• EDISON SW 활용 경진대회 논문집
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• 제4회(2015년)
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• pp.163-166
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• 2015

Intramolecular energy migration in a cyclic porphyrin array is spontaneous transfer of energy from one excited site to another. Since the efficiency of energy migration is inversely proportional to distance, the energy migration is occurred on their adjacent sites more often than distant ones. Therefore, the energy migration in the cyclic porphyrin array is largely dependent on their conformational characters. However, evaluation of conformational information by means of experimental tools is ambiguous since their limited resolution. In this work, we calculate the internal angle and distance distributions of cyclic porphyrin arrays using molecular dynamics simulations to obtain conformational information. To evaluate the angle and distance distributions respect to molecular size, we constructed molecules with n porphyrin dimers (n=1,3,7) in implicit solvent environment. Performing molecular dynamics simulations, we modulated alkyl groups to investigate additional conformational effects of the system.

• Bulletin of the Korean Chemical Society
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• 제27권2호
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• pp.325-328
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• 2006

• Bulletin of the Korean Chemical Society
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• 제22권8호
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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.

• 한국소성가공학회:학술대회논문집
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• 한국소성가공학회 2007년도 추계학술대회 논문집
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• pp.348-351
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• 2007

Simulations of the buckling behavior of a single wall carbon nanotube(SWCNT) was carried out using molecular dynamics simulation. Molecular dynamics simulations were done with 1fs of time step. Tersoff's potential function was used as the interatomic potential function since it has been proved to be reliable to describe the C-C bonds in carbon nanotubes. Compressive force was applied by moving the top end of the nanotube at a constant velocity. Buckling behavior under compressive load was observed for (15,15) armchair SWCNTs with 2nm of diameter and 24.9nm of length. Buckling load and critical strain is obtained from the MD simulation. Deformation occurred on the top region of the CNT because of fast downward velocity.

• Bulletin of the Korean Chemical Society
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• 제32권10호
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• pp.3553-3554
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• 2011

• Bulletin of the Korean Chemical Society
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• 제29권11호
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• pp.2172-2182
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• 2008

• 한국윤활학회:학술대회논문집
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• 한국윤활학회 2002년도 proceedings of the second asia international conference on tribology
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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.

• 대한기계학회:학술대회논문집
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• 대한기계학회 2001년도 추계학술대회논문집A
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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.

• EDISON SW 활용 경진대회 논문집
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• 제4회(2015년)
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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.

• Transactions on Electrical and Electronic Materials
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• 제5권6호
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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 $3.579 eV/{\AA}$.