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MD simulation for nanocrystals
Acta Mechanica Sinica, 2003Molecular dynamic (MD) provided anab initio simulation for nano-scale mechanical behavior of materials, provided that the inter-atomic potential is accurately prescribed. MD is particularly suitable in simulating the formation, the deformation, and the evolution of nanocrystals under a fast strain rate.
Ma Xiling, Yang Wei
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Ligand Binding Affinities from MD Simulations
Accounts of Chemical Research, 2002Simplified free energy calculations based on force field energy estimates of ligand-receptor interactions and thermal conformational sampling have emerged as a useful tool in structure-based ligand design. Here we give an overview of the linear interaction energy (LIE) method for calculating ligand binding free energies from molecular dynamics ...
Johan, Aqvist +2 more
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CONSTANT PRESSURE MD SIMULATION METHOD
Molecular Crystals and Liquid Crystals, 2004By introducing an anisotropic factor in the cell dynamics of constant pressure molecular dynamics simulations, we dramatically reduce the artifacts related to cell shapes and overcome the difficulties of simulating anisotropic molecules under hydrostatic pressure.
K. M. Aoki, M. Yoneya, H. Yokoyama
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MD simulation of beam ordering
Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, 2004A molecular dynamics simulation code using a second-order symplectic integral method is presented. This code is applied to ESR experiments of 1D crystalline beam, and the simulations reproduce the sudden reduction of the momentum spread. Some conditions for obtaining 1D crystalline state are discussed.
H. Tsutsui +6 more
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MD simulation of nanoporous silica
Radiation Effects and Defects in Solids, 1999Abstract The microscopic structure of nanoporous silica is investigated using the Molecular Dynamics simulation method. Porous silica structures are produced by simulated atom aggregation and clustering. The structures are then relaxed at atmospheric pressure.
J. V. L. Beckers, S. W. De Leeuw
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Evaluating Rotational Diffusion from Protein MD Simulations
The Journal of Physical Chemistry B, 2007It is now feasible to carry out molecular dynamics simulations of proteins in water that are long compared to the overall tumbling of the molecule. Here, we examine rotational diffusion in four small, globular proteins (ubiquitin, binase, lysozyme, and fragment B3 of protein G) with the TIP3P, TIP4P/EW, and SPC/E water models, in simulations that are 6
Vance, Wong, David A, Case
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MD-Simulations on Metallic Alloys
2014Strengthening effects in solid materials depend on different mechanisms, which have been analyzed empirically since very long time. The here presented work shows the investigation on atomistic length scale of precipitate hardening, with detailed look on dislocation obstacle interactions, and grain-boundary-strengthening using Molecular Dynamics to ...
Martin Hummel +3 more
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ULK1 kinase domain MD simulations
2019Collection of simulations used in the publication A pan-cancer assessment of alterations of the kinase domain of ULK1, an upstream regulator of autophagy. Kumar M, Papaleo E. Sci Rep. 2020 Sep 10;10(1):14874. doi: 10.1038/s41598-020-71527-4. PMID: 32913252 . The script and input files can be found in the associated Github repository of our group: https:
Papaleo, Elena, mukesh kumar,
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AIP Conference Proceedings, 2004
The microscopic approach applied to shock‐induced phenomena has often brought new understanding of the relevant physical and chemical processes. The interaction of a shock wave with pre‐existing structural or chemical defects in a material can lead to the formation of hot spots, i.e. local regions of significant over heating. These hot spots play a key
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The microscopic approach applied to shock‐induced phenomena has often brought new understanding of the relevant physical and chemical processes. The interaction of a shock wave with pre‐existing structural or chemical defects in a material can lead to the formation of hot spots, i.e. local regions of significant over heating. These hot spots play a key
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