Begin versioning
authorW. Trevor King <wking@tremily.us>
Wed, 29 May 2013 22:15:10 +0000 (18:15 -0400)
committerW. Trevor King <wking@tremily.us>
Wed, 29 May 2013 22:15:10 +0000 (18:15 -0400)
.gitignore [new file with mode: 0644]
Makefile [new file with mode: 0644]
ts.bib [new file with mode: 0644]
ts.tex [new file with mode: 0644]

diff --git a/.gitignore b/.gitignore
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+*.aux
+*.bbl
+*.blg
+*.log
+*.out
+*.pdf
diff --git a/Makefile b/Makefile
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+#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
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+@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 (file)
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--- /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}