• Journal of the Korean GEO-environmental Society
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• v.25 no.4
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• pp.21-28
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• 2024

In this study, a polyhedral domain decomposition method for Smoothed Particle Hydrodynamics (SPH) analysis is introduced. SPH which is one of meshless methods is a numerical analysis method for fluid flow simulation. It can be useful for analyzing fluidic soil or fluid-structure interaction problems. SPH is a particle-based method, where increased particle count generally improves accuracy but diminishes numerical efficiency. To enhance numerical efficiency, parallel processing algorithms are commonly employed with the Cartesian coordinate-based domain decomposition method. However, for parallel analysis of complex geometric shapes or fluidic problems under dynamic boundary conditions, the Cartesian coordinate-based domain decomposition method may not be suitable. The introduced polyhedral domain decomposition technique offers advantages in enhancing parallel efficiency in such problems. It allows partitioning into various forms of 3D polyhedral elements to better fit the problem. Physical properties of SPH particles are calculated using information from neighboring particles within the smoothing length. Methods for sharing particle information physically separable at partitioning and sharing information at cross-points where parallel efficiency might diminish are presented. Through numerical analysis examples, the proposed method's parallel efficiency approached 95% for up to 12 cores. However, as the number of cores is increased, parallel efficiency is decreased due to increased information sharing among cores.

• Journal of the Korean Chemical Society
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• v.58 no.6
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• pp.560-568
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• 2014

The contribution of electrostatic interactions to protein folding reaction was studied by using mutant ubiquitin with lysine to alanine mutation at residue position 29. Based on the three dimensional structure of ubiquitin, lysine 29 is located close to negatively charged glutamate 16 and aspartate 21 and considered to stabilize the native state of ubiquitin by electrostatic interactions between these residues. The equilibrium unfolding experiment showed that the native stability was decreased by about ~20% upon mutation. This observation indicates lysine 29 indeed forms electrostatic interactions with nearby residues. Folding kinetics measurements using stopped-flow device and quantitative analysis of kinetics data indicate that ubiquitin folds from unfolded state to native state via intermediate state as observed previously. This intermediate state was observed to form immediately after the initiation of folding reaction. The folding intermediate was shown to be destabilized considerably upon lysine to alanine mutation. These observations indicate that electrostatic interactions can form early stage of protein folding and hence lead the folding reaction.

• Tunnel and Underground Space
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• v.30 no.6
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• pp.573-590
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• 2020

This study presents the current status of DECOVALEX-2023 project Task G and our research results so far. Task G, named 'Safety ImplicAtions of Fluid Flow, Shear, Thermal and Reaction Processes within Crystalline Rock Fracture NETworks (SAFENET)' aims at developing a numerical method to simulate the fracture creation and propagation, and the coupled thermohydro-mechanical processes in fracture in crystalline rocks. The first research step of Task G is a benchmark simulation, which is designed for research teams to make their modelling codes more robust and verify whether the models can represent an analytical solution for displacements of a single rock fracture. We reproduced the mechanical behavior of rock and embedded single fracture using a three-dimensional grain-based distinct element model for the simulations. In this method, the structure of the rock was represented by an assembly of rigid tetrahedral grains moving independently of each other, and the mechanical interactions at the grains and their contacts were calculated using 3DEC. The simulation results revealed that the stresses induced along the embedded fracture in the model were relatively low compared to those calculated by stress analysis due to stress redistribution and constrained fracture displacements. The fracture normal and shear displacements of the numerical model showed good agreement with the analytical solutions. The numerical model will be enhanced by continuing collaboration and interaction with other research teams of DECOVALEX-2023 Task G and validated using various experiments in a further study.

• Wind and Structures
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• v.34 no.1
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• pp.127-136
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• 2022

In this work a multi-fidelity non-intrusive polynomial chaos (MF-NIPC) has been applied to a structural wind engineering problem in architectural design for the first time. In architectural design it is important to design structures that are safe in a range of wind directions and speeds. For this reason, the computational models used to design buildings and bridges must account for the uncertainties associated with the interaction between the structure and wind. In order to use the numerical simulations for the design, the numerical models must be validated by experi-mental data, and uncertainties contained in the experiments should also be taken into account. Uncertainty Quantifi-cation has been increasingly used for CFD simulations to consider such uncertainties. Typically, CFD simulations are computationally expensive, motivating the increased interest in multi-fidelity methods due to their ability to lev-erage limited data sets of high-fidelity data with evaluations of more computationally inexpensive models. Previous-ly, the multi-fidelity framework has been applied to CFD simulations for the purposes of optimization, rather than for the statistical assessment of candidate design. In this paper MF-NIPC method is applied to flow around a rectan-gular 5:1 cylinder, which has been thoroughly investigated for architectural design. The purpose of UQ is validation of numerical simulation results with experimental data, therefore the radius of curvature of the rectangular cylinder corners and the angle of attack are considered to be random variables, which are known to contain uncertainties when wind tunnel tests are carried out. Computational Fluid Dynamics (CFD) simulations are solved by a solver that employs the Finite Element Method (FEM) for two turbulence modeling approaches of the incompressible Navier-Stokes equations: Unsteady Reynolds Averaged Navier Stokes (URANS) and the Large Eddy simulation (LES). The results of the uncertainty analysis with CFD are compared to experimental data in terms of time-averaged pressure coefficients and bulk parameters. In addition, the accuracy and efficiency of the multi-fidelity framework is demonstrated through a comparison with the results of the high-fidelity model.

• Journal of Korean Society of Coastal and Ocean Engineers
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• v.26 no.3
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• pp.174-183
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• 2014

Seabed beneath and near coastal structures may undergo large excess pore water pressure composed of oscillatory and residual components in the case of long durations of high wave loading. This excess pore water pressure may reduce effective stress and, consequently, the seabed may liquefy. If liquefaction occurs in the seabed, the structure may sink, overturn, and eventually increase the failure potential. In this study, to evaluate the liquefaction potential on the seabed, numerical analysis was conducted using the expanded 2-dimensional numerical wave tank to account for an irregular wave field. In the condition of an irregular wave field, the dynamic wave pressure and water flow velocity acting on the seabed and the surface boundary of the composite breakwater structure were estimated. Simulation results were used as input data in a finite element computer program for elastoplastic seabed response. Simulations evaluated the time and spatial variations in excess pore water pressure, effective stress, and liquefaction potential in the seabed. Additionally, the deformation of the seabed and the displacement of the structure as a function of time were quantitatively evaluated. From the results of the analysis, the liquefaction potential at the seabed in front and rear of the composite breakwater was identified. Since the liquefied seabed particles have no resistance to force, scour potential could increase on the seabed. In addition, the strength decrease of the seabed due to the liquefaction can increase the structural motion and significantly influence the stability of the composite breakwater. Due to limitations of allowable paper length, the studied results were divided into two portions; (I) focusing on the dynamic response of structure, acceleration, deformation of seabed, and (II) focusing on the time variation in excess pore water pressure, liquefaction, effective stress path in the seabed. This paper corresponds to (II).

• Journal of Korean Society of Coastal and Ocean Engineers
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• v.26 no.3
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• pp.160-173
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• 2014

Seabed beneath and near coastal structures may undergo large excess pore water pressure composed of oscillatory and residual components in the case of long durations of high wave loading. This excess pore water pressure may reduce effective stress and, consequently, the seabed may liquefy. If liquefaction occurs in the seabed, the structure may sink, overturn, and eventually increase the failure potential. In this study, to evaluate the liquefaction potential on the seabed, numerical analysis was conducted using the expanded 2-dimensional numerical wave tank to account for an irregular wave field. In the condition of an irregular wave field, the dynamic wave pressure and water flow velocity acting on the seabed and the surface boundary of the composite breakwater structure were estimated. Simulation results were used as input data in a finite element computer program for elastoplastic seabed response. Simulations evaluated the time and spatial variations in excess pore water pressure, effective stress, and liquefaction potential in the seabed. Additionally, the deformation of the seabed and the displacement of the structure as a function of time were quantitatively evaluated. From the results of the analysis, the liquefaction potential at the seabed in front and rear of the composite breakwater was identified. Since the liquefied seabed particles have no resistance to force, scour potential could increase on the seabed. In addition, the strength decrease of the seabed due to the liquefaction can increase the structural motion and significantly influence the stability of the composite breakwater. Due to limitations of allowable paper length, the studied results were divided into two portions; (I) focusing on the dynamic response of structure, acceleration, deformation of seabed, and (II) focusing on the time variation in excess pore water pressure, liquefaction, effective stress path in the seabed. This paper corresponds to (I).

• Transactions of the Korean Society of Mechanical Engineers B
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• v.40 no.9
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• pp.597-604
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• 2016

A parallel algorithm of bi-conjugate gradient method was developed based on CUDA for parallel computation of the incompressible Navier-Stokes equations. The governing equations were discretized using splitting P2P1 finite element method. Asymmetric stenotic flow problem was solved to validate the proposed algorithm, and then the parallel performance of the GPU was examined by measuring the elapsed times. Further, the GPU performance for sparse matrix-vector multiplication was also investigated with a matrix of fluid-structure interaction problem. A kernel was generated to simultaneously compute the inner product of each row of sparse matrix and a vector. In addition, the kernel was optimized to improve the performance by using both parallel reduction and memory coalescing. In the kernel construction, the effect of warp on the parallel performance of the present CUDA was also examined. The present GPU computation was more than 7 times faster than the single CPU by double precision.

• Korean Journal of Food Science and Technology
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• v.6 no.4
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• pp.199-208
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• 1974

An attempt was made to study on new method for the extraction of the regulatory proteins from myofibrils, and the procedures for the preparation of desensitized actomyosin and for complete extraction of troponin-tropomyosin complex were developed. When myofibrils were treated through the procedures developed in this study, actomyosin obtained had no Ca-sensitivity, indicating that Ca-sensitizing protein factor had been removed completely from myofibril. Consequently, it was concluded that the procedures developed in this study were convenient to test whether Ca-sensitizing proteins has been removed or not. When Mg-activated ATPase activity of myofibril were measured, the myofibrillar ATPase turned into the actomyosin type ATPase with the progress of the treatment. This result was interpreted to show that the regulatory proteins of the myofibril seems to play a cementing role on the structure of myofibril. When supernatant containing the regulatory proteins were fractionated with $(NH_4)_2SO_4$ saturation solution, regulatory proteins, ${\alpha}-actinin$ and troponia-tropomyosin complex, could be obtained and they showed their typical phyoislogical activity which modify the actin-myosin interaction. The amount of troponin-tropomyosin complex in myofibril was 72 mg per g myofibril. This result was in good agreement with the results reported by many investigators, and therefore it was concluded that our procedures for the extraction of troponin-tropomyosin complex were desirable to study on the quantitative analysis of troponin-tropomyosin complex.

• Journal of Bio-Environment Control
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• v.23 no.4
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• pp.293-302
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• 2014

This study was carried out to develop rain shelter which can make an appropriate size and environment for Chinese cabbage rainproof cultivation. Fifty three farms with chinese cabbage rainproof cultivation system have been investigated to set up width and height of rain shelter. Mostly the width of 6m was desired for rain shelter and the height of 1.6m for their eaves, so these values were chosen as the dimensions for rain shelter. After an analysis of their structural safety and installation costs by the specifications of the rafter pipe, Ø$25.4{\times}1.5t$ and 90cm have been set as the size of rafter that such size costs the least. This size is stable with $27m{\cdot}s^{-1}$ of wind velocity and 17cm of snow depth. Therefore it is difficult to apply this dimension to area with higher climate load. In order to sort out such problem, the rain shelter has been designed to avoid damage on frame by opening plastic film to the ridge. Once greenhouse band is loosen by turning the manual switch at the both sides of rain shelter and open button of controller is pushed then switch motor rises up along the guide pipe and plastic film is opened to the ridge. Chinese cabbage can be damaged by insects if rain shelter is opened completely as revealed a field. To prevent this, farmers can install an insect-proof net. Further, the greenhouse can be damaged by typhoon while growing Chinese cabbage therefore the effect of an insect-proof net on structural safety has been analyzed. And then structural safety has been analyzed through using flow-structure interaction method at the wind condition of $40m{\cdot}s^{-1}$. And it assumed that wind applied perpendicular to side of the rain shelter which was covered by insect-proof net. The results indicated that plastic film was directly affected by wind therefore high pressure occurred on the surface. But wind load on insect-proof net was smaller than on plastic film and pressure distribution was also uniform. The results of structural analysis by applying pressure data extracted from flow analysis indicated that the maximum stress occurred at the end of pipe which is the ground part and the value has been 54.6MPa. The allowable stress of pipe in the standard of structural safety must be 215 MPa or more therefore structural safety of this rain shelter is satisfied.