• Title/Summary/Keyword: Simulation Model

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Binding Mode Analysis of Bacillus subtilis Obg with Ribosomal Protein L13 through Computational Docking Study

  • Lee, Yu-No;Bang, Woo-Young;Kim, Song-Mi;Lazar, Prettina;Bahk, Jeong-Dong;Lee, Keun-Woo
    • Interdisciplinary Bio Central
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    • v.1 no.1
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    • pp.3.1-3.6
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    • 2009
  • Introduction: GTPases known as translation factor play a vital role as ribosomal subunit assembly chaperone. The bacterial Obg proteins ($Spo{\underline{0B}}$-associated ${\underline{G}}TP$-binding protein) belong to the subfamily of P-loop GTPase proteins and now it is considered as one of the new target for antibacterial drug. The majority of bacterial Obgs have been commonly found to be associated with ribosome, implying that these proteins may play a fundamental role in ribosome assembly or maturation. In addition, one of the experimental evidences suggested that Bacillus subtilis Obg (BsObg) protein binds to the L13 ribosomal protein (BsL13) which is known to be one of the early assembly proteins of the 50S ribosomal subunit in Escherichia coli. In order to investigate binding mode between the BsObg and the BsL13, protein-protein docking simulation was carried out after generating 3D structure of the BsL13 structure using homology modeling method. Materials and Methods: Homology model structure of BsL13 was generated using the EcL13 crystal structure as a template. Protein-protein docking of BsObg protein with ribosomal protein BsL13 was performed by DOT, a macro-molecular docking software, in order to predict a reasonable binding mode. The solvated energy minimization calculation of the docked conformation was carried out to refine the structure. Results and Discussion: The possible binding conformation of BsL13 along with activated Obg fold in BsObg was predicted by computational docking study. The final structure is obtained from the solvated energy minimization. From the analysis, three important H-bond interactions between the Obg fold and the L13 were detected: Obg:Tyr27-L13:Glu32, Obg:Asn76-L13:Glu139, and Obg:Ala136-L13:Glu142. The interaction between the BsObg and BsL13 structures were also analyzed by electrostatic potential calculations to examine the interface surfaces. From the results, the key residues for hydrogen bonding and hydrophobic interaction between the two proteins were predicted. Conclusion and Prospects: In this study, we have focused on the binding mode of the BsObg protein with the ribosomal BsL13 protein. The interaction between the activated Obg and target protein was investigated with protein-protein docking calculations. The binding pattern can be further used as a base for structure-based drug design to find a novel antibacterial drug.

Dynamic Response of Tension Leg Platform (Tension Leg Platform의 동적응답에 관한 연구)

  • Yeo, Woon Kwang;Pyun, Chong Kun
    • KSCE Journal of Civil and Environmental Engineering Research
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    • v.5 no.1
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    • pp.21-30
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    • 1985
  • The tension leg platform (TLP) is a kind of compliant structures, and is also a type of moored stable platform with a buoyancy exceeding the weight because of having tensioned vertical anchor cables. In this paper, among the various kinds of tension leg structures, Deep Oil Technology (DOT) TLP was analyzed because it has large-displacement portions of the immersed surface such as vertical corner pontoons and small-diameter elongated members such as cross-bracing. It also has results of hydraulic model tests, comparable with theorectical analysis. Because of the vertical axes of symmetry in the three vertical buoyant legs and because there are no larger horizontal buoyant members between these three vertical members, it was decided to develop a numerical algorithm which would predict the dynamic response of the DOT TLP using the previously developed numerical algorithm Floating Vessel Response Simulation (FVRS) for vertically axisymmetric bodies of revolution. In addition, a linearized hydroelastic Morison equation subroutine would be developed to account for the hydrodynamic pressure forces on the small member cross bracing. Interaction between the large buoyant members or small member cross bracings is considered to be negligible and is not included in the analysis. The dynamic response of the DOT TLP in the surge mode is compared with the results of the TLP algorithm for various combinations of diffraction and Morison forces and moments. The results which include the Morison equation are better than the results for diffraction only. This is because the vertically axisymmetric buoyant members are only marginally large enough to consider diffractions effects. The prototype TLP results are expected to be more inertially dominated.

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Estimation of fire Experiment Prediction by Utility Tunnels Fire Experiment and Simulation (지하공동구 화재 실험 및 시뮬레이션에 의한 화재 설칠 예측 평가)

  • 윤명오;고재선;박형주;박성은
    • Fire Science and Engineering
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    • v.15 no.1
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    • pp.23-33
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    • 2001
  • The utility tunnels are the important facility as a mainstay of country because of the latest communication developments. However, the utilities tunnel is difficult to deal with in case of a fire accident. When a cable burns, the black smoke containing poisonous gas will be reduced. This black smoke goes into the tunnel, and makes it difficult to extinguish the fire. Therefore, when there was a fire in the utility tunnel, the central nerves of the country had been paralyzed, such as property damage, communication interruption, in addition to inconvenience for people. This paper is based on the fire occurred in the past, and reenacting the fire by making the real utilities tunnel model. The aim of this paper is the scientific analysis of the character image of the fire, and the verification of each fire protection system whether it works well after process of setting up a fire protection system in the utilities tunnel at a constant temperature. The fire experiment was equipped with the linear heat detector, the fire door, the connection water spray system and the ventilation system in the utilities tunnel. Fixed portion of an electric power supply cable was coated with a fire retardant coating, and a heating tube was covered with a fireproof. The result showed that the highest temperature was $932^{\circ}c$ and the linear heat detector was working at the constant temperature, and it pointed at the place of the fire on the receiving board, and Fixed portion of the electric power supply cable coated with the fire retardant coating did not work as the fireproof. The heating tube was covered with the fireproof about 30 minutes.

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Growth and Yield Related Characteristics of Soybeans for the Estimation of Grain Yield in Upland and Drained-Paddy Field (콩 논.밭 재배에서 수랑예측을 위한 생육과 수량 관련 형질의 비교)

  • Cho, Young-Son;Park, Ho-Gi;Kim, Wook-Han;Kim, Sok-Dong;Seo, Jong-Ho;Shin, Jin-Chul
    • KOREAN JOURNAL OF CROP SCIENCE
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    • v.51 no.7
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    • pp.599-607
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    • 2006
  • The experiments were carried out to develop simulation model for estimating the yield of soybean in upland and paddy field condition. Field experiments were done at National Institute of Crop Science in 2005. The evaluated soybean cultivars were Taekwangkong, Daewonkong, and Hwangkeumkong. Soybean seeds were planted by hill seeding with 3-4 seeds and row and hill spacing were $60{\times}10cm$ in upland and $60{\times}15cm$ in paddy field. Seeds were sown on row (without making ridge) and on the top of ridge in upland and paddy field, respectively. Field parameters were measured yield components ($plants/m^{2}$, pod no./plant, and 100-seed weight, seed yield and growth characteristics (stem length, leaf area at each stage, and dry weight of shoot) and after measuring they were compared the relationships with seed yield and yield components and seed yield and growth characteristics. Seed yield of soybean was affected by cultivars and planting density. Seed yield was higher in upland than paddy field due to the higher planting density in upland field. The upland soybeans generally had lower 100-seed weight than that of paddy field. Seed yield of soybean in a paddy field was greatest in Taekwangkong and followed by Daewonkong and Hwangkeumkong. The harvest index of taekwangkong and Hwanggumkong was higher in upland than paddy field, however, it was higher in paddy field than upland in Daewonkong. Seed yield was greatest in Daewonkong in both experimental fields. The greatest stem length was observed in taekwangkong and Hwanggumkong (R6) in late growth stage in paddy field. Dry weight of shoot and pod, pod number, stem length, and stem diameter were higher grown in paddy field than grown in upland. Crop growth rate (CGR) of cultivars was higher in paddy field after 8 WAS(weeks after sowing) and it was greatest at 13 WAS in Daewonkong among the cultivars. In upland field, CGR was greatest in Taekwangkong and then followed by Daewonkong and Hwanggumkong during 12 and 15 WAS. There was no significant relationships between 100-seed weight and seed yield in both experimental fields. A significant positive relationship was observed between seed number and seed yield. The correlation coefficients between leaf area and shoot dry weight were about 0.8 during the whole growth stage except 5 WAS and 4-5 WAS in paddy field and upland, respectively. This experiment was done just one year and drained paddy field condition was not satisfied drained condition successfully at 7th leaf age of soybean by the heavy rain, so we suggest that the excessive soil water reduced seed yield in paddy field and the weather condition should be considered for utilizing of these results.

The Effects of Female Wage on Fertility in Korea (여성의 임금수준이 출산율에 미치는 영향 분석)

  • Kim, Jungho
    • KDI Journal of Economic Policy
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    • v.31 no.1
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    • pp.105-138
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    • 2009
  • Although the decline in fertility rate is generally observed along the history of economic development throughout the world, the continuing decline hitting below the replacement level in Korea over the recent years gathered serious social concerns on the ground that it accelerates the process of population aging. The total fertility rate in Koreareached 2.08 in 1983, and gradually fell to the levels of 1.08 in 2005 and 1.26 in 2007. The policy debate over the role of the government has been focused mainly on the level of theoretical discussion without substantial basis on firm empirical evidence and the determinants of fertility. The objective of the paper is to empirically investigate the fertility effect of the female wage, which is understood as one of the most important determinants of fertility in Koreasince 1980 focusing on one aspect of fertility, namely birth spacing. Using the Korean National Fertility Survey conducted in 2006, I estimate a duration model of first and second births taking into account individual heterogeneity, which turned out to be an important factor to control for. Compared with previous studies in the literature on the Korean fertility, the study has an advantage of using the complete pregnancy history of women in a more representative sample. Unlike the previous studies, the analysis also deals with the endogeneity of marriage by treating a certain age, rather than age at marriage, as the time in which a woman becomes exposed to the risk of pregnancy. The study shares the common problem in the literature on birth spacing of lacking relevant wage information for respondents in a retrospective survey. I estimate the wage series as a function of the basic characteristics using the annual Wage Structure Survey from 1980 to 2005, which is considered as a nationally representative sample for wage information of employees. The results suggest that the increase in female wage by 10 percent leads to a decrease in second birth hazard by 0.56~0.92 percentage points and that the increase in spouse's wage by the equal amount is accompanied by the increase in second birth hazard by 0.36~1.13 percentage points. These estimates are more precisely estimated and of smaller magnitude than those presented by the previous studies. The results are robust to the different specifications of the wage equation. The simulation analysis based on the predicted values shows that about 17% of the change in the second birth hazard over the period 1980 to 2005 was due to the change in the female wage. Although there is some limitation in data, the results can be viewed as one estimate of the role of female wage on the recent fertility decline in Korea. The question raised by the paper is not a normative one of whether a government should promote childbearing but a positive one thatexplains fertility decline. Therefore, if there is a wide consensus on promoting childbearing, the finding suggests that the policies designed to reduce the opportunity cost of women in the labor market would be effective. The recent movement of implementing a wide range of family-friendly policies including child care support, maternity leave, parental leave and tax benefit in developed countries should be understood in this context.

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Numerical Analysis of Unstable Combustion Flows in Normal Injection Supersonic Combustor with a Cavity (공동이 있는 수직 분사 초음속 연소기 내의 불안정 연소유동 해석)

  • Jeong-Yeol Choi;Vigor Yang
    • Proceedings of the Korean Society of Propulsion Engineers Conference
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    • 2003.05a
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    • pp.91-93
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    • 2003
  • A comprehensive numerical study is carried out to investigate for the understanding of the flow evolution and flame development in a supersonic combustor with normal injection of ncumally injecting hydrogen in airsupersonic flows. The formulation treats the complete conservation equations of mass, momentum, energy, and species concentration for a multi-component chemically reacting system. For the numerical simulation of supersonic combustion, multi-species Navier-Stokes equations and detailed chemistry of H2-Air is considered. It also accommodates a finite-rate chemical kinetics mechanism of hydrogen-air combustion GRI-Mech. 2.11[1], which consists of nine species and twenty-five reaction steps. Turbulence closure is achieved by means of a k-two-equation model (2). The governing equations are spatially discretized using a finite-volume approach, and temporally integrated by means of a second-order accurate implicit scheme (3-5).The supersonic combustor consists of a flat channel of 10 cm height and a fuel-injection slit of 0.1 cm width located at 10 cm downstream of the inlet. A cavity of 5 cm height and 20 cm width is installed at 15 cm downstream of the injection slit. A total of 936160 grids are used for the main-combustor flow passage, and 159161 grids for the cavity. The grids are clustered in the flow direction near the fuel injector and cavity, as well as in the vertical direction near the bottom wall. The no-slip and adiabatic conditions are assumed throughout the entire wall boundary. As a specific example, the inflow Mach number is assumed to be 3, and the temperature and pressure are 600 K and 0.1 MPa, respectively. Gaseous hydrogen at a temperature of 151.5 K is injected normal to the wall from a choked injector.A series of calculations were carried out by varying the fuel injection pressure from 0.5 to 1.5MPa. This amounts to changing the fuel mass flow rate or the overall equivalence ratio for different operating regimes. Figure 1 shows the instantaneous temperature fields in the supersonic combustor at four different conditions. The dark blue region represents the hot burned gases. At the fuel injection pressure of 0.5 MPa, the flame is stably anchored, but the flow field exhibits a high-amplitude oscillation. At the fuel injection pressure of 1.0 MPa, the Mach reflection occurs ahead of the injector. The interaction between the incoming air and the injection flow becomes much more complex, and the fuel/air mixing is strongly enhanced. The Mach reflection oscillates and results in a strong fluctuation in the combustor wall pressure. At the fuel injection pressure of 1.5MPa, the flow inside the combustor becomes nearly choked and the Mach reflection is displaced forward. The leading shock wave moves slowly toward the inlet, and eventually causes the combustor-upstart due to the thermal choking. The cavity appears to play a secondary role in driving the flow unsteadiness, in spite of its influence on the fuel/air mixing and flame evolution. Further investigation is necessary on this issue. The present study features detailed resolution of the flow and flame dynamics in the combustor, which was not typically available in most of the previous works. In particular, the oscillatory flow characteristics are captured at a scale sufficient to identify the underlying physical mechanisms. Much of the flow unsteadiness is not related to the cavity, but rather to the intrinsic unsteadiness in the flowfield, as also shown experimentally by Ben-Yakar et al. [6], The interactions between the unsteady flow and flame evolution may cause a large excursion of flow oscillation. The work appears to be the first of its kind in the numerical study of combustion oscillations in a supersonic combustor, although a similar phenomenon was previously reported experimentally. A more comprehensive discussion will be given in the final paper presented at the colloquium.

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Throughfall, Stemflow and Interception Loss of the Natural Old-growth Deciduous and Planted Young Coniferous in Gwangneung and the Rehabilitated Young Mixed Forest in Yangju, Gyeonggido(I) - with a Special Reference on the Results of Measurement - (광릉(光陵) 활엽수(闊葉樹) 천연노령림(天然老齡林)과 침엽수(針葉樹) 인공유령림(人工幼齡林) 그리고 양주(楊洲) 사방지(砂防地) 혼효유령림(混淆幼齡林)의 수관통과우량(樹冠通過雨量), 수간유하량(樹幹流下量) 그리고 차단손실량(遮斷損失量)에 관하여(I) - 실험적(實驗的) 측정결과(測定結果)를 중심(中心)으로 -)

  • Kim, Kyongha;Jun, Jaehong;Yoo, Jaeyun;Jeong, Yongho
    • Journal of Korean Society of Forest Science
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    • v.94 no.6
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    • pp.488-495
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    • 2005
  • This study was conducted to understand the influences of forest structure on throughfall, stemflow and interception loss. The study plots included the natural old-growth deciduous, Pinus koraiensis and Abies holophylla forests in Gwangneung and the rehabilitated young mixed forest in Yangju, Gyeonggido. The Pinus koraiensis and Abies hotophylla had been planted in 1976. The rehabilitated young mixed forest had been established to control erosion in 1974. Total and net rainfall were monitored from March, 2003 to October, 2004. Tipping bucket rain gauge recorded total rainfall. Throughfall and stemflow were measured by custom-made tipping bucket and CR10X data logger at each $10m{\times}10m$ plots at intervals of 30 minutes. Interception loss in the Pinus koraiensis plot were most as 37.2% of total rainfall and least as 22.6% in the rehabilitated young mixed forest. Stemflow in the rehabilitated young mixed forest was 10.7% of total rainfall and stemflow in the Pinus koraiensis plot was 2.4%. The average throughfall ratio ranged from 66% to 77% depending on the canopy coverage. The relationship of stemflow and total rainfall represented in a linear regression equation though the variation of data was large. The ratio of stemflow-conversion was 2% of total rainfall in the Pinus koraiensis plot and 12% in the rehabilitated young mixed forest, respectively. The stem storage of the natural old-growth deciduous was the largest of 0.21 mm whereas that of the Pinus koraiensis plot was the least of 0.003 mm. A deciduous forest produced stemflow more than a coniferous forest due to a smooth bark and steeply angled branches. Interception loss of all study plots increased linearly as total rainfall increased. The distribution of interception loss data related in total rainfall became wider in a deciduous forest than a coniferous. It resulted from seasonality of leaf area index in a deciduous forest. As considered above results, it was confirmed that there were great differences of throughfall, stemflow and interception loss depending on forest stand structures. The simulation model for predicting interception loss must have parameters such as forest stand characteristics and LAI in order to describe the influence of forest structure on interception loss.

Recent Progress in Air-Conditioning and Refrigeration Research : A Review of Papers Published in the Korean Journal of Air-Conditioning and Refrigeration Engineering in 2012 (설비공학 분야의 최근 연구 동향 : 2012년 학회지 논문에 대한 종합적 고찰)

  • Han, Hwataik;Lee, Dae-Young;Kim, Sa Ryang;Kim, Hyun-Jung;Choi, Jong Min;Park, Jun-Seok;Kim, Sumin
    • Korean Journal of Air-Conditioning and Refrigeration Engineering
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    • v.25 no.6
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    • pp.346-361
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    • 2013
  • This article reviews the papers published in the Korean Journal of Air-Conditioning and Refrigeration Engineering during 2012. It is intended to understand the status of current research in the areas of heating, cooling, ventilation, sanitation, and indoor environments of buildings and plant facilities. The conclusions are as follows : (1) The research works on thermal and fluid engineering have been reviewed as groups of fluid machinery, pipes and valves, fuel cells and power plants, ground-coupled heat pumps, and general heat and mass transfer systems. Research issues are mainly focused on new and renewable energy systems, such as fuel cells, ocean thermal energy conversion power plants, and ground-coupled heat pump systems. (2) Research works on the heat transfer area have been reviewed in the categories of heat transfer characteristics, pool boiling and condensing heat transfer, and industrial heat exchangers. Researches on heat transfer characteristics included the results for natural convection in a square enclosure with two hot circular cylinders, non-uniform grooved tube considering tube expansion, single-tube annular baffle system, broadcasting LED light with ion wind generator, mechanical property and microstructure of SA213 P92 boiler pipe steel, and flat plate using multiple tripping wires. In the area of pool boiling and condensing heat transfer, researches on the design of a micro-channel heat exchanger for a heat pump, numerical simulation of a heat pump evaporator considering the pressure drop in the distributor and capillary tubes, critical heat flux on a thermoexcel-E enhanced surface, and the performance of a fin-and-tube condenser with non-uniform air distribution and different tube types were actively carried out. In the area of industrial heat exchangers, researches on a plate heat exchanger type dehumidifier, fin-tube heat exchanger, an electric circuit transient analogy model in a vertical closed loop ground heat exchanger, heat transfer characteristics of a double skin window for plant factory, a regenerative heat exchanger depending on its porous structure, and various types of plate heat exchangers were performed. (3) In the field of refrigeration, various studies were executed to improve refrigeration system performance, and to evaluate the applicability of alternative refrigerants and new components. Various topics were presented in the area of refrigeration cycle. Research issues mainly focused on the enhancement of the system performance. In the alternative refrigerant area, studies on CO2, R32/R152a mixture, and R1234yf were performed. Studies on the design and performance analysis of various compressors and evaporator were executed. (4) In building mechanical system research fields, twenty-nine studies were conducted to achieve effective design of mechanical systems, and also to maximize the energy efficiency of buildings. The topics of the studies included heating and cooling, HVAC system, ventilation, renewable energy systems, and lighting systems in buildings. New designs and performance tests using numerical methods and experiments provide useful information and key data, which can improve the energy efficiency of buildings. (5) In the fields of the architectural environment, studies for various purposes, such as indoor environment, building energy, and renewable energy were performed. In particular, building energy-related researches and renewable energy systems have been mainly studied, reflecting interests in global climate change, and efforts to reduce building energy consumption by government and architectural specialists. In addition, many researches have been conducted regarding indoor environments.

Responses of Soybean Yield to High Temperature Stress during Growing Season: A Case Study of the Korean Soybean (재배기간 동안 이상고온 발생에 따른 콩의 수량반응 탐색)

  • Chung, Uran;Cho, Hyeoun-Suk;Kim, Jun-Hwan;Sang, Wan-Gyu;Shin, Pyeong;Seo, Myung-Chul;Jung, Woo-Seuk
    • Korean Journal of Agricultural and Forest Meteorology
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    • v.18 no.4
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    • pp.188-198
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    • 2016
  • In soybeans, responses of high temperature according to shift of sowing dates during the growing season was explored using the crop model, CROPGRO-soybean. In addition, it analyzed impact on change of sowing dates affects yield potential of soybean under future climate scenario (2041-2070). In Jeonju and Miryang during 1981-2010, if sowing at 15 or ten days ahead from 10 June, namely in shorten of the sowing day (i.e. when sown on 25 or 30 May), the yield potential reduced. However, the yield potential increased when sown 5 June. In the case of delay of sowing day (i.e. when sown on 15 or 20 June), reduction of yield potential in the average -5% was higher than increase in the average +2%. In particular, the relative changes for shorten of the sowing day or delay of the sowing day do not be shown in normal years which high temperatures did not abnormally occur during the growing season from 2003 to 2010 except when sown on 25 May. In abnormal years which high temperatures occurred during the critical period, especially R5 to R7, shorten of the sowing day affected to the increase of yield potential in Miryang, while the yield potential decreased in Jeonju except when sown on 5 June. However, delay of the sowing day influenced on the reduction of yield potential both in two sites. In future climate scenario of Representative Concentration Pathway (RCP) 8.5 during from 2041 to 2070, the increase and decrease of yield potential for shorten of the sowing day were +10/-9% for RCP 8.5 of Jeonju, and +14/-9% for RCP 8.5 of Miryang, respectively. Additionally, it showed +10/-17% for RCP 8.5 in Jeonju, and +10/-29% for RCP 8.5 in Miryang, respectively in the increase and decrease of yield potential for delay of the sowing day.

Determination of proper ground motion prediction equation for reasonable evaluation of the seismic reliability in the water supply systems (상수도 시스템 지진 신뢰성의 합리적 평가를 위한 적정 지반운동예측식 결정)

  • Choi, Jeongwook;Kang, Doosun;Jung, Donghwi;Lee, Chanwook;Yoo, Do Guen;Jo, Seong-Bae
    • Journal of Korea Water Resources Association
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    • v.53 no.9
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    • pp.661-670
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    • 2020
  • The water supply system has a wider installation range and various components of it than other infrastructure, making it difficult to secure stability against earthquakes. Therefore, it is necessary to develop methods for evaluating the seismic performance of water supply systems. Ground Motion Prediction Equation (GMPE) is used to evaluate the seismic performance (e.g, failure probability) for water supply facilities such as pump, water tank, and pipes. GMPE is calculated considering the independent variables such as the magnitude of the earthquake and the ground motion such as PGV (Peak Ground Velocity) and PGA (Peak Ground Acceleration). Since the large magnitude earthquake data has not accumulated much to date in Korea, this study tried to select a suitable GMPE for the domestic earthquake simulation by using the earthquake data measured in Korea. To this end, GMPE formula is calculated based on the existing domestic earthquake and presented the results. In the future, it is expected that the evaluation will be more appropriate if the determined GMPE is used when evaluating the seismic performance of domestic waterworks. Appropriate GMPE can be directly used to evaluate hydraulic seismic performance of water supply networks. In other words, it is possible to quantify the damage rate of a pipeline during an earthquake through linkage with the pipe failure probability model, and it is possible to derive more reasonable results when estimating the water outage or low-pressure area due to pipe damages. Finally, the quantifying result of the seismic performance can be used as a design criteria for preparing an optimal restoration plan and proactive seismic design of pipe networks to minimize the damage in the event of an earthquake.