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.

Molecular Dynamics Simulation of a Pullout Test on a Carbon Nanotube in a Polymer Matrix

2014 ◽  
Vol 1700 ◽  
pp. 61-66
Author(s):  
Guttormur Arnar Ingvason ◽  
Virginie Rollin
Keyword(s):  
Molecular Dynamics ◽  
Polymer Matrix ◽  
Large Scale ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Atomistic Simulations ◽  
Polymer Molecules ◽  
Molecular Potential ◽  
Pull Out ◽  
Walled Carbon Nanotubes

ABSTRACTAdding single walled carbon nanotubes (SWCNT) to a polymer matrix can improve the delamination properties of the composite. Due to the complexity of polymer molecules and the curing process, few 3-D Molecular Dynamics (MD) simulations of a polymer-SWCNT composite have been run. Our model runs on the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS), with a COMPASS (Condensed phase Optimized Molecular Potential for Atomistic Simulations Studies) potential. This potential includes non-bonded interactions, as well as bonds, angles and dihedrals to create a MD model for a SWCNT and EPON 862/DETDA (Diethyltoluenediamine) polymer matrix. Two simulations were performed in order to test the implementation of the COMPASS parameters. The first one was a tensile test on a SWCNT, leading to a Young’s modulus of 1.4 TPa at 300K. The second one was a pull-out test of a SWCNT from an originally uncured EPON 862/DETDA matrix.

Preparation, Structure, And Electronic Properties Of Amorphous Gaas By Tight-Binding Molecular Dynamics

1993 ◽  
Vol 321 ◽  
Author(s):  
C. Molteni ◽  
L. Colombo ◽  
L. Miglio
Keyword(s):  
Molecular Dynamics ◽  
First Principles ◽  
Large Scale ◽  
Tight Binding ◽  
Computer Experiment ◽  
Dynamics Simulation ◽  
First Principles Calculations ◽  
Amorphous Network ◽  
Large Scale Simulations

ABSTRACTWe investigate the short-range structural properties of a-GaAs as obtained in a computer experiment based on a tight-binding molecular dynamics simulation. The amorphous configuration is obtained by quenching a liquid sample well equilibrated at T=1600 K. A detailed characterization of the topology and defect distribution of the amorphous network is presented and discussed. The electronic structure of our sample is calculated as well. Finally, we discuss the reliability and transferability of the present computational scheme for large-scale simulations of compound semiconductor materials by comparing our results to first-principles calculations.

On the Formation of Carbon Nanotube Serpentines: Insights from Multi-Million Atom Molecular Dynamics Simulation

2011 ◽  
Vol 1284 ◽  
Author(s):  
Leonardo D. Machado ◽  
Sergio B. Legoas ◽  
Jaqueline S. Soares ◽  
Nitzan Shadmi ◽  
Ado Jorio ◽  
...  
Keyword(s):  
Carbon Nanotubes ◽  
Molecular Dynamics ◽  
Carbon Nanotube ◽  
Molecular Dynamics Simulations ◽  
Classical Mechanics ◽  
Dynamics Simulation ◽  
Atomistic Simulations ◽  
Molecular Force ◽  
Short Period ◽  
Dynamics Simulations

ABSTRACTIn this work we present preliminary results from molecular dynamics simulations for carbon nanotubes serpentine dynamics formation. These S-like nanostructures consist of a series of parallel and straight nanotube segments connected by alternating U-turn shaped curves. Nanotube serpentines were experimentally synthesized and reported in recent years, but up to now no atomistic simulations have been carried out to address the dynamics of formation of these structures. We have carried out fully atomistic molecular dynamics simulations in the framework of classical mechanics with a standard molecular force field. Multi-million atoms structures formed by stepped substrates with a carbon nanotube (about 1 micron in length) placed on top of them have been considered in our simulations. A force is applied to the upper part of the tube during a short period of time and then turned off and the system set free to evolve in time. Our results showed that these conditions are sufficient to form robust serpentines and validate the general features of the ‘falling spaghetti mechanism’ previously proposed to explain their formation.

scholarly journals Influence of laser nanostructured diamond tools on the cutting behavior of silicon by molecular dynamics simulation

RSC Advances ◽  
2017 ◽  
Vol 7 (25) ◽  
pp. 15596-15612 ◽  
Author(s):  
Houfu Dai ◽  
Genyu Chen ◽  
Shaobo Li ◽  
Qihong Fang ◽  
Bang Hu
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Large Scale ◽  
Diamond Tool ◽  
Single Crystal Silicon ◽  
Dynamics Simulation ◽  
Crystal Silicon ◽  
Nanometric Cutting ◽  
Dynamics Simulations ◽  
Cutting Behavior

In this study, a series of large-scale molecular dynamics simulations have been performed to study the nanometric cutting of single crystal silicon with a laser-fabricated nanostructured diamond tool.

Molecular Dynamics Simulation of the Thermal Conductivity of Silicon-Germanene Nanoribbon (SiGeNR): A Comparison with Silicene Nanoribbon (SiNR) and Germanene Nanoribbon (GeNR)

2015 ◽  
Vol 1105 ◽  
pp. 285-289 ◽  
Author(s):  
Jessa Mae P. Tagalog ◽  
Cachey Girly Alipala ◽  
Giovanni J. Paylaga ◽  
Naomi T. Paylaga ◽  
Rolando V. Bantaculo
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Silicon Germanium ◽  
Large Scale ◽  
Room Temperature ◽  
Single Layer ◽  
Dynamics Simulation ◽  
Two Dimensional ◽  
Silicon And Germanium ◽  
Dynamics Simulations

This study examines the nature of thermal transport properties of single layer two-dimensional honeycomb structures of silicon-germanene nanoribbon (SiGeNR), silicene nanoribbon (SiNR) and germanene nanoribbon (GeNR) which have not yet been characterized experimentally. SiGeNR, SiNR and GeNR are the allotropes of silicon-germanium, silicon and germanium, respectively, withsp2hybridization. The thermal conductivity of the materials has been investigated using Tersoff potential through LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) by performing the molecular-dynamics simulations. The temperature is varied (50 K, 77 K, 150 K, 300 K, 500 K, 700 K, 1000 K, and 1200 K) with fixed nanoribbon dimension of 50 nm × 10 nm. The length is also varied (10 nm, 20 nm, 30 nm, 40 nm, and 50 nm) while the temperature is fixed at room temperature and the width is also fixed at 10 nm. The obtained results showed that the thermal conductivity of SiGeNR at room temperature is approximately 10 times higher than GeNR and approximately 6 times higher compared to SiNR. The thermal conductivity increases as the temperature is increased from 50 K – 300 K, and as the temperature is further increased, the thermal conductivity decreases with temperature. Moreover, the thermal conductivity in SiGeNR, SiNR, and GeNR increases as the length is being increased. Predicting new features of SiGeNR, SiNR and GeNR open new possibilities for nanoelectronic device applications of group IV two-dimensional materials.

scholarly journals A Linked-Cell Domain Decomposition Method for Molecular Dynamics Simulation on a Scalable Multiprocessor

1992 ◽  
Vol 1 (2) ◽  
pp. 153-161 ◽  
Author(s):  
L.H. Yang ◽  
E.D. Brooks III ◽  
J. Belak
Keyword(s):  
Molecular Dynamics ◽  
Large Scale ◽  
Domain Decomposition Method ◽  
Dynamics Simulation ◽  
Parallel Computer ◽  
Interprocessor Communication ◽  
Programming Paradigm ◽  
C Preprocessor ◽  
Large Scale Simulations ◽  
Cell Data

A molecular dynamics algorithm for performing large-scale simulations using the Parallel C Preprocessor (PCP) programming paradigm on the BBN TC2000, a massively parallel computer, is discussed. The algorithm uses a linked-cell data structure to obtain the near neighbors of each atom as time evoles. Each processor is assigned to a geometric domain containing many subcells and the storage for that domain is private to the processor. Within this scheme, the interdomain (i.e., interprocessor) communication is minimized.

Large scale molecular dynamics simulation of native and mutant dihydropteroate synthase–sulphanilamide complexes suggests the molecular basis for dihydropteroate synthase drug resistance

2005 ◽  
Vol 363 (1833) ◽  
pp. 2055-2073 ◽  
Author(s):  
Fabrizio Giordanetto ◽  
Philip W Fowler ◽  
Mansoor Saqi ◽  
Peter V Coveney
Keyword(s):  
Molecular Dynamics ◽  
Drug Resistance ◽  
Molecular Basis ◽  
Large Scale ◽  
Homology Modelling ◽  
Dynamics Simulation ◽  
Dihydropteroate Synthase ◽  
Enzymatic Transformation ◽  
Sulpha Drug ◽  
Dynamics Simulations

Antibiotic resistance is hampering the efficacy of drugs in the treatment of several pathological infections. Dihydropteroate synthase (DHPS) has been targeted by sulphonamide inhibitors for the past 60 years and has developed different amino acid mutations to survive sulpha drug action. We couple homology modelling techniques and massively parallel molecular dynamics simulations to study both the drug-bound and apo forms of native and mutant DHPS. Simulations of the complex between sulphanilamide and Streptomyces pneumoniae , DHPS shows how sulphanilamide is able to position itself close to 6-hydroxymethyl-7, 8-dihydropteridine-phosphate in a suitable position for the enzymatic transformation whereas in the mutant complex the sulpha drug is expelled from the catalytic site. Our simulations, therefore, provide insight into the molecular basis for drug resistance with S. pneumoniae DHPS.

scholarly journals TRILLION-ATOM MOLECULAR DYNAMICS BECOMES A REALITY

2008 ◽  
Vol 19 (09) ◽  
pp. 1315-1319 ◽  
Author(s):  
TIMOTHY C. GERMANN ◽  
KAI KADAU
Keyword(s):  
Molecular Dynamics ◽  
Large Scale ◽  
Shear Instability ◽  
Dynamics Simulation ◽  
Massively Parallel ◽  
Lennard Jones ◽  
Simple Cubic ◽  
Simple Cubic Lattice ◽  
Future Potential ◽  
Large Scale Simulations

By utilizing the molecular dynamics code SPaSM on Livermore's BlueGene/L architecture, consisting of 212 992 IBM PowerPC440 700 MHz processors, a molecular dynamics simulation was run with one trillion atoms. To demonstrate the practicality and future potential of such ultra large-scale simulations, the onset of the mechanical shear instability occurring in a system of Lennard-Jones particles arranged in a simple cubic lattice was simulated. The evolution of the instability was analyzed on-the-fly using the in-house developed massively parallel graphical object-rendering code MD_render.

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