Flocks, herds and schools: A distributed behavioral model
SIGGRAPH '87 Proceedings of the 14th annual conference on Computer graphics and interactive techniques
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From the beginning of biological modeling, simulations were an efficient way to understand local mechanisms linked to whole system behaviors. Cellular automata and more recently Multi-Agent Systems (MAS) are currently used to model ecological systems. Virus dissemination through population or insect collaborations are well known examples of how simple interactions between entities (agents) are able to build a complex situation at the level of the whole population. But use of MAS to design biological system at the cellular or subcellular level, mainly for enzymatic reactions, is a relatively new application of the agent paradigm. In fact, agents used for ecology simulations are 'non-physical' agents, i.e. in general they do not have any explicit representation of their geometry, their space bulk or the articulated movements of their body parts. These characteristics are essential in enzymatic behaviors. The three dimension structure and movements of this structure condition the realisation of the reaction that can be stopped or conversely favored by specific conformations. In order to simulate subcellular biological processes, we defined agents capable of simulating molecular conformational changes. These agents integrate molecular modeling data, for conformational change methods, and biological ontology data, for conformational change conditions. As some biological entities are motor of the enzymatic reactions while others are simple partners, we defined two agent subtypes, active and passive agents. As a proof of concept, we applied our model to the simulation of enzymatic oxydo-reduction reactions.