Using Markov State Models to Study Self-Assembly
arXiv:1402.1784 · doi:10.1063/1.4878494
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 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.
12 pages, 11 figures
References in corpus (10)
- Identification of slow molecular order parameters for Markov model construction
- Reversible self-assembly of patchy particles into monodisperse icosahedral clusters
- Entropically Patchy Particles: Engineering Valence through Shape Entropy
- Role of reversibility in viral capsid growth: A paradigm for self-assembly
- Viral genome structures are optimal for capsid assembly
- Mechanisms of Size Control and Polymorphism in Viral Capsid Assembly
- A theory for viral capsid assembly around electrostatic cores
- Controlling Viral Capsid Assembly with Templating
- Stochastic kinetics of viral capsid assembly based on detailed protein structures
- Common physical framework explains phase behavior and dynamics of atomic, molecular and polymeric network-formers
Cited by in corpus (5)
- Mechanisms of virus assembly
- Recent advances in coarse-grained modeling of virus assembly
- Optimization of Non-Equilibrium Self-Assembly Protocols Using Markov State Models
- Accessing Semi-Addressable Self Assembly with Efficient Structure Enumeration
- Discrete state model of a self-aggregating colloidal system with directional interactions