1 @string{IJBMM = "International Journal of Biological Macromolecules"}
3 @string{WKing = "King, W.~Trevor"}
4 @string{MSu = "Su, Meihong"}
5 @string{GYang = "Yang, Guoliang"}
8 author = WKing #" and "# MSu #" and "# GYang,
9 title = "{M}onte {C}arlo simulation of mechanical unfolding of proteins
10 based on a simple two-state model",
14 address = "Department of Physics, Drexel University, 3141
15 Chestnut Street, Philadelphia, PA 19104, USA.",
21 alternative_issn = "1879-0003",
22 doi = "10.1016/j.ijbiomac.2009.12.001",
23 url = "http://www.sciencedirect.com/science/article/B6T7J-
24 4XWMND2-1/2/7ef768562b4157fc201d450553e5de5e",
26 keywords = "Atomic force microscopy;Mechanical unfolding;Monte Carlo
27 simulation;Worm-like chain;Single molecule methods",
28 abstract = "Single molecule methods are becoming routine biophysical
29 techniques for studying biological macromolecules. In mechanical
30 unfolding of proteins, an externally applied force is used to induce
31 the unfolding of individual protein molecules. Such experiments have
32 revealed novel information that has significantly enhanced our
33 understanding of the function and folding mechanisms of several types
34 of proteins. To obtain information on the unfolding kinetics and the
35 free energy landscape of the protein molecule from mechanical unfolding
36 data, a Monte Carlo simulation based on a simple two-state kinetic
37 model is often used. In this paper, we provide a detailed description
38 of the procedure to perform such simulations and discuss the
39 approximations and assumptions involved. We show that the appearance of
40 the force versus extension curves from mechanical unfolding of proteins
41 is affected by a variety of experimental parameters, such as the length
42 of the protein polymer and the force constant of the cantilever. We
43 also analyze the errors associated with different methods of data
44 pooling and present a quantitative measure of how well the simulation
45 results fit experimental data. These findings will be helpful in
46 experimental design, artifact identification, and data analysis for
47 single molecule studies of various proteins using the mechanical
53 @unpublished{ 2013-05-thesis,
54 title= {Open source single molecule force spectroscopy},
59 note= {Thesis defense, Drexel University},
60 address = {Drexel University},
61 url = {http://blog.tremily.us/posts/Thesis/talk/},
64 @unpublished{ 2013-01-columbia,
65 title= {Collaborative version control with {G}it},
69 note= {Software Carpentry boot camp, Columbia University},
70 address = {Columbia University},
73 @unpublished{ 2009-10-life-cycles,
74 title= {Software life-cycles and alphabet soup},
78 note= {Drexel Physics Graduate Student Association},
79 address = {Drexel University}
82 @unpublished{ 2008-06-locks,
83 title= {Manipulating combination locks \& Ray tracing with polarization},
87 note= {Drexel Physics Graduate Student Association},
88 address = {Drexel University}
91 @unpublished{ 2006-05-quantum-computing,
92 title= {Quantum Computing},
95 note= {Rochester Solid State final},
96 address = {University of Rochester}
102 @unpublished{ 2013-04-swc,
103 title= {Teaching Software Carpentry: Better Science through Science},
107 note= {Drexel CoAS Research Day},
108 address = {Philadelphia, Pennsylvania},
111 @unpublished{ 2012-04-calibcant,
112 title= {Thermally calibrating {AFM} cantilever spring constants},
116 note= {Drexel CoAS Research Day},
117 address = {Philadelphia, Pennsylvania},
120 @unpublished{ 2011-04-saswsim,
121 title= {Flexible parallel simulations and packaging},
125 note= {Drexel CoAS Research Day},
126 address = {Philadelphia, Pennsylvania},
129 @unpublished{ 2010-04-open-source,
130 title= {Open source software in experimental protein unfolding},
134 note= {Drexel CoAS Research Day},
135 address = {Philadelphia, Pennsylvania},
138 @unpublished{ 2009-03-roughness,
139 title= {Experimental Estimation of the Free Energy Landscape
140 Roughness of Protein Molecules},
144 note= {Biophysical Society Annual Meeting},
145 address = {Philadelphia, Pennsylvania},
148 @unpublished{ 2008-04-sawsim,
149 title= {Simulated mechanical unfolding of single proteins},
153 note= {Drexel CoAS Research Day},
154 address = {Philadelphia, Pennsylvania},
157 @unpublished{ 2008-02-stiffness,
158 title= {Effects of Cantilever Stiffness on Unfolding Force in AFM
163 note= {Biophysical Society Annual Meeting},
164 address = {Long Beach, California},