• Journal of the Semiconductor & Display Technology
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• v.3 no.3
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• pp.27-29
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• 2004

The responses of hypothetical silicon nanotubes under torsion have been investigated using an atomistic simulation based on the Tersoff potential. A torque, proportional to the deformation within Hooke's law, resulted in the ribbon-like flattened shapes and eventually led to a breaking of hypothetical silicon nanotubes. Each shape change of hypothetical silicon nanotubes corresponded to an abrupt energy change and a singularity in the strain energy curve as a function of the external tangential force, torque, or twisted angle. The dynamics of silicon nanotubes under torsion can be modelled in the continuum elasticity theory.

• Macromolecular Research
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• v.15 no.7
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• pp.610-616
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• 2007

We developed a coarse-grained force field and have extended it to polystyrene with longer chain length. A systematic method was introduced and was utilized to explain how the coarse-grained force field for polystyrene could be developed from the atomistic simulation in the paper. We elected to use polystyrene with different chain lengths of 20, 40 and 80 monomers in this study. In three cases, we utilized the same new mapping scheme. The coarse-grained force field does reproduce the bond, angle, and radial distribution of the atomistic model. The coarse-grained model proved successful, as shown by analyses of the static and dynamic properties of different chain lengths.

• Proceedings of the Computational Structural Engineering Institute Conference
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• 2006.04a
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• pp.395-402
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• 2006

In analyzing the nano-scale phenomena or behaviors of nano devices or materials, it is often desirable to deal with more atoms than can be treated only with a full atomistic simulation. However, even now, it is advisable to apply the atomistic simulation to the narrow region where the deformation field changes rapidly but to apply the conventional continuum model to the region far from that region. This equivalent continuum model can be formulated by applying the Cauchy-Born rule to the exact atomistic potential as in the quasicontinuum method. To couple the atomistic model with the equivalent continuum model, continuum displacements are conformed to the molecular displacements at the discrete positions of the atoms within the bridging domain. To satisfy the coupling constraints, we apply the Lagrange multiplier method. The continuum model in the bridging model should be applied on the region where the deformation field changes gradually. Then we can make the nodal spacing in the continuum model be much larger than the atomic spacing. In the first step, we generate the atomic-resolution mesh with the nodal spacing equal to the atomic spacing, and then we eliminate the nodal degrees of freedom adaptively using the node deactivation techniques. We eliminate more DOFs as the regions are more far from the atomistic region. Computing time and computational resources can be greatly reduced by the present node deactivation technique in multi scale analysis.

• Interaction and multiscale mechanics
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• v.1 no.4
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• pp.411-422
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• 2008

Atomistic simulation of nanoindentation with spherical indenters was carried out to study dislocation structures, mean contact pressure, and nanohardness of Au and Al thin films. Slip vectors and atomic stresses were used to characterize the dislocation processes. Two different characteristics were found in the induced dislocation structures: wide-spread slip activities in Al, and confined and intact structures in Au. For both samples, the mean contact pressure varied significantly during the early stages of indentation but reached a steady value soon after the first apparent load drop. This indicates that the nanohardness of Al and Au is not affected by the indentation depth for spherical indenters, even at the atomistic scale.

• Journal of the Korean Institute of Electrical and Electronic Material Engineers
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• v.17 no.3
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• pp.249-258
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• 2004

We investigated structural phases of potassium intercalated into carbon nanotubes using a structural optimization process applied to atomistic simulation methods. As the radius of carbon nanotubes increased, structures were found in various phases from an atomistic strand to multishell packs composed of coaxial cylindrical shells and in helical, layed, and crystalline structures. Numbers of helical atom rows composed of coaxial tubes and orthogonal vectors of a circular rolling of a triangular network could explain multishell phases of potassium in carbon nanotubes.

• Journal of the Korean Institute of Electrical and Electronic Material Engineers
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• v.16 no.12S
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• pp.1157-1164
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• 2003

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. The abrasive dynamics was modeled by three cases, such as slipping, rolling, and rotating. Simulation results showed that the different dynamics of the abrasive results the different features of surfaces. This model can be extended to investigate the 3-dimensional chemical mechanical polishing processes.

• Polymer(Korea)
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• v.30 no.6
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• pp.453-463
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• 2006

Molecular simulation is an exceptionally useful method for predicting self-assembled structures in various macromolecular systems, enlightening the origins of many interesting molecular events such as protein folding, polymer micellization, and ordering of molten block copolymer. The length scales of those events ranges widely from sub-nanometer scale to micron-scale or to even larger, which is the main obstacle to simulate all the events in an ab initio principle. In order to detour this major obstacle in the molecular simulation approach, a molecular model can be rebuilt by sacrificing some unimportant molecular details, based on two different perspectives with respect to the resolution of model. These two perspectives are generally referred to as 'atomistic' and 'mesoscopit'. This paper reviews various simulation methods for macromolecular self-assembly in both atomistic and mesoscopic perspectives.

• 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.

• Journal of Korean Vacuum Science & Technology
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• v.6 no.1
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• pp.22-29
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• 2002

The process of energetic deposition has been simulated by using molecular dynamics (W) simulation and kinetic Monte Carlo (KMC) simulation. The atomistic mechanisms of film growth in energetic deposition are discussed.

• Advances in nano research
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• v.3 no.3
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• pp.143-168
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• 2015

Initiation of crack and its growth simulation requires accurate model of traction - separation law. Accurate modeling of traction-separation law remains always a great challenge. Atomistic simulations based prediction has great potential in arriving at accurate traction-separation law. The present paper is aimed at establishing a method to address the above problem. A method for traction-separation law prediction via utilizing atomistic simulations data has been proposed. In this direction, firstly, a simpler approach of common neighbor analysis (CNA) for the prediction of crack growth has been proposed and results have been compared with previously used approach of threshold potential energy. Next, a scheme for prediction of crack speed has been demonstrated based on the stable crack growth criteria. Also, an algorithm has been proposed that utilizes a variable relaxation time period for the computation of crack growth, accurate stress behavior, and traction-separation atomistic law. An understanding has been established for the generation of smoother traction-separation law (including the effect of free surface) from a huge amount of raw atomistic data. A new curve fit has also been proposed for predicting traction-separation data generated from the molecular dynamics simulations. The proposed traction-separation law has also been compared with the polynomial and exponential model used earlier for the prediction of traction-separation law for the bulk materials.