Mersenne twister: a 623-dimensionally equidistributed uniform pseudo-random number generator
ACM Transactions on Modeling and Computer Simulation (TOMACS) - Special issue on uniform random number generation
Physically-based visual simulation on graphics hardware
Proceedings of the ACM SIGGRAPH/EUROGRAPHICS conference on Graphics hardware
Particle-based simulation of granular materials
Proceedings of the 2005 ACM SIGGRAPH/Eurographics symposium on Computer animation
Software and the Concurrency Revolution
Queue - Multiprocessors
Scan primitives for GPU computing
Proceedings of the 22nd ACM SIGGRAPH/EUROGRAPHICS symposium on Graphics hardware
Scalable Parallel Programming with CUDA
Queue - GPU Computing
Data parallel execution challenges and runtime performance of agent simulations on GPUs
Proceedings of the 2008 Spring simulation multiconference
An Exact Brownian Dynamics Method for Cell Simulation
CMSB '08 Proceedings of the 6th International Conference on Computational Methods in Systems Biology
On Parallel Stochastic Simulation of Diffusive Systems
CMSB '08 Proceedings of the 6th International Conference on Computational Methods in Systems Biology
Optimized Parallel Implementation of Gillespie's First Reaction Method on Graphics Processing Units
ICCMS '09 Proceedings of the 2009 International Conference on Computer Modeling and Simulation
Long time-scale simulations of in vivo diffusion using GPU hardware
IPDPS '09 Proceedings of the 2009 IEEE International Symposium on Parallel&Distributed Processing
Experiments with Single Core, Multi-core, and GPU Based Computation of Cellular Automata
SIMUL '09 Proceedings of the 2009 First International Conference on Advances in System Simulation
SpringSim '09 Proceedings of the 2009 Spring Simulation Multiconference
International Journal of High Performance Computing Applications
Parallel Particle-Based Reaction Diffusion: A GPU Implementation
PDMC-HIBI '10 Proceedings of the 2010 Ninth International Workshop on Parallel and Distributed Methods in Verification, and Second International Workshop on High Performance Computational Systems Biology
| Hi-index | 0.00 |
Space is a very important aspect in the simulation of biochemical systems; recently, the need for simulation algorithms able to cope with space is becoming more and more compelling. Complex and detailed models of biochemical systems need to deal with the movement of single molecules and particles, taking into consideration localized fluctuations, transportation phenomena, and diffusion. A common drawback of spatial models lies in their complexity: models can become very large, and their simulation could be time consuming, especially if we want to capture the systems behavior in a reliable way using stochastic methods in conjunction with a high spatial resolution. In order to deliver the promise done by systems biology to be able to understand a system as whole, we need to scale up the size of models we are able to simulate, moving from sequential to parallel simulation algorithms. In this paper, we analyze Smoldyn, a widely diffused algorithm for stochastic simulation of chemical reactions with spatial resolution and single molecule detail, and we propose an alternative, innovative implementation that exploits the parallelism of Graphics Processing Units (GPUs). The implementation executes the most computational demanding steps (computation of diffusion, unimolecular, and bimolecular reaction, as well as the most common cases of molecule-surface interaction) on the GPU, computing them in parallel on each molecule of the system. The implementation offers good speed-ups and real time, high quality graphics output.