An Approach to Constructing Qualitative Models in Computational Cell Biology Using an Artificial Chemistry Based on Pattern Matching and Recombination

摘要

Computational cell biology is a growing research field in which molecular interactions in a cell are modelled and simulated. This paper presents an approach to utilizing an artificial chemistry in computational cell biology. We give example models of genetic mechanisms in natural cells — DNA replication, transcription into mRNA and translation into proteins — described in terms of the artificial chemistry. The descriptions are simple and easily understood, and they run correctly on a simulator of the artificial chemistry. We observed this artificial chemistry has good properties in the modelling and thus we think it is a promising candidate for a tool to construct qualitative models in computational cell biology.