• 한국전산유체공학회:학술대회논문집
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• 2010.05a
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• pp.575-580
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• 2010

In this work, the electrophoretic motion of dsDNA molecule represented by a polymer through an artificial nano-pore in a membrane is simulated using the numerical method combining the lattice Boltzmann and Langevin molecular dynamic method. The polymer motion is represented by Langevin molecular dynamics technique while the fluid flow is taken into account by fluctuating lattice-Boltzmann method. The hydrodynamic interactions between the polymer and solvent in a confined space with a membrane having a hole are considered explicitly through the frictional and the random forces. The electric field intensity over the space is obtained from a finite difference method. Initially, the polymer is placed at one side of the space, and an electric field is applied to drive the polymer to the other side of the space through the nano-pore. In future, we plan to study the effect of the polymer size and the electric field on the electrophoretic velocity.

• 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.

• Proceedings of the Korean Society of Soil and Groundwater Environment Conference
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• 2000.05a
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• pp.163-163
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• 2000

• Bulletin of the Korean Chemical Society
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• v.16 no.5
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• pp.427-432
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• 1995

A model based on two coupled generalized Langevin equations is proposed to investigate the trans-stilbene photoisomerization dynamics. In this model, a system which has two independent coordinates is considered and these two system coordinates are coupled to the same harmonic bath. The direct coupling between the system coordinates is assumed negligible and these two coordinates influence each other through the frictional coupling mediated by solvent molecules. From the Hamiltonian which is equivalent to the coupled generalized Langevin equations, we obtain the transition state theory rate constants of the stilbene photoisomerization. The rates obtained from this model are compared to experimental results in n-alkane solvents.

• 한국전산유체공학회:학술대회논문집
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• 2009.11a
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• pp.97-102
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• 2009

Translocation of biopolymers such as DNA and RNA through a nano-pore is an important process in biotechnology applications. The translocation process of a biopolymer through an artificial nano-pore in the presence of a fluid solvent is simulated. The polymer motion is simulated by Langevin molecular dynamics (MD) techniques while the solvent dynamics are taken into account by lattice-Boltzmann method (LBM). The hydrodynamic interactions are considered explicitly by coupling the polymer and solvent through the frictional and the random forces. From simulation results we found that the hydrodynamic interactions between polymer and solvent speed-up the translocation process. The translocation time ${\tao}_T$ scales with the chain length N as ${{\tau}_T}^{\propto}N^{\alpha}$. The value of scaling exponents($\alpha$) obtained from our simulations are $1.29{\pm}0.03$ and $1.41{\pm}0.03$, with and without hydrodynamic interactions, respectively. Our simulation results are in good agreement with the experimentally observed value of $\alpha$, which is equal to $1.27{\pm}0.03$, particularly when hydrodynamic interaction effects are taken into account.

• The KIPS Transactions:PartD
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• v.12D no.6 s.102
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• pp.921-930
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• 2005

In this paper, a general purpose molecular simulation system which has been developed by the author, are described. One of the most advantageous features is that the molecular simulation system can handle a coarse-grained model as well as an all-atom mode. Therefore, we can simulate mesoscopic phenomena as well as microscopic phenomena with the help of Langevin dynamics simulation and dissipative particle dynamics simulation techniques. Thus we could study anesthesia, protein folding, biopolymer flow in microchannel with single framework, which spans from microscopic to mesoscopic scales. We expect that we can also simulate many other bio/nano systems of technological importance which are not feasible by means of molecular dynamics simulation technique. Finally, performance data are shown and a bottleneck is identified for future optimization.

• Proceedings of the KSME Conference
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• 2008.11a
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• pp.1922-1927
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• 2008

In the present study, deposition of discrete and small particles, which diameter is less than $1{\mu}m$, on a filter element was simulated by stochastic method. Trajectory of each particle was numerically solved by Langevin equation and Brownian random motion was treated by Brownian dynamics. Lattice Boltzmann method (LBM) was used to solve flow field around the filter collector and deposit layer. Interaction between flow field and deposit layer was obtained from a converged solution from an inner-loop calculation. Simulation method is properly validated and collection efficiency due to different filtration parameters are examined and discussed. Morphology of deposit layer and its evolution was visualized in terms of the particle size. The particle loaded effect on collection efficiency was also discussed.

• Bulletin of the Korean Chemical Society
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• v.27 no.10
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• pp.1659-1663
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• 2006

A many-body master equation is constructed by incorporating stochastic terms responsible for chemical reactions into the many-body Smoluchowski equation. Two forms of Langevin-type of memory equations describing the time evolution of dynamical variables under the influence of time-independent perturbation with an arbitrary intensity are derived. One form is convenient in obtaining the dynamics approaching the steady-state attained by the perturbation and the other in describing the fluctuation dynamics at the steady-state and consequently in obtaining the linear response of the system at the steady-state to time-dependent perturbation. In both cases, the kinetics of statistical averages of variables is found to be obtained by analyzing the dynamics of time-correlation functions of the variables.

• Transactions of the Korean Society of Mechanical Engineers B
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• v.33 no.10
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• pp.811-819
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• 2009

In the present study, deposition of discrete and small particles on a filter fiber was simulated by stochastic method. Trajectory of each particle was numerically solved by Langevin equation. And Lattice Boltzmann method (LBM) was used to solve flow field around the filter collector for considering complex shape of deposit layer. Interaction between the flow field and the deposit layer was obtained from a converged solution from an inner-loop calculation. Simulation method is properly validated with filtration theory and collection efficiency due to different filtration parameters are examined and discussed. Morphology of deposit layer and its evolution was visualized in terms of the particle size. The particle loaded effect on collection efficiency was also discussed.

• 한국초전도학회:학술대회논문집
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• 2009.07a
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• pp.4-4
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• 2009