• Interaction and multiscale mechanics
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• v.6 no.4
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• pp.395-409
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• 2013

Molecular dynamics (MD) systems are highly nonlinear and nonlocal, and the conventional model order reduction methods are ineffective for MD systems. The RBF-POD method (Lee and Chen, 2013) employed a radial basis function (RBF) approximated potential energies and inter-atomic forces of MD systems under the framework of the proper orthogonal decomposition (POD) method for the reduced-order modeling of MD systems. In this work, we focus on the numerical procedures of the RBF-POD method and demonstrate how to apply this approach to the modeling of ds-DNA molecules under stretching and bending conditions.

• Interaction and multiscale mechanics
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• v.4 no.3
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• pp.219-237
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• 2011

Recent advances in scientific computing enable the full atomistic simulation of DNA molecules. However, there exists length and time scale limitations in molecular dynamics (MD) simulation for large DNA molecules. In this work, a two-level homogenization of DNA molecules is proposed. A wavelet projection method is first introduced to form a coarse-grained DNA molecule represented with superatoms. The coarsened MD model offers a simplified molecular structure for the continuum description of DNA molecules. The coarsened DNA molecular structure is then homogenized into a three-dimensional beam with embedded molecular properties. The methods to determine the elasticity constants in the continuum model are also presented. The proposed continuum model is adopted for the study of mechanical behavior of DNA loop.

• CELLMED
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• v.6 no.4
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• pp.24.1-24.4
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• 2016

The emergence of influenza virus and antigenic drift are potential cause of world-wide pandemic. There are some commercially available drugs in the market to treat influenza. During past decade, however, critical resistances have been raised for biological targets. Because of structural complexity and flexibility of target proteins, applying a computational modeling tool is very beneficial for developing alternative anti-influenza drugs. In this review, we introduced molecular dynamics (MD) simulations approach to reflect full conformational flexibility of proteins during molecular modeling works. Case studies of MD works were summarized for the drug discovery and drug resistance mechanism of anti-influenza pharmaceuticals.

• Journal of the Computational Structural Engineering Institute of Korea
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• v.27 no.3
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• pp.137-145
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• 2014

We present a design sensitivity analysis(DSA) method for multiscale problems based on bridging scale decomposition. In this paper, we utilize a bridging scale method for the coupled system analysis. Since the analysis of full MD systems requires huge amount of computational costs, a coupled system of MD-level and continuum-level simulation is usually preferred. The information exchange between the MD and continuum levels is taken place at the MD-continuum boundary. In the bridging scale method, a generalized Langevin equation(GLE) is introduced for the reduced MD system and the GLE force using a time history kernel is applied at the boundary atoms in the MD system. Therefore, we can separately analyze the MD and continuum level simulations, which can accelerate the computing process. Once the simulation of coupled problems is successful, the need for the DSA is naturally arising for the optimization of macro-scale design, where the macro scale performance of the system is maximized considering the micro scale effects. The finite difference sensitivity is impractical for the gradient based optimization of large scale problems due to the restriction of computing costs but the analytical sensitivity for the coupled system is always accurate. In this study, we derive the analytical design sensitivity to verify the accuracy and applicability to the design optimization of the coupled system.

• 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.

• Proceedings of the IEEK Conference
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• 2001.06e
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• pp.119-122
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• 2001

This paper deals with new type of active magnetic bearing (AMB) for the linear motors. We adopted optical sensing mechanism for the gap sensing. Using the laser and the PSD (Position Sensitive Device), the absolute rotor position is obtained independent of the profile of the guide rail. With this measurement, the rotor can be controller to follow the straight beam of the laser. Another advantage of optical sensing mechanism might be the elimination of the possible interference between the proximity sensor and the electro-magnet. By adopting the push-full actuating mechanism, the bearing stiffness is increased near the equilibrium position. For the simplicity, distributed control system is constructed. Eight independent PID control algorithm is used with the full order observer. Several simulation md test results are presented.

• Wind and Structures
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• v.37 no.4
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• pp.255-274
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• 2023

The aim of this paper is to enhance the accuracy of predicting time-averaged external surface pressures on low-rise buildings by utilizing Computational Fluid Dynamics (CFD) simulations. To achieve this, benchmark studies of the Silsoe cube and the Texas Tech University (TTU) experimental building are employed for comparison with simulation results. The paper is structured into three main sections. In the initial part, an appropriate domain size is selected based on the precision of mean pressure coefficients on the windward face of the cube, utilizing Reynolds Averaged Navier-Stokes (RANS) turbulence models. Subsequently, recommendations regarding the optimal computational domain size for an isolated building are provided based on revised findings. Moving on to the second part, the Silsoe cube model is examined within a horizontally homogeneous computational domain using more accurate turbulence models, such as Large Eddy Simulation (LES) and hybrid RANS-LES models. For computational efficiency, transient simulation settings are employed, building upon previous studies by the authors at the Windstorm Impact, Science, and Engineering (WISE) Lab, Louisiana State University (LSU). An optimal meshing strategy is determined for LES based on a grid convergence study. Three hybrid RANS-LES cases are investigated to achieve desired enhancements in the distribution of mean pressure coefficients on the Silsoe cube. In the final part, a 1:10 scale model of the TTU building is studied, incorporating the insights gained from the second part. The generated flow characteristics, including vertical profiles of mean velocity, turbulence intensity, and velocity spectra (small and large eddies), exhibit good agreement with full-scale (TTU) measurements. The results indicate promising roof pressures achieved through the careful consideration of meshing strategy, time step, domain size, inflow turbulence, near-wall treatment, and turbulence models. Moreover, this paper demonstrates an improvement in mean roof pressures compared to other state-of-the-art studies, thus highlighting the significance of CFD simulations in building aerodynamics.

• Bulletin of the Korean Chemical Society
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• v.29 no.8
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• pp.1554-1560
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• 2008

The probe diffusion and friction constants of methyl yellow (MY) in liquid n-alkanes of increasing chain length were calculated by equilibrium molecular dynamics (MD) simulations at temperatures of 318, 418, 518 and 618 K. Lennard-Jones particles with masses of 225 and 114 g/mol are modeled for MY. We observed that the diffusion constant of the probe molecule follows a power law dependence on the molecular weight of nalkanes, DMY${\sim}M^{-\gamma}$ well. As the molecular weight of n-alkanes increases, the exponent $\gamma$ shows sharp transitions near n-dotriacontane ($C_{32}$) for the large probe molecule (MY2) at low temperatures of 318 and 418 K. For the small probe molecule (MY1) $D_{MY1}$ in $C_{12}$ to C80 at all the temperatures are always larger than Dself of n-alkanes and longer chain n-alkanes offer a reduced friction relative to the shorter chain n-alkanes, but this reduction in the microscopic friction for MY1 is not large enough to cause a transition in the power law exponent in the log-log plot of DMY1 vs M of n-alkane. For the large probe molecule (MY2) at high temperatures, the situation is very similar to that for MY1. At low temperatures and at low molecular weights of n-alkanes, $D_{MY2}$ are smaller than $D_{self}$ of n-alkanes due to the relatively large molecular size of MY2, and MY2 experiences the full shear viscosity of the medium. As the molecular weight of n-alkane increases, $D_{self}$ of n-alkanes decreases much faster than $D_{MY2}$ and at the higher molecular weights of n-alkane, MY2 diffuses faster than the solvent fluctuations. Therefore there is a large reduction of friction in longer chains compared to the shorter chains, which enhances the diffusion of MY2. The calculated friction constants of MY1 and MY2 in liquid n-alkanes supported these observations. We deem that this is the origin of the so-called“solventoligomer”transition.

• Tunnel and Underground Space
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• v.16 no.3 s.62
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• pp.241-250
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• 2006

Ice ring formation, one of the core techniques in LNG storage in a lined rock cavern, is investigated through hydro-thermal coupled analysis. An ice ring acts as a secondary barrier in case of leakage of cryogenic liquid and as a primary barrier for groundwater intrusion into an LNG cavern. Therefore, the thickness and location of the ice ring are crucial factors for the safe operation of an LNG storage cavern, especially for maintaining the integrity of a primary barrier composed of concrete, PU foam, and steel membrane. Through numerical analyses, the position and thickness of the ice ring are estimated, and the temperature and groundwater level are compared with measured values. The temperature md groundwater level by numerical analyses show good agreement with the field measurements when temperature-dependent properties and phase change are taken into account. The schemes used in this paper can be applied for estimation of ice ring formation in designing a full-scale LNG cavern.