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Abstract Molecular dynamics simulation of sputtering from a cylindrical track: EAM versus pair potentials
"... Molecular dynamics simulations implementing the thermal spike model for sputtering by energetic particle bombardment are performed for a gold target represented with a manybody embedded atom method (EAM) potential. A linear dependence of sputtering yield on the effective energy deposition is observ ..."
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Molecular dynamics simulations implementing the thermal spike model for sputtering by energetic particle bombardment are performed for a gold target represented with a manybody embedded atom method (EAM) potential. A linear dependence of sputtering yield on the effective energy deposition
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
Qualitative Simulation
 Artificial Intelligence
, 2001
"... Qualitative simulation predicts the set of possible behaviors... ..."
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Cited by 513 (31 self)
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Qualitative simulation predicts the set of possible behaviors...
Modeling and simulation of genetic regulatory systems: A literature review
 JOURNAL OF COMPUTATIONAL BIOLOGY
, 2002
"... In order to understand the functioning of organisms on the molecular level, we need to know which genes are expressed, when and where in the organism, and to which extent. The regulation of gene expression is achieved through genetic regulatory systems structured by networks of interactions between ..."
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Cited by 729 (15 self)
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In order to understand the functioning of organisms on the molecular level, we need to know which genes are expressed, when and where in the organism, and to which extent. The regulation of gene expression is achieved through genetic regulatory systems structured by networks of interactions between
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
Simulating Physics with Computers
 SIAM Journal on Computing
, 1982
"... A digital computer is generally believed to be an efficient universal computing device; that is, it is believed able to simulate any physical computing device with an increase in computation time of at most a polynomial factor. This may not be true when quantum mechanics is taken into consideration. ..."
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Cited by 601 (1 self)
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A digital computer is generally believed to be an efficient universal computing device; that is, it is believed able to simulate any physical computing device with an increase in computation time of at most a polynomial factor. This may not be true when quantum mechanics is taken into consideration
A Fast Algorithm for Particle Simulations
, 1987
"... this paper to the case where the potential (or force) at a point is a sum of pairwise An algorithm is presented for the rapid evaluation of the potential and force fields in systems involving large numbers of particles interactions. More specifically, we consider potentials of whose interactions a ..."
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Cited by 1145 (19 self)
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this paper to the case where the potential (or force) at a point is a sum of pairwise An algorithm is presented for the rapid evaluation of the potential and force fields in systems involving large numbers of particles interactions. More specifically, we consider potentials of whose interactions are Coulombic or gravitational in nature. For a the form system of N particles, an amount of work of the order O(N 2 ) has traditionally been required to evaluate all pairwise interactions, un F5F far 1 (F near 1F external ), less some approximation or truncation method is used. The algorithm of the present paper requires an amount of work proportional to N to evaluate all interactions to within roundoff error, making it where F near (when present) is a rapidly decaying potential con
Ptolemy: A Framework for Simulating and Prototyping Heterogeneous Systems
, 1992
"... Ptolemy is an environment for simulation and prototyping of heterogeneous systems. It uses modern objectoriented software technology (C++) to model each subsystem in a natural and efficient manner, and to integrate these subsystems into a whole. Ptolemy encompasses practically all aspects of design ..."
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Cited by 569 (90 self)
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Ptolemy is an environment for simulation and prototyping of heterogeneous systems. It uses modern objectoriented software technology (C++) to model each subsystem in a natural and efficient manner, and to integrate these subsystems into a whole. Ptolemy encompasses practically all aspects
GOLOG: A Logic Programming Language for Dynamic Domains
, 1994
"... This paper proposes a new logic programming language called GOLOG whose interpreter automatically maintains an explicit representation of the dynamic world being modeled, on the basis of user supplied axioms about the preconditions and effects of actions and the initial state of the world. This allo ..."
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Cited by 621 (72 self)
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This paper proposes a new logic programming language called GOLOG whose interpreter automatically maintains an explicit representation of the dynamic world being modeled, on the basis of user supplied axioms about the preconditions and effects of actions and the initial state of the world
MEGA5: Molecular evolutionary genetics analysis using maximum . . .
, 2011
"... Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version ..."
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Cited by 6858 (19 self)
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Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version
Results 1  10
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