From 1327dd9eda62907b9c4b92eee3d25885a8a46ed4 Mon Sep 17 00:00:00 2001 From: "W. Trevor King" Date: Mon, 25 Jun 2012 21:12:27 -0400 Subject: [PATCH] Clean up lattice and off-latice references in the sawsim intro. Also reference the snippet about simulation timescales in introduction/main.tex. --- src/sawsim/introduction.tex | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/src/sawsim/introduction.tex b/src/sawsim/introduction.tex index a0522d9..7c3d3e8 100644 --- a/src/sawsim/introduction.tex +++ b/src/sawsim/introduction.tex @@ -6,15 +6,16 @@ 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 +dynamics simulations\citep{lu98,lu99}, as well as calculations and +simulations using lattice\citep{klimov99,socci99} 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 (TODO: example parameters of each type). As a result, -a Monte Carlo simulation approach based on a simple two-state kinetic +of magnitude smaller than those of the experiments +(\cref{sec:single-molecule}), and the parameters used in the +calculations are often neither experimentally controllable nor +measurable (TODO: example parameters of each type). 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 -- 2.26.2