English
 
User Manual Privacy Policy Disclaimer Contact us
  Advanced SearchBrowse

Item

ITEM ACTIONSEXPORT
  Thermodynamic-Kinetic Modeling

Ederer, M., & Gilles, E. D. (2008). Thermodynamic-Kinetic Modeling. Talk presented at 2nd International Symposium on Biothermodynamics. Frankfurt am Main, Germany. 2008-02-21 - 2008-02-22.

Item is

Basic

show hide
Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0013-95B3-E Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0027-C115-E
Genre: Talk

Files

show Files

Locators

show

Creators

show
hide
 Creators:
Ederer, Michael1, Author              
Gilles, E. D.1, Author              
Affiliations:
1Systems Biology, Max Planck Institute for Dynamics of Complex Technical Systems, Max Planck Society, ou_1738155              

Content

show
hide
Free keywords: -
 Abstract: Motivation: The Wegscheider conditions follow from the principle of detailed balance and the second law of thermodynamics. They constrain possible values of kinetic parameters in reaction networks. A mathematical model that violates these conditions describes a thermodynamically impossible system. Large reaction networks, e.g. in cellular signal transduction or metabolism, contain usually a large number of Wegscheider conditions. This makes thermodynamically consistent modeling difficult [1]. Thermodynamic-Kinetic Modeling (TKM): TKM is a formalism for formulation of kinetic rate equation that is based on thermodynamic flux-force relationships [1]. Chemical potentials and thermodynamic forces (negative Gibbs reaction energies) do not scale linearly with concentrations and fluxes, respectively. Thus they are not suited for kinetic modeling of far-from-equilibrium systems. For this reason TKM uses an alternative system of thermokinetic potentials and forces, that are proportional to concentrations and mass-action fluxes, respectively. By using flux-force relationships we structurally avoid violation of Wegscheider conditions. Features of Thermodynamic-Kinetic Modeling: Since TKM structurally avoids thermodynamically infeasible models, it is suited for modeling large networks with many Wegscheider conditions. Widely used kinetic laws, as mass-action or Michaelis-Menten-kinetics, have a simple expression in TKM; e.g. the thermokinetic resistance of a mass-action reaction is constant. The TKM formalism provides a natural framework for model reduction. In particular, rapid-equilibrium assumptions that correspond to a zero thermokinetic resistance can be applied systematically and easily. This is a further important prerequisite for modeling large network. References: [1] Ederer, M. and Gilles, E.D. Thermodynamically feasible kinetic models of reaction networks. Biophys J, 2007, 92, 1846-1857

Details

show
hide
Language(s):
 Dates: 2008
 Publication Status: Not specified
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Method: -
 Identifiers: eDoc: 367032
 Degree: -

Event

show
hide
Title: 2nd International Symposium on Biothermodynamics
Place of Event: Frankfurt am Main, Germany
Start-/End Date: 2008-02-21 - 2008-02-22

Legal Case

show

Project information

show

Source

show