• Bulletin of the Korean Chemical Society
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• v.26 no.8
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• pp.1203-1208
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• 2005

A computational study based on molecular dynamics (MD) simulations was performed in order to explain the difference in aqueous solubilities of two flavonoid/$\beta$-cyclodextrin ($\beta$-CD) complexes, hesperetin/$\beta$-CD and naringenin/$\beta$-CD. The aqueous solubility of each flavonoid/$\beta$-CD complex could be characterized by complexwater interaction not by flavonoid-CD interaction. The radial distribution of water around each inclusion complex elucidated the difference of an experimentally observed solubility of each flavonoid/$\beta$-CD complex. The analyzed results suggested that a bulky hydrophobic moiety (-$OCH_3$) of B-ring of hesperetin nearby primary rim of $\beta$-CD was responsible for lower aqueous solubility of the hesperetin/$\beta$-CD complex.

• Journal of the Korea Computer Graphics Society
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• v.14 no.4
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• pp.35-39
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• 2008

A computer supported collaborative system provides with a shared virtual workspace over the Internet where its remote users cooperate in order to achieve their goals by overcoming problems caused by distance and time. VRMMS (Virtual Reality Molecular Modeling System) [1] is a VR based collaborative system where biologists can remotely participate in and exercise molecular modeling tasks such as viewing three dimensional structures of molecular models, confirming results of molecular simulations and providing with feedbacks for the next simulations. Biologists can utilize VRMMS in executing molecular simulations. However, first-time users and beginners need to spend some time for studying and practicing in order to skillfully manipulate molecular models and the system. The best way to resolve the problem is to have a face-to-face session of teaching and learning VRMMS. However, it is not practically recommended in the sense that the users are remotely located. It follows that the learning time could last longer than desired. In this paper, we propose to use Second Life [2] combining with VRMMS for removing the problem. It can be used in building a shared workplace over the Internet where molecular simulations using VRMMS can be exercised, taught, learned and practiced. Through the web, users can collaborate with each other using VRMMS. Their avatars and tools of molecular simulations can be remotely utilized in order to provide with senses of 'being there' to the remote users. The users can discuss, teach and learn over the Internet. The shared workspaces for discussion and education are designed and implemented in Second Life. Since the activities in Second Life and VRMMS are designed to realistic, the system is expected to help users in improving their learning and experimental performances.

• Proceedings of the Korean Society of Tribologists and Lubrication Engineers Conference
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• 2002.10b
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• pp.59-60
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• 2002

In this digest, we briefly review our current molecular dynamics (MD) simulations that utilize both the reactive empirical bond order potential (REBO) and the adaptive intermolecular REBO (AIREBO) potential energy functions. The AIREBO potential includes intermolecular interactions, so that self·assembled monolayers, and liquids, can be modeled. We have examined the mechanical and tribological properties of model self assembled monolayers and amorphous carbon films. Self-assembled monolayers are modeled by covalently bonding hydrocarbon chains to diamond substrates. Because the REBO potentials can model chemical reactions, specific compression and sliding induced chemical reactions were identified.

• Proceedings of the KSME Conference
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• 2001.11a
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• pp.252-257
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• 2001

With the help of newly arrived technology such as PC clustering, molecular dynamics (MD) seems to be promising for large-scale materials simulations. A cost-effective cluster is set up using commodity PCs connected over Ethernet with fast switching devices and free software Linux. Executing MD simulations in the parallel sessions makes it possible to carry out large-scale materials simulations at acceptable computation time and costs. In this study, the MD computer code for fracture simulation is modified to comply with MPI (Message Passing Interface) specification, and runs on the PC cluster in parallel mode flawlessly. It is noted that PC clusters can provide a rather inexpensive high-performance computing environment comparing to supercomputers, if properly arranged.

• Proceeding of EDISON Challenge
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• 2015.03a
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• pp.70-75
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• 2015

Fasciclin 1 (FAS1) is an extracellular protein whose aggregation in cornea leads to visual impairment. While a number of FAS1 mutants have been studied that exhibit enhanced/decreased aggregation propensity, no structural information has been provided so far that is associated with distinct aggregation potential. In this study, we have investigated the structural and thermodynamic characteristics of the wild-type FAS1 and its two mutants, R555Q and R555W, by using molecular dynamics simulations and three-dimensional reference interaction site model (3D-RISM) theory. We find that the hydrophobic solvent accessible surface area increases due to hydrophobic core repacking in the C-terminus caused by the mutation. We also find that the solvation free energy of the mutants increases due to the enhanced non-native H-bonding. These structural and thermodynamic changes upon mutation contribute to understand the aggregation of these mutants.

• Current Applied Physics
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• v.18 no.11
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• pp.1352-1358
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• 2018

In recent years, one-dimensional (1D) magnetic nanostructures, such as magnetic nanorods and chains of magnetic nanoparticles have received great attentions due to the breadth of applications. Especially, magnetic nanorods has been opened an area of active research and applications in medicine, sensors, optofluidics, magnetic swimming, and microrheology since they possess the unique magnetic and geometric features. This study focuses on the molecular dynamics (MD) simulations of an infinitely long crystal ${\beta}-Fe_2O_3$ nanorod. To elucidate the structural properties and dynamics behavior of ${\beta}-Fe_2O_3$ nanorods, MD simulation is a powerful technique. The structural properties such as equation of state and radial distribution function of bulk ${\beta}-Fe_2O_3$ are performed by lattice dynamics (LD) simulations. In this work, we consider three main mechanisms affecting on deformation characteristics of a ${\beta}-Fe_2O_3$ nanorod: 1) temperature, 2) the rate of mechanical compression, and 3) the rate of mechanical torsion.

• Bulletin of the Korean Chemical Society
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• v.25 no.2
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• pp.321-324
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• 2004

• Bulletin of the Korean Chemical Society
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• v.33 no.1
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• pp.322-324
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• 2012

• Bulletin of the Korean Chemical Society
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• v.22 no.12
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• pp.1287-1288
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• 2001

• Bulletin of the Korean Chemical Society
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• v.22 no.3
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• pp.253-254
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• 2001