From f1d7ee94bf7d1446f5503fe603c3741a4ce8b1e5 Mon Sep 17 00:00:00 2001
From: "W. Trevor King" <wking@tremily.us>
Date: Wed, 12 Jun 2013 12:05:02 -0400
Subject: [PATCH] introduction/main.tex: Rework the thesis outline

Lay out the current structure.
---
 src/contour-space/main.tex |  4 +++-
 src/introduction/main.tex  | 46 ++++++++++++++++++--------------------
 2 files changed, 25 insertions(+), 25 deletions(-)

diff --git a/src/contour-space/main.tex b/src/contour-space/main.tex
index 9111f72..7ec31f6 100644
--- a/src/contour-space/main.tex
+++ b/src/contour-space/main.tex
@@ -1,4 +1,6 @@
 \chapter{Contour length space}
 \label{sec:contour-space}
 
-TODO\citet{puchner08}.
+Contour length space analysis converts force curves to unfolding
+pathway fingerprints\citet{puchner08}, which is useful for
+identifying and characterizing unfolding behavior.
diff --git a/src/introduction/main.tex b/src/introduction/main.tex
index f05959e..3e094c1 100644
--- a/src/introduction/main.tex
+++ b/src/introduction/main.tex
@@ -204,27 +204,25 @@ behavior.
 \section{Thesis Outline}
 \label{sec:outline}
 
-TODO: fill in once structure has stabilized
-
-%\Cref{sec:unfolding} of this thesis discusses the theory of protein
-%unfolding for single domains.  \Cref{sec:tension} discusses linker
-%tension modeling.  \Cref{sec:unfolding-distributions} pulls
-%\cref{sec:unfolding,sec:tension} together to discuss the theory of
-%mechanical unfolding experiments.  This theory makes straightforward
-%analysis of unfolding results difficult, so \cref{sec:sawsim} presents
-%a Monte Carlo simulation approach to fitting unfolding parameters, and
-%\cref{sec:contour-space} presents the contour-length space analysis
-%for converting force curves to unfolding pathway fingerprints.
-%\Cref{sec:temperature-theory} wraps up the theory section by extending
-%the analysis in \cref{sec:unfolding,sec:unfolding-distributions} to
-%multiple temperatures.
-%
-%\Cref{sec:apparatus} describes our experimental apparatus and methods,
-%as well as calibration procedures.  With both the theory and procedure
-%taken care of, \cref{sec:cantilever,sec:temperature}
-%present and analyze AFM cantilever- and temperature-dependent
-%unfolding behavior of the immunoglobulin-like domain 27 from human
-%Titin (I27).
-%
-%We close with \cref{sec:future}, which presents our conclusions and
-%discusses possible directions for future work.
+\Cref{sec:methods} of this thesis outlines the apparatus and methods
+for single molecule force spectroscopy with an atomic force
+microscope.  \Cref{sec:sawsim} presents my \sawsim\ Monte Carlo
+simulation for modeling unfolding/refolding behavior.  By comparing
+model simulations with experimental measurements, we can gain insight
+into the protein's kinetics.  After \cref{sec:sawsim}, you should have
+a pretty firm grasp of the underlying physics, so we'll move on to
+\cref{sec:pyafm} and discuss my \pyafm\ experiment control software.
+With both the kinetic theory and procedure taken care of,
+\cref{sec:calibcant} discusses thermal cantilever calibration,
+deriving the theoretical approach and presenting my
+\calibcant\ automatic calibration software.
+
+Moving away from experiment control, \cref{sec:hooke} presents the
+\Hooke\ suite for extracting unfolding force histograms (for
+comparison with \sawsim\ simulations).  In \cref{sec:salt}, I pull all
+the pieces together (experiment control, post processing, and
+simulation) to carry out unfolding experiments on the
+immunoglobulin-like domain 27 from human Titin (I27) in buffers with
+different ion strength.  We close with \cref{sec:future}, which
+summarizes my conclusions and discusses possible directions for future
+work.
-- 
2.26.2