\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.
projects / thesis.git / blobdiff