Related papers: Reaction Automata
We consider a reaction-diffusion system where some components react and diffuse on the boundary of a region, while other components diffuse in the interior and react with those on the boundary through mass transport. We establish local…
We present chemlambda (or the chemical concrete machine), an artificial chemistry with the following properties: (a) is Turing complete, (b) has a model of decentralized, distributed computing associated to it, (c) works at the level of…
Validation of a presumably universal theory, such as quantum mechanics, requires a quantum mechanical description of systems that carry out theoretical calculations and experiments. The description of quantum computers is under active…
We provide a category theoretical framework capturing two approaches to graph-based models of chemistry: formal reactions and disconnection rules. We model a translation from the latter to the former as a functor, which is faithful, and…
We propose a new and general formalism for elementary chemical reactions where quantum electronic variables are used as reaction coordinates. This formalism is in principle applicable to all kinds of chemical reactions ionic or covalent.…
Spin-selective reactions of radical pairs have traditionally been modelled theoretically by adding phenomenological rate equations to the quantum mechanical equation of motion of the radical pair spin density matrix. More recently an…
Recent Iterated Response (IR) models of pragmatics conceptualize language use as a recursive process in which agents reason about each other to increase communicative efficiency. These models are generally defined over complete utterances.…
In living cells, chemical reactions form a complex network. Complicated dynamics arising from such networks are the origins of biological functions. We propose a novel mathematical method to analyze bifurcation behaviors of a reaction…
Studying systems where many individual bodies in motion interact with one another is a complex and interesting area. Simple mechanisms that may be determined for biological, chemical, or physical reasons can lead to astonishingly complex…
We introduce the term Super-Reactive Systems to refer to reactive systems whose construction and behavior are complex, constantly changing and evolving, and heavily interwoven with other systems and the physical world. Finding hidden faults…
In this paper, we propose a new method to identify biochemical reaction networks (i.e. both reactions and kinetic parameters) from heterogeneous datasets. Such datasets can contain (a) data from several replicates of an experiment performed…
Quantum computing is concerned with computer technology based on the principles of quantum mechanics, with operations performed at the quantum level. Quantum computational models make it possible to analyze the resources required for…
We consider how the languages of $G$-automata compare with other formal language classes. We prove that if the word problem of a group $G$ is accepted by a machine in the class $\mathcal M$ then the language of any $G$-automaton is in the…
A complex system is a system composed of many interacting parts, often called agents, which displays collective behavior that does not follow trivially from the behaviors of the individual parts. Examples include condensed matter systems,…
Reactive languages are dedicated to the programming of systems which interact continuously and concurrently with their environment. Values take the form of unbounded streams modeling the (discrete) passing of time or the sequence of…
We propose the chemlambda artificial chemistry, whose behavior strongly suggests that real molecules which embed Interaction Nets patterns and real chemical reactions which resemble Interaction Nets graph rewrites could be a realistic path…
This work addresses multistationarity of fully open reaction networks equipped with mass action kinetics. We improve upon the existing results relating existence of positive feedback loops in a reaction network and multistationarity; and we…
Machine learning techniques applied to chemical reactions has a long history. The present contribution discusses applications ranging from small molecule reaction dynamics to platforms for reaction planning. ML-based techniques can be of…
Background: Nuclear reactions are complex, with a large number of possible channels. Understanding how different channels contribute to a given reaction is investigated by perturbing the continuous spectrum. Purpose: To develop tools to…
Large language models (LLMs) are beginning to reshape how chemists plan and run reactions in organic synthesis. Trained on millions of reported transformations, these text-based models can propose synthetic routes, forecast reaction…