• Bulletin of the Korean Chemical Society
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• v.26 no.5
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• pp.769-775
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• 2005

An efficiency of Monte Carlo (MC) docking simulations was examined for the prediction of chiral discrimination by cyclodextrins. Docking simulations were performed with various computational parameters for the chiral discrimination of a series of 17 enantiomers by $\beta$-cyclodextrin ($\beta$-CD) or by 6-amino-6-deoxy-$\beta$-cyclodextrin (am-$\beta$-CD). A total of 30 sets of enantiomeric complexes were tested to find the optimal simulation parameters for accurate predictions. Rigid-body MC docking simulations gave more accurate predictions than flexible docking simulations. The accuracy was also affected by both the simulation temperature and the kind of force field. The prediction rate of chiral preference was improved by as much as 76.7% when rigid-body MC docking simulations were performed at low-temperatures (100 K) with a sugar22 parameter set in the CHARMM force field. Our approach for MC docking simulations suggested that the conformational rigidity of both the host and guest molecule, due to either the low-temperature or rigid-body docking condition, contributed greatly to the prediction of chiral discrimination.

• CELLMED
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• v.6 no.4
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• pp.24.1-24.4
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• 2016

The emergence of influenza virus and antigenic drift are potential cause of world-wide pandemic. There are some commercially available drugs in the market to treat influenza. During past decade, however, critical resistances have been raised for biological targets. Because of structural complexity and flexibility of target proteins, applying a computational modeling tool is very beneficial for developing alternative anti-influenza drugs. In this review, we introduced molecular dynamics (MD) simulations approach to reflect full conformational flexibility of proteins during molecular modeling works. Case studies of MD works were summarized for the drug discovery and drug resistance mechanism of anti-influenza pharmaceuticals.

• Journal of the Korean Institute of Electrical and Electronic Material Engineers
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• v.25 no.7
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• pp.569-573
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• 2012

We investigated the speed change of the diamond spherical abrasive during the substrate surface polishing under the pad compression by using classical molecular dynamics modeling. We performed three-dimensional molecular dynamics simulations using the Morse potential functions for the copper substrate and the Tersoff potential function for the diamond abrasive. As the compressive pressure increased, the indented depth of the diamond abrasive increased and then, the speed of the diamond abrasive along the direction of the pad moving was decreased. Molecular simulation result such as the abrasive speed decreasing due to the pad pressure increasing gave important information for the chemical mechanical polishing including the mechanical removal rate with both the pad speed and the pad compressive pressure.

• Bulletin of the Korean Chemical Society
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• v.34 no.8
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• pp.2515-2518
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• 2013

• Bulletin of the Korean Chemical Society
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• v.32 no.10
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• pp.3553-3554
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• 2011

• 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.

• Transactions of Materials Processing
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• v.21 no.6
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• pp.366-371
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• 2012

Atomistic simulations have become useful tools for exploring new insights in materials science, but the length and time scale that can be handled with atomistic simulations are seriously limiting their practical applications. In order to make meaningful quantitative predictions, atomistic simulations are necessarily combined with higher-scale modeling. The present research is thus concerned with the development of a multi-scale model and its application to the prediction of the mechanical properties of body-centered cubic(BCC) iron with an emphasis on the coupling of atomistic molecular dynamics with meso-scale discrete dislocation dynamics modeling. In order to achieve predictive multi-scale simulations, it is necessary to properly incorporate atomistic details into the meso-scale approach. This challenge is handled with the proposed hierarchical information passing strategy from atomistic to meso-scale by obtaining material properties and dislocation mobility. Finally, this fundamental and physics-based meso-scale approach is employed for quantitative predictions of the mechanical response of single crystal iron.

• Transactions on Electrical and Electronic Materials
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• v.5 no.6
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• pp.227-232
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• 2004

We investigated a nonvolatile nanomemory element based on boron nitride nanopeapods using molecular dynamics simulations. The studied system was composed of two boron-nitride nanotubes filled Cu electrodes and fully ionized endo-fullerenes. The two boron-nitride nanotubes were placed face to face and the endo-fullerenes came and went between the two boron-nitride nanotubes under alternatively applied force fields. Since the endo-fullerenes encapsulated in the boron-nitride nanotubes hardly escape from the boron-nitride nanotubes, the studied system can be considered to be a nonvolatile memory device. The minimum potential energies of the memory element were found near the fullerenes attached copper electrodes and the activation energy barrier was $3{\cdot}579 eV$. Several switching processes were investigated for external force fields using molecular dynamics simulations. The bit flips were achieved from the external force field of above $3.579 eV/{\AA}$.

• Proceedings of the Korean Biophysical Society Conference
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• 1996.07a
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• pp.21-21
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• 1996

The hyperthermostable protein, rubredoxin from Pyrococcus furiosus is 53-residue protein with a three-stranded anti-parallel $\beta$-sheet and several loops. To investigate the effect of changes of electrostatic and hydrophobic interactions on the structure and dynamic property of P. furiosus rubredoxin, molecular dynamics simulations in water were performed on three mesophilic rubredoxins, P, furiosus rubresoxin, and 5 mutants of P. furiosus rubredoxin. (omitted)

• Bulletin of the Korean Chemical Society
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• v.22 no.8
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• pp.847-849
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• 2001

The OSS2(Ojame-Shavitt-Singer 2)[L. Ojame et al., J. Chem. Phys. 109, 5547 (1998)] model as a dissociable water model is examined in order to study the dynamics of H+ in water. MD simulations for 216 water system, 215 water + H+ ion system, and 215 water + OH- ion system using the OSS2 model at 298.15 K with the use of Ewald summation are carried out. The calculated O-H radial distribution functions for these systems are essentially the same and are in very good agreement with that obtained by Ojame.