• 한국전산유체공학회:학술대회논문집
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• 2008.03a
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• pp.208-214
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• 2008

The equilibrium molecular-dynamic simulations have been performed to estimate the properties of the three kinds of fluids (the Lennard-Jones fluid, water and aqueous sodium-chloride solution) confined between two plates that are separated by 1.086 nm; included in the equilibrium properties are the density distribution and the static structure, and the diffusivity in the dynamic property. Three kinds of fluids considered in this study are. The water molecules are modeled by using the SPC/E model and the ions by the charged Lennard-Jones particle model. To treat the water molecules, we combined the quaternion coordinates with Euler angles. We also proposed a plausible algorithm to assign the initial position and direction of molecules. The influence of polarization of water molecules as well as the presence of ions in the solution on the properties will be addressed in this study. In addition, we performed the non-equilibrium molecular-dynamic simulation to compute the flow velocity for the case with the gravitational force acting on molecules.

• 한국전산유체공학회:학술대회논문집
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• 2008.10a
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• pp.208-214
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• 2008

The equilibrium molecular-dynamic simulations have been performed to estimate the properties of the three kinds of fluids (the Lennard-Jones fluid, water and aqueous sodium-chloride solution) confined between two plates that are separated by 1.086 nm; included in the equilibrium properties are the density distribution and the static structure, and the diffusivity in the dynamic property. Three kinds of fluids considered in this study are. The water molecules are modeled by using the SPC/E model and the ions by the charged Lennard-Jones particle model. To treat the water molecules, we combined the quaternion coordinates with Euler angles. We also proposed a plausible algorithm to assign the initial position and direction of molecules. The influence of polarization of water molecules as well as the presence of ions in the solution on the properties will be addressed in this study. In addition, we performed the non-equilibrium molecular-dynamic simulation to compute the flow velocity for the case with the gravitational force acting on molecules.

• Journal of computational fluids engineering
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• v.14 no.1
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• pp.24-34
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• 2009

The equilibrium molecular-dynamic simulations have been performed to estimate the properties of the three kinds of fluids confined between two plates that are separated by 1.086 nm; included in the statical properties are the density distribution and the static structure, and the autocorrelation velocity function in the dynamic property. Three kinds of fluids considered in this study are the Lennard-Jones fluid, water and aqueous sodium-chloride solution. The water molecules are modeled by using the SPC/E model and the ions by the charged Lennard-Jones particle model. To treat the water molecules, we combined the quaternion coordinates with Euler angles. We also proposed a plausible algorithm to assign the initial position and direction of molecules. The influence of polarization of water molecules as well as the presence of ions in the solution on the properties will be addressed in this study. In addition, we performed the non-equilibrium molecular-dynamic simulation to compute the flow velocity for the case with the gravitational force acting on molecules.

• Proceedings of the KSME Conference
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• 2007.05a
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• pp.337-342
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• 2007

In this study, molecular dynamics simulation of nano imprint lithography in which patterned stamp is pressed onto amorphous polyethylene(PE) surface are performed to study the behaviour of polymer. Force fields including bond, angle, torsion, and Lennard Jones potential are used to describe the inter-molecular and intra-molecular force of PE molecules and stamp, substrate. Periodic boundary condition is used in horizontal direction and canonical NVT ensemble is used to control the system temperature. As the simulation results, the behaviour of polymer is investigated during the imprinting process. The mechanism of polymer deformation is studied by means of inspecting the surface shape, volume, density, atom distribution. Deformation of the polymer resist was found for various of the stamp geometry and the alignment state of the polymer molecules.

• Tribology and Lubricants
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• v.36 no.5
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• pp.290-296
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• 2020

When two layers of carbon nanotube (CNT) arrays are loaded to mate, the free ends of individual CNTs come into contact at the interface of the two layers. This leads to a higher contact resistance due to a smaller contact region. However, when the free CNT ends of one array penetrate into the mating array, the contact region increases, effectively lowering the contact resistance. To explore the penetration of mating CNTs, we perform molecular dynamic simulations of a simple unit cell model, incorporating four CNTs in the lower array layer coupled with a single moving CNT on the upper layer. The interaction with neighboring CNTs is modelled by long-range carbon bond order potential (LCBOP I). The model structure is optimized by energy minimization through the conjugate gradient method. A NVT ensemble is used for maintain a room temperature during simulation. The time integration is performed through the velocity-Verlet algorithm. A significant vibrational motion of CNTs is captured when penetration is not available, resulting in a specific vibration mode with a high frequency. Due to this vibrational behavior, the random behaviors of CNT motion for predicting the penetration are confirmed under the specific gap distances between CNTs. Thus, the probability of penetration is examined according to the gap distance between CNTs in the lower array and the aspect ratio of CNTs. The penetration is significantly affected by the vibration mode due to the van der Waals forces between CNTs.

• Current Optics and Photonics
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• v.1 no.5
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• pp.551-555
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• 2017

Tissue optics is a well-established and extensively studied area. In the last decades, Monte Carlo simulation (MCS) has been one of the standard tools for simulation of light propagation in turbid media. The utilization of parallel processing exhibits dramatic increase in the speed of MCS's of photon migration. Some calculations based on MCS can be completed within a few seconds. Since the MCS's have the potential to become a real time calculation method, a dynamic accuracy estimation, which is also known as history by history statistical estimators, is required in the simulation code to automatically terminate the MCS as the results' accuracy achieves a high enough level. In this work, spatial and time-domain GPU-based MCS, adopting the dynamic accuracy estimation, are performed to calculate the light dose/reflectance in homogeneous and heterogeneous tissue media. This dynamic accuracy estimation can effectively derive the statistical error of optical dose/reflectance during the parallel Monte Carlo process.

• Multiscale and Multiphysics Mechanics
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• v.1 no.4
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• pp.327-340
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• 2016

Poly(${\epsilon}$-caprolactone) (PCL) diol, with good biodegradation and biocompatibility, is one of the widely used soft segments (SSs) in composing bio-polyester-urethanes (Bio-PUs), which show great potential in both biomedical and tissue engineering applications. Properties of Bio-PUs are tunable by combining SS monomers with different molecular weights, structures, modifications, and ratio of components. Although numbers of research have reported many Bio-PUs properties, few studies have been done at the molecular scale. In this study, we use molecular dynamic (MD) simulation to construct atomistic models for two commonly used PCL diol SSs with different molecular weights 1247.58 Da and 1932.42 Da. We compare the simulation results by using two widely used classical force fields for organic molecules: Consistent Valence Force Field (CVFF) and CHARMM General Force Field (CGenFF), and discuss the validity and accuracy. Melt density, volume, polymer conformations, transition temperature, and mechanical properties of PCL diols are calculated and compared with experiments. Our results show that both force fields provide accurate predictions on the properties of PCL diol system at the molecular scale and could help the design of future Bio-PUs.

• Journal of the Korean Ceramic Society
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• v.34 no.7
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• pp.713-721
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• 1997

Molecular dynamic (MD) simulations with new interatomic potential function including the covalent bond were performed on the phase transition of $\alpha$-quartz-type GeO2 under high pressure. The optimized crystal structure and the pressure dependence of the lattice constant showed higher reproducibility than the previous models and were in very good agreement with the experimental data. A phase transition of $\alpha$-quartz and $\alpha$-quartz-type GeO2 by simulation was found approximately 24 GPa and 6-7 GPa, respectively. This phase transition involved an abrupt volume shrinkage and showed 4-6 coordination mixed structure with the increasing in the coordination number of cation.

• Journal of the Semiconductor & Display Technology
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• v.10 no.4
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• pp.47-51
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• 2011

We investigated the substrate surface polishing by the spherical rigid abrasive under the compression using classical molecular dynamics modeling. We performed three-dimensional molecular dynamic simulations using the Morse potential functions for the various slide-to-roll ratios, from 0 to 1, and then, the compressive forces acting on the spherical rigid abrasive were calculated as functions of the time and the slide-to-roll ratio. The friction coefficients obtained from the classical molecular dynamics simulations were compared to those obtained from the experiments; and found that the molecular dynamic simulation results with the slide-to-roll ratio of 0 value were in good agreement with the experimental results.

• Bulletin of the Korean Chemical Society
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• v.32 no.12
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• pp.4397-4402
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• 2011

The NF-${\kappa}B$ system of transcription factors plays a crucial role in inflammatory diseases, making it an important drug target. We combined quantitative structure activity relationships for predicting the activity of new compounds and quantitative dynamic models for the NF-${\kappa}B$ network with intracellular concentration models. GFA-MLR QSAR analysis was employed to determine the optimal QSAR equation. To validate the predictability of the $IKK{\beta}$ QSAR model for an external set of inhibitors, a set of ordinary differential equations and mass action kinetics were used for modeling the NF-${\kappa}B$ dynamic system. The reaction parameters were obtained from previously reported research. In the IKKb QSAR model, good cross-validated $q^2$ (0.782) and conventional $r^2$ (0.808) values demonstrated the correlation between the descriptors and each of their activities and reliably predicted the $IKK{\beta}$ activities. Using a developed simulation model of the NF-${\kappa}B$ signaling pathway, we demonstrated differences in $I{\kappa}B$ mRNA expression between normal and different inhibitory states. When the inhibition efficiency increased, inhibitor 1 (PS-1145) led to long-term oscillations. The combined computational modeling and NF-${\kappa}B$ dynamic simulations can be used to understand the inhibition mechanisms and thereby result in the design of mechanism-based inhibitors.