Modeling and Analyzing Reaction Systems in Maude

Fine-Grained Parallel and Distributed Spatial Stochastic Simulation of Biological Reactions

Plug-in context providers for reaction systems

Reaction systems, introduced by Ehrenfeucht and Rozenberg, are computational models inspired by biochemical reactions transpiring within the living cells. Numerous studies focus on rs functions specified by minimal reaction systems, due to their simplicity and rich generative power. Manzoni et al [1] showed that every reaction system can be simulated by a minimal reaction system over an expanded background set. Motivated by their work, we introduce hybrid reaction systems as generalizations of reaction systems. Every rs function is then canonically expressible as a composition of two functions specified by minimal hybrid reaction systems. Using our new approach, the result of Manzoni et al [1] is revisited and strengthened.

Reaction systems are a formal model for computational processing in which reactions operate on sets of entities (molecules) providing a framework for dealing with qualitative aspects of biochemical systems. This paper is concerned with reaction systems in which entities can have discrete concentrations, and so reactions operate on multisets rather than sets of entities. The resulting framework allows one to deal with quantitative aspects of reaction systems, and a bespoke linear-time temporal logic allows one to express and verify a wide range of key behavioural system properties. In practical applications, a reaction system with discrete concentrations may only be partially specified, and the possibility of an effective automated calculation of the missing details provides an attractive design approach. With this idea in mind, the current paper discusses parametric reaction systems with parameters representing unknown parts of hypothetical reactions. The main result is a method aimed at replacing the parameters in such a way that the resulting reaction system operating in a specified external environment satisfies a given temporal logic formula.This paper provides an encoding of parametric reaction systems in smt, and outlines a synthesis procedure based on bounded model checking for solving the synthesis problem. It also reports on the initial experimental results demonstrating the feasibility of the novel synthesis method.

A distributed reaction system consists of a finite set of reaction systems that either interact with a common environment or interact with each other by communicating products or reactions. A reaction system is a well-known qualitative formal model of interactions between biochemical reactions. A reaction is a triplet of nonempty sets representing chemicals, called the set of reactants, the set of inhibitors, and the set of products. A reaction corresponds to a chemical reaction performed on a set of chemicals, and a reaction system is a finite nonempty set of reactions. In this paper, we examine two variants of distributed reaction systems. We introduce the notion of a distributed reaction system with communication by request (a qDRS for short), where sets of products are communicated between the component reaction systems by queries. First, we show that every qDRS can be represented by a reaction system. After that we compare distributed reaction systems with communication by request to extended distributed reaction systems (EDRSs), models that were introduced in a previous paper. We prove that extended distributed reaction systems, where a context automaton provides input for the component reaction systems, simulate distributed reaction systems with communication by request and distributed reaction systems with communication by request simulate special variants of extended distributed reaction systems. Furthermore, we assign languages to these two variants of distributed reaction systems. We prove that the class of agreement languages of extended distributed reaction systems is equal to the class of languages of nondeterministic multihead finite automata and the agreement language of every distributed reaction system with communication by request is an element of a certain subregular language class.

Reaction systems are a formal framework for modeling processes driven by biochemical reactions. They are based on the mechanisms of facilitation and inhibition. A main assumption is that if a resource is available, then it is present in sufficient amounts and as such, several reactions using the same resource will not compete concurrently against each other; this makes reaction systems very different as a modeling framework than traditional frameworks such as ODEs or continuous time Markov chains. We demonstrate in this paper that reaction systems are rich enough to capture the essential characteristics of ODE-based models. We construct a reaction system model for the heat shock response in such a way that its qualitative behavior correlates well with the quantitative behavior of the corresponding ODE model. We construct our reaction system model based on a novel concept of dominance graph that captures the competition on resources in the ODE model. We conclude with a discussion on the expressivity of reaction systems as compared to that of ODE-based models.

The evolution of a reaction system is usually driven by a fixed set of unconstrained rules. In this paper, we present a different approach by imposing some constraints over the rules. Thus, we define restricted reaction systems which are working with mutually exclusive rules, namely rules that are not allowed to be applied together in the same computational step. We investigate the relationship between the reaction systems and the new restricted reaction systems. Additionally, we analyze the notion of reversibility in both reaction systems and restricted reaction systems.

On the analysis of oxygen diffusion and reaction in biological systems

A formal executable semantics of a programming language has the necessary information to develop program debugging and reasoning techniques. In this paper we choose such a particular technique called program slicing and we introduce a generic algorithm which extracts a set of side-effects inducing constructs, directly from the formal executable semantics of a programming language. These constructs are further used to infer program slices, for given programs and specified slicing criteria. Our proposed approach improves on the parametrization of the language tools development because changes in the formal semantics are automatically carried out in the slicing procedure. We use the rewriting logic and the Maude system to implement a prototype and to test our technique.

Modelling of complex liquid–solid reaction systems in semibatch reactors: Claisen condensation in industrial scale

This article discusses the question of when the dynamical systems arising from chemical reaction networks are monotone, preserving an order induced by some proper cone. The reaction systems studied are defined by the reaction network structure while the kinetics is only constrained very weakly. Necessary and sufficient conditions on cones preserved by these systems are presented. Linear coordinate changes which make a given reaction system cooperative are characterized. Also discussed is when a reaction system restricted to an invariant subspace is cone preserving, even when the system fails to be cone preserving on the whole of phase space. Many of the proofs allow explicit construction of preserved cones. Numerous examples of chemical reaction systems are presented to illustrate the results.

Piezoelectric performance can be improved by using crystal-axis oriented materials because piezoelectric properties of the ferroelectric materials are dependent on the crystal-axis direction. In this study, we tried to fabricate Ba1−xCaxTiO3 (BCT) oriented ceramics by reactive template grain growth (RTGG) method using H1.07Ti1.73O4 layered titanate (HTO) plate-like particles as the reactive template. BCT ceramics with [110]-orientation were prepared using HTO-BaCO3-Ca(OH)2 (HBC) and HTO-BaCO3-Ca(OH)2-TiO2 (HBCT) reaction systems. The degree of orientation and the relative density of the BCT ceramics are dependent on the green sheet preparation conditions, such as dispersion condition and added binder amount, calcination temperature and starting material composition. In these reaction systems, firstly oriented BCT particles are formed by a topotactic reaction of HTO template particles with Ba and Ca matrix components, and then, BCT oriented ceramic is formed by the growth of the oriented BCT particles. BCT ceramics with higher density and higher orientation can be fabricated using HBCT reaction system than HBC reaction system, where the orientation degree is dependent strongly on the ratio of HTO template particle to TiO2 matrix particle.

Compositional semantics and behavioural equivalences for reaction systems with restriction

Combustion synthesis of TiN–TiB 2 composites in Ti/BN/N 2 and Ti/BN/B reaction systems

In situ FTIR has been widely used to study polymerization kinetics of different reaction systems. However, lack of humidity control during these studies has generally limited this technique to ambient or nitrogen atmosphere conditions. In this work, a relatively small humidity control chamber was newly designed and introduced into the original FTIR sample chamber in transmission mode to control the humidity during in situ kinetic studies of coatings over a broad range from 5 to 80% RH. With the current setup, it only takes 2–3 min to get to the desired humidity level. Factors that affect the humidity control and FTIR data collection are discussed. Two reaction systems were selected to study the effect of moisture on the kinetics. One is an aliphatic polyisocyanate reacting with moisture in the air, and the other is an acrylic polyol reacting with a polyisocyanate. Relative humidity was studied at three levels: 15, 45, and 75%. In both cases, the reaction rate increases under higher humidity. Formation of different forms of urea in the first system and formation of both urethane and urea in the second system were analyzed. In the second reaction system, more urea is formed under higher humidity or under a higher NCO/OH molar ratio. The humidity control within the transmission FTIR chamber has turned out to be a useful tool to monitor the effect of humidity on the curing kinetics of organic coatings.