From e7b7f5ea0ac2c9242a3596f74542e78865629c6f Mon Sep 17 00:00:00 2001 From: "W. Trevor King" Date: Wed, 29 May 2013 18:15:10 -0400 Subject: [PATCH 1/1] Begin versioning --- .gitignore | 6 ++ Makefile | 18 ++++++ ts.bib | 165 +++++++++++++++++++++++++++++++++++++++++++++++++++++ ts.tex | 31 ++++++++++ 4 files changed, 220 insertions(+) create mode 100644 .gitignore create mode 100644 Makefile create mode 100644 ts.bib create mode 100644 ts.tex diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..9cee8b5 --- /dev/null +++ b/.gitignore @@ -0,0 +1,6 @@ +*.aux +*.bbl +*.blg +*.log +*.out +*.pdf diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..0c726ae --- /dev/null +++ b/Makefile @@ -0,0 +1,18 @@ +#BIBS = ts +#bu1 bu2 bu3 + +ts.pdf: ts.tex $(BIBS:%=%.bbl) $(BIBS:%=%.blg) + pdflatex "$<" + pdflatex "$<" + +$(BIBS:%=%.aux): %.aux: ts.tex + pdflatex "$<" + +$(BIBS:%=%.bbl): %.bbl: %.aux + bibtex "$<" + +$(BIBS:%=%.blg): %.blg: %.aux + bibtex "$<" + +clean: + rm -f *.aux *.bbl *.blg *.log *.out *.pdf diff --git a/ts.bib b/ts.bib new file mode 100644 index 0000000..aefe963 --- /dev/null +++ b/ts.bib @@ -0,0 +1,165 @@ +@string{IJBMM = "International Journal of Biological Macromolecules"} + +@string{WKing = "King, W.~Trevor"} +@string{MSu = "Su, Meihong"} +@string{GYang = "Yang, Guoliang"} + +@article { king10, + author = WKing #" and "# MSu #" and "# GYang, + title = "{M}onte {C}arlo simulation of mechanical unfolding of proteins + based on a simple two-state model", + year = 2010, + month = mar, + day = 1, + address = "Department of Physics, Drexel University, 3141 + Chestnut Street, Philadelphia, PA 19104, USA.", + journal = IJBMM, + volume = 46, + number = 2, + pages = "159--166", + issn = "0141-8130", + alternative_issn = "1879-0003", + doi = "10.1016/j.ijbiomac.2009.12.001", + url = "http://www.sciencedirect.com/science/article/B6T7J- + 4XWMND2-1/2/7ef768562b4157fc201d450553e5de5e", + language = "eng", + keywords = "Atomic force microscopy;Mechanical unfolding;Monte Carlo + simulation;Worm-like chain;Single molecule methods", + abstract = "Single molecule methods are becoming routine biophysical + techniques for studying biological macromolecules. In mechanical + unfolding of proteins, an externally applied force is used to induce + the unfolding of individual protein molecules. Such experiments have + revealed novel information that has significantly enhanced our + understanding of the function and folding mechanisms of several types + of proteins. To obtain information on the unfolding kinetics and the + free energy landscape of the protein molecule from mechanical unfolding + data, a Monte Carlo simulation based on a simple two-state kinetic + model is often used. In this paper, we provide a detailed description + of the procedure to perform such simulations and discuss the + approximations and assumptions involved. We show that the appearance of + the force versus extension curves from mechanical unfolding of proteins + is affected by a variety of experimental parameters, such as the length + of the protein polymer and the force constant of the cantilever. We + also analyze the errors associated with different methods of data + pooling and present a quantitative measure of how well the simulation + results fit experimental data. These findings will be helpful in + experimental design, artifact identification, and data analysis for + single molecule studies of various proteins using the mechanical + unfolding method." +} + +% Talks + +@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 boot camp, 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}, +} diff --git a/ts.tex b/ts.tex new file mode 100644 index 0000000..ec2977c --- /dev/null +++ b/ts.tex @@ -0,0 +1,31 @@ +\documentclass[12pt]{article} + +\topmargin 0.0in +\headheight 0.0in +\headsep 0.0in +\textheight 9in +\oddsidemargin 0in +\textwidth 6in +\pagestyle{empty} % no room for page numbers + +\usepackage{hyperref} +\hypersetup{colorlinks} +\hypersetup{linkcolor=black} +\hypersetup{anchorcolor=black} +\hypersetup{citecolor=black} +\hypersetup{filecolor=black} +\hypersetup{menucolor=black} +\hypersetup{runcolor=black} +\hypersetup{urlcolor=black} + +\title{Teaching Philosophy} +\date{\today} +\author{W.~Trevor King} + +\begin{document} + +\maketitle + +Aloha! + +\end{document} -- 2.26.2