• Proceeding of EDISON Challenge
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• 2015.03a
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• pp.151-155
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• 2015

The molecular interactions between the nucleic acid bases and water molecules are important in organism. Despite Adenine-Thymine Hoogsteen base pair and Guanine-Cytosine Watson-Crick base pair have been demonstrated to be most stable in a gas phase, the effect of water on the stability of these base pairs remains elusive. Here we report the structural and thermodynamic characteristics on possible Adenine-Thymine and Guanine-Cytosine base pairs in a gas phase as well as in an aqueous phase by using quantum mechanical method and statistical mechanical calculations. First, we optimized the direct base-pair interaction energies of four Adenine-Thymine base pairs (Hoogsteen base pair, reverse Hoogsteen base pair, Watson-Crick base pair, and reverse Watson-Crick base pair) and three Guanine-Cytosine base pairs (GC1 base pair, GC2 base pair, and Watson Crick base pair) in a gas phase at the $B3LYP/6-31+G^{**}$ level. Then, the effect of solvent was quantified by the electronic reorganization energy and the solvation free energy by statistical mechanical calculations. Thereby, we discuss the effect of water on the stability of Adenine-Thymine and Guanine-Cytosine base pairs, and argue why Adenine-Thymine Watson-Crick base pair and Guanine-Cytosine Watson-Crick base pair are most stable in an aqueous environment.

• Advances in nano research
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• v.5 no.2
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• pp.141-169
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• 2017

In this paper, a nanobeam connected to a rotating molecular hub is considered. The vibration behavior of rotating functionally graded nanobeam based on Eringen's nonlocal theory and Euler-Bernoulli beam model is investigated. Furthermore, axial preload and porosity effect is studied. It is supposed that the material attributes of the functionally graded porous nanobeam, varies continuously in the thickness direction according to the power law model considering the even distribution of porosities. Porosity at the nanoscopic length scale can affect on the rotating functionally graded nanobeams dynamics. The equations of motion and the associated boundary conditions are derived through the Hamilton's principle and generalized differential quadrature method (GDQM) is utilized to solve the equations. In this paper, the influences of some parameters such as functionally graded power (FG-index), porosity parameter, axial preload, nonlocal parameter and angular velocity on natural frequencies of rotating nanobeams with pure ceramic, pure metal and functionally graded materials are examined and some comparisons about the influence of various parameters on the natural frequencies corresponding to the simply-simply, simplyclamped, clamped-clamped boundary conditions are carried out.

• BMB Reports
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• v.56 no.3
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• pp.184-189
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• 2023

Ovarian cancer (OC) is the most common gynecological malignancy worldwide, and chemoresistance occurs in most patients, resulting in treatment failure. A better understanding of the molecular processes underlying drug resistance is crucial for development of efficient therapies to improve OC patient outcomes. Circular RNAs (circRNAs) and ferroptosis play crucial roles in tumorigenesis and resistance to chemotherapy. However, little is known about the role(s) of circRNAs in regulating ferroptosis in OC. To gain insights into cisplatin resistance in OC, we studied the ferroptosis-associated circRNA circSnx12. We evaluated circSnx12 expression in OC cell lines and tissues that were susceptible or resistant to cisplatin using quantitative real-time PCR. We also conducted in vitro and in vivo assays examining the function and mechanism of lnc-LBCSs. Knockdown of circSnx12 rendered cisplatin-resistant OC cells more sensitive to cisplatin in vitro and in vivo by activating ferroptosis, which was at least partially abolished by downregulation of miR-194-5p. Molecular mechanics studies indicate that circSnx12 can be a molecular sponge of miR-194-5p, which targets SLC7A11. According to our findings, circSnx12 ameliorates cisplatin resistance by blocking ferroptosis via a miR-194-5p/SLC7A11 pathway. CircARNT2 may thus serve as an effective therapeutic target for overcoming cisplatin resistance in OC.

• Bulletin of the Korean Chemical Society
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• v.29 no.8
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• pp.1499-1504
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• 2008

Pyrazine derivatives bind to b-RAF receptor which is important in cancer therapy. The ligand-receptor interactions have been studied by comparative molecular field analysis (CoMFA) and molecular docking methods. Applying conventional ligand-based alignment schemes for the whole set was not successful. However, QM and DFT results suggested that some ligands have electrostatic interaction while others have steric interactions. On the basis of these results, we divided the dataset into two subsets. Electrostatic effect was found to be important in one set while steric effect for the other. Best docking modes were obtained for each subset based on the available crystal structure. These receptor-guided CoMFA models propose an interesting possibility which is difficult to obtain otherwise. i.e., in one binding mode the electrostatic interaction plays a key role for one subset ($q^2$ = 0.46, $r^2$ = 0.98), while in another binding mode steric effect is important with another subset ($q^2$ = 0.43, $r^2$ = 0.74).

• Interaction and multiscale mechanics
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• v.4 no.3
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• pp.173-185
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• 2011

A multiscale modeling scheme that addresses the influence of the nanoparticle size in nanocomposites consisting of nano-sized spherical particles embedded in a polymer matrix is presented. A micromechanics-based constitutive model for nanoparticle-reinforced polymer composites is derived by incorporating the Eshelby tensor considering the interface effects (Duan et al. 2005a) into the ensemble-volume average method (Ju and Chen 1994). A numerical investigation is carried out to validate the proposed micromechanics-based constitutive model, and a parametric study on the interface moduli is conducted to investigate the effect of interface moduli on the overall behavior of the composites. In addition, molecular dynamics (MD) simulations are performed to determine the mechanical properties of the nanoparticles and polymer. Finally, the overall elastic moduli of the nanoparticle-reinforced polymer composites are estimated using the proposed multiscale approach combining the ensemble-volume average method and the MD simulation. The predictive capability of the proposed multiscale approach has been demonstrated through the multiscale numerical simulations.

• Coupled systems mechanics
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• v.1 no.3
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• pp.269-283
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• 2012

In the present paper, a multilevel approach for the local nanobuckling analysis of carbon nanotube (CNT) based composite materials is proposed and described. The approach comprises four levels, all of them at nanoscale. The first level aims to propose the potential that describes the interatomic forces between carbon atoms. In the second level, molecular dynamics simulations are performed to extract the elastic properties of the CNT. The third level aims to determine the stiffness of the material that surrounds the CNT (matrix), using the annular membrane analysis. In the fourth level, finite strip analysis of the CNT elastically restrained by the matrix is performed to calculate the critical strain at which the CNT buckles locally. In order to achieve accurate results and take the CNT-matrix interaction into account, the $3^{rd}$ and $4^{th}$ steps may be repeated iteratively until convergence is achieved. The proposed multilevel approach is applied to several CNTs embedded in a cylindrical representative volume element and illustrated in detail. It shows that (i) the interaction between the CNT and the matrix should be taken into account and (ii) the buckling at nanoscale is sensitive to several types of local buckling modes.

• Proceeding of EDISON Challenge
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• 2013.04a
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• pp.89-100
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• 2013

생물정보학의 다양한 이론적 내용과 계산적 방법들이 갈수록 전문화 되어짐에 따라 신약 개발, 신 물질 합성, 단백질의 구조 예측 등 다양한 분야에서 필요성이 커져가고 있다. 이 중 molecular docking 기술은 단백질과 특정 분자간의 결합 형태를 분자 모델링 기법을 통해 알아내는 방법이며 신약개발 연구에 큰 영향을 미치고 있다. Molecular docking을 통하여 분자간의 결합 형태를 예측하는 과정에서 Protein-ligand complex의 정확한 에너지 측정을 가능하게 하는 scoring function이 필요하다. 그런데 본 연구에서 사용한 B-Raf kinase protein 은 active site 부분에서 ligand와 receptor 간에 aromatic ring로 인한 ${\pi}-{\pi}$ interaction이 정확한 에너지 계산을 어렵게 한다. 이러한 ${\pi}-{\pi}$ interaction 부분의 에너지를 정확하게 계산하기 위해 양자역학 계산을 실시하였다. Active site 부분에서 ligand와 receptor에서 발생하는 각각 다른 5개의 ${\pi}-{\pi}$ interaction 구조를 준비하여 Gaussian을 통해 양자역학 에너지를 계산하였다. 그리고 이러한 결과 값들이 ligand의 활성 값과 어떤 상관관계를 갖는지 살펴보았다. 그 결과 ${\pi}-{\pi}$ interaction을 양자역학으로 계산한 값이 그렇지 않은 것보다 더 좋은 상관관계를 보여주었다. 이는 특별한 구조의 영향으로 ligand와 receptor 간의 결합에너지를 정확하게 계산하기 어려운 문제에서 양자역학을 적용할 경우 더욱 좋은 결과값을 얻을 수 있었다. 또한 이러한 데이터가 신 물질 개발이나 신약 개발 등의 다양한 분야에서 계산화학 방법이 신뢰성을 얻는데 도움 될 수 있다고 생각된다.

• Multiscale and Multiphysics Mechanics
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• v.1 no.1
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• pp.53-64
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• 2016

Amyloid fibrils have recently been considered as an interesting material, since they exhibit the excellent mechanical properties such as elastic modulus in the order of 10 GPa, which is larger than that of other protein materials. Despite recent findings of these excellent mechanical properties for amyloid fibrils, it has not been fully understood how these excellent mechanical properties are achieved. In this work, we have studied the nanomechanical deformation behaviors and properties of amyloid fibrils such as their elastic modulus as well as fracture strength, by using atomistic simulations, particularly steered molecular dynamics simulations. Our simulation results suggest the important role of the length of amyloid fibrils in their mechanical properties such that the fracture force of amyloid fibril is increased when the fibril length decreases. This length scale effect is attributed to the rupture mechanisms of hydrogen bonds that sustain the fibril structure. Moreover, we have investigated the effect of boundary condition on the nanomechanical deformation mechanisms of amyloid fibrils. It is found that the fracture force is critically affected by boundary condition. Our study highlights the crucial role of both fibril length and boundary condition in the nanomechanical properties of amyloid fibrils.

• Genomics & Informatics
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• v.20 no.3
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• pp.33.1-33.17
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• 2022

Nervous necrosis virus (NNV) is a deadly infectious disease that affects several fish species. It has been found that the NNV utilizes grouper heat shock cognate protein 70 (GHSC70) to enter the host cell. Thus, blocking the virus entry by targeting the responsible protein can protect the fishes from disease. The main objective of the study was to evaluate the inhibitory potentiality of 70 compounds of Azadirachta indica (Neem plant) which has been reported to show potential antiviral activity against various pathogens, but activity against the NNV has not yet been reported. The binding affinity of 70 compounds was calculated against the GHSC70 with the docking and molecular dynamics (MD) simulation approaches. Both the docking and MD methods predict 4 (PubChem CID: 14492795, 10134, 5280863, and 11119228) inhibitory compounds that bind strongly with the GHSC70 protein with a binding affinity of -9.7, -9.5, -9.1, and -9.0 kcal/mol, respectively. Also, the ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties of the compounds confirmed the drug-likeness properties. As a result of the investigation, it may be inferred that Neem plant compounds may act as significant inhibitors of viral entry into the host cell. More in-vitro testing is needed to establish their effectiveness.

• Proceedings of the Korean Society of Tribologists and Lubrication Engineers Conference
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• 2002.10b
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• pp.45-46
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• 2002

Based on the fact that the lubricant molecular is with a chain structure, the physical and mathematical models for the thin film lubrication are set up after the analysis of relationship of the chain length and the film thickness is carried out. The basic equations of fluid mechanics with the rotation terms are used to derive the equivalent Reynolds equation. The results show that the load carrying capacity has a significant increase while the length effect is considered. Finally, the calculated results are compared with the experimental results and they have the same tendency.