• Proceeding of EDISON Challenge
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• 2016.03a
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• pp.37-54
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• 2016

The methods for estimating the change of free energy in dissipative particle dynamics (DPD) are discussed on the basis of fluctuation theorems. Fluctuation theorems are tactics to evaluate free energy changes from non-equilibrium work distributions and have several forms, as proposed by Jarzynski, Crooks, and Bennett. The validity of these methods however, has been shown merely with the molecular dynamics or Langevin dynamics. In this study, the appropriate forms of fluctuation theorems for dissipative particle dynamics, which has similar structure to that of Langevin dynamics, are suggested using Liouville's theorem, and they are proved equivalent to original fluctuation theorems. Work distribution functions, which are probability distribution functions of works exerted on the system within the systematic change, are the basics of fluctuation theorems and their shapes are turned out to be dependent on the phase space trajectory of the change of the system. The reliability of Jarzynski and Crooks methods is highly dependent on the number of simulations to measure works and the shapes of the work distribution functions. Bennett method, however, can evaluate free energy changes even when Jarzynski and Crooks methods fail to do so.

• Bulletin of the Korean Chemical Society
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• v.32 no.6
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• pp.1849-1850
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• 2011

• Proceedings of the Korean Society for Noise and Vibration Engineering Conference
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• 2008.04a
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• pp.476-479
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• 2008

Understanding the dynamics of proteins is essential to gain insight into biological functions of proteins. The protein dynamics is delineated by conformational fluctuation (i.e. thermal vibration), and thus, thermal vibration of proteins has to be understood. In this paper, a simple mechanical model was considered for understanding protein's dynamics. Specifically, a mechanical vibration model was developed for understanding the large protein dynamics related to biological functions. The mechanical model for large proteins was constructed based on simple elastic model (i.e. Tirion's elastic model) and model reduction methods (dynamic model condensation). The large protein structure was described by minimal degrees of freedom on the basis of model reduction method that allows one to transform the refined structure into the coarse-grained structure. In this model, it is shown that a simple reduced model is able to reproduce the thermal fluctuation behavior of proteins qualitatively comparable to original molecular model. Moreover, the protein's dynamic behavior such as collective dynamics is well depicted by a simple reduced mechanical model. This sheds light on that the model reduction may provide the information about large protein dynamics, and consequently, the biological functions of large proteins.

• Journal of the Korea Society for Simulation
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• v.6 no.1
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• pp.53-60
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• 1997

Results from a nonequilibrium molecular dynamics (NEMD) simulation are presented for an argon liquid subject to a shear flow. The segmented molecular dynamics method and the subtraction technique used in NEMD program to reduce the thermal fluctuation noise in data are studied with different shear rates. The standard deviation in the shear stress reduced from 0.030 to 0.004 by the segmented molecular dynamics method for 50 repeated segments. On the other hand, the standard deviation of the data remained the same when the subtraction technique was applied, where as the results of shear stress by constant value in a random way.

• 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.

• Transactions of the Korean Society of Mechanical Engineers A
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• v.31 no.2 s.257
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• pp.237-244
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• 2007

In order to obtain mechanical properties of CNT/Polymer nano-composites, molecular dynamics simulation is performed. Overall system was modeled as a flexible unit cell in which carbon nanotubes are embedded into a polyethylene matrix for N $\sigma$ T ensemble simulation. COMPASS force field was chosen to describe inter and intra molecular potential and bulk effect was achieved via periodic boundary conditions. In CNT-polymer interface, only Lennard-Jones non-bond potential was considered. Using Parrinello-Rahman fluctuation method, mechanical properties of orthotropic nano-composites under various temperatures were successfully obtained. Also, we investigated thermal behavior of the short CNT reinforced nanocomposites system with predicting glass transition temperature.

• Proceedings of the KSME Conference
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• 2007.05a
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• pp.332-336
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• 2007

Temperature is an essential process variable in nanoimprint lithography(NIL) where the temperature varies between room temperature and above the glass transition temperature. To simulate NIL process, we employ both the Nose-Poincare method for temperature controlled molecular dynamics(MD) and force field for polymer material i.e. polymethyl methacrylate(PMMA), which is most widely selected as NIL resist. Nose-Poincare method, which convinces the conservation of Hamiltonian structure and time-reversal symmetry, overcomes the drawbacks inherent in the conventional methods such as Nose thermostat and Nose-Hoover thermostat. Thus, this method exhibits enhanced numerical stability even when the temperature fluctuation is large. To describe PMMA, we adopt the force field which account for bond stretch, bending, torsion, inversion, partial charge, and van der Waals energy.

• Bulletin of the Korean Chemical Society
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• v.15 no.2
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• pp.118-122
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• 1994

Molecular dynamics simulation was carried out to study density effects on vibrational dephasing. Because of difficulty due to large time scale difference between vibrational motion and vibrational relaxation, we adopt adiabatic approximation in which the vibrational motion is assumed to be much faster than translational and rotational motion. As a result, we are able to study vibrational dephasing by simulating motion of rigid molecules. It is shown that the dephasing time is decreased as density increases and the contribution to this result is mainly due to the mean-squared frequency fluctuation.

• Bulletin of the Korean Chemical Society
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• v.15 no.7
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• pp.553-559
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• 1994

Dynamics of $CH_2CI$ group in ${\alpha},2,6$-trichlorotoluene dissolved in $CDCl_3$ was studied by observing various relaxation modes for $^{13}C$ under proton undecoupled condition. Partially relaxed $^{13}C$ spectra were obtained at $34^{\circ}C$ as a function of evolution time after applying various designed pulse sequences to this $AX_2$ spin system. It was found that nonlinear regression analysis of the relaxation data for these magnetization modes could provide the information about dipolar and spin-rotational auto-correlation and cross-correlation spectral densities for fluctuation of the $^{13}C-^1H$ internuclear vector in $CH_2Cl$ group. The results show that the effect of cross-correlation is comparable in magnitude to that of auto-correlation and the relaxation in this spin system is dominated by dipolar mechanism rather than spin-rotational one. From the resulting spectral density data we could calculate the bond angle ${\angle}HCH\;(105.1$^{\circ}$) and elements of the rotational diffusion tensor for $CH_2Cl$ group.

• 한국정보디스플레이학회:학술대회논문집
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• 2002.08a
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• pp.419-422
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• 2002

We have studied dielectric properties in the smectic phases of 4-(6-ethoxy-1-trifluoromethyl-hexyloxycarbonyl)-phenyl-4-Nonyloxybiphenyl-4-carboxylat ( TFMEOHPNBC ) having fluorine attached to one of its benzene rings. Homogeneous and homeotropic 1.5 and 5${\mu}m$ thick test cells were prepared to analyze molecular dynamic property. We measured capacitance as a function of temperature in the frequency range between 20 Hz and 100 kHz by using HP4284A LCR meter. We observed that the homogeneous cell has high dielectric constant causing dipole moment in smectic $C^{\ast}$ phase, but we can see the dipole moments are canceled out in antiferroelectric phase. It is found that there are two kind of the relaxation director fluctuation below 100 kHz. The first is ionic or space charge contribution below 10 Hz, and the second is Goldstone mode near 1-2 kHz. We will discuss molecular dynamics in smectic phase from extra information such as x-ray and electrooptic data.