• 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.

• Nuclear Engineering and Technology
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• 제55권6호
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• pp.2298-2304
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• 2023

Titanium alloys are expected to become one of the candidate materials for nuclear-powered spacecraft due to their excellent overall performance. Nevertheless, atomistic mechanisms of the defect accumulation and evolution of the materials due to long-term exposure to irradiation remain scarcely understood by far. Here we investigate the heavy irradiation damage in a-titanium with a dose as high as 4.0 canonical displacements per atom (cDPA) using atomistic simulations of Frenkel pair accumulation. Results show that the content of surviving defects increases sharply before 0.04 cDPA and then decreases slowly to stabilize, exhibiting a strong correlation with the system energy. Under the current simulation conditions, the defect clustering fraction may be not directly dependent on the irradiation dose. Compared to vacancies, interstitials are more likely to form clusters, which may further cause the formation of 1/3<1210> interstitial-type dislocation loops extended along the (1010) plane. This study provides an important insight into the understanding of the irradiation damage behaviors for titanium.

• Kyungpook Mathematical Journal
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• 제34권1호
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• pp.53-57
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• 1994

• 한국섬유공학회:학술대회논문집
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• 한국섬유공학회 1999년도 가을 한국섬유공학회 학술발표회 논문집(Proceedings of the Korean Textile Conference)
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• pp.335-338
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• 1999

• 한국수학사학회:학술대회논문집
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• 한국수학사학회 2005년도 춘계 학술발표회
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• pp.5-5
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• 2005

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• 한국진공학회:학술대회논문집
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• 한국진공학회 1996년도 제10회 학술발표회 논문개요집
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• pp.41-41
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• 1996

• 한국진공학회:학술대회논문집
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• 한국진공학회 2016년도 제50회 동계 정기학술대회 초록집
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• pp.403.2-403.2
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• 2016

Porous materials play a significant role in energy storage and conversion applications such as catalyst support for polymer electrolyte membrane fuel cell. In particular, hierarchical porous materials with both micropores (poresize, ${\delta}$ < 2 nm) and regularly arranged mesopores (2 nm < ${\delta}$ < 50 nm) are known to greatly enhance the efficiency of catalytic reactions by providing enormous surface area as well as fast mass transport channels for both reactants and products from/to active sites. Although it is generally agreed that the microscopic structure of the porous materials directly affects the performance of these catalytic reactions, neither detailed mechanisms nor fundamental understanding are available at hand. In this study, we propose an atomistic model of hierarchical nanostructured porous carbons (HNPCs) in molecular dynamics simulations. By performing a systematic study, we found that structural features of the HNPC can be independently altered by tuning specific synthesis parameters, while remaining other structures unchanged. In addition, we show some structure-property relations including mechanical and gas transport properties.

• Applied Microscopy
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• 제48권1호
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• pp.27-32
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• 2018

Barium titanate ($BaTiO_3$) nanoparticle is one of the most promising materials for future multi-layer ceramic capacitor and ferroelectric random access memory. It is well known that electrical property of nanoparticles depends on the atomistic structure. Although surface may possibly have an impact on the atomistic structure, reconstructed structure at the surface has not been widely investigated. In the present study, Ba-ion position near surface in a $BaTiO_3$ nanoparticle has been quantitatively characterized by scanning transmission electron microscopy. It was found that some Ba ions at the surface were greatly displaced in non-uniform directions.

• 대한기계학회논문집A
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• 제28권9호
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• pp.1306-1313
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• 2004

This paper addresses a theoretical approach to calculate the amount of the stored energy during high strain-rate deformations using atomistic level simulation. The dynamic behavior of materials at high strain-rate deformation are of great interest. At high strain-rates deformations, materials generate heat due to plastic work and the temperature rise can be significant, affecting various properties of the material. It is well known that a small percent of the energy input is stored in the material, and most of input energy is converted into heat. However, microscopic analysis has not been completed without construction of a material model, which can simulate the movement of dislocations and vacancies. A major cause of the temperature rise within materials is traditionally credited to dislocations, vacancies and other defects. In this study, an atomistic material model for FCC such as copper is used to calculate the stored energy.

• 한국고분자학회:학술대회논문집
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• 한국고분자학회 2006년도 IUPAC International Symposium on Advanced Polymers for Emerging Technologies
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• pp.112-112
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• 2006

Detailed surface characteristics of polymer films have been investigated by atomistic molecular dynamics simulations and NEXAFS spectroscopy experiments. The geometric confinement of the surfaces and the necessity to minimize the surface energy lead to the significant molecular organization and orientation in polymer surfaces, with their properties strongly depending upon the atomistic monomer structures. As compared with polymers, oligomeric electronic materials are much more readily aligned by employing various surface anchoring forces, rendering them highly attractive as polarized-light emitting materials and active semiconducting materials in thin film transistors.