• Bulletin of the Korean Chemical Society
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• v.33 no.3
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• pp.848-854
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• 2012

We have studied the oligomerization of a fibril-forming segment of ${\alpha}$-Synulcein using a replica exchange molecular dynamics (REMD) simulation. The simulation was performed with trimers and tetramers of a 12 amino acid residue stretch (residues 71-82) of ${\alpha}$-Synulcein. From extensive REMD simulations, we observed the spontaneous formation of both trimer and tetramer, demonstrating the self-aggregating and fibril-forming properties of the peptides. Secondary structure profile and clustering analysis illustrated that antiparallel ${\beta}$-sheet structures are major species corresponding to the global free energy minimum. As the size of the oligomer increases from a dimer to a tetramer, conformational stability is increased. We examined the evolution of simple order parameters and their free energy profiles to identify the process of aggregation. It was found that the degree of aggregation increased as time passed. Tetramer formation was slower than trimer formation and a transition in order parameters was observed, indicating the full development of tetramer conformation which is more stable than that of the trimer. The shape of free energy surface and change of order parameter distributions indicate that the oligomer formation follows a dock-and-lock process.

• Journal of Korean Society of Water and Wastewater
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• v.28 no.2
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• pp.225-233
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• 2014

This paper presents a Computational Fluid Dynamics(CFD) based simulation and experimental tracer test of flow pattern and turbulent energy dissipation inside a serpentine flocculation basin with continuous operation. Research focused on the evaluation of a specific flow pattern on the hydraulic behavior on the flocculation basin. From the results of CFD simulation and actual tracer test, both results were in good accordance with each other. Also, each Morill index were calculated as 1.5 from CFD simulation and 1.7 from actual tracer test, respectively. Especially, turbulence energy was dissipated relatively higher in the vicinity of inlet to the flocculation basin than other region. The differences between the CFD simulation and actual tracer test were 1.4 min in $T_{50}$, and 1.3 min in $T_p$, respectively.

• Proceedings of the KSME Conference
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• 2007.05a
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• pp.496-501
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• 2007

Recently, as MEMS and NEMS devices have been widely used in the various engineering applications, the characteristics of nanoscale systems are investigated in the limelight. However, as opposed to a macroscale system, the identification of the state of nanoscale systems is extremely hard because they can include only the order of $10^{3}\sim10^{5}$ molecules, which requires highly expensive and accurate experimental apparatus for an investigation. This limitations make the study on nanoscale system use computer simulations. Therefore, it is strongly required to identify the state of nanoscale system simulated in computer simulation. In these molecular dynamics(MD) study, we suggest that the potential energy of individual molecule can be used as criterion for defining the state of clusters or nanoscale systems. In addition, we compared the phase state from the potential energy with one from the radial distribution function(RDF) for verification. The comparison showed that the intermolecular potential energy can be used as a criteria distinguishing the phase state of nanoscale systems (This study will be published soon in the KSME transaction of the section B).

• Transactions of the Korean Society of Mechanical Engineers B
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• v.31 no.5
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• pp.435-447
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• 2007

Recently, as MEMS and NEMS devices have been widely used in the various engineering applications, the characteristics of nanoscale systems are investigated in the limelight. However, as opposed to a macroscale system, the identification of the state of nanoscale systems is extremely hard because they can include only the order of $10^3{\sim}10^5$ molecules, which requires highly expensive and accurate experimental apparatus for an investigation. This limitations make the study on nanoscale system use computer simulations. Therefore, it is strongly required to identify the state of nanoscale system simulated in computer simulation. In this molecular dynamics(MD) study, we suggest that the potential energy of individual molecule can be used as criterion for defining the state of clusters or nanoscale systems. In addition, we compared the phase state from the potential energy with one from the radial distribution function(RDF) for verification. The comparison showed that the intermolecular potential energy can be used as a criteria distinguishing the phase state of nanoscale systems.

• Journal of the Computational Structural Engineering Institute of Korea
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• v.18 no.2
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• pp.141-149
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• 2005

This paper deals with formulations of the energy equilibrium equation by an introduction of the algebraic description, quarternion, which meets conservations of system energy for the equation of motion. Then the equation is discretized to analyze the dynamits analysis of flexible multibody systems in such a way that the work done by the constrained force completely is eliminated. Meanwhile, Rodrigues parameters we used to express the finite rotation lot the proposed method. This method lot the initial essential step to a guarantee of developments of the 3D dynamical problem provides unconditionally stable conditions for the nonlinear problems through the numerical examples.

• Proceeding of EDISON Challenge
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• 2014.03a
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• pp.347-358
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• 2014

본 논문에서는 양자 역학적 분자 동역학(Quantum Mechanical/Molecular Mechanical-Molecular Dynamics, QM/MM-MD)을 통해 수용액에 녹아 있는 Potassium Thiocyanate의 dynamics를 연구했다. Umbrella sampling technique을 활용하여 association/dissociation에 해당하는 Free energy surface를 구했다. 두 개의 Free energy minimum이 녹아 있는 두 이온의 center of mass 사이의 거리가 $4{\AA}$일 때와 $5{\sim}6{\AA}$ 부근일 때 나타났으며 $4{\AA}$일 때 더 안정 했다. 본 논문에서는 $4{\AA}$일 때를 Contact Ion Pair(CIP) $6{\AA}$일 때를 Dissociation Ion Pair(DlP)라고 칭했다. 이 minimum들이 무엇인 지를 밝혀 내기 위해 추가 연구를 수행하였다. Free energy 상에서 가장 안정 할 때(CIP) solute인 Potassium thiocyanate의 구조를 살펴 봤더니 Potassium ion은 Thiocyanate ion의 Sulfur보다 Nitrogen side를 선호하였다. 그 원인을 알아보기 위해 salvation shell의 구조를 Radial distribution function을 통해 살펴 봤더니 물 분자가 Nitrogen보다 Sulfur와 더 강한 상호작용을 하고 있었다. 그로 인해 Potassium ion이 Nitrogen을 선호한단 결과가 나온 것이다. 한편, 두 번째 minimum은 물 분자가 Potassium 이온과 Thiocyanate 이온 사이에 flexible하게 bridging을 하는 구조였다. 또한 단순 양자 계산을 통해서도 비슷한 구조를 얻을 수 있었다. 그러나 QM 계산은 0K에서 수행하는 것이기 때문에 엔트로피 효과가 없는 계산이지만 본 연구는 온도 300K로 실제 용매와 가깝게 수행함으로써 고정되어 있는 구조가 아니라 엔트로피와 엔탈피가 균형적으로 존재하는 실제 용액 속에서의 구조를 처음으로 보여주는 것이다.

• Macromolecular Research
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• v.9 no.3
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• pp.129-142
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• 2001

To efficiently demonstrate the molecular motion, physical properties, and mechanical properties of polycarbonates, we studied the differences between bisphenol-A polycarbonate(BPA-PC) and tetramethyl bisphenol-A-polycarbonate(TMBPA-PC) using molecular modeling techniques. To investigate the conformations of BPA-PC and TMBPA-PC and the effect of the conformation on mechanical properties, we performed conformational energy calculation, molecular dynamics calculation, and stress-strain curves based on molecular mechanics method. From the result obtained from conformational energy calculations of each segment, the molecular motions of the carbonate and the phenylene group in BPA-PC were seen to be more vigorous and have lower restriction to mobility than those in TMBPA-PC, respectively. In addition, from the results of radial distribution function, velocity autocorrelation function, and power spectrum, BPA-PC appeared to have higher diffusion constant than TMBPA-PC and is easier to have various conformations because of the less severe restrictions in molecular motion. The result of stress-strain calculation for TMBPA-PC seemed to be in accordance with the experimental value of strain-to-failure ∼4%. From these results of conformational energy calculations of segments, molecular dynamics, and mechanical properties, it can be concluded that TMBPA-PC has higher modulus and brittleness than BPA-PC because the former has no efficient relaxation mode against the external deformations.

• Korean Journal of Air-Conditioning and Refrigeration Engineering
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• v.26 no.4
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• pp.169-174
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• 2014

Computational fluid dynamics simulation of an apartment underground elevator hall has been carried out to study the effect of dehumidifier locations on condensation problem. In Case 1, horizontal position of humidifier is studied. It is installed at entrance, center or the inside of the elevator hall. In Case 2, installation height is studied, one at 0 m and the other at 1.6 m above the floor. In Case 3, exposed and embedded dehumidifiers are compared for performance. The study shows that the entrance, top and exposed locations are more effective in reducing condensation.

• Bulletin of the Korean Chemical Society
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• v.31 no.10
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• pp.2903-2908
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• 2010

Protein S-nitrosation is common in cells under nitrosative stress. In order to model proteins with S-nitrosocysteine (CysSNO) residues, we first developed an Amber force field for S-nitrosoethanethiol (EtSNO) and then transferred it to CysSNO. Partial atomic charges for EtSNO and CysSNO were obtained by a restrained electrostatic potential approach to be compatible with the Amber-99 force field. The force field parameters for bonds and angles in EtSNO were obtained from a generalized Amber force field (GAFF) by running the Antechamber module of the Amber software package. The GAFF parameters for the CC-SN and CS-NO dihedrals were not accurate and thus determined anew. The CC-SN and CS-NO torsional energy profiles of EtSNO were calculated quantum mechanically at the level of B3LYP/cc-pVTZ//HF/6-$31G^*$. Torsional force constants were obtained by fitting the theoretical torsional energies with those obtained from molecular mechanics energy minimization. These parameters for EtSNO reproduced, to a reasonable accuracy, the corresponding torsional energy profiles of the capped tripeptide ACE-CysSNO-NME as well as their structures obtained from quantum mechanical geometry optimization. A molecular dynamics simulation of myoglobin with a CysSNO residue produced a well-behaved trajectory demonstrating that the parameters may be used in modeling other S-nitrosated proteins.

• International Journal of Fluid Machinery and Systems
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• v.4 no.1
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• pp.14-24
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• 2011

In this paper, design optimization for mixed-flow pump impellers and diffusers has been studied using a commercial computational fluid dynamics (CFD) code and DOE (design of experiments). We also discussed how to improve the performance of the mixed-flow pump by designing the impeller and diffuser. Geometric design variables were defined by the vane plane development, which indicates the blade-angle distributions and length of the impeller and diffusers. The vane plane development was controlled using the blade-angle in a fixed meridional shape. First, the design optimization of the defined impeller geometric variables was achieved, and then the flow characteristics were analyzed in the point of incidence angle at the diffuser leading edge for the optimized impeller. Next, design optimizations of the defined diffuser shape variables were performed. The importance of the geometric design variables was analyzed using $2^k$ factorial designs, and the design optimization of the geometric variables was determined using the response surface method (RSM). The objective functions were defined as the total head and the total efficiency at the design flow rate. Based on the comparison of CFD results between the optimized pump and base design models, the reason for the performance improvement was discussed.