• Tribology and Lubricants
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• 제32권1호
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• pp.9-17
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• 2016

Contact between solid surfaces is one of the most important factors that influence dynamic behavior in micro/nanoscale. Although numerous theories and experimental results on contact behavior have been proposed, a thorough investigation for nanomaterials is still not available owing to technical difficulties. Therefore, molecular dynamics simulation was performed to investigate the contact behavior of nanomaterials, and the application of conventional contact theories to nanoscale was assessed in this work. Particularly, the contact characteristics of cylindrical nanowires were examined via simulation and contact theories. For theoretical analysis, various contact models were utilized and work of adhesion, Hamaker constant and elastic modulus those are required for calculation of the models were obtained from both indentation simulation and tensile simulation. The contact area of the cylindrical nanowire was assessed directly through molecular dynamics simulation and compared with the results obtained from the theories. Determination of the contact area of the nanowires was carried out via simulation by counting each atom, which is within the equilibrium length. The results of the simulation and theoretical calculations were compared, and it was estimated that the discrepancy in the results calculated between the simulation and the theories was less than 10 except in the case of the smallest nanowires. As the result, it was revealed that contact models can be effectively utilized to assess the contact area of nanomaterials.

• Bulletin of the Korean Chemical Society
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• 제31권10호
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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.

• Coupled systems mechanics
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• 제6권1호
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• pp.41-54
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• 2017

Shape-memory alloys (SMA) have interesting behaviors and important mechanical properties due to the solid-solid phase transformation. These phenomena are dominated by the evolution of microstructures. In recent years, the microstructures in SMAs have been studied extensively and modeled using molecular dynamics (MD) simulations. However, it remains difficult to identify the crystal variants in the simulation results, which consist of large numbers of atoms. In the present work, a method is developed to identify the austenite phase and the monoclinic martensite crystal variants in MD results. The transformation matrix of each lattice is calculated to determine the corresponding crystal variant. Evolution of the volume fraction of the crystal variants and the microstructure in Ni-Ti SMAs under thermal and mechanical boundary conditions are examined. The method is validated by comparing MD-simulated interface normals with theoretical solutions. In addition, the results show that, in certain cases, the interatomic potential used in the current study leads to inconsistent monoclinic lattices compared with crystallographic theory. Thus, a specific modification is applied and the applicability of the potential is discussed.

• Coupled systems mechanics
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• 제3권4호
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• pp.329-344
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• 2014

In this work, quantum molecular dynamics simulations (QMD) are preformed to study the hydrogen molecules in three types of carbon nanostructures, $C_{60}$ fullerene, (5,5) and (9,0) carbon nanotubes and graphene layers. Interactions between hydrogen and the nanostructures is of importance to understand hydrogen storage for the development of hydrogen economy. The QMD method overcomes the difficulties with empirical interatomic potentials to model the interaction among hydrogen and carbon atoms in the confined geometry. In QMD, the interatomic forces are calculated by solving the Schrodinger's equation with the density functional theory (DFT) formulation, and the positions of the atomic nucleus are calculated with the Newton's second law in accordance with the Born-Oppenheimer approximation. It is found that the number of hydrogen atoms that is less than 58 can be stored in the $C_{60}$ fullerene. With larger carbon fullerenes, more hydrogen may be stored. For hydrogen molecules passing though the fullerene, a particular orientation is required to obtain least energy barrier. For carbon nanotubes and graphene, adsorption may adhere hydrogen atoms to carbon atoms. In addition, hydrogen molecules can also be stored inside the nanotubes or between the adjacent layers in graphite, multi-layer graphene.

• 한국자원식물학회:학술대회논문집
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• 한국자원식물학회 2020년도 추계국제학술대회
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• pp.14-14
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• 2020

In December 2019, the COVID-19 epidemic was discovered in Wuhan, China, and since has disseminated around the world impacting human health for millions. Herein, in-silico drug discovery approaches were utilized to identify potential candidates as Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) main protease (M^pro) inhibitors. We investigated several databases including natural and natural-like products (>100,000 molecules), DrugBank database (10,036 drugs), major metabolites isolated from daily used spices (32 molecules), and current clinical drug candidates for the treatment of COVID-19 (18 drugs). All tested compounds were prepared and screened using molecular docking techniques. Based on the calculated docking scores, the top ones from each project under investigation were selected and subjected to molecular dynamics (MD) simulations followed by molecular mechanics-generalized Born surface area (MM-GBSA) binding energy calculations. Combined long MD simulations and MM-GBSA calculations revealed the potent compounds with prospective binding affinities against M^pro. Structural and energetic analyses over the simulated time demonstrated the high stabilities of the selected compounds. Our results showed that 4-bis([1,3]dioxolo)pyran-5-carboxamide derivatives (natural and natural-like products database), DB02388 and Cobicistat (DB09065) (DrugBank database), salvianolic acid A (spices secondary metabolites) and TMC-310911 (clinical-trial drugs database) exhibited high binding affinities with SARS-CoV-2 M^pro. In conclusion, these compounds are up-and-coming anti-COVID-19 drug candidates that warrant further detailed in vitro and in vivo experimental estimations.

• Smart Structures and Systems
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• 제8권1호
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• pp.17-37
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• 2011

The microcantilever (MCL) sensor is one of the most promising platforms for next-generation label-free biosensing applications. It outperforms conventional label-free detection methods in terms of portability and parallelization. In this paper, an overview of recent advances in our understanding of the coupling between biomolecular interactions and MCL responses is given. A dual compact optical MCL sensing platform was built to enable biosensing experiments both in gas-phase environments and in solutions. The thermal bimorph effect was found to be an effective nanomanipulator for the MCL platform calibration. The study of the alkanethiol self-assembly monolayer (SAM) chain length effect revealed that 1-octanethiol ($C_8H_{17}SH$) induced a larger deflection than that from 1-dodecanethiol ($C_{12}H_{25}SH$) in solutions. Using the clinically relevant biomarker C-reactive protein (CRP), we revealed that the analytical sensitivity of the MCL reached a diagnostic level of $1{\sim}500{\mu}g/ml$ within a 7% coefficient of variation. Using grazing incident x-ray diffractometer (GIXRD) analysis, we found that the gold surface was dominated by the (111) crystalline plane. Moreover, using X-ray photoelectron spectroscopy (XPS) analysis, we confirmed that the Au-S covalent bonds occurred in SAM adsorption whereas CRP molecular bindings occurred in protein analysis. First principles density functional theory (DFT) simulations were also used to examine biomolecular adsorption mechanisms. Multiscale modeling was then developed to connect the interactions at the molecular level with the MCL mechanical response. The alkanethiol SAM chain length effect in air was successfully predicted using the multiscale scheme.

• 대한화학회지
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• 제34권3호
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• pp.232-238
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• 1990

Zn의 생화학적 역할을 연구하기 위하여, 간단한 모델시스템을 설정하였다. 즉, Zn가 리간드인 $OH_2나 NH_3$와 배위결합을 이루거나 carboxypeptidase A (CPA)의 기질에 해당하는 펩티드의 O=C-와 배위결합을 할 때, 그 기하학적 구조 및 net atomic charge의 변화를 조사하였다. Double Zeta basis set를 사용한 ab initio HF-SCF 계산에 의하면, Zn는 이들 리간드의 O-H, N-H, O=C-를 매우 polar하게 만든다. 특히, 펩티드의 탄소는 친전자성이 매우 증가하여, nucleophile의 공격을 용이하게 받을 수 있을 것으로 예측되었다. 또한, CPA에서 Zn 주위에 있는 리간드의 분자배위 상태를 조사하기 위하여, CPA+glycyltyrosine complex에 관한 molecular mechanics방법을 적용하였다. 이 결과를 X-ray 결과와 비교하였을 때, Zn는 4배위 결합 이외에 물분자도 관여할 것으로 예측된다.

• Bulletin of the Korean Chemical Society
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• 제35권5호
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• pp.1479-1484
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• 2014

Based on the full optimized molecular geometric structures at B3LYP/cc-pvtz method, a new designed compound, 4,6,8-trinitro-4,5,7,8-tetrahydro-6H-furazano[3,4-f ]-1,3,5-triazepine was investigated in order to look for high energy density compounds (HEDCs). The analysis of the molecular structure indicates that the seven-membered ring adopts chair conformation and there exist intramolecular hydrogen bond interactions. IR spectrum and heat of formation (HOF) were predicted. The detonation velocity and pressure were evaluated by using Kamlet-Jacobs equations based on the theoretical density and condensed HOF. The bond dissociation energies and bond orders for the weakest bonds were analyzed to investigate the thermal stability of the title compound. The results show that $N_1-N_6$ bond is the trigger bond. The crystal structure obtained by molecular mechanics belongs to $Pna2_1$ space group, with lattice parameters Z = 4, a = 15.3023 ${\AA}$, b = 5.7882 ${\AA}$, c = 11.0471 ${\AA}$, ${\rho}=2.06gcm^{-3}$. In addition, the analysis of frontier molecular orbital shows the title compound has good stability and high chemical hardness.

• 한국전산구조공학회논문집
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• 제26권5호
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• pp.393-399
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• 2013

본 논문은 그래핀의 모드 I 균열 진전에 대한 분자동역학 해석과 수치보조장을 사용하는 영역 투영 방법의 역문제 해석 방법을 결합하여 균열 선단 응집 법칙을 평가하는 효율적인 방법을 제시하고 있다. 그래핀의 균열 선단 응집 법칙을 결정하는 것은 균열 선단에서 멀리 떨어진 영역의 변위를 사용하여 균열 면에서 미지의 응집 트랙션과 열림 변위를 구하는 역문제를 해석해야 하는데 상호 J-적분과 M-적분의 경로 보존성과 효율적인 수치보조장을 사용하는 방법을 적용하였다. 분자동역학 해석에서 원자 변위를 유한요소 절점 변위로 이동최소자승법을 사용하여 근사하였으며 안정적인 역문제 해석을 통하여 원자 단위의 거동을 연속체 해석으로 연결시킬 수 있는 새로운 방법을 보여주었다.

• 한국전산유체공학회:학술대회논문집
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• 한국전산유체공학회 2005년도 추계 학술대회논문집
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• pp.11-19
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• 2005

First, methods of numerical analysis of gas-particle flows is classified into micro, meso and macro scale approaches based on the concept of multi-scale mechanics. Next, the explanation moves on to discrete particle simulation where motion of individual particles is calculated numerically using the Newtonian equations of motion. The author focuses on the cases where particle-to-particle interaction has significant effects on the phenomena. Concerning the particle-to-particle interaction, two cases are considered: the one is collision-dominated flows and the other is the contact-dominated flows. To treat this interaction mathematically, techniques named DEM(Distinct Element Method) or DSMC (Direct Simulation Monte Carlo) have been developed DEM, which has been developed in the field of soil mechanics, is useful for the contact -dominated flows and DSMC method, developed in molecular gas flows, is for the collision-dominated flows. Combining DEM or DSMC with CFD (computer fluid dynamics), the discrete particle simulation becomes a more practical tool for industrial flows because not only the particle-particle interaction but particle-fluid interaction can be handled. As examples of simulations, various results are shown, such as hopper flows, particle segregation phenomena, particle mixing in a rotating drum, dense phase pneumatic conveying, spouted bed, dense phase fluidized bed, fast circulating fluidized bed and so on.