相关论文: Computing weakly reversible realizations of chemic…
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…
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…
Mass-action kinetics is frequently used in systems biology to model the behaviour of interacting chemical species. Many important dynamical properties are known to hold for such systems if they are weakly reversible and have a low…
We prove that if a given reaction network $\mathcal{N}$ has a weakly reversible deficiency zero realization for all choice of rate constants, then there exists a $\textit{unique}$ weakly reversible deficiency zero network $\mathcal{N}'$…
Reversibility, weak reversibility and deficiency, detailed and complex balancing are generally not "encoded" in the kinetic differential equations but they are realization properties that may imply local or even global asymptotic stability…
A numerically effective procedure for determining weakly reversible chemical reaction networks that are linearly conjugate to a known reaction network is proposed in this paper. The method is based on translating the structural and…
Chemical reaction networks, or CRNs, are known to stably compute semilinear Boolean-valued predicates and functions, provided that all reactions are irreversible. However, this property does not hold for wet-lab implementations, as all…
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…
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…
Reaction networks can display a wide array of dynamics. However, it is possible for different reaction networks to display the same dynamics. This phenomenon is called dynamical equivalence and makes network identification a hard problem to…
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.…
Given a dynamical system with polynomial right-hand side, can it be generated by a reaction network that possesses certain properties? This question is important because some network properties may guarantee specific dynamical properties,…
Across many disciplines, chemical reaction networks (CRNs) are an established population model defined as a system of coupled nonlinear ordinary differential equations. In many applications, for example, in systems biology and epidemiology,…
Coupled chemical interactions in a well-mixed solution are commonly formalized as chemical reaction networks (CRNs). However, despite the widespread use of CRNs in the natural sciences, the range of computational behaviors exhibited by CRNs…
We present a computational method for performing structural translation, which has been studied recently in the context of analyzing the steady states and dynamical behavior of mass-action systems derived from biochemical reaction networks.…
Chemical reaction networks (CRNs) provide a convenient language for modelling a broad variety of biological systems. These models are commonly studied with respect to the time series they generate in deterministic or stochastic simulations.…
We consider how to generate chemical reaction networks (CRNs) from functional specifications. We propose a two-stage approach that combines synthesis by satisfiability modulo theories and Markov chain Monte Carlo based optimisation. First,…
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.…
We explore the range of probabilistic behaviours that can be engineered with Chemical Reaction Networks (CRNs). We show that at steady state CRNs are able to "program" any distribution with finite support in $\mathbb{N}^m$, with $m \geq 1$.…
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…