相关论文: Sign patterns for chemical reaction networks
A system made up of N interacting species is considered. Self-reaction terms are assumed of the logistic type. Pairwise interactions take place among species according to different modalities, thus yielding a complex asymmetric disordered…
Two networks are said to be linearly conjugate if the solution of their dynamic equations can be transformed into each other by a positive linear transformation. The study on dynamical equivalence in chemical kinetic systems was initiated…
We develop a matrix-based approach to predict and verify indirect interactions in gene and protein regulatory networks. It is based on the approximate transitivity of indirect regulations (e.g. A regulates B and B regulates C often implies…
Chemical reaction networks (CRNs) formally model chemistry in a well-mixed solution. CRNs are widely used to describe information processing occurring in natural cellular regulatory networks, and with upcoming advances in synthetic biology,…
Reaction networks are commonly used to model the evolution of populations of species subject to transformations following an imposed stoichiometry. This paper focuses on the efficient characterisation of dynamical properties of Discrete…
We derive the Hessian geometric structure of nonequilibrium chemical reaction networks (CRN) on the flux and force spaces induced by the Legendre duality of convex dissipation functions and characterize their dynamics as a generalized flow.…
We identify the thermodynamic conditions necessary to observe indefinite growth in homogeneous open chemical reaction networks (CRNs) satisfying mass action kinetics. We also characterize the thermodynamic efficiency of growth by…
Chemical reactions that couple to systems that phase separate have been implicated in diverse contexts from biology to materials science. However, how a particular set of chemical reactions (chemical reaction network, CRN) would affect the…
Reaction currents in chemical networks usually increase when increasing their driving affinities. But far from equilibrium the opposite can also happen. We find that such negative differential response (NDR) occurs in reaction schemes of…
Artificial neural networks (NNs) can be implemented using chemical reaction networks (CRNs), where the concentrations of species act as inputs and outputs. In such biochemical computing, noise-robust computing is crucial due to the…
Inferring chemical reaction networks (CRN) from concentration time series is a challenge encouragedby the growing availability of quantitative temporal data at the cellular level. This motivates thedesign of algorithms to infer the…
Predicting how systems respond to external perturbations far from equilibrium remains a fundamental challenge across physics, chemistry, and biology. We present a unified response framework for stochastic Markov dynamics that integrates…
We examine reaction networks (CRNs) through their associated continuous-time Markov processes. Studying the dynamics of such networks is in general hard, both analytically and by simulation. In particular, stationary distributions of…
We study two specific measures of quality of chemical reaction networks, Precision and Sensitivity. The two measures arise in the study of sensory adaptation, in which the reaction network is viewed as an input-output system. Given a step…
Motivated by biochemical reaction networks, a generalization of the classical secant condition for the stability analysis of cyclic interconnected commensurate fractional-order systems is provided. The main result presents a sufficient…
Reaction networks have been widely used as generic models in diverse areas of applied sciences, such as biology, chemistry, ecology, epidemiology, and computer science. A reaction network incorporating noisy effects is modeled as a…
Reaction rate equations are ordinary differential equations that are frequently used to describe deterministic chemical kinetics at the macroscopic scale. At the microscopic scale, the chemical kinetics is stochastic and can be captured by…
Thermodynamic constraints on reactions directions are inherent in the structure of a given biochemical network. However, concrete procedures for determining feasible reaction directions for large-scale metabolic networks are not well…
Embedding computation in biochemical environments incompatible with traditional electronics is expected to have wide-ranging impact in synthetic biology, medicine, nanofabrication and other fields. Natural biochemical systems are typically…
We establish a new relationship between monotonicity and contractivity and use this connection to describe a new general class of weakly contractive reaction networks. The new class is characterized by the stoichiometry matrix of the…