Simulating biochemical networks at the particle level and in time and space: Green's function reaction dynamics
We present a technique, called Green's function reaction dynamics (GFRD), for particle-based simulations of reaction-diffusion systems. GFRD uses a maximum time step such that only single particles or pairs of particles have to be considered. For these particles, the Smoluchowski equations are...
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| Veröffentlicht in: | Physical review letters 2005-04, Vol.94 (12), p.128103.1-128103.4, Article 128103 |
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| container_end_page | 128103.4 |
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| container_issue | 12 |
| container_start_page | 128103.1 |
| container_title | Physical review letters |
| container_volume | 94 |
| creator | VAN ZON, Jeroen S TEN WOLDE, Pieter Rein |
| description | We present a technique, called Green's function reaction dynamics (GFRD), for particle-based simulations of reaction-diffusion systems. GFRD uses a maximum time step such that only single particles or pairs of particles have to be considered. For these particles, the Smoluchowski equations are solved analytically using Green's functions, which are used to set up an event-driven algorithm. We apply the technique to a model of gene expression. Under biologically relevant conditions, GFRD is up to 5 orders of magnitude faster than conventional particle-based schemes. |
| doi_str_mv | 10.1103/physrevlett.94.128103 |
| format | Article |
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Under biologically relevant conditions, GFRD is up to 5 orders of magnitude faster than conventional particle-based schemes.</description><identifier>ISSN: 0031-9007</identifier><identifier>EISSN: 1079-7114</identifier><identifier>DOI: 10.1103/physrevlett.94.128103</identifier><identifier>PMID: 15903966</identifier><identifier>CODEN: PRLTAO</identifier><language>eng</language><publisher>Ridge, NY: American Physical Society</publisher><subject>Algorithms ; Chemistry ; Diffusion ; DNA - genetics ; DNA-Directed RNA Polymerases - metabolism ; Exact sciences and technology ; Gene Expression ; General and physical chemistry ; Kinetics ; Models, Genetic ; Poisson Distribution ; Promoter Regions, Genetic ; Theory of reactions, general kinetics ; Theory of reactions, general kinetics. Catalysis. 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GFRD uses a maximum time step such that only single particles or pairs of particles have to be considered. For these particles, the Smoluchowski equations are solved analytically using Green's functions, which are used to set up an event-driven algorithm. We apply the technique to a model of gene expression. Under biologically relevant conditions, GFRD is up to 5 orders of magnitude faster than conventional particle-based schemes.</description><subject>Algorithms</subject><subject>Chemistry</subject><subject>Diffusion</subject><subject>DNA - genetics</subject><subject>DNA-Directed RNA Polymerases - metabolism</subject><subject>Exact sciences and technology</subject><subject>Gene Expression</subject><subject>General and physical chemistry</subject><subject>Kinetics</subject><subject>Models, Genetic</subject><subject>Poisson Distribution</subject><subject>Promoter Regions, Genetic</subject><subject>Theory of reactions, general kinetics</subject><subject>Theory of reactions, general kinetics. Catalysis. Nomenclature, chemical documentation, computer chemistry</subject><issn>0031-9007</issn><issn>1079-7114</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2005</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpFkU1P3DAQhq0KBMvHT2jlC-WUrT_WTswNoUKRVmpV6DlynHHXreME21m0_76muxKneTV6ZkZ6BqGPlCwpJfzLtNmlCFsPOS_VaklZU7of0IKSWlU1pasjtCCE00oRUp-is5T-EEIok80JOqVCEa6kXKDxyQ2z19mF37hzo9nA4Iz2OEB-HePfhHXGeQN40jE74wF72ILHOvTYBZzdAP9zmrSBG_wQAcJ1wnYOJrsx4Ah6H_pd0GVzukDHVvsEl4d6jn7df32--1atvz883t2uKyOYyJWgwDtuVVf3tWTaKqoUU5r3trGE9SsOignLJe9Fxw3lICU0TWdqzoSxXPBz9Hm_d4rjywwpt4NLBrzXAcY5tbJuhBCMFVDsQRPHVIzadopu0HHXUtK-mW5_FNM_Ybsuplu1avemy9ynw4G5G6B_nzqoLcDVAdCpGLVRB-PSOyfr8ikl-D--Toub</recordid><startdate>20050401</startdate><enddate>20050401</enddate><creator>VAN ZON, Jeroen S</creator><creator>TEN WOLDE, Pieter Rein</creator><general>American Physical Society</general><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope></search><sort><creationdate>20050401</creationdate><title>Simulating biochemical networks at the particle level and in time and space: Green's function reaction dynamics</title><author>VAN ZON, Jeroen S ; TEN WOLDE, Pieter Rein</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c525t-51e3b3f9b7d762af919929a3df8f02d43e925f363d5b3c13e66e88bc7325cf353</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2005</creationdate><topic>Algorithms</topic><topic>Chemistry</topic><topic>Diffusion</topic><topic>DNA - genetics</topic><topic>DNA-Directed RNA Polymerases - metabolism</topic><topic>Exact sciences and technology</topic><topic>Gene Expression</topic><topic>General and physical chemistry</topic><topic>Kinetics</topic><topic>Models, Genetic</topic><topic>Poisson Distribution</topic><topic>Promoter Regions, Genetic</topic><topic>Theory of reactions, general kinetics</topic><topic>Theory of reactions, general kinetics. 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Nomenclature, chemical documentation, computer chemistry</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>VAN ZON, Jeroen S</creatorcontrib><creatorcontrib>TEN WOLDE, Pieter Rein</creatorcontrib><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Physical review letters</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>VAN ZON, Jeroen S</au><au>TEN WOLDE, Pieter Rein</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Simulating biochemical networks at the particle level and in time and space: Green's function reaction dynamics</atitle><jtitle>Physical review letters</jtitle><addtitle>Phys Rev Lett</addtitle><date>2005-04-01</date><risdate>2005</risdate><volume>94</volume><issue>12</issue><spage>128103.1</spage><epage>128103.4</epage><pages>128103.1-128103.4</pages><artnum>128103</artnum><issn>0031-9007</issn><eissn>1079-7114</eissn><coden>PRLTAO</coden><abstract>We present a technique, called Green's function reaction dynamics (GFRD), for particle-based simulations of reaction-diffusion systems. 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| ispartof | Physical review letters, 2005-04, Vol.94 (12), p.128103.1-128103.4, Article 128103 |
| issn | 0031-9007 1079-7114 |
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| source | MEDLINE; American Physical Society Journals |
| subjects | Algorithms Chemistry Diffusion DNA - genetics DNA-Directed RNA Polymerases - metabolism Exact sciences and technology Gene Expression General and physical chemistry Kinetics Models, Genetic Poisson Distribution Promoter Regions, Genetic Theory of reactions, general kinetics Theory of reactions, general kinetics. Catalysis. Nomenclature, chemical documentation, computer chemistry |
| title | Simulating biochemical networks at the particle level and in time and space: Green's function reaction dynamics |
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