Visualization in three dimensions is invaluable for understanding the nature of condensed and fluid systems, but it is not always easy. In nature it is hard to view sample interiors, but on computers it is possible. W...
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Slow flow of a single fluid through a porous medium is well understood on a macroscopic level through Darcy's law, a linear relation between flow rate and a combination of pressure differences, viscosity, and grav...
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We report Brownian dynamics (BD) simulation results for a coarse-grained (CG) model semi-flexible polymer threading through two nanopores. Particularly we study a "tug-of-war" situation where equal and oppos...
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Origin of a power-law in traffic-volume distribution found in traffic simulations of Kobe city was studied. The traffic distribution which was obtained from a shortest path search with randomized OD (origin-destinatio...
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We are discussing a model to understand previously obtained results on Weyl semimetals as realized in MoTe2 using DFT and DFT+U calculations. The model is motivated from general principles and we use it to investigate...
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Classification and data reconstruction using a restricted Boltzmann machine (RBM) is presented. RBM is an energy-based model which assigns low energy values to the configurations of interest. It is a generative model,...
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Design and examples of a sixty-four bit quantum dragon data-set are presented. A quantum dragon is a tight-binding model for a strongly disordered nanodevice, but when connected to appropriate semi-infinite leads has ...
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Molecular dynamics (MD) methods suitable for treating anisotropic fluctuations in condensedmatter are discussed. Barostats with two anisotropic factors to control the simulation cell dynamics are introduced in three ...
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Molecular dynamics (MD) methods suitable for treating anisotropic fluctuations in condensedmatter are discussed. Barostats with two anisotropic factors to control the simulation cell dynamics are introduced in three MD simulation methods;constant pressure, constant surface tension, and canonical hydrostatic. To demonstrate the possibilities of these methods, calculations of two systems, one consisting of anisotropic particles and other consisting of isotropic particles, are presented.
Tertiary structure formation underlies the folding mechanics of many classes of polymers. A simplified model of helical polymers is a useful system in which to begin studying the formation and properties of compact co...
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Tertiary structure formation underlies the folding mechanics of many classes of polymers. A simplified model of helical polymers is a useful system in which to begin studying the formation and properties of compact conformations known from biomolecules. Hyper-phase diagrams and structural transitions are presented for polymers of length 40 and 50 over an array of model parameters.
The putative ground-state structures of 13-atom Cu and Ag clusters have been studied using ab initio molecular-dynamics (AIMD) based on density-functional theory (DFT). An ensemble of low-energy configurations, collec...
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The putative ground-state structures of 13-atom Cu and Ag clusters have been studied using ab initio molecular-dynamics (AIMD) based on density-functional theory (DFT). An ensemble of low-energy configurations, collected along the AIMD trajectory and optimized to nearest local minimum-energy configurations, were studied. An analysis of the results suggests the existence of low-symmetric bilayer structures as strong candidates for the putative ground-state structure of Cu 13 and Ag 13 clusters. These bilayer structures are markedly different from a buckled bi-planar (BBP) configuration and energetically favorable, by about 0.4-0.5 eV, than the latter proposed earlier by others. Our study reveals that the structure of the resulting putative global-minimum configuration is essentially independent of the nature of basis functions (i.e., plane waves vs. pseudoatomic orbitals) employed in the calculations, for a given exchange-correlation functional. The structural configurations obtained from plane-wave-based DFT calculations show a noticeably tighter or dense first-shell of Cu and Ag atoms. A comparison of our results with recent full-potential DFT simulations is presented.
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