From: W. Trevor King <wking@tremily.us>
Date: Fri, 14 Jun 2013 18:37:13 +0000 (-0400)
Subject: sawsim/methods.tex: Fix (or hide) outstanding TODO issues
X-Git-Tag: v1.0~67
X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=2659d1be33d4be1930a8f9162120a5861240fa47;p=thesis.git

sawsim/methods.tex: Fix (or hide) outstanding TODO issues
---

diff --git a/src/sawsim/methods.tex b/src/sawsim/methods.tex
index d513d73..c54716e 100644
--- a/src/sawsim/methods.tex
+++ b/src/sawsim/methods.tex
@@ -188,7 +188,7 @@ chosen for the folded domains has negligible effect on the unfolding
 forces (\cref{eq:sawsim:x-total}), which was also suggested by
 \citet{staple08}.  Force curves simulated using different models to
 describe the folded domains yielded almost identical unfolding force
-distributions (data not shown, TODO: show data).
+distributions (data not shown).% TODO: show data
 
 As an alternative to modeling the folded domains explicitly or
 ignoring them completely, another approach is to subtract the
@@ -376,10 +376,11 @@ the cantilever deflection induced by liquid motion and fitting the
 time dependence of the deflection to an exponential
 function\citep{jones05}.  For a $200\U{$\mu$m}$ rectangular cantilever
 with a bending spring constant of $20\U{pN/nm}$, the measured
-relaxation time in water is $\sim50\U{$\mu$/s}$ (data not shown.
-TODO: show data).  This relatively large relaxation time constant
-makes the cantilever act as a low-pass filter and also causes a lag in
-the force measurement.
+relaxation time in water is $\sim50\U{$\mu$/s}$ (data not shown).
+% TODO: show data
+This relatively large relaxation time constant makes the cantilever
+act as a low-pass filter and also causes a lag in the force
+measurement.
 %
 \nomenclature{$\eta$}{Dynamic viscocity (\cref{eq:sawsim:tau-wlc}).}
 
@@ -495,6 +496,7 @@ Although the Bell model (\cref{eq:sawsim:bell}) is the most widely
 used unfolding model due to its simplicity and its applicability to
 various biopolymers\citep{rief98}, other theoretical models have been
 proposed to interpret mechanical unfolding data.  For example,
+\citet{walton08} uses a stiffness-corrected Bell model.
 \citet{schlierf06} used the mechanical unfolding data of the protein
 ddFLN4 to demonstrate that Kramers' diffusion model (in the
 spatial-diffusion-limited case, a.k.a. the Smoluchowski
@@ -565,9 +567,6 @@ region (\cref{fig:kramers:integrand}).  The steepest-descent
 formulation has less to say about the underlying energy landscape, but
 it may be more robust in the face of noisy data.
 
-Other tension models in use include a stiffness-corrected
-Bell model\citep{walton08}, and TODO.
-
 How to choose which unfolding model to use?  For proteins with
 relatively narrow folded and transition states, the Bell model
 provides a good approximation, and it is the model used by the vast