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Optimisation of a molecular dynamics simulation of chromosome condensation
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Law, Timothy R., Hancox, Jonny, Cheng, Tammy M. K., Chaleil, Raphael A. G., Wright, Steven A., Bates, Paul A. and Jarvis, Stephen A. (2016) Optimisation of a molecular dynamics simulation of chromosome condensation. In: 28th International Symposium on Computer Architecture and High Performance Computing, LA, USA, 26-28 Oct 2016. Published in: 2016 28th International Symposium on Computer Architecture and High Performance Computing (SBAC-PAD) ISBN 9781509061099. doi:10.1109/SBAC-PAD.2016.24
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WRAP-optimisation-molecular-dynamics-simulation-chromosome-condensation-Hancox-2018.pdf - Accepted Version - Requires a PDF viewer. Download (934Kb) | Preview |
Official URL: https://doi.org/10.1109/SBAC-PAD.2016.24
Abstract
We present optimisations applied to a bespoke biophysical molecular dynamics simulation designed to investigate chromosome condensation. Our primary focus is on domain specific algorithmic improvements to determining short-range interaction forces between particles, as certain qualities of the simulation render traditional methods less effective. We implement tuned versions of the code for both traditional CPU architectures and the modern many-core architecture found in the Intel Xeon Phi coprocessor and compare their effectiveness. We achieve speed-ups starting at a factor of 10 over the original code, facilitating more detailed and larger-scale experiments.
Item Type: | Conference Item (Paper) | |||||||||||||||
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Subjects: | Q Science > QH Natural history > QH426 Genetics | |||||||||||||||
Divisions: | Faculty of Science, Engineering and Medicine > Science > Computer Science | |||||||||||||||
Library of Congress Subject Headings (LCSH): | Molecular dynamics -- Simulation methods, Chromatin, Chromosomes, Algorithms, Coprocessors -- Xeon (Firm), Genomes | |||||||||||||||
Journal or Publication Title: | 2016 28th International Symposium on Computer Architecture and High Performance Computing (SBAC-PAD) | |||||||||||||||
Publisher: | IEEE | |||||||||||||||
ISBN: | 9781509061099 | |||||||||||||||
Official Date: | 19 December 2016 | |||||||||||||||
Dates: |
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DOI: | 10.1109/SBAC-PAD.2016.24 | |||||||||||||||
Status: | Peer Reviewed | |||||||||||||||
Publication Status: | Published | |||||||||||||||
Access rights to Published version: | Restricted or Subscription Access | |||||||||||||||
Date of first compliant deposit: | 12 September 2016 | |||||||||||||||
Date of first compliant Open Access: | 12 September 2016 | |||||||||||||||
RIOXX Funder/Project Grant: |
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Conference Paper Type: | Paper | |||||||||||||||
Title of Event: | 28th International Symposium on Computer Architecture and High Performance Computing | |||||||||||||||
Type of Event: | Conference | |||||||||||||||
Location of Event: | LA, USA | |||||||||||||||
Date(s) of Event: | 26-28 Oct 2016 |
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