From f3fdcc1be5f6390298809c705ed3a4544a5c7306 Mon Sep 17 00:00:00 2001 From: "W. Trevor King" Date: Wed, 15 May 2013 11:38:00 -0400 Subject: [PATCH] sawsim/introduction.tex: Add a lead in paragraph (why this chapter?) A number of my readers have been confused about why I lead off my contributions with the sawsim chapter. This paragraph is an attempt to lay that out for them. --- src/sawsim/introduction.tex | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/src/sawsim/introduction.tex b/src/sawsim/introduction.tex index 094ea76..c828758 100644 --- a/src/sawsim/introduction.tex +++ b/src/sawsim/introduction.tex @@ -1,3 +1,22 @@ +% Why simulations? And why are we leading with them? +Unfolding proteins by pulling on them with an AFM yields a series of +force curves (\cref{fig:expt-sawtooth}). How do we get from the +unfolding curves to a deeper understanding of the unfolding physics? +In this chapter, I present my \sawsim\ simulator, which performs +discrete-state unfolding simulations using theoretical models of +protein unfolding. By finding the models and parameters that best +reproduce the experimental data, we can find unforced unfolding rates +and other unfolded polymer distances that can be cross checked in +chemical unfolding experiments and used to validate more detailed +molecular dynamics simulations. The \sawsim\ simulations discussed +here are carried out after the unfolding experiments +(\cref{sec:pyafm}), cantilever calibration (\cref{sec:calibcant}), and +post-processing (\cref{sec:hooke}), but I discuss \sawsim\ first +because it provides the cleanest description of the underlying +physical processes. After we cover the theory here, we will be better +prepared for the realistic complications discussed in the following +chapters. + % AFM unfolding analysis, what we'll do. Much theoretical and computational work has been done in order to extract information about the structural, kinetic, and energetic -- 2.26.2