Related papers: Regulated Multiset Rewriting Systems
A modeling formalism is proposed for the description and study of living and life-like systems. It provides an abstract conceptual model framework for real life and evolution of biological organisms. It is proposed, that this model…
The classical attenuation regulation of gene expression in bacteria is considered. We propose to represent the secondary RNA structure in the leader region of a gene or an operon by a term, and we give a probabilistic term rewriting system…
Graph rewrite formalisms are a powerful approach to modeling complex molecular systems. They capture the intrinsic concurrency of molecular interactions, thereby enabling a formal notion of mechanism (a partially ordered set of events) that…
Social norms are powerful formalism in coordinating autonomous agents' behaviour to achieve certain objectives. In this paper, we propose a dynamic normative system to enable the reasoning of the changes of norms under different…
Modelling gene regulatory networks not only requires a thorough understanding of the biological system depicted but also the ability to accurately represent this system from a mathematical perspective. Throughout this chapter, we aim to…
Rewriting is a formalism widely used in computer science and mathematical logic. The classical formalism has been extended, in the context of functional languages, with an order over the rules and, in the context of rewrite based languages,…
Bigraphs are a versatile modelling formalism that allows easy expression of placement and connectivity relations in a graphical format. System evolution is user defined as a set of rewrite rules. This paper presents a practical, yet…
Term rewriting has a significant presence in various areas, not least in automated theorem proving where it is used as a proof technique. Many theorem provers employ specialised proof tactics for rewriting. This results in an interleaving…
Norms with sanctions have been widely employed as a mechanism for controlling and coordinating the behavior of agents without limiting their autonomy. The norms enforced in a multi-agent system can be revised in order to increase the…
A rewriting system is a set of equations over a given set of terms called rules that characterize a system of computation and is a powerful general method for providing decision procedures of equational theories, based upon the principle of…
In this paper we consider the problem of proving properties of infinite behaviour of formalisms suitable to describe (infinite state) systems with recursion and parallelism. As a formal setting, we consider the framework of Process…
Mathematical methods provide useful framework for the analysis and design of complex systems. In newer contexts such as biology, however, there is a need to both adapt existing methods as well as to develop new ones. Using a combination of…
We develop a multiset query and update language executable in a term rewriting system. Its most remarkable feature, besides non-standard approach to quantification and introduction of fresh values, is non-determinism - a query result is not…
The last decade has witnessed a surge of theoretical and computational models to describe the dynamics of complex gene regulatory networks, and how these interactions can give rise to multistable and heterogeneous cell populations. As the…
Probabilistic programming is becoming increasingly popular thanks to its ability to specify problems with a certain degree of uncertainty. In this work, we focus on term rewriting, a well-known computational formalism. In particular, we…
Specifying the intended behaviour of autonomous systems is becoming increasingly important but is fraught with many challenges. This technical report provides an overview of existing work on specifications of autonomous systems and places a…
The analysis of industrial processes, modelled as descriptor systems, is often computationally hard due to the presence of both algebraic couplings and difference equations of high order. In this paper, we introduce a control refinement…
Multi-valued logical models can be used to describe biological networks on a high level of abstraction based on the network structure and logical parameters capturing regulatory effects. Interestingly, the dynamics of two distinct models…
Artificial neurons built on synthetic gene networks have potential applications ranging from complex cellular decision-making to bioreactor regulation. Furthermore, due to the high information throughput of natural systems, it provides an…
Most available tools propose simulation frameworks to study models of biological systems, but simulation only explores a few of the most probable behaviours of the system. On the contrary, techniques such as model checking, coming from…