TITLE:
Refined Agent Model Using Shape-Based Grained Structure: Application to Membrane Molecules
AUTHORS:
François Vallée, Marie Beurton-Aimar, Hien T. Tran, Nicolas Parisey
KEYWORDS:
Biological Simulations, 3D Reactive Agent, Sub-Cellular Level, Molecule Interactions
JOURNAL NAME:
Journal of Computer and Communications,
Vol.4 No.13,
October
18,
2016
ABSTRACT: Multi-agent model is well-known to suit
design of complex systems. This paradigm allows describing autonomous entities
to interact together directly or through their environment. It is specially
adapted to design 3D simulations taking into account spatial constraints on
agents. In this work, we have designed a multi-agent model which adds a feature
to the classical representation of agent: a body, encapsulating a physical
model of the agent. We have applied this model to lipids and proteins belonging
to the inner mitochondrial membrane, a biological membrane. Information provided
by atomic structures is available through international databases and has been
used to design a shape-based grain model for the agent body. We selected a
model with three grains per molecule in which each grain is characterized by a
type determining how they interact together and consequently the agent
behaviors. Lipids and two kinds of protein structures have been described
within this model allowing us to simulate their organization in membranes.