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We report our group’s performance for protein-protein complex structure prediction and scoring in Round 37 of the Critical Assessment of PRediction of Interactions (CAPRI), an objective assessment of protein-protein complex modeling. We demonstrated noticeable improvement in both prediction and scoring compared to previous rounds of CAPRI, with our human predictor group near the top of the rankings and our server scorer group at the top. This is the first time in CAPRI that a server has been the top scorer group. To predict protein-protein complex structures, we used both multi-chain template-based modeling (TBM) and our protein-protein docking program, LZ-erD. LZerD represents protein surfaces using 3D Zernike descriptors (3DZD), which are based on a mathematical series expansion of a 3D function. Because 3DZD are a soft representation of the protein surface, LZerD is tolerant to small conformational changes, making it well suited to docking unbound and TBM structures. The key to our improved performance in CAPRI Round 37 was to combine multi-chain TBM and docking. As opposed to our previous strategy of performing docking for all target complexes, we used TBM when multi-chain templates were available and docking otherwise. We also describe the combination of multiple scoring functions used by our server scorer group, which achieved the top rank for the scorer phase.

We report the performance of protein-protein docking predictions by our group for recent rounds of the Critical Assessment of Prediction of Interactions (CAPRI), a community-wide assessment of state-of-the-art docking methods. Our prediction procedure uses a protein-protein docking program named LZerD developed in our group. LZerD represents a protein surface with 3D Zernike descriptors (3DZD), which are based on a mathematical series expansion of a 3D function. The appropriate soft representation of protein surface with 3DZD makes the method more tolerant to conformational change of proteins upon docking, which adds an advantage for unbound docking. Docking was guided by interface residue prediction performed with BindML and cons-PPISP as well as literature information when available. The generated docking models were ranked by a combination of scoring functions, including PRESCO, which evaluates the native-likeness of residues' spatial environments in structure models. First, we discuss the overall performance of our group in the CAPRI prediction rounds and investigate the reasons for unsuccessful cases. Then, we examine the performance of several knowledge-based scoring functions and their combinations for ranking docking models. It was found that the quality of a pool of docking models generated by LZerD, that is whether or not the pool includes near-native models, can be predicted by the correlation of multiple scores. Although the current analysis used docking models generated by LZerD, findings on scoring functions are expected to be universally applicable to other docking methods. Proteins 2017; 85:513-527. © 2016 Wiley Periodicals, Inc.

This paper proposes a nonlinear model for more accurate and efficient dynamic analysis of a rotating cantilever beam with elastic deformation. The proposed nonlinear model is described by partial integro-differential equations with non-Cartesian deformation variables, i.e., the stretch, chordwise and flapwise deformations. After the equations of motion are discretized by using the mode superposition method, dynamic responses are computed by applying the Newmark time integration method to the discretized equations. To show the accuracy and efficiency of the proposed model, convergence characteristics and dynamic responses for the present model are compared with those for previous models. This study shows that the proposed model not only yields good accuracy and efficiency in terms of computation, but also overcomes the limitations of a previous conventional nonlinear model expressed by Cartesian variables.

SMART is a small sized integral type pressurized water reactor and its design minimizes the potential for an occurrence of transients and accidents. To achieve these purposes, engineered safety features enhance the accident resistance. A large volume of semi-passive pressurizer can accommodate a wide range of pressure transients. Low core power density increases the thermal margin, and negative fuel and moderator temperature coefficients yield beneficial effects on a core self-stabilization, and limit the reactor power during accidents. Considering the enhanced engineered safety features and design characteristics, anticipated transient without scram scenarios are adopted to evaluate the strength of the SMART design. The peak pressure does not exceed 116% of the nominal pressure and the fuel can maintain its integrity for the transient. The intrinsic SMART design characteristics having passive safety features and a large primary coolant inventory can maintain a stable condition safely although the reactor protection and diverse protection systems are not available for the anticipated transient without scram transients.

An accurate scoring function that can select near-native structure models from a pool of alternative models is key for successful protein structure prediction. For the critical assessment of techniques for protein structure prediction (CASP) 11, we have built a protocol of protein structure prediction that has novel coarse-grained scoring functions for selecting decoys as the heart of its pipeline. The score named PRESCO (Protein Residue Environment SCOre) developed recently by our group evaluates the native-likeness of local structural environment of residues in a structure decoy considering positions and the depth of side-chains of spatially neighboring residues. We also introduced a helix interaction potential as an additional scoring function for selecting decoys. The best models selected by PRESCO and the helix interaction potential underwent structure refinement, which includes side-chain modeling and relaxation with a short molecular dynamics simulation. Our protocol was successful, achieving the top rank in the free modeling category with a significant margin of the accumulated Z-score to the subsequent groups when the top 1 models were considered. Proteins 2016; 84(Suppl 1):105-117. © 2015 Wiley Periodicals, Inc.

Pectin methylesterases (PMEs) catalyze the demethylesterification of homogalacturonan domains of pectin in plant cell walls and are regulated by endogenous pectin methylesterase inhibitors (PMEIs). In Arabidopsis dark-grown hypocotyls, one PME (AtPME3) and one PMEI (AtPMEI7) were identified as potential interacting proteins. Using RT-quantitative PCR analysis and gene promoter::GUS fusions, we first showed that AtPME3 and AtPMEI7 genes had overlapping patterns of expression in etiolated hypocotyls. The two proteins were identified in hypocotyl cell wall extracts by proteomics. To investigate the potential interaction between AtPME3 and AtPMEI7, both proteins were expressed in a heterologous system and purified by affinity chromatography. The activity of recombinant AtPME3 was characterized on homogalacturonans (HGs) with distinct degrees/patterns of methylesterification. AtPME3 showed the highest activity at pH 7.5 on HG substrates with a degree of methylesterification between 60 and 80% and a random distribution of methyl esters. On the best HG substrate, AtPME3 generates long non-methylesterified stretches and leaves short highly methylesterified zones, indicating that it acts as a processive enzyme. The recombinant AtPMEI7 and AtPME3 interaction reduces the level of demethylesterification of the HG substrate but does not inhibit the processivity of the enzyme. These data suggest that the AtPME3·AtPMEI7 complex is not covalently linked and could, depending on the pH, be alternately formed and dissociated. Docking analysis indicated that the inhibition of AtPME3 could occur via the interaction of AtPMEI7 with a PME ligand-binding cleft structure. All of these data indicate that AtPME3 and AtPMEI7 could be partners involved in the fine tuning of HG methylesterification during plant development.

CUPID-SG (CUPID code for Steam Generators) is a computer code for analyzing two-phase flows and heat transfer in PWR steam generators. It was derived from CUPID (Component Unstructured Program for Interfacial Dynamics), which is a component-scale thermo-hydraulic analysis code developed at KAERI (Korea Atomic Energy Research Institute). CUPID-SG shares the code structure with CUPID, which adopts two-fluid, three-field conservation equations, and semi-implicit numerical algorithms. CUPID-SG supports unstructured meshes to handle complex geometries, and adopts constitutive models of two-fluid model based system analysis codes for two-phase boiling flows. FRIGG tests are the benchmark in confirming the correct implementation of the transport models and the applicability of CUPID-SG to two-phase flows over heated tube bundles. A comparison with the FRIGG experiments showed that the constitutive models are properly implemented, and that CUPID-SG is capable of analyzing vertical two-phase boiling flows over tube bundles typically appearing in steam generators.

We developed a new representation of local amino acid environments in protein structures called the Side-chain Depth Environment (SDE). An SDE defines a local structural environment of a residue considering the coordinates and the depth of amino acids that locate in the vicinity of the side-chain centroid of the residue. SDEs are general enough that similar SDEs are found in protein structures with globally different folds. Using SDEs, we developed a procedure called PRESCO (Protein Residue Environment SCOre) for selecting native or near-native models from a pool of computational models. The procedure searches similar residue environments observed in a query model against a set of representative native protein structures to quantify how native-like SDEs in the model are. When benchmarked on commonly used computational model datasets, our PRESCO compared favorably with the other existing scoring functions in selecting native and near-native models.

The CUPID code has been developed at KAERI for a transient, three-dimensional analysis of a two-phase flow in light water nuclear reactor components. It can provide both a component-scale and a CFD-scale simulation by using a porous media or an open media model for a two-phase flow. In this paper, recent advances in the CUPID code are presented in three sections. First, the domain decomposition parallel method implemented in the CUPID code is described with the parallel efficiency test for multiple processors. Then, the coupling of CUPID-MARS via heat structure is introduced, where CUPID has been coupled with a system-scale thermal-hydraulics code, MARS, through the heat structure. The coupled code has been applied to a multi-scale thermal-hydraulic analysis of a pool mixing test. Finally, CUPID-SG is developed for analyzing two-phase flows in PWR steam generators. Physical models and validation results of CUPID-SG are discussed.

A new modeling method for the vibration analysis of a rotating cantilever beam is proposed and compared to the other modeling methods. Applying the Hamilton principle, the equations for the axial, chordwise and flapwise motions are derived. During the derivation of these equations, the nonlinear von Karman strain and the corresponding linear stress are used to consider the stiffening effect due to rotation. The derived equations of motion obtained from the proposed method are analytically and numerically compared to equations from the previous modeling methods. Computations of the natural frequencies and time responses show that the described equations of motion are more reliable than the equations of the other modeling methods.

Clinical risk factors (CRFs), either alone or in combination with bone mineral density, are used to determine the fracture risk for clinical assessment and to determine intervention thresholds. Because fracture risk is strongly affected by ethnicity and population-specific differences, we sought to identify Korean-specific CRFs for fracture, in combination with quantitative ultrasound (qUS) measurements of the radius and tibia. A total of 9351 subjects (4732 men and 4619 women) aged 40 to 69 years were followed for a mean of 46.3 ± 2.2 months. We obtained CRF information using a standardized questionnaire and measured anthropometric variables. Speed of sound at the radius (SoSR) and tibia (SoST) were measured by qUS. Fracture events were recorded using a questionnaire, and a height-loss threshold was used as an indicator of vertebral fracture. Relative risks were calculated by Cox regression analysis. A total of 195 subjects (61 men and 134 women) suffered low-trauma fractures. Older age, lower body mass index (BMI), and previous fracture history were positively associated with fracture risk in both sexes. Decreased hip circumference, lack of regular exercise, higher alcohol intake, menopause, and osteoarthritis history were further independent CRFs for fracture in women. However, neither SoSR nor SoST was independently associated with fracture risk. In this study, we identified the major Korean-specific CRFs for fracture and found that smaller hip circumference was a novel risk factor. This information will allow optimal risk-assessment targeting Koreans for whom treatment would provide the greatest benefit. © 2010 American Society for Bone and Mineral Research

The SuperCritical Water-cooled Reactor (SCWR) is one of the candidates for the fourth-generation nuclear power plant, and it uses light water as a coolant. Heat transfer between a fuel assembly and...

Heat transfer experiments in an annulus passage were performed using SPHINX(Supercritical Pressure Heat Transfer Investigation for NeXt Generation), which was constructed at KAERI(Korea Atomic Energy Research Institute), to investigate the heat transfer behaviors of supercritical . was selected as the working fluid to utilize its low critical pressure and temperature when compared with water. The mass flux was in the range of 400 to 1200 and the heat flux was chosen at rates up to 150 . The selected pressures were 7.75 and 8.12 MPa. At lower mass fluxes, heat transfer deterioration occurs if the heat flux increases beyond a certain value. Comparison with the tube test results showed that the degree of heat transfer deterioration in the heat flux was smaller than that in the tube. In addition, the Nusselt number correlation for a normal heat transfer mode is presented.

A heat transfer test facility, SPHINX, which uses carbon dioxide as a medium at supercritical pressures, has been built at KAERI. A series of experiments are under way for various geometries including tubes of several diameters and narrow annulus passages of a concentric and eccentric layout. The experiments aim to collect heat transfer data and to provide an empirical heat transfer correlation required for a SCWR design. In this paper the test results for tubes of 4.4 mm and 9.0 mm IDs, and a concentric annular passage (ϕ8 mm × ϕ10 mm × L1800 mm) are presented for certain combinations of the heat fluxes and mass fluxes. The heat transfer coefficients produced in the tests were compared with those from the existing heat transfer correlations with different media. A new correlation was introduced for the experiment data presented in this paper.

The determination of the hydrogen concentrations in coal and metal samples were investigated by using the PGAA system at the HANARO Research Reactor, KAERI. The calibration curve of the hydrogen concentration was obtained from a standard sample and the effects of the interference peaks near the gamma-energy region of hydrogen were investigated. The background in the hydrogen peak of a prompt gamma-ray spectrum was measured for the sample chamber and shielding materials of an atmospheric state. The combined uncertainties estimated for the analysis procedure were in the range of 4–5%. Two kinds of certified reference materials, NIST SRM 1632c (Coal), NIST SRM 173c (Titaniumbase Alloy) and NIST SRM 2453 (Titanium Alloy) were used to verify the accuracy and precision of the measurement. The relative error was in the range of 3–6% and the relative standard deviation were less than 4%.

In the boron neutron capture therapy, an accurate determination of the boron content in a biological sample is very important. The boron content was investigated with a standard solution of boron which was administered intraperitoneally with a dose of 750 mg/kg body weight into mice induced cancer cells and tumors. The boron content for two types of a sample was compared to the boronophenylalanine for the tumor and the ethylamine derivatives for the induced cancer cell, which were also investigated for their accumulation rate in each organ such as blood, spleen, liver, kidney and brain. An analytical quality control was carried out by using certified reference materials such as Peach Leaves, Apple Leaves and Spinach Leaves. The relative error of the measured values was in good agreement within 2% to the certified values.

Heat transfer test facility, SPHINX (Supercritical Pressure Heat Transfer Investigation for NeXt Generation), was constructed at KAERI (Korea Atomic Energy Research Institute) for an investigation of the thermal-hydraulic behaviors of supercritical CO 2 at the various geometries of the test section. The test data will be used for the reactor core design of the SCWR (Supercritical Water-cooled Reactor). As a working fluid, CO 2 was selected to make use of the low critical pressure and temperature of CO 2 compared with water. An experimental study was carried out in the SPHINX to investigate the characteristics of heat transfer and pressure drop at a vertical single tube with an inside diameter of 4.4 mm in case of an upward flow of supercritical CO 2 . The heat and mass fluxes were varied at a given pressure. The mass flux was in the range of 400∼1,200kg/m 2 s and the heat flux was chosen up to 150kW/m 2 . The selected pressures were 7.75, 8.12, and 8.85MPa. A heat transfer deterioration occurred at the lower mass fluxes. The experimental heat transfer coefficients were compared with the ones predicted by several existing correlations. The standard deviation was about 20% for each correlation and an apparent discrepancy was not found among the correlations. The major components of the pressure drop were a gravitational pressure drop and a frictional pressure drop. The frictional pressure drop increases as the mass flux and heat flux increase.

This paper presents a set of numerical procedure to innovate CFD code into a PWR component analysis code. A porous media approach is adapted to two-fluid model and conductor model, and a pack of constitutive relations close the numerical model into a PWR component analysis code. The separate verification calculations on conductor model and porous media approach, and the validation calculation for the integrated component-scale code are introduced.Copyright © 2014 by ASME

CUPID-SG is a component scale thermal-hydraulic analysis tool based on CUPID, which is intended to be a computer code for analyzing two-phase flows in porous media with tube bundles such as PWR steam generators. CUPID-SG adopts two-fluid, three-field conservation equations, and uses an in-house semi-implicit solver to obtain numerical efficiency. CUPID-SG can handle unstructured meshes that enable its application in complex geometries. CUPID-SG also has constitutive models for a two-phase flow map, interfacial heat and mass transfer, interfacial drag, wall friction, wall heating, and heat partitioning. CUPID-SG is benchmarked against a few cases of FRIGG tests to confirm that the transport models are correctly implemented and the code is applicable to a two-phase flow over tube bundles. The comparison showed that the constitutive models are properly implemented and CUPID-SG is capable of analyzing a two-phase boiling flow over tube bundles.Copyright © 2013 by ASME

The technique of simultaneous localization and mapping has received much attention recently in mobile robotics. When map is being built, robot memorizes environmental information on the plane of grid or topology. Several approaches about this research have been presented so far, but most of them use mapping technique as either grid-based map or topology-based map. This paper proposes some algorithms integrating grid and topology map and its performance is faster and more stable. The proposed scheme uses an occupancy grid map in representing the environment and then formulate topological information in path finding by A* algorithm. The localization process and the dynamic obstacle avoidance can be accomplished by topological information on grid map. On simulator mapping process is shown and the shortest path is decided on grid based map. Then topological information such as direction, distance is calculated on simulator program then transmitted to robot hardware devices. Three ultrasonic sensors and electronic compass are implemented on our mobile robot and two DC geared motor wheels are individually controlled by PD control method. Simulations and experimental results show the performance and efficiency of the proposed scheme.