% Journals @string{IJBMM = "International Journal of Biological Macromolecules"} @string{SCI = "Science"} % Institutions @string{Drexel = "Drexel University"} % Addresses @string{DrexelPhysics = "Department of Physics, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, USA."} % People @string{WKing = "King, W.~Trevor"} @string{JFernandez = "Fernandez, Julio M."} @string{HEGaub = "Gaub, Hermann E."} @string{MGautel = "Gautel, Mathias"} @string{TGuy = "Guy, Tommy"} @string{CKoch = "Koch, Christina"} @string{FOesterhelt = "Oesterhelt, Filipp"} @string{MRief = "Rief, Matthias"} @string{TSibley = "Sibley, Thomas"} @string{MSu = "Su, Meihong"} @string{GYang = "Yang, Guoliang"} % Papers @phdthesis { king13, author = WKing, title = "Open source single molecule force spectroscopy", school = Drexel, year = 2013, month = jun, address = DrexelPhysics, url = "http://hdl.handle.net/1860/4188", eprint = "https://idea.library.drexel.edu/islandora/object/idea%3A4188/datastream/OBJ/download/Open_source_single_molecule_force_spectroscopy.pdf", keywords = "Physics; Molecular spectroscopy; Biophysics", abstract = "Single molecule force spectroscopy (SMFS) experiments provide an experimental benchmark for testing simulated and theoretical predictions of protein unfolding behavior. Despite it use since 1997\citep{rief97a}, the labs currently engaged in SMFS use in-house software and procedures for critical tasks such as cantilever calibration and Monte Carlo unfolding simulation. Besides wasting developer time producing and maintaining redundant implementations, the lack of transparency makes it more difficult to share data and techniques between labs, which slows progress. In some cases it can also lead to ambiguity as to which of several similar approaches, correction factors, etc.\ were used in a particular paper. % \par In this thesis, I introduce an SMFS sofware suite for cantilever calibration (\href{https://pypi.python.org/pypi/calibcant/}{calibcant}), experiment control (\href{https://pypi.python.org/pypi/unfold-protein}{unfold-protein}), analysis (\href{https://pypi.python.org/pypi/Hooke}{Hooke}), and postprocessing (\href{http://blog.tremily.us/posts/sawsim/}{sawsim}) in the context of velocity clamp unfolding of I27 octomers in buffers with varying concentrations of \CaCl\textsubscript{2}. All of the tools are licensed under open source licenses, which allows SMFS researchers to centralize future development. Where possible, care has been taken to keep these packages operating system (OS) agnostic. The experiment logic in unfold-protein and calibcant is still nominally OS agnostic, but those packages depend on \href{https://pypi.python.org/pypi/pyafm}{more fundamental packages} that control the physical hardware in use. At the bottom of the physical-interface stack are the \href{http://www.comedi.org/}{Comedi} drivers from the Linux kernel. Users running other operating systems should be able to swap in analogous low level physical-interface packages if Linux is not an option.", } @article { king10, author = WKing #" and "# MSu #" and "# GYang, title = "{M}onte {C}arlo simulation of mechanical unfolding of proteins based on a simple two-state model", year = 2010, month = mar, day = 1, address = DrexelPhysics, journal = IJBMM, volume = 46, number = 2, pages = "159--166", issn = "0141-8130", alternative_issn = "1879-0003", doi = "10.1016/j.ijbiomac.2009.12.001", url = "http://www.sciencedirect.com/science/article/B6T7J- 4XWMND2-1/2/7ef768562b4157fc201d450553e5de5e", language = "eng", keywords = "Atomic force microscopy;Mechanical unfolding;Monte Carlo simulation;Worm-like chain;Single molecule methods", abstract = "Single molecule methods are becoming routine biophysical techniques for studying biological macromolecules. In mechanical unfolding of proteins, an externally applied force is used to induce the unfolding of individual protein molecules. Such experiments have revealed novel information that has significantly enhanced our understanding of the function and folding mechanisms of several types of proteins. To obtain information on the unfolding kinetics and the free energy landscape of the protein molecule from mechanical unfolding data, a Monte Carlo simulation based on a simple two-state kinetic model is often used. In this paper, we provide a detailed description of the procedure to perform such simulations and discuss the approximations and assumptions involved. We show that the appearance of the force versus extension curves from mechanical unfolding of proteins is affected by a variety of experimental parameters, such as the length of the protein polymer and the force constant of the cantilever. We also analyze the errors associated with different methods of data pooling and present a quantitative measure of how well the simulation results fit experimental data. These findings will be helpful in experimental design, artifact identification, and data analysis for single molecule studies of various proteins using the mechanical unfolding method." } % Talks @unpublished{ 2015-04-uw, title= {Databases and and {SQL}}, author = TSibley #" and "# WKing, year = 2015, month = apr, note= {Software Carpentry workshop, University of Washington}, address = {University of Washington}, } % Message-ID: <54D3F261.7040808 at uw.edu> @unpublished{ 2014-03-uw, title= {Bash, {P}ython, and {SQL}}, author = TGuy #" and "# WKing #" and "# CKoch, year = 2014, month = mar, note= {Software Carpentry workshop, University of Washington}, address = {University of Washington}, } % Message-ID: <20140226041514.GE13371 at odin.tremily.us> @unpublished{ 2013-05-thesis, title= {Open source single molecule force spectroscopy}, author = WKing, year = 2013, month = may, day = 28, note= {Thesis defense, Drexel University}, address = {Drexel University}, url = {http://blog.tremily.us/posts/Thesis/talk/}, } @unpublished{ 2013-01-columbia, title= {Collaborative version control with {G}it}, author = WKing, year = 2013, month = jan, note= {Software Carpentry workshop, Columbia University}, address = {Columbia University}, } @unpublished{ 2009-10-life-cycles, title= {Software life-cycles and alphabet soup}, author = WKing, year = 2009, month = oct, note= {Drexel Physics Graduate Student Association}, address = {Drexel University} } @unpublished{ 2008-06-locks, title= {Manipulating combination locks \& Ray tracing with polarization}, author = WKing, year = 2008, month = jun, note= {Drexel Physics Graduate Student Association}, address = {Drexel University} } @unpublished{ 2006-05-quantum-computing, title= {Quantum Computing}, author = WKing, year = 2006, note= {Rochester Solid State final}, address = {University of Rochester} } % month = may, % Posters @unpublished{ 2013-04-swc, title= {Teaching Software Carpentry: Better Science through Science}, author = WKing, year = 2013, month = apr, note= {Drexel CoAS Research Day}, address = {Philadelphia, Pennsylvania}, } @unpublished{ 2012-04-calibcant, title= {Thermally calibrating {AFM} cantilever spring constants}, author = WKing, year = 2012, month = apr, note= {Drexel CoAS Research Day}, address = {Philadelphia, Pennsylvania}, } @unpublished{ 2011-04-saswsim, title= {Flexible parallel simulations and packaging}, author = WKing, year = 2011, month = apr, note= {Drexel CoAS Research Day}, address = {Philadelphia, Pennsylvania}, } @unpublished{ 2010-04-open-source, title= {Open source software in experimental protein unfolding}, author = WKing, year = 2010, month = apr, note= {Drexel CoAS Research Day}, address = {Philadelphia, Pennsylvania}, } @unpublished{ 2009-03-roughness, title= {Experimental Estimation of the Free Energy Landscape Roughness of Protein Molecules}, author = WKing, year = 2009, month = mar, note= {Biophysical Society Annual Meeting}, address = {Philadelphia, Pennsylvania}, } @unpublished{ 2008-04-sawsim, title= {Simulated mechanical unfolding of single proteins}, author = WKing, year = 2008, month = apr, note= {Drexel CoAS Research Day}, address = {Philadelphia, Pennsylvania}, } @unpublished{ 2008-02-stiffness, title= {Effects of Cantilever Stiffness on Unfolding Force in AFM Protein Unfolding}, author = WKing, year = 2008, month = feb, note= {Biophysical Society Annual Meeting}, address = {Long Beach, California}, } % References @article { rief97a, author = MRief #" and "# MGautel #" and "# FOesterhelt #" and "# JFernandez #" and "# HEGaub, title = "Reversible Unfolding of Individual Titin Immunoglobulin Domains by {AFM}", year = 1997, journal = SCI, volume = 276, number = 5315, pages = "1109--1112", doi = "10.1126/science.276.5315.1109", eprint = "http://www.sciencemag.org/cgi/reprint/276/5315/1109.pdf", url = "http://www.sciencemag.org/cgi/content/abstract/276/5315/1109", note = "Seminal paper for force spectroscopy on Titin.", }