• 대한기계학회논문집B
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• 제36권8호
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• pp.873-876
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• 2012

Ionic Liquids (ILs) 는 표준상태에서 액체이온으로 존재하는 물질로 여러 가지 방법으로 다양한 특성을 띄게 할 수 있다. 이런 성질을 적절하게 이용하여 계면활성제 등 다양한 분야로의 응용이 가능하다. ILs의 한 종류인 1-10-alkyl-3-methylimidazolium bromide([C10mim][Br]) 은 특정한 환경에서 양친매성을 가진다. 이번 논문에서 우리는 분자동역학을 이용하여 수용액에서의 [C10mim][Br]의 응집 거동에 대한 연구를 진행하였다. 정준모듬(canonical ensemble)을 이용하여 모사 간 시스템의 부피와 온도를 일정하게 유지시키고 5ns 동안의 전산모사를 통하여 얻은 radial distribution function(RDF)을 이용하여 [C10mim][Br]과 물 분자간의 상호작용 및 그 분포의 특성에 대하여 논의하였다. 분자동역학적 계산을 위하여 LAMMPS 코드를 사용하였고, VMD 코드를 이용하여 후처리(post processing)을 진행하였다.

• 멤브레인
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• 제25권2호
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• pp.162-170
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• 2015

본 연구에서는 다양한 아민기를 가지는 폴리이미드 소재 및 분리막을 제조하여 그들의 구조의 변화에 따른 기체 투과도를 측정하였으며 동력학(Molecular dynamics; MD) 기술을 이용하여 해당 기체의 시간의 변화에 따른 위치와 속도를 계산하여, 기체분자의 동적 특성을 분석하는데 활용하였다. 투과도 측정결과 합성된 고분자 소재의 경우 고분자 내의 free volume을 증가시키는 치환기를 도입시켰을 경우 기체투과도가 증가되었으나 rigid한 구조가 도입된 폴리이미드는 투과도가 감소되는 경향을 확인하였다. 또한 분자동력학 시뮬레이션을 이용하여 기체투과거동 변화를 분석한 결과 실제 기체투과도 측정결과와 유사한 결과를 나타냄을 확인할 수 있었다.

• 터널과지하공간
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• 제10권1호
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• pp.70-79
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• 2000

입자수, 압력, 온도일정의 앙상블(NPT-ensemble) 분자동력학(MD) 시뮬레이션을 이용하여 300$^{\circ}$K에서 $\alpha$-quartz의 결정축에 따른 일축압축강도를 계산하고, 자연산 $\alpha$-quartz 단결정 코아를 제작하여 일축압축강도시험을 실시하였다. $\alpha$-quartz 단결정 코아에 대한 일축압축시험에서 측정된 결과에 의하면 재하 방향이 c축에 평행한 경우가 수직인 경우보다 높은 강도를 나타내지만, MD 시뮬레이션에서 계산된 완전무결함 $\alpha$-quartz의 경우 이와 반대의 결과를 보이고 있다. 두 경우 모두 재하방향에 따른 강도 이방성을 보이고 있으나, 그 이유는 서로 다르다. MD 시뮬레이션에 의해 계산된 무결함 $\alpha$-quartz의 강도 이방성은 결정구조의 차이에 기인하는 것으로 사료된다. 이에 반해 일축압축시험을 통해 측정된 $\alpha$-quartz의 강도 이방성은 결정성장과정에서 생기는 주상 미세결함에 의해 영향을 받는다.

• Composites Research
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• 제37권1호
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• pp.32-39
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• 2024

고체수소저장은 수소 기반 경제 발전과 에너지 저장 기술 혁신의 핵심 주제로 부각되고 있다. 이러한 저장 방식은 압축 및 액화수소 저장 등 기존 방식에 비해 안전성과 저장 및 운용 효율성 측면에서 우수한 특성을 보여주고 있다. 본 연구에서는 다양한 구조적 설계 요소 별로 나노튜브 표면에서의 고체수소저장 성능을 평가하고자 한다. 본 연구는 나노튜브의 저장 메커니즘을 밝히고자 분자 역학 시뮬레이션(MD)을 도입하여 수행되었다. 본 연구의 시뮬레이션에는 다양한 직경, 다중벽 구조(MWNT), 단일벽 구조(SWNT)의 탄소나노튜브(CNT) 및 붕소-질소 나노튜브(BNNT)가 도입되어 진행되었다. 방사형 밀도 함수(RDF)를 통해 다양한 조건에서 수소의 저장 및 효과적인 방출을 분석한 결과, 반경 감소와 이중벽 구조가 고체 수소 저장을 높이는 데 기여하는 것으로 나타났다. 또한, 붕소-질소 나노튜브의 수소 저장 용량은 탄소 나노튜브에 비해 낮게 측정되었지만, 유효 수소 저장 측면에서는 탄소 나노튜브를 훨씬 능가하는 것으로 나타났다.

• Bulletin of the Korean Chemical Society
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• 제31권9호
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• pp.2581-2587
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• 2010

Nitration of tyrosine and tryptophan residues is common in cells under nitrative stress. However, physiological consequences of protein nitration are not well characterized on a molecular level due to limited availability of the 3D structures of nitrated proteins. Molecular dynamics (MD) simulation can be an alternative tool to probe the structural perturbations induced by nitration. In this study we developed molecular mechanics parameters for 3-nitrotyrosine (NIY) and 6-nitrotryptophan (NIW) that are compatible with the AMBER-99 force field. Partial atomic charges were derived by using a multi-conformational restrained electrostatic potential (RESP) methodology that included the geometry optimized structures of both $\alpha$- and $\beta$-conformers of a capped tripeptide ACE-NIY-NME or ACE-NIW-NME. Force constants for bonds and angles were adopted from the generalized AMBER force field. Torsional force constants for the proper dihedral C-C-N-O and improper dihedral C-O-N-O of the nitro group in NIY were determined by fitting the torsional energy profiles obtained from quantum mechanical (QM) geometry optimization with those from molecular mechanical (MM) energy minimization. Force field parameters obtained for NIY were transferable to NIW so that they reproduced the QM torsional energy profiles of ACE-NIW-NME accurately. Moreover, the QM optimized structures of the tripeptides containing NIY and NIW were almost identical to the corresponding structures obtained from MM energy minimization, attesting the validity of the current parameter set. Molecular dynamics simulations of thioredoxin nitrated at the single tyrosine and tryptophan yielded well-behaved trajectories suggesting that the parameters are suitable for molecular dynamics simulations of a nitrated protein.

• Genomics & Informatics
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• 제21권1호
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• pp.9.1-9.13
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• 2023

Matrix metalloproteinase-9 (MMP-9) is a zinc and calcium-dependent proteolytic enzyme involved in extracellular matrix degradation. Overexpression of MMP-9 has been confirmed in several disorders, including cancers, Alzheimer's disease, autoimmune diseases, cardiovascular diseases, and dental caries. Therefore, MMP-9 inhibition is recommended as a therapeutic strategy for combating various diseases. Cinnamic acid derivatives have shown therapeutic effects in different cancers, Alzheimer's disease, cardiovascular diseases, and dental caries. A computational drug discovery approach was performed to evaluate the binding affinity of selected cinnamic acid derivatives to the MMP-9 active site. The stability of docked poses for top-ranked compounds was also examined. Twelve herbal cinnamic acid derivatives were tested for possible MMP-9 inhibition using the AutoDock 4.0 tool. The stability of the docked poses for the most potent MMP-9 inhibitors was assessed by molecular dynamics (MD) in 10 nanosecond simulations. Interactions between the best MMP-9 inhibitors in this study and residues incorporated in the MMP-9 active site were studied before and after MD simulations. Cynarin, chlorogenic acid, and rosmarinic acid revealed a considerable binding affinity to the MMP-9 catalytic domain (ΔG_binding < -10 kcal/ mol). The inhibition constant value for cynarin and chlorogenic acid were calculated at the picomolar scale and assigned as the most potent MMP-9 inhibitor from the cinnamic acid derivatives. The root-mean-square deviations for cynarin and chlorogenic acid were below 2 Å in the 10 ns simulation. Cynarin, chlorogenic acid, and rosmarinic acid might be considered drug candidates for MMP-9 inhibition.

• Bulletin of the Korean Chemical Society
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• 제32권11호
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• pp.4027-4034
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• 2011

$CaCO_3$ crystalline structures having novel assemblies were in situ fabricated as analogs of naturally occurring proteins and polysaccharides for biomineralization. The calcite crystal was mineralized in a poly(vinyl alcohol)-$Ca^{2+}$ complex film immersed in a $Na_2CO_3$ solution containing poly(aspartic acid). The morphology and size of the $CaCO_3$ crystals were tuned by varying the concentration of poly(aspartic acid). The mechanisms of their nucleation orientation and formation were investigated experimentally and through molecular dynamics (MD) simulations in order to obtain a better understanding of the interactions between the polymers and the crystal at the molecular level. Both the MD results and experimental results indicate that the interaction between PVA and calcite mainly depends on the concentration of the polymer. The novel approach proposed herein for the fabrication of inorganic crystalline assembly structures can be used to fabricate precise crystalline structures.

• 대한기계학회:학술대회논문집
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• 대한기계학회 2003년도 춘계학술대회
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• pp.1366-1371
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• 2003

Molecular dynamics (MD) simulations are conducted to investigate the thermophysical characteristics and the stability of liquid threads for various conditions. A cylindrical thread in the simulation domain is made of Lennard-Jones molecules. The surface tension of liquid threads can be determined from local densities, local normal and transverse components of the pressure force. In order to understand the effects of thread radii on surface tensions, the Tolman equation is modified on the basis of the cylindrical coordinates for prediction of surface tensions. Surface tensions calculated from the MD simulation agree with the prediction from the modified Tolman equation. In addition, surface tensions decrease linearly with increasing system temperature. For a binary system, the surface tension decreased linearly compared to that for a pure system with increasing binary ratio of solute molecules which have relatively large value of the affinity coefficient. For a fixed binary ratio, the surface tension increased slightly with the affinity coefficient and the maximum value appear around where the affinity coefficient is 1.5 and decreased rapidly for upper value of 1.5. In addition, the critical wavelengths of perturbations are proven to be directly proportional to the equimolar dividing radii of the liquid threads.

• 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.

• Bulletin of the Korean Chemical Society
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• 제25권6호
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• pp.838-842
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• 2004

Amyloid peptide (A${\beta}$) is the major component of senile plaques found in the brain of patient of Alzheimer's disease. ${\beta}$-amyloid peptide (25-35) (A${\beta}$25-35) is biologically active fragment of A${\beta}$. The three-dimensional structure of A${\beta}$25-35 in aqueous solution with 50% (vol/vol) TFE determined by NMR spectroscopy previously adopts an ${\alpha}$-helical conformation from $Ala^{30}$ to $Met^{35}$. It has been proposed that A${\beta}$(25-35) exhibits pH- and concentration-dependent ${\alpha}-helix{\leftrightarrow}{\beta}$sheet transition. This conformational transition with concomitant peptide aggregation is a possible mechanism of plaque formation. Here, in order to gain more insight into the mechanism of ${\alpha}$-helix formation of A${\beta}$25-35 peptide by TFE, which particularly stabilizes ${\alpha}$-helical conformation, we studied the secondary-structural elements of A${\beta}$25-35 peptide by molecular dynamics simulations. Secondary structural elements determined from NMR spectroscopy in aqueous TFE solution are preserved during the MD simulation. TFE/water mixed solvent has reduced capacity for forming hydrogen bond to the peptide compared to pure water solvent. TFE allows A${\beta}$25-35 to form bifurcated hydrogen bonds to TFE as well as to residues in peptide itself. MD simulation in this study supports the notion that TFE can act as an ${\alpha}$-helical structure forming solvent.