相关论文: Heuristics-Guided Exploration of Reaction Mechanis…
Understanding the evolution of electrified solid-liquid interfaces during electrochemical reactions is crucial. However, capturing the dynamic behavior of the interfaces with high temporal resolution and accuracy over long timescales…
Chemical and biological networks can describe a wide variety of processes, from gene regulatory networks to biochemical oscillations. Modeled by chemical master equations, these processes are inherently stochastic, as fluctuations dominate…
This paper analyses of a stochastic model of a chemical reaction network with three types of chemical species ${\cal R}$, ${\cal M}$ and ${\cal U}$ that interact to transform a flow of external resources, the chemical species ${\cal Q}$, to…
Understanding the set of elementary steps and kinetics in each reaction is extremely valuable to make informed decisions about creating the next generation of catalytic materials. With physical and mechanistic complexity of industrial…
Atom tracing is essential for understanding the fate of labeled atoms in biochemical reaction networks, yet existing computational methods either simplify label correlations or suffer from combinatorial explosion. We introduce a…
An algorithm is given in this paper for the computation of dynamically equivalent weakly reversible realizations with the maximal number of reactions, for chemical reaction networks (CRNs) with mass action kinetics. The original problem…
The catalytic reaction system (CRS) formalism by Hordijk and Steel is a versatile method to model autocatalytic biochemical reaction networks. It is particularly suited, and has been widely used, to study self-sustainment and…
Prediction of complete step-by-step chemical reaction mechanisms (CRMs) remains a major challenge. Whereas the traditional approaches in CRM tasks rely on expert-driven experiments or costly quantum chemical computations, contemporary deep…
This paper proposes an optimization-based framework for the analysis of multiperiod directed multihypergraphs aimed at identifying self-amplifying structures that sustain endogenous growth in complex systems. The approach captures the…
The study of chemical reactions in aqueous media is very important for its implications in several fields of science, from biology to industrial processes. Modelling these reactions is however difficult when water directly participates in…
Chemical reaction network theory provides powerful tools for rigorously understanding chemical reactions and the dynamical systems and differential equations that represent them. A frequent issue with mathematical analyses of these networks…
Thermodynamic constraints on reactions directions are inherent in the structure of a given biochemical network. However, concrete procedures for determining feasible reaction directions for large-scale metabolic networks are not well…
The Bond Graph approach and the Chemical Reaction Network approach to modelling biomolecular systems developed independently. This paper brings together the two approaches by providing a bond graph interpretation of the chemical reaction…
We present an experimental system of networks of coupled non-linear chemical reactors, which we theoretically model within a reaction-diffusion framework. The networks consist of patterned arrays of diffusively coupled nanoliter-scale…
Chemical reaction networks (CRNs) formally model chemistry in a well-mixed solution. CRNs are widely used to describe information processing occurring in natural cellular regulatory networks, and with upcoming advances in synthetic biology,…
We present a differentiable formulation of abstract chemical reaction networks (CRNs) that can be trained to solve a variety of computational tasks. Chemical reaction networks are one of the most fundamental computational substrates used by…
We lay the foundation of a circuit theory for chemical reaction networks. Chemical reactions are grouped into chemical modules solely characterized by their current-concentration characteristic, as electrical devices by their…
Deep generative models have been shown powerful in generating novel molecules with desired chemical properties via their representations such as strings, trees or graphs. However, these models are limited in recommending synthetic routes…
A chemical reaction network (CRN) is composed of reactions that can be seen as interactions among entities called species, which exist within the system. Endowed with kinetics, CRN has a corresponding set of ordinary differential equations…
Chemical reactions often proceed through the formation and the consumption of intermediate species. An example is the creation and subsequent degradation of the substrate-enzyme complexes in an enzymatic reaction. In this paper we provide a…