Theoretical Computer Science
BioAmbients: an abstraction for biological compartments
Theoretical Computer Science - Special issue: Computational systems biology
CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
Abstract interpretation based verification of temporal properties for BioAmbients
Information and Computation
Compartmental rule-based modeling of biochemical systems
Winter Simulation Conference
CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
Electronic Notes in Theoretical Computer Science (ENTCS)
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Inspired by the alternating orientations of cellular membranes, we describe a structure of nested membranes that are colored in two alternating tones. We investigate a class of reactions that maintain the colored regions largely invariant at each step (bitonal reactions). These coloring constraints guide us towards a small and non-obvious set of basic reactions that are both realistic and complete. They are realistic because bitonality is related to an independent notion of locality, and because similar reactions are implemented by molecular machinery. They are complete because any bitonal reaction can be obtained from them. Such a set of reactions can then be used as the basis for descriptions of biological processes, and in particular for the description of transport networks in cellular biology.