Parallel Solutions for Voxel-Based Simulations of Reaction-Diffusion Systems
Joint Authors
D’Agostino, Daniele
Mosca, Ettore
Clematis, Andrea
Milanesi, Luciano
Maj, Carlo
Pasquale, Giulia
Merelli, Ivan
Source
Issue
Vol. 2014, Issue 2014 (31 Dec. 2014), pp.1-10, 10 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2014-06-12
Country of Publication
Egypt
No. of Pages
10
Main Subjects
Abstract EN
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.
American Psychological Association (APA)
D’Agostino, Daniele& Pasquale, Giulia& Clematis, Andrea& Maj, Carlo& Mosca, Ettore& Milanesi, Luciano…[et al.]. 2014. Parallel Solutions for Voxel-Based Simulations of Reaction-Diffusion Systems. BioMed Research International،Vol. 2014, no. 2014, pp.1-10.
https://search.emarefa.net/detail/BIM-513199
Modern Language Association (MLA)
D’Agostino, Daniele…[et al.]. Parallel Solutions for Voxel-Based Simulations of Reaction-Diffusion Systems. BioMed Research International No. 2014 (2014), pp.1-10.
https://search.emarefa.net/detail/BIM-513199
American Medical Association (AMA)
D’Agostino, Daniele& Pasquale, Giulia& Clematis, Andrea& Maj, Carlo& Mosca, Ettore& Milanesi, Luciano…[et al.]. Parallel Solutions for Voxel-Based Simulations of Reaction-Diffusion Systems. BioMed Research International. 2014. Vol. 2014, no. 2014, pp.1-10.
https://search.emarefa.net/detail/BIM-513199
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-513199