相关论文: Thermodynamics of Growth in Open Chemical Reaction…
Some results are presented on how oscillation is inherited by chemical reaction networks (CRNs) when they are built in natural ways from smaller oscillatory networks. The main results describe four important ways in which a CRN can be…
It is widely recognized that reciprocal interactions between cells and their microenvironment, via mechanical forces and biochemical signaling pathways, regulate cell behaviors during normal development, homeostasis and disease progression…
We derive the nonequilibrium conductance matrix for open stationary Chemical Reaction Networks (CRNs) described by a deterministic mass action kinetic equation. As an illustration, we determine the nonequilibrium conductance matrix of a CRN…
In this and a companion paper we outline a general framework for the thermodynamic description of open chemical reaction networks, with special regard to metabolic networks regulating cellular physiology and biochemical functions. We first…
Random graph models have been instrumental in characterizing complex networks, but chemical reaction networks (CRNs) are better represented as hypergraphs. Traditional models of random CRNs often reduce CRNs to bipartite graphs,…
We generalize thermodynamic uncertainty relation (TUR) and thermodynamic speed limit (TSL) for deterministic chemical reaction networks (CRNs). The scaled diffusion coefficient derived by considering the connection between macroscopic CRNs…
We extend the traditional framework of steady state energy transduction -- typically characterized by a single input and output -- to multi-resource transduction in open chemical reaction networks (CRNs). Transduction occurs when…
We investigate the dynamics of chemical reaction networks (CRNs) with the goal of deriving an upper bound on their reaction rates. This task is challenging due to the nonlinear nature and discrete structure inherent in CRNs. To address…
Chemical reaction networks (CRN) comprise an important class of models to understand biological functions such as cellular information processing, the robustness and control of metabolic pathways, circadian rhythms, and many more. However,…
A reaction system exhibits "absolute concentration robustness" (ACR) in some species if the positive steady-state value of that species does not depend on initial conditions. Mathematically, this means that the positive part of the variety…
We show that if a chemical reaction network (CRN) admits nondegenerate (resp., linearly stable) oscillation, and we add new reversible reactions involving new species to this CRN, then the new CRN so created also admits nondegenerate…
The asymptotic properties of some Markov processes associated to stochastic chemical reaction networks (CRNs) driven by the kinetics of the law of mass action are analyzed. The scaling regime introduced in the paper assumes that the norm of…
Biological regulatory networks depend upon chemical interactions to process information. Engineering such molecular computing systems is a major challenge for synthetic biology and related fields. The chemical reaction network (CRN) model…
Coupled chemical interactions in a well-mixed solution are commonly formalized as chemical reaction networks (CRNs). However, despite the widespread use of CRNs in the natural sciences, the range of computational behaviors exhibited by CRNs…
Chemical systems are interpreted through the species they contain and the reactions they may undergo, i.e., their chemical reaction network (CRN). In spite of their central importance to chemistry, the structure of CRNs continues to be…
Stochastic chemical reaction networks (CRNs) are complex systems which combine the features of concurrent transformation of multiple variables in each elementary reaction event, and nonlinear relations between states and their rates of…
Many reaction networks arising in applications are multistationary, that is, they have the capacity for more than one steady state; while some networks exhibit absolute concentration robustness (ACR), which means that some species…
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…
Much of the theory on chemical-reaction networks (CRNs) has been developed in the ideal-solution limit, where interactions between the solutes are negligible. However, there is a large variety of phenomena in biological cells and…
Chemical reaction networks (CRNs) are foundational models for describing complex biochemical processes. We study noncompetitive CRNs, a class of networks whose static states are rate-independent, and that can implement ReLU neural networks.…