相关论文: Heuristics-Guided Exploration of Reaction Mechanis…
Biomolecular networks underpin emerging technologies in synthetic biology-from robust biomanufacturing and metabolic engineering to smart therapeutics and cell-based diagnostics-and also provide a mechanistic language for understanding…
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…
Many important phenomena in biochemistry and biology exploit dynamical features such as multi-stability, oscillations, and chaos. Construction of novel chemical systems with such rich dynamics is a challenging problem central to the fields…
We consider the problem of learning data-driven replicas for stiff systems of ordinary differential equations arising in chemical kinetics that can be evaluated with high computational efficiency. We first focus on training emulators for…
A stochastic model for a chemical reaction network is embedded in a one-parameter family of models with species numbers and rate constants scaled by powers of the parameter. A systematic approach is developed for determining appropriate…
Multistationary chemical reaction networks are of interest to scientists and mathematicians alike. While some criteria for multistationarity exist, obtaining explicit reaction rates and steady states that exhibit multistationarity for a…
Dynamic graphs are rife with higher-order interactions, such as co-authorship relationships and protein-protein interactions in biological networks, that naturally arise between more than two nodes at once. In spite of the ubiquitous…
Accurately modeling chemical reactions in molecular dynamics simulations requires detailed pre- and post-reaction templates, often created through labor-intensive manual workflows. This work introduces a Python-based algorithm that…
39 detailed mechanisms for combustion of hydrogen, carbon monoxide and methanol are investigated using ReactionKinetics, a Mathematica based package. The obtained results in most cases do not depend on the choice of reaction rate…
This paper presents new results about the optimization based generation of chemical reaction networks (CRNs) of higher deficiency. Firstly, it is shown that the graph structure of the realization containing the maximal number of reactions…
Biology is perhaps the most complex of the sciences, given the incredible variety of chemical species that are interconnected in spatial and temporal pathways that are daunting to understand. Their interconnections lead to emergent…
Many biochemical and industrial applications involve complicated networks of simultaneously occurring chemical reactions. Under the assumption of mass action kinetics, the dynamics of these chemical reaction networks are governed by systems…
In the study of grain-surface chemistry in the interstellar medium, there exists much uncertainty regarding the reaction mechanisms with few constraints on the abundances of grain-surface molecules. Bayesian inference can be performed to…
We mathematically prove that chemical reaction networks without hidden layers can solve tasks for which spiking neural networks require hidden layers. Our proof uses the deterministic mass-action kinetics formulation of chemical reaction…
The large-scale properties of chemical reaction systems, such as the metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information -- lists of chemical reactions -- available in databases. Even for the…
Chemical reaction networks (CRNs) model the behavior of chemical reactions in well-mixed solutions and they can be designed to perform computations. In this tutorial we give an overview of various computational models for CRNs. Moreover, we…
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 address a fundamental question: under which conditions do the dynamics and thermodynamics of open chemical reaction networks (CRNs), grounded on the notion of idealized chemostats that exchange selected species, emerge from underlying…
Chemical kinetics plays an important role in governing the thermal evolution in reactive flows problems. The possible interactions between chemical species increase drastically with the number of species considered in the system. Various…
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…