• Bulletin of the Korean Chemical Society
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• 제28권12호
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• pp.2426-2430
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• 2007

Dissipative particle dynamics simulations of bead-spring dumbbell models under microchannel flow were performed and the effects of the deformation on their migration behavior were discussed. Dumbbells were found to migrate toward the walls or the channel center depending on the stiffness. Stiff dumbbells migrated toward the walls. In any cases, the dumbbells were found to have a stronger tendency to move toward the channel center in more deformable conditions.

• 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.

• 한국기계가공학회지
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• 제17권5호
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• pp.117-122
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• 2018

3D printing technology and its applications have grown rapidly in academia and industry. We consider a 3D printing system designed for the selective laser sintering (SLS) method, which is one of the powder bed fusion (PBF) techniques to build up the final product by layering sintered powder slices. Thermal distortion of printing products is a critical challenge in 3D printing. This study investigates temperature-dependent conformational behaviors of 3D printed samples of sintered poly-ether-ether-ketone (PEEK) powders using molecular dynamics simulations. The wear and chemical resistance properties of PEEK are understood, as it is a well-known biocompatible material used for implants. However, studies on physical phenomena at nanoscale in PEEK are rarely published in public. We simulate dissipative particle dynamics to elucidate how a cavity regime forms in PEEK at different system temperatures. We demonstrate how PEEK structures deform subject to the system temperature distribution.

• Journal of the Korean Physical Society
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• 제73권12호
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• pp.1899-1903
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• 2018

The effects of introducing hybrid lipids to a lipid bilayer containing saturated and unsaturated lipids immersed in water were studied. The lipid and water molecules were modeled as coarse-grained particles. All particles were simulated by using the dissipative particle dynamics method. The results showed that the hybrid lipids accumulated at the interface between the saturated and the unsaturated lipid domains. The relation between the hybrid lipid concentration and the equilibrium domain size was obtained. Moreover, the sizes of the simulated lipid domains are consistent with that given by the lipid raft definition.

• Interaction and multiscale mechanics
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• 제5권4호
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• pp.399-405
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• 2012

A dissipative particle dynamics (DPD) simulation was presented to analyze surface wettability and contact angles of a droplet on a solid platform. The many-body DPD, capable of modeling vapor-liquid coexistence, was used to resolve the vapor-liquid interface of a droplet. We found a constant density inside a droplet with a transition along the droplet boundary where the density decreased rapidly. The contact angle of a droplet was extracted from the isosurfaces of the density generated by the marching cube and a spline interpolation of 2D cutting planes of the isosurfaces. A wide range of contact angles from $55^{\circ}$ to $165^{\circ}$ predicted by the normalized parameter ($|A_{SL}|/B_{SL}$) were reported. Droplet with the parameters $|A_{SL}|>5.84B{_{SL}}^{0.297}$ was found to be hydrophilic. If $|A_{SL}|$ was much smaller than $5.84B{_{SL}}^{0.297}$, the droplet was found to be superhydrophobic.

• 대한화학회지
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• 제56권4호
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• pp.431-439
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• 2012

Dissipative particle dynamics (DPD) was carried out to study the nucleation and crystal growth process of $CeO_2$ nanoparticles in different alcohol aqueous solutions. The results showed that the nucleation and crystal growth process of $CeO_2$ can be classified into three stages: nuclei growth, crystal stabilization and crystal aggregation except the initial induction stage, which could be reproduced by collecting simulation results after different simulation time. Properly selecting the sizes of $CeO_2$ and water bead was crucial in the simulation system. The influence of alcohol type and content in solutions, and precipitation temperature on the particle dimension were investigated in detail and compared with the experimental results. The consistency between simulation results and experimental data verify that the simulation can reproduce the macroscopic particle aggregation process. The effect of solvent on the nucleation and crystal growth of $CeO_2$ nanoparticles are different at three stages and can not be simply described by Derjaguin-Landau-Verwey-Overbeek (DLVO) theory or nucleation thermodynamics theory. Our work demonstrated that DPD methods can be applied to study nanoparticle forming process.

• Interaction and multiscale mechanics
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• 제6권2호
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• pp.157-172
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• 2013

This paper presented an investigation of macromolecular suspension in a grooved channel by using the dissipative particle dynamics (DPD) with finitely extensible non-linear elastic (FENE) bead spring chains model. Before studying the movement and evolution of macromolecules, the DPD method was first validated by modeling the simple fluid flow in the grooved channel. For both simple fluid flow and macromolecular suspension, the flow fields were analyzed in detail. It is found that the structure of the grooved channel with sudden contraction and expansion strongly affects the velocity distribution. As the width of the channel reduces, the horizontal velocity increases simultaneously. Vortices can also be found at the top and bottom corners behind the contraction section. For macromolecular suspension, the macromolecular chains influence velocity and density distribution rather than the temperature and pressure. Macromolecules tend to drag simple fluid particles, reducing the velocity with density and velocity fluctuations. Particle trajectories and evolution of macromolecular conformation were investigated. The structure of the grooved channel with sudden contraction and expansion significantly influence the evolution of macromolecular conformation, while macromolecules display adaptivity to adjust their own conformation and angle to suit the structure so as to pass the channel smoothly.

• 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.

• EDISON SW 활용 경진대회 논문집
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• 제2회(2013년)
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• pp.139-151
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• 2013

Understanding interactions between nanoparticles and lipid bilayer membranes is of great importance due to the potential applications in bio-nanotechnology such as drug deliveries, carrying genes, and utilization of integral membrane proteins. To investigate the dynamics of nanoparticle penetration and translocation into membranes, we performed dissipative particle dynamics simulations which use simple and intuitive coarse-grained models yet effectively describe hydrodynamic interactions in cell environment. We discuss the influence of the shape of nanoparticles as well as the properties of membranes including large membrane-embedded proteins that are found to significantly affect orientation of nanoparticles within membranes and, in turn, the minimum force required to translocate nanoparticles.

• Journal of the Korean Physical Society
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• 제73권12호
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• pp.1840-1844
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• 2018

Working in an arbitrary Lorentz frame, we address the question of formulating the covariant variational principle for classical, single-particle, dissipative, relativistic mechanics. First, within a Minkowskian geometry, the basic properties of the proper time ${\tau}$ and the covariant velocity $u_{\mu}$ are recapitulated. Next, using a scalar function ${\psi}(x)$ and its negative derivatives ${\varphi}_{\mu}{^{\prime}}s$, we construct a covariant Lagrangian ${\Lambda}$ that generalizes the famous Bateman-Caldirola-Kanai Lagrangian of nonrelativistic frictional mechanics. Finally, we propose a deterministic model for ${\psi}$ (involving the drag coefficient A) whose explicit solution leads to relativistic damped Rayleigh motion in the rest frame of the medium.