-
1
-
-
34147177681
-
Using FPGA Devices to Accelerate Biomolecular Simulations
-
S.R. Alam, P. Agarwal, M.C Smith, J.S Vetter and D. Caliga, "Using FPGA Devices to Accelerate Biomolecular Simulations," IEEE Computer, vol 40, pp.66-73, 2007.
-
(2007)
IEEE Computer
, vol.40
, pp. 66-73
-
-
Alam, S.R.1
Agarwal, P.2
Smith, M.C.3
Vetter, J.S.4
Caliga, D.5
-
2
-
-
18644385256
-
Reconfigurable Molecular Dynamics Simulator
-
N. Azizi, I. Kuon, A Egier, et al, "Reconfigurable Molecular Dynamics Simulator," Proc. FCCM, 2004.
-
(2004)
Proc. FCCM
-
-
Azizi, N.1
Kuon, I.2
Egier, A.3
-
3
-
-
20844453811
-
-
S. Banerjee and J.A. Board, Efficient Charge Assignment and Back Interpolation in Multigrid Methods for Molecular Dynamics, J. Comp. Chem. 26, 2005.
-
S. Banerjee and J.A. Board, "Efficient Charge Assignment and Back Interpolation in Multigrid Methods for Molecular Dynamics," J. Comp. Chem. vol. 26, 2005.
-
-
-
-
4
-
-
0001027112
-
Multilevel Evaluation of Integral Transforms with Asymptotically Smooth Kernels
-
A. Brandt and C.H. Venner, "Multilevel Evaluation of Integral Transforms with Asymptotically Smooth Kernels," SIAM J Scientific Computing, vol. 19, pp. 468-492, 1998.
-
(1998)
SIAM J Scientific Computing
, vol.19
, pp. 468-492
-
-
Brandt, A.1
Venner, C.H.2
-
5
-
-
0000054413
-
Real-space multigrid-based approach to large-scale electronic structure calculations
-
E.L. Briggs, D.J. Sullivan, and J. Bernholc, "Real-space multigrid-based approach to large-scale electronic structure calculations," Phys. Rev. B, vol. 54, pp. 14362-14375, 1996.
-
(1996)
Phys. Rev. B
, vol.54
, pp. 14362-14375
-
-
Briggs, E.L.1
Sullivan, D.J.2
Bernholc, J.3
-
6
-
-
33846823909
-
Particle mesh Ewald: An O(N log N) method for Ewald sums in large systems
-
T. Darden, D. York, and L. Pedersen, "Particle mesh Ewald: an O(N log N) method for Ewald sums in large systems," J. Chem. Phys, vol. 98, pp. 10089-10092, 1993.
-
(1993)
J. Chem. Phys
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
7
-
-
33645961739
-
A smooth particle mesh Ewald method
-
U. Essmann, L. Perera, and M.L. Berkowitz, "A smooth particle mesh Ewald method," J. Chem. Phys, vol. 103, pp. 8577-8593, 1995.
-
(1995)
J. Chem. Phys
, vol.103
, pp. 8577-8593
-
-
Essmann, U.1
Perera, L.2
Berkowitz, M.L.3
-
8
-
-
33644848399
-
Molecular Dynamics Simulations of the Complete Satellite Tobacco Mosaic Virus
-
P.L. Freddolino, A.S. Arkhipov, S.B. Larson, et al, "Molecular Dynamics Simulations of the Complete Satellite Tobacco Mosaic Virus," Structure, vol. 14, pp. 437-49, 2006.
-
(2006)
Structure
, vol.14
, pp. 437-449
-
-
Freddolino, P.L.1
Arkhipov, A.S.2
Larson, S.B.3
-
9
-
-
44049101194
-
Improved Interpolation and System Integration for FPGA-Based Molecular Dynamics Simulations
-
Y. Gu, T. VanCourt, and M.C. Herbordt, "Improved Interpolation and System Integration for FPGA-Based Molecular Dynamics Simulations," Proc. FPL, 2006.
-
(2006)
Proc. FPL
-
-
Gu, Y.1
VanCourt, T.2
Herbordt, M.C.3
-
10
-
-
33646396757
-
Accelerating Molecular Dynamics Simulations with Configurable Circuits
-
Y. Gu, T. VanCourt, and M. C. Herbordt, "Accelerating Molecular Dynamics Simulations with Configurable Circuits," IEE Proc. CDT, vol. 153 (3), 2006.
-
(2006)
IEE Proc. CDT
, vol.153
, Issue.3
-
-
Gu, Y.1
VanCourt, T.2
Herbordt, M.C.3
-
11
-
-
20444461136
-
Parallel Multigrid Summation for the N-Body Problem
-
J.A. Izaguirre, S.S. Hampton, and T. Matthey, "Parallel Multigrid Summation for the N-Body Problem," J. Parallel Distrib. Comput, vol. 65, pp. 949-962, 2005.
-
(2005)
J. Parallel Distrib. Comput
, vol.65
, pp. 949-962
-
-
Izaguirre, J.A.1
Hampton, S.S.2
Matthey, T.3
-
12
-
-
33846844133
-
A case study in porting a production scientific supercomputing application to a reconfigurable computer
-
V. Kindratenko and D. Pointer, "A case study in porting a production scientific supercomputing application to a reconfigurable computer," Proc. FCCM, 2006.
-
(2006)
Proc. FCCM
-
-
Kindratenko, V.1
Pointer, D.2
-
13
-
-
0001489848
-
Fast and Accurate Molecular Dynamics Simulation of a Protein Using a Special-Purpose Computer
-
Y. Komeiji, M. Uebayasi, R. Takata, et al, "Fast and Accurate Molecular Dynamics Simulation of a Protein Using a Special-Purpose Computer," J. Comp. Chem, vol. 18, pp. 1546-1563, 1997.
-
(1997)
J. Comp. Chem
, vol.18
, pp. 1546-1563
-
-
Komeiji, Y.1
Uebayasi, M.2
Takata, R.3
-
15
-
-
8344261362
-
ProtoMol, An Object-Oriented Framework for Prototyping Novel Algorithms for Molecular Dynamics
-
T. Matthey, "ProtoMol, An Object-Oriented Framework for Prototyping Novel Algorithms for Molecular Dynamics," ACM Trans. Mathematical Software, vol. 30, pp. 237-265, 2004.
-
(2004)
ACM Trans. Mathematical Software
, vol.30
, pp. 237-265
-
-
Matthey, T.1
-
16
-
-
0035870662
-
Multigrid methods for classical molecular dynamics simulations of biomolecules
-
C. Sagui amd T. Darden, "Multigrid methods for classical molecular dynamics simulations of biomolecules," J. Chem. Phys, vol. 114, pp. 6578-6591, 2001.
-
(2001)
J. Chem. Phys
, vol.114
, pp. 6578-6591
-
-
Sagui, C.1
Darden, T.2
-
17
-
-
0035339718
-
Multiscale Fast Summation of Long-Range Charge and Dipolar Interactions
-
B. Sandak, "Multiscale Fast Summation of Long-Range Charge and Dipolar Interactions," J. Comput.Chem, vol. 22, pp. 717-731, 2001.
-
(2001)
J. Comput.Chem
, vol.22
, pp. 717-731
-
-
Sandak, B.1
-
18
-
-
47349126346
-
Preliminary Investigation of Advanced Electrostatics in Molecular Dynamics on Reconfigurable Computers
-
R. Scrofano and V. Prasanna, "Preliminary Investigation of Advanced Electrostatics in Molecular Dynamics on Reconfigurable Computers," Proc. Supercomputing, 2006.
-
(2006)
Proc. Supercomputing
-
-
Scrofano, R.1
Prasanna, V.2
-
19
-
-
47349133350
-
A Hardware/Software Approach to Molecular Dynamics on Reconfigurable Computers
-
R. Scrofano and V. Prasanna, "A Hardware/Software Approach to Molecular Dynamics on Reconfigurable Computers," , Proc. FCCM, 2006.
-
(2006)
Proc. FCCM
-
-
Scrofano, R.1
Prasanna, V.2
-
20
-
-
0037197257
-
Multiple Grid Methods for Classical Molecular Dynamics
-
R.D. Skeel, I. Tezcan, and D.J. Hardy, "Multiple Grid Methods for Classical Molecular Dynamics," J. Comput. Chem, vol. 23, pp. 673-684, 2002.
-
(2002)
J. Comput. Chem
, vol.23
, pp. 673-684
-
-
Skeel, R.D.1
Tezcan, I.2
Hardy, D.J.3
-
22
-
-
47349119825
-
Application-Dependent Memory Interleaving Enables High Performance in FPGA-Based Grid Computations
-
T. VanCourt and M.C. Herbordt, "Application-Dependent Memory Interleaving Enables High Performance in FPGA-Based Grid Computations," Proc. FPL, 2006.
-
(2006)
Proc. FPL
-
-
VanCourt, T.1
Herbordt, M.C.2
-
23
-
-
47349109771
-
FPGA Acceleration of Rigid Molecule Interactions
-
T. VanCourt, Y. Gu, and M.C. Herbordt, "FPGA Acceleration of Rigid Molecule Interactions," Proc. FPL, 2004.
-
(2004)
Proc. FPL
-
-
VanCourt, T.1
Gu, Y.2
Herbordt, M.C.3
-
24
-
-
33750799898
-
Why Multigrid method are so efficient
-
I. Yavneh, "Why Multigrid method are so efficient," Computing in Science & Engineering, vol. 8, pp. 12-22, 2006.
-
(2006)
Computing in Science & Engineering
, vol.8
, pp. 12-22
-
-
Yavneh, I.1
-
25
-
-
33744994616
-
The fast Fourier Poisson method for calculating Ewald sums
-
D. York and W. Yang, "The fast Fourier Poisson method for calculating Ewald sums," J. Chem. Phys, vol. 101, pp. 3298-3300, 1994.
-
(1994)
J. Chem. Phys
, vol.101
, pp. 3298-3300
-
-
York, D.1
Yang, W.2
|