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Title: Population dynamics, information transfer, and spatial organization in a chemical reaction network under spatial confinement and crowding conditions

Here, we investigate, via Brownian dynamics simulations, the reaction dynamics of a generic, nonlinear chemical network under spatial confinement and crowding conditions. In detail, the Willamowski-Rossler chemical reaction system has been “extended” and considered as a prototype reaction-diffusion system. These results are potentially relevant to a number of open problems in biophysics and biochemistry, such as the synthesis of primitive cellular units (protocells) and the definition of their role in the chemical origin of life and the characterization of vesicle-mediated drug delivery processes. More generally, the computational approach presented in this work makes the case for the use of spatial stochastic simulation methods for the study of biochemical networks in vivo where the “well-mixed” approximation is invalid and both thermal and intrinsic fluctuations linked to the possible presence of molecular species in low number copies cannot be averaged out.
Authors:
 [1] ;  [2]
  1. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  2. Univ. of California, Santa Barbara, CA (United States). Dept. of Computer Science
Publication Date:
Report Number(s):
LA-UR-15-28942
Journal ID: ISSN 2470-0045; PLEEE8; TRN: US1800619
Grant/Contract Number:
AC52-06NA25396; 1R01EB014877-01
Type:
Accepted Manuscript
Journal Name:
Physical Review E
Additional Journal Information:
Journal Volume: 94; Journal Issue: 4; Journal ID: ISSN 2470-0045
Publisher:
American Physical Society (APS)
Research Org:
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Sponsoring Org:
National Institutes of Health (NIH)
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
OSTI Identifier:
1414084

Bellesia, Giovanni, and Bales, Benjamin B. Population dynamics, information transfer, and spatial organization in a chemical reaction network under spatial confinement and crowding conditions. United States: N. p., Web. doi:10.1103/PhysRevE.94.042306.
Bellesia, Giovanni, & Bales, Benjamin B. Population dynamics, information transfer, and spatial organization in a chemical reaction network under spatial confinement and crowding conditions. United States. doi:10.1103/PhysRevE.94.042306.
Bellesia, Giovanni, and Bales, Benjamin B. 2016. "Population dynamics, information transfer, and spatial organization in a chemical reaction network under spatial confinement and crowding conditions". United States. doi:10.1103/PhysRevE.94.042306. https://www.osti.gov/servlets/purl/1414084.
@article{osti_1414084,
title = {Population dynamics, information transfer, and spatial organization in a chemical reaction network under spatial confinement and crowding conditions},
author = {Bellesia, Giovanni and Bales, Benjamin B.},
abstractNote = {Here, we investigate, via Brownian dynamics simulations, the reaction dynamics of a generic, nonlinear chemical network under spatial confinement and crowding conditions. In detail, the Willamowski-Rossler chemical reaction system has been “extended” and considered as a prototype reaction-diffusion system. These results are potentially relevant to a number of open problems in biophysics and biochemistry, such as the synthesis of primitive cellular units (protocells) and the definition of their role in the chemical origin of life and the characterization of vesicle-mediated drug delivery processes. More generally, the computational approach presented in this work makes the case for the use of spatial stochastic simulation methods for the study of biochemical networks in vivo where the “well-mixed” approximation is invalid and both thermal and intrinsic fluctuations linked to the possible presence of molecular species in low number copies cannot be averaged out.},
doi = {10.1103/PhysRevE.94.042306},
journal = {Physical Review E},
number = 4,
volume = 94,
place = {United States},
year = {2016},
month = {10}
}