Related papers: Reaction Automata
The ability to reason beyond established knowledge allows Organic Chemists to solve synthetic problems and to invent novel transformations. Here, we propose a model which mimics chemical reasoning and formalises reaction prediction as…
Reactive lattice gas automata provide a microscopic approachto the dynamics of spatially-distributed reacting systems. After introducing the subject within the wider framework of lattice gas automata (LGA) as a microscopic approach to the…
Chemical reactivity models are developed to predict chemical reaction outcomes in the form of classification (success/failure) or regression (product yield) tasks. The vast majority of the reported models are trained solely on chemical…
Due to the intrinsic complexity and nonlinearity of chemical reactions, direct applications of traditional machine learning algorithms may face with many difficulties. In this study, through two concrete examples with biological background,…
Reaction networks, or equivalently Petri nets, are a general framework for describing processes in which entities of various kinds interact and turn into other entities. In chemistry, where the reactions are assigned "rate constants", any…
A reaction network is a chemical system involving multiple reactions and chemical species. Stochastic models of such networks treat the system as a continuous time Markov chain on the number of molecules of each species with reactions as…
We introduce a new class of cellular automata to model reaction-diffusion systems in a quantitatively correct way. The construction of the CA from the reaction-diffusion equation relies on a moving average procedure to implement diffusion,…
A reaction-diffusion model of receptor-toxin-antibody (RTA) interaction is studied numerically. The protective properties of an antibody against a given toxin are evaluated for a spherical cell placed into a toxin-antibody solution. The…
We study general linear transport-reaction systems on an arbitrary dimensional hypercube with periodic boundary conditions. Transport-reaction systems are often used to model the finite speed movement and interaction of particles, bacteria…
This article introduces a formal model to specify, model and validate hierarchical complex systems described at different levels of analysis. It relies on concepts that have been developed in the multi-agent-based simulation (MABS)…
Team Automata is a formalism for interacting component-based systems proposed in 1997, whereby multiple sending and receiving actions from concurrent automata can synchronise. During the past 25+ years, team automata have been studied and…
Complex systems of intracellular biochemical reactions have a central role in regulating cell identities and functions. Biochemical reaction systems are typically studied using the language and tools of graph theory. However, graph…
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…
We investigate the computational power of particle methods, a well-established class of algorit hms with applications in scientific computing and computer simulation. The computational power of a compute model determines the class of…
The current work addresses a virtual environment with self-replicating agents whose decisions are based on a form of "somatic computation" (soma - body) in which basic emotional responses, taken in parallelism to actual living organisms,…
Reaction-diffusion processes are the foundational model for a diverse range of complex systems, ranging from biochemical reactions to social agent-based phenomena. The underlying dynamics of these systems occur at the individual…
Linearly bounded Turing machines have been mainly studied as acceptors for context-sensitive languages. We define a natural class of infinite automata representing their observable computational behavior, called linearly bounded graphs.…
Chemical reaction mechanisms are the foundation of how chemists evaluate reactivity and feasibility, yet current Computer-Assisted Synthesis Planning (CASP) systems operate without this mechanistic reasoning. We introduce a computational…
Chemical reaction networks (CRNs) are prototypical complex systems because reactions are nonlinear and connected in intricate ways, and they are also essential to understand living systems. Here, I discuss how recent developments in…
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…