sawsim: Shift review of past research into the introduction

diff --git a/src/sawsim/discussion.tex b/src/sawsim/discussion.tex
index dade809e51b80cd8529f1f749ea156524f1b49b9..4dabc9370f083bb876a79388d3a1274ff563b3a2 100644 (file)
--- a/src/sawsim/discussion.tex
+++ b/src/sawsim/discussion.tex
@@ -755,49 +755,3 @@ $l_{ts}$ is the characteristic length of the transition state.
 
 \citet{evans97} solved this unfolding rate for both inverse power law
 potentials and cusp potentials.
-
-\section{Review of current research}
-
-There is a long history of protein unfolding and unbinding
-simulations.  Early work by \citet{grubmuller96} and
-\citet{izrailev97} focused on molecular dynamics (MD) simulations of
-receptor-ligand breakage.  Around the same time, \citet{evans97}
-introduced a Monte Carlo Kramers' simulation in the context of
-receptor-ligand breakage.  The approach pioneered by \citet{evans97}
-was used as the basis for analysis of the initial protein unfolding
-experiments\citep{rief97a}.  However, none of these earlier
-implementations were open source, which made it difficult to reuse or
-validate their results.
-%
-\nomenclature[text ]{MD}{Molecular dynamics simulation.  Simulate the
-  physical motion of atoms and molecules by numerically solving
-  Newton's equations.}
-
-Within the Monte Carlo simulation approach, there are two main models
-for protein domain unfolding under tension: Bell's and
-Kramers'\citep{schlierf06,hummer03,dudko06}.  Bell introduced his
-model in the context of cell adhesion\citep{bell78}, but it has been
-widely used to model mechanical unfolding in
-proteins\citep{rief97a,carrion-vazquez99b,schlierf06} due to its
-simplicity and ease of use\citep{hummer03}.  Kramers introduced his
-theory in the context of thermally activated barrier crossings, which
-is how we use it here.
-
-Evans introduced the saddle-point Kramers' approximation in a protein
-unfolding context in 1997 (\xref{evans97}{equation}{3}).  However,
-early work on mechanical unfolding focused on the simpler Bell
-model\citep{rief97a}.  In the early 2000's, the
-saddle-point/steepest-descent approximation to Kramer's model
-(\xref{hanggi90}{equation}{4.56c}) was introduced into our
-field\citep{dudko03,hyeon03}.  By the mid 2000's, the full-blown
-double-integral form of Kramer's model
-(\xref{hanggi90}{equation}{4.56b}) was in use\citep{schlierf06}.
-
-There have been some tangential attempts towards even fancier models:
-\citet{dudko03} attempted to reduce the restrictions of the
-single-unfolding-path model and \citet{hyeon03} attempted to measure
-the local roughness using temperature dependent unfolding.  However,
-further work on these lines has been slow, because the Bell model fits
-the data well despite its simplicity.  For more complicated models to
-gain ground, we need larger, more detailed datasets that expose
-features which the Bell model doesn't capture.

diff --git a/src/sawsim/introduction.tex b/src/sawsim/introduction.tex
index 295b6f5339697c126fb05e4b3f66d3e2fb8f0a47..2eb19eb16e3cfbcf6b156057709047fc7c617839 100644 (file)
--- a/src/sawsim/introduction.tex
+++ b/src/sawsim/introduction.tex
@@ -57,3 +57,50 @@ demonstrated, and the errors associated with different methods of data
 pooling are discussed.  These results should be useful in future
 experimental design, artifact identification, and data analysis for
 single molecule mechanical unfolding experiments.
+
+\section{Review of current research}
+
+There is a long history of protein unfolding and unbinding
+simulations.  Early work by \citet{grubmuller96} and
+\citet{izrailev97} focused on molecular dynamics (MD) simulations of
+receptor-ligand breakage.  Around the same time, \citet{evans97}
+introduced a Monte Carlo Kramers' simulation in the context of
+receptor-ligand breakage.  The approach pioneered by \citet{evans97}
+was used as the basis for analysis of the initial protein unfolding
+experiments\citep{rief97a}.  However, none of these earlier
+implementations were open source, which made it difficult to reuse or
+validate their results.
+%
+\nomenclature[text ]{MD}{Molecular dynamics simulation.  Simulate the
+  physical motion of atoms and molecules by numerically solving
+  Newton's equations.}
+
+Within the Monte Carlo simulation approach, there are two main models
+for protein domain unfolding under tension: Bell's and
+Kramers'\citep{schlierf06,hummer03,dudko06}.  Bell introduced his
+model in the context of cell adhesion\citep{bell78}, but it has been
+widely used to model mechanical unfolding in
+proteins\citep{rief97a,carrion-vazquez99b,schlierf06} due to its
+simplicity and ease of use\citep{hummer03}
+(\cref{sec:sawsim:rate:bell}).  Kramers introduced his theory in the
+context of thermally activated barrier crossings, which is how we use
+it here (\cref{sec:sawsim:rate:other}).
+
+Evans introduced the saddle-point Kramers' approximation in a protein
+unfolding context in 1997 (\xref{evans97}{equation}{3}).  However,
+early work on mechanical unfolding focused on the simpler Bell
+model\citep{rief97a}.  In the early 2000's, the
+saddle-point/steepest-descent approximation to Kramer's model
+(\xref{hanggi90}{equation}{4.56c}) was introduced into our
+field\citep{dudko03,hyeon03}.  By the mid 2000's, the full-blown
+double-integral form of Kramer's model
+(\xref{hanggi90}{equation}{4.56b}) was in use\citep{schlierf06}.
+
+There have been some tangential attempts towards even fancier models:
+\citet{dudko03} attempted to reduce the restrictions of the
+single-unfolding-path model and \citet{hyeon03} attempted to measure
+the local roughness using temperature dependent unfolding.  However,
+further work on these lines has been slow, because the Bell model fits
+the data well despite its simplicity.  For more complicated transition
+rate models to gain ground, we need larger, more detailed datasets
+that expose features which the Bell model doesn't capture.