• Journal of Biomedical Engineering Research
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• v.34 no.3
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• pp.123-128
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• 2013

The 'Dielectrophoretic Tweezers(DEP Tweezers)' can be used as a facile, economical toolkit for quantitative measurement of chemical and biological binding forces related to many biological interactions within a microfluidic device. Our experimental setup can probe the interaction between a single receptor molecule and its specific ligand. Immunoglobulin G(IgG) functionalized on polystyrene microspheres has been used to detect individual surface linked Staphylococcus protein A(SpA) molecules and to characterize the strength of the noncovalent IgG-SpA bond. It was measured and compared with the existing measurements. Measured single binding force of between Goat, Rabbit IgG and SpA were $17{\pm}7pN$, $74{\pm}16pN$. This work can be used to investigate several different ligand-receptor interactions and antigen-antibody interactions.

• Interdisciplinary Bio Central
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• v.2 no.2
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• pp.6.1-6.5
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• 2010

Fragment molecular orbital (FMO) method provides a novel tool for ab initio calculations of large biomolecules. This method overcomes the size limitation difficulties in conventional molecular orbital methods and has several advantages compared to classical force field approaches. While there are many features in this method, we here focus on explaining the issues related to protein-ligand binding: FMO method provides useful interaction-analysis tools such as IFIE, CAFI and FILM. FMO calculations can provide not only binding energies, which are well correlated with experimental binding affinity, but also QSAR descriptors. In addition, FMO-derived charges improve the descriptions of electrostatic properties and the correlations between docking scores and experimental binding affinities. These calculations can be performed by the ABINIT-MPX program and the calculation results can be visualized by its proper BioStation Viewer. The acceleration of FMO calculations on various computer facilities is ongoing, and we are also developing methods to deal with cytochrome P450, which belongs to the family of drug metabolic enzymes.

• Journal of the Korean Magnetics Society
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• v.26 no.6
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• pp.206-212
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• 2016

The shape of a iron bed supporting a permanent magnet in a large-sized motor is a important factor for determining the coupling strength with the yoke. In a large-sized motor, there is a difference in electromagnetic force with the yoke depending on the shape of the iron bed. In this paper, we show the differences and problems by calculating the electromagnetic force between the double bed and the single bed through the virtual air gap, and show that the single bed is superior in terms of the binding force. It is also shown that the binding force between the bed and the yoke is improved by carving the groove shape under the bed.

• Bulletin of the Korean Chemical Society
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• v.34 no.2
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• pp.545-548
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• 2013

It has been shown that calculating atomic charges using quantum mechanical level theory greatly improves the accuracy of docking. A protocol was developed and shown to be effective. That this protocol works is just a manifestation of the fact that electrostatic interactions are important in protein-ligand binding. In order to investigate how the same protocol helps in prediction of binding affinities, we took a series of known cocrystal structures of influenza neuraminidase inhibitors with the receptor and performed docking with Glide SP, Glide XP, and QPLD, the last being a workflow that incorporates QM/MM calculations to replace the fixed atomic charges of force fields with quantum mechanically recalculated ones at a given docking pose, and predicted the binding affinities of each cocrystal. The correlation with experimental binding affinities considerably improved with QPLD compared to Glide SP/XP yielding $r^2$ = 0.83. The results suggest that for binding sites, such as that of neuraminidase, which are laden with hydrophilic residues, protocols such as QPLD which utilizes QM-based atomic charges can better predict the binding affinities.

• Proceedings of the Korea Concrete Institute Conference
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• 2006.11a
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• pp.537-540
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• 2006

Over the past few decades, a considerable number of studies on the durability of concrete have been carried out extensively. A lot of improvements have been achieved especially in modeling of ionic flows. However, the majority of these researches have not dealt with the chloride binding isotherm based on the mechanism, although chloride binding capacity can significantly impact on the total service life of concrete under marine environment. The purpose of this study is to develop the model of chloride binding isotherm based on the individual mechanism. It is well known that chlorides ions in concrete can be present; free chlorides dissolved in the pore solution, chemical bound chlorides reacted with the hydration compounds of cement, and physical bound attracted to the surface of C-S-H grains. First, sub-model for water soluble chloride content is suggested as a function of pore solution and degree of saturation. Second, chemical model is suggested separately to estimate the response of binding capacity due to C-S-H and Friedel's salt. Finally, physical bound chloride content is estimated to consider a surface area of C-S-H nano-grains and the distance limited by the Van der Waals force. The new model of chloride binding isotherm suggested in this study is based on their intrinsic binding mechanisms and hydration reaction of concrete. Accordingly, it is possible to characterize chloride binding isotherm at the arbitrary stage of hydration time and arbitrary location from the surface of concrete. Comparative study with experimental data of published literature is accomplished to validity this model.

• KIEE International Transactions on Electrophysics and Applications
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• v.3C no.5
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• pp.182-188
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• 2003

We have demonstrated a fluidic technique for self-assembly of microfabricated parts onto substrate using patterned shapes of magnetic force self-assembled monolayers (SAMs). The metal particles and the array were fabricated using the micromachining technique. The metal particles were in a multilayer structure (Au, Ti, and Ni). Sidewalls of patterned Ni dots on the array were covered by thick negative photoresist (SU-8), and the array was magnetized. The array and the particles were mixed in buffer solution, and were arranged by magnetic force interaction. Binding direction of the metal particle onto Ni dots was controlled by multilayer structure and direction of magnetization. A quarter of total Ni dots were covered by the particles. The binding direction of the particles was controllable, and condition of particles was almost even with the Au surface on top. The particles were successfully arranged on the array.

• Proceedings of the IEEK Conference
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• 2001.06b
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• pp.169-172
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• 2001

We have investigated the mechanical deformation of carbon nanotube using TBMD(tight-binding molecular dynamics) simulation. We have studied four carbon nanotubes, armchair (6, 6), (7, 7), (8, 8), and (9, 9) carbon nanotubes whose length were same. As a result of study, we have known that the nanotube's yield force increases with incresing their diameter. It is similar between (6, 6) and (8, 8) CNT's force-strain curves. Also force-strain curve between (7,7) and (9, 9) CNTs are nearly same.

• Journal of the Korean Chemical Society
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• v.59 no.2
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• pp.132-135
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• 2015

Bonding force and stiffness in amine-linked single-molecule junctions for Ag electrodes were measured using a home-built conducting atomic force microscope under ambient conditions at room temperature. For comparison, Au electrodes were used to measure the rupture force and stiffness of the molecular junctions. The traces of the force along with the conductance showed a characteristic saw-tooth pattern owing to the breaking of the metal atomic contacts or the metal-molecule- metal junctions. We found the rupture force and stiffness for Ag are smaller than those for Au electrodes. Furthermore, we observed that the force required to break the amine-Ag bond in the conjugated molecule, 1,4-benzenediamine, is smaller than in 1,4-butanediamine which is fully saturated. These results consist with the previous theoretical calculations for the binding energies of the nitrogen bonded to Ag or Au atoms.

• Journal of Integrative Natural Science
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• v.3 no.1
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• pp.49-53
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• 2010

Molecular docking is a critical event which mostly forms Van der waals complex in molecular recognition. Since the majority of developed drugs are small molecules, docking them into proteins has been a prime concern in drug discovery community. Since the binding pose space is too vast to cover completely, many search algorithms such as genetic algorithm, Monte Carlo, simulated annealing, distance geometry have been developed. Proper evaluation of the quality of binding is an essential problem. Scoring functions derived from force fields handle the ligand binding prediction with the use of potential energies and sometimes in combination with solvation and entropy contributions. Knowledge-based scoring functions are based on atom pair potentials derived from structural databases. Forces and potentials are collected from known protein-ligand complexes to get a score for their binding affinities (e.g. PME). Empirical scoring functions are derived from training sets of protein-ligand complexes with determined affinity data. Because non of any single scoring function performs generally better than others, some other approaches have been tried. Although numerous scoring functions have been developed to locate the correct binding poses, it still remains a major hurdle to derive an accurate scoring function for general targets. Recently, consensus scoring functions and target specific scoring functions have been studied to overcome the current limitations.

• Journal of the Korean Ceramic Society
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• v.47 no.5
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• pp.381-386
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• 2010

Some basic properties of inorganic coatings hardened by the room temperature reaction with alkalies were examined. The coating paste was prepared from the powders in the system $Al_2O_3-SiO_2$-CaO using blast furnace slag, fly ash and amorphous ceramic fiber after mixing with a solution of sodium hydroxide and water glass. The mineralogical and morphological examinations were performed for the coatings prepared at room temperature and after heating to $1200^{\circ}C$ respectively. The binding force of the coating hardened at room temperature was caused by the formation of fairly dense matrix mainly composed of oyelite-containing amorphous phase formed by the reaction between blast furnace slag and alkali solution. At the temperature, fly ash and ceramic fiber was not reacted but imbedded in the binding phase, giving the fluidity to the paste and reinforcing the coating respectively. During heating up to $1200^{\circ}C$, instead of a break in the coating, anorthite and gehlenite was crystallized out by the reaction among the binding phase and unreacted components in ternary system. The crystallization of these minerals revealed to be a reason that the coating maintains dense morphology after heating. The maintenance of binding force after heat treatment is seemed to be also caused by the formation of welldispersed fiber-like mineral phase which is originated from the shape of the amorphous ceramic fiber used as a raw materials.