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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 ...
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 ...