NDLI: Parallelized agent-based simulation on CPU and graphics hardware for spatial and stochastic models in biology

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Parallelized agent-based simulation on CPU and graphics hardware for spatial and stochastic models in biology

Content Provider	ACM Digital Library
Author	Falk, Martin Ertl, Thomas Koeppl, Heinz Ott, Michael Klann, Michael
Abstract	The complexity of biological systems is enormous, even when considering a single cell where a multitude of highly parallel and intertwined processes take place on the molecular level. This paper focuses on the parallel simulation of signal transduction processes within a cell carried out solely on the graphics processing unit (GPU). Each signaling molecule is represented by an agent performing a discretetime continuous-space random walk to model its diffusion through the cell. Since the interactions and reactions between the agents can be competitive and are interdependent, we propose spatial partitioning for the reaction detection to overcome the data dependencies in the parallel execution of reactions. In addition, we present a simple way to simulate the Michaelis-Menten kinetics in our particle-based method using a per-particle delay. We apply this agent-based simulation to model signal transduction in the MAPK (Mitogen-Activated Protein Kinase) cascade both with and without cytoskeletal filaments. Finally, we compare the speed-up of our GPU simulation with a parallelized CPU version resulting in a twelvefold speedup.
Starting Page	73
Ending Page	82
Page Count	10
File Format	PDF
ISBN	9781450308175
DOI	10.1145/2037509.2037521
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2011-09-21
Publisher Place	New York
Access Restriction	Subscribed
Subject Keyword	Agent-based simulation Systems biology Gpu computing Gpu parallelization Mapk
Content Type	Text
Resource Type	Article

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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