相关论文: Fundamental Decompositions and Multistationarity o…

Networks of filamentous proteins play a crucial role in cell mechanics. These cytoskeletal networks, together with various crosslinking and other associated proteins largely determine the (visco)elastic response of cells. In this letter we…

We answer several fundamental geometric questions about reaction networks with power-law kinetics, on topics such as generic finiteness of the number of steady states, robustness, and nondegenerate multistationarity. In particular, we give…

Stochastic reaction networks are dynamical models of biochemical reaction systems and form a particular class of continuous-time Markov chains on $\mathbb{N}^n$. Here we provide a fundamental characterisation that connects structural…

A reaction network together with a choice of rate constants uniquely gives rise to a system of differential equations, according to the law of mass-action kinetics. On the other hand, different networks can generate the same dynamical…

In small systems, quantitative discrepancies between stochastic and deterministic descriptions of chemical kinetics can be significant, with their magnitude depending on the specific reaction network. Here, we study the Finke-Watzky…

For dynamical systems arising from chemical reaction networks, persistence is the property that each species concentration remains positively bounded away from zero, as long as species concentrations were all positive in the beginning. We…

Analyzing qualitative behaviors of biochemical reactions using its associated network structure has proven useful in diverse branches of biology. As an extension of our previous work, we introduce a graph-based framework to calculate steady…

Thomas's necessary conditions for the existence of multiple steady states in gene networks have been proved by Soul\'e with high generality for dynamical systems defined by differential equations. When applied to (protein) reaction networks…

This paper considers the problem of decentralized analysis and control synthesis to verify and ensure properties like stability and dissipativity of a large-scale networked system comprised of linear subsystems interconnected in an…

We investigate the quantum reaction-diffusion dynamics of fermionic particles which coherently hop in a one-dimensional lattice and undergo annihilation reactions. The latter are modelled as dissipative processes which involve losses of…

Computational studies of chemical reactions in complex environments such as proteins, nanostructures, or on surfaces require accurate and efficient atomistic models applicable to the nanometer scale. In general, an accurate parametrization…

Reaction networks (RNs) comprise a set $X$ of species and a set $\mathscr{R}$ of reactions $Y\to Y'$, each converting a multiset of educts $Y\subseteq X$ into a multiset $Y'\subseteq X$ of products. RNs are equivalent to directed…

Networks are characterized by structural features, such as degree distribution, triangular closures, and assortativity. This paper addresses the problem of reconstructing instances of continuously (and non-negatively) weighted networks from…

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…

It is well known that tensor network regression models operate on an exponentially large feature space, but questions remain as to how effectively they are able to utilize this space. Using a polynomial featurization, we propose the…

Network meta-analysis (NMA) is widely used in evidence synthesis to estimate the effects of several competing interventions for a given clinical condition. One of the challenges is that it is not possible in disconnected networks. Component…

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 perform a set of flow and reactive transport simulations within three-dimensional fracture networks to learn the factors controlling mineral reactions. CO$_2$ mineralization requires CO$_2$-laden water, dissolution of a mineral that then…

Complex mechanic systems simulation is important in many real-world applications. The de-facto numeric solver using Finite Element Method (FEM) suffers from computationally intensive overhead. Though with many progress on the reduction of…

Motivated by the fact that the pseudo-Helmholtz function is a valid Lyapunov function for characterizing asymptotic stability of complex balanced mass action systems (MASs), this paper develops the generalized pseudo-Helmholtz function for…