Special Purpose Parallel Computer for Modelling Supramolecular Systems based on the Dynamic Lattice Liquid Model
Polanowski Piotr 1*, Jung Jarosław 1, Kiełbik Rafał 2
1Technical University of Łódź, Department of Molecular Physics,
Żeromskiego 116, 90-924 Łódź, Poland
2Technical University of Łódź, Department of Microelectronics and Computer Science
al. Politechniki 11, 90-924 Łódź, Poland
*e-mail: ppolanow@p.lodz.pl
Received:
Received: 30 March 2010; accepted: 2 June 2010; published online: 3 September 2010
DOI: 10.12921/cmst.2010.16.02.147-153
OAI: oai:lib.psnc.pl:722
Abstract:
A predictive description of the synthetic processes leading to complex macromolecules requires consideration of the spatial models. Hierarchical, structural and dynamic complexities of such systems require new methodological developments. The presented work provides effective tools for the modelling of the complex synthetic processes in the 3D space under controlled conditions. We propose constructing a parallel computing system which realizes the 3D architecture and the cooperative dynamics based on the dynamic lattice liquid (DLL) model. This can create new standards in the spatial resolution of the models allowing simulations of the systems comparable in sizes and complexity with the biological cells in the future.
Key words:
dedicated parallel computer, FPGA, liquid dynamics, Monte Carlo simulations
References:
[1] B.J. Alder, T.E. Wainwright, Studies of molecular dynamics I: general method. J. Chem. Phys. 31, 459 (1959).
[2] R. Zangi, S. Rice, Coopertive Dynamics it Two Dimension. Phys. Rev. Letter 93, 35502 (2004).
[3] B.G. Fitch, A. Rayshubsky, M. Elftheriou, T.J.C. Ward, M.E. Giampapa, M.C. Pitman, J.W. Pitera, W.C. Swope, R.S. Germain. Blue Matter: Scalling of N-body simulations to one atom per node. IBM J. Res & Dev. 52, 145 (2008).
[4] J. Makino, Grape project special-purpose computers for many-body simulation. Comp. Phys. Communication 139, 45-56 (2001).
[5] R. Scrofano, M.B. Gokhale, F. Trouw, V.K. Prasanna, Accelerating Molecular Dynamics Simulation with Reconfigurable Computers. IEEE Transaction on Parallel and Distributed
System 19, 765 (2008).
[6] B. Chopard, M. Droz, Cellular Automata Modeling of Physical Systems. Cambridge University Press (1998).
[7] I. Teraoka, Polymer solution – an introduction to physical properties. Wiley-Interscience, (2002).
[8] P. Polanowski, T. Pakula, Studies of mobility, interdiffusion and self-diffusion in two-component mixtures using the dynamic lattice liquid model. J. Chem. Phys. 118, 11139-11146
(2003)
A predictive description of the synthetic processes leading to complex macromolecules requires consideration of the spatial models. Hierarchical, structural and dynamic complexities of such systems require new methodological developments. The presented work provides effective tools for the modelling of the complex synthetic processes in the 3D space under controlled conditions. We propose constructing a parallel computing system which realizes the 3D architecture and the cooperative dynamics based on the dynamic lattice liquid (DLL) model. This can create new standards in the spatial resolution of the models allowing simulations of the systems comparable in sizes and complexity with the biological cells in the future.
Key words:
dedicated parallel computer, FPGA, liquid dynamics, Monte Carlo simulations
References:
[1] B.J. Alder, T.E. Wainwright, Studies of molecular dynamics I: general method. J. Chem. Phys. 31, 459 (1959).
[2] R. Zangi, S. Rice, Coopertive Dynamics it Two Dimension. Phys. Rev. Letter 93, 35502 (2004).
[3] B.G. Fitch, A. Rayshubsky, M. Elftheriou, T.J.C. Ward, M.E. Giampapa, M.C. Pitman, J.W. Pitera, W.C. Swope, R.S. Germain. Blue Matter: Scalling of N-body simulations to one atom per node. IBM J. Res & Dev. 52, 145 (2008).
[4] J. Makino, Grape project special-purpose computers for many-body simulation. Comp. Phys. Communication 139, 45-56 (2001).
[5] R. Scrofano, M.B. Gokhale, F. Trouw, V.K. Prasanna, Accelerating Molecular Dynamics Simulation with Reconfigurable Computers. IEEE Transaction on Parallel and Distributed
System 19, 765 (2008).
[6] B. Chopard, M. Droz, Cellular Automata Modeling of Physical Systems. Cambridge University Press (1998).
[7] I. Teraoka, Polymer solution – an introduction to physical properties. Wiley-Interscience, (2002).
[8] P. Polanowski, T. Pakula, Studies of mobility, interdiffusion and self-diffusion in two-component mixtures using the dynamic lattice liquid model. J. Chem. Phys. 118, 11139-11146
(2003)
