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Phys Rev E. 2016 Oct;94(4-1):042306. Epub 2016 Oct 10.

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

Author information

1
Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA.
2
Department of Computer Science, University of California Santa Barbara, Santa Barbara, California 93106, USA.

Abstract

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. Our 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.

PMID:
27841639
DOI:
10.1103/PhysRevE.94.042306

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