相关论文: Modeling of chemical reaction systems with detaile…
A central feature of complex systems is the relevance and entanglement of different levels of description. For instance, the dynamics of ecosystems can be alternatively described in terms of large ecological processes and classes of…
For many real physico-chemical complex systems detailed mechanism includes both reversible and irreversible reactions. Such systems are typical in homogeneous combustion and heterogeneous catalytic oxidation. Most complex enzyme reactions…
Analyzing qualitative behaviors of biochemical reactions using its associated network structure has proven useful in diverse branches of biology. As an extension of our previous work, we introduce a graph-based framework to calculate steady…
A finite-volume method for the steady, compressible, reacting, turbulent Navier-Stokes equations is developed by using a steady-state preserving splitting scheme for the stiff source terms in chemical reaction. Laminar and turbulent…
We analyse a dynamic control problem for scalar reaction-diffusion equations, focusing on the emulation of pattern formation through the selection of appropriate active controls. While boundary controls alone prove inadequate for…
Most biochemical reactions in living cells are open systems interacting with environment through chemostats to exchange both energy and materials. At a mesoscopic scale, the number of each species in those biochemical reactions can be…
Discrete-state, continuous-time Markov models are becoming commonplace in the modelling of biochemical processes. The mathematical formulations that such models lead to are opaque, and, due to their complexity, are often considered…
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 developed for determining appropriate…
Motivated by recent progress on the interplay between graph theory, dynamics, and systems theory, we revisit the analysis of chemical reaction networks described by mass action kinetics. For reaction networks possessing a thermodynamic…
Recent work of M.D. Johnston et al. has produced sufficient conditions on the structure of a chemical reaction network which guarantee that the corresponding discrete state space system exhibits an extinction event. The conditions consist…
The evolution of a system of chemical reactions can be studied, in the eikonal approximation, by means of a Hamiltonian dynamical system. The fixed points of this dynamical system represent the different states in which the chemical system…
Complex systems of intracellular biochemical reactions have a central role in regulating cell identities and functions. Biochemical reaction systems are typically studied using the language and tools of graph theory. However, graph…
The modern thermodynamics of discrete systems is based on graph theory, which provides both algebraic methods to define observables and a geometric intuition of their meaning and role. However, because chemical reactions are usually…
We develop a systematic approach to the linear-noise approximation for stochastic reaction systems with distributed delays. Unlike most existing work our formalism does not rely on a master equation, instead it is based upon a dynamical…
Chemical reaction networks can undergo nonequilibrium phase transitions upon variation of external control parameters like the chemical potential of a species. We investigate the flux in the associated chemostats that is proportional to the…
We investigate the nonequilibrium stationary states of systems consisting of chemical reactions among molecules of several chemical species. To this end we introduce and develop a stochastic formulation of nonequilibrium thermodynamics of…
Stochasticity plays a fundamental role in various biochemical processes, such as cell regulatory networks and enzyme cascades. Isothermal, well-mixed systems can be modelled as Markov processes, typically simulated using the Gillespie…
In the first part of this paper, we propose new optimization-based methods for the computation of preferred (dense, sparse, reversible, detailed and complex balanced) linearly conjugate reaction network structures with mass action dynamics.…
We present a systematic mathematical analysis of the qualitative steady-state response to rate perturbations in large classes of reaction networks. This includes multimolecular reactions and allows for catalysis, enzymatic reactions,…
We consider the forward Kolmogorov equation corresponding to measure-valued processes stemming from a class of interacting particle systems in population dynamics, including variations of the Bolker-Pacala-Dieckmann-Law model. Under the…