• Transactions of the Korean Society of Mechanical Engineers A
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• v.33 no.8
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• pp.733-738
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• 2009

Mechanical properties of <001> silicon nanowires are presented. In particular, predictions from the calculations based on different length scales, first principles calculations, atomistic calculations, and continuum nanomechanical theory, are compared for <001> silicon nanowires. There are several elements that determine the mechanics of silicon nanowires, and the complicated balance between these elements is studied. Specifically, the role of the increasing surface effects and reduced dimensionality predicted from theories of different length scales are compared. As a prototype, a Tersoff-based empirical potential has been used to study the mechanical properties of silicon nanowires including the Young's modulus. The results significantly deviates from the first principles predictions as the size of wire is decreased.

• Proceedings of the Korean Vacuum Society Conference
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• 2014.02a
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• pp.425.1-425.1
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• 2014

Thermal transport in nanomaterials is not only scientifically interesting but also technological important for various future electronic, bio, and energy device applications. Among the various computation approaches to investigate lattice thermal transport phenomena in nanoscale, the atomistic nonequilibrium Green's function approach based on first-principles density functional theory calculations appeared as a promising method given the continued miniaturization of devices and the difficulty of developing classical force constants for novel nanoscale interfaces. Among the nanometerials, carbon atomic chains, namely the cumulene (all-doulble bonds, ${\cdots}C=C=C=C{\cdots}$) and polyyne (alternation of single and triple bonds, ${\cdots}C{\equiv}C-C{\equiv}C{\cdots}$) can be considered as the extream cases of interconnction materials for nanodevices. After the discovery and realization of carbon atomic chains, their electronic transport properties have been widely studied. For the thermal transport properties, however, there have been few literatures for this simple linear chain system. In this work, we first report on the development of a non-equilibrium Green's function theory-based computational tool for atomistic thermal transport calculations of nanojunctions. Using the developed tool, we investigated phonon dispersion and transmission properties of polyethylene (${\cdots}CH2-CH2-CH2-CH2{\cdots}$) and polyene (${\cdots}CH-CH-CH-CH{\cdots}$) structures as well as the cumulene and polyyne. The resulting phonon dispersion from polyethylene and polyene showed agreement with previous results. Compared to the cumulene, the gap was found near the ${\Gamma}$ point of the phonon dispersion of polyyne as the prediction of Peierls distortion, and this feature was reflected in the phonon transmission of polyyne. We also investigated the range of interatomic force interactions with increase in the size of the simulation system to check the convergence criteria. Compared to polyethylene and polyene, polyyne and cumulene showed spatially long-ranged force interactions. This is reflected on the differences in phonon transport caused by the delicate differences in electronic structure.

• Journal of the Computational Structural Engineering Institute of Korea
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• v.22 no.4
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• pp.331-334
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• 2009

In this paper, we present a surface relaxation model in atomistic calculations for thin nanofilms. This surface relaxation model is very simple model which have only two degrees of freedoms to determine the atomic positions of nanofilms. Whereas in conventional molecular statics simulations, the same number of degrees of freedoms at all atom positions are used as unknown variables. In order to prove the reliability of the presented model, we present the results of self-equilibrium strain calculations with the surface parameters obtained from this model.

• Journal of the Korean Magnetic Resonance Society
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• v.19 no.1
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• pp.1-10
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• 2015

Refinements with atomistic molecular dynamics (MD) simulation have contributed to improving the qualities of NMR structures. In most cases, the calculations with atomistic MD simulation for NMR structures employ generalized-Born implicit solvent model (GBIS) to take into accounts solvation effects. Developments in algorithms and computational capacities have ameliorated GBIS to approximate solvation effects that explicit solvents bring about. However, the quantitative comparison of NMR structures in the latest GBIS and explicit solvents is lacking. In this study, we report the direct comparison of NMR structures that atomistic MD simulation coupled with GBIS and water molecules refined. Two model proteins, GB1 and ubiquitin, were recalculated with experimental distance and torsion angle restraints, under a series of simulated annealing time steps. Whereas the root mean square deviations of the resulting structures were apparently similar, AMBER energies, the most favored regions in Ramachandran plot, and MolProbity clash scores witnessed that GBIS-refined structures had the better geometries. The outperformance by GBIS was distinct in the structure calculations with sparse experimental restraints. We show that the superiority stemmed, at least in parts, from the inclusion of all the pairs of non-bonded interactions. The shorter computational times with GBIS than those for explicit solvents makes GBIS a powerful method for improving structural qualities particularly under the conditions that experimental restraints are insufficient. We also propose a method to separate the native-like folds from non-violating diverged structures.

• Interaction and multiscale mechanics
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• v.7 no.1
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• pp.543-561
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• 2014

We present a full energy and force formulation of the quasicontinuum method with non-local and local transition elements. Non-local transition elements are developed to transmit inhomogeneity from the atomistic to the continuum regions. Local transition elements are developed to resolve the mathematical mismatch between non-local atoms and the local continuum. The rationale behind these transition elements is provided by analyzing the energy and force transitions between atoms and continuum under the Cauchy-Born rule. We show that breakdown of the Cauchy-Born rule occurs for slaved atoms of local elements within the cutoff of non-local atoms. The inadequacy of the Cauchy-Born rule at the transition region naturally leads to the need of atomistic treatment of transition slaved and transition representative atoms. Such an atomistic treatment together with a full or cutoff sampling allows non-local transition elements containing these transition entities to transmit inhomogeneity. Different force formulations for transition representative atoms and pure local representative atoms allow the local transition elements to resolve non-local and local mismatches. The method presented herein is validated by force calculations in an unstressed perfect crystal as well as an unrelaxed grain boundary model. A nanoindentation simulation in 3D is conducted to demonstrate the accuracy and efficiency of the proposed method.

• Korean Journal of Crystallography
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• v.11 no.3
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• pp.176-181
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• 2000

Computer-based atomistic simulation methods are applied to address quantitatively the crystal defect chemistry of strontium hexaaluminate, SrAl/sub 12/O/sub 19/. Our calculations show that oxygen Frenkel disorder is the dominant intrinsic defect mode to be expected in the multi-component oxide, though Schottky disorder may also exist. When La and Mg enter into SrAl/sub 12/O/sub 19/. Mg prefers to occupy Al(3)4f tetrahedral sites in the magnetoplumbite structure. Our calculations also indicate that O/sub Sr/ defect is improbable in the structure.

• Nuclear Engineering and Technology
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• v.41 no.1
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• pp.39-52
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• 2009

Theory-based models and high performance simulations are briefly reviewed starting with atomistic methods, such as Electronic Structure calculations, Molecular Dynamics, and Monte Carlo, continuing with meso-scale methods, such as Dislocation Dynamics and Phase Field, and ending with continuum methods that include Finite Element and Finite Volume. Special attention is paid to relating thermo-mechanical and chemical properties of the fuel to reactor parameters. By inserting atomistic models of point defects into continuum thermo-chemical calculations, a model of oxygen diffusivity in $UO_{2+x}$ is developed and used to predict point defect concentrations, oxygen diffusivity, and fuel stoichiometry at various temperatures and oxygen pressures. The simulations of coupled heat transfer and species diffusion demonstrate that including the dependence of thermal conductivity and density on composition can lead to changes in the calculated centerline temperature and thermal expansion displacements that exceed 5%. A review of advanced nuclear fuel performance codes reveals that the many codes are too dedicated to specific fuel forms and make excessive use of empirical correlations in describing properties of materials. The paper ends with a review of international collaborations and a list of lessons learned that includes the importance of education in creating a large pool of experts to cover all necessary theoretical, experimental, and computational tasks.

• Journal of the Korean Magnetic Resonance Society
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• v.26 no.1
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• pp.1-9
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• 2022

There are two distinct approaches to improving the quality of protein NMR structures during refinement: all-atom force fields and accumulated knowledge-assisted methods that include Rosetta. Mao et al. reported that, for 40 proteins, Rosetta increased the accuracies of their NMR-determined structures with respect to the X-ray crystal structures (Mao et al., J. Am. Chem. Soc. 136, 1893 (2014)). In this study, we calculated 32 structures of those studied by Mao et al. using all-atom force field and implicit solvent model, and we compared the results with those obtained from Rosetta. For a single protein, using only the experimental NOE-derived distances and backbone torsion angle restraints, 20 of the lowest energy structures were extracted as an ensemble from 100 generated structures. Restrained simulated annealing by molecular dynamics simulation searched conformational spaces with a total time step of 1-ns. The use of GPU-accelerated AMBER code allowed the calculations to be completed in hours using a single GPU computer-even for proteins larger than 20 kDa. Remarkably, statistical analyses indicated that the structures determined in this way showed overall higher accuracies to their X-ray structures compared to those refined by Rosetta (p-value < 0.01). Our data demonstrate the capability of sophisticated atomistic force fields in refining NMR structures, particularly when they are coupled with the latest GPU-based calculations. The straightforwardness of the protocol allows its use to be extended to all NMR structures.

• Proceedings of the Korean Vacuum Society Conference
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• 2012.08a
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• pp.75-75
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• 2012

This presentation will focus on computational materials research carried out across length scales. Examples will be presented that illustrate the way in which state-of-the-art quantum mechanical calculations and atomistic simulations can be applied to explain experimental data, design new structures, determine mechanisms, and enable new investigations. In particular, the presentation will present key findings from an integrated experimental and computational investigation of the tribological properties of polytetrafluoroethylene and its composites and predictions regarding the mechanical and tribological properties of inorganic nanostructured materials.

• Proceedings of the Polymer Society of Korea Conference
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• 2006.10a
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• pp.11-12
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• 2006

Incorporation of chromophores into multi-chromophore-containing dendrimers is shown to lead to a significant enhancement in electro-optic activity. These results are reasonably well simulated by pseudo-atomistic Monte Carlo calculations that permit dendrimers to interpenetrate (entangle). Calculations also lead to the correct prediction of material densities. An even greater enhancement in electro-optic activity is observed when such dendrimer materials are doped with a second chromophore. This latter effect may reflect an Ising-lattice-type phenomenon where one chromophore impacts the ordering of the other and vice versa.