Related papers: Reaction Automata
A plausible definition of "reasoning" could be "algebraically manipulating previously acquired knowledge in order to answer a new question". This definition covers first-order logical inference or probabilistic inference. It also includes…
We introduce Network Automata, a framework which couples the topological evolution of a network to its structure. It is useful for dealing with networks in which the topology evolves according to some specified microscopic rules and,…
Stochastic reaction-diffusion processes may be presented in terms of integrable quantum chains and can be used to describe various biological and chemical systems. Exploiting the integrability of the models one finds in some cases good…
In many scientific fields, there is an interest in understanding the way in which complex chemical networks evolve. The chemical networks which researchers focus upon, have become increasingly complex and this has motivated the development…
It has been recently observed that the dynamical properties of mass action systems arising from many models of biochemical reaction networks can be derived by considering the corresponding properties of a related generalized mass action…
The construction of a reaction network containing all relevant intermediates and elementary reactions is necessary for the accurate description of chemical processes. In the case of a complex chemical reaction (involving, for instance, many…
This paper grew out of three tutorial lectures on automatic structures given by the first author at the Logic Colloquium 2007. We discuss variants of automatic structures related to several models of computation: word automata, tree…
An inverse problem framework for constructing reaction systems with prescribed properties is presented. Kinetic transformations are defined and analysed as a part of the framework, allowing an arbitrary polynomial ordinary differential…
Multi-agent models are a suitable starting point to model complex social interactions. However, as the complexity of the systems increase, we argue that novel modeling approaches are needed that can deal with inter-dependencies at different…
We present counting reward automata-a finite state machine variant capable of modelling any reward function expressible as a formal language. Unlike previous approaches, which are limited to the expression of tasks as regular languages, our…
Cellular automata are arrays of finite state machines that can exist in a finite number of states. These machines update their states simultaneously based on specific local rules that govern their interactions. This framework provides a…
Multispecies reaction-diffusion systems, for which the time evolution equation of correlation functions become a closed set, are considered. A formal solution for the average densities is found. Some special interactions and the exact time…
The theory of computational complexity focuses on functions and, hence, studies programs whose interactive behavior is reduced to a simple question/answer pattern. We propose a broader theory whose ultimate goal is expressing and analyzing…
A chemical reaction mechanism (CRM) is a sequence of molecular-level events involving bond-breaking/forming processes, generating transient intermediates along the reaction pathway as reactants transform into products. Understanding such…
Relating formal re nement techniques with commercial object oriented software development methods is important to achieve enhancement of the power and exibility of these software development methods and tools. We will present an automata…
Chemical systems are traditionally described by lists of species, reactions, and externally imposed kinetic laws, a framework that lacks an intrinsic algebraic structure governing how transformations compose. We propose an axiomatic…
Dynamical systems are a broad class of mathematical tools used to describe the evolution of physical and computational processes. Traditionally these processes model changing entities in a static world. Picture a ball rolling on an empty…
Hybrid automata are a natural framework for modeling and analyzing systems which exhibit a mixed discrete continuous behaviour. However, the standard operational semantics defined over such models implicitly assume perfect knowledge of the…
Autonomous reaction network exploration algorithms offer a systematic approach to explore mechanisms of complex chemical processes. However, the resulting reaction networks are so vast that an exploration of all potentially accessible…
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,…