Sciweavers

DAGSTUHL
2011
12 years 10 months ago
Salient Frame Detection for Molecular Dynamics Simulations
Saliency-based analysis can be applied to time-varying 3D datasets purpose of summarization, abstraction, and motion analysis. As the sizes of time-varying datasets continue to gro...
Youngmin Kim, Robert Patro, Cheuk Yiu Ip, Dianne P...
JCC
2011
87views more  JCC 2011»
13 years 6 months ago
Determining equilibrium constants for dimerization reactions from molecular dynamics simulations
Abstract: With today’s available computer power, free energy calculations from equilibrium molecular dynamics simulations “via counting” become feasible for an increasing num...
Djurre H. De Jong, Lars V. Schäfer, Alex H. D...
JCC
2002
94views more  JCC 2002»
13 years 10 months ago
Modern protein force fields behave comparably in molecular dynamics simulations
: Several molecular dynamics simulations were performed on three proteins--bovine apo-calbindin D9K, human interleukin-4 R88Q mutant, and domain IIA of bacillus subtilis glucose pe...
Daniel J. Price, Charles L. Brooks III
JCC
2007
63views more  JCC 2007»
13 years 11 months ago
Quantum correction to the pair distribution function
: We report a numerical technique that allows the quantum effects of zero-point motion to be incorporated into Pair Distribution Functions calculated classically for molecules usin...
V. A. Levashov, S. J. L. Billinge, M. F. Thorpe
CPHYSICS
2008
97views more  CPHYSICS 2008»
13 years 11 months ago
Parallel algorithms for molecular dynamics with induction forces
We examine parallel algorithms for molecular dynamics simulations involving long-range induction interactions. The algorithms are tested by performing molecular dynamics simulatio...
Jianhui Li, Zhongwu Zhou, Richard J. Sadus
ISCAPDCS
2008
14 years 13 days ago
Accelerating Molecular Dynamics Simulations with GPUs
Molecular dynamics simulations are known to run for many days or weeks before completion. In this paper we explore the use of GPUs to accelerate a LennardJones-based molecular dyn...
John Paul Walters, Vidyananth Balu, Vipin Chaudhar...
VRML
1999
ACM
14 years 3 months ago
VRML Molecular Dynamics Trajectories
One application of VRML is visualisation of scientific data. Using VRML results of simulations and other scientific endeavours can be published on the web with all the advantage...
Geoff Leach, James Gilbert
EUROGP
2004
Springer
14 years 4 months ago
Constrained Molecular Dynamics as a Search and Optimization Tool
Abstract. In this paper we consider a new class of search and optimization algorithms inspired by molecular dynamics simulations in physics.
Riccardo Poli, Christopher R. Stephens
HIPC
2007
Springer
14 years 5 months ago
Molecular Dynamics Simulations on Commodity GPUs with CUDA
Molecular dynamics simulations are a common and often repeated task in molecular biology. The need for speeding up this treatment comes from the requirement for large system simula...
Weiguo Liu, Bertil Schmidt, Gerrit Voss, Wolfgang ...
RECOMB
2009
Springer
14 years 11 months ago
An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations
Collective behavior involving distally separate regions in a protein is known to widely affect its function. In this paper, we present an online approach to study and characterize ...
Arvind Ramanathan, Pratul K. Agarwal, Maria Kurnik...