Accelerating Atomistic Simulations of Defect Dynamics: Hyperdynamics, Parallel Replica Dynamics, and Temperature-Accelerated Dynamics

1998 ◽  
Vol 538 ◽  
Author(s):  
Arthur F. Voter ◽  
Mads R. Sørensen
Keyword(s):  
Molecular Dynamics ◽  
State Theory ◽  
Atomistic Simulations ◽  
New Methods ◽  
Diffusion Dynamics ◽  
Daunting Task ◽  
System Temperature ◽  
Dynamics Simulations ◽  
Dynamics Method ◽  
Infrequent Event

AbstractObtaining a good atomistic description of diffusion dynamics in materials remains a daunting task due to the time-scale limitations of the molecular dynamics method. We discuss new methods, derived from transition state theory, for accelerating molecular dynamics simulations of these infrequent-event processes. Two of these methods (hyperdynamics and parallel replica dynamics) have been presented previously, and are briefly reviewed here. The third, temperature-accelerated dynamics (TAD), is presented in detail. In TAD, the system temperature is raised to stimulate more rapid escape out of each potential basin, but attempted transitions are filtered to allow only those that would have occurred at the normal temperature. The characteristics of the methods are compared.

Interface Conditions for Coupled Atomistic and Continuum Models of Solids for Dynamics Problems at Finite Temperature

2006 ◽  
Vol 978 ◽  
Author(s):  
Xiantao Li ◽  
Weinan E
Keyword(s):  
Molecular Dynamics ◽  
Boundary Conditions ◽  
Finite Temperature ◽  
Langevin Equations ◽  
Continuum Models ◽  
Interface Conditions ◽  
System Temperature ◽  
Dynamics Simulations ◽  
Dynamics Problems ◽  
Generalized Langevin Equations

AbstractWe will present a general formalism for deriving boundary conditions for molecular dynamics simulations of crystalline solids in the context of atomistic/continuum coupling. These boundary conditions are modeled by generalized Langevin equations, derived from Mori-Zwanzig's formalism. Such boundary conditions are useful in suppressing phonon reflections, and maintaining the system temperature.

scholarly journals Anomalous dynamics of water at the octopeptide lanreotide surface

RSC Advances ◽  
2020 ◽  
Vol 10 (56) ◽  
pp. 33903-33910
Author(s):  
Florian Pinzan ◽  
Franck Artzner ◽  
Aziz Ghoufi
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Water Dynamics ◽  
Atomistic Simulations ◽  
Hydration State ◽  
Dynamics Simulations ◽  
Anomalous Dynamics ◽  
Cyclic Octapeptide

Molecular dynamics simulations of a hydrated mutated lanreotide, a cyclic octapeptide, were carried out to characterize its hydration state. We studied the water dynamics close to the peptide using atomistic simulations.

Tunable Gigahertz Oscillators of Gliding Incommensurate Bilayer Graphene Sheets

2013 ◽  
Vol 80 (4) ◽  
Author(s):  
Ming Luo ◽  
Zhuhua Zhang ◽  
Boris I. Yakobson
Keyword(s):  
Molecular Dynamics ◽  
Surface Energy ◽  
Molecular Dynamics Simulations ◽  
Friction Force ◽  
Function Theory ◽  
Bilayer Graphene ◽  
Atomistic Simulations ◽  
Graphene Sheets ◽  
Dynamics Simulations ◽  
Oscillation Frequencies

Oscillators composed of incommensurate graphene sheets have been investigated by molecular dynamics simulations. The oscillation frequencies can reach tens of gigahertz range and depend on the surface energy of the bilayer graphene and the oscillatory amplitude. We demonstrate the tunability of such an oscillator in terms of frequency and friction by its varying geometric parameters. Exploration of the damping mechanism by combining the autocorrelation function theory and the direct atomistic simulations reveals that the friction force is proportional to the velocity of oscillatory motion. The results should help optimize the design of graphene-based nanoelectromechanical devices.

Atomistic simulations of TeO2-based glasses: interatomic potentials and molecular dynamics

2014 ◽  
Vol 16 (27) ◽  
pp. 14150-14160 ◽  
Author(s):  
Anastasia Gulenko ◽  
Olivier Masson ◽  
Abid Berghout ◽  
David Hamani ◽  
Philippe Thomas
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Interatomic Potential ◽  
Atomistic Simulations ◽  
Interatomic Potentials ◽  
First Results ◽  
Dynamics Simulations

This article derives the interatomic potential for the TeO2 system and presents the first results of molecular dynamics simulations of the pure TeO2 structure.

Study on the Effect of Different Factors of Displacement Cascades in Alpha-Fe by Molecular Dynamics Simulations

2020 ◽  
Author(s):  
Pandong Lin ◽  
Junfeng Nie ◽  
Meidan Liu
Keyword(s):  
Molecular Dynamics ◽  
Tensile Strain ◽  
Vacancy Concentration ◽  
Irradiation Damage ◽  
Effect Of Temperature ◽  
Displacement Cascade ◽  
Rpv Steel ◽  
Dynamics Simulations ◽  
Dynamics Method

Abstract As the key component of RPV steel, α-Fe is under neutron irradiation during its long-term service, and lattice atoms of α-Fe are knocked by neutrons, which leads to irradiation damage. In this paper, molecular dynamics method is conducted to investigate the effect of temperature, vacancy concentration and tensile strain on irradiation-induced damage by displacement cascade simulations in α-Fe. The simulations are performed with primary knock-on atom energies ranging from 0.1 to 5 keV, temperature ranging from 100 to 500K, vacancy concentration ranging from 0% to 1% and applied tensile strain ranging from 0 to 5%. The time evolution of defects produced during displacement cascade can be obtained where the surviving number of Frenkel pairs increases rapidly at first, then decrease and comes to stability finally. The influence of these factors on defect production can be concluded as following: The increase of PKA energy, vacancy concentration and applied tensile strain can lead to the increase of defect numbers. In contrast, the increase of temperature decreases the defect numbers. Vacancies and interstitials cluster size distributions are varied in different case. The results are meaningful to describe some microcosmic mechanisms of RPV steels in nuclear system.

scholarly journals Thermodynamics of the self-assembly of non-ionic chromonic molecules using atomistic simulations. The case of TP6EO2M in aqueous solution

Soft Matter ◽  
2015 ◽  
Vol 11 (4) ◽  
pp. 680-691 ◽  
Author(s):  
Anna Akinshina ◽  
Martin Walker ◽  
Mark R. Wilson ◽  
Gordon J. T. Tiddy ◽  
Andrew J. Masters ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Liquid Crystal ◽  
Molecular Dynamics Simulations ◽  
Self Assembly ◽  
The Self ◽  
Atomistic Simulations ◽  
Aggregation Behaviour ◽  
Dynamics Simulations

Molecular dynamics simulations of non-ionic triphenylene-based chromonic liquid crystal molecules demonstrate self-assembly of the molecules into stacks and “quasi-isodesmic” aggregation behaviour.

LARGE-SCALE MOLECULAR-DYNAMICS SIMULATION OF 19 BILLION PARTICLES

2004 ◽  
Vol 15 (01) ◽  
pp. 193-201 ◽  
Author(s):  
KAI KADAU ◽  
TIMOTHY C. GERMANN ◽  
PETER S. LOMDAHL
Keyword(s):  
Molecular Dynamics ◽  
Large Scale ◽  
Dynamics Simulation ◽  
Atomistic Simulations ◽  
Huge Number ◽  
Physical Problems ◽  
Efficient Data ◽  
Dynamics Simulations ◽  
Large Scale Simulations ◽  
Efficient Data Analysis

We have performed parallel large-scale molecular-dynamics simulations on the QSC-machine at Los Alamos. The good scalability of the SPaSM code is demonstrated together with its capability of efficient data analysis for enormous system sizes up to 19 000 416 964 particles. Furthermore, we introduce a newly-developed graphics package that renders in a very efficient parallel way a huge number of spheres necessary for the visualization of atomistic simulations. These abilities pave the way for future atomistic large-scale simulations of physical problems with system sizes on the μ-scale.

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