Query: molecular dynamics simulation

Candidate papers:

abstract: We present ab initio quantum mechanical molecular dynamics simulations of the liquid metal amorphous semiconductor transition in Ge. Our simulations are based on (a) finite temperature density functional theory of the one electron states, (b) exact energy minimization and hence calculation of the exact Hellmann Feynman forces after each molecular dynamics step using preconditioned conjugate gradient techniques, (c) accurate nonlocal pseudopotentials, and (d) Nos\'e dynamics for generating a canonical ensemble. This method gives perfect control of the adiabaticity of the electron ion ensemble and allows us to perform simulations over more than 30 ps. The computer generated ensemble describes the structural, dynamic, and electronic properties of liquid and amorphous Ge in very good agreement with experiment. The simulation allows us to study in detail the changes in the structure property relationship through the metal semiconductor transition. We report a detailed analysis of the local structural properties and their changes induced by an annealing process. The geometrical, bonding, and spectral properties of defects in the disordered tetrahedral network are investigated and compared with experiment.
title: Ab initio molecular dynamics simulation of the liquid metal amorphous semiconductor transition in germanium.
venue: Physical review. B, Condensed matter
year: 1994

abstract: From the Publisher: This book describes the extremely powerful technique of molecular dynamics simulation, which involves solving the classical many body problem in contexts relevant to the study of matter at the atomic level. The method allows the prediction of the static and dynamic properties of substances directly from the underlying interactions between the molecules. Because there is no alternative approach capable of handling such a broad range of problems at the required level of detail, molecular dynamics methods have proved themselves indispensable in both pure and applied research.
author_names: D C Rapaport
title: The Art of Molecular Dynamics Simulation
year: 1997

abstract: A new method for performing molecular dynamics simulations under constant pressure is presented. In the method, which is based on the extended system formalism introduced by Andersen, the deterministic equations of motion for the piston degree of freedom are replaced by a Langevin equation; a suitable choice of collision frequency then eliminates the unphysical 'ringing' of the volume associated with the piston mass. In this way it is similar to the 'weak coupling algorithm' developed by Berendsen and co workers to perform molecular dynamics simulation without piston mass effects. It is shown, however, that the weak coupling algorithm induces artifacts into the simulation which can be quite severe for inhomogeneous systems such as aqueous biopolymers or liquid/liquid interfaces.
author_names: Scott Feller

Yuhong Zhang

Richard W Pastor

Bernard R Brooks
title: Constant pressure molecular dynamics simulation: The Langevin piston method
year: 1995

abstract: The impact of molecular dynamics (MD) simulations in molecular biology and drug discovery has expanded dramatically in recent years. These simulations capture the behavior of proteins and other biomolecules in full atomic detail and at very fine temporal resolution. Major improvements in simulation speed, accuracy, and accessibility, together with the proliferation of experimental structural data, have increased the appeal of biomolecular simulation to experimentalists a trend particularly noticeable in, although certainly not limited to, neuroscience. Simulations have proven valuable in deciphering functional mechanisms of proteins and other biomolecules, in uncovering the structural basis for disease, and in the design and optimization of small molecules, peptides, and proteins. Here we describe, in practical terms, the types of information MD simulations can provide and the ways in which they typically motivate further experimental work.
author_names: Scott A Hollingsworth

Ron O Dror
title: Molecular Dynamics Simulation for All
venue: Neuron
year: 2018

abstract: Can completely homogeneous nucleation occur? Large scale molecular dynamics simulations performed on a graphics processing unit rich supercomputer can shed light on this long standing issue. Here, a billion atom molecular dynamics simulation of homogeneous nucleation from an undercooled iron melt reveals that some satellite like small grains surrounding previously formed large grains exist in the middle of the nucleation process, which are not distributed uniformly. At the same time, grains with a twin boundary are formed by heterogeneous nucleation from the surface of the previously formed grains. The local heterogeneity in the distribution of grains is caused by the local accumulation of the icosahedral structure in the undercooled melt near the previously formed grains. This insight is mainly attributable to the multi graphics processing unit parallel computation combined with the rapid progress in high performance computational environments.Nucleation is a fundamental physical process, however it is a long standing issue whether completely homogeneous nucleation can occur. Here the authors reveal, via a billion atom molecular dynamics simulation, that local heterogeneity exists during homogeneous nucleation in an undercooled iron melt.
author_names: Yasushi Shibuta

Shinji Sakane

Eisuke Miyoshi

Shinpei Okita

Tomohiro Takaki

Munekazu Ohno
title: Heterogeneity in homogeneous nucleation from billion atom molecular dynamics simulation of solidification of pure metal
venue: Nature Communications
year: 2017

abstract: We present an extensive molecular dynamics simulation for a bead spring model of a melt of linear polymers. The number of monomers N covers the range from N=5 to N=400. Since the entanglement length Ne is found to be approximately 35, our chains cover the crossover from the nonentangled to the entangled regime. The Rouse model provides an excellent description for short chains N<Ne, while the dynamics of the long chains can be described by the reptation model. By mapping the model chains onto chemical species we give estimates of the times and distances of onset of the slowing down in motion due to reptation. Comparison to neutron spin echo data confirm our mapping procedure, resolving a discrepancy between various experiments. By considering the primitive chain we are able to directly visualize the confinement to a tube. Analyzing the Rouse mode relaxation allows us to exclude the generalized Rouse models, while the original reptation prediction gives a good description of the data.
author_names: Kurt Kremer

Gary S Grest
title: Dynamics of entangled linear polymer melts: A molecular dynamics simulation
year: 1990

abstract: molecular dynamics simulation elementary methods is available in our book collection an online access to it is set as public so you can get it instantly. Our digital library spans in multiple locations, allowing you to get the most less latency time to download any of our books like this one. Merely said, the molecular dynamics simulation elementary methods is universally compatible with any devices to read.
author_names: Matthias Durr
title: Molecular Dynamics Simulation Elementary Methods
year: 2016

abstract: Abstract Corrosion inhibition mechanism of two mercapto quinoline Schiff bases, eg. 3 (phenylimino)methyl)quinoline 2 thiol (PMQ) and 3 (5 methylthiazol 2 ylimino)methyl) quinoline 2 thiol (MMQT) on mild steel surface is investigated by quantum chemical calculation and molecular dynamics simulation. Quantum chemical parameters such as EHOMO, ELUMO, energy gap (DE) dipolemoment (u) electronegativity (kh) global hardness (e) and fraction of electron transfers from the inhibitor molecule to the metallic atom surface (DN) have been studied to investigate their relative corrosion inhibition performance. Parameters like local reactive sites of the present molecule have been analyzed through Fukui indices. Moreover, adsorption behavior of the inhibitor molecules on Fe (1 1 0) surface have been analyzed using molecular dynamics simulation. The binding strength of the concerned inhibitor molecules on mild steel surface follows the order MMQT>PMQ, which is in good agreement with the experimentally determined inhibition efficiencies. In view of the above, our approach will be helpful for quick prediction of a potential inhibitor from a lot of similar inhibitors and subsequently in their rational designed synthesis for corrosion inhibition application following a wet chemical synthetic route.
author_names: Sourav Saha

Pritam Ghosh

Abhiram Hens

Naresh Chandra Murmu

Priyabrata Banerjee
title: Density functional theory and molecular dynamics simulation study on corrosion inhibition performance of mild steel by mercapto quinoline Schiff base corrosion inhibitor
year: 2015

abstract: Molecular dynamics (MD) simulation has enhanced our understanding about ductile regime machining of brittle materials such as silicon and germanium. In particular, MD simulation has helped understand the occurrence of brittle ductile transition due to the high pressure phase transformation (HPPT) which induces Herzfeld Mott transition. In this paper, relevant MD simulation studies in conjunction with experimental studies are reviewed with a focus on (i) the importance of machining variables: undeformed chip thickness, feed rate, depth of cut, geometry of the cutting tool in influencing the state of the deviatoric stresses to cause HPPT in silicon, (ii) the influence of material properties: role of fracture toughness and hardness, crystal structure and anisotropy of the material, and (iii) phenomenological understanding of the wear of diamond cutting tools, which are all non trivial for cost effective manufacturing of silicon. The ongoing developmental work on potential energy functions is reviewed to identify opportunities for overcoming the current limitations of MD simulations. Potential research areas relating to how MD simulation might help improve existing manufacturing technologies are identified which may be of particular interest to early stage researchers.
author_names: Saurav Goel

Xichun Luo

Anupam Agrawal

Robert L Reuben
title: Diamond machining of silicon: A review of advances in molecular dynamics simulation
year: 2015

author_names: Zhigang Li
title: Molecular dynamics simulation
year: 2018