• Proceeding of EDISON Challenge
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• 2015.03a
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• pp.70-75
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• 2015

Fasciclin 1 (FAS1) is an extracellular protein whose aggregation in cornea leads to visual impairment. While a number of FAS1 mutants have been studied that exhibit enhanced/decreased aggregation propensity, no structural information has been provided so far that is associated with distinct aggregation potential. In this study, we have investigated the structural and thermodynamic characteristics of the wild-type FAS1 and its two mutants, R555Q and R555W, by using molecular dynamics simulations and three-dimensional reference interaction site model (3D-RISM) theory. We find that the hydrophobic solvent accessible surface area increases due to hydrophobic core repacking in the C-terminus caused by the mutation. We also find that the solvation free energy of the mutants increases due to the enhanced non-native H-bonding. These structural and thermodynamic changes upon mutation contribute to understand the aggregation of these mutants.

• Bulletin of the Korean Chemical Society
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• v.28 no.9
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• pp.1485-1488
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• 2007

Photodissociation dynamics of cyanamide (NH2CN) at 212 nm has been investigated by measuring rotationally resolved laser induced fluorescence spectra of CN fragments exclusively produced in the ground electronic state. From the spectra, rotational population distributions of CN as well as translational energy releases in the products were obtained. The measured average rotational energies of CN were 12.4 ± 0.5 and 11.6 ± 0.5 kJ/ mol for v'' = 0 and v'' = 1, respectively and the center of mass average translational energy release among products was 41.8 ± 6.4 kJ/mol. The observed energy partitioning was well represented by statistical prior calculations, from which it was suggested that the dissociation takes place on the ground electronic surface after rapid internal conversion.

• Journal of the Korean Vacuum Society
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• v.4 no.S2
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• pp.139-147
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• 1995

The mechanism of the ionized cluster beam deposition has been studied using Molecular Dynamics Simulation. The Embedded Atom Method(EAM) potential were used in the simulation. The impact of a Au95-cluster on Au(100) substrate was studied for the impact energies 0.15-10eV/atom. The dependency of the impact energy of cluster beam was observed. For the cluster energy impact of 10eV per atom, the defects on surface were created and the cluster embedded into substrate as an amorphous state. For the energy of 0.5eV per atom, the defect free homoepitaxial growth was observed and atomic scale nucleation was formated, which are in good agreement with experiment. Thus molecular dynamics simulation is very useful to study the mechanism of the ionized cluster beam deposition.

• Transactions of the Korean Society of Mechanical Engineers A
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• v.24 no.4 s.175
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• pp.830-838
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• 2000

The paper addresses an application of molecular dynamics technique for fracture mechanics. Molecular dynamics simulation is an atomistic approach, while typical numerical methods such as finite element methods are macroscopic. Using the potential functions, which express the energy of a molecular system, a virtual specimen with molecules is set up and the trajectory of every molecule can be calculated by Newton's equation of motion. Several three-dimensional models with various types of cracks are considered. The stress intensity factors, the sizes of plastic zone as well as the dislocation emission are sought to be compared with the analytical solutions, which result in good agreement.

• Bulletin of the Korean Chemical Society
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• v.32 no.2
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• pp.515-518
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• 2011

We investigated how temperature influences the structural and energetic dynamics of carbon nanotubes (CNTs) undergoing a high-speed impact with a Si (110) surface. By performing molecular dynamics simulations in the temperature range of 100 - 300 K, we found that a low temperature CNT ends up with a higher vibrational energy after collision than a high temperature CNT. The vibrational temperature of CNT increases by increasing the surface temperature. Overall, the structural and energy relaxation of low temperature CNTs are faster than those of high temperature CNTs.

• Bulletin of the Korean Chemical Society
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• v.26 no.1
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• pp.151-156
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• 2005

The conformational dynamics of heme pocket, a small vacant site near the binding site of heme proteins -myoglobin (Mb) and hemoglobin (Hb), was investigated after photolysis of carbon monoxide from MbCO and HbCO in D$_2$O solution at 283 K by probing time-resolved vibrational spectra of photolyzed CO. Two absorption bands, arising from CO in the heme pocket, evolve nonexponentially in time. The band at higher energy side blue shifts and broadens with time and the one at lower energy side narrows significantly with a negligible shift. These spectral evolutions are induced by protein conformational changes following photolysis that modify structure and electric field of heme pocket, and ligand dynamics in it. The conformational changes affecting the spectrum of photolyzed CO in heme pocket likely modulates ligand-binding activity.

• Structural Engineering and Mechanics
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• v.30 no.4
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• pp.427-444
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• 2008

A mathematical model for the nonlinear dynamics of a rotating beam with flexible root attached to a rotating hub with elastic foundation is developed. The model is developed based on the large planar and flexural deformation theory and the potential energy method to account for axial shortening due to bending deformation. In addition the exact nonlinear curvature is used in the system potential energy. The Lagrangian dynamics and the assumed mode method is used to derive the nonlinear coupled equations of motion hub rotation, beam tip deflection and hub horizontal and vertical displacements. The derived nonlinear model is simulated numerically and the results are presented and discussed for the effect of root flexibility, hub stiffness, torque type, torque period and excitation frequency and amplitude on the dynamic behavior of the rotating beam-hub and on its stability.

• Proceedings of the Korean System Dynamics Society
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• 2005.04a
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• pp.149-162
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• 2005

• Journal of Hydrogen and New Energy
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• v.32 no.1
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• pp.1-10
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• 2021

Water electrolysis technology, which generates hydrogen using renewable energy resources, has recently attracted great attention. Especially, the polymer electrolyte membrane water electrolysis system has several advantages over other water electrolysis technologies, such as high efficiency, low operating temperature, and optimal operating point. Since research that analyzes performance characteristics using test bench have high cost and long test time, however, model based approach is very important. Therefore, in this study, a system model for water electrolysis dynamics of a polymer electrolyte membrane was developed based on MATLAB/Simulink®. The water electrolysis system developed in this study can take into account the heat and mass transfer characteristics in the cell with the load variation. In particular, the performance of the system according to the stack temperature control can be analyzed and evaluated. As a result, the developed water electrolysis system can analyze water pump dynamics and hydrogen generation according to temperature dynamics by reflecting the dynamics of temperature.

• Journal of Power System Engineering
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• v.21 no.2
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• pp.35-40
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• 2017

In this study, the multi-body dynamics model for a wave energy converter is established. The equations of motions for the mechanical parts of the wave energy converter are derived to analyze the dynamic behavior. A spring method with the same performance as the counter weight method is proposed. The counter weight method and spring method are analyzed for evaluating the performance of the wave energy converter. RecurDyn program which is a kind of commercial multi-body dynamics program is used to perform the dynamic simulation of the wave energy converter.