相关论文: Maximal and minimal realizations of reaction kinet…
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…
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.
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…
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,…
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 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,…
Motivation: A Chemical Reaction Network (CRN) is a set of chemical reactions, which can be very complex and difficult to analyze. Indeed, dynamical properties of CRNs can be described by a set of non-linear differential equations that…
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…
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…
Formal methods have enabled breakthroughs in many fields, such as in hardware verification, machine learning and biological systems. The key object of interest in systems biology, synthetic biology, and molecular programming is chemical…
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…
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.…
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.…
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 investigate the dynamics of chemical reaction networks (CRNs) with the goal of deriving an upper bound on their reaction rates. This task is challenging due to the nonlinear nature and discrete structure inherent in CRNs. To address…
We propose a unified framework that allows for the full mechanistic reconstruction of chemical reaction networks (CRNs) from concentration data. The framework utilizes an integral formulation of the differential equations governing the…
Molecular computation based on chemical reaction networks (CRNs) has emerged as a promising paradigm for designing programmable biochemical systems. However, the implementation of complex computations still requires excessively large and…
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,…
In this paper an algorithm is given to determine all possible structurally different linearly conjugate realizations of a given kinetic polynomial system. The solution is based on the iterative search for constrained dense realizations…
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…