• 한국군사과학기술학회지
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• 제14권1호
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• pp.147-153
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• 2011

A series of nonequilibrium molecular dynamics(NEMD) simulations are performed to investigate the kinetic energy and velocity distributions of molecules in shock waves. In the simulations, argon molecules are used as a medium gas through which shock waves are propagating. The kinetic energy distribution profiles reveals that as a strong shock wave whose Mach number is 27.1 is applied, 39.6% of argon molecules inside the shock wave have larger kinetic energy than molecular ionization energy. This indicates that an application of a strong shock wave to argon gas can give rise to an intense light. The velocity distribution profiles in z direction along which shock waves propagate clearly represent two Maxwell-Boltzmann distributions of molecular velocities in two equilibrium regions and one bimodal velocity distribution profile that is attributed to a nonequilibrium region. The peak appearing in the directional temperature in z direction is discussed on a basis of the bimodal velocity distribution in the nonequilibrium region.

• Bulletin of the Korean Chemical Society
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• 제32권12호
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• pp.4397-4402
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• 2011

The NF-${\kappa}B$ system of transcription factors plays a crucial role in inflammatory diseases, making it an important drug target. We combined quantitative structure activity relationships for predicting the activity of new compounds and quantitative dynamic models for the NF-${\kappa}B$ network with intracellular concentration models. GFA-MLR QSAR analysis was employed to determine the optimal QSAR equation. To validate the predictability of the $IKK{\beta}$ QSAR model for an external set of inhibitors, a set of ordinary differential equations and mass action kinetics were used for modeling the NF-${\kappa}B$ dynamic system. The reaction parameters were obtained from previously reported research. In the IKKb QSAR model, good cross-validated $q^2$ (0.782) and conventional $r^2$ (0.808) values demonstrated the correlation between the descriptors and each of their activities and reliably predicted the $IKK{\beta}$ activities. Using a developed simulation model of the NF-${\kappa}B$ signaling pathway, we demonstrated differences in $I{\kappa}B$ mRNA expression between normal and different inhibitory states. When the inhibition efficiency increased, inhibitor 1 (PS-1145) led to long-term oscillations. The combined computational modeling and NF-${\kappa}B$ dynamic simulations can be used to understand the inhibition mechanisms and thereby result in the design of mechanism-based inhibitors.

• 멤브레인
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• 제30권6호
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• pp.433-442
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• 2020

본 연구에서는 수전해용 ionomer의 분자동역학 전산모사 모델 제작을 위하여, 과량의 물 분자가 존재하는 수전해 시스템의 특성을 반영한 ionomer 모델을 제작한 후, 기존 연료전지용 전해질막 전산모사 조건에 맞춰 제작한 ionomer 모델과 비교하였다. 최종적으로 얻어진 모델은 과불소계 ionomer의 중요 특징 중 하나인 명확한 상분리 및 수화채널이 관찰되었으며, 과량의 물 및 높은 운전 온도 조건에서도 물에 녹지 않고 안정된 구조를 나타내었다. 제조된 ionomer 모델에서는 과량의 물분자로 인한 이온 희석 효과로 이온 전달 성능 감소가 나타났으며, 반대로 수소 기체의 투과는 더 증가할 것으로 분석되었다. 따라서 이러한 수전해 시스템의 특성을 반영한 수전해용 ionomer 분자 구조 설계 전략이 필요하고, 분자동역학 전산모사 연구 시에도 이를 감안한 수전해용 ionomer 모델 제작이 필요하다.

• Bulletin of the Korean Chemical Society
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• 제35권5호
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• pp.1440-1448
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• 2014

Co(II)-tetrasulfonated phthalocyanine (CoTSP) is known to be aggregated to dimer at high concentration levels in water. A study on the aggregation of CoTSP using multivariate curve resolution analysis of the visible absorbance spectra over a concentration range of 30, 40 and 50 ${\mu}M$ in the presence of dimethyl sulfoxide (DMSO), dimethyl formamide (DMF), acetonitrile (AN) and ethanol (EtOH) in the concentration range of 0 to 3.57 M is conducted. A hard modeling-based multivariate curve resolution method was applied to determine the dissociation constants of the CoTSP aggregates at various temperatures ranging from 25, 45 and $65^{\circ}C$ and in the presence of various co-solvents. Dissociation constant for aggregation was increased and then decrease by temperature and concentration of phthalocyanine, respectively. Utilizing the vant Hoff relation, the enthalpy and entropy of the dissociation equilibriums were calculated. For the dissociation of both aggregates, the enthalpy and entropy changes were positive and negative, respectively. Molecular dynamics simulation of cosolvent effect on CoTSP aggregation was done to confirm spectroscopy results. Results of radial distribution function (RDF), root mean square deviation (RMSD) and distance curves confirmed more effect of polar solvent to decrease monomer formation.

• Bulletin of the Korean Chemical Society
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• 제28권10호
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• pp.1689-1696
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• 2007

Equilibrium molecular dynamics (EMD) simulations are used to evaluate the transport coefficients of argonkrypton mixtures at two liquid states (state A: 94.4 K and 1 atm; state B: 135 K and 39.5 atm) via modified Green-Kubo formulas. The composition dependency of the volume at state A obeys close to the linear model for ideal liquid mixture, while that at state B differs from the linear model probably due to the high pressure. The radial distribution functions for the Ar-Kr mixture (x = 2/3) show a mixing effect: the first peak of g11 is higher than that of g(r) for pure Ar and the first peak of g22 is lower than that of g(r) for pure Kr. An exponential model of engineering correlation for diffusion coefficient (D) and shear viscosity (η) is superior to the simple linear model for ideal liquid mixtures. All three components of thermal conductivity (λpm, λtm, and λti) at state A and hence the total thermal conductivity decrease with the increase of x. At state B, the change in λtm is dominant over those in λpm and λti, and hence the total thermal conductivity decrease with the increase of x.

• Macromolecular Research
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• 제17권5호
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• pp.289-295
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• 2009

Low viscosity aromatic hyperbranched polyester epoxy resin (HTBE) was synthesized by the reaction between epichlorohydrin (ECH) and carboxyl-end hyperbranched polyester (HTB) which was prepared from inexpensive materials $A_2$ (1,4-butanediol glycol, BEG) and $B_3$ (trimellitic anhydride, TMA) by pseudo one-step method. The molar mass of the HTB was calculated from its acid value by "Recursive Probability Approach". The degree of branching (DB) of the HTB was characterized by model compounds and $^1H$ NMR-minus spectrum technology, and the DB of the HTB was about $0.47{\sim}0.63$. The viscosity and epoxy equivalent weight of the HTBE were $3,600{\sim}5,000\;cp$ and lower than 540 g/mol respectively. The reaction mechanism and structure of the $AB_2$ monomer, HTB and HTBE were investigated by MS, $^1H$ NMR and FTIR spectra technology. The molecular size of HTBE is under 8.65 nm and its shape is ellipsoid-like as determined by molecular simulation.

• 한국윤활학회:학술대회논문집
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• 한국윤활학회 2004년도 학술대회지
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• pp.215-220
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• 2004

Molecular Dynamics(MD) method was used to investigate the change of friction force due to interaction between dislocations and a grain boundary when a Ni tip was scratched on a Cu bicrystal. The substrate comprised a Cu bicrystal containing a vertical$\Sigma=5(210)$ grain boundary. The moving tip for scratching simulation was consisted of fixed Ni atoms emulating a rigid tip. The indentation depth was $3.6\AA$ and the scratching was performed along <110>direction in the first grain. As the scratching was continued, nucleation and propagation of dislocations were observed. In the early stage, the grain boundary played as a barrier to moving dislocations and interrupting further dislocation movement with no dislocation resulting in no propagation across the grain boundary. As the Ni tip approached the grain boundary, dislocations were nucleated at the grain boundary and propagated to the second grain. However, stick-slip phenomena that were observed on a single crystal scratching were not observed in the bicrystal. And, instead, irregular oscillation of friction force was observed during the scratching due to the presence of a grain boundary.

• BMB Reports
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• 제49권8호
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• pp.431-436
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• 2016

Human papillomavirus (HPV) is the major cause of cervical cancer, a deadly threat to millions of females. The early oncogene product (E7) of the high-risk HPV16 is the primary agent associated with HPV-related cervical cancers. In order to understand how E7 contributes to the transforming activity, we investigated the structural features of the flexible N-terminal region (46 residues) of E7 by carrying out N-15 heteronuclear NMR experiments and replica exchange molecular dynamics simulations. Several NMR parameters as well as simulation ensemble structures indicate that this intrinsically disordered region of E7 contains two transient (10-20% populated) helical pre-structured motifs that overlap with important target binding moieties such as an E2F-mimic motif and a pRb-binding LXCXE segment. Presence of such target-binding motifs in HPV16 E7 provides a reasonable explanation for its promiscuous target-binding behavior associated with its transforming activity.

• Structural Engineering and Mechanics
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• 제30권2호
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• pp.177-190
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• 2008

Material failure behavior is generally dependent on loading rate. Especially in brittle and quasi-brittle materials, rate dependent material behavior can be significant. Empirical formulations are often used to predict the rate dependency, but such methods depend on extensive experimental works and are limited by practical constraints of physical testing. Numerical simulation can be an effective means for extracting knowledge about rate dependent behavior and for complementing the results obtained by testing. In this paper, the failure behavior of a brittle material under different loading rates is simulated by molecular dynamics analysis. A notched specimen is modeled by sub-million particles with a normalization scheme. Lennard-Jones potential is used to describe the interparticle force. Numerical simulations are performed with six different loading rates in a direct tensile test, where the loading velocity is normalized to the ratio of the pseudo-sonic speed. As a consequence, dynamic features are achieved from the numerical experiments. Remarkable failure characteristics, such as crack surface interaction/crack arrest, branching, and void nucleation, vary in case of the six loading cases. These characteristics are interpreted by the energy concept approach. This study provides insight into the change in dynamic failure mechanism under different loading rates.

• 대한기계학회:학술대회논문집
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• 대한기계학회 2008년도 추계학술대회A
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• pp.1885-1890
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• 2008

3-D heterogeneous nucleation was simulated by classical molecular dynamics (MD), where the Lennard-Jones (LJ) gas and solid cluster-seed molecules have argon and aluminum properties, respectively. There are three shapes of cluster-seeds, cube, rod, and sphere, and three classes of masses and the simulation took place under nine supersaturation ratios, making a total of 81 calculations. Results show that the dimension of the cluster-seed highly affects the rates of cluster development. In order to analyze heterogeneous nucleation above and below the critical supersaturation ratio, growth rate and liquefaction rate were separately defined to supplement the investigation. Design of experiments (DOE) was used for analysis which displayed that the shape and mass of the cluster-seed are prominent for the growth rate, while the supersaturation ratio is most significant followed by the mass for liquefaction rate. The significance of the supersaturation ratio for overall liquefaction suggests that thermal diffusion is more dominant than mass interactions for this system.