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Interactive Molecular Dynamics: Scaling up to Large Systems
, 2013
"... Combining molecular dynamics simulations with user interaction would have various applications in both education and research. By enabling interactivity the scientist will be able to visualize the experiment in real time and drive the simulation to a desired state more easily. However, interacting w ..."
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Combining molecular dynamics simulations with user interaction would have various applications in both education and research. By enabling interactivity the scientist will be able to visualize the experiment in real time and drive the simulation to a desired state more easily. However, interacting
The LargeScale Organization of Metabolic Networks
, 2000
"... In a cell or microorganism the processes that generate mass, energy, information transfer, and cell fate specification are seamlessly integrated through a complex network of various cellular constituents and reactions. However, despite the key role these networks play in sustaining various cellular ..."
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Cited by 599 (7 self)
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and errortolerant networks, and may represent a common blueprint for the largescale organization of interactions among all cellular constituents.
Network Coding for Large Scale Content Distribution
"... We propose a new scheme for content distribution of large files that is based on network coding. With network coding, each node of the distribution network is able to generate and transmit encoded blocks of information. The randomization introduced by the coding process eases the scheduling of bloc ..."
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Cited by 497 (6 self)
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We propose a new scheme for content distribution of large files that is based on network coding. With network coding, each node of the distribution network is able to generate and transmit encoded blocks of information. The randomization introduced by the coding process eases the scheduling
Fast Parallel Algorithms for ShortRange Molecular Dynamics
 JOURNAL OF COMPUTATIONAL PHYSICS
, 1995
"... Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of interatomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dyn ..."
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Cited by 622 (6 self)
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Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of interatomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular
RealTime Dynamic Voltage Scaling for LowPower Embedded Operating Systems
, 2001
"... In recent years, there has been a rapid and wide spread of nontraditional computing platforms, especially mobile and portable computing devices. As applications become increasingly sophisticated and processing power increases, the most serious limitation on these devices is the available battery lif ..."
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Cited by 498 (4 self)
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life. Dynamic Voltage Scaling (DVS) has been a key technique in exploiting the hardware characteristics of processors to reduce energy dissipation by lowering the supply voltage and operating frequency. The DVS algorithms are shown to be able to make dramatic energy savings while providing
Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of nalkanes
 J. Comput. Phys
, 1977
"... A numerical algorithm integrating the 3N Cartesian equations of motion of a system of N points subject to holonomic constraints is formulated. The relations of constraint remain perfectly fulfilled at each step of the trajectory despite the approximate character of numerical integration. The method ..."
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Cited by 682 (6 self)
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is applied to a molecular dynamics simulation of a liquid of 64 nbutane molecules and compared to a simulation using generalized coordinates. The method should be useful for molecular dynamics calculations on large molecules with internal degrees of freedom. 1. INTR~D~JCTI~N The method of molecular dynamics
CYC: A LargeScale Investment in Knowledge Infrastructure
 Communications of the ACM
, 1995
"... This article examines the fundamental ..."
SNOPT: An SQP Algorithm For LargeScale Constrained Optimization
, 2002
"... Sequential quadratic programming (SQP) methods have proved highly effective for solving constrained optimization problems with smooth nonlinear functions in the objective and constraints. Here we consider problems with general inequality constraints (linear and nonlinear). We assume that first deriv ..."
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Cited by 582 (23 self)
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Sequential quadratic programming (SQP) methods have proved highly effective for solving constrained optimization problems with smooth nonlinear functions in the objective and constraints. Here we consider problems with general inequality constraints (linear and nonlinear). We assume that first derivatives are available, and that the constraint gradients are sparse. We discuss
GPFS: A SharedDisk File System for Large Computing Clusters
 In Proceedings of the 2002 Conference on File and Storage Technologies (FAST
, 2002
"... GPFS is IBM's parallel, shareddisk file system for cluster computers, available on the RS/6000 SP parallel supercomputer and on Linux clusters. GPFS is used on many of the largest supercomputers in the world. GPFS was built on many of the ideas that were developed in the academic community ove ..."
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Cited by 518 (3 self)
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over the last several years, particularly distributed locking and recovery technology. To date it has been a matter of conjecture how well these ideas scale. We have had the opportunity to test those limits in the context of a product that runs on the largest systems in existence. While in many cases
GloMoSim: A Library for Parallel Simulation of Largescale Wireless Networks
 in Workshop on Parallel and Distributed Simulation
, 1998
"... A number of librarybased parallel and sequential network simulators have been designed. This paper describes a library, called GloMoSim (for Global Mobile system Simulator), for parallel simulation of wireless networks. GloMoSim has been designed to be extensible and composable: the communication p ..."
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Cited by 645 (30 self)
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A number of librarybased parallel and sequential network simulators have been designed. This paper describes a library, called GloMoSim (for Global Mobile system Simulator), for parallel simulation of wireless networks. GloMoSim has been designed to be extensible and composable: the communication
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