• Asia-pacific Journal of Multimedia Services Convergent with Art, Humanities, and Sociology
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• v.8 no.6
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• pp.939-946
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• 2018

In this work, we present simple schematics for a three-terminal graphene-based nanoelectromechanical switch with the vertical electrode, and we investigated their operational dynamics via classical molecular dynamics simulations. The main structure is both the vertical pin electrode grown in the center of the square hole and the graphene covering on the hole. The potential difference between the bottom gate of the hole and the graphene of the top cover is applied to deflect the graphene. By performing classical molecular dynamic simulations, we investigate the nanoelectromechanical properties of a three-terminal graphene-based nanoelectromechanical switch with vertical pin electrode, which can be switched by the externally applied force. The elastostatic energy of the deflected graphene is also very important factor to analyze the three-terminal graphene-based nanoelectromechanical switch. This simulation work explicitly demonstrated that such devices are applicable to nanoscale sensors and quantum computing, as well as ultra-fast-response switching devices.

• Composites Research
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• v.36 no.5
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• pp.369-376
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• 2023

This study focuses on investigating the influence of epoxy polymer crosslinking density, a crucial aspect in composite material matrices, on the yield surface using molecular dynamics simulations. Our approach involved generating epoxy models with diverse crosslinking densities and subjecting them to both uniaxial and multiaxial deformation simulations, accounting for the elasto-plastic deformation behaviors. Through this, we obtained key mechanical parameters including elastic modulus, yield point, and strain hardening coefficient, all correlated with crosslinking conversion ratios. A particularly noteworthy finding is the rapid expansion of the yield surface in the biaxial compression region with increasing crosslinking ratios, compared to the uniaxial tensile region. This unique behavior led to observable yield surface variations, indicating a significant pressure-dependent relationship of the yield surface considering plastic strain and crosslinking conversion ratio. These results contribute to a deeper understanding of the complex interplay between crosslinking density and plastic mechanical response, especially in the aspect of multiaxial deformation behaviors.

• Composites Research
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• v.37 no.1
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• pp.32-39
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• 2024

Solid-state hydrogen storage is gaining prominence as a crucial subject in advancing the hydrogen-based economy and innovating energy storage technology. This storage method shows superior characteristics in terms of safety, storage, and operational efficiency compared to existing methods such as compression and liquefied hydrogen storage. In this study, we aim to evaluate the solid hydrogen storage performance on the nanotube surface by various structural design factors. This is accomplished through molecular dynamics simulations (MD) with the aim of uncovering the underlying ism. The simulation incorporates diverse carbon nanotubes (CNTs) - encompassing various diameters, multi-walled structures (MWNT), single-walled structures (SWNT), and boron-nitrogen nanotubes (BNNT). Analyzing the storage and effective release of hydrogen under different conditions via the radial density function (RDF) revealed that a reduction in radius and the implementation of a double-wall configuration contribute to heightened solid hydrogen storage. While the hydrogen storage capacity of boron-nitrogen nanotubes falls short of that of carbon nanotubes, they notably surpass carbon nanotubes in terms of effective hydrogen storage capacity.

• Genomics & Informatics
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• v.21 no.1
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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.

• Proceedings of the Membrane Society of Korea Conference
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• 2003.07a
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• pp.57-59
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• 2003

Molecular dynamics simulations have been performed on $\beta$-cyclodextrins octyl-derivative (b-CD) encapsulated into a polymer matrix of glassy poly(ether ether ketone) (PEEK-WC) material to investigate the effects of the complexation of p-nitrophenilacetate and naringin molecules with the aim to study the recognition properties of b-CD.

• Nuclear Engineering and Technology
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• v.41 no.1
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• pp.39-52
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• 2009

Theory-based models and high performance simulations are briefly reviewed starting with atomistic methods, such as Electronic Structure calculations, Molecular Dynamics, and Monte Carlo, continuing with meso-scale methods, such as Dislocation Dynamics and Phase Field, and ending with continuum methods that include Finite Element and Finite Volume. Special attention is paid to relating thermo-mechanical and chemical properties of the fuel to reactor parameters. By inserting atomistic models of point defects into continuum thermo-chemical calculations, a model of oxygen diffusivity in $UO_{2+x}$ is developed and used to predict point defect concentrations, oxygen diffusivity, and fuel stoichiometry at various temperatures and oxygen pressures. The simulations of coupled heat transfer and species diffusion demonstrate that including the dependence of thermal conductivity and density on composition can lead to changes in the calculated centerline temperature and thermal expansion displacements that exceed 5%. A review of advanced nuclear fuel performance codes reveals that the many codes are too dedicated to specific fuel forms and make excessive use of empirical correlations in describing properties of materials. The paper ends with a review of international collaborations and a list of lessons learned that includes the importance of education in creating a large pool of experts to cover all necessary theoretical, experimental, and computational tasks.

• Genomics & Informatics
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• v.15 no.4
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• pp.142-146
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• 2017

More effective production of human insulin is important, because insulin is the main medication that is used to treat multiple types of diabetes and because many people are suffering from diabetes. The current system of insulin production is based on recombinant DNA technology, and the expression vector is composed of a preproinsulin sequence that is a fused form of an artificial leader peptide and the native proinsulin. It has been reported that the sequence of the leader peptide affects the production of insulin. To analyze how the leader peptide affects the maturation of insulin structurally, we adapted several in silico simulations using 13 artificial proinsulin sequences. Three-dimensional structures of models were predicted and compared. Although their sequences had few differences, the predicted structures were somewhat different. The structures were refined by molecular dynamics simulation, and the energy of each model was estimated. Then, protein-protein docking between the models and trypsin was carried out to compare how efficiently the protease could access the cleavage sites of the proinsulin models. The results showed some concordance with experimental results that have been reported; so, we expect our analysis will be used to predict the optimized sequence of artificial proinsulin for more effective production.

• Bulletin of the Korean Chemical Society
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• v.28 no.10
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• pp.1689-1696
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• 2007

Equilibrium molecular dynamics (EMD) simulations are used to evaluate the transport coefficients of argonkrypton mixtures at two liquid states (state A: 94.4 K and 1 atm; state B: 135 K and 39.5 atm) via modified Green-Kubo formulas. The composition dependency of the volume at state A obeys close to the linear model for ideal liquid mixture, while that at state B differs from the linear model probably due to the high pressure. The radial distribution functions for the Ar-Kr mixture (x = 2/3) show a mixing effect: the first peak of g11 is higher than that of g(r) for pure Ar and the first peak of g22 is lower than that of g(r) for pure Kr. An exponential model of engineering correlation for diffusion coefficient (D) and shear viscosity (η) is superior to the simple linear model for ideal liquid mixtures. All three components of thermal conductivity (λpm, λtm, and λti) at state A and hence the total thermal conductivity decrease with the increase of x. At state B, the change in λtm is dominant over those in λpm and λti, and hence the total thermal conductivity decrease with the increase of x.

• Journal of Advanced Marine Engineering and Technology
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• v.29 no.1
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• pp.60-67
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• 2005

Generally. in the molecular dynamics simulations. the Verlet neighboring list algorithm is used for the reduction of a simulation time On the other hand. the application of the Verlet neighboring list forces the time evolution of a simulation system to follow an unrealistic path in a phase space. In equilibrium state, it does not matter with the simulation results because the individual molecule's motion is originally random and any effect due to a small deviation from a real time evolution can be completely ignored. However, if an unsteady state is involved. such a deviation may significantly affect to the results. That is, there is a Possibility that the simulation results Provide ones with any misleading data In this study we evaluated the effect due to the Verlet neighboring list in performing the simulation of a non-equilibrium state and suggested the method to avoid it.

• Journal of the Korean Ceramic Society
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• v.44 no.3 s.298
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• pp.175-181
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• 2007

Molecular dynamics simulation (MD) of $(62-x)CaO{\cdot}38Al_{2}O_{3}{\cdot}xBaO$ glasses has been carried out using empirical potentials with the covalent term. The simulations closely reproduce the total neutron correlation functions of glass with 5 mol% BaO and physical properties of these glasses such as elastic constants. For these glasses, aluminum is tetrahedrally coordinated by oxygen, but there is a part of five-fold and six-fold coordination of aluminum. There are no major changes to the mid-range structure of glass, as barium is substituted for calcium. To predict the barium coordination number, we have used the bond valence (BV) theory and also compared the results of simulation with Bond valence. The coordination number for oxygen around barium atoms is close to 8 and the average distance of barium and oxygen is nearly 2.80 A. The viscosity of these glasses increases with the content of barium oxide substituted for calcium oxide.