Start fleshing out "Related work" section in the manual.

To facilitate this, I've added the following new keys to sawsim.bib:
  jollymore09, kellermayer97, king10, marszalek98, oberhauser98, rief97a
I also renamed the old rief97 -> rief97b to avoid confusion with rief97a.

Also, run a second bibtex/pdflatex pass on compilation to handle a
single layer of cross referencing in the `note` field.

diff --git a/src/sawsim.bib b/src/sawsim.bib
index 948c196871cbe84058328d336c2dfbe42e24071e..417de258a52b7237d99f61adcf1c4a249a6ed788 100644 (file)
--- a/src/sawsim.bib
+++ b/src/sawsim.bib
@@ -101,7 +101,7 @@
 @string{JGlaser = "Glaser, Jens"}
 @string{BGompertz = "Gompertz, Benjamin"}
 @string{BGough = "Gough, Brian"}
 @string{JGlaser = "Glaser, Jens"}
 @string{BGompertz = "Gompertz, Benjamin"}
 @string{BGough = "Gough, Brian"}

-@string{HGranzier = "Granzier, Henk"}
+@string{HLGranzier = "Granzier, Henk L."}

 @string{FGrater = "Grater, Frauke"}
 @string{CGrossman = "Grossman, C."}
 @string{HGrubmuller = {Grubm{\"u}ller, Helmut}}
 @string{FGrater = "Grater, Frauke"}
 @string{CGrossman = "Grossman, C."}
 @string{HGrubmuller = {Grubm{\"u}ller, Helmut}}


@@ -127,6 +127,7 @@
 @string{WLHung = "Hung, Wen-Liang"}
 @string{JLHutter = "Hutter, Jeffrey L."}
 @string{CHyeon = "Hyeon, Changbong"}
 @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{AIrback = "Irback, Anders"}
 @string{SIzrailev = "Izrailev, S."}
 @string{JBiotechnol = "J Biotechnol"}


@@ -138,13 +139,16 @@
 @string{YJia = "Jia, Yiwei"}
 @string{SJiang = "Jiang, Shaoyi"}
 @string{CPJohnson = "Johnson, Colin P."}
 @string{YJia = "Jia, Yiwei"}
 @string{SJiang = "Jiang, Shaoyi"}
 @string{CPJohnson = "Johnson, Colin P."}

+@string{AJollymore = "Jollymore, Ashlee"}

 @string{EJones = "Jones, Eric"}
 @string{EJones = "Jones, Eric"}

+@string{JMB = "Journal of Molecular Biology"}

 @string{DAJuckett = "Juckett, D. A."}
 @string{GJungman = "Jungman, Gerard"}
 @string{DKaftan = "Kaftan, David"}
 @string{RKapon = "Kapon, Ruti"}
 @string{AKardinal = "Kardinal, Angelika"}
 @string{MKarplus = "Karplus, Martin"}
 @string{DAJuckett = "Juckett, D. A."}
 @string{GJungman = "Jungman, Gerard"}
 @string{DKaftan = "Kaftan, David"}
 @string{RKapon = "Kapon, Ruti"}
 @string{AKardinal = "Kardinal, Angelika"}
 @string{MKarplus = "Karplus, Martin"}

+@string{MSZKellermayer = "Kellermayer, Mikl\'os S. Z."}

 @string{FKienberger = "Kienberger, Ferry"}
 @string{WTKing = "King, W. Trevor"}
 @string{JKlafter = "Klafter, J."}
 @string{FKienberger = "Kienberger, Ferry"}
 @string{WTKing = "King, W. Trevor"}
 @string{JKlafter = "Klafter, J."}


@@ -168,6 +172,7 @@
 @string{SLee = "Lee, Sunyoung"}
 @string{RLemmen = "Lemmen, Robert"}
 @string{OLequin = "Lequin, Olivier"}
 @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{HLi = "Li, Hongbin"}
 @string{MSLi = "Li, Mai Suan"}
 @string{FCLin = "Lin, Fan-Chi"}


@@ -202,6 +207,7 @@
 @string{VMontana = "Montana, Vedrana"}
 @string{LMontanaro = "Montanaro, Lucio"}
 @string{SMukamel = "Mukamel, Shaul"}
 @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{NSB = "Nat Struct Biol"}
 @string{NSMB = "Nat Struct Mol Biol"}
 @string{CNeagoe = "Neagoe, Ciprian"}


@@ -227,6 +233,7 @@
 @string{EOroudjev = "Oroudjev, E."}
 @string{OUP = "Oxford University Press"}
 @string{EPaci = "Paci, Emanuele"}
 @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{VParpura = "Parpura, Vladimir"}
 @string{QPeng = "Peng, Qing"}
 @string{OPerisic = "Perisic, Ognjen"}


@@ -270,7 +277,7 @@
 @string{KSchulten = "Schulten, Klaus"}
 @string{ZSchulten = "Schulten, Zan"}
 @string{ISchwaiger = "Schwaiger, Ingo"}
 @string{KSchulten = "Schulten, Klaus"}
 @string{ZSchulten = "Schulten, Zan"}
 @string{ISchwaiger = "Schwaiger, Ingo"}

-@string{Science = "Science"}
+@string{SCI = "Science"}

 @string{USeifert = "Seifert, Udo"}
 @string{BSenger = "Senger, B."}
 @string{EShakhnovich = "Shakhnovich, Eugene"}
 @string{USeifert = "Seifert, Udo"}
 @string{BSenger = "Senger, B."}
 @string{EShakhnovich = "Shakhnovich, Eugene"}


@@ -280,7 +287,7 @@
 @string{EDSiggia = "Siggia, Eric D."}
 @string{CLSmith = "Smith, Corey L."}
 @string{DASmith = "Smith, D. Alastair"}
 @string{EDSiggia = "Siggia, Eric D."}
 @string{CLSmith = "Smith, Corey L."}
 @string{DASmith = "Smith, D. Alastair"}

-@string{SSmith = "Smith, S."}
+@string{SBSmith = "Smith, S. B."}

 @string{JSoares = "Soares, J."}
 @string{NDSocci = "Socci, N. D."}
 @string{DWSpeicher = "Speicher, David W."}
 @string{JSoares = "Soares, J."}
 @string{NDSocci = "Socci, N. D."}
 @string{DWSpeicher = "Speicher, David W."}


@@ -288,6 +295,7 @@
 @string{AStout = "Stout, A."}
 @string{CStroh = "Stroh, Cordula"}
 @string{TStrunz = "Strunz, Torsten"}
 @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{ASzabo = "Szabo, Attila"}
 @string{DSTalaga = "Talaga, David S."}
 @string{PTalkner = "Talkner, Peter"}


@@ -447,7 +455,7 @@
     year = 1978,
     month = may,
     day = 12,
     year = 1978,
     month = may,
     day = 12,

-    journal = Science,
+    journal = SCI,

     volume = 200,
     number = 4342,
     pages = "618--627",
     volume = 200,
     number = 4342,
     pages = "618--627",


@@ -480,6 +488,8 @@
     title = "{A simple method for probing the mechanical unfolding pathway of
         proteins in detail}",
     year = 2002,
     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,
     journal = PNAS,
     volume = 99,
     number = 19,


@@ -702,12 +712,12 @@
 
 @article { bustamante94,
     author = CBustamante #" and "# JFMarko #" and "# EDSiggia #" and "#
 
 @article { bustamante94,
     author = CBustamante #" and "# JFMarko #" and "# EDSiggia #" and "#

-        SSmith,
+        SBSmith,

     title = "Entropic elasticity of lambda-phage {DNA}.",
     year = 1994,
     month = sep,
     day = 09,
     title = "Entropic elasticity of lambda-phage {DNA}.",
     year = 1994,
     month = sep,
     day = 09,

-    journal = Science,
+    journal = SCI,

     volume = 265,
     number = 5178,
     pages = "1599--1600",
     volume = 265,
     number = 5178,
     pages = "1599--1600",


@@ -1584,6 +1594,54 @@
         rupture."
 }
 
         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
 @article { juckett93,
     author = DAJuckett #" and "# BRosenberg,
     title = "Comparison of the Gompertz and Weibull functions as descriptors


@@ -1620,6 +1678,41 @@
         Weibull models."
 }
 
         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}
 @article { king09,
     author = WTKing #" and "# GYang,
     title = "Effects of Cantilever Stiffness on Unfolding Force in {AFM}


@@ -1630,6 +1723,43 @@
     journal = BPS:P
 }
 
     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
 @article { kleiner07,
     author = AKleiner #" and "# EShakhnovich,
     title = "The mechanical unfolding of ubiquitin through all-atom Monte Carlo


@@ -1776,7 +1906,7 @@
 @article { labeit03,
     author = DLabeit #" and "# KWatanabe #" and "# CWitt #" and "# HFujita #"
         and "# YWu #" and "# SLahmers #" and "# TFunck #" and "# SLabeit #" and
 @article { labeit03,
     author = DLabeit #" and "# KWatanabe #" and "# CWitt #" and "# HFujita #"
         and "# YWu #" and "# SLahmers #" and "# TFunck #" and "# SLabeit #" and

-        "# HGranzier,
+        "# HLGranzier,

     title = "Calcium-dependent molecular spring elements in the giant protein
         titin",
     year = 2003,
     title = "Calcium-dependent molecular spring elements in the giant protein
         titin",
     year = 2003,


@@ -1952,6 +2082,43 @@
     note = "Derivation of the Worm-like Chain interpolation function."
 }
 
     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,
 @article { marszalek02,
     author = PEMarszalek #" and "# HLi #" and "# AFOberhauser #" and "#
         JMFernandez,


@@ -2287,6 +2454,50 @@
         under different conditions."
 }
 
         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,
 @article { oberhauser01,
     author = AFOberhauser #" and "# PKHansma #" and "# MCarrion-Vazquez #" and
         "# JMFernandez,


@@ -2627,23 +2838,54 @@
     project = "Cantilever Calibration"
 }
 
     project = "Cantilever Calibration"
 }
 

-@article { rief97,
-    author = MRief #" and "# MGautel #" and "# FOesterhelt #" and "#
-        JMFernandez #" and "# HEGaub,
-    title = "{Reversible Unfolding of Individual Titin Immunoglobulin Domains
-        by AFM}",
+@article { rief97a,
+    author = MRief #" and "# FOesterhelt #" and "# BHeymann #" and "# HEGaub,
+    title = "Single Molecule Force Spectroscopy on Polysaccharides by Atomic
+        Force Microscopy",

     year = 1997,
     year = 1997,

-    journal = Science,
+    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",
     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 Dietz
-        '04\cite{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 it's globular-chain
+    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"
 }
         structure.",
     project = "Energy Landscape Roughness"
 }


@@ -2661,7 +2903,10 @@
     numpages = 3,
     publisher = APS,
     doi = "10.1103/PhysRevLett.81.4764",
     numpages = 3,
     publisher = APS,
     doi = "10.1103/PhysRevLett.81.4764",

-    eprint = "http://prola.aps.org/pdf/PRL/v81/i21/p4764_1"
+    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,
 }
 
 @article { sarkar04,

diff --git a/src/sawsim.nw b/src/sawsim.nw
index f70f9861dc17f7ef7a11bda9d627fc78dc4b2036..c4ba0716600679b8a9f94cc11bcaa7abafdc3648 100644 (file)
--- a/src/sawsim.nw
+++ b/src/sawsim.nw
@@ -127,7 +127,29 @@ to share the burden and increase the transparency of data analysis.
 
 \subsection{Related work}
 
 
 \subsection{Related work}
 

-TODO References
+Sawim has been published\citep{king10}!  It is, as far as I know, the
+only open-source Monte Carlo force spectroscopy simulator, but similar
+closed source simulators have been around since the seminal paper by
+\citet{rief97a}.  In chronological order, major contributions have
+come from
+
+\begin{packed_item}
+  \item \citet{rief97a} \citeyear{rief97a}:
+  \item \citet{rief97b} \citeyear{rief97b}:
+  \item \citet{kellermayer97} \citeyear{kellermayer97}:
+  \item \citet{rief98} \citeyear{rief98}:
+    first paper to focus mainly on the simulation
+  \item \citet{oberhauser98} \citeyear{oberhauser98}:
+  \item \citet{carrion-vazquez99a} \citeyear{carrion-vazquez99a}:
+  \item \citet{best02} \citeyear{best02}:
+    pointed out large fit valley
+  \item \citet{zinober02} \citeyear{zinober02}:
+    introduced the scaffold effect
+  \item \citet{jollymore09} \citeyear{jollymore09}:
+  \item \citet{king10} \citeyear{king10}:
+    introduced sawsim
+\end{packed_item}
+

 
 \subsection{About this document}
 
 
 \subsection{About this document}
 


@@ -6531,6 +6553,8 @@ $(DOC_DIR)/sawsim.pdf : $(BUILD_DIR)/sawsim.tex $(BUILD_DIR)/sawsim.bib \
        $(SHELL) -e -c "cd $(BUILD_DIR) && pdflatex sawsim"
        $(SHELL) -e -c "cd $(BUILD_DIR) && bibtex sawsim"
        $(SHELL) -e -c "cd $(BUILD_DIR) && pdflatex sawsim"
        $(SHELL) -e -c "cd $(BUILD_DIR) && pdflatex sawsim"
        $(SHELL) -e -c "cd $(BUILD_DIR) && bibtex sawsim"
        $(SHELL) -e -c "cd $(BUILD_DIR) && pdflatex sawsim"

+       $(SHELL) -e -c "cd $(BUILD_DIR) && bibtex sawsim"
+       $(SHELL) -e -c "cd $(BUILD_DIR) && pdflatex sawsim"

        $(SHELL) -e -c "cd $(BUILD_DIR) && pdflatex sawsim"
        mv $(BUILD_DIR)/sawsim.pdf $@
 @
        $(SHELL) -e -c "cd $(BUILD_DIR) && pdflatex sawsim"
        mv $(BUILD_DIR)/sawsim.pdf $@
 @


@@ -6626,7 +6650,7 @@ clean : $(CHECK_BINS:%=clean_%) $(SAWSIM_MODS:%=clean_%) \
                $(BUILD_DIR)/interp.c $(BUILD_DIR)/interp.h \
                $(BUILD_DIR)/tavl.c $(BUILD_DIR)/tavl.h \
                $(BUILD_DIR)/global.h ./gmon.out
                $(BUILD_DIR)/interp.c $(BUILD_DIR)/interp.h \
                $(BUILD_DIR)/tavl.c $(BUILD_DIR)/tavl.h \
                $(BUILD_DIR)/global.h ./gmon.out

-       $(SHELL) -e -c "rmdir $(BUILD_DIR) $(BIN_DIR) $(DOC_DIR)"
+       $(SHELL) -e -c "rmdir $(BUILD_DIR) $(DOC_DIR)"

 
 # Various builds of sawsim
 $(BIN_DIR)/sawsim : $(SAWSIM_SRC) | $(BIN_DIR)
 
 # Various builds of sawsim
 $(BIN_DIR)/sawsim : $(SAWSIM_SRC) | $(BIN_DIR)