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Study on MPI-based parallel sequence similarity search in the LINUX cluster (클러스터 환경에서의 MPI 기반 병렬 서열 유사성 검색에 관한 연구)

  • Hong, Chang-Bum;Cha, Jeoung-Ho;Lee, Sung-Hoon;Shin, Seung-Woo;Park, Keun-Joon;Park, Keun-Young
    • Journal of the Korea Society of Computer and Information
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    • v.11 no.6 s.44
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    • pp.69-78
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    • 2006
  • In the field of the bioinformatics, it plays an important role in predicting functional information or structure information to search similar sequence in biological DB. Biolrgical sequences have been increased dramatically since Human Genome Project. At this point, because the searching speed for the similar sequence is highly regarded as the important factor for predicting function or structure, the SMP(Sysmmetric Multi-Processors) computer or cluster is being used in order to improve the performance of searching time. As the method to improve the searching time of BLAST(Basic Local Alighment Search Tool) being used for the similarity sequence search, We suggest the nBLAST algorithm performing on the cluster environment in this paper. As the nBLAST uses the MPI(Message Passing Interface), the parallel library without modifying the existing BLAST source code, to distribute the query to each node and make it performed in parallel, it is possible to easily make BLAST parallel without complicated procedures such as the configuration. In addition, with the experiment performing the nBLAST in the 28 nodes of LINUX cluster, the enhanced performance according to the increase in the number of the nodes has been confirmed.

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PROPERTIES SCUBA-2 850 ㎛ SOURCES AKARI NEP-DEEP FIELD

  • Seo, Hyunjong;Jeong, Woong-Seob;Kim, Minjin;Kim, Seong Jin;Ko, Jongwan;Pyo, Jeonghyun;Kim, Min Gyu;Pearson, Chris;Barrufet, Laia;Varillas, Maria del Carmen Campos;Matsuhara, Hideo;Malkan, Matt;Kim, Helen K.;Takagi, Toshinobu;Miyaji, Takamitsu;Tello, Jorge Diaz;Goto, Tomotsugu;Oi, Nagisa
    • Journal of The Korean Astronomical Society
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    • v.51 no.3
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    • pp.49-63
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    • 2018
  • We carry out a study of Sub-Millimeter Galaxies (SMGs) in the AKARI NEP-Deep field using the James Clerk Maxwell Telescope (JCMT) SCUBA-2 $850{\mu}m$ source catalog, released as part of the SCUBA-2 Cosmology Legacy Survey (S2CLS) program. The SCUBA-2 $850{\mu}m$ map has a root mean square (rms) noise of $1.2mJy\;beam^{-1}$ and covers an area of $0.60degree^2$. We find four SMGs which have counterparts to Herschel sources with spectroscopic redshifts in the literature. In addition, three dust obscured galaxies (DOGs) detected in Herschel bands are selected as a comparison sample. We derive IR luminosities of SMGs using the CIGALE code, which are similar to those of high redshift SMGs from previous studies. The contribution of AGN to the total IR luminosity in SMGs (2%-11%) is smaller than the lower limit for the one in DOGs (19%-35%), which is consistent with the expectation from the evolutionary scenario of massive galaxies. We search for SMGs in overdense regions as protocluster candidates and investigate four regions, including candidates around three DOGs. Finally, we argue that follow-up spectroscopic observation for the NEP-Deep field will provide crucial information to understand the role of SMGs in the evolution of massive galaxies.

A study on the method for the Integrated Cost Estimate based on Project(ICEP) of program management with typical model (기준모델을 사용한 종합사업관리용역비 산정방법(ICEP) 연구)

  • Baek, Myeongchang;Park, Junmo;Park, Gilbeom;Kim, Okkyue
    • Korean Journal of Construction Engineering and Management
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    • v.16 no.1
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    • pp.119-128
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    • 2015
  • Domestic dominant method in subcontract cost estimate for comprehensive program management is estimation by referencing similar cases or relying on the experience and expertise of the engaged. However, this method is not reliable due to lack of accuracy, making it harder for clients to plan and budget the program. Since budget itself is roughly estimated, it becomes a source of cost rise in the course of management due to design modifications. Therefore, the client and service providers shall calculate more accurate service cost by applying objective and scientific method in order to minimize cost rise and cost related dispute. Traditional cases, in estimating program management cost, took Top-Down approach based on precedents and experience. On the contrary, this study will categorize management structure into phases and activities, issue WBS for each phase to estimated schedule and cost for each code, and take Bottom-UP approach. By taking this approach named ICEP (Integrated Cost Estimate based on Project), Set project typical model will be developed for service cost estimating, calculate cost by applying project-specific factors. Also, by analyzing progress data and allocated management cost to complement them, more efficient construction management will take shape based on program management cost standards which reflect project-specific features.

An FSI Simulation of the Metal Panel Deflection in a Shock Tube Using Illinois Rocstar Simulation Suite (일리노이 록스타 해석환경을 활용한 충격파관 내 금속패널 변형의 유체·구조 연성 해석)

  • Shin, Jung Hun;Sa, Jeong Hwan;Kim, Han Gi;Cho, Keum Won
    • Transactions of the Korean Society of Mechanical Engineers A
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    • v.41 no.5
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    • pp.361-366
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    • 2017
  • As the recent development of computing architecture and application software technology, real world simulation, which is the ultimate destination of computer simulation, is emerging as a practical issue in several research sectors. In this paper, metal plate motion in a square shock tube for small time interval was calculated using a supercomputing-based fluid-structure-combustion multi-physics simulation tool called Illinois Rocstar, developed in a US national R amp; D program at the University of Illinois. Afterwards, the simulation results were compared with those from experiments. The coupled solvers for unsteady compressible fluid dynamics and for structural analysis were based on the finite volume structured grid system and the large deformation linear elastic model, respectively. In addition, a strong correlation between calculation and experiment was shown, probably because of the predictor-corrector time-integration scheme framework. In the future, additional validation studies and code improvements for higher accuracy will be conducted to obtain a reliable open-source software research tool.

Characterization of Radiation Field in the Steam Generator Water Chambers and Effective Doses to the Workers (증기발생기 수실의 방사선장 특성 및 작업자 유효선량의 평가)

  • Lee, Choon-Sik;Lee, Jai-Ki
    • Journal of Radiation Protection and Research
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    • v.24 no.4
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    • pp.215-223
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    • 1999
  • Characteristics of radiation field in the steam generator(S/G) water chamber of a PWR were investigated and the anticipated effective dose rates to the worker in the S/G chamber were evaluated by Monte Carlo simulation. The results of crud analysis in the S/G of the Kori nuclear power plant unit 1 were adopted for the source term. The MCNP4A code was used with the MIRD type anthropomorphic sex-specific mathematical phantoms for the calculation of effective doses. The radiation field intensity is dominated by downward rays, from the U-tube region, having approximate cosine distribution with respect to the polar angle. The effective dose rates to adults of nominal body size and of small body size(The phantom for a 15 year-old person was applied for this purpose) appeared to be 36.22 and 37.06 $mSvh^{-1}$) respectively, which implies that the body size effect is negligible. Meanwhile, the equivalent dose rates at three representative positions corresponding to head, chest and lower abdomen of the phantom, calculated using the estimated exposure rates, the energy spectrum and the conversion coefficients given in ICRU47, were 118, 71 and 57 $mSvh^{-1}$, respectively. This implies that the deep dose equivalent or the effective dose obtained from the personal dosimeter reading would be the over-estimate the effective dose by about two times. This justifies, with possible under- or over- response of the dosimeters to radiation of slant incidence, necessity of very careful planning and interpretation for the dosimetry of workers exposed to a non-regular radiation field of high intensity.

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Assessment of Effective Doses in the Radiation Field of Contaminated Ground Surface by Monte Carlo Simulation (몬테칼로 시뮬레이션에 의한 지표면 오염 방사선장에서의 유효선량 평가)

  • Chang, Jai-Kwon;Lee, Jai-Ki;Chang, Si-Young
    • Journal of Radiation Protection and Research
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    • v.24 no.4
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    • pp.205-213
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    • 1999
  • Effective dose conversion coefficients from unit activity radionuclides contaminated on the ground surface were calculated by using MCNP4A rode and male/female anthropomorphic phantoms. The simulation calculations were made for 19 energy points in the range of 40 keV to 10 MeV. The effective doses E resulting from unit source intensity for different energy were compared to the effective dose equivalent $H_E$ of previous studies. Our E values are lower by 30% at low energy than the $H_E$ values given in the Federal Guidance Report of USEPA. The effective dose response functions derived by polynomial fitting of the energy-effective dose relationship are as follows: $f({\varepsilon})[fSv\;m^2]=\;0.0634\;+\;0.727{\varepsilon}-0.0520{\varepsilon}^2+0.00247{\varepsilon}^3,\;where\;{\varepsilon}$ is the gamma energy in MeV. Using the response function and the radionuclide decay data given in ICRP 38, the effective dose conversion coefficients for unit activity contamination on the ground surface were calculated with addition of the skin dose contribution of beta particles determined by use of the DOSEFACTOR code. The conversion coefficients for 90 important radionuclides were evaluated and tabulated. Comparison with the existing data showed that a significant underestimates could be resulted when the old conversion coefficients were used, especially for the nuclides emitting low energy photons or high energy beta particles.

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A Study on the Optimal Design of Soft X-ray Ionizer using the Monte Carlo N-Particle Extended Code (Monte Carlo N-Particle Extended 코드를 이용한 연X선 정전기제거장치의 최적설계에 관한 연구)

  • Jeong, Phil hoon;Lee, Dong Hoon
    • Journal of the Korean Society of Safety
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    • v.32 no.2
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    • pp.34-37
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    • 2017
  • In recent emerging industry, Display field becomes bigger and bigger, and also semiconductor technology becomes high density integration. In Flat Panel Display, there is an issue that electrostatic phenomenon results in fine dust adsorption as electrostatic capacity increases due to bigger size. Destruction of high integrated circuit and pattern deterioration occur in semiconductor and this causes the problem of weakening of thermal resistance. In order to solve this sort of electrostatic failure in this process, Soft X-ray ionizer is mainly used. Soft X-ray Ionizer does not only generate electrical noise and minute particle but also is efficient to remove electrostatic as it has a wide range of ionization. X-ray Generating efficiency has an effect on soft X-ray Ionizer affects neutralizing performance. There exist variable factors such as type of anode, thickness, tube voltage etc., and it takes a lot of time and financial resource to find optimal performance by manufacturing with actual X-ray tube source. MCNPX (Monte Carlo N-Particle Extended) is used for simulation to solve this kind of problem, and optimum efficiency of X-ray generation is anticipated. In this study, X-ray generation efficiency was measured according to target material thickness using MCNPX under the conditions that tube voltage is 5 keV, 10 keV, 15 keV and the target Material is Tungsten(W), Gold(Au), Silver(Ag). At the result, Gold(Au) shows optimum efficiency. In Tube voltage 5 keV, optimal target thickness is $0.05{\mu}m$ and Largest energy of Light flux appears $2.22{\times}10^8$ x-ray flux. In Tube voltage 10 keV, optimal target Thickness is $0.18{\mu}m$ and Largest energy of Light flux appears $1.97{\times}10^9$ x-ray flux. In Tube voltage 15 keV, optimal target Thickness is $0.29{\mu}m$ and Largest energy of Light flux appears $4.59{\times}10^9$ x-ray flux.

Real-time Implementation of the AMR Speech Coder Using $OakDSPCore^{\circledR}$ ($OakDSPCore^{\circledR}$를 이용한 적응형 다중 비트 (AMR) 음성 부호화기의 실시간 구현)

  • 이남일;손창용;이동원;강상원
    • The Journal of the Acoustical Society of Korea
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    • v.20 no.6
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    • pp.34-39
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    • 2001
  • An adaptive multi-rate (AMR) speech coder was adopted as a standard of W-CDMA by 3GPP and ETSI. The AMR coder is based on the CELP algorithm operating at rates ranging from 12.2 kbps down to 4.75 kbps, and it is a source controlled codec according to the channel error conditions and the traffic loading. In this paper, we implement the DSP S/W of the AMR coder using OakDSPCore. The implementation is based on the CSD17C00A chip developed by C&S Technology, and it is tested using test vectors, for the AMR speech codec, provided by ETSI for the bit exact implementation. The DSP B/W requires 20.6 MIPS for the encoder and 2.7 MIPS for the decoder. Memories required by the Am coder were 21.97 kwords, 6.64 kwords and 15.1 kwords for code, data sections and data ROM, respectively. Also, actual sound input/output test using microphone and speaker demonstrates its proper real-time operation without distortions or delays.

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Numerical Analysis on Aerodynamic Performances and Characteristics of Quad Tilt Rotor during Forward Flight (전진 비행하는 쿼드 틸트 로터의 공력성능 및 특징에 대한 수치적 연구)

  • Lee, Seonggi;Oh, Sejong;Choi, Seongwook;Lee, Yunggyo;Park, Donghun
    • Journal of the Korean Society for Aeronautical & Space Sciences
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    • v.46 no.3
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    • pp.197-209
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    • 2018
  • In this study, numerical analyses on Quad Tilt Rotor(QTR) are carried out to investigate the interference effect of components and effect of operating condition during forward flight. Actuator Surface Method(ASM) which is implemented in an open source CFD code, OpenFOAM, is used to calculate the flow field around QTR with high computational efficiency. The lift of the front and rear wing is found to increase or decrease depending on the rotation direction of the rotor. At the rear wing, the interference effects of the front and rear rotor appear as a combined manner. Performance change due to the phase difference is found to be insignificant. For both rotors, the locally higher thrust is generated by the blockage effect of the wing. The interference effect of wake from the front nacelle contributes to higher local thrust for the rear rotor compared to the front rotor. And it is observed that the amplitude of thrust oscillation can decrease depending on the phase difference between the rotors. Aerodynamic performances of both rotors and the entire aircraft were compared and analyzed for various operating conditions.

A Study on the Research Model for the Standardization of Software-Similarity-Appraisal Techniques (소프트웨어 복제도 감정기법의 표준화 모델에 관한 연구)

  • Bahng, Hyo-Keun;Cha, Tae-Own;Chung, Tai-Myoung
    • The KIPS Transactions:PartD
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    • v.13D no.6 s.109
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    • pp.823-832
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    • 2006
  • The Purpose of Similarity(Reproduction) Degree Appraisal is to determine the equality or similarity between two programs and it is a system that presents the technical grounds of judgment which is necessary to support the resolution of software intellectual property rights through expert eyes. The most important things in proceeding software appraisal are not to make too much of expert's own subjective judgment and to acquire the accurate-appraisal results. However, up to now standard research and development for its systematic techniques are not properly made out and as different expert as each one could approach in a thousand different ways, even the techniques for software appraisal types have not exactly been presented yet. Moreover, in the analyzing results of all the appraisal cases finished before, through a practical way, we blow that there are some damages on objectivity and accuracy in some parts of the appraisal results owing to the problems of existing appraisal procedures and techniques or lack of expert's professional knowledge. In this paper we present the model for the standardization of software-similarity-appraisal techniques and objective-evaluation methods for decreasing a tolerance that could make different results according to each expert in the same-evaluation points. Especially, it analyzes and evaluates the techniques from various points of view concerning the standard appraisal process, setting a range of appraisal, setting appraisal domains and items in detail, based on unit processes, setting the weight of each object to be appraised, and the degree of logical and physical similarity, based on effective solutions to practical problems of existing appraisal techniques and their objective and quantitative standardization. Consequently, we believe that the model for the standardization of software-similarity-appraisal techniques will minimizes the possibility of mistakes due to an expert's subjective judgment as well as it will offer a tool for improving objectivity and reliability of the appraisal results.