A Biochemically-inspired Coordination-based Model for Simulating Biochemical Patterns

Sara Montagna, Andrea Omicini, Pedro Pablo González Pérez

Given the prominence of the interaction issues in the simulation of complex systems, coordination models and infrastructures have the potential to work as the core of non-trivial simulation frameworks. In particular, self-organising, nature-inspired coordination models are seemingly well-suited for the simulation of complex biochemical systems, where molecules massively interact arising patterns that underlie cell functioning.
In this paper we adopt a self-organising coordination model based on biochemical tuple spaces (BTS-SOC), and show how it can be straightforwardly and effectively applied to the simulation of complex interaction patterns of intracellular signalling pathways. We discuss the model and the high-level simulation architecture, where tuples represent chemical substances, coordination rules evolve tuple concentrations over time, tuple spaces represent single-compartment solutions, and a network of tuple spaces resemble a set of compartments in a biological system. Then we develop and discuss a simple case study, that is, a single signalling pathway from the complex network of the Ras signalling pathways.

(keywords) Self-organising coordination; Simulation; Biochemical tuple spaces; Computational Biology; Intracellular signalling pathways

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