|InterJournal Complex Systems, 516
|Manuscript Number: |
Submission Date: 20430
|Design Patterns for the Generation and the Analysis of Chemical Reaction Networks|
Subject(s): CX.21, CX.06, CX.13
Category: Brief Article
Chemical reactions among molecules rapidly create a complex web of interactions where it is nearly impossible by analytical means to predict which molecule will emerge in high concentration and which will not « survive » the network interactions. Computer simulations may help to achieve these predictions provided those simulations are written in a clear and easy to manage modelling language. The work presented here could play two roles. Following an easy-to-do and adequate parametrization, they could be proposed to chemical or biological practitioners to model a particular system. On the other hand, they could also stand on their own and allow the discovery of generic laws characterizing the behavior of emergent complex systems. To ease the parametrization and ease the manipulation of the software by not computer specialists, object-oriented approaches, by the use of the UML diagrams, is proposed as the natural way to follow. In this paper, the basic chemical objects will be presented. Technical problems like the canonization of the molecular graphs, the calculation of the kinetic reaction rates, and the combinatorial explosion of the number of molecules will be faced. Some preliminary results will be presented, departing from trivial molecules, but already showing the difficulty to predict the emerging molecules and the reaction network, as well as the benefits gained by resorting to computer simulations.
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