Close parens in gamma calculation in manual's timescale discussion.

[sawsim.git] / src / sawsim.bib

@string{AAPT = "AAPT"}
@string{AIP = "AIP"}
@string{DAbramavicius = "Abramavicius, Darius"}
@string{SRKAinavarapu = "Ainavarapu, Sri Rama Koti"}
@string{MDAllen = "Allen, Mark D."}
@string{AJP = "American Journal of Physics"}
@string{APS = "American Physical Society"}
@string{IAndricioaei = "Andricioaei, Ioan"}
@string{DAnselmetti = "Anselmetti, D."}
@string{AMC = "Applied Mathematics and Computation"}
@string{SArcidiacono = "Arcidiacono, S."}
@string{CRArciola = "Arciola, Carla Renata"}
@string{WABaase = "Baase, Walter A."}
@string{CLBadilla = "Badilla, Carmen L."}
@string{MMBalamurali = "Balamurali, M. M."}
@string{MBalsera = "Balsera, M."}
@string{GBaneyx = "Baneyx, Gretchen"}
@string{RBar-Ziv = "Bar-Ziv, Roy"}
@string{DBarrick = "Barrick, Doug"}
@string{FWBartels = "Bartels, F. W."}
@string{BBarz = "Barz, Bogdan"}
@string{TBasche = "Basche, Th."}
@string{LBaugh = "Baugh, Loren"}
@string{JBechhoefer = "Bechhoefer, John"}
@string{GSBeddard = "Beddard, Godfrey S."}
@string{GIBell = "Bell, G. I."}
@string{VBenes = "Benes, Vladimir"}
@string{FBerkemeier = "Berkemeier, Felix"}
@string{BJBerne = "Berne, Bruce J."}
@string{MBertz = "Bertz, Morten"}
@string{RBBest = "Best, Robert B."}
@string{NBhasin = "Bhasin, Nishant"}
@string{KSBillings = "Billings, Kate S."}
@string{Biochemistry = "Biochemistry"}
@string{BiophysJ = "Biophys J"}
@string{BPS:P = "Biophysical Society Annual Meeting (Poster)"}
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@string{AWBlake = "Blake, Anthony W."}
@string{MBooth = "Booth, Michael"}
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@string{EBraverman = "Braverman, Elena"}
@string{WABreyer = "Breyer, Wendy A."}
@string{pub-NETWORK-THEORY:adr = "Bristol, UK"}
@string{DJBrockwell = "Brockwell, David J."}
@string{SEBroedel = "Broedel, Sheldon E."}
@string{BDBrower-Toland = "Brower-Toland, Brent D."}
@string{VBrumfeld = "Brumfeld, Vlad"}
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@string{BBullard = "Bullard, Belinda"}
@string{CBustamante = "Bustamante, Carlos"}
@string{YBustanji = "Bustanji, Yasser"}
@string{CUP = "Cambridge University Press"}
@string{IDCampbell = "Campbell, Iain D."}
@string{YCao = "Cao, Yi"}
@string{PCarl = "Carl, Philippe"}
@string{BACarnes = "Carnes, B. A."}
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@string{CCecconi = "Cecconi, Ciro"}
@string{ERChapman = "Chapman, Edwin R."}
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@string{JChoy = "Choy, Jason"}
@string{JClarke = "Clarke, Jane"}
@string{JClarkson = "Clarkson, John"}
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@string{GCowan = "Cowan, Glen"}
@string{DCraig = "Craig, David"}
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@string{MElbaum = "Elbaum, Michael"}
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@string{HPErickson = "Erickson, Harold P."}
@string{MEsaki = "Esaki, Masatoshi"}
@string{EEvans = "Evans, E."}
@string{MEvstigneev = "Evstigneev, M."}
@string{JMFernandez = "Fernandez, Julio M."}
@string{AEFilippov = "Filippov, A. E."}
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@string{FoldDes = "Fold Des"}
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@string{SBFowler = "Fowler, Susan B."}
@string{HFujita = "Fujita, Hideaki"}
@string{TFunck = "Funck, Theodor"}
@string{MGalassi = "Galassi, Mark"}
@string{MGao = "Gao, Mu"}
@string{TGarcia = "Garcia, Tzintzuni"}
@string{HEGaub = "Gaub, Hermann E."}
@string{MGautel = "Gautel, Mathias"}
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@string{BGough = "Gough, Brian"}
@string{HLGranzier = "Granzier, Henk L."}
@string{FGrater = "Grater, Frauke"}
@string{CGrossman = "Grossman, C."}
@string{HGrubmuller = {Grubm{\"u}ller, Helmut}}
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@string{JAHaack = "Haack, Julie A."}
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@string{FHan = "Han, Fangpu"}
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@string{PKHansma = "Hansma, Paul K."}
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@string{CKHu = "Hu, Chin-Kun"}
@string{HHHuang = "Huang, Hector H."}
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@string{WLHung = "Hung, Wen-Liang"}
@string{JLHutter = "Hutter, Jeffrey L."}
@string{CHyeon = "Hyeon, Changbong"}
@string{IJBMM = "International Journal of Biological Macromolecules"}
@string{AIrback = "Irback, Anders"}
@string{SIzrailev = "Izrailev, S."}
@string{JBiotechnol = "J Biotechnol"}
@string{JMathBiol = "J Math Biol"}
@string{JTheorBiol = "J Theor Biol"}
@string{JChemPhys = "J. Chem. Phys."}
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@string{YJia = "Jia, Yiwei"}
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@string{CPJohnson = "Johnson, Colin P."}
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@string{EJones = "Jones, Eric"}
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@string{DAJuckett = "Juckett, D. A."}
@string{GJungman = "Jungman, Gerard"}
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@string{RKapon = "Kapon, Ruti"}
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@string{MKarplus = "Karplus, Martin"}
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@string{WTKing = "King, W. Trevor"}
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@string{AKleiner = "Kleiner, Ariel"}
@string{DKKlimov = "Klimov, Dmitri K."}
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@string{AKrammer = "Krammer, Andre"}
@string{KKroy = "Kroy, Klaus"}
@string{MKulke = "Kulke, Michael"}
@string{CHKwok = "Kwok, Carol H."}
@string{DLabeit = "Labeit, Dietmar"}
@string{SLabeit = "Labeit, Siegfried"}
@string{SLahmers = "Lahmers, Sunshine"}
@string{CLam = "Lam, Canaan"}
@string{JCLamb = "Lamb, Jonathan C."}
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@string{MCLeake = "Leake, Mark C."}
@string{HLee = "Lee, Haeshin"}
@string{SLee = "Lee, Sunyoung"}
@string{RLemmen = "Lemmen, Robert"}
@string{OLequin = "Lequin, Olivier"}
@string{CLethias = "Lethias, Claire"}
@string{HLi = "Li, Hongbin"}
@string{MSLi = "Li, Mai Suan"}
@string{FCLin = "Lin, Fan-Chi"}
@string{WALinke = "Linke, Wolfgang A."}
@string{JTLis = "Lis, John T."}
@string{WLiu = "Liu, W."}
@string{HLu = "Lu, Hui"}
@string{ZLuthey-Schulten = "Luthey-Schulten, Z."}
@string{MMaaloum = "Maaloum, M."}
@string{Macromolecules = "Macromolecules"}
@string{SMajid = "Majid, Sophia"}
@string{DEMakarov = "Makarov, Dmitrii E."}
@string{AMalec = "Malec, Arien"}
@string{RMamdani = "Mamdani, Reneeta"}
@string{EMandello = "Mandello, Enrico"}
@string{GManderson = "Manderson, Gavin"}
@string{JFMarko = "Marko, John F."}
@string{PEMarszalek = "Marszalek, Piotr E."}
@string{JMathe = "Math{\'e}, J{\'e}r{\^o}me"}
@string{AMatouschek = "Matouschek, Andreas"}
@string{BWMatthews = "Matthews, Brian W."}
@string{McGraw-Hill = "McGraw-Hill"}
@string{MechAgeingDev = "Mech Ageing Dev"}
@string{AMeller = "Meller, Amit"}
@string{CCMello = "Mello, Cecilia C."}
@string{RMerkel = "Merkel, R."}
@string{HMetiu = "Metiu, Horia"}
@string{MMickler = "Mickler, Moritz"}
@string{SMitternacht = "Mitternacht, Simon"}
@string{SMohanty = "Mohanty, Sandipan"}
@string{UMohideen = "Mohideen, U."}
@string{VMontana = "Montana, Vedrana"}
@string{LMontanaro = "Montanaro, Lucio"}
@string{SMukamel = "Mukamel, Shaul"}
@string{NAT = "Nature"}
@string{NSB = "Nat Struct Biol"}
@string{NSMB = "Nat Struct Mol Biol"}
@string{CNeagoe = "Neagoe, Ciprian"}
@string{NetworkTheoryLtd = "Network Theory Ltd."}
@string{RNevo = "Nevo, Reinat"}
@string{NJP = "New Journal of Physics"}
@string{SPNg = "Ng, Sean P."}
@string{MNguyen-Duong = "Nguyen-Duong, M."}
@string{SNie = "Nie, S."}
@string{AANoegel = "Noegel, Angelika A."}
@string{RANome = "Nome, Rene A."}
@string{JNummela = "Nummela, Jeremiah"}
@string{AFOberhauser = "Oberhauser, Andres F."}
@string{FOesterhelt = "Oesterhelt, Filipp"}
@string{TOhashi = "Ohashi, Tomoo"}
@string{TOliphant = "Oliphant, Travis"}
@string{PDOlmsted = "Olmsted, Peter D."}
@string{SJOlshansky = "Olshansky, S. J."}
@string{JNOnuchic = "Onuchic, J. N."}
@string{YOono = "Oono, Y."}
@string{CAOpitz = "Opitz, Christiane A."}
@string{KOroszlan = "Oroszlan, Krisztina"}
@string{EOroudjev = "Oroudjev, E."}
@string{OUP = "Oxford University Press"}
@string{EPaci = "Paci, Emanuele"}
@string{YPPang = "Pang, Y. P."}
@string{VParpura = "Parpura, Vladimir"}
@string{QPeng = "Peng, Qing"}
@string{OPerisic = "Perisic, Ognjen"}
@string{CLPeterson = "Peterson, Craig L."}
@string{PPeterson = "Peterson, Pearu"}
@string{PTRSL = "Philosophical Transactions of the Royal Society of London"}
@string{PRL = "Phys Rev Lett"}
@string{PRE = "Phys. Rev. E"}
@string{Physica = "Physica"}
@string{CPickett = "Pickett, Chris"}
@string{WPress = "Press, W."}
@string{PNAS = "Proceedings of the National Academy of Sciences U.S.A"}
@string{ProtSci = "Protein Sci"}
@string{Proteins = "Proteins"}
@string{SRQuake = "Quake, Stephen R."}
@string{SERadford = "Radford, Sheena E."}
@string{MRaible = "Raible, M."}
@string{NRamsey = "Ramsey, Norman"}
@string{LGRandles = "Randles, Lucy G."}
@string{SDRedick = "Redick, Sambra D."}
@string{ZReich = "Reich, Ziv"}
@string{PReimann = "Reimann, P."}
@string{RMP = "Rev. Mod. Phys."}
@string{RSI = "Review of Scientific Instruments"}
@string{FRief = "Rief, Frederick"}
@string{MRief = "Rief, Matthias"}
@string{KRitchie = "Ritchie, K."}
@string{RBRobertson = "Robertson, Ragan B."}
@string{HRoder = "Roder, Heinrich"}
@string{RRos = "Ros, R."}
@string{BRosenberg = "Rosenberg, B."}
@string{FRossi = "Rossi, Fabrice"}
@string{BSamori = "Samori, Bruno"}
@string{ASarkar = "Sarkar, Atom"}
@string{TSato = "Sato, Takehiro"}
@string{PSchaaf = "Schaaf, P."}
@string{RSchafer = "Schafer, Rolf"}
@string{NFScherer = "Scherer, Norbert F."}
@string{MSchleicher = "Schleicher, Michael"}
@string{MSchlierf = "Schlierf, Michael"}
@string{KSchulten = "Schulten, Klaus"}
@string{ZSchulten = "Schulten, Zan"}
@string{ISchwaiger = "Schwaiger, Ingo"}
@string{SCI = "Science"}
@string{USeifert = "Seifert, Udo"}
@string{BSenger = "Senger, B."}
@string{EShakhnovich = "Shakhnovich, Eugene"}
@string{DSharma = "Sharma, Deepak"}
@string{YJSheng = "Sheng, Yu-Jane"}
@string{JShillcock = "Shillcock, Julian"}
@string{EDSiggia = "Siggia, Eric D."}
@string{CLSmith = "Smith, Corey L."}
@string{DASmith = "Smith, D. Alastair"}
@string{SBSmith = "Smith, S. B."}
@string{JSoares = "Soares, J."}
@string{NDSocci = "Socci, N. D."}
@string{DWSpeicher = "Speicher, David W."}
@string{SStepaniants = "Stepaniants, S."}
@string{AStout = "Stout, A."}
@string{CStroh = "Stroh, Cordula"}
@string{TStrunz = "Strunz, Torsten"}
@string{MSu = "Su, Meihong"}
@string{ASzabo = "Szabo, Attila"}
@string{DSTalaga = "Talaga, David S."}
@string{PTalkner = "Talkner, Peter"}
@string{JTang = "Tang, Jianyong"}
@string{STeukolsky = "Teukolsky, S."}
@string{JCP = "The Journal of Chemical Physics"}
@string{RS = "The Royal Society"}
@string{JTheiler = "Theiler, James"}
@string{DThirumalai = "Thirumalai, D."}
@string{JBThompson = "Thompson, J. B."}
@string{TTlusty = "Tlusty, Tsvi"}
@string{JLToca-Herrera = "Toca-Herrera, Jose L."}
@string{JTrinick = "Trinick, John"}
@string{CHTsai = "Tsai, Chih-Hui"}
@string{HKTsao = "Tsao, Heng-Kwong"}
@string{MUrbakh = "Urbakh, M."}
@string{IRVetter = "Vetter, Ingrid R."}
@string{WVetterling = "Vetterling, W."}
@string{JCVoegel = "Voegel, J.-C."}
@string{VVogel = "Vogel, Viola"}
@string{KAWalther = "Walther, Kirstin A."}
@string{EBWalton = "Walton, Emily B."}
@string{MDWang = "Wang, Michelle D."}
@string{KWatanabe = "Watanabe, Kaori"}
@string{APWiita = "Wiita, Arun P."}
@string{Wikipedia = "Wikipedia"}
@string{AJWilcox = "Wilcox, Alexander J."}
@string{SWilson = "Wilson, Scott"}
@string{CWitt = "Witt, Christian"}
@string{PGWolynes = "Wolynes, P. G."}
@string{JWWu = "Wu, Jong-Wuu"}
@string{YWu = "Wu, Yiming"}
@string{GYang = "Yang, Guoliang"}
@string{YYang = "Yang, Yao"}
@string{RCYeh = "Yeh, Richard C."}
@string{WYu = "Yu, Weichang"}
@string{JMZhao = "Zhao, Jason Ming"}
@string{WZhuang = "Zhuang, Wei"}
@string{RCZinober = "Zinober, Rebecca C."}
@string{others = "others"}
@string{NGvanKampen = "van Kampen, N.G."}
@string{GvanRossum = "van Rossum, Guido"}
@string{KJvanVliet = "van Vliet, Krystyn J."}

@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 = BiophysJ,
    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 "# JMFernandez,
    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"
}

@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.
        Excellent detail on power spectrum derivation and thermal noise for
        extremely overdamped oscillators in Appendix A (references
        \cite{reif65}). References work on deconvolving thermal noise from
        other noise\cite{cowan98}",
    project = "Cantilever Calibration"
}

@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 { best02,
    author = RBBest #" and "# SBFowler #" and "# JLToca-Herrera #" and "#
        JClarke,
    title = "{A simple method for probing the mechanical unfolding pathway of
        proteins in detail}",
    year = 2002,
    month = sep,
    day = 17,
    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."
}

@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 { 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 = BiophysJ,
    volume = 83,
    number = 1,
    pages = "458--472",
    issn = "0006-3495",
    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 { brower-toland02,
    author = BDBrower-Toland #" and "# CLSmith #" and "# RCYeh #" and "# JTLis
        #" and "# CLPeterson #" 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 = Proteins,
    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 "# MCLeake #"
        and "# WALinke #" and "# AFOberhauser,
    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 { bustamante94,
    author = CBustamante #" and "# JFMarko #" and "# EDSiggia #" and "#
        SBSmith,
    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",
    keywords = "Bacteriophage lambda; DNA, Viral; Least-Squares Analysis;
        Thermodynamics",
    note = "WLC interpolation formula."
}

@article { bustanji03,
    author = YBustanji #" and "# CRArciola #" 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 { cao07,
    author = YCao #" and "# MMBalamurali #" 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 = "Proteinligand interactions, including proteinprotein
        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
        proteinligand 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
        proteinligand 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 proteinligand interactions in
        a functional context, and we anticipate that it will find broad
        application in diverse proteinligand systems."
}

@article { carl01,
    author = PCarl #" and "# CHKwok #" and "# GManderson #" and "# DWSpeicher
        #" and "# DEDischer,
    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-vazquez99a,
    author = MCarrion-Vazquez #" and "# AFOberhauser #" and "# SBFowler #" and
        "# PEMarszalek #" and "# SEBroedel #" and "# JClarke #" and "#
        JMFernandez,
    title = "Mechanical and chemical unfolding of a single protein: A
        comparison",
    year = 1999,
    month = mar,
    day = 30,
    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 { carrion-vazquez99b,
    author = MCarrion-Vazquez #" and "# PEMarszalek #" and "# AFOberhauser #"
        and "# JMFernandez,
    title = "Atomic force microscopy captures length phenotypes in single
        proteins",
    year = 1999,
    month = sep,
    day = 28,
    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 = ""
}

@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 { 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 {approx}35 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 = "Nice energy-landscape-to-one-dimension compression graphic.
        Unfolding Green Flourescent Protein (GFP) towards using it as an
        embedded force probe.",
    project = "Energy landscape roughness"
}

@article { dietz06a,
    author = HDietz #" and "# FBerkemeier #" and "# MBertz #" and "# MRief,
    title = "{Anisotropic deformation response of single protein molecules}",
    year = 2006,
    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 { dietz06b,
    author = HDietz #" and "# MRief,
    title = "{Protein structure by mechanical triangulation}",
    year = 2006,
    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 { 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 { discher06,
    author = DEDischer #" and "# NBhasin #" and "# CPJohnson,
    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"
}

@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 = BiophysJ,
    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 { evans97,
    author = EEvans #" and "# KRitchie,
    title = "Dynamic strength of molecular adhesion bonds.",
    year = 1997,
    month = apr,
    journal = BiophysJ,
    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 = BiophysJ,
    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"
}

@book { galassi05,
    author = MGalassi #" and "# JDavies #" and "# JTheiler #" and "# BGough #"
        and "# GJungman #" and "# MBooth #" and "# FRossi,
    title = "{GNU} Scientific Library: Reference Manual",
    year = 2005,
    edition = "Second Revised",
    pages = "xvi + 601",
    xxpages = "xvi + 580",
    isbn = "0-9541617-3-4",
    isbn-13 = "978-0-9541617-3-6",
    lccn = "QA76.73.C15",
    publisher = NetworkTheoryLtd,
    address = pub-NETWORK-THEORY:adr,
    bibdate = "Wed Oct 30 10:44:22 2002",
    url = "http://www.network-theory.co.uk/gsl/manual/",
    note = "This is the revised and updated second edition of the manual, and
        corresponds to version 1.6 of the library."
}

@article { gao03,
    author = MGao #" and "# DCraig #" and "# OLequin #" and "# IDCampbell #"
        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 = JTheorBiol,
    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 "# JKHHorber #" 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 = ""
}

@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 section 4.3., cites
        \cite{tlusty98} and \cite{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 \cite{bechhoefer02} and
        \cite{press92} respectively instead.",
    project = "Cantilever Calibration"
}

@article { hanggi90,
    author = PHanggi #" and "# PTalkner #" and "# MBorkovec,
    title = "Reaction-rate theory: fifty years after Kramers",
    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"
}

@article { hummer03,
    author = GHummer #" and "# ASzabo,
    title = "Kinetics from nonequilibrium single-molecule pulling experiments.",
    year = 2003,
    month = jul,
    journal = BiophysJ,
    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 { hutter93,
    author = JLHutter #" and "# JBechhoefer,
    title = "Calibration of atomic-force microscope tips",
    collaboration = "",
    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 = "Seminal paper for thermal calibration of AFM cantilevers.",
    project = "Cantilever Calibration"
}

@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 Hanggi Eq. 4.56c (page 275)\cite{hanggi90}.",
    project = "Energy Landscape Roughness"
}

@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 { 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 = BiophysJ,
    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 { 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 { juckett93,
    author = DAJuckett #" and "# BRosenberg,
    title = "Comparison of the Gompertz and Weibull functions as descriptors
        for human mortality distributions and their intersections.",
    year = 1993,
    month = jun,
    journal = MechAgeingDev,
    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 { kellermayer97,
    author = MSZKellermayer #" 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 { king09,
    author = WTKing #" and "# GYang,
    title = "Effects of Cantilever Stiffness on Unfolding Force in {AFM}
        Protein Unfolding",
    year = 2009,
    month = mar,
    day = 01,
    journal = BPS:P
}

@article { king10,
    author = WTKing #" and "# MSu #" and "# GYang,
    title = "{M}onte {C}arlo simulation of mechanical unfolding of proteins
        based on a simple two-state model",
    year = 2010,
    journal = IJBMM,
    volume = 46,
    number = 2,
    pages = "159--166",
    issn = "0141-8130",
    doi = "10.1016/j.ijbiomac.2009.12.001",
    url = "http://www.sciencedirect.com/science/article/B6T7J-4XWMND2-1/2/7ef768562b4157fc201d450553e5de5e",
    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 = BiophysJ,
    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 = DKKlimov #" 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 timescales for Ig27-like S1 and S2 domains"
}

@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 = JChemPhys,
    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://www.sciencedirect.com/science/article/B6X42-4CB752H-3G/1/1d9e8dc558b822877c9e1ad55bb08831",
    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 { 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 { li00,
    author = HLi #" and "# AFOberhauser #" and "# SBFowler #" and "# JClarke
        #" and "# JMFernandez,
    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 = ""
}

@article { li01,
    author = HLi #" and "# AFOberhauser #" and "# SDRedick #" and "#
        MCarrion-Vazquez #" and "# HPErickson #" and "# JMFernandez,
    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 { li06,
    author = MSLi #" and "# CKHu #" and "# DKKlimov #" 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 { liu03,
    author = WLiu #" and "# VMontana #" and "# ERChapman #" 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 { makarov01,
    author = DEMakarov #" and "# PKHansma #" 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 = Macromolecules,
    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 { marszalek98,
    author = PEMarszalek #" and "# AFOberhauser #" and "# YPPang #" and "#
        JMFernandez,
    title = "Polysaccharide elasticity governed by chair-boat transitions of
        the glucopyranose ring.",
    year = 1998,
    month = dec,
    day = 17,
    journal = NAT,
    volume = 396,
    number = 6712,
    pages = "661--664",
    issn = "0028-0836",
    doi = "10.1038/25322",
    keywords = "Amylose;Dextrans;Elasticity;Glucans;Glucose;Microscopy, Atomic
        Force;Oxidation-Reduction;Polysaccharides",
    abstract = "Many common, biologically important polysaccharides contain
        pyranose rings made of five carbon atoms and one oxygen atom. They
        occur in a variety of cellular structures, where they are often
        subjected to considerable tensile stress. The polysaccharides are
        thought to respond to this stress by elastic deformation, but the
        underlying molecular rearrangements allowing such a response remain
        poorly understood. It is typically assumed, however, that the pyranose
        ring structure is inelastic and locked into a chair-like conformation.
        Here we describe single-molecule force measurements on individual
        polysaccharides that identify the pyranose rings as the structural unit
        controlling the molecule's elasticity. In particular, we find that the
        enthalpic component of the polymer elasticity of amylose, dextran and
        pullulan is eliminated once their pyranose rings are cleaved. We
        interpret these observations as indicating that the elasticity of the
        three polysaccharides results from a force-induced elongation of the
        ring structure and a final transition from a chair-like to a boat-like
        conformation. We expect that the force-induced deformation of pyranose
        rings reported here plays an important role in accommodating mechanical
        stresses and modulating ligand binding in biological systems."
}

@article { marszalek02,
    author = PEMarszalek #" and "# HLi #" and "# AFOberhauser #" and "#
        JMFernandez,
    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 { 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 { mickler07,
    author = MMickler #" and "# RIDima #" 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 (See
        Figure 2). The unfolding timescale in GFP is about 6 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 = BiophysJ,
    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 = EMBORep,
    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 H&T\cite{hyeon03} to ligand-receptor binding.",
    project = "Energy Landscape Roughness"
}

@article { ng07,
    author = SPNg #" and "# KSBillings #" and "# TOhashi #" and "# MDAllen #"
        and "# RBBest #" and "# LGRandles #" and "# HPErickson #" and "#
        JClarke,
    title = "{Designing an extracellular matrix protein with enhanced
        mechanical stability}",
    year = 2007,
    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 { nome07,
    author = RANome #" and "# JMZhao #" and "# WDHoff #" and "# NFScherer,
    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."
}

@article { nummela07,
    author = JNummela #" and "# IAndricioaei,
    title = "{Exact Low-Force Kinetics from High-Force Single-Molecule
        Unfolding Events}",
    year = 2007,
    journal = BiophysJ,
    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 { oberhauser98,
    author = AFOberhauser #" and "# PEMarszalek #" and "# HPErickson #" and "#
        JMFernandez,
    title = "The molecular elasticity of the extracellular matrix protein
        tenascin.",
    year = 1998,
    month = may,
    day = 14,
    journal = NAT,
    volume = 393,
    number = 6681,
    pages = "181--185",
    issn = "0028-0836",
    doi = "10.1038/30270",
    eprint = "http://www.nature.com/nature/journal/v393/n6681/pdf/393181a0.pdf",
    url = "http://www.nature.com/nature/journal/v393/n6681/abs/393181a0.html",
    keywords = "Alternative Splicing;Binding
        Sites;Elasticity;Fibronectins;Humans;Microscopy, Atomic Force;Monte
        Carlo Method;Peptide Fragments;Protein Folding;Recombinant
        Proteins;Tenascin",
    abstract = "Extracellular matrix proteins are thought to provide a rigid
        mechanical anchor that supports and guides migrating and rolling cells.
        Here we examine the mechanical properties of the extracellular matrix
        protein tenascin by using atomic-force-microscopy techniques. Our
        results indicate that tenascin is an elastic protein. Single molecules
        of tenascin could be stretched to several times their resting length.
        Force-extension curves showed a saw-tooth pattern, with peaks of force
        at 137pN. These peaks were approximately 25 nm apart. Similar results
        have been obtained by study of titin. We also found similar results by
        studying recombinant tenascin fragments encompassing the 15 fibronectin
        type III domains of tenascin. This indicates that the extensibility of
        tenascin may be due to the stretch-induced unfolding of its fibronectin
        type III domains. Refolding of tenascin after stretching, observed when
        the force was reduced to near zero, showed a double-exponential
        recovery with time constants of 42 domains refolded per second and 0.5
        domains per second. The former speed of refolding is more than twice as
        fast as any previously reported speed of refolding of a fibronectin
        type III domain. We suggest that the extensibility of the modular
        fibronectin type III region may be important in allowing
        tenascin-ligand bonds to persist over long extensions. These properties
        of fibronectin type III modules may be of widespread use in
        extracellular proteins containing such domain."
}

@article { oberhauser01,
    author = AFOberhauser #" and "# PKHansma #" and "# MCarrion-Vazquez #" and
        "# JMFernandez,
    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 { olshansky97,
    author = SJOlshansky #" and "# BACarnes,
    title = "Ever since Gompertz.",
    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 { opitz03,
    author = CAOpitz #" and "# MKulke #" and "# MCLeake #" and "# CNeagoe #"
        and "# HHinssen #" and "# RJHajjar #" 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 "#
        JBThompson #" and "# SAFossey #" and "# HGHansma,
    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 { 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 { 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 = JBiotechnol,
    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 = BiophysJ,
    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 { rief02,
    author = MRief #" and "# HGrubmuller,
    title = "Force spectroscopy of single biomolecules.",
    year = 2002,
    month = mar,
    day = 12,
    journal = Chemphyschem,
    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 SHOs, in Chapter 15, Sections 6 and 10.",
    project = "Cantilever Calibration"
}

@article { rief97a,
    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 { rief97b,
    author = MRief #" and "# MGautel #" and "# FOesterhelt #" and "# JMFernandez
        #" and "# HEGaub,
    title = "Reversible Unfolding of Individual Titin Immunoglobulin Domains by
        {AFM}",
    year = 1997,
    month = may,
    day = 16,
    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 { rief98,
    author = MRief #" and "# JMFernandez #" 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 { sarkar04,
    author = ASarkar #" and "# RBRobertson #" and "# JMFernandez,
    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 "# JMFernandez #" 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 "# JMFernandez,
    title = "{The unfolding kinetics of ubiquitin captured with single-molecule
        force-clamp techniques}",
    year = 2004,
    journal = PNAS,
    volume = 101,
    number = 19,
    pages = "7299--7304",
    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",
    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 = BiophysJ,
    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 $v$. Eqn.~3 in the supplement is Evans-Ritchie 1999's
        Eqn.~2\cite{evans99}, but it is just ``[dying percent] * [surviving
        population] = [deaths]'' (TODO, check). $\nu \equiv k$ is the force
        /time-dependent off rate... (TODO) The Kramers' rate equation (second
        equation in the paper) is Hanggi Eq.~4.56b (page 275)\cite{hanggi90}.
        It is important to extract $k_0$ and $\Delta x$ using every available
        method."
}

@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 = PRE,
    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 { 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 { 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"
}

@misc { sw:check,
    author = AMalec #" and "# CPickett #" and "# FHugosson #" and "# RLemmen,
    key = "sw:check",
    title = "Check",
    year = 2006,
    month = oct,
    day = 13,
    version = "version 0.9.4",
    url = "http://check.sourceforge.net",
    abstract = "Check is a unit testing framework for C. It features a simple
        interface for defining unit tests, putting little in the way of the
        developer. Tests are run in a separate address space, so Check can
        catch both assertion failures and code errors that cause segmentation
        faults or other signals. The output from unit tests can be used within
        source code editors and IDEs."
}

@misc { sw:noweb,
    author = NRamsey,
    key = "sw:noweb",
    title = "Noweb",
    year = 1997,
    month = nov,
    day = 18,
    version = "version 2.11b",
    url = "http://www.eecs.harvard.edu/nr/noweb/",
    abstract = "Noweb is a simple, extensible literate programming tool.",
    note = "Debian package by Federico Di Gregorio"
}

@misc { sw:python,
    author = GvanRossum #" and "# others,
    key = "sw:python",
    title = "Python",
    year = 2007,
    month = apr,
    day = 18,
    version = "version 2.5.1",
    url = "http://www.python.org/",
    abstract = "Python is a dynamic object-oriented programming language."
}

@misc { sw:scipy,
    author = EJones #" and "# TOliphant #" and "# PPeterson #" and "# others,
    key = "sw:scipy",
    title = "{SciPy}: Open source scientific tools for {Python}",
    year = "2001--",
    url = "http://www.scipy.org/"
}

@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 = DSTalaga #" and "# WLLau #" and "# HRoder #" and "# JTang #" and
        "# YJia #" and "# WFDeGrado #" and "# RMHochstrasser,
    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 = Biochemistry,
    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"
}

@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 \cite{grossman05} for derivation of thermal response fn.
        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"
}

@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 { walther07,
    author = KAWalther #" and "# FGrater #" and "# LDougan #" and "# CLBadilla
        #" and "# BJBerne #" and "# JMFernandez,
    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 Bell's model: how force transducer stiffness alters
        measured unbinding forces and kinetics of molecular complexes.",
    year = 2008,
    month = apr,
    day = 01,
    journal = BiophysJ,
    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 { wiita06,
    author = APWiita #" and "# SRKAinavarapu #" and "# HHHuang #" and "#
        JMFernandez,
    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 { wikipedia_cubic_function,
    author = Wikipedia,
    key = "wikipedia_cubic_function",
    title = "Cubic function",
    year = 2009,
    month = mar,
    day = 23,
    journal = Wikipedia,
    url = "http://en.wikipedia.org/wiki/Cubic_equation"
}

@article { wilcox05,
    author = AJWilcox #" 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 { 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://www.sciencedirect.com/science/article/B6TY8-4B3NR1W-B/1/bbaa47878ada03c6ef8e681d03bb65d3",
    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 "# WABaase #" and "# IRVetter #"
        and "# WABreyer #" and "# JAHaack #" and "# BWMatthews #" and "#
        FWDahlquist #" 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 "# JCLamb #" and "# FHan #" and "# JABirchler,
    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 = JMZhao #" and "# HLee #" and "# RANome #" and "# SMajid #" and "#
        NFScherer #" and "# WDHoff,
    title = "{Single-molecule detection of structural changes during Per-Arnt-
        Sim (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 = ProtSci,
    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 = "READ",
    project = "sawtooth simulation"
}