From: W. Trevor King Date: Fri, 14 Jun 2013 18:38:32 +0000 (-0400) Subject: sawsim/introduction.tex: Hide parameter TODO (no time to look this up) X-Git-Tag: v1.0~66 X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=99611baea952728ec6423824f59786423502b470;p=thesis.git sawsim/introduction.tex: Hide parameter TODO (no time to look this up) --- diff --git a/src/sawsim/introduction.tex b/src/sawsim/introduction.tex index 9440afd..295b6f5 100644 --- a/src/sawsim/introduction.tex +++ b/src/sawsim/introduction.tex @@ -30,16 +30,17 @@ However, these simulations often involve time scales that are orders of magnitude smaller than those of the experiments (\cref{sec:single-molecule}), and the parameters used in the calculations are often neither experimentally controllable nor -measurable (TODO: example parameters of each type). As a result, a -Monte Carlo simulation approach based on a simple two-state kinetic -model for the protein is usually used to analyze data from mechanical -unfolding experiments. A comparison of the force curves measured -experimentally and those generated from simulations can yield the -unfolding rate constant of the protein in the absence of force as well -as the distance from the native state to the transition state along -the pulling direction. The Monte Carlo simulation method has been -used since the first report of mechanical unfolding experiments using -the AFM% +measurable. +% (TODO: example parameters of each type). +As a result, a Monte Carlo simulation approach based on a simple +two-state kinetic model for the protein is usually used to analyze +data from mechanical unfolding experiments. A comparison of the force +curves measured experimentally and those generated from simulations +can yield the unfolding rate constant of the protein in the absence of +force as well as the distance from the native state to the transition +state along the pulling direction. The Monte Carlo simulation method +has been used since the first report of mechanical unfolding +experiments using the AFM% \citep{rief97b,rief97a,rief98,carrion-vazquez99b,best02,zinober02,jollymore09}, but these previous implementations are neither fully described nor publicly available.