title: Parallel solutions for voxel-based simulations of reaction-diffusion systems.
abstract: There is an increasing awareness of the pivotal role of noise in biochemical processes and of the effect of molecular crowding on the dynamics of biochemical systems. This necessity has given rise to a strong need for suitable and sophisticated algorithms for the simulation of biological phenomena taking into account both spatial effects and noise. However, the high computational effort characterizing simulation approaches, coupled with the necessity to simulate the models several times to achieve statistically relevant information on the model behaviours, makes such kind of algorithms very time-consuming for studying real systems. So far, different parallelization approaches have been deployed to reduce the computational time required to simulate the temporal dynamics of biochemical systems using stochastic algorithms. In this work we discuss these aspects for the spatial TAU-leaping in crowded compartments (STAUCC) simulator, a voxel-based method for the stochastic simulation of reaction-diffusion processes which relies on the Sτ-DPP algorithm. In particular we present how the characteristics of the algorithm can be exploited for an effective parallelization on the present heterogeneous HPC architectures.
authors.affiliation: Institute of Applied Mathematics and Information Technologies, National Research Council of Italy, Via de Marini, 16149 Genoa, Italy.
authors.forename: Daniele
authors.initials: D
authors.lastname: D'Agostino
authors.affiliation: Institute of Applied Mathematics and Information Technologies, National Research Council of Italy, Via de Marini, 16149 Genoa, Italy.
authors.forename: Giulia
authors.initials: G
authors.lastname: Pasquale
authors.affiliation: Institute of Applied Mathematics and Information Technologies, National Research Council of Italy, Via de Marini, 16149 Genoa, Italy.
authors.forename: Andrea
authors.initials: A
authors.lastname: Clematis
authors.affiliation: Genetic Unit, IRCCS Saint John of God, Clinical Research Centre, Via Pilastroni 4, 25125 Brescia, Italy.
authors.forename: Carlo
authors.initials: C
authors.lastname: Maj
authors.affiliation: Institute of Biomedical Technologies, National Research Council of Italy, Via Fratelli Cervi 93, 20090 Segrate, Milan, Italy.
authors.forename: Ettore
authors.initials: E
authors.lastname: Mosca
authors.affiliation: Institute of Biomedical Technologies, National Research Council of Italy, Via Fratelli Cervi 93, 20090 Segrate, Milan, Italy.
authors.forename: Luciano
authors.initials: L
authors.lastname: Milanesi
authors.affiliation: Institute of Biomedical Technologies, National Research Council of Italy, Via Fratelli Cervi 93, 20090 Segrate, Milan, Italy.
authors.forename: Ivan
authors.initials: I
authors.lastname: Merelli
mesh_terms: D000465:Algorithms; D001669:Biochemical Phenomena; D003198:Computer Simulation; D004058:Diffusion; D007700:Kinetics; D008954:Models, Biological; D009622:Noise; D013269:Stochastic Processes