Mass conserved elementary kinetics is sufficient for the existence of a non-equilibrium steady state concentration
Living systems are forced away from thermodynamic equilibrium by exchange of mass and energy with their environment. In order to model a biochemical reaction network in a non-equilibrium state one requires a mathematical formulation to mimic this forcing. We provide a general formulation to force an...
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Veröffentlicht in: | Journal of theoretical biology 2012-12, Vol.314, p.173-181 |
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creator | Fleming, R.M.T. Thiele, I. |
description | Living systems are forced away from thermodynamic equilibrium by exchange of mass and energy with their environment. In order to model a biochemical reaction network in a non-equilibrium state one requires a mathematical formulation to mimic this forcing. We provide a general formulation to force an arbitrary large kinetic model in a manner that is still consistent with the existence of a non-equilibrium steady state. We can guarantee the existence of a non-equilibrium steady state assuming only two conditions; that every reaction is mass balanced and that continuous kinetic reaction rate laws never lead to a negative molecule concentration. These conditions can be verified in polynomial time and are flexible enough to permit one to force a system away from equilibrium. With expository biochemical examples we show how reversible, mass balanced perpetual reaction(s), with thermodynamically infeasible kinetic parameters, can be used to perpetually force various kinetic models in a manner consistent with the existence of a steady state. Easily testable existence conditions are foundational for efforts to reliably compute non-equilibrium steady states in genome-scale biochemical kinetic models.
► Forcing a chemical reaction network away from thermodynamic equilibrium. ► Sufficient conditions for the existence of a non-equilibrium steady state. ► Mass conservation, continuous kinetic rate laws and concentration non-negativity. ► Exchange of mass with the environment is not necessary. |
doi_str_mv | 10.1016/j.jtbi.2012.08.021 |
format | Article |
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► Forcing a chemical reaction network away from thermodynamic equilibrium. ► Sufficient conditions for the existence of a non-equilibrium steady state. ► Mass conservation, continuous kinetic rate laws and concentration non-negativity. ► Exchange of mass with the environment is not necessary.</description><subject>Anaerobiosis</subject><subject>Chemical reaction network</subject><subject>Enzymes - metabolism</subject><subject>Glycolysis</subject><subject>Kinetics</subject><subject>Models, Biological</subject><subject>Molecular Weight</subject><subject>Stoichiometric consistency</subject><subject>Thermodynamic forcing</subject><subject>Thermodynamics</subject><subject>Trypanosoma brucei brucei - metabolism</subject><issn>0022-5193</issn><issn>1095-8541</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kLtOHTEQhq0oUTgheYEUyGWaXcaXvUk0CAFBIkoDteW1x4oPu2uwvSi8PV4dSJnqL_6LZj5CvjOoGbD2dF_v8-hrDozX0NfA2QeyYzA0Vd9I9pHsADivGjaII_IlpT0ADFK0n8kR54PseNfsSPylU6ImLAnjM1qKE864ZB1f6INfMHuTqE80rc5544tDXYg0_0GKf33KuBikwVFNl7BU-LT6yY_RrzMtnrYvRXTGbd-UbtTZh-Ur-eT0lPDbmx6T-6vLu4uf1e3v65uL89vKSIBc7mZ9h6NsHBMWrW5a3XPG2g6EHKEbe2lN241tDxYEImrZiKFzQgM4MbQgjsmPw-5jDE8rpqxmnwxOk14wrEkxxmQ7NIMQJcoPURNDShGdeox-LhAUA7WxVnu1sVYbawW9KqxL6eRtfx1ntP8q73BL4OwQwPLls8eo0obQoPURTVY2-P_tvwK2OZGp</recordid><startdate>20121207</startdate><enddate>20121207</enddate><creator>Fleming, R.M.T.</creator><creator>Thiele, I.</creator><general>Elsevier Ltd</general><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>20121207</creationdate><title>Mass conserved elementary kinetics is sufficient for the existence of a non-equilibrium steady state concentration</title><author>Fleming, R.M.T. ; Thiele, I.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c400t-51187eb45f13deda56a821167034b07b84dc67b680d03eeea45397f3a00f39603</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>Anaerobiosis</topic><topic>Chemical reaction network</topic><topic>Enzymes - metabolism</topic><topic>Glycolysis</topic><topic>Kinetics</topic><topic>Models, Biological</topic><topic>Molecular Weight</topic><topic>Stoichiometric consistency</topic><topic>Thermodynamic forcing</topic><topic>Thermodynamics</topic><topic>Trypanosoma brucei brucei - metabolism</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Fleming, R.M.T.</creatorcontrib><creatorcontrib>Thiele, I.</creatorcontrib><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>Journal of theoretical biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Fleming, R.M.T.</au><au>Thiele, I.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Mass conserved elementary kinetics is sufficient for the existence of a non-equilibrium steady state concentration</atitle><jtitle>Journal of theoretical biology</jtitle><addtitle>J Theor Biol</addtitle><date>2012-12-07</date><risdate>2012</risdate><volume>314</volume><spage>173</spage><epage>181</epage><pages>173-181</pages><issn>0022-5193</issn><eissn>1095-8541</eissn><abstract>Living systems are forced away from thermodynamic equilibrium by exchange of mass and energy with their environment. In order to model a biochemical reaction network in a non-equilibrium state one requires a mathematical formulation to mimic this forcing. We provide a general formulation to force an arbitrary large kinetic model in a manner that is still consistent with the existence of a non-equilibrium steady state. We can guarantee the existence of a non-equilibrium steady state assuming only two conditions; that every reaction is mass balanced and that continuous kinetic reaction rate laws never lead to a negative molecule concentration. These conditions can be verified in polynomial time and are flexible enough to permit one to force a system away from equilibrium. With expository biochemical examples we show how reversible, mass balanced perpetual reaction(s), with thermodynamically infeasible kinetic parameters, can be used to perpetually force various kinetic models in a manner consistent with the existence of a steady state. Easily testable existence conditions are foundational for efforts to reliably compute non-equilibrium steady states in genome-scale biochemical kinetic models.
► Forcing a chemical reaction network away from thermodynamic equilibrium. ► Sufficient conditions for the existence of a non-equilibrium steady state. ► Mass conservation, continuous kinetic rate laws and concentration non-negativity. ► Exchange of mass with the environment is not necessary.</abstract><cop>England</cop><pub>Elsevier Ltd</pub><pmid>22947275</pmid><doi>10.1016/j.jtbi.2012.08.021</doi><tpages>9</tpages><oa>free_for_read</oa></addata></record> |
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source | MEDLINE; Elsevier ScienceDirect Journals |
subjects | Anaerobiosis Chemical reaction network Enzymes - metabolism Glycolysis Kinetics Models, Biological Molecular Weight Stoichiometric consistency Thermodynamic forcing Thermodynamics Trypanosoma brucei brucei - metabolism |
title | Mass conserved elementary kinetics is sufficient for the existence of a non-equilibrium steady state concentration |
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