# MCargill #" and "#
        IChandramouliswaran #" and "# RCharlab #" and "# KChaturvedi #" and "#
        ZDeng #" and "# VDiFrancesco #" and "# PDunn #" and "# KEilbeck #" and
        "# CEvangelista #" and "# AEGabrielian #" and "# WGan #" and "# WGe #"
        and "# FGong #" and "# ZGu #" and "# PGuan #" and "# TJHeiman #" and "#
        MEHiggins #" and "# RRJi #" and "# ZKe #" and "# KAKetchum #" and "#
        ZLai #" and "# YLei #" and "# ZLi #" and "# JLi #" and "# YLiang #" and
        "# XLin #" and "# FLu #" and "# GVMerkulov #" and "# NMilshina #" and
        "# HMMoore #" and "# AKNaik #" and "# VANarayan #" and "# BNeelam #"
        and "# DNusskern #" and "# DBRusch #" and "# SSalzberg #" and "# WShao
        #" and "# BShue #" and "# JSun #" and "# ZWang #" and "# AWang #" and
        "# XWang #" and "# JWang #" and "# MWei #" and "# RWides #" and "#
        CXiao #" and "# CYan #" and "# AYao #" and "# JYe #" and "# MZhan #"
        and "# WZhang #" and "# HZhang #" and "# QZhao #" and "# LZheng #" and
        "# FZhong #" and "# WZhong #" and "# SZhu #" and "# SZhao #" and "#
        DGilbert #" and "# SBaumhueter #" and "# GSpier #" and "# CCarter #"
        and "# ACravchik #" and "# TWoodage #" and "# FAli #" and "# HAn #" and
        "# AAwe #" and "# DBaldwin #" and "# HBaden #" and "# MBarnstead #" and
        "# IBarrow #" and "# KBeeson #" and "# DBusam #" and "# ACarver #" and
        "# ACenter #" and "# MLCheng #" and "# LCurry #" and "# SDanaher #" and
        "# LDavenport #" and "# RDesilets #" and "# SDietz #" and "# KDodson #"
        and "# LDoup #" and "# SFerriera #" and "# NGarg #" and "# AGluecksmann
        #" and "# BHart #" and "# JHaynes #" and "# CHaynes #" and "# CHeiner
        #" and "# SHladun #" and "# DHostin #" and "# JHouck #" and "# THowland
        #" and "# CIbegwam #" and "# JJohnson #" and "# FKalush #" and "#
        LKline #" and "# SKoduru #" and "# ALove #" and "# FMann #" and "# DMay
        #" and "# SMcCawley #" and "# TMcIntosh #" and "# IMcMullen #" and "#
        MMoy #" and "# LMoy #" and "# BMurphy #" and "# KNelson #" and "#
        CPfannkoch #" and "# EPratts #" and "# VPuri #" and "# HQureshi #" and
        "# MReardon #" and "# RRodriguez #" and "# YHRogers #" and "# DRomblad
        #" and "# BRuhfel #" and "# RScott #" and "# CSitter #" and "#
        MSmallwood #" and "# EStewart #" and "# RStrong #" and "# ESuh #" and
        "# RThomas #" and "# NNTint #" and "# STse #" and "# CVech #" and "#
        GWang #" and "# JWetter #" and "# SWilliams #" and "# MWilliams #" and
        "# SWindsor #" and "# EWinn-Deen #" and "# KWolfe #" and "# JZaveri #"
        and "# KZaveri #" and "# JFAbril #" and "# RGuigo #" and "# MJCampbell
        #" and "# KVSjolander #" and "# BKarlak #" and "# AKejariwal #" and "#
        HMi #" and "# BLazareva #" and "# THatton #" and "# ANarechania #" and
        "# KDiemer #" and "# AMuruganujan #" and "# NGuo #" and "# SSato #" and
        "# VBafna #" and "# SIstrail #" and "# RLippert #" and "# RSchwartz #"
        and "# BWalenz #" and "# SYooseph #" and "# DAllen #" and "# ABasu #"
        and "# JBaxendale #" and "# LBlick #" and "# MCaminha #" and "#
        JCarnes-Stine #" and "# PCaulk #" and "# YHChiang #" and "# MCoyne #"
        and "# CDahlke #" and "# AMays #" and "# MDombroski #" and "# MDonnelly
        #" and "# DEly #" and "# SEsparham #" and "# CFosler #" and "# HGire #"
        and "# SGlanowski #" and "# KGlasser #" and "# AGlodek #" and "#
        MGorokhov #" and "# KGraham #" and "# BGropman #" and "# MHarris #" and
        "# JHeil #" and "# SHenderson #" and "# JHoover #" and "# DJennings #"
        and "# CJordan #" and "# JJordan #" and "# JKasha #" and "# LKagan #"
        and "# CKraft #" and "# ALevitsky #" and "# MLewis #" and "# XLiu #"
        and "# JLopez #" and "# DMa #" and "# WMajoros #" and "# JMcDaniel #"
        and "# SMurphy #" and "# MNewman #" and "# TNguyen #" and "# NNguyen #"
        and "# MNodell #" and "# SPan #" and "# JPeck #" and "# MPeterson #"
        and "# WRowe #" and "# RSanders #" and "# JScott #" and "# MSimpson #"
        and "# TSmith #" and "# ASprague #" and "# TStockwell #" and "# RTurner
        #" and "# EVenter #" and "# MWang #" and "# MWen #" and "# DWu #" and
        "# MWu #" and "# AXia #" and "# AZandieh #" and "# XZhu,
    title = "The sequence of the human genome.",
    year = 2001,
    month = "Feb",
    day = 16,
    journal = SCI,
    volume = 291,
    number = 5507,
    pages = "1304--1351",
    issn = "0036-8075",
    doi = "10.1126/science.1058040",
    eprint = "http://www.sciencemag.org/cgi/content/pdf/291/5507/1304",
    url = "http://www.sciencemag.org/cgi/content/short/291/5507/1304",
    keywords = "Algorithms;Animals;Chromosome Banding;Chromosome
        Mapping;Chromosomes, Artificial, Bacterial;Computational
        Biology;Consensus Sequence;CpG Islands;DNA, Intergenic;Databases,
        Factual;Evolution, Molecular;Exons;Female;Gene
        Duplication;Genes;Genetic Variation;Genome, Human;Human Genome
        Project;Humans;Introns;Male;Phenotype;Physical Chromosome
        Mapping;Polymorphism, Single Nucleotide;Proteins;Pseudogenes;Repetitive
        Sequences, Nucleic Acid;Retroelements;Sequence Analysis, DNA;Species
        Specificity",
    abstract = "A 2.91-billion base pair (bp) consensus sequence of the
        euchromatic portion of the human genome was generated by the whole-
        genome shotgun sequencing method. The 14.8-billion bp DNA sequence was
        generated over 9 months from 27,271,853 high-quality sequence reads
        (5.11-fold coverage of the genome) from both ends of plasmid clones
        made from the DNA of five individuals. Two assembly strategies-a whole-
        genome assembly and a regional chromosome assembly-were used, each
        combining sequence data from Celera and the publicly funded genome
        effort. The public data were shredded into 550-bp segments to create a
        2.9-fold coverage of those genome regions that had been sequenced,
        without including biases inherent in the cloning and assembly procedure
        used by the publicly funded group. This brought the effective coverage
        in the assemblies to eightfold, reducing the number and size of gaps in
        the final assembly over what would be obtained with 5.11-fold coverage.
        The two assembly strategies yielded very similar results that largely
        agree with independent mapping data. The assemblies effectively cover
        the euchromatic regions of the human chromosomes. More than 90\% of the
        genome is in scaffold assemblies of 100,000 bp or more, and 25\% of the
        genome is in scaffolds of 10 million bp or larger. Analysis of the
        genome sequence revealed 26,588 protein-encoding transcripts for which
        there was strong corroborating evidence and an additional approximately
        12,000 computationally derived genes with mouse matches or other weak
        supporting evidence. Although gene-dense clusters are obvious, almost
        half the genes are dispersed in low G+C sequence separated by large
        tracts of apparently noncoding sequence. Only 1.1\% of the genome is
        spanned by exons, whereas 24\% is in introns, with 75\% of the genome
        being intergenic DNA. Duplications of segmental blocks, ranging in size
        up to chromosomal lengths, are abundant throughout the genome and
        reveal a complex evolutionary history. Comparative genomic analysis
        indicates vertebrate expansions of genes associated with neuronal
        function, with tissue-specific developmental regulation, and with the
        hemostasis and immune systems. DNA sequence comparisons between the
        consensus sequence and publicly funded genome data provided locations
        of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of
        human haploid genomes differed at a rate of 1 bp per 1250 on average,
        but there was marked heterogeneity in the level of polymorphism across
        the genome. Less than 1\% of all SNPs resulted in variation in
        proteins, but the task of determining which SNPs have functional
        consequences remains an open challenge."
}

@article { verdier70,
    author = PHVerdier,
    title = "Relaxation Behavior of the Freely Jointed Chain",
    collaboration = "",
    year = 1970,
    journal = JCP,
    volume = 52,
    number = 11,
    pages = "5512--5517",
    publisher = AIP,
    doi = "10.1063/1.1672818",
    url = "http://link.aip.org/link/?JCP/52/5512/1"
}

@article { walther07,
    author = KWalther #" and "# FGrater #" and "# LDougan #" and "# CBadilla #"
        and "# BBerne #" and "# JFernandez,
    title = "Signatures of hydrophobic collapse in extended proteins captured
        with force spectroscopy",
    year = 2007,
    journal = PNAS,
    volume = 104,
    number = 19,
    pages = "7916--7921",
    doi = "10.1073/pnas.0702179104",
    eprint = "http://www.pnas.org/cgi/reprint/104/19/7916.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/104/19/7916",
    abstract = "We unfold and extend single proteins at a high force and then
        linearly relax the force to probe their collapse mechanisms. We observe
        a large variability in the extent of their recoil. Although chain
        entropy makes a small contribution, we show that the observed
        variability results from hydrophobic interactions with randomly varying
        magnitude from protein to protein. This collapse mechanism is common to
        highly extended proteins, including nonfolding elastomeric proteins
        like PEVK from titin. Our observations explain the puzzling differences
        between the folding behavior of highly extended proteins, from those
        folding after chemical or thermal denaturation. Probing the collapse of
        highly extended proteins with force spectroscopy allows separation of
        the different driving forces in protein folding."
}

@article { walton08,
    author = EBWalton #" and "# SLee #" and "# KJVanVliet,
    title = "Extending {B}ell's model: How force transducer stiffness alters
        measured unbinding forces and kinetics of molecular complexes",
    year = 2008,
    month = apr,
    day = 01,
    journal = BPJ,
    volume = 94,
    number = 7,
    pages = "2621--2630",
    issn = "1542-0086",
    doi = "10.1529/biophysj.107.114454",
    keywords = "Biotin;Computer
        Simulation;Elasticity;Kinetics;Mechanotransduction, Cellular;Models,
        Chemical;Models, Molecular;Molecular Motor
        Proteins;Motion;Streptavidin;Stress, Mechanical;Transducers",
    abstract = "Forced unbinding of complementary macromolecules such as
        ligand-receptor complexes can reveal energetic and kinetic details
        governing physiological processes ranging from cellular adhesion to
        drug metabolism. Although molecular-level experiments have enabled
        sampling of individual ligand-receptor complex dissociation events,
        disparities in measured unbinding force F(R) among these methods lead
        to marked variation in inferred binding energetics and kinetics at
        equilibrium. These discrepancies are documented for even the ubiquitous
        ligand-receptor pair, biotin-streptavidin. We investigated these
        disparities and examined atomic-level unbinding trajectories via
        steered molecular dynamics simulations, as well as via molecular force
        spectroscopy experiments on biotin-streptavidin. In addition to the
        well-known loading rate dependence of F(R) predicted by Bell's model,
        we find that experimentally accessible parameters such as the effective
        stiffness of the force transducer k can significantly perturb the
        energy landscape and the apparent unbinding force of the complex for
        sufficiently stiff force transducers. Additionally, at least 20\%
        variation in unbinding force can be attributed to minute differences in
        initial atomic positions among energetically and structurally
        comparable complexes. For force transducers typical of molecular force
        spectroscopy experiments and atomistic simulations, this energy barrier
        perturbation results in extrapolated energetic and kinetic parameters
        of the complex that depend strongly on k. We present a model that
        explicitly includes the effect of k on apparent unbinding force of the
        ligand-receptor complex, and demonstrate that this correction enables
        prediction of unbinding distances and dissociation rates that are
        decoupled from the stiffness of actual or simulated molecular linkers.",
    note = "Some detailed estimates at U(x)."
}

@article { walton86,
    author = AJWalton,
    title = "The Abbe theory of imaging: an alternative derivation of the
        resolution limit",
    year = 1986,
    journal = EJP,
    volume = 7,
    number = 1,
    pages = "62--63",
    url = "http://stacks.iop.org/0143-0807/7/62"
}

@article { watanabe05,
    author = HWatanabe #" and "# TInoue,
    title = "Conformational dynamics of Rouse chains during creep/recovery
        processes: a review",
    year = 2005,
    journal = JP:CM,
    volume = 17,
    number = 19,
    pages = "R607--R636",
    doi = "10.1088/0953-8984/17/19/R01",
    eprint = "http://www.iop.org/EJ/article/0953-8984/17/19/R01/cm5_19_R01.pdf",
    url = "http://stacks.iop.org/0953-8984/17/R607",
    abstract = "The Rouse model is a well-established model for non-entangled
        polymer chains and also serves as a fundamental model for entangled
        chains. The dynamic behaviour of this model under strain-controlled
        conditions has been fully analysed in the literature. However, despite
        the importance of the Rouse model, no analysis has been made so far of
        the orientational anisotropy of the Rouse eigenmodes during the stress-
        controlled, creep and recovery processes. For completeness of the
        analysis of the model, the Rouse equation of motion is solved to
        calculate this anisotropy for monodisperse chains and their binary
        blends during the creep/recovery processes. The calculation is simple
        and straightforward, but the result is intriguing in the sense that
        each Rouse eigenmode during these processes has a distribution in the
        retardation times. This behaviour, reflecting the interplay/correlation
        among the Rouse eigenmodes of different orders (and for different
        chains in the blends) under the constant stress condition, is quite
        different from the behaviour under rate-controlled flow (where each
        eigenmode exhibits retardation/relaxation associated with a single
        characteristic time). Furthermore, the calculation indicates that the
        Rouse chains exhibit affine deformation on sudden imposition/removal of
        the stress and the magnitude of this deformation is inversely
        proportional to the number of bond vectors per chain. In relation to
        these results, a difference between the creep and relaxation properties
        is also discussed for chains obeying multiple relaxation mechanisms
        (Rouse and reptation mechanisms).",
    note = "Middly-detailed Rouse model review."
}

@article { wiita06,
    author = AWiita #" and "# SAinavarapu #" and "# HHuang #" and "# JFernandez,
    title = "From the Cover: Force-dependent chemical kinetics of disulfide
        bond reduction observed with single-molecule techniques",
    year = 2006,
    journal = PNAS,
    volume = 103,
    number = 19,
    pages = "7222--7227",
    doi = "10.1073/pnas.0511035103",
    eprint = "http://www.pnas.org/cgi/reprint/103/19/7222.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/103/19/7222",
    abstract = "The mechanism by which mechanical force regulates the kinetics
        of a chemical reaction is unknown. Here, we use single-molecule force-
        clamp spectroscopy and protein engineering to study the effect of force
        on the kinetics of thiol/disulfide exchange. Reduction of disulfide
        bonds through the thiol/disulfide exchange chemical reaction is crucial
        in regulating protein function and is known to occur in mechanically
        stressed proteins. We apply a constant stretching force to single
        engineered disulfide bonds and measure their rate of reduction by DTT.
        Although the reduction rate is linearly dependent on the concentration
        of DTT, it is exponentially dependent on the applied force, increasing
        10-fold over a 300-pN range. This result predicts that the disulfide
        bond lengthens by 0.34 A at the transition state of the thiol/disulfide
        exchange reaction. Our work at the single bond level directly
        demonstrates that thiol/disulfide exchange in proteins is a force-
        dependent chemical reaction. Our findings suggest that mechanical force
        plays a role in disulfide reduction in vivo, a property that has never
        been explored by traditional biochemistry. Furthermore, our work also
        indicates that the kinetics of any chemical reaction that results in
        bond lengthening will be force-dependent."
}

@article { wilcox05,
    author = AWilcox #" and "# JChoy #" and "# CBustamante #" and "#
        AMatouschek,
    title = "Effect of protein structure on mitochondrial import",
    year = 2005,
    journal = PNAS,
    volume = 102,
    number = 43,
    pages = "15435--15440",
    doi = "10.1073/pnas.0507324102",
    eprint = "http://www.pnas.org/cgi/reprint/102/43/15435.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/102/43/15435",
    abstract = "Most proteins that are to be imported into the mitochondrial
        matrix are synthesized as precursors, each composed of an N-terminal
        targeting sequence followed by a mature domain. Precursors are
        recognized through their targeting sequences by receptors at the
        mitochondrial surface and are then threaded through import channels
        into the matrix. Both the targeting sequence and the mature domain
        contribute to the efficiency with which proteins are imported into
        mitochondria. Precursors must be in an unfolded conformation during
        translocation. Mitochondria can unfold some proteins by changing their
        unfolding pathways. The effectiveness of this unfolding mechanism
        depends on the local structure of the mature domain adjacent to the
        targeting sequence. This local structure determines the extent to which
        the unfolding pathway can be changed and, therefore, the unfolding rate
        increased. Atomic force microscopy studies find that the local
        structures of proteins near their N and C termini also influence their
        resistance to mechanical unfolding. Thus, protein unfolding during
        import resembles mechanical unfolding, and the specificity of import is
        determined by the resistance of the mature domain to unfolding as well
        as by the properties of the targeting sequence."
}

@article { wolfsberg01,
    author = TGWolfsberg #" and "# JMcEntyre #" and "# GDSchuler,
    title = "Guide to the draft human genome.",
    year = 2001,
    month = feb,
    day = 15,
    journal = NAT,
    volume = 409,
    number = 6822,
    pages = "824--826",
    issn = "0028-0836",
    doi = "10.1038/35057000",
    eprint = "http://www.nature.com/nature/journal/v409/n6822/pdf/409824a0.pdf",
    url = "http://www.nature.com/nature/journal/v409/n6822/full/409824a0.html",
    keywords = "Amino Acid Sequence;Chromosome Mapping;Computational
        Biology;Genes;Genetic Variation;Genome, Human;Human Genome
        Project;Humans;Internet;Molecular Sequence Data;Sequence Analysis, DNA",
    abstract = "There are a number of ways to investigate the structure,
        function and evolution of the human genome. These include examining the
        morphology of normal and abnormal chromosomes, constructing maps of
        genomic landmarks, following the genetic transmission of phenotypes and
        DNA sequence variations, and characterizing thousands of individual
        genes. To this list we can now add the elucidation of the genomic DNA
        sequence, albeit at 'working draft' accuracy. The current challenge is
        to weave together these disparate types of data to produce the
        information infrastructure needed to support the next generation of
        biomedical research. Here we provide an overview of the different
        sources of information about the human genome and how modern
        information technology, in particular the internet, allows us to link
        them together."
}

@article { wu04,
    author = JWWu #" and "# WLHung #" and "# CHTsai,
    title = "Estimation of parameters of the {G}ompertz distribution using the
        least squares method",
    year = 2004,
    month = oct,
    day = 25,
    journal = AMC,
    volume = 158,
    number = 1,
    pages = "133--147",
    issn = "0096-3003",
    doi = "10.1016/j.amc.2003.08.086",
    url = "http://dx.doi.org/10.1016/j.amc.2003.08.086",
    keywords = "Gompertz distribution; Least squares estimate; Maximum
        likelihood estimate; First failure-censored; Series system",
    abstract = "The Gompertz distribution has been used to describe human
        mortality and establish actuarial tables. Recently, this distribution
        has been again studied by some authors. The maximum likelihood
        estimates for the parameters of the Gompertz distribution has been
        discussed by Garg et al. [J. R. Statist. Soc. C 19 (1970) 152]. The
        purpose of this paper is to propose unweighted and weighted least
        squares estimates for parameters of the Gompertz distribution under the
        complete data and the first failure-censored data (series systems; see
        [J. Statist. Comput. Simulat. 52 (1995) 337]). A simulation study is
        carried out to compare the proposed estimators and the maximum
        likelihood estimators. Results of the simulation studies show that the
        performance of the weighted least squares estimators is acceptable."
}

@article { yang00,
    author = GYang #" and "# CCecconi #" and "# WBaase #" and "# IVetter #" and
        "# WBreyer #" and "# JHaack #" and "# BMatthews #" and "# FDahlquist #"
        and "# CBustamante,
    title = "Solid-state synthesis and mechanical unfolding of polymers of {T4}
        lysozyme",
    year = 2000,
    journal = PNAS,
    volume = 97,
    number = 1,
    pages = "139--144",
    doi = "10.1073/pnas.97.1.139",
    eprint = "http://www.pnas.org/cgi/reprint/97/1/139.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/97/1/139"
}

@article { yang06,
    author = YYang #" and "# FCLin #" and "# GYang,
    title = "Temperature control device for single molecule measurements using
        the atomic force microscope",
    collaboration = "",
    year = 2006,
    journal = RSI,
    volume = 77,
    number = 6,
    pages = 063701,
    numpages = 5,
    publisher = AIP,
    eid = 063701,
    doi = "10.1063/1.2204580",
    url = "http://link.aip.org/link/?RSI/77/063701/1",
    keywords = "temperature control; atomic force microscopy; thermocouples;
        heat sinks",
    note = "Introduces our temperature control system",
    project = "Energy Landscape Roughness"
}

@article { yu06,
    author = WYu #" and "# JLamb #" and "# FHan #" and "# JBirchler,
    title = "Telomere-mediated chromosomal truncation in maize",
    year = 2006,
    journal = PNAS,
    volume = 103,
    number = 46,
    pages = "17331--17336",
    doi = "10.1073/pnas.0605750103",
    eprint = "http://www.pnas.org/cgi/reprint/103/46/17331.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/103/46/17331",
    abstract = "Direct repeats of Arabidopsis telomeric sequence were
        constructed to test telomere-mediated chromosomal truncation in maize.
        Two constructs with 2.6 kb of telomeric sequence were used to transform
        maize immature embryos by Agrobacterium-mediated transformation. One
        hundred seventy-six transgenic lines were recovered in which 231
        transgene loci were revealed by a FISH analysis. To analyze chromosomal
        truncations that result in transgenes located near chromosomal termini,
        Southern hybridization analyses were performed. A pattern of smear in
        truncated lines was seen as compared with discrete bands for internal
        integrations, because telomeres in different cells are elongated
        differently by telomerase. When multiple restriction enzymes were used
        to map the transgene positions, the size of the smears shifted in
        accordance with the locations of restriction sites on the construct.
        This result demonstrated that the transgene was present at the end of
        the chromosome immediately before the integrated telomere sequence.
        Direct evidence for chromosomal truncation came from the results of
        FISH karyotyping, which revealed broken chromosomes with transgene
        signals at the ends. These results demonstrate that telomere-mediated
        chromosomal truncation operates in plant species. This technology will
        be useful for chromosomal engineering in maize as well as other plant
        species."
}

@article { zhao06,
    author = JZhao #" and "# HLee #" and "# RNome #" and "# SMajid #" and "#
        NScherer #" and "# WHoff,
    title = "Single-molecule detection of structural changes during
        {P}er-{A}rnt-{S}im ({PAS}) domain activation",
    year = 2006,
    journal = PNAS,
    volume = 103,
    number = 31,
    pages = "11561--11566",
    doi = "10.1073/pnas.0601567103",
    eprint = "http://www.pnas.org/cgi/reprint/103/31/11561.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/103/31/11561",
    abstract = "The Per-Arnt-Sim (PAS) domain is a ubiquitous protein module
        with a common three-dimensional fold involved in a wide range of
        regulatory and sensory functions in all domains of life. The activation
        of these functions is thought to involve partial unfolding of N- or
        C-terminal helices attached to the PAS domain. Here we use atomic force
        microscopy to probe receptor activation in single molecules of
        photoactive yellow protein (PYP), a prototype of the PAS domain family.
        Mechanical unfolding of Cys-linked PYP multimers in the presence and
        absence of illumination reveals that, in contrast to previous studies,
        the PAS domain itself is extended by {approx}3 nm (at the 10-pN
        detection limit of the measurement) and destabilized by {approx}30% in
        the light-activated state of PYP. Comparative measurements and steered
        molecular dynamics simulations of two double-Cys PYP mutants that probe
        different regions of the PAS domain quantify the anisotropy in
        stability and changes in local structure, thereby demonstrating the
        partial unfolding of their PAS domain upon activation. These results
        establish a generally applicable single-molecule approach for mapping
        functional conformational changes to selected regions of a protein. In
        addition, the results have profound implications for the molecular
        mechanism of PAS domain activation and indicate that stimulus-induced
        partial protein unfolding can be used as a signaling mechanism."
}

@article { zhuang06,
    author = WZhuang #" and "# DAbramavicius #" and "# SMukamel,
    title = "Two-dimensional vibrational optical probes for peptide fast
        folding investigation",
    year = 2006,
    journal = PNAS,
    volume = 103,
    number = 50,
    pages = "18934--18938",
    doi = "10.1073/pnas.0606912103",
    eprint = "http://www.pnas.org/cgi/reprint/103/50/18934.pdf",
    url = "http://www.pnas.org/cgi/content/abstract/103/50/18934",
    abstract = "A simulation study shows that early protein folding events may
        be investigated by using a recently developed family of nonlinear
        infrared techniques that combine the high temporal and spatial
        resolution of multidimensional spectroscopy with the chirality-specific
        sensitivity of amide vibrations to structure. We demonstrate how the
        structural sensitivity of cross-peaks in two-dimensional correlation
        plots of chiral signals of an {alpha} helix and a [beta] hairpin may be
        used to clearly resolve structural and dynamical details undetectable
        by one-dimensional techniques (e.g. circular dichroism) and identify
        structures indistinguishable by NMR."
}

@article { zinober02,
    author = RCZinober #" and "# DJBrockwell #" and "# GSBeddard #" and "#
        AWBlake #" and "# PDOlmsted #" and "# SERadford #" and "# DASmith,
    title = "Mechanically unfolding proteins: the effect of unfolding history
        and the supramolecular scaffold",
    year = 2002,
    month = dec,
    journal = PS,
    volume = 11,
    number = 12,
    pages = "2759--2765",
    issn = "0961-8368",
    doi = "10.1110/ps.0224602",
    eprint = "http://www.proteinscience.org/cgi/reprint/11/12/2759.pdf",
    url = "http://www.proteinscience.org/cgi/content/abstract/11/12/2759",
    keywords = "Computer Simulation; Models, Molecular; Monte Carlo Method;
        Protein Folding; Protein Structure, Tertiary; Proteins",
    abstract = "The mechanical resistance of a folded domain in a polyprotein
        of five mutant I27 domains (C47S, C63S I27)(5)is shown to depend on the
        unfolding history of the protein. This observation can be understood on
        the basis of competition between two effects, that of the changing
        number of domains attempting to unfold, and the progressive increase in
        the compliance of the polyprotein as domains unfold. We present Monte
        Carlo simulations that show the effect and experimental data that
        verify these observations. The results are confirmed using an
        analytical model based on transition state theory. The model and
        simulations also predict that the mechanical resistance of a domain
        depends on the stiffness of the surrounding scaffold that holds the
        domain in vivo, and on the length of the unfolded domain. Together,
        these additional factors that influence the mechanical resistance of
        proteins have important consequences for our understanding of natural
        proteins that have evolved to withstand force.",
    note = "Introduces unfolding-order \emph{scaffold effect} on average
        unfolding force.",
    project = "sawtooth simulation"
}

@article { zwanzig92,
    author = RZwanzig #" and "# ASzabo #" and "# BBagchi,
    title = "Levinthal's paradox.",
    year = 1992,
    month = jan,
    day = 01,
    journal = PNAS,
    volume = 89,
    number = 1,
    pages = "20--22",
    issn = "0027-8424",
    eprint =
        "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC48166/pdf/pnas01075-0036.p
        df",
    url = "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC48166/",
    keywords = "Mathematics;Models, Theoretical;Protein Conformation;Proteins",
    abstract = "Levinthal's paradox is that finding the native folded state of
        a protein by a random search among all possible configurations can take
        an enormously long time. Yet proteins can fold in seconds or less.
        Mathematical analysis of a simple model shows that a small and
        physically reasonable energy bias against locally unfavorable
        configurations, of the order of a few kT, can reduce Levinthal's time
        to a biologically significant size."
}

@article { hong10,
  author =       XHong #" and "# XChu #" and "# PZou #" and "# YLiu
                 #" and "# GYang,
  title =        "Magnetic-field-assisted rapid ultrasensitive
                 immunoassays using Fe3{O4}/Zn{O}/Au nanorices as Raman
                 probes.",
  journal =      BIOSENSE,
  year =         2010,
  month =        oct,
  day =          15,
  address =      "Centre for Advanced Optoelectronic Functional
                 Materials Research, Key Laboratory for UV
                 Light-Emitting Materials and Technology of Ministry of
                 Education, Northeast Normal University, Changchun
                 130024, PR China.",
  volume =       26,
  number =       2,
  pages =        "918--922",
  keywords =     "Biosensing Techniques",
  keywords =     "Electromagnetic Fields",
  keywords =     "Equipment Design",
  keywords =     "Equipment Failure Analysis",
  keywords =     "Immunoassay",
  keywords =     "Magnetite Nanoparticles",
  keywords =     "Spectrum Analysis, Raman",
  keywords =     "Zinc Oxide",
  abstract =     "Rapid and ultrasensitive immunoassays were developed
                 by using biofunctional Fe3O4/ZnO/Au nanorices as Raman
                 probes. Taking advantage of the superparamagnetic
                 property of the nanorices, the labeled proteins can
                 rapidly be separated and purified with a commercial
                 permanent magnet. The unsusceptible multiphonon
                 resonant Raman scattering of the nanorices provided a
                 characteristic spectroscopic fingerprint function,
                 which allowed an accurate detection of the analyte.
                 High specificity and selectivity of the assay were
                 demonstrated. It was found that the diffusion barriers
                 and the boundary layer effects had a great influence on
                 the detection limit. Manipulation of the nanorice
                 probes using an external magnetic field can enhance the
                 assay sensitivity by several orders of magnitude, and
                 reduce the detection time from 1 h to 3 min. This
                 magnetic-field-assisted rapid and ultrasensitive
                 immunoassay based on the resonant Raman scatting of
                 semiconductor shows significant value for potential
                 applications in biomedicine, food safety, and
                 environmental defence.",
  ISSN =         "1873-4235",
  doi =          "10.1016/j.bios.2010.06.066",
  URL =          "http://www.ncbi.nlm.nih.gov/pubmed/20667438",
  language =     "eng",
}

@article { zhao10,
  author =       LZhao #" and "# ABulhassan #" and "# GYang #" and "#
                 HFJi #" and "# JXi,
  title =        "Real-time detection of the morphological change in
                 cellulose by a nanomechanical sensor.",
  journal =      BIOTECH,
  year =         2010,
  month =        sep,
  day =          01,
  address =      "Department of Physics, Drexel University,
                 Philadelphia, Pennsylvania, USA.",
  volume =       107,
  number =       1,
  pages =        "190--194",
  keywords =     "Cellulose",
  keywords =     "Computer Systems",
  keywords =     "Equipment Design",
  keywords =     "Equipment Failure Analysis",
  keywords =     "Micro-Electrical-Mechanical Systems",
  keywords =     "Molecular Conformation",
  keywords =     "Nanotechnology",
  keywords =     "Transducers",
  abstract =     "Up to now, experimental limitations have prevented
                 researchers from achieving the molecular-level
                 understanding for the initial steps of the enzymatic
                 hydrolysis of cellulose, where cellulase breaks down
                 the crystal structure on the surface region of
                 cellulose and exposes cellulose chains for the
                 subsequent hydrolysis by cellulase. Because one of
                 these non-hydrolytic enzymatic steps could be the
                 rate-limiting step for the entire enzymatic hydrolysis
                 of crystalline cellulose by cellulase, being able to
                 analyze and understand these steps is instrumental in
                 uncovering novel leads for improving the efficiency of
                 cellulase. In this communication, we report an
                 innovative application of the microcantilever technique
                 for a real-time assessment of the morphological change
                 of cellulose induced by a treatment of sodium chloride.
                 This sensitive nanomechanical approach to define
                 changes in surface structure of cellulose has the
                 potential to permit a real-time assessment of the
                 effect of the non-hydrolytic activities of cellulase on
                 cellulose and thereby to provide a comprehensive
                 understanding of the initial steps of the enzymatic
                 hydrolysis of cellulose.",
  ISSN =         "1097-0290",
  doi =          "10.1002/bit.22754",
  URL =          "http://www.ncbi.nlm.nih.gov/pubmed/20653025",
  language =     "eng",
}

@article { liu10,
  author =       RLiu #" and "# MRoman #" and "# GYang,
  title =        "Correction of the viscous drag induced errors in
                 macromolecular manipulation experiments using atomic
                 force microscope.",
  journal =      RSI,
  year =         2010,
  month =        jun,
  address =      "Department of Physics, Drexel University,
                 Philadelphia, Pennsylvania 19104, USA.",
  volume =       81,
  number =       6,
  pages =        "063703",
  keywords =     "Algorithms",
  keywords =     "Artifacts",
  keywords =     "Macromolecular Substances",
  keywords =     "Mechanical Processes",
  keywords =     "Microscopy, Atomic Force",
  keywords =     "Models, Theoretical",
  keywords =     "Motion",
  keywords =     "Protein Folding",
  keywords =     "Signal Processing, Computer-Assisted",
  keywords =     "Viscosity",
  abstract =     "We describe a method to correct the errors induced by
                 viscous drag on the cantilever in macromolecular
                 manipulation experiments using the atomic force
                 microscope. The cantilever experiences a viscous drag
                 force in these experiments because of its motion
                 relative to the surrounding liquid. This viscous force
                 superimposes onto the force generated by the
                 macromolecule under study, causing ambiguity in the
                 experimental data. To remove this artifact, we analyzed
                 the motions of the cantilever and the liquid in
                 macromolecular manipulation experiments, and developed
                 a novel model to treat the viscous drag on the
                 cantilever as the superposition of the viscous force on
                 a static cantilever in a moving liquid and that on a
                 bending cantilever in a static liquid. The viscous
                 force was measured under both conditions and the
                 results were used to correct the viscous drag induced
                 errors from the experimental data. The method will be
                 useful for many other cantilever based techniques,
                 especially when high viscosity and high cantilever
                 speed are involved.",
  ISSN =         "1089-7623",
  doi =          "10.1063/1.3436646",
  URL =          "http://www.ncbi.nlm.nih.gov/pubmed/20590242",
  language =     "eng",
}

@phdthesis { roman12,
  author = MRoman,
  title = "Macromolecular crowding effects in the mechanical unfolding
    forces of proteins",
  school = Drexel,
  year = 2012,
  month = may,
  url = "http://hdl.handle.net/1860/3854",
  eprint = "http://idea.library.drexel.edu/bitstream/1860/3854/1/Roman_Marisa.pdf",
  keywords = "Physics",
  keywords = "Biophysics",
  keywords = "Protein folding",
  abstract = "Macromolecules can occupy a large fraction of the volume
    of a cell and this crowded environment influences the behavior and
    properties of the proteins, such as mechanical unfolding forces,
    thermal stability and rates of folding and diffusion. Although
    much is already known about molecular crowding, it is not well
    understood how it affects a protein’s resistance to mechanical
    stress in a crowded environment and how the size of the crowders
    affect those changes. An atomic force microscope-based single
    molecule method was used to measure the effects of the crowding on
    the mechanical stability of a model protein, in this case I-27. As
    proteins tend to aggregate, single molecule methods provided a way
    to prevent aggregation because of the very low concentration of
    proteins in the solution under study. Dextran was used as the
    crowding agent with three different molecular weights 6kDa, 10 kDa
    and 40 kDa, with concentrations varying from zero to 300 grams per
    liter in a pH neutral buffer solution at room temperature. Results
    showed that the forces required to unfold biomolecules were
    increased when a high concentration of crowder molecules were
    added to the buffer solution and that the maximum force required
    to unfold a domain was when the crowder size was 10 kDa, which is
    comparable to the protein size. Unfolding rates obtained from
    Monte Carlo simulations showed that they were also affected in the
    presence of crowders. As a consequence, the energy barrier was
    also affected. These effects were most notable when the size of
    the crowder was 10 kDa, comparable to the size of the protein. On
    the other hand, distances to the transition state did not seem to
    change when crowders were added to the solution. The effect of
    Dextran on the energy barrier was modeled by using established
    theories such as Ogston’s and scaled particle theory, neither of
    which was completely convincing at describing the results. It can
    be hypothesized that the composition of Dextran plays a role in
    the deviation of the predicted behavior with respect to the
    experimental data.",
  language = "eng",
}

@article { measey09,
  author =       TMeasey #" and "# KBSmith #" and "# SDecatur #" and "#
                 LZhao #" and "# GYang #" and "# RSchweitzerStenner,
  title =        "Self-aggregation of a polyalanine octamer promoted by
                 its {C}-terminal tyrosine and probed by a strongly
                 enhanced vibrational circular dichroism signal.",
  journal =      JACS,
  year =         2009,
  month =        dec,
  day =          30,
  address =      "Department of Chemistry, Drexel University, 3141
                 Chestnut Street, Philadelphia, Pennsylvania 19104,
                 USA.",
  volume =       131,
  number =       51,
  pages =        "18218--18219",
  keywords =     "Amyloid",
  keywords =     "Circular Dichroism",
  keywords =     "Dimerization",
  keywords =     "Oligopeptides",
  keywords =     "Peptides",
  keywords =     "Protein Conformation",
  keywords =     "Tyrosine",
  abstract =     "The eight-residue alanine oligopeptide
                 Ac-A(4)KA(2)Y-NH(2) (AKY8) was found to form
                 amyloid-like fibrils upon incubation at room
                 temperature in acidified aqueous solution at peptide
                 concentrations >10 mM. The fibril solution exhibits an
                 enhanced vibrational circular dichroism (VCD) couplet
                 in the amide I' band region that is nearly 2 orders of
                 magnitude larger than typical polypeptide/protein
                 signals in this region. The UV-CD spectrum of the
                 fibril solution shows CD in the region associated with
                 the tyrosine side chain absorption. A similar peptide,
                 Ac-A(4)KA(2)-NH(2) (AK7), which lacks a terminal
                 tyrosine residue, does not aggregate. These results
                 suggest a pivotal role for the C-terminal tyrosine
                 residue in stabilizing the aggregation state of this
                 peptide. It is speculated that interactions between the
                 lysine and tyrosine side chains of consecutive strands
                 in an antiparallel arrangement (e.g., cation-pi
                 interactions) are responsible for the stabilization of
                 the resulting fibrils. These results offer
                 considerations and insight regarding the de novo design
                 of self-assembling oligopeptides for biomedical and
                 biotechnological applications and highlight the
                 usefulness of VCD as a tool for probing amyloid fibril
                 formation.",
  ISSN =         "1520-5126",
  doi =          "10.1021/ja908324m",
  URL =          "http://www.ncbi.nlm.nih.gov/pubmed/19958029",
  language =     "eng",
}

@article { shan09,
  author =       GShan #" and "# SWang #" and "# XFei #" and "# YLiu
                 #" and "# GYang,
  title =        "Heterostructured Zn{O}/Au nanoparticles-based resonant
                 Raman scattering for protein detection.",
  journal =      JPC:B,
  year =         2009,
  month =        feb,
  day =          05,
  address =      "Center for Advanced Optoelectronic Functional
                 Materials Research, Northeast Normal University,
                 Changchun 130024, P. R. China.",
  volume =       113,
  number =       5,
  pages =        "1468--1472",
  keywords =     "Animals",
  keywords =     "Gold",
  keywords =     "Humans",
  keywords =     "Immunoglobulin G",
  keywords =     "Metal Nanoparticles",
  keywords =     "Microscopy, Electron, Transmission",
  keywords =     "Spectrum Analysis, Raman",
  keywords =     "Zinc Oxide",
  abstract =     "A new method of protein detection was explored on the
                 resonant Raman scattering signal of ZnO nanoparticles.
                 A probe for the target protein was constructed by
                 binding the ZnO/Au nanoparticles to secondary protein
                 by eletrostatic interaction. The detection of proteins
                 was achieved by an antibody-based sandwich assay. A
                 first antibody, which could be specifically recognized
                 by target protein, was attached to a solid silicon
                 surface. The ZnO/Au protein probe could specifically
                 recognize and bind to the complex of the target protein
                 and first antibody. This method on the resonant Raman
                 scattering signal of ZnO nanoparticles showed good
                 selectivity and sensitivity for the target protein.",
  ISSN =         "1520-6106",
  doi =          "10.1021/jp8046032",
  URL =          "http://www.ncbi.nlm.nih.gov/pubmed/19138135",
  language =     "eng",
}

@article { yuan08,
  author =       JMYuan #" and "# CLChyan #" and "# HXZhou #" and "#
                 TYChung #" and "# HPeng #" and "# GPing #" and "#
                 GYang,
  title =        "The effects of macromolecular crowding on the
                 mechanical stability of protein molecules.",
  journal =      PS,
  year =         2008,
  month =        dec,
  day =          09,
  address =      "Department of Physics, Drexel University,
                 Philadelphia, Pennsylvania 19104, USA.",
  volume =       17,
  number =       12,
  pages =        "2156--2166",
  keywords =     "Circular Dichroism",
  keywords =     "Dextrans",
  keywords =     "Kinetics",
  keywords =     "Microscopy, Atomic Force",
  keywords =     "Microscopy, Scanning Probe",
  keywords =     "Protein Folding",
  keywords =     "Protein Stability",
  keywords =     "Protein Structure, Secondary",
  keywords =     "Thermodynamics",
  keywords =     "Ubiquitin",
  abstract =     "Macromolecular crowding, a common phenomenon in the
                 cellular environments, can significantly affect the
                 thermodynamic and kinetic properties of proteins. A
                 single-molecule method based on atomic force microscopy
                 (AFM) was used to investigate the effects of
                 macromolecular crowding on the forces required to
                 unfold individual protein molecules. It was found that
                 the mechanical stability of ubiquitin molecules was
                 enhanced by macromolecular crowding from added dextran
                 molecules. The average unfolding force increased from
                 210 pN in the absence of dextran to 234 pN in the
                 presence of 300 g/L dextran at a pulling speed of 0.25
                 microm/sec. A theoretical model, accounting for the
                 effects of macromolecular crowding on the native and
                 transition states of the protein molecule by applying
                 the scaled-particle theory, was used to quantitatively
                 explain the crowding-induced increase in the unfolding
                 force. The experimental results and interpretation
                 presented could have wide implications for the many
                 proteins that experience mechanical stresses and
                 perform mechanical functions in the crowded environment
                 of the cell.",
  ISSN =         "1469-896X",
  doi =          "10.1110/ps.037325.108",
  URL =          "http://www.ncbi.nlm.nih.gov/pubmed/18780817",
  language =     "eng",
}

@article { liu08,
  author =       YLiu #" and "# MZhong #" and "# GShan #" and "# YLi
                 #" and "# BHuang #" and "# GYang,
  title =        "Biocompatible Zn{O}/Au nanocomposites for
                 ultrasensitive {DNA} detection using resonance Raman
                 scattering.",
  journal =      JPC:B,
  year =         2008,
  month =        may,
  day =          22,
  address =      "Centre for Advanced Optoelectronic Functional
                 Materials Research, Institute of Genetics and Cytology,
                 Northeast Normal University, Changchun, People's
                 Republic of China. ycliu@nenu.edu.cn",
  volume =       112,
  number =       20,
  pages =        "6484--6489",
  keywords =     "Base Sequence",
  keywords =     "DNA",
  keywords =     "Gold",
  keywords =     "Microscopy, Electron, Transmission",
  keywords =     "Nanocomposites",
  keywords =     "Sensitivity and Specificity",
  keywords =     "Spectrum Analysis, Raman",
  keywords =     "Zinc Oxide",
  abstract =     "A novel method for identifying DNA microarrays based
                 on ZnO/Au nanocomposites functionalized with
                 thiol-oligonucleotide as probes is descried here. DNA
                 labeled with ZnO/Au nanocomposites has a strong Raman
                 signal even without silver acting as a surface-enhanced
                 Raman scattering promoter. X-ray photoelectron spectra
                 confirmed the formation of a three-component sandwich
                 assay, i.e., constituted DNA and ZnO/Au nanocomposites.
                 The resonance multiple-phonon Raman signal of the
                 ZnO/Au nanocomposites as a spectroscopic fingerprint is
                 used to detect a target sequence of oligonucleotide.
                 This method exhibits extraordinary sensitivity and the
                 detection limit is at least 1 fM.",
  ISSN =         "1520-6106",
  doi =          "10.1021/jp710399d",
  URL =          "http://www.ncbi.nlm.nih.gov/pubmed/18444675",
  language =     "eng",
}

@article { guo08,
  author =       YGuo #" and "# AMylonakis #" and "# ZZhang #" and "#
                 GYang #" and "# PLelkes #" and "# SChe #" and "#
                 QLu #" and "# YWei,
  title =        "Templated synthesis of electroactive periodic
                 mesoporous organosilica bridged with oligoaniline.",
  journal =      CHEM,
  year =         2008,
  address =      "Department of Chemistry, Drexel University,
                 Philadelphia, Pennsylvania 19104, USA.",
  volume =       14,
  number =       9,
  pages =        "2909--2917",
  keywords =     "Aniline Compounds",
  keywords =     "Cetrimonium Compounds",
  keywords =     "Electrochemistry",
  keywords =     "Hydrolysis",
  keywords =     "Microscopy, Electron, Transmission",
  keywords =     "Molecular Structure",
  keywords =     "Organosilicon Compounds",
  keywords =     "Particle Size",
  keywords =     "Porosity",
  keywords =     "Spectroscopy, Fourier Transform Infrared",
  keywords =     "Surface Properties",
  keywords =     "Thermogravimetry",
  keywords =     "X-Ray Diffraction",
  abstract =     "The synthesis and characterization of novel
                 electroactive periodic mesoporous organosilica (PMO)
                 are reported. The silsesquioxane precursor,
                 N,N'-bis(4'-(3-triethoxysilylpropylureido)phenyl)-1,4-quinonene-diimine
                 (TSUPQD), was prepared from the emeraldine base of
                 amino-capped aniline trimer (EBAT) using a one-step
                 coupling reaction and was used as an organic silicon
                 source in the co-condensation with tetraethyl
                 orthosilicate (TEOS) in proper ratios. By means of a
                 hydrothermal sol-gel approach with the cationic
                 surfactant cetyltrimethyl-ammonium bromide (CTAB) as
                 the structure-directing template and acetone as the
                 co-solvent for the dissolution of TSUPQD, a series of
                 novel MCM-41 type siliceous materials (TSU-PMOs) were
                 successfully prepared under mild alkaline conditions.
                 The resultant mesoporous organosilica were
                 characterized by Fourier transform infrared (FT-IR)
                 spectroscopy, thermogravimetry, X-ray diffraction,
                 nitrogen sorption, and transmission electron microscopy
                 (TEM) and showed that this series of TSU-PMOs exhibited
                 hexagonally patterned mesostructures with pore
                 diameters of 2.1-2.8 nm. Although the structural
                 regularity and pore parameters gradually deteriorated
                 with increasing loading of organic bridges, the
                 electrochemical behavior of TSU-PMOs monitored by
                 cyclic voltammetry demonstrated greater
                 electroactivities for samples with higher concentration
                 of the incorporated TSU units.",
  ISSN =         "0947-6539",
  doi =          "10.1002/chem.200701605",
  URL =          "http://www.ncbi.nlm.nih.gov/pubmed/18224650",
  language =     "eng",
}

@article { li07,
  author =       LiLi #" and "# BLi #" and "# GYang #" and "# CYLi,
  title =        "Polymer decoration on carbon nanotubes via physical
                 vapor deposition.",
  journal =      LANG,
  year =         2007,
  month =        jul,
  day =          31,
  address =      "A. J. Drexel Nanotechnology Institute and Department
                 of Materials Science and Engineering, Drexel
                 University, Philadelphia, Pennsylvania 19104, USA.",
  volume =       23,
  number =       16,
  pages =        "8522--8525",
  keywords =     "Microscopy, Atomic Force",
  keywords =     "Microscopy, Electron, Transmission",
  keywords =     "Nanotubes, Carbon",
  keywords =     "Polymers",
  keywords =     "Surface Properties",
  keywords =     "Volatilization",
  abstract =     "The polymer decoration technique has been widely used
                 to study the chain folding behavior of polymer single
                 crystals. In this article, we demonstrate that this
                 method can be successfully adopted to pattern a variety
                 of polymers on carbon nanotubes (CNTs). The resulting
                 structure is a two-dimensional nanohybrid shish kebab
                 (2D NHSK), wherein the CNT forms the shish and the
                 polymer crystals form the kebabs. 2D NHSKs consisting
                 of CNTs and polymers such as polyethylene, nylon 66,
                 polyvinylidene fluoride and poly(L-lysine) have been
                 achieved. Transmission electron microscopy and atomic
                 force microscopy were used to study the nanoscale
                 morphology of these hybrid materials. Relatively
                 periodic decoration of polymers on both single-walled
                 and multi-walled CNTs was observed. It is envisaged
                 that this unique method offers a facile means to
                 achieve patterned CNTs for nanodevice applications.",
  ISSN =         "0743-7463",
  doi =          "10.1021/la700480z",
  URL =          "http://www.ncbi.nlm.nih.gov/pubmed/17602575",
  language =     "eng",
}

@article { su06,
  author =       MSu #" and "# YYang #" and "# GYang,
  title =        "Quantitative measurement of hydroxyl radical induced
                 {DNA} double-strand breaks and the effect of
                 {N}-acetyl-{L}-cysteine.",
  journal =      FEBS,
  year =         2006,
  month =        jul,
  day =          24,
  address =      "Department of Physics, Drexel University,
                 Philadelphia, PA 19104, USA.",
  volume =       580,
  number =       17,
  pages =        "4136--4142",
  keywords =     "Acetylcysteine",
  keywords =     "Animals",
  keywords =     "DNA Damage",
  keywords =     "Humans",
  keywords =     "Hydroxyl Radical",
  keywords =     "Microscopy, Atomic Force",
  keywords =     "Nucleic Acid Conformation",
  keywords =     "Plasmids",
  abstract =     "Reactive oxygen species, such as hydroxyl or
                 superoxide radicals, can be generated by exogenous
                 agents as well as from normal cellular metabolism.
                 Those radicals are known to induce various lesions in
                 DNA, including strand breaks and base modifications.
                 These lesions have been implicated in a variety of
                 diseases such as cancer, arteriosclerosis, arthritis,
                 neurodegenerative disorders and others. To assess these
                 oxidative DNA damages and to evaluate the effects of
                 the antioxidant N-acetyl-L-cysteine (NAC), atomic force
                 microscopy (AFM) was used to image DNA molecules
                 exposed to hydroxyl radicals generated via Fenton
                 chemistry. AFM images showed that the circular DNA
                 molecules became linear after incubation with hydroxyl
                 radicals, indicating the development of double-strand
                 breaks. The occurrence of the double-strand breaks was
                 found to depend on the concentration of the hydroxyl
                 radicals and the duration of the reaction. Under the
                 conditions of the experiments, NAC was found to
                 exacerbate the free radical-induced DNA damage.",
  ISSN =         "0014-5793",
  doi =          "10.1016/j.febslet.2006.06.060",
  URL =          "http://www.ncbi.nlm.nih.gov/pubmed/16828758",
  language =     "eng",
}

@article { lli06,
  author =       LiLi #" and "# YYang #" and "# GYang #" and "# XuChen
                 #" and "# BHsiao #" and "# BChu #" and "#
                 JSpanier #" and "# CYLi,
  title =        "Patterning polyethylene oligomers on carbon nanotubes
                 using physical vapor deposition.",
  journal =      NANO,
  year =         2006,
  month =        may,
  address =      "A. J. Drexel Nanotechnology Institute and Department
                 of Materials Science and Engineering, Drexel
                 University, Philadelphia, Pennsylvania 19104, USA.",
  volume =       6,
  number =       5,
  pages =        "1007--1012",
  keywords =     "Microscopy, Atomic Force",
  keywords =     "Nanotechnology",
  keywords =     "Nanotubes, Carbon",
  keywords =     "Polyethylenes",
  keywords =     "Volatilization",
  abstract =     "Periodic patterning on one-dimensional (1D) carbon
                 nanotubes (CNTs) is of great interest from both
                 scientific and technological points of view. In this
                 letter, we report using a facile physical vapor
                 deposition method to achieve periodic polyethylene (PE)
                 oligomer patterning on individual CNTs. Upon heating
                 under vacuum, PE degraded into oligomers and
                 crystallized into rod-shaped single crystals. These PE
                 rods periodically decorate on CNTs with their long axes
                 perpendicular to the CNT axes. The formation mechanism
                 was attributed to ``soft epitaxy'' growth of PE
                 oligomer crystals on CNTs. Both SWNTs and MWNTs were
                 decorated successfully with PE rods. The intermediate
                 state of this hybrid structure, MWNTs absorbed with a
                 thin layer of PE, was captured successfully by
                 depositing PE vapor on MWNTs detached from the solid
                 substrate, and was observed using high-resolution
                 transmission electron microscopy. Furthermore, this
                 hybrid structure formation depends critically on CNT
                 surface chemistry: alkane-modification of the MWNT
                 surface prohibited the PE single-crystal growth on the
                 CNTs. We anticipate that this work could open a gateway
                 for creating complex CNT-based nanoarchitectures for
                 nanodevice applications.",
  ISSN =         "1530-6984",
  doi =          "10.1021/nl060276q",
  URL =          "http://www.ncbi.nlm.nih.gov/pubmed/16683841",
  language =     "eng",
}

@article{ kuhn05,
  author = MKuhn #" and "# HJanovjak #" and "# MHubain #" and "# DJMuller,
  title = {Automated alignment and pattern recognition of
    single-molecule force spectroscopy data.},
  year = 2005,
  month = may,
  address = {Division of Computer Science, California Institute of
             Technology, Pasadena, California 91125, USA.},
  journal = JMicro,
  volume = 218,
  number = 2,
  pages = {125--132},
  ISSN = {0022-2720},
  doi = {10.1111/j.1365-2818.2005.01478.x},
  URL = {http://www.ncbi.nlm.nih.gov/pubmed/15857374},
  language = {eng},
  keywords = {Algorithms},
  keywords = {Bacteriorhodopsins},
  keywords = {Data Interpretation, Statistical},
  keywords = {Escherichia coli Proteins},
  keywords = {Microscopy, Atomic Force},
  keywords = {Protein Folding},
  keywords = {Sodium-Hydrogen Antiporter},
  keywords = {Software},
  abstract = {Recently, direct measurements of forces stabilizing
    single proteins or individual receptor-ligand bonds became
    possible with ultra-sensitive force probe methods like the atomic
    force microscope (AFM). In force spectroscopy experiments using
    AFM, a single molecule or receptor-ligand pair is tethered between
    the tip of a micromachined cantilever and a supporting
    surface. While the molecule is stretched, forces are measured by
    the deflection of the cantilever and plotted against extension,
    yielding a force spectrum characteristic for each biomolecular
    system. In order to obtain statistically relevant results, several
    hundred to thousand single-molecule experiments have to be
    performed, each resulting in a unique force spectrum. We developed
    software and algorithms to analyse large numbers of force
    spectra. Our algorithms include the fitting polymer extension
    models to force peaks as well as the automatic alignment of
    spectra.  The aligned spectra allowed recognition of patterns of
    peaks across different spectra. We demonstrate the capabilities of
    our software by analysing force spectra that were recorded by
    unfolding single transmembrane proteins such as bacteriorhodopsin
    and NhaA. Different unfolding pathways were detected by
    classifying peak patterns. Deviant spectra, e.g. those with no
    attachment or erratic peaks, can be easily identified.  The
    software is based on the programming language C++, the GNU
    Scientific Library (GSL), the software WaveMetrics IGOR Pro and
    available open-source at http://bioinformatics.org/fskit/.},
  note = {Development stalled in 2005 after Michael graduated.},
}

@article{ janovjak05,
  author = HJanovjak #" and "# JStruckmeier #" and "# DJMuller,
  title = {Hydrodynamic effects in fast {AFM} single-molecule
    force measurements.},
  year = 2005,
  month = feb,
  day = 15,
  address = {BioTechnological Center, University of Technology
             Dresden, 01307 Dresden, Germany.},
  journal = EBJ,
  volume = 34,
  number = 1,
  pages = {91--96},
  issn = {0175-7571},
  doi = {10.1007/s00249-004-0430-3},
  url = {http://www.ncbi.nlm.nih.gov/pubmed/15257425},
  language = {eng},
  keywords = {Algorithms},
  keywords = {Computer Simulation},
  keywords = {Elasticity},
  keywords = {Microfluidics},
  keywords = {Microscopy, Atomic Force},
  keywords = {Models, Chemical},
  keywords = {Models, Molecular},
  keywords = {Physical Stimulation},
  keywords = {Protein Binding},
  keywords = {Proteins},
  keywords = {Stress, Mechanical},
  keywords = {Viscosity},
  abstract = {Atomic force microscopy (AFM) allows the critical forces
    that unfold single proteins and rupture individual receptor-ligand
    bonds to be measured. To derive the shape of the energy landscape,
    the dynamic strength of the system is probed at different force
    loading rates. This is usually achieved by varying the pulling
    speed between a few nm/s and a few $\mu$m/s, although for a more
    complete investigation of the kinetic properties higher speeds are
    desirable. Above 10 $\mu$m/s, the hydrodynamic drag force acting
    on the AFM cantilever reaches the same order of magnitude as the
    molecular forces. This has limited the maximum pulling speed in
    AFM single-molecule force spectroscopy experiments. Here, we
    present an approach for considering these hydrodynamic effects,
    thereby allowing a correct evaluation of AFM force measurements
    recorded over an extended range of pulling speeds (and thus
    loading rates). To support and illustrate our theoretical
    considerations, we experimentally evaluated the mechanical
    unfolding of a multi-domain protein recorded at $30\U{$mu$m/s}$
    pulling speed.},
}

@article{ sandal09,
  author = MSandal #" and "# FBenedetti #" and "# MBrucale #" and "#
    AGomezCasado #" and "# BSamori,
  title = "Hooke: An open software platform for force spectroscopy.",
  journal = BIOINFO,
  year = 2009,
  month = jun,
  day = 01,
  address = "Department of Biochemistry, University of Bologna,
             Bologna, Italy. massimo.sandal@unibo.it",
  volume = 25,
  number = 11,
  pages = "1428--1430",
  keywords = "Algorithms",
  keywords = "Computational Biology",
  keywords = "Internet",
  keywords = "Microscopy, Atomic Force",
  keywords = "Proteome",
  keywords = "Proteomics",
  keywords = "Software",
  abstract = "SUMMARY: Hooke is an open source, extensible software
    intended for analysis of atomic force microscope (AFM)-based
    single molecule force spectroscopy (SMFS) data. We propose it as a
    platform on which published and new algorithms for SMFS analysis
    can be integrated in a standard, open fashion, as a general
    solution to the current lack of a standard software for SMFS data
    analysis. Specific features and support for file formats are coded
    as independent plugins. Any user can code new plugins, extending
    the software capabilities.  Basic automated dataset filtering and
    semi-automatic analysis facilities are included. AVAILABILITY:
    Software and documentation are available at
    (http://code.google.com/p/hooke). Hooke is a free software under
    the GNU Lesser General Public License.",
  ISSN = "1367-4811",
  doi = "10.1093/bioinformatics/btp180",
  URL = "http://www.ncbi.nlm.nih.gov/pubmed/19336443",
  language = "eng",
}

@article{ materassi09,
  author = DMaterassi #" and "# PBaschieri #" and "# BTiribilli #" and "#
    GZuccheri #" and "# BSamori,
  title = {An open source/real-time atomic force microscope
    architecture to perform customizable force spectroscopy
    experiments},
  year = 2009,
  month = aug,
  address = {Department of Electrical and Computer Engineering,
             University of Minnesota, 200 Union St. SE, Minneapolis,
             Minnesota 55455, USA. mater013@umn.edu},
  journal = RSI,
  volume = 80,
  number = 8,
  pages = 084301,
  issn = "1089-7623",
  doi = "10.1063/1.3194046",
  url = "http://www.ncbi.nlm.nih.gov/pubmed/19725671",
  language = "eng",
  keywords = {Algorithms},
  keywords = {Animals},
  keywords = {Calibration},
  keywords = {Gold},
  keywords = {Microscopy, Atomic Force},
  keywords = {Muscle Proteins},
  keywords = {Myocardium},
  keywords = {Optics and Photonics},
  keywords = {Ownership},
  keywords = {Protein Kinases},
  keywords = {Software},
  keywords = {Spectrum Analysis},
  keywords = {Time Factors},
  abstract = {We describe the realization of an atomic force
    microscope architecture designed to perform customizable
    experiments in a flexible and automatic way. Novel technological
    contributions are given by the software implementation platform
    (RTAI-LINUX), which is free and open source, and from a functional
    point of view, by the implementation of hard real-time control
    algorithms. Some other technical solutions such as a new way to
    estimate the optical lever constant are described as well. The
    adoption of this architecture provides many degrees of freedom in
    the device behavior and, furthermore, allows one to obtain a
    flexible experimental instrument at a relatively low cost. In
    particular, we show how such a system has been employed to obtain
    measures in sophisticated single-molecule force spectroscopy
    experiments\citep{fernandez04}. Experimental results on proteins
    already studied using the same methodologies are provided in order
    to show the reliability of the measure system.},
  note = {Although this paper claims to present an open source
    experiment control framework (on Linux!), it doesn't actually link
    to any source code.  This is puzzling and frusterating.},
}

@article{ aioanei11,
  author = DAioanei #" and "# MBrucale #" and "# BSamori,
  title = {Open source platform for the execution and analysis of
    mechanical refolding experiments.},
  year = 2011,
  month = feb,
  day = 1,
  address = {Department of Biochemistry G.~Moruzzi,
             University of Bologna, Via Irnerio 48, 40126 Bologna, Italy.
             aioaneid@gmail.com},
  journal = BIOINFO,
  volume = 27,
  number = 3,
  pages = {423--425},
  issn = {1367-4811},
  doi = {10.1093/bioinformatics/btq663},
  url = {http://www.ncbi.nlm.nih.gov/pubmed/21123222},
  language = {eng},
  keywords = {Computational Biology},
  keywords = {Kinetics},
  keywords = {Protein Denaturation},
  keywords = {Protein Refolding},
  keywords = {Software},
  abstract = {Single-molecule force spectroscopy has facilitated the
    experimental investigation of biomolecular force-coupled kinetics,
    from which the kinetics at zero force can be extrapolated via
    explicit theoretical models. The atomic force microscope (AFM) in
    particular is routinely used to study protein unfolding kinetics,
    but only rarely protein folding kinetics. The discrepancy arises
    because mechanical protein refolding studies are more technically
    challenging.},
  note = {\href{http://code.google.com/p/refolding/}{Refolding} is a
    suite for performing and analyzing double-pulse refolding
    experiments.  The experiment-driver is mostly written in Java with
    the analysis code in Python. The driver is curious; it uses the
    NanoScope scripting interface to drive the experiment through the
    NanoScope software by impersonating a mouse-wielding user (like
    Selenium does for web browsers). See the
    \imint{sh}|RobotNanoDriver.java| code for details. There is also
    support for automatic velocity clamp analysis.},
}

@article{ benedetti11,
  author = FBenedetti #" and "# CMicheletti #" and "# GBussi #" and "#
    SKSekatskii #" and "# GDietler,
  title = {Nonkinetic modeling of the mechanical unfolding of
    multimodular proteins: theory and experiments.},
  year = 2011,
  month = sep,
  day = 21,
  address = {Laboratory of Physics of Living Matter,
             Ecole Polytechnique F{\'e}d{\'e}rale de Lausanne,
             Lausanne, Switzerland.},
  journal = BPJ,
  volume = 101,
  number = 6,
  pages = {1504--1512},
  issn = {1542-0086},
  doi = {10.1016/j.bpj.2011.07.047},
  url = {http://www.ncbi.nlm.nih.gov/pubmed/21943432},
  language = {eng},
  keywords = {Kinetics},
  keywords = {Microscopy, Atomic Force},
  keywords = {Models, Molecular},
  keywords = {Monte Carlo Method},
  keywords = {Protein Unfolding},
  keywords = {Stochastic Processes},
  abstract = {We introduce and discuss a novel approach called
    back-calculation for analyzing force spectroscopy experiments on
    multimodular proteins. The relationship between the histograms of
    the unfolding forces for different peaks, corresponding to a
    different number of not-yet-unfolded protein modules, is exploited
    in such a manner that the sole distribution of the forces for one
    unfolding peak can be used to predict the unfolding forces for
    other peaks. The scheme is based on a bootstrap prediction method
    and does not rely on any specific kinetic model for multimodular
    unfolding. It is tested and validated in both
    theoretical/computational contexts (based on stochastic
    simulations) and atomic force microscopy experiments on (GB1)(8)
    multimodular protein constructs. The prediction accuracy is so
    high that the predicted average unfolding forces corresponding to
    each peak for the GB1 construct are within only 5 pN of the
    averaged directly-measured values. Experimental data are also used
    to illustrate how the limitations of standard kinetic models can
    be aptly circumvented by the proposed approach.},
}

@phdthesis{ benedetti12,
  author = FBenedetti,
  title = {Statistical Study of the Unfolding of Multimodular Proteins
    and their Energy Landscape by Atomic Force Microscopy},
  year = 2012,
  address = {Lausanne},
  affiliation = {EPFL},
  doctoral = {EDPY},
  pagecount = {153},
  doi = {10.5075/epfl-thesis-5440},
  url = {http://infoscience.epfl.ch/record/181215},
  eprint = {http://infoscience.epfl.ch/record/181215/files/EPFL_TH5440.pdf},
  keywords = {atomic force microscope (AFM); single molecule force
    spectrosopy; velocity clamp AFM; Monte carlo simulations; force
    modulation spectroscopy; energy barrier model; non kinetic methods
    for force spectroscopy},
  abstract = {The aim of the present thesis is to investigate several
    aspects of: the proteins mechanics, interprotein interactions and
    to study also new techniques, theoretical and technical, to obtain
    and analyze the force spectroscopy experiments. The first section
    is dedicated to the statistical properties of the unfolding forces
    in a chain of homomeric multimodular proteins. The basic idea of
    this kind of statistic is to divide the peaks observed in a force
    extension curve in separate groups and then analyze these groups
    considering their position in the force curves. In fact in a
    multimodular homomeric protein the unfolding force is related to
    the number of not yet unfolded modules (we call it "N"). Such
    effect yields to a linear dependence of the most probable
    unfolding force of a peak on ln(N). We demonstrate how such
    dependence can be used to extract the kinetic parameters and how,
    ignoring it, could lead to significant errors. Following this
    topic we continue with non kinetic methods that, using the
    resampling from the rupture forces of any peak, could reconstruct
    the rupture forces for all the other peaks in a chain. Then a
    discussion about the Monte Carlo simulation for protein pulling is
    present. In fact a theoretical framework for such methodology has
    to be introduced to understand the various simulations done. In
    this chapter we also introduce a methodology to study the ligand
    receptor interactions when we directly functionalize the AFM tip
    and the substrate. In fact, in many of our experiments, we see a
    "cloud of points" in the force vs loading rate graph. We have
    modeled a system composed by "N" parallel springs, and studying
    the distribution of forces obtained in the force vs loading rate
    graph we have establish a procedure to restore the kinetic
    parameters used. Such procedure has then been used to discuss real
    experiments similar to biotin-avidin interaction. In the following
    chapter we discuss a first order approximation of the Bell-Evans
    model where a more explicit form of the potential is
    considered. In particular the dependence of the curvature of the
    potential on the applied force at the minimum and at the
    metastable state is considered. In the well known Bell-Evans model
    the prefactors of the transition rate are fixed at any force,
    however this is not what happen in nature, where the prefactors
    (that are the second local derivative of the interacting energy
    with respect to the reaction coordinate in its minimum and
    maximum) depend on the force applied. The results obtained with
    the force spectroscopy of the Laminin-binding-protein are
    discussed, in particular this protein showed a phase transition
    when the pH was changed. The behavior of this protein changes,
    from a normal WLC behavior to a plateau behavior. The analysis of
    the force spectroscopy curves shows a distribution of length where
    the maximum of the first prominent peak correspond to the full
    length of the protein. However, length that could be associated
    with dimers and trymers are also present in this
    distribution. Later a new approach to study the lock and key
    mechanism, using "handles" with a specific force extension
    pattern, is introduced. In particular handles of (I27)3 and
    (I27–SNase)3 were biochemically attached to: strept-actin
    molecules, biotin molecules, RNase and Angiogenin. The main idea
    is to have a system composed by "handle-(molecule A)-(molecule
    B)-handle" where the handles are covalently attached to the
    respective molecules and the two molecules "A and B" are attached
    by secondary bonds. This approach allows a better recognition of
    the protein-protein interaction enabling us to filter out spurious
    events. Doing a statistic on the rupture forces and comparing this
    with the statistic of the detachments of the system of the bare
    handles, we are able to extract the information of the interaction
    between the molecule A and B. The two last chapters are of more
    preliminary character that the previous part of the thesis. A
    section is dedicated to the estimation of effective mass and
    viscous drag of the cantilevers studied by autocorrelation and
    noise power spectrum. Usually the noise power spectrum method is
    the most used, however the autocorrelation should give
    approximately the same information. The parameters obtained are
    important in high frequency modulation techniques. In fact, they
    are needed to interpret the results. The results of these two
    methods show a good agreement in the estimation of the mass and
    the viscous drag of the various cantilever used. Afterwards a
    chapter is dedicated to the discussion of the force spectroscopy
    experiments using a low frequency modulation of the cantilever
    base. Such experiments allow us to record the phase and the
    amplitude shift of the modulation signal used. Using the amplitude
    channel we managed to restore the static force signal with a lower
    level of noise. Moreover these signals give us direct information
    about the dynamic stiffness and the lose of energy in the system,
    information that, using the standard technique would be difficult
    (or even impossible) to obtain.},
}

@article{ kempe85,
  author = TKempe #" and "# SBHKent #" and "# FChow #" and "# SMPeterson
    #" and "# WSundquist #" and "# JLItalien #" and "# DHarbrecht
    #" and "# DPlunkett #" and "# WDeLorbe,
  title = "Multiple-copy genes: Production and modification of
    monomeric peptides from large multimeric fusion proteins.",
  journal = GENE,
  year = 1985,
  volume = 39,
  number = "2-3",
  pages = "239--245",
  keywords = "Cloning, Molecular",
  keywords = "Cyanogen Bromide",
  keywords = "DNA, Recombinant",
  keywords = "Escherichia coli",
  keywords = "Gene Expression Regulation",
  keywords = "Genetic Vectors",
  keywords = "Humans",
  keywords = "Molecular Weight",
  keywords = "Peptide Fragments",
  keywords = "Plasmids",
  keywords = "Substance P",
  keywords = "beta-Galactosidase",
  abstract = "A vector system has been designed for obtaining high
    yields of polypeptides synthesized in Escherichia coli.  Multiple
    copies of a synthetic gene encoding the neuropeptide substance P
    (SP) (Arg-Pro-Lys-Pro-Gln-Gln-Phe-Phe-Gly-Leu-Met-NH2) have been
    linked and fused to the lacZ gene. Each copy of the SP gene was
    flanked by codons for methionine to create sites for cleavage by
    cyanogen bromide (CNBr).  The isolated multimeric SP fusion
    protein was converted to monomers of SP analog, each containing a
    carboxyl-terminal homoserine lactone (Hse-lactone) residue
    (Arg-Pro-Lys-Pro-Gln-Gln-Phe-Phe-Gly-Leu-Hse-lactone), upon
    treatment with CNBr in formic acid. The Hse-lactone moiety was
    subjected to chemical modifications to produce an SP Hse
    amide. This method permits synthesis of peptide amide analogs and
    other peptide derivatives by combining recombinant DNA techniques
    and chemical methods.",
  ISSN = "0378-1119",
  URL = "http://www.ncbi.nlm.nih.gov/pubmed/2419204",
  language = "eng",
}

@article{ honda08,
  author = MHonda #" and "# YBaba #" and "# NHiaro #" and "# TSekiguchi,
  title = "Metal-molecular interface of sulfur-containing amino acid
    and thiophene on gold surface",
  journal = JP:CON,
  volume = 100,
  number = 5,
  pages = "052071",
  url = "http://dx.doi.org/10.1088/1742-6596/100/5/052071",
  year = 2008,
  abstract = "Chemical-bonding states of metal-molecular interface
    have been investigated for L-cysteine and thiophene on gold by
    x-ray photoelectron spectroscopy (XPS) and near edge x-ray
    adsorption fine structure (NEXAFS). A remarkable difference in
    Au-S bonding states was found between L-cysteine and
    thiophene. For mono-layered L-cysteine on gold, the binding energy
    of S 1s in XPS and the resonance energy at the S K-edge in NEXAFS
    are higher by 8–9 eV than those for multi-layered film (molecular
    L-cysteine). In contrast, the S K-edge resonance energy for
    mono-layered thiophene on gold was 2475.0 eV, which is the same as
    that for molecular L-cysteine. In S 1s XPS for mono-layered
    thiophene, two peaks were observed. The higher binging-energy and
    more intense peak at 2473.4 eV are identified as gold sulfide. The
    binding energy of smaller peak, whose intensity is less than 1/3
    of the higher binding energy peak, is 2472.2 eV, which is the same
    as that for molecular thiophene. These observations indicate that
    Au-S interface behavior shows characteristic chemical bond only
    for the Au-S interface of L-cysteine monolayer on gold
    substrate.",
}

@article{ ulman96,
  author = AUlman,
  title = "Formation and Structure of Self-Assembled Monolayers.",
  journal = CHEMREV,
  year = 1996,
  month = jun,
  day = 20,
  address = "Department of Chemical Engineering, Chemistry and
    Materials Science, and the Herman F. Mark Polymer Research
    Institute, Polytechnic University, Six MetroTech Center, Brooklyn,
    New York 11201.",
  volume = 96,
  number = 4,
  pages = "1533--1554",
  ISSN = "1520-6890",
  URL = "http://www.ncbi.nlm.nih.gov/pubmed/11848802",
  language = "eng",
}

@article{ hager02,
  author = GHager #" and "# ABrolo,
  title = "Adsorption/desorption behaviour of cysteine and cystine in
    neutral and basic media: electrochemical evidence for differing
    thiol and disulfide adsorption to a {Au(111)} single crystal
    electrode",
  journal = JEChem,
  volume = "550--551",
  number = 0,
  pages = "291--301",
  year = 2003,
  issn = "1572-6657",
  doi = "10.1016/S0022-0728(03)00052-4",
  url = "http://www.sciencedirect.com/science/article/pii/S0022072803000524",
  keywords = "Thiol",
  keywords = "Disulfide",
  keywords = "Thiol adsorption",
  keywords = "Self-assembled monolayers",
  keywords = "Au(111) single crystal electrode",
  keywords = "Cysteine",
  keywords = "Cystine",
  abstract = "The adsorption/desorption behaviour of the
    thiol/disulfide redox couple, cysteine/cystine, was monitored at a
    Au(111) single crystal electrode. The monolayers were formed
    electrochemically from 0.1 M KClO4 and 0.1 M NaOH solutions
    containing either the thiol or the disulfide. Distinct features in
    the adsorption potential were noted. An adsorption peak was
    observed in the cyclic voltammograms (CVs) from Au(111) in 0.1 M
    KClO4 solutions containing cystine at $-0.57$ V vs. saturated
    calomel electrode. Under the same conditions, the CVs from
    solutions containing cysteine showed an adsorption peak at $-0.43$
    V (0.14 V more positive than the corresponding peak from disulfide
    solutions). This showed that the thiol and disulfide species have
    different adsorption properties. Similar behaviour was observed in
    0.1 M NaOH. Cyclic voltammetric and chronocoulometric data were
    employed to determine the surface coverage of the different
    monolayers. Cysteine solutions prepared in 0.1 M KClO4 provided
    coverages of $3.0\times10^{-10}$ and $2.5\times10^{-10}$
    mol~cm$^{-2}$ for the L and the D--L species, respectively as
    evaluated from the desorption peaks. Desorption of cystine in the
    same medium yielded coverages of $1.2\times10^{-10}$ mol~cm$^{-2}$
    for both L and D--L solutions (or $2.4\times10^{-10}$
    mol~cm$^{-2}$ in cysteine equivalents). Surface coverages obtained
    from Au(111) in 0.1 M NaOH corresponded to $3.9\times10^{10}$
    mol~cm$^{-2}$ for L-cysteine, and $1.2\times10^{-10}$
    mol~cm$^{-2}$ (or $2.4\times10^{-10}$ mol~cm$^{-2}$ cysteine
    equivalents) for L and D--L cystine.",
}

@phdthesis{ ma10,
  author = LMa,
  title = "The Nanomechanics of Polycystin-1: A Kidney Mechanosensor",
  school = UTMB,
  year = 2010,
  month = aug,
  url = "http://etd.utmb.edu/theses/available/etd-07072010-132038/",
  keywords = "ADPKD",
  keywords = "Polycystin-1",
  keywords = "Missense mutations",
  keywords = "Atomic Force Microscopy",
  keywords = "Osmolyte",
  keywords = "Mechanosensor",
  abstract = "Mutations in polycystin-1 (PC1) can cause Autosomal
    Dominant Polycystic Kidney Disease (ADPKD), which is a leading
    cause of renal failure. The available evidence suggests that PC1
    acts as a mechanosensor, receiving signals from the primary cilia,
    neighboring cells, and extracellular matrix. PC1 is a large
    membrane protein that has a long N-terminal extracellular region
    (about 3000 aa) with a multimodular structure including sixteen
    Ig-like PKD domains, which are targeted by many naturally
    occurring missense mutations. Nothing is known about the effects
    of these mutations on the biophysical properties of PKD
    domains. In addition, PC1 is expressed along the renal tubule,
    where it is exposed to a wide range of concentration of urea. Urea
    is known to destabilize proteins. Other osmolytes found in the
    kidney such as sorbitol, betaine and TMAO are known to counteract
    urea's negative effects on proteins. Nothing is known about how
    the mechanical properties of PC1 are affected by these
    osmolytes. Here I use nano-mechanical techniques to study the
    effects of missense mutations and effects of denaturants and
    various osmolytes on the mechanical properties of PKD
    domains. Several missense mutations were found to alter the
    mechanical stability of PKD domains resulting in distinct
    mechanical phenotypes. Based on these findings, I hypothesize that
    missense mutations may cause ADPKD by altering the stability of
    the PC1 ectodomain, thereby perturbing its ability to sense
    mechanical signals. I also found that urea has a significant
    impact on both the mechanical stability and refolding rate of PKD
    domains. It not only lowers their mechanical stability, but also
    slows down their refolding rate. Moreover, several osmolytes were
    found to effectively counteract the effects of urea. Our data
    provide the evidence that naturally occurring osmolytes can help
    to maintain Polycystin-1 mechanical stability and folding
    kinetics. This study has the potential to provide new therapeutic
    approaches (e.g. through the use of osmolytes or chemical
    chaperones) for rescuing destabilized and misfolded PKD domains.",
  language = "eng",
}

@article{ sundberg03,
  author = MSundberg #" and "# JRosengren #" and "# RBunk
    #" and "# JLindahl #" and "# INicholls #" and "# STagerud
    #" and "# POmling #" and "# LMontelius #" and "# AMansson,
  title = "Silanized surfaces for in vitro studies of actomyosin
    function and nanotechnology applications.",
  journal = ABioChem,
  year = 2003,
  month = dec,
  day = 01,
  address = "Department of Chemistry and Biomedical Sciences,
    University of Kalmar, SE-391 82 Kalmar, Sweden.",
  volume = 323,
  number = 1,
  pages = "127--138",
  keywords = "Actomyosin",
  keywords = "Adsorption",
  keywords = "Animals",
  keywords = "Collodion",
  keywords = "Kinetics",
  keywords = "Methods",
  keywords = "Movement",
  keywords = "Nanotechnology",
  keywords = "Rabbits",
  keywords = "Silicon",
  keywords = "Surface Properties",
  keywords = "Trimethylsilyl Compounds",
  abstract = "We have previously shown that selective heavy meromyosin
    (HMM) adsorption to predefined regions of nanostructured polymer
    resist surfaces may be used to produce a nanostructured in vitro
    motility assay.  However, actomyosin function was of lower quality
    than on conventional nitrocellulose films. We have therefore
    studied actomyosin function on differently derivatized glass
    surfaces with the aim to find a substitute for the polymer
    resists. We have found that surfaces derivatized with
    trimethylchlorosilane (TMCS) were superior to all other surfaces
    tested, including nitrocellulose. High-quality actin filament
    motility was observed up to 6 days after incubation with HMM and
    the fraction of motile actin filaments and the velocity of smooth
    sliding were generally higher on TMCS than on nitrocellulose. The
    actomyosin function on TMCS-derivatized glass and nitrocellulose
    is considered in relation to roughness and hydrophobicity of these
    surfaces. The results suggest that TMCS is an ideal substitute for
    polymer resists in the nanostructured in vitro motility
    assay. Furthermore, TMCS derivatized glass also seems to offer
    several advantages over nitrocellulose for HMM adsorption in the
    ordinary in /vitro motility assay.",
  ISSN = "0003-2697",
  URL = "http://www.ncbi.nlm.nih.gov/pubmed/14622967",
  doi = "10.1016/j.ab.2003.07.022",
  language = "eng",
}

@article{ itoh04,
  author = HItoh #" and "# ATakahashi #" and "# KAdachi #" and "#
    HNoji #" and "# RYasuda #" and "# MYoshida #" and "#
    KKinosita,
  title = "Mechanically driven {ATP} synthesis by {F1}-{ATP}ase.",
  journal = NAT,
  year = 2004,
  month = jan,
  day = 29,
  address = "Tsukuba Research Laboratory, Hamamatsu Photonics KK,
    Joko, Hamamatsu 431-3103, Japan.
    hiritoh@hpk.trc-net.co.jp",
  volume = 427,
  number = 6973,
  pages = "465--468",
  keywords = "Adenosine Diphosphate",
  keywords = "Adenosine Triphosphate",
  keywords = "Bacillus",
  keywords = "Catalysis",
  keywords = "Glass",
  keywords = "Magnetics",
  keywords = "Microchemistry",
  keywords = "Microspheres",
  keywords = "Molecular Motor Proteins",
  keywords = "Proton-Translocating ATPases",
  keywords = "Rotation",
  keywords = "Torque",
  abstract = "ATP, the main biological energy currency, is synthesized
    from ADP and inorganic phosphate by ATP synthase in an
    energy-requiring reaction. The F1 portion of ATP synthase, also
    known as F1-ATPase, functions as a rotary molecular motor: in
    vitro its gamma-subunit rotates against the surrounding
    alpha3beta3 subunits, hydrolysing ATP in three separate catalytic
    sites on the beta-subunits. It is widely believed that reverse
    rotation of the gamma-subunit, driven by proton flow through the
    associated F(o) portion of ATP synthase, leads to ATP synthesis in
    biological systems. Here we present direct evidence for the
    chemical synthesis of ATP driven by mechanical energy. We attached
    a magnetic bead to the gamma-subunit of isolated F1 on a glass
    surface, and rotated the bead using electrical magnets. Rotation
    in the appropriate direction resulted in the appearance of ATP in
    the medium as detected by the luciferase-luciferin reaction. This
    shows that a vectorial force (torque) working at one particular
    point on a protein machine can influence a chemical reaction
    occurring in physically remote catalytic sites, driving the
    reaction far from equilibrium.",
  ISSN = "1476-4687",
  doi = "10.1038/nature02212",
  URL = "http://www.ncbi.nlm.nih.gov/pubmed/14749837",
  language = "eng",
}

@article{ sakaki05,
  author = NSakaki #" and "# RShimoKon #" and "# KAdachi
    #" and "# HItoh #" and "# SFuruike #" and "# EMuneyuki
    #" and "# MYoshida #" and "# KKinosita,
  title = "One rotary mechanism for {F1}-{ATP}ase over {ATP}
    concentrations from millimolar down to nanomolar.",
  journal = BPJ,
  year = 2005,
  month = mar,
  day = 30,
  address = "Department of Functional Molecular Science, The Graduate
    University for Advanced Studies, Nishigonaka 38, Myodaiji, Okazaki
    444-8585, Japan.",
  volume = 88,
  number = 3,
  pages = "2047--2056",
  keywords = "Adenosine Triphosphate",
  keywords = "Hydrolysis",
  keywords = "Kinetics",
  keywords = "Microchemistry",
  keywords = "Molecular Motor Proteins",
  keywords = "Nanostructures",
  keywords = "Protein Binding",
  keywords = "Protein Conformation",
  keywords = "Proton-Translocating ATPases",
  keywords = "Rotation",
  keywords = "Torque",
  abstract = "F(1)-ATPase is a rotary molecular motor in which the
    central gamma-subunit rotates inside a cylinder made of
    alpha(3)beta(3)-subunits. The rotation is driven by ATP hydrolysis
    in three catalytic sites on the beta-subunits. How many of the
    three catalytic sites are filled with a nucleotide during the
    course of rotation is an important yet unsettled question. Here we
    inquire whether F(1) rotates at extremely low ATP concentrations
    where the site occupancy is expected to be low. We observed under
    an optical microscope rotation of individual F(1) molecules that
    carried a bead duplex on the gamma-subunit. Time-averaged rotation
    rate was proportional to the ATP concentration down to 200 pM,
    giving an apparent rate constant for ATP binding of 2 x 10(7)
    M(-1)s(-1). A similar rate constant characterized bulk ATP
    hydrolysis in solution, which obeyed a simple Michaelis-Menten
    scheme between 6 mM and 60 nM ATP. F(1) produced the same torque
    of approximately 40 pN.nm at 2 mM, 60 nM, and 2 nM ATP.  These
    results point to one rotary mechanism governing the entire range
    of nanomolar to millimolar ATP, although a switchover between two
    mechanisms cannot be dismissed. Below 1 nM ATP, we observed less
    regular rotations, indicative of the appearance of another
    reaction scheme.",
  ISSN = "0006-3495",
  doi = "10.1529/biophysj.104.054668",
  URL = "http://www.ncbi.nlm.nih.gov/pubmed/15626703",
  language = "eng",
}

@article{ schmidt02,
  author = JSchmidt #" and "# XJiang #" and "# CMontemagno,
  title = "Force Tolerances of Hybrid Nanodevices",
  journal = NANO,
  volume = 2,
  number = 11,
  pages = "1229--1233",
  year = 2002,
  doi = "10.1021/nl025773v",
  URL = "http://pubs.acs.org/doi/abs/10.1021/nl025773v",
  eprint = "http://pubs.acs.org/doi/pdf/10.1021/nl025773v",
  abstract = "We have created hybrid devices consisting of nanoscale
    fabricated inorganic components integrated with and powered by a
    genetically engineered motor protein. We wish to increase the
    assembly yield and lifetime of these devices through
    identification, measurement, and improvement of weak internal
    bonds. Using dynamic force spectroscopy, we have measured the bond
    rupture force of (histidine)\textsubscript{6} on a number of
    different surfaces as a function of loading rate. The bond sizes,
    lifetimes, and energy barrier heights were derived from these
    measurements. We compare the (His)\textsubscript{6}--nickel bonds
    to other bonds composing the hybrid device and describe
    preliminary measurements of the force tolerances of the protein
    itself. Pathways for improvement of device longevity and
    robustness are discussed.",
}

@article{ lo01,
  author = YSLo #" and "# YJZhu #" and "# TBeebe,
  title = "Loading-Rate Dependence of Individual Ligand−Receptor
    Bond-Rupture Forces Studied by Atomic Force Microscopy",
  journal = LANG,
  volume = 17,
  number = 12,
  pages = "3741--3748",
  year = 2001,
  doi = "10.1021/la001569g",
  URL = "http://pubs.acs.org/doi/abs/10.1021/la001569g",
  eprint = "http://pubs.acs.org/doi/pdf/10.1021/la001569g",
  abstract = "It is known that bond strength is a dynamic property
    that is dependent upon the force loading rate applied during the
    rupturing of a bond. For biotin--avidin and biotin--streptavidin
    systems, dynamic force spectra, which are plots of bond strength
    vs loge(loading rate), have been acquired in a recent biomembrane
    force probe (BFP) study at force loading rates in the range
    0.05--60 000 pN/s. In the present study, the dynamic force spectrum
    of the biotin--streptavidin bond strength in solution was extended
    from loading rates of ∼104 to ∼107 pN/s with the atomic force
    microscope (AFM). A Poisson statistical analysis method was
    applied to extract the magnitude of individual bond-rupture forces
    and nonspecific interactions from the AFM force--distance curve
    measurements. The bond strengths were found to scale linearly with
    the logarithm of the loading rate. The nonspecific interactions
    also exhibited a linear dependence on the logarithm of loading
    rate, although not increasing as rapidly as the specific
    interactions. The dynamic force spectra acquired here with the AFM
    combined well with BFP measurements by Merkel et al. The combined
    spectrum exhibited two linear regimes, consistent with the view
    that multiple energy barriers are present along the unbinding
    coordinate of the biotin--streptavidin complex. This study
    demonstrated that unbinding forces measured by different
    techniques are in agreement and can be used together to obtain a
    dynamic force spectrum covering 9 orders of magnitude in loading
    rate.",
  note = "These guys seem to be pretty thorough, give this one another read.",
}

@article{ baljon96,
  author = ABaljon #" and "# MRobbins,
  title = "Energy Dissipation During Rupture of Adhesive Bonds",
  journal = SCI,
  volume = 271,
  number = 5248,
  pages = "482--484",
  year = 1996,
  month = jan,
  doi = "10.1126/science.271.5248.482",
  URL = "http://www.sciencemag.org/content/271/5248/482.abstract",
  eprint = "http://www.sciencemag.org/content/271/5248/482.full.pdf",
  abstract = "Molecular dynamics simulations were used to study
    energy-dissipation mechanisms during the rupture of a thin
    adhesive bond formed by short chain molecules. The degree of
    dissipation and its velocity dependence varied with the state of
    the film. When the adhesive was in a liquid phase, dissipation was
    caused by viscous loss. In glassy films, dissipation occurred
    during a sequence of rapid structural rearrangements. Roughly
    equal amounts of energy were dissipated in each of three types of
    rapid motion: cavitation, plastic yield, and bridge rupture. These
    mechanisms have similarities to nucleation, plastic flow, and
    crazing in commercial polymeric adhesives.",
}

@article{ fisher99a,
  author = TEFisher #" and "# PMarszalek #" and "# AOberhauser
    #" and "# MCarrionVazquez #" and "# JFernandez,
  title = "The micro-mechanics of single molecules studied with
    atomic force microscopy.",
  journal = JPhysio,
  year = 1999,
  month = oct,
  day = 01,
  address = "Department of Physiology and Biophysics, Mayo Foundation,
    1-117 Medical Sciences Building, Rochester, MN 55905, USA.",
  volume = "520 Pt 1",
  pages = "5--14",
  keywords = "Animals",
  keywords = "Extracellular Matrix",
  keywords = "Extracellular Matrix Proteins",
  keywords = "Humans",
  keywords = "Microscopy, Atomic Force",
  keywords = "Polysaccharides",
  abstract = "The atomic force microscope (AFM) in its force-measuring
    mode is capable of effecting displacements on an angstrom scale
    (10 A = 1 nm) and measuring forces of a few piconewtons. Recent
    experiments have applied AFM techniques to study the mechanical
    properties of single biological polymers.  These properties
    contribute to the function of many proteins exposed to mechanical
    strain, including components of the extracellular matrix
    (ECM). The force-bearing proteins of the ECM typically contain
    multiple tandem repeats of independently folded domains, a common
    feature of proteins with structural and mechanical
    roles. Polysaccharide moieties of adhesion glycoproteins such as
    the selectins are also subject to strain. Force-induced extension
    of both types of molecules with the AFM results in conformational
    changes that could contribute to their mechanical function. The
    force-extension curve for amylose exhibits a transition in
    elasticity caused by the conversion of its glucopyranose rings
    from the chair to the boat conformation. Extension of multi-domain
    proteins causes sequential unraveling of domains, resulting in a
    force-extension curve displaying a saw tooth pattern of peaks. The
    engineering of multimeric proteins consisting of repeats of
    identical domains has allowed detailed analysis of the mechanical
    properties of single protein domains. Repetitive extension and
    relaxation has enabled direct measurement of rates of domain
    unfolding and refolding. The combination of site-directed
    mutagenesis with AFM can be used to elucidate the amino acid
    sequences that determine mechanical stability. The AFM thus offers
    a novel way to explore the mechanical functions of proteins and
    will be a useful tool for studying the micro-mechanics of
    exocytosis.",
  ISSN = "0022-3751",
  URL = "http://www.ncbi.nlm.nih.gov/pubmed/10517795",
  language = "eng",
}

@article{ fisher99b,
  author = TEFisher #" and "# AOberhauser #" and "# MCarrionVazquez
    #" and "# PMarszalek #" and "# JFernandez,
  title = "The study of protein mechanics with the atomic force microscope.",
  journal = "Trends in biochemical sciences",
  year = "1999",
  month = oct,
  address = "Dept of Physiology and Biophysics, Mayo Foundation, 1-117
    Medical Sciences Building, Rochester, MN 55905, USA.",
  volume = 24,
  number = 10,
  pages = "379--384",
  keywords = "Entropy",
  keywords = "Kinetics",
  keywords = "Microscopy, Atomic Force",
  keywords = "Protein Binding",
  keywords = "Protein Folding",
  keywords = "Proteins",
  abstract = "The unfolding and folding of single protein molecules
    can be studied with an atomic force microscope (AFM).  Many
    proteins with mechanical functions contain multiple, individually
    folded domains with similar structures. Protein engineering
    techniques have enabled the construction and expression of
    recombinant proteins that contain multiple copies of identical
    domains.  Thus, the AFM in combination with protein engineering
    has enabled the kinetic analysis of the force-induced unfolding
    and refolding of individual domains as well as the study of the
    determinants of mechanical stability.",
  ISSN = "0968-0004",
  URL = "http://www.ncbi.nlm.nih.gov/pubmed/10500301",
  language = "eng",
}

@article{ zlatanova00,
  author = JZlatanova #" and "# SLindsay #" and "# SLeuba,
  title = "Single molecule force spectroscopy in biology using the
    atomic force microscope.",
  journal = PBPMB,
  year = 2000,
  address = "Biochip Technology Center, Argonne National Laboratory,
    9700 South Cass Avenue, Bldg. 202-A253, Argonne, IL 60439,
    USA. jzlatano@duke.poly.edu",
  volume = 74,
  number = "1--2",
  pages = "37--61",
  keywords = "Biophysics",
  keywords = "Cell Adhesion",
  keywords = "DNA",
  keywords = "Elasticity",
  keywords = "Microscopy, Atomic Force",
  keywords = "Polysaccharides",
  keywords = "Proteins",
  keywords = "Signal Processing, Computer-Assisted",
  keywords = "Viscosity",
  abstract = "The importance of forces in biology has been recognized
    for quite a while but only in the past decade have we acquired
    instrumentation and methodology to directly measure interactive
    forces at the level of single biological macromolecules and/or
    their complexes. This review focuses on force measurements
    performed with the atomic force microscope. A general introduction
    to the principle of action is followed by review of the types of
    interactions being studied, describing the main results and
    discussing the biological implications.",
  ISSN = "0079-6107",
  URL = "http://www.ncbi.nlm.nih.gov/pubmed/11106806",
  language = "eng",
  note = "Lots of great force-clamp cartoons explaining different
    approach/retract features.",
}

@article{ viani99,
  author = MViani #" and "# TESchafer #" and "# AChand #" and "# MRief
    #" and "# HEGaub #" and "# HHansma,
  title = "Small cantilevers for force spectroscopy of single molecules",
  journal = JAP,
  year = 1999,
  volume = 86,
  number = 4,
  pages = "2258--2262",
  abstract = "We have used a simple process to fabricate small
    rectangular cantilevers out of silicon nitride. They have lengths
    of 9--50 $\mu$m, widths of 3--5 $\mu$m, and thicknesses of 86 and
    102 nm. We have added metallic reflector pads to some of the
    cantilever ends to maximize reflectivity while minimizing
    sensitivity to temperature changes. We have characterized small
    cantilevers through their thermal spectra and show that they can
    measure smaller forces than larger cantilevers with the same
    spring constant because they have lower coefficients of viscous
    damping. Finally, we show that small cantilevers can be used for
    experiments requiring large measurement bandwidths, and have used
    them to unfold single titin molecules over an order of magnitude
    faster than previously reported with conventional cantilevers.",
  ISSN = "0021-8979",
  issn_online = "1089-7550",
  doi = "10.1063/1.371039",
  URL = "http://jap.aip.org/resource/1/japiau/v86/i4/p2258_s1",
  language = "eng",
}

@article{ capitanio02,
  author = MCapitanio #" and "# GRomano #" and "# RBallerini #" and "#
    MGiuntini #" and "# FPavone #" and "# DDunlap #" and "# LFinzi,
  title = "Calibration of optical tweezers with differential
    interference contrast signals",
  journal = RSI,
  year = 2002,
  volume = 73,
  number = 4,
  pages = "1687--1696",
  abstract = "A comparison of different calibration methods for
    optical tweezers with the differential interference contrast (DIC)
    technique was performed to establish the uses and the advantages
    of each method. A detailed experimental and theoretical analysis
    of each method was performed with emphasis on the anisotropy
    involved in the DIC technique and the noise components in the
    detection. Finally, a time of flight method that permits the
    reconstruction of the optical potential well was demonstrated.",
  ISSN = "0034-6748",
  issn_online = "1089-7623",
  doi = "10.1063/1.1460929",
  URL = "http://rsi.aip.org/resource/1/rsinak/v73/i4/p1687_s1",
  language = "eng",
}

@article{ binnig86,
  author = GBinnig #" and "# CQuate #" and "# CGerber,
  title = "Atomic force microscope",
  journal = PRL,
  year = 1986,
  month = mar,
  day = 03,
  volume = 56,
  number = 9,
  pages = "930--933",
  abstract = "The scanning tunneling microscope is proposed as a
    method to measure forces as small as $10^{-18}$ N. As one
    application for this concept, we introduce a new type of
    microscope capable of investigating surfaces of insulators on an
    atomic scale. The atomic force microscope is a combination of the
    principles of the scanning tunneling microscope and the stylus
    profilometer. It incorporates a probe that does not damage the
    surface. Our preliminary results in air demonstrate a lateral
    resolution of 30 \AA and a vertical resolution less than 1 \AA.",
  ISSN = "1079-7114",
  doi = "10.1103/PhysRevLett.56.930",
  URL = "http://www.ncbi.nlm.nih.gov/pubmed/10033323",
  eprint = {http://prl.aps.org/pdf/PRL/v56/i9/p930_1},
  language = "eng",
  note = "Original AFM paper.",
}

@article{ drake89,
  author = BDrake #" and "# CBPrater #" and "# ALWeisenhorn #" and "#
    SAGould #" and "# TRAlbrecht #" and "# CQuate #" and "#
    DSCannell #" and "# HHansma #" and "# PHansma,
  title = {Imaging crystals, polymers, and processes in water with the
    atomic force microscope},
  year = 1989,
  month = mar,
  day = 24,
  journal = SCI,
  volume = 243,
  number = 4898,
  pages = {1586--1589},
  doi = {10.1126/science.2928794},
  url = {http://www.sciencemag.org/content/243/4898/1586.abstract},
  eprint = {http://www.sciencemag.org/content/243/4898/1586.full.pdf},
  abstract ={The atomic force microscope (AFM) can be used to image
    the surface of both conductors and nonconductors even if they are
    covered with water or aqueous solutions. An AFM was used that
    combines microfabricated cantilevers with a previously described
    optical lever system to monitor deflection. Images of mica
    demonstrate that atomic resolution is possible on rigid materials,
    thus opening the possibility of atomic-scale corrosion experiments
    on nonconductors. Images of polyalanine, an amino acid polymer,
    show the potential of the AFM for revealing the structure of
    molecules important in biology and medicine. Finally, a series of
    ten images of the polymerization of fibrin, the basic component of
    blood clots, illustrate the potential of the AFM for revealing
    subtle details of biological processes as they occur in real
    time.},
}

@article{ radmacher92,
  author = MRadmacher #" and "# RWTillmann #" and "# MFritz #" and "# HEGaub,
  title = {From molecules to cells: imaging soft samples with the
    atomic force microscope},
  year = 1992,
  month = sep,
  day = 25,
  journal = SCI,
  volume = 257,
  number = 5078,
  pages = {1900--1905},
  doi = {10.1126/science.1411505},
  url = {http://www.sciencemag.org/content/257/5078/1900.abstract},
  eprint = {http://www.sciencemag.org/content/257/5078/1900.full.pdf},
  abstract ={Since its invention a few years ago, the atomic force microscope has become one of the most widely used near-field microscopes. Surfaces of hard sample are imaged routinely with atomic resolution. Soft samples, however, remain challenging. An overview is presented on the application of atomic force microscopy to organic samples ranging from thin ordered films at molecular resolution to living cells. Fundamental mechanisms of the image formation are discussed, and novel imaging modes are introduced that exploit different aspects of the tip-sample interaction for local measurements of the micromechanical properties of the sample. As examples, images of Langmuir-Blodgett films, which map the local viscoelasticity as well as the friction coefficient, are presented.},
}

@article{ williams86,
  author = CCWilliams #" and "# HKWickramasinghe,
  title = "Scanning thermal profiler",
  journal = APL,
  year = 1986,
  month = dec,
  day = 8,
  volume = 49,
  number = 23,
  pages = "1587--1589",
  abstract = "A new high-resolution profilometer has been demonstrated
    based upon a noncontacting near-field thermal probe. The thermal
    probe consists of a thermocouple sensor with dimensions
    approaching 100 nm. Profiling is achieved by scanning the heated
    sensor above but close to the surface of a solid. The conduction
    of heat between tip and sample via the air provides a means for
    maintaining the sample spacing constant during the lateral
    scan. The large difference in thermal properties between air and
    solids makes the profiling technique essentially independent of
    the material properties of the solid. Noncontact profiling of
    resist and metal films has shown a lateral resolution of 100 nm
    and a depth solution of 3 nm. The basic theory of the new probe is
    described and the results presented.",
  issn = "0003-6951",
  issn_online = "1077-3118",
  doi = "10.1063/1.97288",
  URL = "http://apl.aip.org/resource/1/applab/v49/i23/p1587_s1",
  language = "eng",
}

@article{ meyer88,
  author = GMeyer #" and "# NMAmer,
  title = "Novel optical approach to atomic force microscopy",
  journal = APL,
  year = 1988,
  month = sep,
  day = 19,
  volume = 53,
  number = 12,
  pages = "1045--1047",
  abstract = "A sensitive and simple optical method for detecting the
    cantilever deflection in atomic force microscopy is described. The
    method was incorporated in an atomic force microscope, and imaging
    and force measurements, in ultrahigh vacuum, were successfully
    performed.",
  issn = "0003-6951",
  issn_online = "1077-3118",
  doi = "10.1063/1.100061",
  URL = "http://apl.aip.org/resource/1/applab/v53/i12/p1045_s1",
  language = "eng",
}

@book{ dijkstra70,
  author = EDijkstra,
  title = {Notes on Structured Programming},
  year = 1970,
  month = apr,
  url = {http://www.cs.utexas.edu/users/EWD/ewd02xx/EWD249.PDF},
  publisher = THEMath,
  note = {T.H. Report 70-WSK-03},
}

@article{ wirth74,
 author = NWirth,
 title = {On the Composition of Well-Structured Programs},
 journal = ACM:CSur,
 year = 1974,
 month = dec,
 volume = 6,
 number = 4,
 pages = {247--259},
 numpages = {13},
 issn = {0360-0300},
 doi = {10.1145/356635.356639},
 url = {http://doi.acm.org/10.1145/356635.356639},
 publisher = ACM,
 address = {New York, NY, USA},
}

@article{ shneiderman79,
  author = BShneiderman #" and "# RMayer,
  title = {Syntactic/semantic interactions in programmer behavior: A
    model and experimental results},
  year = 1979,
  journal = IJCIS,
  volume = 8,
  number = 3,
  pages = {219--238},
  issn = {0091-7036},
  doi = {10.1007/BF00977789},
  url = {http://dx.doi.org/10.1007/BF00977789},
  publisher = KAPPP,
  keywords = {Programming; programming languages; cognitive models;
    program composition; program comprehension; debugging;
    modification; learning; education; information processing},
  language = {English},
}

@article{ hughes89,
  author = JHughes,
  title = {Why Functional Programming Matters},
  journal = CJ,
  year = 1989,
  volume = 32,
  number = 2,
  pages = {98--107},
  doi = {10.1093/comjnl/32.2.98},
  URL = {http://comjnl.oxfordjournals.org/content/32/2/98.abstract},
  eprint = {http://comjnl.oxfordjournals.org/content/32/2/98.full.pdf+html},
  abstract ={As software becomes more and more complex, it is more and
    more important to structure it well. Well-structured software is
    easy to write, easy to debug, and provides a collection of modules
    that can be re-used to reduce future programming
    costs. Conventional languages place conceptual limits on the way
    problems can be modularised. Functional languages push those
    limits back. In this paper we show that two features of functional
    languages in particular, higher-order functions and lazy
    evaluation, can contribute greatly to modularity. As examples, we
    manipulate lists and trees, program several numerical algorithms,
    and implement the alpha-beta heuristics (an Artificial
    Intelligence algorithm used in game-playing programs). Since
    modularity is the key to successful programming, functional
    languages are vitally important to the real world.},
}

@article{ hilburn93,
 author = THilburn,
 title = {A top-down approach to teaching an introductory computer science course},
 journal = ACM:SIGCSE,
 year = 1993,
 month = mar,
 volume = 25,
 number = 1,
 issn = {0097-8418},
 pages = {58--62},
 numpages = 5,
 doi = {10.1145/169073.169349},
 url = {http://doi.acm.org/10.1145/169073.169349},
 acmid = {169349},
 publisher = ACM,
 address = {New York, NY, USA},
}

@book{ brooks95,
  author = FBrooks,
  title = {The mythical man-month},
  edition = {20$^\text{th}$ anniversary},
  year = 1995,
  isbn = {0-201-83595-9},
  publisher = AW,
  address = {Boston, MA, USA},
  url = {http://dl.acm.org/citation.cfm?id=207583},
  note = {First published in 1975},
}

@inproceedings{ claerbout92,
  author = JClaerbout #" and "# MKarrenbach,
  title = {Electronic documents give reproducible research a new meaning},
  booktitle = {SEG Technical Program Expanded Abstracts 1992},
  chapter = 161,
  year = 1992,
  pages = {601--604},
  doi = {10.1190/1.1822162},
  issn = {1052-3812},
  publisher = SEG,
  url = {http://library.seg.org/doi/abs/10.1190/1.1822162},
  eprint = {http://sepwww.stanford.edu/doku.php?id=sep:research:reproducible:seg92},
}

@incollection{ buckheit95,
  author = JBuckheit #" and "# DDonoho,
  title = {WaveLab and Reproducible Research},
  booktitle = {Wavelets and Statistics},
  series = {Lecture Notes in Statistics},
  editor = AAntoniadis #" and "# GOppenheim,
  year = 1995,
  volume = 103,
  pages = {55--81},
  isbn = {978-0-387-94564-4},
  doi = {10.1007/978-1-4612-2544-7_5},
  url = {http://dx.doi.org/10.1007/978-1-4612-2544-7_5},
  eprint = {http://www-stat.stanford.edu/~wavelab/Wavelab_850/wavelab.pdf},
  publisher = SPRINGER,
  language = {English},
}

@article{ schwab00,
  author = MSchwab #" and "# MKarrenbach #" and "# JClaerbout,
  title = {Making scientific computations reproducible},
  journal = CSE,
  year = 2000,
  month = {November--December},
  volume = 2,
  number = 6,
  pages = {61--67},
  doi = {10.1109/5992.881708},
  ISSN = {1521-9615},
  keywords = {document handling;file organisation;natural sciences
    computing;research and development
    management;ReDoc;authors;computational results;reproducible
    scientific computations;research paper;software filing
    system;standardized rules;Computer
    interfaces;Documentation;Electronic
    publishing;Laboratories;Organizing;Reproducibility of
    results;Software maintenance;Software systems;Software
    testing;Technological innovation},
  abstract = {To verify a research paper's computational results,
    readers typically have to recreate them from scratch. ReDoc is a
    simple software filing system for authors that lets readers easily
    reproduce computational results using standardized rules and
    commands},
}

@article{ wilson06a,
  author = GWilson,
  title = {Where's the Real Bottleneck in Scientific Computing?},
  journal = AS,
  year = 2006,
  month = {January--February},
}

@article{ wilson06b,
  author = GWilson ,
  title = {Software Carpentry: Getting Scientists to Write Better
    Code by Making Them More Productive},
  journal = CSE,
  year = 2006,
  month = {November--December},
}

@article{ vandewalle09,
  author = PVandewalle #" and "# JKovacevic #" and "# MVetterli ,
  title = {Reproducible Research in Signal Processing - What, why, and how},
  journal = IEEE:SPM,
  year = 2009,
  month = may,
  volume = 26,
  number = 3,
  pages = {37--47},
  doi = {10.1109/MSP.2009.932122},
  issn = {1053-5888},
  url = {http://rr.epfl.ch/17/},
  eprint = {http://rr.epfl.ch/17/1/VandewalleKV09.pdf},
  keywords={research and development;signal processing;high-quality
    reviewing process;large data set;reproducible research;signal
    processing;win-win situation;Advertising;Digital signal
    processing;Education;Programming;Reproducibility of
    results;Scholarships;Signal processing;Signal processing
    algorithms;Testing;Wikipedia},
  abstract = {Have you ever tried to reproduce the results presented
    in a research paper? For many of our current publications, this
    would unfortunately be a challenging task. For a computational
    algorithm, details such as the exact data set, initialization or
    termination procedures, and precise parameter values are often
    omitted in the publication for various reasons, such as a lack of
    space, a lack of self-discipline, or an apparent lack of interest
    to the readers, to name a few. This makes it difficult, if not
    impossible, for someone else to obtain the same results. In our
    experience, it is often even worse as even we are not always able
    to reproduce our own experiments, making it difficult to answer
    questions from colleagues about details. Following are some
    examples of e-mails we have received: ``I just read your paper
    X. It is very completely described, however I am confused by
    Y. Could you provide the implementation code to me for reference
    if possible?'' ``Hi! I am also working on a project related to
    X. I have implemented your algorithm but cannot get the same
    results as described in your paper. Which values should I use for
    parameters Y and Z?''},
}

@article{ aruliah12,
  author = DAruliah #" and "# CTBrown #" and "# MPCHong #" and "#
    MDavis #" and "# RTGuy #" and "# SHaddock #" and "# KHuff #" and "#
    IMitchell #" and "# MPlumbley #" and "# BWaugh #" and "#
    EPWhite #" and "# GWilson #" and "# PWilson,
  title = {Best Practices for Scientific Computing},
  journal = CoRR,
  volume = {abs/1210.0530},
  year = 2012,
  month = nov,
  day = 29,
  numpages = 6,
  url = {http://arxiv.org/abs/1210.0530},
  eprint = {http://arxiv.org/pdf/1210.0530v3},
  note = {v3: Thu, 29 Nov 2012 19:28:27 GMT},
}

@article{ ziegler42,
  author = JZiegler #" and "# NNichols,
  title = {Optimum Settings for Automatic Controllers},
  journal = TASME,
  year = 1942,
  month = nov,
  volume = 64,
  pages = {759--765},
  url = {http://www.driedger.ca/Z-N/Z-N.html},
  eprint = {http://www.driedger.ca/Z-N/Z-n.pdf},
}

@article{ cohen53,
  author = GHCohen #" and "# GACoon,
  title = {Theoretical considerations of retarded control},
  year = 1953,
  journal = TASME,
  volume = 75,
  pages = {827--834},
}

@article{ wang95,
  author = FSWang #" and "# WSJuang #" and "# CTChan,
  title = {Optimal tuning of {PID} controllers for single and
    cascade control loops},
  year = 1995,
  journal = CEC,
  volume = 132,
  number = 1,
  pages = {15--34},
  publisher = GordonBreach,
  issn = {0098-6445},
  doi = {10.1080/00986449508936294},
  url = {http://www.tandfonline.com/doi/abs/10.1080/00986449508936294},
  keywords = {process control; cascade control; controller tuning},
  abstract = {Design of one parameter tuning of three-mode PID
    controller was developed in this present study. The integral time
    and the derivative time of the controller were expressed in terms
    of the time constant and dead time of the process. Only the
    proportional gain was observed to be dependent on the implemented
    tunable parameter in which the stable region could be
    predetermined by the Routh test. Extension of the concept towards
    designing cascade PID controllers was straightforward such that
    only two parameters for the inner and outer PID controllers
    required to be tuned, respectively. The optimal tuning correlative
    formulas of the proportional gain for single and cascade control
    systems were obtained by the least square regression method.},
}

@article{ astrom93,
  author = KAstrom #" and "# THagglund #" and "# CCHang #" and "# WKHo,
  title = {Automatic tuning and adaptation for {PID} controllers---a survey},
  journal = CEP,
  year = 1993,
  volume = 1,
  number = 4,
  pages = {699--714},
  issn = "0967-0661",
  doi = "10.1016/0967-0661(93)91394-C",
  url = "http://www.sciencedirect.com/science/article/pii/096706619391394C",
  keywords = {Adaptive control},
  keywords = {automatic tuning},
  keywords = {gain scheduling},
  keywords = {{PID} control},
  abstract = {Adaptive techniques such as gain scheduling, automatic
    tuning and continuous adaptation have been used in industrial
    single-loop controllers for about ten years. This paper gives a
    survey of the different adaptive techniques, the underlying
    process models and control designs. An overview of industrial
    products is also presented, which includes a fairly detailed
    investigation of four different adaptive single-loop
    controllers.},
}

@article{ ku66,
  author = HHKu,
  title = {Notes on the use of propagation of error formulas},
  year = 1966,
  month = oct,
  journal = JRNBS:C,
  volume = {70C},
  number = 4,
  pages = {263--273},
  publisher = NBS,
  issn = {0022-4316},
  url = {http://nistdigitalarchives.contentdm.oclc.org/cdm/compoundobject/collection/p13011coll6/id/78003/rec/5},
  eprint = {http://nistdigitalarchives.contentdm.oclc.org/utils/getfile/collection/p13011coll6/id/78003/filename/print/page/download},
  keywords = {Approximation; error; formula; imprecision; law of
    error; products; propagation of error; random; ratio; systematic;
    sum},
  abstract = {The ``law of propagation of error'' is a tool that
    physical scientists have conveniently and frequently used in their
    work for many years, yet an adequate reference is difficult to
    find. In this paper an expository review of this topic is
    presented, particularly in the light of current practices and
    interpretations. Examples on the accuracy of the approximations
    are given. The reporting of the uncertainties of final results is
    discussed.},
}

@article{ livadaru03,
  author = LLivadaru #" and "# RRNetz #" and "# HJKreuzer,
  title = {Stretching Response of Discrete Semiflexible Polymers},
  year = 2003,
  month = apr,
  day = 25,
  journal = Macromol,
  volume = 36,
  number = 10,
  pages = {3732--3744},
  doi = {10.1021/ma020751g},
  URL = {http://pubs.acs.org/doi/abs/10.1021/ma020751g},
  eprint = {http://pubs.acs.org/doi/pdf/10.1021/ma020751g},
  abstract = {We demonstrate that semiflexible polymer chains
    (characterized by a persistence length $l$) made up of discrete
    segments or bonds of length $b$ show at large stretching forces a
    crossover from the standard wormlike chain (WLC) behavior to a
    discrete-chain (DC) behavior. In the DC regime, the stretching
    response is independent of the persistence length and shows a
    different force dependence than in the WLC regime. We perform
    extensive transfer-matrix calculations for the force-response of a
    freely rotating chain (FRC) model as a function of varying bond
    angle $\gamma$ (and thus varying persistence length) and chain
    length. The FRC model is a first step toward the understanding of
    the stretching behavior of synthetic polymers, denatured proteins,
    and single-stranded DNA under large tensile forces. We also
    present scaling results for the force response of the elastically
    jointed chain (EJC) model, that is, a chain made up of freely
    jointed bonds that are connected by joints with some bending
    stiffness; this is the discretized version of the continuum WLC
    model. The EJC model might be applicable to stiff biopolymers such
    as double-stranded DNA or Actin. Both models show a similar
    crossover from the WLC to the DC behavior, which occurs at a force
    $f/k_BT\sim l/b^2$ and is thus (for polymers with a moderately
    large persistence length) in the piconewton range probed in many
    AFM experiments. We also give a heuristic simple function for the
    force--distance relation of a FRC, valid in the global force
    range, which can be used to fit experimental data. Our findings
    might help to resolve the discrepancies encountered when trying to
    fit experimental data for the stretching response of polymers in a
    broad force range with a single effective persistence length.},
  note = {There are two typos in \fref{equation}{46}.
    \citet{livadaru03} have
    \begin{equation}
      \frac{R_z}{L} = \begin{cases}
          \frac{fa}{3k_BT}  &  \frac{fb}{k_BT} < \frac{b}{l} \\
          1 - \p({\frac{fl}{4k_BT}})^{-0.5}
            &  \frac{b}{l} < \frac{fb}{k_BT} < \frac{l}{b} \\
          1 - \p({\frac{fb}{ck_BT}})^{-1}  &  \frac{1}{b} < \frac{fb}{k_BT} \;,
        \end{cases}
    \end{equation}
    but the correct formula is
    \begin{equation}
      \frac{R_z}{L} = \begin{cases}
          \frac{fa}{3k_BT}  &  \frac{fb}{k_BT} < \frac{b}{l} \\
          1 - \p({\frac{4fl}{k_BT}})^{-0.5}
            &  \frac{b}{l} < \frac{fb}{k_BT} < \frac{l}{b} \\
          1 - \p({\frac{cfb}{k_BT}})^{-1}  &  \frac{1}{b} < \frac{fb}{k_BT} \;,
        \end{cases}
    \end{equation}
    with both the $4$ and the $c$ moved into their respective
    numerators.  I pointed these errors out to Roland Netz in 2012,
    along with the fact that even with the corrected formula there is
    a discontinuity between the low- and moderate-force regimes.  Netz
    confirmed the errors, and pointed out that the discontinuity is
    because \fref{equation}{46} only accounts for the scaling (without
    prefactors).  Unfortunately, there does not seem to be a published
    erratum pointing out the error and at least \citet{puchner08} have
    quoted the incorrect form.},
}

@misc{ punias,
  author = PCarl #" and "# PDalhaimer,
  title = {{PUNIAS}: Protein Unfolding and Nano-indentation Analysis
    Software},
  year = 2005,
  month = oct,
  day = 13,
  note = {4 Int. Workshop, Scanning Probe Microscopy in Life Sciences},
  address = {Berlin},
  url = {http://punias.voila.net/},
}

@article{ carl08,
  author = PCarl #" and "# HSchillers,
  title = {Elasticity measurement of living cells with an atomic force
    microscope: data acquisition and processing.},
  year = 2008,
  month = nov,
  day = 15,
  address = {Institute of Physiology II, University of M{\"u}nster,
             Robert-Koch-Str. 27b, 48149, M{\"u}nster, Germany.},
  journal = PA,
  volume = 457,
  number = 2,
  pages = {551--559},
  issn = {0031-6768},
  doi = {10.1007/s00424-008-0524-3},
  url = {http://www.ncbi.nlm.nih.gov/pubmed/18481081},
  language = {eng},
  keywords = {Animals},
  keywords = {Biomechanics},
  keywords = {CHO Cells},
  keywords = {Cricetinae},
  keywords = {Cricetulus},
  keywords = {Cystic Fibrosis Transmembrane Conductance Regulator},
  keywords = {Elastic Modulus},
  keywords = {Equipment Design},
  keywords = {Microscopy, Atomic Force},
  keywords = {Models, Biological},
  keywords = {Reproducibility of Results},
  keywords = {Signal Processing, Computer-Assisted},
  keywords = {Transfection},
  abstract = {Elasticity of living cells is a parameter of increasing
    importance in cellular physiology, and the atomic force microscope
    is a suitable instrument to quantitatively measure it. The
    principle of an elasticity measurement is to physically indent a
    cell with a probe, to measure the applied force, and to process
    this force-indentation data using an appropriate model. It is
    crucial to know what extent the geometry of the indenting probe
    influences the result. Therefore, we indented living Chinese
    hamster ovary cells at 37 degrees C with sharp tips and colloidal
    probes (spherical particle tips) of different sizes and
    materials. We furthermore developed an implementation of the Hertz
    model, which simplifies the data processing. Our results show (a)
    that the size of the colloidal probe does not influence the result
    over a wide range (radii $0.5$-$26\U{$\mu$m}$) and (b) indenting
    cells with sharp tips results in higher Young's moduli
    (approximately $1,300\U{Pa}$) than using colloidal probes
    (approximately $400\U{Pa}$).},
  note = {Mentions \citetalias{punias} as if it was in-house software,
    which makes sense because Philippe Carl seems to be a major author.},
}

@article{ struckmeier08,
  author = JStruckmeier #" and "# RWahl #" and "# MLeuschner #" and "#
    JNunes #" and "# HJanovjak #" and "# UGeisler #" and "#
    GHofmann #" and "# TJahnke #" and "# DJMuller,
  title = {Fully automated single-molecule force spectroscopy for
    screening applications},
  year = 2008,
  month = sep,
  day = 24,
  address = {Cellular Machines, Biotechnology Center,
             Technische Universit{\"a}t Dresden, Tatzberg 47, D-01307
             Dresden, Germany},
  journal = NT,
  volume = 19,
  number = 38,
  pages = 384020,
  issn = {0957-4484},
  doi = {10.1088/0957-4484/19/38/384020},
  url = {http://www.ncbi.nlm.nih.gov/pubmed/21832579},
  language = {eng},
  abstract = {With the introduction of single-molecule force
    spectroscopy (SMFS) it has become possible to directly access the
    interactions of various molecular systems. A bottleneck in
    conventional SMFS is collecting the large amount of data required
    for statistically meaningful analysis. Currently, atomic force
    microscopy (AFM)-based SMFS requires the user to tediously `fish'
    for single molecules. In addition, most experimental and
    environmental conditions must be manually adjusted.  Here, we
    developed a fully automated single-molecule force
    spectroscope. The instrument is able to perform SMFS while
    monitoring and regulating experimental conditions such as buffer
    composition and temperature.  Cantilever alignment and calibration
    can also be automatically performed during experiments. This,
    combined with in-line data analysis, enables the instrument, once
    set up, to perform complete SMFS experiments autonomously.},
  note = {An advertisement for JPK's \citetalias{force-robot}.},
}

@article{ andreopoulos11,
  author = BAndreopoulos #" and "# DLabudde,
  title = {Efficient unfolding pattern recognition in single molecule
    force spectroscopy data},
  year = 2011,
  month = jun,
  day = 06,
  address = {Department of Bioinformatics, Biotechnological Center,
             University of Technology Dresden, Dresden, Germany.
             williama@biotec.tu-dresden.de},
  journal = AMB,
  volume = 6,
  number = 1,
  pages = 16,
  issn = {1748-7188},
  doi = {10.1186/1748-7188-6-16},
  url = {http://www.ncbi.nlm.nih.gov/pubmed/21645400},
  language = {eng},
  abstract = {Single-molecule force spectroscopy (SMFS) is a technique
    that measures the force necessary to unfold a protein. SMFS
    experiments generate Force-Distance (F-D) curves. A statistical
    analysis of a set of F-D curves reveals different unfolding
    pathways. Information on protein structure, conformation,
    functional states, and inter- and intra-molecular interactions can
    be derived.},
}

@book{ turnbull59,
  editor = HWTurnbull,
  author = INewton,
  title = {The correspondence of Isaac Newton},
  year = 1959,
  publisher = RSUP,
  volume = 1,
  numpages = 445,
  url = {http://books.google.com/books?id=pr8WAQAAMAAJ},
  note = {The ``Giants'' quote is on page 416, in a letter to Robert
    Hooke dated February 5, 1676.},
}

@book{ whitehead11,
  author = ANWhitehead,
  title = {An introduction to mathematics},
  year = 1911,
  publisher = WN,
  numpages = 274,
  address = {London},
  url = {http://archive.org/details/introductiontoma00whitiala},
  note = {The ``civilization'' quote is on page 61.},
}

@article{ mlot11,
  author = NJMlot #" and "# CATovey #" and "# DLHu,
  title = {Fire ants self-assemble into waterproof rafts to survive floods},
  year = 2011,
  month = may,
  day = 10,
  address = {Schools of Mechanical Engineering, Industrial and
             Systems Engineering, and Biology,
             Georgia Institute of Technology, Atlanta, GA 30318, USA.},
  journal = PNAS,
  volume = 108,
  number = 19,
  pages = {7669--7673},
  issn = {1091-6490},
  doi = {10.1073/pnas.1016658108},
  url = {http://www.ncbi.nlm.nih.gov/pubmed/21518911},
  language = {eng},
  keywords = {Animals},
  keywords = {Ants},
  keywords = {Behavior, Animal},
  keywords = {Biophysical Phenomena},
  keywords = {Floods},
  keywords = {Hydrophobic and Hydrophilic Interactions},
  keywords = {Microscopy, Electron, Scanning},
  keywords = {Models, Biological},
  keywords = {Social Behavior},
  keywords = {Surface Properties},
  keywords = {Time-Lapse Imaging},
  keywords = {Video Recording},
  keywords = {Water},
  abstract = {Why does a single fire ant \species{Solenopsis invicta}
    struggle in water, whereas a group can float effortlessly for
    days? We use time-lapse photography to investigate how fire ants
    \species{S.~invicta} link their bodies together to build
    waterproof rafts. Although water repellency in nature has been
    previously viewed as a static material property of plant leaves
    and insect cuticles, we here demonstrate a self-assembled
    hydrophobic surface. We find that ants can considerably enhance
    their water repellency by linking their bodies together, a process
    analogous to the weaving of a waterproof fabric. We present a
    model for the rate of raft construction based on observations of
    ant trajectories atop the raft.  Central to the construction
    process is the trapping of ants at the raft edge by their
    neighbors, suggesting that some ``cooperative'' behaviors may rely
    upon coercion.},
  note = {Higher resolution pictures are available at
    \url{http://antlab.gatech.edu/antlab/The_Ant_Raft.html}.},
}

@article{ chauhan97,
  author = VPChauhan #" and "# IRay #" and "# AChauhan #" and "#
    JWegiel #" and "# HMWisniewski,
  title = {Metal cations defibrillize the amyloid beta-protein fibrils.},
  year = 1997,
  month = jul,
  address = {New York State Institute for Basic Research in
             Developmental Disabilities, Staten Island 10314-6399,
             USA.},
  journal = NR,
  volume = 22,
  number = 7,
  pages = {805--809},
  issn = {0364-3190},
  url = {http://www.ncbi.nlm.nih.gov/pubmed/9232632},
  doi = {10.1023/A:1022079709085},
  language = {eng},
  keywords = {Alzheimer Disease},
  keywords = {Amyloid beta-Peptides},
  keywords = {Drug Evaluation, Preclinical},
  keywords = {Humans},
  keywords = {Metals},
  keywords = {Peptide Fragments},
  keywords = {Solubility},
  abstract = {Amyloid beta-protein (A beta) is the major constituent
    of amyloid fibrils composing beta-amyloid plaques and
    cerebrovascular amyloid in Alzheimer's disease (AD). We studied
    the effect of metal cations on preformed fibrils of synthetic A
    beta by Thioflavin T (ThT) fluorescence spectroscopy and
    electronmicroscopy (EM) in negative staining. The amount of cross
    beta-pleated sheet structure of A beta 1-40 fibrils was found to
    decrease by metal cations in a concentration-dependent manner as
    measured by ThT fluorescence spectroscopy.  The order of
    defibrillization of A beta 1-40 fibrils by metal cations was: Ca2+
    and Zn2+ (IC50 = 100 microM) > Mg3+ (IC50 = 300 microM) > Al3+
    (IC50 = 1.1 mM). EM analysis in negative staining showed that A
    beta 1-40 fibrils in the absence of cations were organized in a
    fine network with a little or no amorphous material.  The addition
    of Ca2+, Mg2+, and Zn2+ to preformed A beta 1-40 fibrils
    defibrillized the fibrils or converted them into short rods or to
    amorphous material. Al3+ was less effective, and reduced the
    fibril network by about 80\% of that in the absence of any metal
    cation. Studies with A beta 1-42 showed that this peptide forms
    more dense network of fibrils as compared to A beta 1-40. Both ThT
    fluorescence spectroscopy and EM showed that similar to A beta
    1-40, A beta 1-42 fibrils are also defibrillized in the presence
    of millimolar concentrations of Ca2+. These studies suggest that
    metal cations can defibrillize the fibrils of synthetic A beta.},
  note = {From page 806, ``The exact mechanism by which these metal
    ions affect the fibrillization of A$\beta$ is not known.''},
}

@article{ friedman05,
  author = RFriedman #" and "# ENachliel #" and "# MGutman,
  title = {Molecular dynamics of a protein surface: ion-residues
    interactions.},
  year = 2005,
  month = aug,
  day = 13,
  address = {Laser Laboratory for Fast Reactions in Biology,
             Department of Biochemistry, The George S. Wise Faculty
             for Life Sciences, Tel Aviv University, Israel.},
  journal = BPJ,
  volume = 89,
  number = 2,
  pages = {768--781},
  issn = {0006-3495},
  doi = {10.1529/biophysj.105.058917},
  url = {http://www.ncbi.nlm.nih.gov/pubmed/15894639},
  language = {eng},
  keywords = {Amino Acids},
  keywords = {Binding Sites},
  keywords = {Chlorine},
  keywords = {Computer Simulation},
  keywords = {Ions},
  keywords = {Models, Chemical},
  keywords = {Models, Molecular},
  keywords = {Motion},
  keywords = {Protein Binding},
  keywords = {Protein Conformation},
  keywords = {Ribosomal Protein S6},
  keywords = {Sodium},
  keywords = {Solutions},
  keywords = {Static Electricity},
  keywords = {Surface Properties},
  keywords = {Water},
  abstract = {Time-resolved measurements indicated that protons could
    propagate on the surface of a protein or a membrane by a special
    mechanism that enhanced the shuttle of the proton toward a
    specific site. It was proposed that a suitable location of
    residues on the surface contributes to the proton shuttling
    function.  In this study, this notion was further investigated by
    the use of molecular dynamics simulations, where Na(+) and Cl(-)
    are the ions under study, thus avoiding the necessity for quantum
    mechanical calculations.  Molecular dynamics simulations were
    carried out using as a model a few Na(+) and Cl(-) ions enclosed
    in a fully hydrated simulation box with a small globular protein
    (the S6 of the bacterial ribosome). Three independent 10-ns-long
    simulations indicated that the ions and the protein's surface were
    in equilibrium, with rapid passage of the ions between the
    protein's surface and the bulk. However, it was noted that close
    to some domains the ions extended their duration near the surface,
    thus suggesting that the local electrostatic potential hindered
    their diffusion to the bulk. During the time frame in which the
    ions were detained next to the surface, they could rapidly shuttle
    between various attractor sites located under the electrostatic
    umbrella. Statistical analysis of the molecular dynamics and
    electrostatic potential/entropy consideration indicated that the
    detainment state is an energetic compromise between attractive
    forces and entropy of dilution. The similarity between the motion
    of free ions next to a protein and the proton transfer on the
    protein's surface are discussed.},
}

@article{ friedman11,
  author = RFriedman,
  title = {Ions and the protein surface revisited: extensive molecular
    dynamics simulations and analysis of protein structures in
    alkali-chloride solutions.},
  year = 2011,
  month = jul,
  day = 28,
  address = {School of Natural Sciences, Linn{\ae}us University,
             391 82 Kalmar, Sweden. ran.friedman@lnu.se},
  journal = JPC:B,
  volume = 115,
  number = 29,
  pages = {9213--9223},
  issn = {1520-5207},
  doi = {10.1021/jp112155m},
  URL = {http://www.ncbi.nlm.nih.gov/pubmed/21688775},
  language = {eng},
  keywords = {Alkalies},
  keywords = {Amyloid},
  keywords = {Chlorides},
  keywords = {Databases, Protein},
  keywords = {Fungal Proteins},
  keywords = {HIV Protease},
  keywords = {Humans},
  keywords = {Molecular Dynamics Simulation},
  keywords = {Protein Multimerization},
  keywords = {Protein Structure, Secondary},
  keywords = {Proteins},
  keywords = {Ribosomal Protein S6},
  keywords = {Solutions},
  keywords = {Solvents},
  keywords = {Surface Properties},
  abstract = {Proteins interact with ions in various ways. The surface
    of proteins has an innate capability to bind ions, and it is also
    influenced by the screening of the electrostatic potential owing
    to the presence of salts in the bulk solution. Alkali metal ions
    and chlorides interact with the protein surface, but such
    interactions are relatively weak and often transient.  In this
    paper, computer simulations and analysis of protein structures are
    used to characterize the interactions between ions and the protein
    surface. The results show that the ion-binding properties of
    protein residues are highly variable. For example, alkali metal
    ions are more often associated with aspartate residues than with
    glutamates, whereas chlorides are most likely to be located near
    arginines. When comparing NaCl and KCl solutions, it was found
    that certain surface residues attract the anion more strongly in
    NaCl. This study demonstrates that protein-salt interactions
    should be accounted for in the planning and execution of
    experiments and simulations involving proteins, particularly if
    subtle structural details are sought after.},
}

@article{ zhang06,
  author = YZhang #" and "# PSCremer,
  title = {Interactions between macromolecules and ions: The
    {H}ofmeister series.},
  year = 2006,
  month = dec,
  day = 10,
  address = {Department of Chemistry, Texas A\&M University,
             College Station, TX 77843, USA.},
  journal = COCB,
  volume = 10,
  number = 6,
  pages = {658--663},
  issn = {1367-5931},
  doi = {10.1016/j.cbpa.2006.09.020},
  url = {http://www.ncbi.nlm.nih.gov/pubmed/17035073},
  language = {eng},
  keywords = {Acrylamides},
  keywords = {Biopolymers},
  keywords = {Solubility},
  keywords = {Thermodynamics},
  keywords = {Water},
  abstract = {The Hofmeister series, first noted in 1888, ranks the
    relative influence of ions on the physical behavior of a wide
    variety of aqueous processes ranging from colloidal assembly to
    protein folding. Originally, it was thought that an ion's
    influence on macromolecular properties was caused at least in part
    by `making' or `breaking' bulk water structure. Recent
    time-resolved and thermodynamic studies of water molecules in salt
    solutions, however, demonstrate that bulk water structure is not
    central to the Hofmeister effect.  Instead, models are being
    developed that depend upon direct ion-macromolecule interactions
    as well as interactions with water molecules in the first
    hydration shell of the macromolecule.},
  note = {A quick pass through Hofmeister history, but no discussion
    of cations (``A complete picture will inevitably involve an
    integrated understanding of the role of cations (including
    guanidinium ions) and osmolytes (such as urea and tri-methylamine
    N-oxide) as well. There has been some progress in these fields,
    although such subjects are generally beyond the scope of this
    short review.'').},
}

@article{ isaacs06,
  author = AMIsaacs #" and "# DBSenn #" and "# MYuan #" and "#
    JPShine #" and "# BAYankner,
  title = {Acceleration of amyloid beta-peptide aggregation by
    physiological concentrations of calcium.},
  year = 2006,
  month = sep,
  day = 22,
  address = {Department of Neurology and Division of Neuroscience,
             The Children's Hospital, Harvard Medical School,
             Boston, Massachusetts 02115, USA.},
  journal = JBC,
  volume = 281,
  number = 38,
  pages = {27916--27923},
  issn = {0021-9258},
  doi = {10.1074/jbc.M602061200},
  url = {http://www.ncbi.nlm.nih.gov/pubmed/16870617},
  language = {eng},
  keywords = {Alzheimer Disease},
  keywords = {Amyloid},
  keywords = {Amyloid beta-Peptides},
  keywords = {Animals},
  keywords = {Calcium},
  keywords = {Cells, Cultured},
  keywords = {Copper},
  keywords = {Neurons},
  keywords = {Rats},
  keywords = {Zinc},
  abstract = {Alzheimer disease is characterized by the accumulation
    of aggregated amyloid beta-peptide (Abeta) in the brain. The
    physiological mechanisms and factors that predispose to Abeta
    aggregation and deposition are not well understood. In this
    report, we show that calcium can predispose to Abeta aggregation
    and fibril formation. Calcium increased the aggregation of early
    forming protofibrillar structures and markedly increased
    conversion of protofibrils to mature amyloid fibrils. This
    occurred at levels 20-fold below the calcium concentration in the
    extracellular space of the brain, the site at which amyloid plaque
    deposition occurs. In the absence of calcium, protofibrils can
    remain stable in vitro for several days. Using this approach, we
    directly compared the neurotoxicity of protofibrils and mature
    amyloid fibrils and demonstrate that both species are inherently
    toxic to neurons in culture. Thus, calcium may be an important
    predisposing factor for Abeta aggregation and toxicity. The high
    extracellular concentration of calcium in the brain, together with
    impaired intraneuronal calcium regulation in the aging brain and
    Alzheimer disease, may play an important role in the onset of
    amyloid-related pathology.},
  note = {Physiological levels of \NaCl\ are $\sim 150\U{mM}$.  \Ca\
    is $\sim 2\U{mM}$.},
}

@article{ itkin11,
  author = AItkin #" and "# VDupres #" and "# YFDufrene #" and "#
    BBechinger #" and "# JMRuysschaert #" and "# VRaussens,
  title = {Calcium ions promote formation of amyloid $\beta$-peptide
    (1-40) oligomers causally implicated in neuronal toxicity of
    {A}lzheimer's disease.},
  year = 2011,
  month = mar,
  day = 28,
  address = {Laboratory of Structure and Function of Biological
             Membranes, Center for Structural Biology and
             Bioinformatics, Universit{\'e} Libre de Bruxelles,
             Brussels, Belgium.},
  journal = PLOS:ONE,
  volume = 6,
  number = 3,
  pages = {e18250},
  keywords = {Alzheimer Disease},
  keywords = {Amyloid beta-Peptides},
  keywords = {Blotting, Western},
  keywords = {Calcium},
  keywords = {Fluorescence},
  keywords = {Humans},
  keywords = {Ions},
  keywords = {Models, Biological},
  keywords = {Mutant Proteins},
  keywords = {Neurons},
  keywords = {Protein Structure, Quaternary},
  keywords = {Protein Structure, Secondary},
  keywords = {Spectroscopy, Fourier Transform Infrared},
  keywords = {Thiazoles},
  ISSN = {1932-6203},
  doi = {10.1371/journal.pone.0018250},
  URL = {http://www.ncbi.nlm.nih.gov/pubmed/21464905},
  language = {eng},
  abstract = {Amyloid $\beta$-peptide (A$\beta$) is directly linked to
    Alzheimer's disease (AD). In its monomeric form, A$\beta$
    aggregates to produce fibrils and a range of oligomers, the latter
    being the most neurotoxic.  Dysregulation of Ca(2+) homeostasis in
    aging brains and in neurodegenerative disorders plays a crucial
    role in numerous processes and contributes to cell dysfunction and
    death. Here we postulated that calcium may enable or accelerate
    the aggregation of A$\beta$. We compared the aggregation pattern
    of A$\beta$(1-40) and that of A$\beta$(1-40)E22G, an amyloid
    peptide carrying the Arctic mutation that causes early onset of
    the disease.  We found that in the presence of Ca(2+),
    A$\beta$(1-40) preferentially formed oligomers similar to those
    formed by A$\beta$(1-40)E22G with or without added Ca(2+), whereas
    in the absence of added Ca(2+) the A$\beta$(1-40) aggregated to
    form fibrils.  Morphological similarities of the oligomers were
    confirmed by contact mode atomic force microscopy imaging. The
    distribution of oligomeric and fibrillar species in different
    samples was detected by gel electrophoresis and Western blot
    analysis, the results of which were further supported by
    thioflavin T fluorescence experiments. In the samples without
    Ca(2+), Fourier transform infrared spectroscopy revealed
    conversion of oligomers from an anti-parallel $\beta$-sheet to the
    parallel $\beta$-sheet conformation characteristic of
    fibrils. Overall, these results led us to conclude that calcium
    ions stimulate the formation of oligomers of A$\beta$(1-40), that
    have been implicated in the pathogenesis of AD.},
  note = {$2\U{mM}$ of \Ca\ is the \emph{extracellular} concentration.
    Cytosol concetrations are in the $\mu$M range.},
}

@article{ zidar11,
  author = JZidar #" and "# FMerzel,
  title = {Probing amyloid-beta fibril stability by increasing ionic
    strengths.},
  year = 2011,
  month = mar,
  day = 10,
  address = {National Institute of Chemistry, Hajdrihova 19,
             SI-1000 Ljubljana, Slovenia.},
  journal = JPC:B,
  volume = 115,
  number = 9,
  pages = {2075--2081},
  issn = {1520-5207},
  doi = {10.1021/jp109025b},
  URL = {http://www.ncbi.nlm.nih.gov/pubmed/21329333},
  language = {eng},
  keywords = {Amyloid beta-Peptides},
  keywords = {Entropy},
  keywords = {Hydrogen Bonding},
  keywords = {Molecular Dynamics Simulation},
  keywords = {Osmolar Concentration},
  keywords = {Protein Multimerization},
  keywords = {Protein Stability},
  keywords = {Protein Structure, Secondary},
  keywords = {Solvents},
  keywords = {Vibration},
  abstract = {Previous experimental studies have demonstrated changing
    the ionic strength of the solvent to have a great impact on the
    mechanism of aggregation of amyloid-beta (A$\beta$) protein
    leading to distinct fibril morphology at high and low ionic
    strength. Here, we use molecular dynamics simulations to elucidate
    the ionic strength-dependent effects on the structure and dynamics
    of the model A$\beta$ fibril. The change in ionic strength was
    brought forth by varying the NaCl concentration in the environment
    surrounding the A$\beta$ fibril. Comparison of the calculated
    vibrational spectra of A$\beta$ derived from 40 ns all-atom
    molecular dynamics simulations at different ionic strength reveals
    the fibril structure to be stiffer with increasing ionic
    strength. This finding is further corroborated by the calculation
    of the stretching force constants. Decomposition of binding and
    dynamical properties into contributions from different structural
    segments indicates the elongation of the fibril at low ionic
    strength is most likely promoted by hydrogen bonding between
    N-terminal parts of the fibril, whereas aggregation at higher
    ionic strength is suggested to be driven by the hydrophobic
    interaction.},
  note = {Only study \NaCl\ over the range to $308\U{mM}$, but show a
    general decreased hydrogen bonding as concentration increases.},
}

@article{ miao11,
  author = LMiao #" and "# HQin #" and "# PKoehl #" and "# JSong,
  title = {Selective and specific ion binding on proteins at
    physiologically-relevant concentrations.},
  year = 2011,
  month = oct,
  day = 03,
  address = {Department of Biological Sciences, Faculty of Science,
             National University of Singapore, Singapore.},
  journal = FEBS,
  volume = 585,
  number = 19,
  pages = {3126--3132},
  issn = {1873-3468},
  doi = {10.1016/j.febslet.2011.08.048},
  url = {http://www.ncbi.nlm.nih.gov/pubmed/21907714},
  language = {eng},
  keywords = {Amino Acid Sequence},
  keywords = {Ephrin-B2},
  keywords = {Ions},
  keywords = {Models, Molecular},
  keywords = {Molecular Sequence Data},
  keywords = {Nuclear Magnetic Resonance, Biomolecular},
  keywords = {Protein Binding},
  keywords = {Protein Folding},
  keywords = {Protein Structure, Tertiary},
  keywords = {Salts},
  keywords = {Solutions},
  keywords = {Thermodynamics},
  keywords = {Water},
  abstract = {Insoluble proteins dissolved in unsalted water appear to
    have no well-folded tertiary structures. This raises a fundamental
    question as to whether being unstructured is due to the absence of
    salt ions. To address this issue, we solubilized the insoluble
    ephrin-B2 cytoplasmic domain in unsalted water and first confirmed
    using NMR spectroscopy that it is only partially folded. Using NMR
    HSQC titrations with 14 different salts, we further demonstrate
    that the addition of salt triggers no significant folding of the
    protein within physiologically relevant ion concentrations. We
    reveal however that their 8 anions bind to the ephrin-B2 protein
    with high affinity and specificity at biologically-relevant
    concentrations.  Interestingly, the binding is found to be both
    salt- and residue-specific.},
  note = {They suggest that for low concentrations ($<100\U{mM}$),
    protein-ion interactions are mostly electrostatic.  The Hofmeister
    effects only kick in at higher consentrations.},
}

@article{ dyson05,
  author = HJDyson #" and "# PEWright,
  title = {Intrinsically unstructured proteins and their functions.},
  journal = NRMCB,
  year = 2005,
  month = mar,
  address = {Department of Molecular Biology and Skaggs Institute
             for Chemical Biology, The Scripps Research Institute,
             10550 North Torrey Pines Road, La Jolla, California
             92037, USA. dyson@scripps.edu},
  volume = 6,
  number = 3,
  pages = {197--208},
  issn = {1471-0072},
  doi = {10.1038/nrm1589},
  url = {http://www.ncbi.nlm.nih.gov/pubmed/15738986},
  language = {eng},
  keywords = {CREB-Binding Protein},
  keywords = {Humans},
  keywords = {Nuclear Proteins},
  keywords = {Nucleic Acids},
  keywords = {Protein Binding},
  keywords = {Protein Processing, Post-Translational},
  keywords = {Protein Structure, Tertiary},
  keywords = {Proteins},
  keywords = {Trans-Activators},
  keywords = {Tumor Suppressor Protein p53},
  abstract = {Many gene sequences in eukaryotic genomes encode entire
    proteins or large segments of proteins that lack a well-structured
    three-dimensional fold. Disordered regions can be highly conserved
    between species in both composition and sequence and, contrary to
    the traditional view that protein function equates with a stable
    three-dimensional structure, disordered regions are often
    functional, in ways that we are only beginning to discover. Many
    disordered segments fold on binding to their biological targets
    (coupled folding and binding), whereas others constitute flexible
    linkers that have a role in the assembly of macromolecular
    arrays.},
}

@article{ cleland64,
  author = WWCleland,
  title = {Dithiothreitol, a New Protective Reagent for SH Groups},
  journal = Biochem,
  year = 1964,
  month = apr,
  volume = 3,
  number = 4,
  pages = {480--482},
  keywords = {Alcohols},
  keywords = {Chromatography},
  keywords = {Coenzyme A},
  keywords = {Oxidation-Reduction},
  keywords = {Research},
  keywords = {Sulfhydryl Compounds},
  keywords = {Sulfides},
  keywords = {Ultraviolet Rays},
  issn = {0006-2960},
  doi = {10.1021/bi00892a002},
  url = {http://www.ncbi.nlm.nih.gov/pubmed/14192894},
  eprint = {http://pubs.acs.org/doi/pdf/10.1021/bi00892a002},
  language = {eng},
}