相关论文: Sign patterns for chemical reaction networks

Growth and decay are system-level properties of chemical reaction networks (CRNs) relevant from prebiotic chemistry to cellular metabolism. Their properties are typically analyzed through the kinetics of particular models, which requires…

Formal methods have enabled breakthroughs in many fields, such as in hardware verification, machine learning and biological systems. The key object of interest in systems biology, synthetic biology, and molecular programming is chemical…

A natural condition on the structure of the underlying chemical reaction network, namely weak reversibility, is shown to guarantee the existence of an equilibrium (steady state) in each positive stoichiometric compatibility class for the…

Stochastic reaction networks (SRNs) provide models of many real-world networks. Examples include networks in epidemiology, pharmacology, genetics, ecology, chemistry, and social sciences. Here, we model stochastic reaction networks by…

We continue recent attempts to put together concepts and results of Chemical Reaction Networks theory (CRNT) and Mathematical Epidemiology (ME), for solving problems of stability of positive ODEs. We provide first an elegant CRN-flavored…

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…

Chemical reaction networks (CRNs) are a standard formalism used in chemistry and biology to reason about the dynamics of molecular interaction networks. In their interpretation by ordinary differential equations, CRNs provide a…

Chemical reaction networks (CRNs) model systems where molecules interact according to a finite set of reactions such as $A + B \to C$, representing that if a molecule of $A$ and $B$ collide, they disappear and a molecule of $C$ is produced.…

This paper answers an open question of Chen, Doty, and Soloveichik [1], who showed that a function f:N^k --> N^l is deterministically computable by a stochastic chemical reaction network (CRN) if and only if the graph of f is a semilinear…

Autocatalytic cores are minimal units in reaction networks (RNs) responsible for the emergence of autocatalysis. In the absence of explicit catalysis, i.e., when an entity appears both as reactant and product in the same reaction, they are…

The stable functionality of networked systems is a hallmark of their natural ability to coordinate between their multiple interacting components. Yet, strikingly, real-world networks seem random and highly irregular, apparently lacking any…

Detailed balance of a chemical reaction network can be defined in several different ways. Here we investigate the relationship among four types of detailed balance conditions: deterministic, stochastic, local, and zero-order local detailed…

The thermodynamic and dynamical conditions necessary to observe indefinite growth in homogeneous open chemical reaction networks (CRNs) satisfying mass action kinetics were presented in Srinivas et al. (2023): Unimolecular CRNs can only…

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…

We introduce a unifying and generalizing framework for complex and detailed balanced steady states in chemical reaction network theory. To this end, we generalize the graph commonly used to represent a reaction network. Specifically, we…

We present determinant criteria for the preclusion of non-degenerate multiple steady states in networks of interacting species. A network is modeled as a system of ordinary differential equations in which the form of the species formation…

Reaction networks are mathematical models of interacting chemical species that are primarily used in biochemistry. There are two modeling regimes that are typically used, one of which is deterministic and one that is stochastic. 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.…

Associated with a chemical reaction network is a natural labelled bipartite multigraph termed an SR graph, and its directed version, the DSR graph. These objects are closely related to Petri nets. The construction of SR and DSR graphs for…

We establish a generalized work theorem for stochastic chemical reaction networks (CRNs). By using a compensated Poisson jump process, we identify a martingale structure in a generalized entropy defined relative to an auxiliary backward…