Related papers: Simulation Of Reaction Systems By The Strictly Min…
Particle-based simulations are an essential tool for the study of biochemical systems for scales between molecular/Brownian dynamics and the reaction-diffusion master equation. These simulations utilise proximity-based reaction conditions…
Explaining the origin of life requires us to explain how self-replication arises. To be specific, how can a self-replicating entity develop spontaneously from a chemical reaction system in which no reaction is self-replicating? Previously…
Radiation technologies have found wide application in power engineering, medicine, biology and other areas of human activities. However, theoretical calculations of nuclear reactions and, correspondingly, the interpretation of experimental…
Ab initio techniques have revolutionised the way in which theory can help practitioners to explore critical mechanisms that govern reactions or properties, and to develop new strategies for materials discovery and design. Yet, their…
Reaction-diffusion equations are commonly used to model a diverse array of complex systems, including biological, chemical, and physical processes. Typically, these models are phenomenological, requiring the fitting of parameters to…
A general framework for the simulation of reaction-diffusion systems with probabilistic cellular automata is presented. The basic reaction probabilities of the chemical model translate directly into the transition rules of the automaton,…
Biologists and physicists have a rich tradition of modeling living systems with simple models composed of a few interacting components. Despite the remarkable success of this approach, it remains unclear how to use such finely tuned models…
The Comment's author argues that a correct description of reactive systems should incorporate the explicit interaction with reservoirs, leading to a unified system-reservoirs entity. However, this proposition has two major flaws. Firstly,…
The building of minimal self-reproducing systems with a physical embodiment (generically called protocells) is a great challenge, with implications for both theory and applied sciences. Although the classical view of a living protocell…
Mathematical models are increasingly being used to understand complex biochemical systems, to analyze experimental data and make predictions about unobserved quantities. However, we rarely know how robust our conclusions are with respect to…
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…
We study a system of diffusing point particles in which any triplet of particles reacts and is removed from the system when the relative proximity of the constituent particles satisfies a predefined condition. Proximity-based reaction…
Cross-reactions and other systematic issues generated by the coupling of functional chemical subsystems pose the largest challenge for assembling a viable protocell in the laboratory. Our current work seeks to identify and clarify such key…
Reaction Systems (RSs) are a successful computational framework inspired by biological systems. A RS pairs a set of entities with a set of reactions over them. Entities can be used to enable or inhibit each reaction, and are produced by…
Simulation of stochastic spatially-extended systems is a challenging problem. The fundamental quantities in these models are individual entities such as molecules, cells, or animals, which move and react in a random manner. In big systems,…
Autocatalytic systems are very often incorporated in the "origin of life" models, a connection that has been analyzed in the context of the classical hypercycles introduced by Manfred Eigen. We investigate the dynamics of certain networks…
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…
The multi-level method for discrete state systems, first introduced by Anderson and Higham [Multiscale Model. Simul. 10:146--179, 2012], is a highly efficient simulation technique that can be used to elucidate statistical characteristics of…
The paper has two goals: It presents basic ideas, notions, and methods for reduction of reaction kinetics models: quasi-steady-state, quasi-equilibrium, slow invariant manifolds, and limiting steps. It describes briefly the current state of…
The primary goal of this paper is to characterize solutions to coupled reaction-diffusion systems. Indeed, we use operators theory to show that under suitable assumptions, then the solutions to the reaction-diffusion equations exist. As…