• 대한기계학회논문집A
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• 제33권8호
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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.

• 한국진공학회:학술대회논문집
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• 한국진공학회 2014년도 제46회 동계 정기학술대회 초록집
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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.

• 한국전산구조공학회논문집
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• 제22권4호
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• pp.331-334
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• 2009

본 논문에서는 원자적 계산(atomistic calculation)을 위한 해석적 모델로 surface relaxation model을 제시한다. 기존의 분자정역학(molecular statics)이 모든 원자의 위치를 자유도로 선정하여 사용하는데 반하여, 이 모델은 면내방향에 해당하는 두 개의 자유도로 나노박막의 원자 위치를 기술하는 매우 간단한 방법이다. 본 연구에서는 surface relaxation model을 이용하여 표면응력(surface stress)과 표면강성계수(surface stiffness tensor)와 같은 표면인자(surface parameter)의 계산을 수행하고, surface stress model을 이용하여 평형상태에서의 원자의 위치정보를 계산한다. 그리고 surface relaxation model을 검증하기 위하여 분자동역학 전산모사(molecular dynamics simulation)의 수치 결과가 제시되며, 본 연구에서 계산한 equilibrium strain과 비교 검증한다.

• 한국자기공명학회논문지
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• 제19권1호
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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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• 제7권1호
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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.

• 한국결정학회지
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• 제11권3호
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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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• 제41권1호
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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.

• 한국자기공명학회논문지
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• 제26권1호
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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.

• 한국진공학회:학술대회논문집
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• 한국진공학회 2012년도 제43회 하계 정기 학술대회 초록집
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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.

• 한국고분자학회:학술대회논문집
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• 한국고분자학회 2006년도 IUPAC International Symposium on Advanced Polymers for Emerging Technologies
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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.