Multiscale modeling of stochastic dynamics processes with MBN Explorer

Stochastic dynamics describes processes in complex systems having the probabilistic nature. They can involve very different dynamical systems and occur on very different temporal and spatial scale. This paper discusses the concept of stochastic dynamics and its implementation in the popular program...

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Bibliographic Details
Published in:Journal of computational chemistry 2022-08, Vol.43 (21), p.1442-1458
Main Authors: Solov'yov, Ilia A., Sushko, Gennady, Friis, Ida, Solov'yov, Andrey V.
Format: Article
Language:English
Subjects:
Biological activity
Cell membranes
Complex systems
diffusion
Dynamical systems
Dynamics
MBN Explorer
multiscale methods
Nanoparticles
random walk
stochastic dynamics
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Summary:Stochastic dynamics describes processes in complex systems having the probabilistic nature. They can involve very different dynamical systems and occur on very different temporal and spatial scale. This paper discusses the concept of stochastic dynamics and its implementation in the popular program MBN Explorer. Stochastic dynamics in MBN Explorer relies on the Monte Carlo approach and permits simulations of physical, chemical, and biological processes. The paper presents the basic theoretical concepts underlying stochastic dynamics implementation and provides several examples highlighting its applicability to different systems, such as diffusing proteins seeking an anchor point on a cell membrane, deposition of nanoparticles on a surface leading to structures with fractal morphologies, and oscillations of compounds in an autocatalytic reaction. The chosen examples illustrate the diversity of applications that can be modeled by means of stochastic dynamics with MBN Explorer. The computational approach developed in this work describes the dynamics of systems in which all their constituent elements can move stochastically and may experience transformations and reactions. These include different diffusion modes, dissociation and attachment (decay, fission, and fusion), uptake and injections (creation and annihilation) processes, reactive transformations and particle type alteration. Each particle in the system can experience transformations according to a set of pre‐defined rules with given probabilities.
ISSN:0192-8651
1096-987X
DOI:10.1002/jcc.26948