UZH-Logo

Maintenance Infos

Exact on-lattice stochastic reaction-diffusion simulations using partial-propensity methods


Ramaswamy, Rajesh; Sbalzarini, Ivo F (2011). Exact on-lattice stochastic reaction-diffusion simulations using partial-propensity methods. Journal of Chemical Physics, 135(24):244103.

Abstract

Stochastic reaction-di usion systems frequently exhibit behavior that is not predicted by deterministic simulation models. Stochastic simulation methods, however, are computationally expensive. We present a more efficient stochastic reaction-di usion simulation algorithm that samples realizations from the exact solution of the reaction-di usion master equation. The present algorithm, called Partial-propensity Stochastic Reaction-Di usion (PSRD) method, uses an on-lattice discretization of the reaction-di usion system and relies on partial-propensity methods for computational efficiency. We describe the algorithm in detail, provide a theoretical analysis of its computational cost, and demonstrate its computational performance in benchmarks. We then illustrate the application of PSRD to two- and three-dimensional pattern-forming Gray-Scott systems, highlighting the role of intrinsic noise in these systems.

Stochastic reaction-di usion systems frequently exhibit behavior that is not predicted by deterministic simulation models. Stochastic simulation methods, however, are computationally expensive. We present a more efficient stochastic reaction-di usion simulation algorithm that samples realizations from the exact solution of the reaction-di usion master equation. The present algorithm, called Partial-propensity Stochastic Reaction-Di usion (PSRD) method, uses an on-lattice discretization of the reaction-di usion system and relies on partial-propensity methods for computational efficiency. We describe the algorithm in detail, provide a theoretical analysis of its computational cost, and demonstrate its computational performance in benchmarks. We then illustrate the application of PSRD to two- and three-dimensional pattern-forming Gray-Scott systems, highlighting the role of intrinsic noise in these systems.

Citations

7 citations in Web of Science®
7 citations in Scopus®
Google Scholar™

Altmetrics

Downloads

51 downloads since deposited on 05 Jul 2013
22 downloads since 12 months
Detailed statistics

Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:Special Collections > SystemsX.ch
Special Collections > SystemsX.ch > Research, Technology and Development Projects > LipidX
Special Collections > SystemsX.ch > Research, Technology and Development Projects > WingX
Special Collections > SystemsX.ch > Research, Technology and Development Projects
Dewey Decimal Classification:570 Life sciences; biology
Date:2011
Deposited On:05 Jul 2013 10:46
Last Modified:17 May 2016 16:22
Publisher:American Institute of Physics
ISSN:0021-9606
Publisher DOI:https://doi.org/10.1063/1.3666988
PubMed ID:22225140
Permanent URL: https://doi.org/10.5167/uzh-79200

Download

[img]
Preview
Content: Accepted Version
Filetype: PDF
Size: 3MB
View at publisher
[img]
Preview
Content: Published Version
Filetype: PDF
Size: 1MB

TrendTerms

TrendTerms displays relevant terms of the abstract of this publication and related documents on a map. The terms and their relations were extracted from ZORA using word statistics. Their timelines are taken from ZORA as well. The bubble size of a term is proportional to the number of documents where the term occurs. Red, orange, yellow and green colors are used for terms that occur in the current document; red indicates high interlinkedness of a term with other terms, orange, yellow and green decreasing interlinkedness. Blue is used for terms that have a relation with the terms in this document, but occur in other documents.
You can navigate and zoom the map. Mouse-hovering a term displays its timeline, clicking it yields the associated documents.

Author Collaborations