From: W. Trevor King <wking@drexel.edu>
Date: Tue, 23 Feb 2010 14:46:10 +0000 (-0500)
Subject: Move Sawsim into paragraph fully into sawsim/introduction.tex
X-Git-Tag: v1.0~444
X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=6fa7a7c750f638ea66b23e9057597f8f3ab9f650;p=thesis.git

Move Sawsim into paragraph fully into sawsim/introduction.tex
---

diff --git a/tex/src/introduction/main.tex b/tex/src/introduction/main.tex
index 95f3ba1..19f9004 100644
--- a/tex/src/introduction/main.tex
+++ b/tex/src/introduction/main.tex
@@ -53,7 +53,6 @@ remarkably difficult.
 \end{figure}
 
 % the free energy landscape
-
 Folding a protein via a brute force sampling of all possible
 conformations is impossibly inefficient, due to the exponential
 scaling of possible conformations with protein length, as outlined by
@@ -121,6 +120,7 @@ cantilever and incident on a position sensitive photodetector
 cantilever is known\citep{levy02}, the force applied to the sample can
 be calculated.
 
+% really, AFM can do this ;)
 The forces that can be applied and measured with an AFM range from
 tens of piconewtons to hundreds of nanonewtons.  The investigation of
 the unfolding and refolding processes of individual protein molecules
@@ -196,26 +196,3 @@ time, facilitating single molecule studies.
   \end{center}
 \end{figure}
 
-% 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
-properties of the protein molecules from the experimental data of
-force-induced protein unfolding measurements.  Steered molecular
-dynamics simulations\citep{lu98}, as well as calculations and
-simulations using lattice\citep{lu99} and off-lattice
-models\citep{klimov00,li01}, have provided insights into structural
-and energetic changes during force-induced protein unfolding.
-However, these simulations often involve time scales that are orders
-of magnitude smaller than those of the experiments, and the parameters
-used in the calculations are often neither experimentally controllable
-nor measurable.  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 experiment using
-AFM\citep{rief97a,rief97b,rief98,carrion-vazquez99b,best02,zinober02,jollymore09},
-however...
diff --git a/tex/src/sawsim/introduction.tex b/tex/src/sawsim/introduction.tex
index ad42142..c66afba 100644
--- a/tex/src/sawsim/introduction.tex
+++ b/tex/src/sawsim/introduction.tex
@@ -1,8 +1,27 @@
 \section{Introduction}
 \label{sec:sawsim:introduction}
 
-The Monte Carlo simulation method has been used since the first report
-of mechanical unfolding experiment using
+% 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
+properties of the protein molecules from the experimental data of
+force-induced protein unfolding measurements.  Steered molecular
+dynamics simulations\citep{lu98}, as well as calculations and
+simulations using lattice\citep{lu99} and off-lattice
+models\citep{klimov00,li01}, have provided insights into structural
+and energetic changes during force-induced protein unfolding.
+However, these simulations often involve time scales that are orders
+of magnitude smaller than those of the experiments, and the parameters
+used in the calculations are often neither experimentally controllable
+nor measurable.  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 experiment using
 AFM\citep{rief97a,rief97b,rief98,carrion-vazquez99b,best02,zinober02,jollymore09},
 however, a comprehensive description and discussion of the simulation
 procedures and the intricacies involved has not been reported.  In