title: High performance computing for three-dimensional agent-based molecular models.
abstract: Agent-based simulations are increasingly popular in exploring and understanding cellular systems, but the natural complexity of these systems and the desire to grasp different modelling levels demand cost-effective simulation strategies and tools. In this context, the present paper introduces novel sequential and distributed approaches for the three-dimensional agent-based simulation of individual molecules in cellular events. These approaches are able to describe the dimensions and position of the molecules with high accuracy and thus, study the critical effect of spatial distribution on cellular events. Moreover, two of the approaches allow multi-thread high performance simulations, distributing the three-dimensional model in a platform independent and computationally efficient way. Evaluation addressed the reproduction of molecular scenarios and different scalability aspects of agent creation and agent interaction. The three approaches simulate common biophysical and biochemical laws faithfully. The distributed approaches show improved performance when dealing with large agent populations while the sequential approach is better suited for small to medium size agent populations. Overall, the main new contribution of the approaches is the ability to simulate three-dimensional agent-based models at the molecular level with reduced implementation effort and moderate-level computational capacity. Since these approaches have a generic design, they have the major potential of being used in any event-driven agent-based tool.
authors.affiliation: ESEI - Escuela Superior de Ingeniería Informática, Edificio Politécnico, Campus Universitario As Lagoas s/n, Universidad de Vigo, 32004 Ourense, Spain. Electronic address: gprodriguez2@esei.uvigo.es.
authors.forename: G
authors.initials: G
authors.lastname: Pérez-Rodríguez
authors.affiliation: ESEI - Escuela Superior de Ingeniería Informática, Edificio Politécnico, Campus Universitario As Lagoas s/n, Universidad de Vigo, 32004 Ourense, Spain. Electronic address: mpperez3@esei.uvigo.es.
authors.forename: M
authors.initials: M
authors.lastname: Pérez-Pérez
authors.affiliation: ESEI - Escuela Superior de Ingeniería Informática, Edificio Politécnico, Campus Universitario As Lagoas s/n, Universidad de Vigo, 32004 Ourense, Spain. Electronic address: riverola@uvigo.es.
authors.forename: F
authors.initials: F
authors.lastname: Fdez-Riverola
authors.affiliation: ESEI - Escuela Superior de Ingeniería Informática, Edificio Politécnico, Campus Universitario As Lagoas s/n, Universidad de Vigo, 32004 Ourense, Spain; CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-0668 Braga, Portugal. Electronic address: analia@uvigo.es.
authors.forename: A
authors.initials: A
authors.lastname: Lourenço
mesh_terms: D003198:Computer Simulation; D019746:Intramolecular Oxidoreductases / Q000737:chemistry; D008958:Models, Molecular; D013597:Systems Analysis
chemical_list: D019746:Intramolecular Oxidoreductases
keywords: Agent-based modelling; Cellular systems; Distributed computing; Individual molecule simulation; Three-dimensional model representation