2014
DOI: 10.1063/1.4878494
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Using Markov state models to study self-assembly

Abstract: Markov state models (MSMs) have been demonstrated to be a powerful method for computationally studying intramolecular processes such as protein folding and macromolecular conformational changes. In this article, we present a new approach to construct MSMs that is applicable to modeling a broad class of multi-molecular assembly reactions. Distinct structures formed during assembly are distinguished by their undirected graphs, which are defined by strong subunit interactions. Spatial inhomogeneities of free sub… Show more

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Cited by 54 publications
(57 citation statements)
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References 139 publications
(248 reference statements)
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“…[35] In particular, recent millisecond simulations [34] revealed unexpected intermediate stages in the processing of DNA by RNA polymerase. These simulations used a multi-scale approach that extrapolates from conventional sub-microsecond molecular dynamics models using Markov models [36] to approach the real timescale for translocation (at least tens of microseconds). They also represent an important step forward in the state of the art for using modeling to describe features that are important for rational design but which are difficult if not impossible to measure experimentally.…”
Section: Reviewmentioning
confidence: 99%
“…[35] In particular, recent millisecond simulations [34] revealed unexpected intermediate stages in the processing of DNA by RNA polymerase. These simulations used a multi-scale approach that extrapolates from conventional sub-microsecond molecular dynamics models using Markov models [36] to approach the real timescale for translocation (at least tens of microseconds). They also represent an important step forward in the state of the art for using modeling to describe features that are important for rational design but which are difficult if not impossible to measure experimentally.…”
Section: Reviewmentioning
confidence: 99%
“…Finally, enhanced sampling methods can focus computational time on critical but rare events, such as crossing nucleation barriers. Methods well-suited for the diverse pathways typical of assembly systems include multiple state transition path sampling [36], Markov state models [37], weighted ensemble dynamics [35], and diffusion maps [38].…”
Section: Coarse-grained Models For Capsid Assemblymentioning
confidence: 99%
“…Minimizing φ b ij creates an interaction that resists torsion and enforces angular specificity commensurate with a complete capsid. The potentials are given by Eqs (16) [68,89] Conformational dynamics. In our BD simulations with conformational dynamics, free subunits stochastically switch between inactive and active conformations.…”
Section: Brownian Dynamics Model Detailsmentioning
confidence: 99%