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» Reconfigurable Molecular Dynamics Simulator
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COMPGEOM
2005
ACM
14 years 28 days ago
Dynamic maintenance of molecular surfaces under conformational changes
We present an efficient algorithm for maintaining the boundary and surface area of protein molecules as they undergo conformational changes. We also describe a robust implementati...
Eran Eyal, Dan Halperin
CSC
2010
13 years 6 months ago
Performance Modeling, Analysis, and Optimization of Cell-List Based Molecular Dynamics
- We have developed a performance prediction model for non-bonded interaction computations in molecular dynamics simulations, thereby predicting the optimal cell dimension in a lin...
Manaschai Kunaseth, Rajiv K. Kalia, Aiichiro Nakan...
IJIPM
2010
57views more  IJIPM 2010»
13 years 8 months ago
A Design and Simulation for Dynamically Reconfigurable Systolic Array
Toshiyuki Ishimura, Akinori Kanasugi
ARCS
2004
Springer
14 years 2 months ago
Evaluation of Run-Time Reconfiguration for General-Purpose Computing
: In order to investigate the impact of dynamic hardware reconfiguration on general-purpose applications, we present a superscalar micro-architecture that includes a variable numbe...
Adronis Niyonkuru, Hans Christoph Zeidler
CPHYSICS
2008
161views more  CPHYSICS 2008»
13 years 11 months ago
Implementing peridynamics within a molecular dynamics code
Peridynamics (PD) is a continuum theory that employs a nonlocal model to describe material properties. In this context, nonlocal means that continuum points separated by a finite ...
Michael L. Parks, Richard B. Lehoucq, Steven J. Pl...