From 2659d1be33d4be1930a8f9162120a5861240fa47 Mon Sep 17 00:00:00 2001 From: "W. Trevor King" Date: Fri, 14 Jun 2013 14:37:13 -0400 Subject: [PATCH] sawsim/methods.tex: Fix (or hide) outstanding TODO issues --- src/sawsim/methods.tex | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) 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 -- 2.26.2