Using Markov state models to study self-assembly.
نویسندگان
چکیده
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 subunits are accounted for using a recently developed Gaussian-based signature. Simplifications to this state identification are also investigated. The feasibility of this approach is demonstrated on two different coarse-grained models for virus self-assembly. We find good agreement between the dynamics predicted by the MSMs and long, unbiased simulations, and that the MSMs can reduce overall simulation time by orders of magnitude.
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[37] M. R. Perkett, M. F. Hagan, Using Markov state models to study self-assembly, J. Chem. Phys. 140 (21) (2014) 214101. doi:10.1063/1.4878494.
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ورودعنوان ژورنال:
- The Journal of chemical physics
دوره 140 21 شماره
صفحات -
تاریخ انتشار 2014