A Rule-Based Approach for Automated Generation of Kinetic Chemical Mechanisms

Abstract

Abstract. Several software systems have been developed recently for the automated generation of combustion reactions kinetic mechanisms using different representations of species and reactions and different generation algorithms. In parallel, several software systems based on rewriting have been developed for the easy modeling and prototyping of systems using rules controlled by strategies. This paper presents our current experience in using the rewrite system ELAN for the automated generation of the combustion reactions mechanisms previously implemented in the EXGAS kinetic mechanism generator system. We emphasize the benefits of using rewriting and rule-based programming controlled by strategies for the generation of kinetic mechanisms.

Graph Rewriting and Strategies for Modeling Biochemical Networks

“…Based on our previous experience on implementing molecular chemistry [8,2], we are currently implementing this calculus using TOM, a tool providing matching, normalization, and strategic rewriting in high-level programming languages like Java. An aspect we cannot neglect in modeling protein-protein interactions is the combinatorial complexity [20].…”

“…Different control strategies may be easily prototyped and experimented by selecting specific rules, grouping rules and applying each group with different strategies, and then linking them up. The advantages of using strategic rewriting for the network generation have already been experimented in [8,2] for a chemical application.…”

Non-intrusive Formal Methods and Strategic Rewriting for a Chemical Application

“…In GasEl project [6,7,15] we already have explored the use of rule-based systems and strategies for the problem of automated generation of kinetics mechanisms [23,9] in the whole context of its use by chemists and industrial partners. In GasEl the representation of chemical species uses the notion of molecular graphs, encoded by a term structure called GasEl terms [6] which is inspired by the linear notation SMILES [30].…”

“…In GasEl the representation of chemical species uses the notion of molecular graphs, encoded by a term structure called GasEl terms [6] which is inspired by the linear notation SMILES [30]. The graph isomorphism test is based on the Unique SMILES algorithm [30].…”

“…The control of the chemical reactions chaining (i.e. reactor dynamics) is described using a strategy language [6]. GasEl prototype is implemented in ELAN [5,17], encoding a set of nine reaction patterns.…”