Modeling and Analysis of Stochastic Reaction Kinetics in Biomolecular Systems

Yutaka Hori

doi:10.1007/s00354-020-00095-y

Modeling and Analysis of Stochastic Reaction Kinetics in Biomolecular Systems

Yutaka Hori

Department of Applied Physics and Physico-Informatics

Research output: Contribution to journal › Article › peer-review

1 Citation (Scopus)

Abstract

Chemical reactions in small-volume reactors such as biological cells are highly variable due to the stochastic collision events of the small number of molecules. To analyze and design these stochastic biomolecular reactions, computational tools have been developed based on rigorous mathematical foundations. This paper reviews fundamental theory and computational tools for the modeling, analysis, and design of stochastic biomolecular systems. Specifically, we first review the governing equation of the stochastic kinetics using the first principle modeling. Then, three computational approaches are introduced for simulating and/or analyzing the governing equation.

Original language	English
Journal	New Generation Computing
DOIs	https://doi.org/10.1007/s00354-020-00095-y
Publication status	Accepted/In press - 2020 Jan 1

Keywords

Mathematical optimization
Monte Carlo simulations
Stochastic chemical reactions
Stochastic systems

ASJC Scopus subject areas

Software
Theoretical Computer Science
Hardware and Architecture
Computer Networks and Communications

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10.1007/s00354-020-00095-y

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abstract = "Chemical reactions in small-volume reactors such as biological cells are highly variable due to the stochastic collision events of the small number of molecules. To analyze and design these stochastic biomolecular reactions, computational tools have been developed based on rigorous mathematical foundations. This paper reviews fundamental theory and computational tools for the modeling, analysis, and design of stochastic biomolecular systems. Specifically, we first review the governing equation of the stochastic kinetics using the first principle modeling. Then, three computational approaches are introduced for simulating and/or analyzing the governing equation.",

keywords = "Mathematical optimization, Monte Carlo simulations, Stochastic chemical reactions, Stochastic systems",

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AB - Chemical reactions in small-volume reactors such as biological cells are highly variable due to the stochastic collision events of the small number of molecules. To analyze and design these stochastic biomolecular reactions, computational tools have been developed based on rigorous mathematical foundations. This paper reviews fundamental theory and computational tools for the modeling, analysis, and design of stochastic biomolecular systems. Specifically, we first review the governing equation of the stochastic kinetics using the first principle modeling. Then, three computational approaches are introduced for simulating and/or analyzing the governing equation.

KW - Mathematical optimization

KW - Monte Carlo simulations

KW - Stochastic chemical reactions

KW - Stochastic systems

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JF - New Generation Computing

ER -

Modeling and Analysis of Stochastic Reaction Kinetics in Biomolecular Systems

Abstract

Keywords

ASJC Scopus subject areas

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