From: W. Trevor King Date: Sat, 16 Oct 2010 15:58:52 +0000 (-0400) Subject: Corrections to saswim.bib before reformating with pybtex. X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=dfc1fd3faf40b9958fb9a66d0069b2e0baf2846b;p=sawsim.git Corrections to saswim.bib before reformating with pybtex. --- diff --git a/src/sawsim.bib b/src/sawsim.bib index 6977cdf..574cec7 100644 --- a/src/sawsim.bib +++ b/src/sawsim.bib @@ -1,50 +1,11 @@ -% Good, very basic tutorial -% http://cmtw.harvard.edu/Documentation/TeX/Bibtex/Example.html -% More detail on the whole process -% http://www.andy-roberts.net/misc/latex/latextutorial3.html -% Entry types reference -% http://newton.ex.ac.uk/tex/pack/bibtex/btxdoc/node6.html -% Fields reference -% http://newton.ex.ac.uk/tex/pack/bibtex/btxdoc/node7.html -% Entry and field reference, but with little discussion -% http://en.wikipedia.org/wiki/BibTeX -% Examples of assorted styles -% http://www.cs.stir.ac.uk/~kjt/software/latex/showbst.html -% Assorted BibTeX tools -% http://liinwww.ira.uka.de/bibliography/Bib.Format.html -% -% at some point in your latex document -% \bibliographystyle{prsty} % Phys. Rev. style -% other syles include abbrv, alpha, plain, unsrt -% -% and in your latex document where you want the bibliography: -% \bibliography{wtk} % wtk.bib is the name of the database -% -% compile (using latex for example) with -% $ latex example -% $ bibtex example -% $ latex example -% $ latex example -% -% See possibly the Natbib package for other citation styles & link formats -% Customize bibliography with Makebst (`latex makebst`), -% makes .bst bib-style format files according to your specifications. -% -% My key style is '', -% which I can kindof achieve with -% $ bibtool -f '%-1n(author)%2d(year)' wtk.bib -o wtk1.bib -% Except any paper with more than one author has a '.ea' appended to the name -% and bibtool removes all comments :(. - -% Define some Journal name shortcuts -% @String{PRL = "Phys. Rev. Lett."} - -% @String{RMP = "Rev. Mod. Phys."} - -% @String{LANG = "Langmuir"} - -% @String(PNAS="Proc. Nat. Acad. Sci.") -% @String{RSI = "Rev. Sci. Instrum."} +@String{PRL = "Phys. Rev. Lett."} +@String{RMP = "Rev. Mod. Phys."} +@String{LANG = "Langmuir"} +@String(PNAS="Proc. Nat. Acad. Sci.") +@String{RSI = "Rev. Sci. Instrum."} +@String{pub-NETWORK-THEORY = "Network Theory Ltd."} +@String{pub-NETWORK-THEORY:adr = "Bristol, UK"} +@String{BPJ = "Biophys J" @Article{hyeon03, author = "Changbong Hyeon and D. Thirumalai", @@ -58,11 +19,7 @@ volume = "100", number = "18", pages = "10249--10253", - keywords = "Protein Folding", - keywords = "Proteins", - keywords = "RNA", - keywords = "Temperature", - keywords = "Thermodynamics", + 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 @@ -98,13 +55,7 @@ volume = "6", number = "5", pages = "482--486", - keywords = "Models, Molecular", - keywords = "Protein Binding", - keywords = "Protein Folding", - keywords = "Spectrum Analysis", - keywords = "Thermodynamics", - keywords = "beta Karyopherins", - keywords = "ran GTP-Binding Protein", + 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 @@ -810,6 +761,8 @@ pages = "11288--11292", doi = "10.1073/pnas.96.20.11288", year = "1999", + month = sep, + day = 28, abstract = "", URL = "http://www.pnas.org/cgi/content/abstract/96/20/11288", eprint = "http://www.pnas.org/cgi/reprint/96/20/11288.pdf", @@ -1151,11 +1104,7 @@ year = "2000", month = jun, day = "20", - keywords = "Animals", - keywords = "Humans", - keywords = "Protein Folding", - keywords = "Proteins", - keywords = "Spectrin", + 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 @@ -1191,7 +1140,6 @@ concentration of denaturants.", ISSN = "0027-8424", URL = "http://www.pnas.org/cgi/content/abstract/97/13/7254", - URLB = "http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=16532", eprint = "http://www.pnas.org/cgi/reprint/97/13/7254.pdf", note = "Simulated unfolding timescales for Ig27-like S1 and S2 domains", } @@ -1222,26 +1170,10 @@ volume = "104", number = "52", pages = "20799--20804", - doi = "10.1073/pnas.0701281105", year = "2007", month = dec, day = "26", - keywords = "Anisotropy", - keywords = "Bacterial Proteins", - keywords = "Biophysics", - keywords = "Computer Simulation", - keywords = "Cysteine", - keywords = "Halorhodospira halophila", - keywords = "Hydrogen Bonding", - keywords = "Kinetics", - keywords = "Luminescent Proteins", - keywords = "Microscopy, Atomic Force", - keywords = "Molecular Conformation", - keywords = "Protein Binding", - keywords = "Protein Conformation", - keywords = "Protein Denaturation", - keywords = "Protein Folding", - keywords = "Protein Structure, Secondary", + 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 @@ -1785,6 +1717,8 @@ pages = "3694--3699", doi = "10.1073/pnas.96.7.3694", year = "1999", + month = mar, + day = 30, URL = "http://www.pnas.org/cgi/content/abstract/96/7/3694", eprint = "http://www.pnas.org/cgi/reprint/96/7/3694.pdf", } @@ -1800,20 +1734,7 @@ volume = "87", number = "4", pages = "2630--2634", - keywords = "Elasticity", - keywords = "Enzyme Activation", - keywords = "Micromanipulation", - keywords = "Microscopy, Atomic Force", - keywords = "Models, Chemical", - keywords = "Models, Molecular", - keywords = "Multiprotein Complexes", - keywords = "Nuclear Proteins", - keywords = "Physical Stimulation", - keywords = "Protein Binding", - keywords = "Stress, Mechanical", - keywords = "Structure-Activity Relationship", - keywords = "beta Karyopherins", - keywords = "ran GTP-Binding Protein", + 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, @@ -1850,13 +1771,7 @@ volume = "10", number = "7", pages = "553--557", - keywords = "Guanosine Diphosphate", - keywords = "Guanosine Triphosphate", - keywords = "Microscopy, Atomic Force", - keywords = "Protein Binding", - keywords = "Protein Conformation", - keywords = "beta Karyopherins", - keywords = "ran GTP-Binding Protein", + 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 @@ -2000,10 +1915,7 @@ volume = "90", number = "4", pages = "L33--L35", - keywords = "Models, Molecular", - keywords = "Protein Folding", - keywords = "Proteins", - keywords = "Thermodynamics", + 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 @@ -2093,16 +2005,7 @@ volume = "92", number = "6", pages = "2054--2061", - keywords = "Computer Simulation", - keywords = "Models, Chemical", - keywords = "Models, Molecular", - keywords = "Models, Statistical", - keywords = "Monte Carlo Method", - keywords = "Motion", - keywords = "Protein Conformation", - keywords = "Protein Denaturation", - keywords = "Protein Folding", - keywords = "Ubiquitin", + 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 @@ -2179,12 +2082,7 @@ volume = "11", number = "12", pages = "2759--2765", - keywords = "Computer Simulation", - keywords = "Models, Molecular", - keywords = "Monte Carlo Method", - keywords = "Protein Folding", - keywords = "Protein Structure, Tertiary", - keywords = "Proteins", + 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 @@ -2225,23 +2123,7 @@ volume = "83", number = "1", pages = "458--472", - keywords = "Amino Acid Sequence", - keywords = "Dose-Response Relationship, Drug", - keywords = "Kinetics", - keywords = "Magnetic Resonance Spectroscopy", - keywords = "Models, Molecular", - keywords = "Molecular Sequence Data", - keywords = "Monte Carlo Method", - keywords = "Muscle Proteins", - keywords = "Mutation", - keywords = "Peptide Fragments", - keywords = "Protein Denaturation", - keywords = "Protein Folding", - keywords = "Protein Kinases", - keywords = "Protein Structure, Secondary", - keywords = "Protein Structure, Tertiary", - keywords = "Proteins", - keywords = "Thermodynamics", + 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 @@ -2283,24 +2165,7 @@ volume = "85", number = "1", pages = "5--15", - keywords = "Computer Simulation", - keywords = "Crystallography", - keywords = "Energy Transfer", - keywords = "Kinetics", - keywords = "Lasers", - keywords = "Micromanipulation", - keywords = "Microscopy, Atomic Force", - keywords = "Models, Molecular", - keywords = "Molecular Conformation", - keywords = "Motion", - keywords = "Muscle Proteins", - keywords = "Nanotechnology", - keywords = "Physical Stimulation", - keywords = "Protein Conformation", - keywords = "Protein Denaturation", - keywords = "Protein Folding", - keywords = "Protein Kinases", - keywords = "Stress, Mechanical", + 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 @@ -2390,15 +2255,7 @@ volume = "6", number = "1", pages = "46--51", - keywords = "Animals", - keywords = "Contractile Proteins", - keywords = "Dictyostelium", - keywords = "Immunoglobulins", - keywords = "Kinetics", - keywords = "Microfilament Proteins", - keywords = "Models, Molecular", - keywords = "Protein Folding", - keywords = "Protein Structure, Tertiary", + 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 @@ -2437,17 +2294,7 @@ volume = "76", number = "5", pages = "2439--2447", - keywords = "Animals", - keywords = "Biophysics", - keywords = "Biopolymers", - keywords = "Microscopy, Atomic Force", - keywords = "Models, Chemical", - keywords = "Muscle Proteins", - keywords = "Protein Folding", - keywords = "Protein Kinases", - keywords = "Stochastic Processes", - keywords = "Stress, Mechanical", - keywords = "Thermodynamics", + 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. @@ -2498,13 +2345,7 @@ note= {Develops Kramers improvement on Bell model for domain unfolding. volume = "72", number = "4", pages = "1541--1555", - keywords = "Avidin", - keywords = "Biotin", - keywords = "Chemistry, Physical", - keywords = "Computer Simulation", - keywords = "Mathematics", - keywords = "Monte Carlo Method", - keywords = "Protein Binding", + 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 @@ -2620,11 +2461,7 @@ eprint = {http://www.biophysj.org/cgi/reprint/72/4/1541.pdf}, volume = "1", number = "6", pages = "441--450", - keywords = "Animals", - keywords = "Cytochrome c Group", - keywords = "Humans", - keywords = "Infant", - keywords = "Protein Folding", + 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 @@ -2709,19 +2546,7 @@ note = {A nice introduction to some quantitative ramifications of the funnel ene volume = "11", number = "1", pages = "81--85", - keywords = "Actins", - keywords = "Animals", - keywords = "Contractile Proteins", - keywords = "Cross-Linking Reagents", - keywords = "Dictyostelium", - keywords = "Dimerization", - keywords = "Microfilament Proteins", - keywords = "Microscopy, Atomic Force", - keywords = "Mutagenesis, Site-Directed", - keywords = "Protein Denaturation", - keywords = "Protein Folding", - keywords = "Protein Structure, Tertiary", - keywords = "Protozoan Proteins", + 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 @@ -2778,18 +2603,7 @@ note = "Gives appropriate Einstein-S... relation for diffusion to damping", volume = "200", number = "4342", pages = "618--627", - keywords = "Antigen-Antibody Reactions", - keywords = "Cell Adhesion", - keywords = "Cell Membrane", - keywords = "Chemistry, Physical", - keywords = "Electrophysiology", - keywords = "Enzymes", - keywords = "Glycoproteins", - keywords = "Kinetics", - keywords = "Ligands", - keywords = "Membrane Proteins", - keywords = "Models, Biological", - keywords = "Receptors, Drug", + 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 @@ -2823,20 +2637,7 @@ note = "Gives appropriate Einstein-S... relation for diffusion to damping", volume = "101", number = "39", pages = "14102--14107", - keywords = "Animals", - keywords = "Ankyrin Repeat", - keywords = "Circular Dichroism", - keywords = "Drosophila Proteins", - keywords = "Drosophila melanogaster", - keywords = "Gene Deletion", - keywords = "Models, Chemical", - keywords = "Models, Molecular", - keywords = "Protein Denaturation", - keywords = "Protein Folding", - keywords = "Protein Structure, Tertiary", - keywords = "Spectrometry, Fluorescence", - keywords = "Thermodynamics", - keywords = "Urea", + 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 @@ -2873,18 +2674,7 @@ note = "Gives appropriate Einstein-S... relation for diffusion to damping", volume = "21", number = "3", pages = "167--195", - keywords = "Amino Acid Sequence", - keywords = "Chemistry, Physical", - keywords = "Computer Simulation", - keywords = "Data Interpretation, Statistical", - keywords = "Kinetics", - keywords = "Models, Chemical", - keywords = "Molecular Sequence Data", - keywords = "Protein Biosynthesis", - keywords = "Protein Conformation", - keywords = "Protein Folding", - keywords = "Proteins", - keywords = "Thermodynamics", + 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 @@ -2931,12 +2721,7 @@ note = "Gives appropriate Einstein-S... relation for diffusion to damping", volume = "84", number = "21", pages = "7524--7528", - keywords = "Kinetics", - keywords = "Mathematics", - keywords = "Models, Theoretical", - keywords = "Protein Conformation", - keywords = "Proteins", - keywords = "Stochastic Processes", + 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 @@ -2960,20 +2745,11 @@ note = "Gives appropriate Einstein-S... relation for diffusion to damping", volume = "265", number = "5178", pages = "1599--1600", - keywords = "Bacteriophage lambda", - keywords = "DNA, Viral", - keywords = "Least-Squares Analysis", - keywords = "Thermodynamics", + keywords = "Bacteriophage lambda; DNA, Viral; Least-Squares Analysis; Thermodynamics", ISSN = "0036-8075", note = "WLC interpolation formula.", } -% see the list of BibTeX databases Beebe has compiled -% http://www.math.utah.edu/~beebe/bibliographies.html - -% Beebe: http://www.math.utah.edu/pub/tex/bib/gnu.html -@String{pub-NETWORK-THEORY = "Network Theory Ltd."} -@String{pub-NETWORK-THEORY:adr = "Bristol, UK"} @Book{galassi05, author = "Mark Galassi and Jim Davies and James Theiler and Brian Gough and Gerard Jungman and Michael Booth and @@ -2988,8 +2764,7 @@ note = "Gives appropriate Einstein-S... relation for diffusion to damping", ISBN-13 = "978-0-9541617-3-6", LCCN = "QA76.73.C15", bibdate = "Wed Oct 30 10:44:22 2002", - acknowledgement = ack-nhfb, - remark = "This is the revised and updated second edition of the + note = "This is the revised and updated second edition of the manual, and corresponds to version 1.6 of the library.", URL = "http://www.network-theory.co.uk/gsl/manual/", @@ -2997,6 +2772,7 @@ note = "Gives appropriate Einstein-S... relation for diffusion to damping", } @Misc{sw:check, + key = "sw:check", title = {Check}, author = {Arien Malec and Chris Pickett and Fredrik Hugosson and Robert Lemmen}, version = {version 0.9.4}, @@ -3008,6 +2784,7 @@ note = "Gives appropriate Einstein-S... relation for diffusion to damping", } @Misc{sw:noweb, + key="sw:noweb", title = {Noweb}, author = {Norman Ramsey}, version = {version 2.11b}, @@ -3020,8 +2797,9 @@ note = "Gives appropriate Einstein-S... relation for diffusion to damping", } @Misc{sw:python, + key="sw:python", title = {Python}, - author = {Guido {van Rossum} and others}, + author = {van Rossum, Guido and others}, version = {version 2.5.1}, year = "2007", month = apr, @@ -3031,6 +2809,7 @@ note = "Gives appropriate Einstein-S... relation for diffusion to damping", } @Misc{sw:scipy, + key="sw:scipy", author = {Eric Jones and Travis Oliphant and Pearu Peterson and others}, title = {{SciPy}: Open source scientific tools for {Python}}, year = {2001--}, @@ -3053,21 +2832,17 @@ eprint = {http://www.biophysj.org/cgi/reprint/93/10/3373.pdf} } @article{gompertz25, - jstor_articletype = {primary_article}, 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}, author = {Gompertz, Benjamin}, journal = {Philosophical Transactions of the Royal Society of London}, - jstor_issuetitle = {}, volume = {115}, number = {}, - jstor_formatteddate = {1825}, pages = {513--583}, url = {http://www.jstor.org/stable/107756}, ISSN = {02610523}, abstract = {}, publisher = {The Royal Society}, - language = {}, - copyright = {Copyright © 1825 The Royal Society}, + copyright = {Copyright \copy 1825 The Royal Society}, year = {1825}, } @@ -3083,18 +2858,7 @@ eprint = {http://www.biophysj.org/cgi/reprint/93/10/3373.pdf} volume = "92", number = "12", pages = "4188--4195", - keywords = "Computer Simulation", - keywords = "DNA", - keywords = "Elasticity", - keywords = "Mechanics", - keywords = "Micromanipulation", - keywords = "Microscopy, Atomic Force", - keywords = "Models, Chemical", - keywords = "Models, Molecular", - keywords = "Nanostructures", - keywords = "Nucleic Acid Conformation", - keywords = "Porosity", - keywords = "Stress, Mechanical", + 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 @@ -3134,24 +2898,7 @@ eprint = {http://www.biophysj.org/cgi/reprint/93/10/3373.pdf} volume = "96", number = "10", pages = "108101", - keywords = "Biophysics", - keywords = "Computer Simulation", - keywords = "Data Interpretation, Statistical", - keywords = "Kinetics", - keywords = "Micromanipulation", - keywords = "Models, Chemical", - keywords = "Models, Molecular", - keywords = "Molecular Conformation", - keywords = "Muscle Proteins", - keywords = "Nucleic Acid Conformation", - keywords = "Protein Binding", - keywords = "Protein Denaturation", - keywords = "Protein Folding", - keywords = "Protein Kinases", - keywords = "RNA", - keywords = "Stress, Mechanical", - keywords = "Thermodynamics", - keywords = "Time Factors", + 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 @@ -3227,16 +2974,7 @@ eprint = {http://www.biophysj.org/cgi/reprint/93/10/3373.pdf} volume = "213", number = "4", pages = "527--545", - keywords = "Adult", - keywords = "Aged", - keywords = "Aging", - keywords = "Animals", - keywords = "Humans", - keywords = "Longevity", - keywords = "Middle Aged", - keywords = "Models, Biological", - keywords = "Survival Rate", - keywords = "Systems Theory", + 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 @@ -3290,14 +3028,7 @@ eprint = {http://www.biophysj.org/cgi/reprint/93/10/3373.pdf} volume = "34", number = "1", pages = "1--15", - keywords = "Aging", - keywords = "Biometry", - keywords = "History, 19th Century", - keywords = "History, 20th Century", - keywords = "Humans", - keywords = "Life Tables", - keywords = "Mortality", - keywords = "Sexual Maturation", + 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 @@ -3320,7 +3051,7 @@ eprint = {http://www.biophysj.org/cgi/reprint/93/10/3373.pdf} of his observations and insights in light of research on aging that has taken place since then.", ISSN = "0070-3370", -notes = "Hardly any actual math, but the references might be interesting. +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.", url = "http://www.jstor.org/stable/2061656", @@ -3337,25 +3068,7 @@ url = "http://www.jstor.org/stable/2061656", volume = "69", number = "1-2", pages = "1--31", - keywords = "Adolescent", - keywords = "Adult", - keywords = "Aged", - keywords = "Aged, 80 and over", - keywords = "Aging", - keywords = "Biometry", - keywords = "Child", - keywords = "Child, Preschool", - keywords = "Data Interpretation, Statistical", - keywords = "Female", - keywords = "Humans", - keywords = "Infant", - keywords = "Infant, Newborn", - keywords = "Longitudinal Studies", - keywords = "Male", - keywords = "Middle Aged", - keywords = "Models, Biological", - keywords = "Models, Statistical", - keywords = "Mortality", + 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 @@ -3379,7 +3092,7 @@ url = "http://www.jstor.org/stable/2061656", and the probable errors in those analyses are discussed.", ISSN = "0047-6374", -notes = "Nice table of various functions associated with Gompertz and Weibull models.", +note = "Nice table of various functions associated with Gompertz and Weibull models.", doi = "10.1016/0047-6374(93)90068-3" } @@ -3393,11 +3106,7 @@ doi = "10.1016/0047-6374(93)90068-3" volume = "3", number = "3", pages = "255--261", - keywords = "Ligands", - keywords = "Microscopy, Atomic Force", - keywords = "Polysaccharides", - keywords = "Protein Denaturation", - keywords = "Proteins", + 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 @@ -3432,22 +3141,7 @@ doi = "10.1016/0047-6374(93)90068-3" volume = "112", number = "1-2", pages = "13--23", - keywords = "Binding Sites", - keywords = "Computer Simulation", - keywords = "DNA", - keywords = "DNA-Binding Proteins", - keywords = "Elasticity", - keywords = "Ligands", - keywords = "Macromolecular Substances", - keywords = "Micromanipulation", - keywords = "Microscopy, Atomic Force", - keywords = "Models, Chemical", - keywords = "Molecular Biology", - keywords = "Nucleic Acid Conformation", - keywords = "Physical Stimulation", - keywords = "Protein Binding", - keywords = "Protein Conformation", - keywords = "Stress, Mechanical", + 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 @@ -3479,11 +3173,7 @@ doi = "10.1016/0047-6374(93)90068-3" volume = "90", number = "11", pages = "3851--3864", - keywords = "Biomechanics", - keywords = "Microscopy, Atomic Force", - keywords = "Models, Molecular", - keywords = "Statistical Distributions", - keywords = "Thermodynamics", + 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 @@ -3525,8 +3215,7 @@ doi = {10.1063/1.439715} volume = "100", number = "20", pages = "11378--11381", - keywords = "Spectrum Analysis", - keywords = "Temperature", + 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, @@ -3559,18 +3248,7 @@ doi = {10.1063/1.439715} volume = "73", number = "3", pages = "1281--1287", - keywords = "Binding Sites", - keywords = "Biopolymers", - keywords = "Kinetics", - keywords = "Ligands", - keywords = "Microscopy, Atomic Force", - keywords = "Models, Chemical", - keywords = "Molecular Conformation", - keywords = "Protein Conformation", - keywords = "Proteins", - keywords = "Reproducibility of Results", - keywords = "Stochastic Processes", - keywords = "Thermodynamics", + 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 @@ -3603,20 +3281,7 @@ doi = {10.1063/1.439715} volume = "72", number = "4", pages = "1568--1581", - keywords = "Avidin", - keywords = "Binding Sites", - keywords = "Biotin", - keywords = "Computer Simulation", - keywords = "Hydrogen Bonding", - keywords = "Mathematics", - keywords = "Microscopy, Atomic Force", - keywords = "Microspheres", - keywords = "Models, Molecular", - keywords = "Molecular Structure", - keywords = "Protein Binding", - keywords = "Protein Conformation", - keywords = "Protein Folding", - keywords = "Sepharose", + 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 @@ -3709,8 +3374,8 @@ doi = {10.1063/1.439715} @Book{vanKampen07, title = "Stochastic Processes in Physics and Chemistry", - author = "N.G. {van Kampen}", - editin = "3", + author = "van Kampen, N.G.", + edition = "3", publisher = "Elsevier, North-Holland Personal Library", address = "Amsterdam", year = "2007", @@ -3734,8 +3399,7 @@ doi = {10.1063/1.439715} } @Article{walton08, - author = "Emily B. Walton and Sunyoung Lee and Krystyn J. {Van - Vliet}", + author = "Emily B. Walton and Sunyoung Lee and van Vliet, Krystyn J.", title = "Extending Bell's model: how force transducer stiffness alters measured unbinding forces and kinetics of molecular complexes.", @@ -3746,18 +3410,7 @@ doi = {10.1063/1.439715} volume = "94", number = "7", pages = "2621--2630", - keywords = "Biotin", - keywords = "Computer Simulation", - keywords = "Elasticity", - keywords = "Kinetics", - keywords = "Mechanotransduction, Cellular", - keywords = "Models, Chemical", - keywords = "Models, Molecular", - keywords = "Molecular Motor Proteins", - keywords = "Motion", - keywords = "Streptavidin", - keywords = "Stress, Mechanical", - keywords = "Transducers", + 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 @@ -3809,6 +3462,7 @@ doi = {10.1063/1.439715} } @Article{wikipedia_cubic_function, + key="wikipedia_cubic_function", author = "Wikipedia", title = "Cubic function", journal = "Wikipedia",