相关论文: On Quantitative Comparison of Chemical Reaction Ne…
The main motivation of this work is to assess the validity of a LWR traffic flow model to model measurements obtained from trajectory data, and propose extensions of this model to improve it. A formulation for a discrete dynamical system is…
We present here a combination of two networks, Recurrent Neural Networks (RNN) and Temporarily Convolutional Neural Networks (TCN) in de novo reaction generation using the novel Reaction Smiles-like representation of reactions (CGRSmiles)…
A molecule traveling in a realistic propagation environment can experience stochastic interactions with other molecules and the environment boundary. The statistical behavior of some isolated phenomena, such as dilute unbounded molecular…
In living cells, chemical reactions form a complex network. Complicated dynamics arising from such networks are the origins of biological functions. We propose a novel mathematical method to analyze bifurcation behaviors of a reaction…
We present a novel multiscale simulation approach for modeling stochasticity in chemical reaction networks. The approach seamlessly integrates exact-stochastic and "leaping" methodologies into a single "partitioned leaping" algorithmic…
Inspired by Anderson et al. [J. R. Soc. Interface, 2014] we study the long-term behavior of discrete chemical reaction networks (CRNs). In particular, using techniques from both Petri net theory and CRN theory, we provide a powerful…
We present a method for estimating parameters in stochastic models of biochemical reaction networks by fitting steady-state distributions using Wasserstein distances. We simulate a reaction network at different parameter settings and train…
We propose a universal approach for analysis and fast simulations of stiff stochastic biochemical kinetics networks, which rests on elimination of fast chemical species without a loss of information about mesoscopic, non-Poissonian…
Steady state is an essential concept in reaction networks. Its stability reflects fundamental characteristics of several biological phenomena such as cellular signal transduction and gene expression. Because biochemical reactions occur at…
We show that adding new chemical species into the reactions of a chemical reaction network (CRN) in such a way that the rank of the network remains unchanged preserves its capacity for multiple nondegenerate equilibria and/or periodic…
Biochemical reaction networks in living cells usually involve reversible covalent modification of signaling molecules, such as protein phosphorylation. Under conditions of small molecule numbers, as is frequently the case in living cells,…
Many dynamical systems can be successfully analyzed by representing them as networks. Empirically measured networks and dynamic processes that take place in these situations show heterogeneous, non-Markovian, and intrinsically correlated…
We initiate the study of rate-constant-independent computation of Boolean predicates and numerical functions in the continuous model of chemical reaction networks (CRNs), which model the amount of a chemical species as a nonnegative,…
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.…
Chemical kinetic mechanisms can be represented by sets of elementary reactions that are easily translated into mathematical terms using physicochemical relationships. The schematic representation of reactions captures the interactions…
We investigate, via Brownian dynamics simulations, the reaction dynamics of a simple, non-linear chemical network (the Willamowski-Rossler network) under spatial confinement and crowding conditions. Our results show that the presence of…
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…
We obtain bounds on the Kullback--Leibler divergence to equilibrium for mass-action chemical reaction networks (CRNs) with equilibrium. The associated decay rates are characterized in terms of the singular values of the stoichiometric…
In this paper we study a class of stochastic chemical reaction networks (CRNs) for which chemical species are created by a sequence of chain reactions. We prove that under some convenient conditions on the initial state, some of these…
Within a fully microscopic setting, we derive a variational principle for the non-equilibrium steady states of chemical reaction networks, valid for time-scales over which chemical potentials can be taken to be slowly varying: at…