• Korea-Australia Rheology Journal
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• v.13 no.1
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• pp.1-12
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• 2001

This paper describes the application of our recently developed two-phase model for flow-induced crystallization (FIC) to the simulation of fiber spinning and film blowing. 1-D and 2-D simulations of fiber spinning include the combined effects of (FIC), viscoelasticity, filament cooling, air drag, inertia, surface tension and gravity and the process dynamics are modeled from the spinneret to the take-up roll device (below the freeze point). 1-D model fits and predictions are in very good quantitative agreement with high- and low-speed spinline data for both nylon and PET systems. Necking and the associated extensional softening are also predicted. Consistent with experimental observations, the 2-D model also predicts a skin-core structure at low and intermediate spin speeds, with the stress, chain extension and crystallinity being highest at the surface. Film blowing is simulated using a "quasi-cylindrical" approximation for the momentum equations, and simulations include the combined effects of flow-induced crystallization, viscoelasticity, and bubble cooling. The effects of inflation pressure, melt extrusion temperature and take-up ratio on the bubble shape are predicted to be in agreement with experimental observations, and the location of the frost line is predicted naturally as a consequence of flow-induced crystallization. An important feature of our FIC model is the ability to predict stresses at the freeze point in fiber spinning and the frost line in film blowing, both of which are related to the physical and mechanical properties of the final product.l product.

• Advances in nano research
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• v.1 no.3
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• pp.133-151
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• 2013

The availability of advanced nanotechnological methodologies (experimental and theoretical) has widened the investigation of biological/organic matter in interaction with substrates. Minerals are good candidates as substrates because they may present a wide variety of physico-chemical properties and surface nanostructures that can be used to actively condense and manipulate the biomolecules. Scanning Probe Microscopy (SPM) is one of the best suited techniques used to investigate at a single molecule level the surface interactions. In addition, the recent availability of high performance computing has increased the possibility to study quantum mechanically the interaction phenomena extending the number of atoms involved in the simulation. In the present paper, firstly we will briefly introduce new SPM technological developments and applications to investigate mineral surfaces and mineral-biomolecule interaction, then we will present results on the specific RNA-mineral interaction and recent basics and applicative achievements in the field of the interactions between other fundamental biological molecules and mineral surfaces from both an experimental and theoretical point of view.

• Bulletin of the Korean Chemical Society
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• v.14 no.4
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• pp.491-496
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• 1993

A class A ${\beta}$-lactamase from Staphylococcus aureus PC1 complexed with 3R,5R-clavulanate is studied. The starting geometry for the computation is the crystal structure of the ${\beta}$-lactamase. Docking of the clavulanate to the enzyme is done exploiting the requirements of electrostatic and shape complementarity between the enzyme and clavulanate. This structure is then hydrated by water molecules and refined by energy minimization and short molecular dynamics simulation. In the energy refined structure of this complex, the carboxyl group of the clavulanate is hydrogen bonded to Lys-234, and the the carbonyl carbon atom of the clavulanate is adjacent to the $O_{\gamma}$ of Ser-70. It is found that a crystallographic water molecule initially located at the oxyanion hole, which is formed by the two -NH group of Ser-70 and Gln-237, is replaced by the carbonyl oxygen atom of the 3R,5R-clavulanate after docking and energy reginement. The crystallographic water molecules are proved to be important in ligand binding. Glu-166 residue is found to be repulsive to the binding of clavulanate, which is in agreement with experimental observation. Arg-244 residue is found to be important to the binding of clavulanate as well as to interaction with C2 side chain of the clavulanate. The electron density redistribution of the clavulanate on binding to the ${\beta}$-lactamase in studied by an ab initio quantum-mechanical calculation. A significant redistribution of electron density of the clavulanate is induced by the enzyme, toward the enzyme, toward the transition state of the enzymatic reaction.

• Bulletin of the Korean Chemical Society
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• v.5 no.4
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• pp.162-167
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• 1984

Equilibrium and dynamical behaviors of an n-alkane poymer (decane) in solution have been investigated by a molecuar dynamics simulation method. The polymer is assumed to be a chain of elements $(CH_2)$ interconnected by bonds having a fixed bond length and bond angle, but esch bond of the polymer is allowed to execute hindered internal rotation. The calculation explicitly considers the molecular naturer of solvent by including the intermolecular interactions between slovent-solvent molecules and chain element-solvent molecule. We present the results of calculations on (1) equilibrium properties (the solvent molecule-chain element pair correlation function, chain element-chain element pair correlation function, the mean square end-to-end distance and the mean square radius of gyration of the polymer) and (2) dynamic properties (four different autocorrelation functions, namely, the autocorrelation functions for the end-to-end distance and the radius of gyration, and the velocity autocorrelation functions for the center of mass and the end point of the chain). We found that the physical properties of the polymer chain depends sensitively on temperature. Comparison of the present work with other authors' results is also presented.

• Nuclear Engineering and Technology
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• v.54 no.8
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• pp.2801-2808
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• 2022

The synergistic effect of ZrC nanoparticle pining and Re solution in W matrix on the thermal stability of tungsten was studied by investigating the evolution of the microstructure, hardness and tensile properties after annealing in a temperature range of 1000-1700 ℃. The results of metallography, electron backscatter diffraction pattern and Vickers micro-hardness indicate that the rolled W-1wt%Re-0.5 wt% ZrC alloy has a higher recrystallization temperature (1600 ℃-1700 ℃) than that of the rolled pure W (1200 ℃), W-0.5 wt%ZrC (1300 ℃), W-0.5 wt%HfC (1400-1500 ℃) and W-K-3wt%Re alloy fabricated by the same technology. The molecular dynamics simulation results indicated that solution Re atoms in W matrix can slow down the self-diffusion of W atoms and form dragging effect to delay the growth of W grain, moreover, the diffusion coefficient decrease with increasing Re content. In addition, the ZrC nanoparticles can pin the grain boundaries and dislocations effectively, preventing the recrystallization. Therefore, synergistic effect of solid solution Re element and dispersed ZrC nanoparticles significantly increase recrystallization temperature.

• Journal of the Korean Magnetic Resonance Society
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• v.26 no.1
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• pp.1-9
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• 2022

There are two distinct approaches to improving the quality of protein NMR structures during refinement: all-atom force fields and accumulated knowledge-assisted methods that include Rosetta. Mao et al. reported that, for 40 proteins, Rosetta increased the accuracies of their NMR-determined structures with respect to the X-ray crystal structures (Mao et al., J. Am. Chem. Soc. 136, 1893 (2014)). In this study, we calculated 32 structures of those studied by Mao et al. using all-atom force field and implicit solvent model, and we compared the results with those obtained from Rosetta. For a single protein, using only the experimental NOE-derived distances and backbone torsion angle restraints, 20 of the lowest energy structures were extracted as an ensemble from 100 generated structures. Restrained simulated annealing by molecular dynamics simulation searched conformational spaces with a total time step of 1-ns. The use of GPU-accelerated AMBER code allowed the calculations to be completed in hours using a single GPU computer-even for proteins larger than 20 kDa. Remarkably, statistical analyses indicated that the structures determined in this way showed overall higher accuracies to their X-ray structures compared to those refined by Rosetta (p-value < 0.01). Our data demonstrate the capability of sophisticated atomistic force fields in refining NMR structures, particularly when they are coupled with the latest GPU-based calculations. The straightforwardness of the protocol allows its use to be extended to all NMR structures.

• Nuclear Engineering and Technology
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• v.55 no.6
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• pp.2298-2304
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• 2023

Titanium alloys are expected to become one of the candidate materials for nuclear-powered spacecraft due to their excellent overall performance. Nevertheless, atomistic mechanisms of the defect accumulation and evolution of the materials due to long-term exposure to irradiation remain scarcely understood by far. Here we investigate the heavy irradiation damage in a-titanium with a dose as high as 4.0 canonical displacements per atom (cDPA) using atomistic simulations of Frenkel pair accumulation. Results show that the content of surviving defects increases sharply before 0.04 cDPA and then decreases slowly to stabilize, exhibiting a strong correlation with the system energy. Under the current simulation conditions, the defect clustering fraction may be not directly dependent on the irradiation dose. Compared to vacancies, interstitials are more likely to form clusters, which may further cause the formation of 1/3<1210> interstitial-type dislocation loops extended along the (1010) plane. This study provides an important insight into the understanding of the irradiation damage behaviors for titanium.

• Genomics & Informatics
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• v.21 no.3
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• pp.41.1-41.11
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• 2023

The Dengue virus M protein is a 75 amino acid polypeptide with two helical transmembranes (TM). The TM domain oligomerizes to form an ion channel, facilitating viral release from the host cells. The M protein has a critical role in the virus entry and life cycle, making it a potent drug target. The oligomerization of the monomeric protein was studied using ab initio modeling and molecular dynamics simulation in an implicit membrane environment. The representative structures obtained showed pentamer as the most stable oligomeric state, resembling an ion channel. Glutamic acid, threonine, serine, tryptophan, alanine, isoleucine form the pore-lining residues of the pentameric channel, conferring an overall negative charge to the channel with approximate length of 51.9 Å. Residue interaction analysis for M protein shows that Ala94, Leu95, Ser112, Glu124, and Phe155 are the central hub residues representing the physicochemical interactions between domains. The virtual screening with 165 different ion channel inhibitors from the ion channel library shows monovalent ion channel blockers, namely lumacaftor, glipizide, gliquidone, glisoxepide, and azelnidipine to be the inhibitors with high docking scores. Understanding the three-dimensional structure of M protein will help design therapeutics and vaccines for Dengue infection.

• Bulletin of the Korean Chemical Society
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• v.35 no.8
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• pp.2494-2504
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• 2014

P38 mitogen activated protein (MAP) kinase is an important anti-inflammatory drug target, which can be activated by responding to various stimuli such as stress and immune response. Based on the conformation of the conserved DFG loop (in or out), binding inhibitors are termed as type-I and II. Type-I inhibitors are ATP competitive, whereas type-II inhibitors bind in DFG-out conformation of allosteric pocket. It remains unclear that how these allosteric inhibitors stabilize the DFG-out conformation and interact. Organosilicon compounds provide unusual opportunity to enhance potency and diversity of drug molecules due to their low toxicity. However, very few examples have been reported to utilize this property. In this regard, we performed docking of an inhibitor (BIRB) and its silicon analog (Si-BIRB) in an allosteric binding pocket of p38. Further, molecular dynamics (MD) simulations were performed to study the dynamic behavior of the simulated complexes. The difference in the biological activity and mechanism of action of the simulated inhibitors could be explained based on the molecular mechanics/generalized Born surface area (MM/GBSA) binding free energy per residue decomposition. MM/GBSA showed that biological activities were related with calculated binding free energy of inhibitors. Analyses of the per-residue decomposed energy indicated that van der Waals and non-polar interactions were predominant in the ligand-protein interactions. Further, crucial residues identified for hydrogen bond, salt bridge and hydrophobic interactions were Tyr35, Lys53, Glu71, Leu74, Leu75, Ile84, Met109, Leu167, Asp168 and Phe169. Our results indicate that stronger hydrophobic interaction of Si-BIRB with the binding site residues could be responsible for its greater binding affinity compared with BIRB.

• Membrane Journal
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• v.29 no.1
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• pp.11-17
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• 2019

In the field of water treatment membranes, polymers are used together with ceramics as the most important materials. In this review, I tried to analyze the technology trends of polymer membrane materials based on commercial products. For this purpose, according to the types of water treatment membranes such as MF (Microfiltration), UF (Ultrafiltration) and NF (Nanofiltration), the trends of polymer membrane products were investigated by countries, materials, and companies. Through this, we were able to classify the types of materials that are mainly used for each type of membrane, and at the same time, identify the companies that are dominant in the market, and analyze which materials constitute the product portfolio. Based on these results, we have presented the characteristics of the material market according to each type of membrane, and proposed a technology development strategy to enter each market based on these characteristics.