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A theorem for the thermodynamics of chemical reaction networks at steady state
thermodynamics of chemical reaction networks steady state Biological Physics
2012/5/3
In this article the Gordan theorem is applied to the thermodynamics of a chemical reaction network at steady state. From a theoretical viewpoint it states that the exclusion (presence) of closed react...
Stochastic theory of large-scale enzyme-reaction networks: Finite copy number corrections to rate equation models
Stochastic theory large-scale enzyme-reaction networks Finite copy number corrections
2011/8/18
Abstract: Chemical reactions inside cells occur in compartment volumes in the range of atto- to femtolitres. Physiological concentrations realized in such small volumes imply low copy numbers of inter...
Variable elimination in post-translational modification reaction networks with mass-action kinetics
Polynomial equations Mass-action kinetics MAPK cascade Rational functions Chemical Reaction Networks
2011/10/8
Abstract: We define a subclass of Chemical Reaction Networks called Post-Translational Modification systems. Important biological examples of such systems include MAPK cascades and two-component syste...
A Linear Programming Approach to Weak Reversibility and Linear Conjugacy of Chemical Reaction Networks
chemical kinetics stability theory weak reversibility linear programming dynamical equivalence
2011/8/30
Abstract: A numerically effective procedure for determining weakly reversible chemical reaction networks that are linearly conjugate to a known reaction network is proposed in this paper. The method i...
Separation of time-scales and model reduction for stochastic reaction networks
Separation time-scales stochastic reaction networks
2010/11/12
A stochastic model for a chemical reaction network is embedded in a one-parameter family of models with species numbers and rate constants scaled by powers of the parameter. A systematic approach is ...
Reaction Networks For Interstellar Chemical Modelling: Improvements and Challenges
Reaction Networks Interstellar Chemical Modelling
2010/11/11
We survey the current situation regarding chemical modelling of the synthesis of molecules in the interstellar medium. The present state of knowledge concerning the rate coecients and their uncertain...
Finding complex balanced and detailed balanced realizations of chemical reaction networks
Finding complex balanced detailed balanced realizations chemical reaction networks
2010/11/15
Reversibility, weak reversibility and deficiency, detailed and complex balancing are generally not "encoded" in the kinetic differential equations but they are realization properties that may imply lo...
Chemical Master versus Chemical Langevin for First-Order Reaction Networks
Birth-and-death process Chemical Master Equation chemical ki-netics correlation matrix Euler{Maruyama gene regulation network Gillespie Ito Lemma stochastic simulation algorithm
2008/11/10
Markov jump processes are widely used to model interacting species in circumstances where discreteness and stochasticity are relevant. Such mod- els have been particularly successful in computational ...