• KIISE Transactions on Computing Practices
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• v.20 no.10
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• pp.534-542
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• 2014

Multiscale modeling is a new simulation approach which can manage different spatial and temporal scales of system. In this study, as part of multiscale modeling research, we propose the way of combining two different simulation methods, molecular dynamics(MD) and stochastic rotation dynamics(SRD). Our conceptual implementations are based on LAMMPS, one of the well-known molecular dynamics programs. Our prototype of multiscale modeling follows the form of the third party implementation of LAMMPS. It added MD to SRD in order to simulate the boundary area of the simulation box. Because it is important to guarantee the seamless simulation, we also designed the overlap zones and communication zones. The preliminary experimental results showed that our proposed scheme is properly worked out and the execution time is also reduced.

• 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 Photoscience
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• v.9 no.2
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• pp.134-137
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• 2002

PYP consists of a water-soluble apoprotein and 4-hydroxycinnamyl chromophore bound to Cys69 via thiolester linkage, Upon absorption of a photon, the photocycle is initiated, leading to formation of several photo-intermediates. Among them, M intermediate is important to understand the signal transduction mechanism of PYP, because it is a putative signaling state. As well known, the dynamics of a protein is closely correlated with the occurrence of its function. Here we report the results of IO ns molecular dynamics (MD) simulation for the M intermediate in aqueous solution and discuss the characteristic feature of this state from a viewpoint of structural fluctuation.

• Proceedings of the Korean Society for Technology of Plasticity Conference
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• 2003.10a
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• pp.347-354
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• 2003

The dynamics of fluid flow through nanomachines is completely different from that of continuum. In this study, molecular dynamics simulations were performed for the flow of helium, neon, argon inside carbon(graphite) nanotubes of several sizes. The fluid was introduced into the nanotube at a given initial velocity according to given temperature. Diffusion coefficients were evaluated by Green-Kubo equation derived from Einstein relationship. The behaviour of the fluid was strongly dependent on the density of fluid and tube diameter, not on the tube length. It was found that the diffusion Coefficients increased With decreasing the density of molecules and increasing the diameter and temperature.

• Bulletin of the Korean Chemical Society
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• v.27 no.8
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• pp.1154-1158
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• 2006

Anomalously high ionic mobilities of H+ and $OH^-$ are owing to the transfer of $H^+$ by the Grotthus chain mechanism. Molecular dynamics simulations for the system of 215 water including $OH^-$ ion at 298.15 K using the OSS2 model [J. Chem. Phys. 109, 5547 (1998)] as a dissociable water model with the use of Ewald summation were carried out in order to study the dynamics of $OH^-$ in water. The calculated ionic mobility of $OH^-$ is in good agreement with the experimental result and the Grotthus chain mechanism is fully understood.

• Bulletin of the Korean Chemical Society
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• v.25 no.5
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• pp.737-741
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• 2004

We presents new results for transport properties of dumbbell fluids by equilibrium molecular dynamics (EMD) simulations using Green-Kubo and Einstein formulas. It is evident that the interaction between dumbbell molecules is less attractive than that between spherical molecules which leads to higher diffusion and to lower friction. The calculated viscosity, however, is almost independent on the molecular elongation within statistical error bar, which is contradicted to the Stokes' law. The calculated thermal conductivity increases and then decreases as molecular elongation increases. These results of viscosity and thermal conductivity for dumbbell molecules by EMD simulations are inconsistent with the earlier results of those by non-equilibrium molecular dynamics (NEMD) simulations. The possible limitation of the Green-Kubo and Einstein formulas with regard to the calculations of viscosity and thermal conductivity for molecular fluids such as the missing rotational degree of freedom is pointed out.

• Korea-Australia Rheology Journal
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• v.14 no.4
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• pp.161-174
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• 2002

A new technique for numerical calculation of viscoelastic flow based on the combination of Neural Net-works (NN) and Brownian Dynamics simulation or Stochastic Simulation Technique (SST) is presented in this paper. This method uses a "universal approximator" based on neural network methodology in combination with the kinetic theory of polymeric liquid in which the stress is computed from the molecular configuration rather than from closed form constitutive equations. Thus the new method obviates not only the need for a rheological constitutive equation to describe the fluid (as in the original Calculation Of Non-Newtonian Flows: Finite Elements St Stochastic Simulation Techniques (CONNFFESSIT) idea) but also any kind of finite element-type discretisation of the domain and its boundary for numerical solution of the governing PDE's. As an illustration of the method, the time development of the planar Couette flow is studied for two molecular kinetic models with finite extensibility, namely the Finitely Extensible Nonlinear Elastic (FENE) and FENE-Peterlin (FENE-P) models.P) models.

• Bulletin of the Korean Chemical Society
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• v.30 no.9
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• pp.2087-2092
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• 2009

We performed molecular dynamics simulations on dimyristoylphosphatidylcholine lipid bilayer with 50 mol% halothane. The structural properties, electron density profile, segmental order parameter of acyl chains, headgroup orientation distribution, water dipole orientation distribution, have been examined. Overall the effects of the halothane molecules on structural properties of DMPC lipid bilayer were found to be small. The electron density profiles, the segmental order parameter, the headgroup orientation, the water dipole orientation were not affected significantly by the halothane molecules. Pressure tensor calculations shows that the lateral pressure increases at the hydrocarbon tail region and the headgroup region, and decreases at the water-headgroup interfacial region.

• Transactions of the Korean Society of Mechanical Engineers A
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• v.23 no.7 s.166
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• pp.1223-1230
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• 1999

This paper addresses a novel optimization technique based on molecular dynamics simulation which has been utilized for physical model simulation at various disciplines. In this study, objective functions are considered to be potential functions, which depict molecular interactions. Comparisons of typical optimization method such as the steepest descent and the present method for several test functions are made. The present method shows applicability and stability in finding a global optimum.

• Bulletin of the Korean Chemical Society
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• v.23 no.3
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• pp.441-446
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• 2002

We have presented the results of thermodynamic, structural and dynamic properties of liquid benzene, toluene, and p-xylene in canonical (NVT) ensemble at 293.15 K by molecular dynamics (MD) simulations. The molecular model adopted for these molecules is a combination of the rigid body treatment for the benzene ring and an atomistically detailed model for the methyl hydrogen atoms. The calculated pressures are too low in the NVT ensemble MD simulations. The various thermodynamic properties reflect that the intermolecular interactions become stronger as the number of methyl group attached into the benzene ring increases. The pronounced nearest neighbor peak in the center of mass g(r) of liquid benzene at 293.15 K, provides the interpretation that nearest neighbors tend to be perpendicular. Two self-diffusion coefficients of liquid benzene at 293.15 K calculated from MSD and VAC function are in excellent agreement with the experimental measures. The self-diffusion coefficients of liquid toluene also agree well with the experimental ones for toluene in benzene and for toluene in cyclohexane.