Related papers: Decomposition of Complex Reaction Networks into Re…
Graph transformation systems have the potential to be realistic models of chemistry, provided a comprehensive collection of reaction rules can be extracted from the body of chemical knowledge. A first key step for rule learning is the…
Background: A classical problem in metabolic design is to maximize the production of desired compound in a given chemical reaction network by appropriately directing the mass flow through the network. Computationally, this problem is…
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 present a computational method for performing structural translation, which has been studied recently in the context of analyzing the steady states and dynamical behavior of mass-action systems derived from biochemical reaction networks.…
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…
A decomposition of a chemical reaction network (CRN) is produced by partitioning its set of reactions. The partition induces networks, called subnetworks, that are "smaller" than the given CRN which, at this point, can be called parent…
In this paper we derive a compact mathematical formulation describing the dynamics of chemical reaction networks that are complex-balanced and are governed by mass action kinetics. The formulation is based on the graph of (substrate and…
Reaction networks, or equivalently Petri nets, are a general framework for describing processes in which entities of various kinds interact and turn into other entities. In chemistry, where the reactions are assigned "rate constants", any…
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,…
Sensitivity studies the network response to perturbations. We consider local perturbations of the concentrations of metabolites at an equilibrium. We investigate the responses in the network, both of the metabolite concentrations and of the…
Reaction networks in the bulk and on surfaces are widespread in physical, chemical and biological systems. In macroscopic systems, which include large populations of reactive species, stochastic fluctuations are negligible and the reaction…
Robustness of biochemical systems has become one of the central questions in systems biology although it is notoriously difficult to formally capture its multifaceted nature. Maintenance of normal system function depends not only on the…
We consider the chemical reaction networks and study currents in these systems. Reviewing recent decomposition of rate functionals from large deviation theory for Markov processes, we adapt these results for reaction networks. In…
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.…
Many real networks can be understood as two complementary networks with two kind of nodes. This is the case of metabolic networks where the first network has chemical compounds as nodes and the second one has nodes as reactions. The second…
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…
We formally characterize a set of causality-based properties of metabolic networks. This set of properties aims at making precise several notions on the production of metabolites, which are familiar in the biologists' terminology. From a…
The spatially distributed reaction networks are indispensable for the understanding of many important phenomena concerning the development of organisms, coordinated cell behavior, and pattern formation. The purpose of this brief discussion…
Biological networks provide insight into the complex organization of biological processes in a cell at the system level. They are an effective tool for understanding the comprehensive map of functional interactions, finding the functional…
Simulating chemical reaction networks is often computationally demanding, in particular due to stiffness. We propose a novel simulation scheme where long runs are not simulated as a whole but assembled from shorter precomputed segments of…