• 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.

• Advances in nano research
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• v.2 no.3
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• pp.157-172
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• 2014

The three-dimensional Nano-Electronic Modeling toolkit (NEMO 3-D) is an open source software package that allows the atomistic calculation of single-particle electronic states and optical response of various semiconductor structures including bulk materials, quantum dots, impurities, quantum wires, quantum wells and nanocrystals containing millions of atoms. This paper, first, describes a software module introduced in the NEMO 3-D toolkit for the calculation of electronic bandstructure and interband optical transitions in nanowires having wurtzite crystal symmetry. The energetics (Hamiltonian) of the quantum system under study is described via the tight-binding (TB) formalism (including $sp^3$, $sp^3s^*$ and $sp^3d^5s^*$ models as appropriate). Emphasis has been given in the treatment of surface atoms that, if left unpassivated, can lead to the creation of energy states within the bandgap of the sample. Furthermore, the developed software has been validated via the calculation of: a) modulation of the energy bandgap and the effective masses in [0001] oriented wurtzite nanowires as compared to the experimentally reported values in bulk structures, and b) the localization of wavefunctions and the optical anisotropy in GaN/AlN disk-in-wire nanowires.

• Journal of the Korean Magnetic Resonance Society
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• v.18 no.1
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• pp.24-29
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• 2014

Atomistic molecular dynamics (MD) simulation has become mature enabling close approximation of the real behaviors of biomolecules. In biomolecular NMR field, atomistic MD simulation coupled with generalized implicit solvent model (GBIS) has contributed to improving the qualities of NMR structures in the refinement stage with experimental restraints. Here all-atom force fields play important roles in defining the optimal positions between atoms and angles, resulting in more precise and accurate structures. Despite successful applications in refining NMR structure, however, the research that has studied the influence of force fields in GBIS is limited. In this study, we compared the qualities of NMR structures of two model proteins, ubiquitin and GB1, under a series of AMBER force fields-ff99SB, ff99SB-ILDN, ff99SB-NMR, ff12SB, and ff13-with experimental restraints. The root mean square deviations of backbone atoms and packing scores that reflect the apparent structural qualities were almost indistinguishable except ff13. Qualitative comparison of parameters, however, indicates that ff99SB-ILDN is more recommendable, at least in the cases of ubiquitin and GB1.

• Journal of the Korean Institute of Electrical and Electronic Material Engineers
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• v.18 no.5
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• pp.414-422
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• 2005

This paper shows the results of atomistic modeling for the Interaction between spherical nano abrasive and substrate In chemical mechanical polishing processes. Atomistic modeling was achieved from 2-dimensional molecular dynamics simulations using the Lennard-jones 12-6 potentials. We proposed and investigated three mechanical models: (1) Constant Force Model; (2) Constant Depth Model, (3) Variable Force Model, and three chemical models, such as (1) Chemically Reactive Surface Model, (2) Chemically Passivating Surface Model, and (3) Chemically Passivating-reactive Surface Model. From the results obtained from classical molecular dynamics simulations for these models, we concluded that atomistic chemical mechanical polishing model based on both Variable Force Model and Chemically Passivating-reactive Surface Model were the most suitable for realistic simulation of chemical mechanical polishing in the atomic scale. The proposed model can be extended to investigate the 3-dimensional chemical mechanical polishing processes in the atomic scale.

• Transactions of the Korean Society of Mechanical Engineers A
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• v.28 no.9
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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.

• Journal of the Korean Society of Manufacturing Process Engineers
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• v.8 no.1
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• pp.43-47
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• 2009

Recently, an approach for nano-scale material deformation has been developed that couples the atomistic and continuum approaches using Finite Element Method (FEM) and Molecular Dynamics (MD). However, this approach still has problems to connect two approaches because of the difference of basic assumptions, continuum and atomistic modeling. To solve this problem, an alternative way is developed that connects the QuasiMolecular Dynamics (QMD) and molecular dynamics. In this paper, we suggest the way to make and validate the MD-QMD coupled model.

• Proceedings of the Korean Magnestics Society Conference
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• 2007.05a
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• pp.90.2-90.2
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• 2007

• Journal of the Korean Institute of Electrical and Electronic Material Engineers
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• v.19 no.2
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• pp.116-125
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• 2006

We have presented a nanoelectromechanical (NEM) model based on atomistic simulations. Our models were applied to a NEM device as called a nanotube random access memory (NRAM) operated by an atomistic capacitive model including a tunneling current model. We have performed both static and dynamic analyses of a NRAM device. The turn-on voltage obtained from molecular dynamics simulations was less than the half of the turn-on voltage obtained from the static simulation. Since the suspended carbon nanotube (CNT) oscillated with the amplitude for the oscillation center under an externally applied force, the quantity of the CNT-gold interaction in the static analysis was different from that in the dynamic analysis. When the gate bias was applied, the oscillation centers obtained from the static analysis were different from those obtained from the dynamics analysis. Therefore, for the range of the potential difference that the CNT-gold interaction effects in the static analysis were negligible, the vibrations of the CNT in the dynamics analysis significantly affected the CNT-gold interaction energy and the turn-on voltage. The turn-on voltage and the tunneling resistance obtained from our tunneling current model were in good agreement with previous experimental and theoretical works.

• 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.

• Nuclear Engineering and Technology
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• v.55 no.6
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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.