• Genomics & Informatics
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• v.15 no.1
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• pp.11-18
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• 2017

Nowadays, huge volumes of chromatin immunoprecipitation-sequencing (ChIP-Seq) data are generated to increase the knowledge on DNA-protein interactions in the cell, and accordingly, many tools have been developed for ChIP-Seq analysis. Here, we provide an example of a streamlined workflow for ChIP-Seq data analysis composed of only four packages in Bioconductor: dada2, QuasR, mosaics, and ChIPseeker. 'dada2' performs trimming of the high-throughput sequencing data. 'QuasR' and 'mosaics' perform quality control and mapping of the input reads to the reference genome and peak calling, respectively. Finally, 'ChIPseeker' performs annotation and visualization of the called peaks. This workflow runs well independently of operating systems (e.g., Windows, Mac, or Linux) and processes the input fastq files into various results in one run. R code is available at github: https://github.com/ddhb/Workflow_of_Chipseq.git.

• Journal of computational fluids engineering
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• v.14 no.1
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• pp.9-17
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• 2009

In this study we investigated the characteristics of fluid flow and heat transfer within a coolant passage in the cylinder head assembly of an internal combustion engine by using a commercial CFD code, CFX The complex coolant passage of the cylinder head assembly was modelled by suitable choice of a grid system and careful attention was paid in the construction of meshes near the walls where significant cooling occurs. To treat the simultaneous heating and cooling of the combustion walls we invented a methodology allowing a heat source within the solid wall and the convective cooling at the interface between the solid and the fluid. We managed to reproduce the experimental results by adjusting parameters appropriately. We have found that high temperature was concentrated at the surface of the cylinder jacket. It turned out that the effect of oil cooling from the piston head was unexpectedly significant. On the other hand the effect of cooling from the ambient air is almost negligible. The CFD method proposed in this study is believed to be useful in the early stage of the design of the engine-cooling system.

• Transactions of The Korea Fluid Power Systems Society
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• v.8 no.3
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• pp.1-7
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• 2011

As the technologies of electronic device have advanced these days, most of mechanical systems are designed with electronic control unit to take advantage of control parameter adaption to operating conditions and firmware flexibilities as well. On-board diagnosis, which detects the system malfunction and identifies potential source of error with its own diagnostic criteria, and fail-safe that can switch the mode of operation in view of recognized error characteristics enables easy maintenance and troubleshooting as well as system protection. This paper dealt with the development of diagnosis and fail-safe function for proportional flow control valve. All type of errors related to valve control system components are investigated and assigned to a specific hexadecimal codes. Cumulative error detection algorithm is applied in order for the sensitivity and reliability to be appropriate. Embedded simulator which runs simultaneously with system program provides the virtual error simulation environment for expeditious development of error detection algorithm. The diagnosis function was verified both with solenoid valve and embedded simulator test and it will enhance the valve control system monitoring function.

• Journal of Power System Engineering
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• v.11 no.4
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• pp.103-108
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• 2007

In general, the swing motion of the crane is controlled and suppressed by activating the trolley motion. In many papers reported by us, we suggested a new type of anti-sway control system of the crane. In the proposed control system, a small auxiliary mass(moving-mass) is installed on the spreader and the swing motion is controlled by moving the auxiliary mass. The actuator reaction against the auxiliary mass applies inertial control forces to the container in order to reduce the swing motion in the desired manner. The measuring system is based on laser sensor or others. However it is not so useful in real world. Especially, in this paper, the image sensor is used to measures the motions of the spreader and the measured data are fed back to the controller in real time. The applied image processing technique is a kind of robust template matching method which is named Vector Code Correlation (VCC) and devised to consider the real environmental conditions. And the $H_{\infty}$ based control technique is applied to suppress swing motion of the crane. And the experimental result shows that the proposed measurement system based on image sensor and control system is useful and robust to disturbances.

• Proceedings of the Korean Society of Precision Engineering Conference
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• 2006.05a
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• pp.657-658
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• 2006

Although there are many numerical models to simulate fs laser ablation of metals, no model can analyze the ablation phenomena over a wide range of fluence. In this work, a numerical code for simulating the fs laser ablation phenomena of metals has been developed. The two temperature model is employed to predict the ablation rate and the crater shape of metals using phase explosion mechanism in the relatively high fluence regime. Also, the ultrashort thermoelastic model is used for the low fluence regime to account for spallation of the sample by high strain rate. It has been demonstrated that the thermoelastic stress generated within the sample can exceed the yield stress of the material even near the threshold fluence. Numerical computation results are compared with the experiment for Cu and Ni and show good agreement. Discussions are made on the hydrodynamic model considering phase change and hydrodynamic flow.

• Journal of the Korean Society for Precision Engineering
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• v.18 no.10
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• pp.168-177
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• 2001

Reverse engineering has been widely used for the shape reconstruction of an object without CAD data and the measurement of clay or wood models fur the development of new products. To generate a surface from measured points by a laser scanner, typical steps include the scanning of a clay or wood model, the generation of compatible input curves, the generation of a surface and manufacturing data like G code or STL file. A laser scanner has a great potential to get geometrical data of a model for its frost measuring speed and higher precision. The data from a laser scanner are composed of many line stripes of points including small spikes and noise. A new approach using automated surface generating algorithm is introduced to deal with problems during reverse engineering process. And the input data and the generated surface are represented in IGES format, thus can be supplied to other CAD/CAM software without any data manipulation.

• Journal of the Korean Society for Heat Treatment
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• v.16 no.3
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• pp.148-158
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• 2003

In this study, a user oriented CFD program for optimum design of a regenerative combustion furnace, REBURN was developed. For user's convenience, user friendly Graphic User Interface was made and the renumbering interface program was developed in order to directly input any generated mesh system from ICEM CFD/FEA. Also an automatic processing system for switching mode was developed. The program was verified through compahng with commercial CFD code about regenerative combustion furnace. Then, numerical simulation of real walking beam furnace used in real industry was performed and the parametric analysis was studied about the arrangement mode. As a results, the uniform temperature was appeared in the cross mode.

• Journal of the Society of Naval Architects of Korea
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• v.34 no.4
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• pp.53-60
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• 1997

Nonlinear free surface flow phenomena have teen studied by several kinds of numerical methods, of which boundary element method has been known as most promising one. There, however, remain many difficulties to be solved in the numerical procedures by boundary element analysis. In this paper, an efficient calculation of elemental integrals and iterative solution algorithm for the resulting system of equations were thoroughly investigated in order to enhance the procedure of the boundary element analysis. Advantages of the herein developed boundary element analysis code are demonstrated in terms of accuracy and convergence for typical boundary-value problems with free surface.

• Transactions of Materials Processing
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• v.16 no.3 s.93
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• pp.172-177
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• 2007

The process design for large-scale ring rolling of Ti-6Al-4V alloy was performed by calculation method, processing map approach and FEM simulation. The ring rolling design includes geometry design and optimization of process variables. The calculation method was used to make geometry design such as initial billet and blank sizes, and final rolled ring shape. A commercial FEM code, SHAPE-RR was used to simulate the effect of process variables in ring rolling on the distribution of the internal state variables such as strain, strain rate and temperature. In order to predict the forming defects during ring rolling and the formation of over-heating above $\beta$-transus temperature due to deformation heating, the process-map approach based on Ziegler's instability criterion was used with FEM simulation. Finally, an optimum process design to obtain sound Ti-6Al-4V rings without forming defects was suggested through combined approach of Ziegler's instability map and FEM simulation results.

• Journal of ILASS-Korea
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• v.8 no.4
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• pp.9-16
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• 2003

The Purpose of this study is to investigate the relationships between the local heat release rate and CH concentration have been investigated by numerical simulations of methane-air premixed flames. And simultaneous CH and OH PLIF(Planar Laser Induced Fluorescence) measurement has been also conducted for lean premixed flame as well as for laminar flames. Numerical simulations are conducted for laminar premixed flames and turbulent ones by using PREMIX in CHEMKIN and two dimensional DNS code with GRI mechanism version 2.11, respectively. In the case of laminar premixed flame, the distance between the peak of heat release rate and that of CH concentration is under $91{\mu}m$ for all equivalence ratio calculated in present work. Even for the premixed flame in high intensity turbulence, the distribution of the heat release rate coincides with that of CH mole fraction. For CH PLIF measurements in the laminar premixed flame burner, CH fluorescence intensity as a function of equivalence ratio shows a similar trend with CH mole fraction computed by GRI mechanism. Simultaneous CH and OH PLIF measurement gave us useful information of instantaneous reaction zone. In addition, CH fluorescence can be measured even for lean conditions where CH mole fraction significantly decreases compared with that of stoichiometric condition. It was found that CH PLIF measurements can be applicable to the estimation of the spatial fluctuations of heat release rate in the engine combustion.