相关论文: Computing Weakly Reversible Deficiency Zero Networ…
Long-term behaviors of biochemical systems are described by steady states in deterministic models and stationary distributions in stochastic models. Obtaining their analytic solutions can be done for limited cases, such as linear or…
An algorithm is given in this paper for the computation of dynamically equivalent weakly reversible realizations with the maximal number of reactions, for chemical reaction networks (CRNs) with mass action kinetics. The original problem…
Mass-action kinetics is frequently used in systems biology to model the behaviour of interacting chemical species. Many important dynamical properties are known to hold for such systems if they are weakly reversible and have a low…
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 is based on translating the structural and…
An algorithm is given in this paper for the computation of dynamically equivalent weakly reversible realizations with the maximal number of reactions, for chemical reaction networks (CRNs) with mass action kinetics.
A dynamical system obtains a wide variety of kinetic realizations, which is advantageous for the analysis of biochemical systems. A reaction network, derived from a dynamical system, may or may not possess some properties needed for a…
It has been recently observed that the dynamical properties of mass action systems arising from many models of biochemical reaction networks can be derived by considering the corresponding properties of a related generalized mass action…
Many biochemical and industrial applications involve complicated networks of simultaneously occurring chemical reactions. Under the assumption of mass action kinetics, the dynamics of these chemical reaction networks are governed by systems…
We introduce the notion of corresponding a chemical reaction network to a split network translation, and use this novel process to extend the scope of existing network-based theory for characterizing the steady state set of mass-action…
Biochemical networks are used in computational biology, to model the static and dynamical details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as…
Network translation has recently been used to establish steady state properties of mass action systems by corresponding the given system to a generalized one which is either dynamically or steady state equivalent. In this work we further…
The automated inference of physically interpretable (bio)chemical reaction network models from measured experimental data is a challenging problem whose solution has significant commercial and academic ramifications. It is demonstrated,…
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,…
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…
We prove that if a given reaction network $\mathcal{N}$ has a weakly reversible deficiency zero realization for all choice of rate constants, then there exists a $\textit{unique}$ weakly reversible deficiency zero network $\mathcal{N}'$…
The analysis of complex reaction networks is of great importance in several chemical and biochemical fields (interstellar chemistry, prebiotic chemistry, reaction mechanism, etc). In this article, we propose to simultaneously refine and…
We discuss a method of approximate model reduction for networks of biochemical reactions. This method can be applied to networks with polynomial or rational reaction rates and whose parameters are given by their orders of magnitude. In…
Reaction networks are widely used models to describe biochemical processes. Stochastic fluctuations in the counts of biological macromolecules have amplified consequences due to their small population sizes. This makes it necessary to favor…
The large-scale properties of chemical reaction systems, such as the metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information -- lists of chemical reactions -- available in databases. Even for the…
Reliability on complex biological networks reconstructions remains a concern. Although observations are getting more and more precise, the data collection process is yet error prone and the proofs display uneven certitude. In the case of…