相关论文: Determining the Equivalence of Small Zero-one Reac…
A variety of natural phenomena comprises a huge number of competing reactions and short-lived intermediates. Any study of such processes requires the discovery and accurate modeling of their underlying reaction network. However, this task…
This paper considers optimization problems over networks where agents have individual objectives to meet, or individual parameter vectors to estimate, subject to subspace constraints that require the objectives across the network to lie in…
Stochastic reaction networks, which are usually modeled as continuous-time Markov chains on $\mathbb Z^d_{\ge 0}$, and simulated via a version of the "Gillespie algorithm," have proven to be a useful tool for the understanding of processes,…
The balance between excitation and inhibition is crucial for neuronal computation. It is observed that the balanced state of neuronal networks exists in many experiments, yet its underlying mechanism remains to be fully clarified.…
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 investigate the possibility that for any given reaction rate vector $k$ associated with a network $G$, there exists another network $G'$ with a corresponding reaction rate vector that reproduces the mass-action dynamics generated by…
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…
We study the decay process for the reaction-diffusion process of three species on the small-world network. The decay process is manipulated from the deterministic rate equation of three species in the reaction-diffusion system. The particle…
The number of units of a network dynamical system, its size, arguably constitutes its most fundamental property. Many units of a network, however, are typically experimentally inaccessible such that the network size is often unknown. Here…
We consider a natural class of reaction networks which consist of reactions where either two species can inactivate each other (i.e., sequestration), or some species can be transformed into another (i.e., transmutation), in a way that gives…
Recent algorithmic developments have enabled computers to automatically determine and prove the capacity regions of small hypergraph networks under network coding. A structural theory relating network coding problems of different sizes is…
This paper deals with identifiability of undirected dynamical networks with single-integrator node dynamics. We assume that the graph structure of such networks is known, and aim to find graph-theoretic conditions under which the state…
It is useful to have complete lists of nonisomorphic chemical reaction networks (CRNs) of a given size, with or without various restrictions. One may, for example, be interested in exploring how often certain dynamical behaviours occur in…
This paper (parts I and II) provides an expository introduction to monotone and near-monotone dynamical systems associated to biochemical networks, those whose graphs are consistent or near-consistent. Many conclusions can be drawn from…
We present a computational procedure to characterize the signs of sensitivities of steady states to parameter perturbations in chemical reaction networks.
Resonator networks are ubiquitous in natural and engineered systems, such as solid-state materials, neural tissue, and electrical circuits. To understand and manipulate these networks, it is essential to characterize their building blocks,…
Analog electrical networks have long been investigated as energy-efficient computing platforms for machine learning, leveraging analog physics during inference. More recently, resistor networks have sparked particular interest due to their…
Understanding the emergent behavior of chemical reaction networks (CRNs) is a fundamental aspect of biology and its origin from inanimate matter. A closed CRN monotonically tends to thermal equilibrium, but when it is opened to external…
We consider linear elimination of variables in steady state equations of a chemical reaction network. Particular subsets of variables corresponding to sets of so-called reactant-noninteracting species, are introduced. The steady state…
It is well-known that biological and social interaction networks have a varying degree of redundancy, though a consensus of the precise cause of this is so far lacking. In this paper, we introduce a topological redundancy measure for…