• Journal of the Mineralogical Society of Korea
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• v.25 no.4
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• pp.211-220
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• 2012

The numerical modeling and simulation have been used increasingly as tools for examining and interpreting the bulk structure and properties of materials. The use of molecular dynamics (MD) simulations to model the structure of materials is now both widespread and reasonably well understood. In this research, we introduced the numerical method to calculate the physico-chemical properties such as a diffusion coefficient and a viscosity of clay mineral. In this research, a series of MD calculations were performed for clay mineral and clay-water systems, appropriate to a saturated deep geological setting. Then, by using homogenization analysis (HA), the diffusion coefficients are calculated for conditions of the spatial distribution of the water viscosity associated with some configuration of clay minerals. This result of numerical analysis is quite similar to the previous experimental results. It means that the introduced numerical method is very useful to calculate the physico-chemical properties of clay minerals under various environmental conditions.

• Genomics & Informatics
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• v.21 no.3
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• pp.42.1-42.23
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• 2023

Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis, one of the most deadly infections in humans. The emergence of multidrug-resistant and extensively drug-resistant Mtb strains presents a global challenge. Mtb has shown resistance to many frontline antibiotics, including rifampicin, kanamycin, isoniazid, and capreomycin. The only licensed vaccine, Bacille Calmette-Guerin, does not efficiently protect against adult pulmonary tuberculosis. Therefore, it is urgently necessary to develop new vaccines to prevent infections caused by these strains. We used a subtractive proteomics approach on 23 virulent Mtb strains and identified a conserved membrane protein (MmpL4, NP_214964.1) as both a potential drug target and vaccine candidate. MmpL4 is a non-homologous essential protein in the host and is involved in the pathogen-specific pathway. Furthermore, MmpL4 shows no homology with anti-targets and has limited homology to human gut microflora, potentially reducing the likelihood of adverse effects and cross-reactivity if therapeutics specific to this protein are developed. Subsequently, we constructed a highly soluble, safe, antigenic, and stable multi-subunit vaccine from the MmpL4 protein using immunoinformatics. Molecular dynamics simulations revealed the stability of the vaccine-bound Tolllike receptor-4 complex on a nanosecond scale, and immune simulations indicated strong primary and secondary immune responses in the host. Therefore, our study identifies a new target that could expedite the design of effective therapeutics, and the designed vaccine should be validated. Future directions include an extensive molecular interaction analysis, in silico cloning, wet-lab experiments, and evaluation and comparison of the designed candidate as both a DNA vaccine and protein vaccine.

• Composites Research
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• v.31 no.5
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• pp.282-287
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• 2018

In this paper, we explore interfacial properties of the mineralized CNTs when they are employed as reinforcing fillers in a polymer nanocomposite using molecular dynamics (MD) simulations. Recently, several studies on mineralizing carbon nanotubes (CNTs) with an aid of nitrogen doping to CNTs have been reported. However, there is a lack of studies on the reinforcing effects of the mineralized CNTs when it is employed as a filler of nanocomposites. Silica ($SiO_2$) is used as a mineral material and poly (methyl metacrylate) (PMMA) is used as a polymer matrix. Pull-out simulations are conducted to obtain the interfacial energy and the interfacial shear stress. It was found that the silica mineralized CNTs have higher interfacial interaction with the polymer matrix. In the future, by examining various thermomechanical properties of the mineralized-CNT-filler/polymer nanocomposites, we will search for potential applications of the novel reinforcing filler.

• Bulletin of the Korean Chemical Society
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• v.35 no.6
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• pp.1713-1719
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• 2014

1FSD is a 28-residue designed protein with a ${\beta}{\beta}{\alpha}$ motif. Since this protein displays most essential features of protein structures in such a small size, this model protein can be an outstanding system for evaluating the balance in the propensity of the secondary structures and the quality of all-atom protein force fields. Particularly, this protein would be difficult to fold to its correct native structure without establishing proper balances between the secondary structure elements in all-atom energy functions. In this work, a series of the recently optimized five amber protein force fields [$ff03^*$, $f99sb^*$-ildn, ff99sb-${\phi}^{\prime}$-ildn, ff99sb-nmr1-ildn, ff99sb-${\Phi}{\Psi}$(G24, CS)-ildn] were investigated for the simulations of 1FSD using a conventional molecular dynamics (MD) and a biased-exchange meta-dynamics (BEMD) methods. Among those tested force fields, we found that ff99sb-nmr1-ildn and ff99sb-${\Phi}{\Psi}$(G24, CS)-ildn are promising in that both force fields can locate the native state of 1FSD with a high accuracy (backbone rmsd ${\leq}1.7{\AA}$) in the global free energy minimum basin with a reasonable energetics conforming to a previous circular dichroism (CD) experiment. Furthermore, both force fields led to a common set of two distinct folding pathways with a heterogeneous nature of the transition state to the folding. We anticipate that these force fields are reasonably well balanced, thereby transferable to many other protein folds.

• Bulletin of the Korean Chemical Society
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• v.24 no.2
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• pp.178-182
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• 2003

The stress and the heat-flux auto-correlation functions in the Green-Kubo formulas for shear viscosity and thermal conductivity have non-decaying long-time tails. This problem can be overcome by improving the statistical accuracy by N (number of particles) times, considering the stress and the heat-flux of the system as properties of each particle. The mean square stress and the heat-flux displacements in the Einstein formulas for shear viscosity and thermal conductivity are non linear functions of time since the quantities in the mean square stress and the heat-flux displacements are not continuous under periodic boundary conditions. An alternative to these quantities is to integrate the stress and the heat-flux with respect to time, but the resulting mean square stress and heat-flux displacements are still not linear versus time. This problem can be also overcome by improving the statistical accuracy. The results for transport coefficients of liquid argon obtained are discussed.

• Proceedings of the KSME Conference
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• 2008.11a
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• pp.1784-1787
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• 2008

Molecular dynamics (MD) simulations are used to analyze behavior of copper nanowires under cyclic loading. The embedded atom method (EAM) potential is employed to represent atomic interaction. Cyclic load is applied in two ways (Forward Tension / Reverse Compression and Forward Compression / Reverse Tension). The results show that dislocations are piled up as a result of plastic deformation during alternate tensile and compressive loading. After cyclic loading with a change of direction, yield stress decreases in consequence of the effect by the dislocation pileups. On the other hand, under FC/RT cyclic load, phase transformation represent associated with mechanical twinning. And copper nanowire can return to almost former undeformed condition during tensile loading at 300K.

• Korean Membrane Journal
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• v.1 no.1
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• pp.50-58
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• 1999

Symmetric asymmetric and composite perfluoropolymer membranes made with HYFLON AD have been prepared and evaluated. Porous and non porous symmetric membranes have been prepared by solvent evaporation with various processing conditions. Non-contact atomic force microscopy (AFM) was used to investigate the membrane morphology in air. Analysis of the images gave quantitative imformation on the surface pore strcture in particular on the pore size distributin. Possible useful uses of porous membranes are envisaged in the field of gas-liquid separations such as membrane contactors (MSc) Molecular Dynamics(MD) simulations structure of HYFLON AD 60X copolymer supporting these results are also reported. Amorphous perfluoropolymer membranes appears to be ideal other than in MCs when separation processes have to be performed in hostile environments i.e. high temperatures and aggressive non-aqueous media such as chemicals and solvents. In these cases HYFLON AD mem-branes can exploit the outstanding resistance of perfluoropolymers.

• Bulletin of the Korean Chemical Society
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• v.31 no.6
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• pp.1519-1526
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• 2010

The behavior of peptide or protein solutes in saline aqueous solution is a fundamental topic in physical chemistry. Addition of ions can strongly alter the thermodynamic and physical properties of peptide molecules in solution. In order to study the effects of added ionic salts on protein conformation and dynamics, we have used the molecular dynamics (MD) simulations to investigate the behavior of Staphylococcus aureus Hfq protein under two different ionic concentrations: 0.1 M NaCl and 1.0 M NaCl in presence and absence of RNA (a hepta-oligoribonucleotide AU5G). Hfq, a global regulator of gene expression is highly conserved and abundant RNA-binding protein. It is already reported that in vivo the increase of ionic strength results in a drastic reduction of Hfq affinity for $Q{\beta}$ RNA and reduces the tendency of aggregation of Escherichia coli host factor hexamers. Our results revealed the crucial role of 0.1 M NaCl Hfq system on the bases with strong hydrogen bonding interactions and by stabilizing the aromatic stacking of Tyr42 residue of the adjacent subunits/monomers with the adenine and uridine nucleobases. An increase in RNA pore diameter and weakened compactness of the Hfq-RNA complex was clearly observed in 1.0 M NaCl Hfq system with bound RNA. Aggregation of monomers in Hfq and the interaction of Hfq with RNA are greatly affected due to the presence of high ionic strength. Higher the ionic concentration, weaker is the aggregation and interaction. Our results were compatible with the experimental data and this is the first theoretical report for the experimental study done in 1980 by Uhlenbeck group for the present system.

• Proceedings of the Korean Institute of Building Construction Conference
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• 2023.05a
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• pp.255-256
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• 2023

The development of corrosion inhibitors with outstanding performance is a never-ending and complex process engaged in by researchers, engineers and practitioners. Computational assessment of organic corrosion inhibitors performance is a crucial step towards the design of new task-pecific materials. Herein, electronic features, adsorption characteristics and bonding mechanisms of two pyridine oximes, namely 2-pyridylaldoxime (2POH) and 3-pyridylaldoxime (3POH) with the iron surface were investigated using molecular dynamics (MD), and self-consistent-charge density-unctional tight-binding (SCC-DFTB) simulations. SCC-DFTB simulations revealed that 3POH molecule can form covalent bonds with iron atoms in its neutral and protonated states, while 2POH molecule can only bond with iron through its protonated form, resulting in interaction energies of -2.534, -2.007, -1.897, and -0.007 eV for 3POH, 3POH+, 2POH+, and 2POH, respectively. Projected density of states (PDOSs) analysis of pyridines-Fe(110) interactions indicated that pyridine molecules chemically adsorbed on the iron surface.

• Journal of the Korean Ceramic Society
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• v.54 no.6
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• pp.506-510
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• 2017

One of the characteristics of polycrystalline graphene that determines its material properties is grain size. Mechanical properties such as Young's modulus, yield strain and tensile strength depend on the grain size and show a reverse Hall-Petch effect at small grain size limit for some properties under certain conditions. While there is agreement on the grain size effect for Young's modulus and yield strain, certain MD simulations have led to disagreement for tensile strength. Song et al. showed a decreasing behavior for tensile strength, that is, a pseudo Hall-Petch effect for the small grain size domain up to 5 nm. On the other hand, Sha et al. showed an increasing behavior, a reverse Hall-Petch effect, for grain size domain up to 10 nm. Mortazavi et al. also showed results similar to those of Sha et al. We suspect that the main difference of these two inconsistent results is due to the different modeling. The modeling of polycrystalline graphene with regular size and (hexagonal) shape shows the pseudo Hall-Petch effect, while the modeling with random size and shape shows the reverse Hall-Petch effect. Therefore, this study is conducted to confirm that different modeling is the main reason for the different behavior of tensile strength of the polycrystalline structures. We conducted MD simulations with models derived from the Voronoi tessellation for two types of grain size distributions. One type is grains of relatively similar sizes; the other is grains of random sizes. We found that the pseudo Hall-Petch effect and the reverse Hall-Petch effect of tensile strength were consistently shown for the two different models. We suspect that this result comes from the different crack paths, which are related to the grain patterns in the models.