• Bulletin of the Korean Chemical Society
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• v.31 no.10
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• pp.2903-2908
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• 2010

Protein S-nitrosation is common in cells under nitrosative stress. In order to model proteins with S-nitrosocysteine (CysSNO) residues, we first developed an Amber force field for S-nitrosoethanethiol (EtSNO) and then transferred it to CysSNO. Partial atomic charges for EtSNO and CysSNO were obtained by a restrained electrostatic potential approach to be compatible with the Amber-99 force field. The force field parameters for bonds and angles in EtSNO were obtained from a generalized Amber force field (GAFF) by running the Antechamber module of the Amber software package. The GAFF parameters for the CC-SN and CS-NO dihedrals were not accurate and thus determined anew. The CC-SN and CS-NO torsional energy profiles of EtSNO were calculated quantum mechanically at the level of B3LYP/cc-pVTZ//HF/6-$31G^*$. Torsional force constants were obtained by fitting the theoretical torsional energies with those obtained from molecular mechanics energy minimization. These parameters for EtSNO reproduced, to a reasonable accuracy, the corresponding torsional energy profiles of the capped tripeptide ACE-CysSNO-NME as well as their structures obtained from quantum mechanical geometry optimization. A molecular dynamics simulation of myoglobin with a CysSNO residue produced a well-behaved trajectory demonstrating that the parameters may be used in modeling other S-nitrosated proteins.

• International Journal of Fluid Machinery and Systems
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• v.4 no.1
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• pp.14-24
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• 2011

In this paper, design optimization for mixed-flow pump impellers and diffusers has been studied using a commercial computational fluid dynamics (CFD) code and DOE (design of experiments). We also discussed how to improve the performance of the mixed-flow pump by designing the impeller and diffuser. Geometric design variables were defined by the vane plane development, which indicates the blade-angle distributions and length of the impeller and diffusers. The vane plane development was controlled using the blade-angle in a fixed meridional shape. First, the design optimization of the defined impeller geometric variables was achieved, and then the flow characteristics were analyzed in the point of incidence angle at the diffuser leading edge for the optimized impeller. Next, design optimizations of the defined diffuser shape variables were performed. The importance of the geometric design variables was analyzed using $2^k$ factorial designs, and the design optimization of the geometric variables was determined using the response surface method (RSM). The objective functions were defined as the total head and the total efficiency at the design flow rate. Based on the comparison of CFD results between the optimized pump and base design models, the reason for the performance improvement was discussed.

• International Journal of Naval Architecture and Ocean Engineering
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• v.1 no.2
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• pp.64-69
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• 2009

The two-dimensional unsteady flow around a vertical axis turbine for tidal stream energy conversion was investigated using a computational fluid dynamics tool solving the Reynolds-Averaged Navier-Stokes equations. The geometry of the turbine blade section was NACA653-018 aiifoil. The computational analysis was done at several different angles of attack and the results were compared with the corresponding experimental data for validation and calibration. Simulations were then carried out for the two-dimensional cross section of a vertical axis turbine. The simulation results demonstrated the usefulness of the method for the typical unsteady flows around vertical axis turbines. The optimum turbine efficiency was achieved for carefully selected combinations of the number of blades and tip speed ratios.

• Journal of Hydrogen and New Energy
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• v.21 no.5
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• pp.364-374
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• 2010

Design of a reformer consisting of combustion chamber and reforming chamber was investigated for a 1 kW and a 5 kW polymer electrolyte membrane fuel cell (PEMFC), respectively, using the computational fluid dynamics (CFD). First, the 1kW reformer was considered to obtain the reliability of the numerical study. It was modeled, calculated and compared with experimental data. Second, the 5kW reformer was considered for a geometric study. Three tip sizes (35, 40, and 45 mm) and five aspect ratios was selected. It was found that the optimum was at tip sizes of 40 and 45 mm, at aspect ratios of -10% and -20% of the standard length.

• Tribology and Lubricants
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• v.37 no.2
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• pp.77-80
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• 2021

In this study, we investigated the effect of the spring constant on frictional behavior at a nanoscale through molecular dynamics simulation. A small cube-shaped tip was modeled and placed on a flat substrate. We did not apply the normal force to the tip but applied adhesive force between the tip and the substrate. The tip was horizontally pulled by a virtual spring to generate relative motion against the substrate. The controlled spring constant of the virtual spring ranged from 0.3 to 70 N/m to reveal its effect on frictional behavior. During the sliding simulation, we monitored the frictional force and the position of the tip. As the spring constant decreased from 70 to 0.3 N/m, the frictional force increased from 0.1 to 0.25 nN. A logarithmic relationship between the frictional force and spring constant was established. The stick-slip instability and potential energy slope increased with a decreasing spring constant. Based on the results, an increase in the spring constant reduces the probability of trapping in the local minima on the potential energy surface. Thus, the energy loss of escaping the potential well is minimized as the spring constant increases.

• Journal of Ocean Engineering and Technology
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• v.35 no.4
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• pp.247-256
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• 2021

In order to minimize carbon emissions and greenhouse gas, the Energy Efficiency Design Index (EEDI) has become a major factor to be considered in recent years in a ship's design and operation phases. Energy-Saving Devices (ESDs) improve the EEDI of a vessel and make them environmentally friendly. In this research, the performance of an equalizing duct-type ESD installed upstream of a Korea Research Institute of Ships & Ocean Engineering (KRISO) Container Ship (KCS) model's propeller was investigated by computational fluid dynamics (CFD). Open-source CFD libraries, OpenFOAM, were used for computational analysis of the KCS with and without the ESD to verify the performance improvement. The flow field near the stern region and propulsive coefficients were considered for comparison. The results showed a considerable improvement when an ESD was used on the model. Using different sizes of the duct, the performance of the ESD was also compared. It was observed that with an increased duct size, the propulsive performance was improved.

• Nuclear Engineering and Technology
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• v.54 no.11
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• pp.4022-4029
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• 2022

We investigated the possibility of using graphene for control of hydrogen isotopes by exploring adsorption, reflection, and penetration of hydrogen isotopes on graphene using molecular dynamics. Reflection is the dominant interaction when hydrogen isotopes have low incident energy. Adsorption rates increase with increasing incident energy until 5 eV is reached. After 5 eV, adsorption rates decrease as incident energy increases. At incident energies greater than 5 eV, adsorption rates increase with the number of graphene layers. At low incident energies (<1 eV), no isotopic effects on interactions are observed since the predominant interaction is derived from the force of π electrons. Between 1 eV and 50 eV, heavier isotopes exhibit higher adsorption rates and lower reflection rates than lighter isotopes, due to the greater momentum of heavier isotopes. Adsorption rates are consistently higher when the incident angle of the impacting atoms is smaller between 0.5 eV and 5 eV. At higher energies (>5 eV), larger incident angles lead to higher reflection and lower penetration rates. At high incident energies (>5 eV), crumpled graphene has higher adsorption and lower penetration rates than wrinkled or unwrinkled graphene. The results obtained in this research study will be used to develop novel nanomaterials that can be employed for tritium control.

• Nuclear Engineering and Technology
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• v.54 no.8
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• pp.3117-3129
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• 2022

Deeply understanding the phase change of thin liquid sodium film inside wick pore is very important for further studying high-temperature sodium heat pipe's heat transfer. For the first time, the evaporation and condensation of thin liquid sodium film are investigated by the Lennard-Jones potential of molecular dynamics. Based on the startup and normal operation of the sodium heat pipe, three different cases are simulated. First, the equilibrium is achieved and the Mass Accommodation Coefficients of the three cases are 0.3886, 0.2119, 0.2615 respectively. Secondly, the non-equilibrium is built. The change of liquid film thickness, the number of gas atoms, the net evaporation flux (J_net), the heat transfer coefficient (h) at the liquid-gas interface are acquired. Results indicate that the magnitude of the J_net and the h increase with the basic equilibrium temperature. In 520-600 K (the startup of the heat pipe), the h has approached 5-6 W m^-2 K^-1 while liquid film thickness is in 11-13 nm. The fact shows that during the initial startup of the sodium heat pipe, the thermal resistance at the liquid-gas interface can't be negligible. This work is the complement and extension for macroscopic investigation of heat transfer inside sodium heat pipe. It can provide a reference for further numerical simulation and optimal design of the sodium heat pipe in the future.

• Journal of Mechanical Science and Technology
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• v.16 no.11
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• pp.1440-1447
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• 2002

Adhesion of a hemispherical tip to the flat surface in nano-structures is simulated using the molecular dynamics technique. The tip and plates are modeled with the Lennard-Jones molecules. The simulation focuses on the deformation of the tip. Detailed descriptions on the evolution of interaction force, the energy dissipation due to adhesion hysteresis, the forma- tion-growth-breakage of adhesive junction as well as the evolution of molecular distribution during the process are presented. The effects of the tip size, the maximum tip approach, the tip temperature, and the affinity between the tip and the mating plate are also discussed.

• Proceedings of the Korean Society of Tribologists and Lubrication Engineers Conference
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• 2002.10b
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• pp.59-60
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• 2002

In this digest, we briefly review our current molecular dynamics (MD) simulations that utilize both the reactive empirical bond order potential (REBO) and the adaptive intermolecular REBO (AIREBO) potential energy functions. The AIREBO potential includes intermolecular interactions, so that self·assembled monolayers, and liquids, can be modeled. We have examined the mechanical and tribological properties of model self assembled monolayers and amorphous carbon films. Self-assembled monolayers are modeled by covalently bonding hydrocarbon chains to diamond substrates. Because the REBO potentials can model chemical reactions, specific compression and sliding induced chemical reactions were identified.