Report: GPU Based Massive Parallel Kawasaki Kinetics In Monte Carlo Modelling of Lipid Microdomains.

作者: Lukasz Pintal , Mateusz Lis

DOI:

关键词:

摘要: This paper introduces novel method of simulation lipid biomembranes based on Metropolis Hastings algorithm and Graphic Processing Unit computational power. Method gives up to 55 times boost in comparison classical computations. Extensive study correctness is provided. Analysis results obtained with methodologies are presented.

参考文章(9)
Neil G. Dickson, Kamran Karimi, Firas Hamze, Importance of explicit vectorization for CPU and GPU software performance Journal of Computational Physics. ,vol. 230, pp. 5383- 5398 ,(2011) , 10.1016/J.JCP.2011.03.041
Jens Ehrig, Eugene P. Petrov, Petra Schwille, Near-critical fluctuations and cytoskeleton-assisted phase separation lead to subdiffusion in cell membranes. Biophysical Journal. ,vol. 100, pp. 80- 89 ,(2011) , 10.1016/J.BPJ.2010.11.002
Nicholas Metropolis, Arianna W. Rosenbluth, Marshall N. Rosenbluth, Augusta H. Teller, Edward Teller, Equation of State Calculations by Fast Computing Machines The Journal of Chemical Physics. ,vol. 21, pp. 1087- 1092 ,(1953) , 10.1063/1.1699114
Tobias Preis, Peter Virnau, Wolfgang Paul, Johannes J. Schneider, GPU accelerated Monte Carlo simulation of the 2D and 3D Ising model Journal of Computational Physics. ,vol. 228, pp. 4468- 4477 ,(2009) , 10.1016/J.JCP.2009.03.018
Tal Levy, Eran Rabani, Guy Cohen, Simulating Lattice Spin Models on Graphics Processing Units arXiv: Computational Physics. ,(2012) , 10.1021/CT100385B
Agnieszka E. Hac, Heiko M. Seeger, Matthias Fidorra, Thomas Heimburg, Diffusion in two-component lipid membranes--a fluorescence correlation spectroscopy and monte carlo simulation study. Biophysical Journal. ,vol. 88, pp. 317- 333 ,(2005) , 10.1529/BIOPHYSJ.104.040444
Mateusz Lis, Lukasz Pintal, Jerzy Swiatek, Lukasz Cwiklik, GPU-Based Massive Parallel Kawasaki Kinetics in the Dynamic Monte Carlo Simulations of Lipid Nanodomains. Journal of Chemical Theory and Computation. ,vol. 8, pp. 4758- 4765 ,(2012) , 10.1021/CT300587W
Christopher C. Holmes, Arnaud Doucet, Christopher Yau, Anthony Lee, Michael B. Giles, On the utility of graphics cards to perform massively parallel simulation of advanced Monte Carlo methods arXiv: Computation. ,(2009) , 10.1198/JCGS.2010.10039