• 한국전산유체공학회:학술대회논문집
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• 2008.03b
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• pp.660-661
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• 2008

Nanotubes fabricated with diverse materials show different hydrophobic properties. The hydrophobic property is one of key properties for possible applications to ion channels due to their affinity. This study focuses on the structures of water molecules inside nanotubes with varying hydrophobicity using molecular dynamics simulation. Hydrophobicity here is determined by varying the attraction term in Lennard-Jones potential. The number of water molecules inside hydrophilic nanotubes increase, as expected, and their mobilities also increase. This trend is rather discrete with increasing number of water molecules and this discreteness is attributed to hydrogen bond. We plan to perform energy analysis to understand these structural results.

• Journal of Information Display
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• v.5 no.1
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• pp.34-40
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• 2004

Time resolved infrared IR absorption spectroscopy is carried out to investigate the dynamics of electric field induced reorientation of the biphenyl molecular core and alkyl tail sub-fragments of the nematic liquid crystal 5CB (4-pentyl-4-cyano-biphenyl). The planar to homeotropic transition for high pre-tilt planar aligned cells, is studied for switching times ranging from 200 ${\mu}sec$ down to 80 ${\mu}sec$, the latter a factor of 1000 times faster than any previous nematic IR study. The reorientation rates of the core and tail are found to be the same to within experimental error and scale inversely with applied field squared, as expected for the balance of field and viscous torques. Thus any molecular conformation change during switching must relax on a shorter time scale. A simple model shows that no substantial differences exist between the reorientational dynamics of the tails and cores on the time scales longer than on the order of 10 ${\mu}s$.

• Bulletin of the Korean Chemical Society
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• v.34 no.2
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• pp.574-578
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• 2013

In this work, the friction and diffusion coefficients of a tracer in a mesoscopic solvent are evaluated as a function of the tracer size by a hybrid molecular dynamics simulation where solute molecules evolve by Newton's equations of motion but the solvent evolves through the multi-particle collision dynamics. The friction coefficient is shown to scale linearly with the tracer size for larger tracers in accord with predictions of hydrodynamic theories. The diffusion coefficient of tracer is found to be inversely proportional to tracer size. The behavior of Stokes-Einstein formula is validated as a function of tracer size.

• Bulletin of the Korean Chemical Society
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• v.33 no.3
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• pp.862-868
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• 2012

Based on the recently derived general expression for the rates of diffusion-controlled reactions, we calculate the rates of dismutation of the superoxide anion radical catalyzed by Cu/Zn superoxide dismutases (SOD). This is the first attempt to calculate the absolute rates of diffusion-controlled enzyme reactions based on the atomiclevel molecular dynamics simulations. All solvent molecules are included explicitly and the effects of the structural flexibility of enzyme, especially those of side chain motions near the active site, are included in the present calculation. In addition, the actual mobility of the substrate molecule is taken into account, which may change as the molecule approaches the active site of enzyme from the bulk solution. The absolute value of the rate constant for the wild type SOD reaction obtained from MD simulation is shown to be in good agreement with the experimental value. The calculated reactivity of a mutant SOD is also in agreement with the experimental result.

• Bulletin of the Korean Chemical Society
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• v.35 no.5
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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.

• Genomics & Informatics
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• v.15 no.4
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• pp.142-146
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• 2017

More effective production of human insulin is important, because insulin is the main medication that is used to treat multiple types of diabetes and because many people are suffering from diabetes. The current system of insulin production is based on recombinant DNA technology, and the expression vector is composed of a preproinsulin sequence that is a fused form of an artificial leader peptide and the native proinsulin. It has been reported that the sequence of the leader peptide affects the production of insulin. To analyze how the leader peptide affects the maturation of insulin structurally, we adapted several in silico simulations using 13 artificial proinsulin sequences. Three-dimensional structures of models were predicted and compared. Although their sequences had few differences, the predicted structures were somewhat different. The structures were refined by molecular dynamics simulation, and the energy of each model was estimated. Then, protein-protein docking between the models and trypsin was carried out to compare how efficiently the protease could access the cleavage sites of the proinsulin models. The results showed some concordance with experimental results that have been reported; so, we expect our analysis will be used to predict the optimized sequence of artificial proinsulin for more effective production.

• Bulletin of the Korean Chemical Society
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• v.28 no.10
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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.

• Journal of Advanced Marine Engineering and Technology
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• v.29 no.1
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• pp.60-67
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• 2005

Generally. in the molecular dynamics simulations. the Verlet neighboring list algorithm is used for the reduction of a simulation time On the other hand. the application of the Verlet neighboring list forces the time evolution of a simulation system to follow an unrealistic path in a phase space. In equilibrium state, it does not matter with the simulation results because the individual molecule's motion is originally random and any effect due to a small deviation from a real time evolution can be completely ignored. However, if an unsteady state is involved. such a deviation may significantly affect to the results. That is, there is a Possibility that the simulation results Provide ones with any misleading data In this study we evaluated the effect due to the Verlet neighboring list in performing the simulation of a non-equilibrium state and suggested the method to avoid it.

• Journal of the Korean Ceramic Society
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• v.44 no.3 s.298
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• pp.175-181
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• 2007

Molecular dynamics simulation (MD) of $(62-x)CaO{\cdot}38Al_{2}O_{3}{\cdot}xBaO$ glasses has been carried out using empirical potentials with the covalent term. The simulations closely reproduce the total neutron correlation functions of glass with 5 mol% BaO and physical properties of these glasses such as elastic constants. For these glasses, aluminum is tetrahedrally coordinated by oxygen, but there is a part of five-fold and six-fold coordination of aluminum. There are no major changes to the mid-range structure of glass, as barium is substituted for calcium. To predict the barium coordination number, we have used the bond valence (BV) theory and also compared the results of simulation with Bond valence. The coordination number for oxygen around barium atoms is close to 8 and the average distance of barium and oxygen is nearly 2.80 A. The viscosity of these glasses increases with the content of barium oxide substituted for calcium oxide.

• Tribology and Lubricants
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• v.22 no.5
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• pp.243-251
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• 2006

Molecular dynamics simulations of nanoimprint lithography NIL) are performed in order to investigate effects of process parameters, such as stamp shape, imprinting temperature and adhesive energy, on nanoimprint lithography process and pattern transfer. The simulation model consists of an amorphous $SiO_{2}$ stamp with line pattern, an amorphous poly-(methylmethacrylate) (PMMA) film and an Si substrate under periodic boundary condition in horizontal direction to represent a real NIL process imprinting long line patterns. The pattern transfer behavior and its related phenomena are investigated by analyzing polymer deformation characteristics, stress distribution and imprinting force. In addition, their dependency on the process parameters are also discussed by varying stamp pattern shapes, adhesive energy between stamp and polymer film, and imprinting temperature. Simulation results indicate that triangular pattern has advantages of low imprinting force, small elastic recovery after separation, and low pattern failure. Adhesive energy between surface is found to be critical to successful pattern transfer without pattern failure. Finally, high imprinting temperature above glass transition temperature reduces the imprinting force.