• 한국전산유체공학회:학술대회논문집
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• 한국전산유체공학회 2010년 춘계학술대회논문집
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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.

• EDISON SW 활용 경진대회 논문집
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• 제5회(2016년)
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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.

• 한국지하수토양환경학회:학술대회논문집
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• 한국지하수토양환경학회 2000년도 창립총회 및 춘계학술발표회
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• pp.163-163
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• 2000

• Bulletin of the Korean Chemical Society
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• 제16권5호
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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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• 한국전산유체공학회 2009년 추계학술대회논문집
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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.

• 정보처리학회논문지D
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• 제12D권6호
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• pp.921-930
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• 2005

본 논문에서는 개발된 범용 분자 시뮬레이션 시스템에 대해 기술하고자 한다. 본 연구에서 개발된 분자 시뮬레이션 시스템의 가장 큰 장점은 다른 무엇보다도 Langevin dynamics simulation이나 dissipative particle dynamics simulation 기법을 도입하여 all-atom 모델뿐만 아니라coarse-grain 모델까지도 다룰 수 있도록 설계하였고 따라서 미시영역은 물론 중간영역에서 일어나는 현상까지도 시뮬레이션 할 수 있도록 설계하였다는 점이다. 이를 통해 하나의 통합된 분자 시뮬레이션 시스템으로 생체막 내에서 마취제의 분포, 단백질 접힘 현상, 마이크로 채널 내에서 생체고분자의 구조와 유동 특성 등과 같이 미시영역에서부터 중간영역에 이르는 다양한 현상을 연구할 수 있게 되었다 개발된 시스템을 이용하면 molecular dynamics simulation에 기반한 분자 시뮬레이션 시스템으로는 불가능한 여러 중요한 바이오/나노 시스템을 시뮬레이션 할 수 있을 것으로 기대한다 마지막으로 벤치마크 결과를 통해 개발된 분자 시뮬레이션 시스템의 성능을 측정하였고 성능 최적화를 위한 병목지점을 조사하였다.

• 대한기계학회:학술대회논문집
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• 대한기계학회 2008년도 추계학술대회A
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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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• 제27권10호
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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.

• 대한기계학회논문집B
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• 제33권10호
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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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• 한국초전도학회 2009년도 Korea Superconductivity Society Meeting 2009
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• pp.4-4
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• 2009