Approaches for Modelling the Residual Service Life of Marine Concrete Structures

Directory of Open Access Journals (Sweden)

Amir Rahimi

2014-01-01

Full Text Available This paper deals with the service life design of existing reinforced concrete structures in a marine environment. The general procedure of condition assessment for estimating the residual service life of structures before a repair measure is illustrated. For assessment of the residual service life of structures which have undergone a repair measure a simplified mathematical model of chloride diffusion in a 2-layer system is presented. Preliminary probabilistic calculations demonstrate the effect of various conditions on the residual service life. First studies of the chloride diffusion in a 2-layer system have been conducted using the finite element method. Results of a long-term exposure test are presented to illustrate the performance of two different repair materials. The distribution of residual chlorides after application of a repair material is being studied in laboratory investigations. The residual chlorides migrate from the concrete layer into the new layer immediately after the repair material has been applied to the concrete member. The content and gradient of residual chlorides, along with the thickness and the chloride ingress resistance of both the remaining and the new layer of cover, will determine the residual service life of the repaired structures.

The Effect of Stochastically Varying Creep Parameters on Residual Stresses in Ceramic Matrix Composites

Science.gov (United States)

Pineda, Evan J.; Mital, Subodh K.; Bednarcyk, Brett A.; Arnold, Steven M.

2015-01-01

Constituent properties, along with volume fraction, have a first order effect on the microscale fields within a composite material and influence the macroscopic response. Therefore, there is a need to assess the significance of stochastic variation in the constituent properties of composites at the higher scales. The effect of variability in the parameters controlling the time-dependent behavior, in a unidirectional SCS-6 SiC fiber-reinforced RBSN matrix composite lamina, on the residual stresses induced during processing is investigated numerically. The generalized method of cells micromechanics theory is utilized to model the ceramic matrix composite lamina using a repeating unit cell. The primary creep phases of the constituents are approximated using a Norton-Bailey, steady state, power law creep model. The effect of residual stresses on the proportional limit stress and strain to failure of the composite is demonstrated. Monte Carlo simulations were conducted using a normal distribution for the power law parameters and the resulting residual stress distributions were predicted.

BLAST-based structural annotation of protein residues using Protein Data Bank.

Science.gov (United States)

Singh, Harinder; Raghava, Gajendra P S

2016-01-25

In the era of next-generation sequencing where thousands of genomes have been already sequenced; size of protein databases is growing with exponential rate. Structural annotation of these proteins is one of the biggest challenges for the computational biologist. Although, it is easy to perform BLAST search against Protein Data Bank (PDB) but it is difficult for a biologist to annotate protein residues from BLAST search. A web-server StarPDB has been developed for structural annotation of a protein based on its similarity with known protein structures. It uses standard BLAST software for performing similarity search of a query protein against protein structures in PDB. This server integrates wide range modules for assigning different types of annotation that includes, Secondary-structure, Accessible surface area, Tight-turns, DNA-RNA and Ligand modules. Secondary structure module allows users to predict regular secondary structure states to each residue in a protein. Accessible surface area predict the exposed or buried residues in a protein. Tight-turns module is designed to predict tight turns like beta-turns in a protein. DNA-RNA module developed for predicting DNA and RNA interacting residues in a protein. Similarly, Ligand module of server allows one to predicted ligands, metal and nucleotides ligand interacting residues in a protein. In summary, this manuscript presents a web server for comprehensive annotation of a protein based on similarity search. It integrates number of visualization tools that facilitate users to understand structure and function of protein residues. This web server is available freely for scientific community from URL http://crdd.osdd.net/raghava/starpdb .

Residual stress improving method for reactor structural component and residual stress improving device therefor

Energy Technology Data Exchange (ETDEWEB)

Enomoto, Kunio; Otaka, Masahiro; Kurosawa, Koichi; Saito, Hideyo; Tsujimura, Hiroshi; Tamai, Yasukata; Urashiro, Keiichi; Mochizuki, Masato

1996-09-03

The present invention is applied to a BWR type reactor, in which a high speed jetting flow incorporating cavities is collided against the surface of reactor structural components to form residual compression stresses on the surface layer of the reactor structural components thereby improving the stresses on the surface. Namely, a water jetting means is inserted into the reactor container filled with reactor water. Purified water is pressurized by a pump and introduced to the water jetting means. The purified water jetted from the water jetting means and entraining cavities is abutted against the surface of the reactor structural components. With such procedures, since the purified water is introduced to the water jetting means by the pump, the pump is free from contamination of radioactive materials. As a result, maintenance and inspection for the pump can be facilitated. Further, since the purified water injection flow entraining cavities is abutted against the surface of the reactor structural components being in contact with reactor water, residual compression stresses are exerted on the surface of the reactor structural components. As a result, occurrence of stress corrosion crackings of reactor structural components is suppressed. (I.S.)

Residual stress improving method for reactor structural component and residual stress improving device therefor

International Nuclear Information System (INIS)

Enomoto, Kunio; Otaka, Masahiro; Kurosawa, Koichi; Saito, Hideyo; Tsujimura, Hiroshi; Tamai, Yasukata; Urashiro, Keiichi; Mochizuki, Masato.

1996-01-01

The present invention is applied to a BWR type reactor, in which a high speed jetting flow incorporating cavities is collided against the surface of reactor structural components to form residual compression stresses on the surface layer of the reactor structural components thereby improving the stresses on the surface. Namely, a water jetting means is inserted into the reactor container filled with reactor water. Purified water is pressurized by a pump and introduced to the water jetting means. The purified water jetted from the water jetting means and entraining cavities is abutted against the surface of the reactor structural components. With such procedures, since the purified water is introduced to the water jetting means by the pump, the pump is free from contamination of radioactive materials. As a result, maintenance and inspection for the pump can be facilitated. Further, since the purified water injection flow entraining cavities is abutted against the surface of the reactor structural components being in contact with reactor water, residual compression stresses are exerted on the surface of the reactor structural components. As a result, occurrence of stress corrosion crackings of reactor structural components is suppressed. (I.S.)

Standard test method for determining the effective elastic parameter for X-ray diffraction measurements of residual stress

CERN Document Server

American Society for Testing and Materials. Philadelphia

1998-01-01

1.1 This test method covers a procedure for experimentally determining the effective elastic parameter, Eeff, for the evaluation of residual and applied stresses by X-ray diffraction techniques. The effective elastic parameter relates macroscopic stress to the strain measured in a particular crystallographic direction in polycrystalline samples. Eeff should not be confused with E, the modulus of elasticity. Rather, it is nominally equivalent to E/(1 + ν) for the particular crystallographic direction, where ν is Poisson's ratio. The effective elastic parameter is influenced by elastic anisotropy and preferred orientation of the sample material. 1.2 This test method is applicable to all X-ray diffraction instruments intended for measurements of macroscopic residual stress that use measurements of the positions of the diffraction peaks in the high back-reflection region to determine changes in lattice spacing. 1.3 This test method is applicable to all X-ray diffraction techniques for residual stress measurem...

Structural and sequence features of two residue turns in beta-hairpins.

Science.gov (United States)

Madan, Bharat; Seo, Sung Yong; Lee, Sun-Gu

2014-09-01

Beta-turns in beta-hairpins have been implicated as important sites in protein folding. In particular, two residue β-turns, the most abundant connecting elements in beta-hairpins, have been a major target for engineering protein stability and folding. In this study, we attempted to investigate and update the structural and sequence properties of two residue turns in beta-hairpins with a large data set. For this, 3977 beta-turns were extracted from 2394 nonhomologous protein chains and analyzed. First, the distribution, dihedral angles and twists of two residue turn types were determined, and compared with previous data. The trend of turn type occurrence and most structural features of the turn types were similar to previous results, but for the first time Type II turns in beta-hairpins were identified. Second, sequence motifs for the turn types were devised based on amino acid positional potentials of two-residue turns, and their distributions were examined. From this study, we could identify code-like sequence motifs for the two residue beta-turn types. Finally, structural and sequence properties of beta-strands in the beta-hairpins were analyzed, which revealed that the beta-strands showed no specific sequence and structural patterns for turn types. The analytical results in this study are expected to be a reference in the engineering or design of beta-hairpin turn structures and sequences. © 2014 Wiley Periodicals, Inc.

Residue-based Coordinated Selection and Parameter Design of Multiple Power System Stabilizers (PSSs)

DEFF Research Database (Denmark)

Su, Chi; Hu, Weihao; Fang, Jiakun

2013-01-01

data from time domain simulations. Then a coordinated approach for multiple PSS selection and parameter design based on residue method is proposed and realized in MATLAB m-files. Particle swarm optimization (PSO) is adopted in the coordination process. The IEEE 39-bus New England system model...

Residual strength evaluation of concrete structural components ...

Indian Academy of Sciences (India)

This paper presents methodologies for residual strength evaluation of concrete structural components using linear elastic and nonlinear fracture mechanics principles. The effect of cohesive forces due to aggregate bridging has been represented mathematically by employing tension softening models. Various tension ...

On the relationship between residue structural environment and sequence conservation in proteins.

Science.gov (United States)

Liu, Jen-Wei; Lin, Jau-Ji; Cheng, Chih-Wen; Lin, Yu-Feng; Hwang, Jenn-Kang; Huang, Tsun-Tsao

2017-09-01

Residues that are crucial to protein function or structure are usually evolutionarily conserved. To identify the important residues in protein, sequence conservation is estimated, and current methods rely upon the unbiased collection of homologous sequences. Surprisingly, our previous studies have shown that the sequence conservation is closely correlated with the weighted contact number (WCN), a measure of packing density for residue's structural environment, calculated only based on the C α positions of a protein structure. Moreover, studies have shown that sequence conservation is correlated with environment-related structural properties calculated based on different protein substructures, such as a protein's all atoms, backbone atoms, side-chain atoms, or side-chain centroid. To know whether the C α atomic positions are adequate to show the relationship between residue environment and sequence conservation or not, here we compared C α atoms with other substructures in their contributions to the sequence conservation. Our results show that C α positions are substantially equivalent to the other substructures in calculations of various measures of residue environment. As a result, the overlapping contributions between C α atoms and the other substructures are high, yielding similar structure-conservation relationship. Take the WCN as an example, the average overlapping contribution to sequence conservation is 87% between C α and all-atom substructures. These results indicate that only C α atoms of a protein structure could reflect sequence conservation at the residue level. © 2017 Wiley Periodicals, Inc.

A tool for calculating binding-site residues on proteins from PDB structures

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Hu Jing

2009-08-01

Full Text Available Abstract Background In the research on protein functional sites, researchers often need to identify binding-site residues on a protein. A commonly used strategy is to find a complex structure from the Protein Data Bank (PDB that consists of the protein of interest and its interacting partner(s and calculate binding-site residues based on the complex structure. However, since a protein may participate in multiple interactions, the binding-site residues calculated based on one complex structure usually do not reveal all binding sites on a protein. Thus, this requires researchers to find all PDB complexes that contain the protein of interest and combine the binding-site information gleaned from them. This process is very time-consuming. Especially, combing binding-site information obtained from different PDB structures requires tedious work to align protein sequences. The process becomes overwhelmingly difficult when researchers have a large set of proteins to analyze, which is usually the case in practice. Results In this study, we have developed a tool for calculating binding-site residues on proteins, TCBRP http://yanbioinformatics.cs.usu.edu:8080/ppbindingsubmit. For an input protein, TCBRP can quickly find all binding-site residues on the protein by automatically combining the information obtained from all PDB structures that consist of the protein of interest. Additionally, TCBRP presents the binding-site residues in different categories according to the interaction type. TCBRP also allows researchers to set the definition of binding-site residues. Conclusion The developed tool is very useful for the research on protein binding site analysis and prediction.

Simultaneous determination of aquifer parameters and zone structures with fuzzy c-means clustering and meta-heuristic harmony search algorithm

Science.gov (United States)

Ayvaz, M. Tamer

2007-11-01

This study proposes an inverse solution algorithm through which both the aquifer parameters and the zone structure of these parameters can be determined based on a given set of observations on piezometric heads. In the zone structure identification problem fuzzy c-means ( FCM) clustering method is used. The association of the zone structure with the transmissivity distribution is accomplished through an optimization model. The meta-heuristic harmony search ( HS) algorithm, which is conceptualized using the musical process of searching for a perfect state of harmony, is used as an optimization technique. The optimum parameter zone structure is identified based on three criteria which are the residual error, parameter uncertainty, and structure discrimination. A numerical example given in the literature is solved to demonstrate the performance of the proposed algorithm. Also, a sensitivity analysis is performed to test the performance of the HS algorithm for different sets of solution parameters. Results indicate that the proposed solution algorithm is an effective way in the simultaneous identification of aquifer parameters and their corresponding zone structures.

Efficient identification of critical residues based only on protein structure by network analysis.

Directory of Open Access Journals (Sweden)

Michael P Cusack

2007-05-01

Full Text Available Despite the increasing number of published protein structures, and the fact that each protein's function relies on its three-dimensional structure, there is limited access to automatic programs used for the identification of critical residues from the protein structure, compared with those based on protein sequence. Here we present a new algorithm based on network analysis applied exclusively on protein structures to identify critical residues. Our results show that this method identifies critical residues for protein function with high reliability and improves automatic sequence-based approaches and previous network-based approaches. The reliability of the method depends on the conformational diversity screened for the protein of interest. We have designed a web site to give access to this software at http://bis.ifc.unam.mx/jamming/. In summary, a new method is presented that relates critical residues for protein function with the most traversed residues in networks derived from protein structures. A unique feature of the method is the inclusion of the conformational diversity of proteins in the prediction, thus reproducing a basic feature of the structure/function relationship of proteins.

Main Parameters Characterization of Bulk CMOS Cross-Like Hall Structures

Directory of Open Access Journals (Sweden)

Maria-Alexandra Paun

2016-01-01

Full Text Available A detailed analysis of the cross-like Hall cells integrated in regular bulk CMOS technological process is performed. To this purpose their main parameters have been evaluated. A three-dimensional physical model was employed in order to evaluate the structures. On this occasion, numerical information on the input resistance, Hall voltage, conduction current, and electrical potential distribution has been obtained. Experimental results for the absolute sensitivity, offset, and offset temperature drift have also been provided. A quadratic behavior of the residual offset with the temperature was obtained and the temperature points leading to the minimum offset for the three Hall cells were identified.

Verification and Validation of Residual Stresses in Bi-Material Composite Rings

Energy Technology Data Exchange (ETDEWEB)

Nelson, Stacy Michelle [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Hanson, Alexander Anthony [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Briggs, Timothy [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Werner, Brian T. [Sandia National Lab. (SNL-CA), Livermore, CA (United States)

2017-07-01

Process-induced residual stresses commonly occur in composite structures composed of dissimilar materials. These residual stresses form due to differences in the composite materials’ coefficients of thermal expansion and the shrinkage upon cure exhibited by polymer matrix materials. Depending upon the specific geometric details of the composite structure and the materials’ curing parameters, it is possible that these residual stresses could result in interlaminar delamination or fracture within the composite. Therefore, the consideration of potential residual stresses is important when designing composite parts and their manufacturing processes. However, the experimental determination of residual stresses in prototype parts can be time and cost prohibitive. As an alternative to physical measurement, it is possible for computational tools to be used to quantify potential residual stresses in composite prototype parts. Therefore, the objectives of the presented work are to demonstrate a simplistic method for simulating residual stresses in composite parts, as well as the potential value of sensitivity and uncertainty quantification techniques during analyses for which material property parameters are unknown. Specifically, a simplified residual stress modeling approach, which accounts for coefficient of thermal expansion mismatch and polymer shrinkage, is implemented within the Sandia National Laboratories’ developed SIERRA/SolidMechanics code. Concurrent with the model development, two simple, bi-material structures composed of a carbon fiber/epoxy composite and aluminum, a flat plate and a cylinder, are fabricated and the residual stresses are quantified through the measurement of deformation. Then, in the process of validating the developed modeling approach with the experimental residual stress data, manufacturing process simulations of the two simple structures are developed and undergo a formal verification and validation process, including a mesh

The effects of machine parameters on residual stress determined using micro-Raman spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Sparks, R.G.; Enloe, W.S.; Paesler, M.A.

1988-12-01

The effects of machine parameters on residual stresses in single point diamond turned silicon and germanium have been investigated using micro-Raman spectroscopy. Residual stresses were sampled across ductile feed cuts in < 100 > silicon and germanium which were single point diamond turned using a variety of feed rates, rake angles and clearance angles. High spatial resolution micro-Raman spectra (1{mu}m spot) were obtained in regions of ductile cutting where no visible surface damage was present. The use of both 514-5nm and 488.0nm excitation wavelengths, by virtue of their differing characteristic penetration depths in the materials, allowed determinations of stress profiles as a function of depth into the sample. Previous discussions have demonstrated that such Raman spectra will exhibit asymmetrically broadened peaks which are characteristic of the superposition of a continuum of Raman scatterers from the various depths probed. Depth profiles of residual stress were obtained using computer deconvolution of the resulting asymmetrically broadened raman spectra.

Residual stresses in laser direct metal deposited Waspaloy

Energy Technology Data Exchange (ETDEWEB)

Moat, R.J., E-mail: richard.moat@manchester.ac.uk [School of Materials, University of Manchester, Grosvenor Street, Manchester M1 7HS (United Kingdom); Pinkerton, A.J.; Li, L. [Laser Processing Research Centre, School of Mechanical, Aerospace and Civil Engineering, University of Manchester, M60 1QD (United Kingdom); Withers, P.J.; Preuss, M. [School of Materials, University of Manchester, Grosvenor Street, Manchester M1 7HS (United Kingdom)

2011-03-15

Research highlights: {yields} Neutron diffraction and the contour method show good agreement. {yields} Tensile stresses found parallel to the surfaces. {yields} Compressive stresses within the bulk of the structures. {yields} Residual stress weakly dependent on the laser pulse parameters. {yields} Maximum tensile residual stress unaffected across range of pulse parameters used. - Abstract: This paper reports a study into the effect of laser pulse length and duty cycle on the residual stress distributions in multi-track laser direct metal deposits of Waspaloy onto an Inconel 718 substrate. The residual stresses have been evaluated using neutron diffraction and the contour method, while electron microscopy and micro hardness indentation have been used to map the concomitant microstructural variation. In all cases, near the tops of the deposited walls, the longitudinal stresses are tensile towards the mid-length of the wall, while the stresses perpendicular to the substrate are negligible. By contrast near the base of the walls, the stresses along the direction of deposition are small, while the stresses perpendicular to the substrate are compressive at the centre and tensile towards the ends. Consistent with previous observations, the stresses parallel to free surfaces are tensile, balanced by compressive stresses in the interior (an inverse quench stress profile). These profiles have been found to be weakly dependent on the laser pulse parameters, most notably an increase in tensile stress gradient with increasing duty cycle, but the maximum residual stresses are largely unaffected. Furthermore, microstructural analysis has shown that the effect of laser pulse parameters on grain morphology in multi-track thick walls is less marked than previously reported for single-track wall structures.

Residual stresses in laser direct metal deposited Waspaloy

International Nuclear Information System (INIS)

Moat, R.J.; Pinkerton, A.J.; Li, L.; Withers, P.J.; Preuss, M.

2011-01-01

Research highlights: → Neutron diffraction and the contour method show good agreement. → Tensile stresses found parallel to the surfaces. → Compressive stresses within the bulk of the structures. → Residual stress weakly dependent on the laser pulse parameters. → Maximum tensile residual stress unaffected across range of pulse parameters used. - Abstract: This paper reports a study into the effect of laser pulse length and duty cycle on the residual stress distributions in multi-track laser direct metal deposits of Waspaloy onto an Inconel 718 substrate. The residual stresses have been evaluated using neutron diffraction and the contour method, while electron microscopy and micro hardness indentation have been used to map the concomitant microstructural variation. In all cases, near the tops of the deposited walls, the longitudinal stresses are tensile towards the mid-length of the wall, while the stresses perpendicular to the substrate are negligible. By contrast near the base of the walls, the stresses along the direction of deposition are small, while the stresses perpendicular to the substrate are compressive at the centre and tensile towards the ends. Consistent with previous observations, the stresses parallel to free surfaces are tensile, balanced by compressive stresses in the interior (an inverse quench stress profile). These profiles have been found to be weakly dependent on the laser pulse parameters, most notably an increase in tensile stress gradient with increasing duty cycle, but the maximum residual stresses are largely unaffected. Furthermore, microstructural analysis has shown that the effect of laser pulse parameters on grain morphology in multi-track thick walls is less marked than previously reported for single-track wall structures.

Parameter identification of civil engineering structures

Science.gov (United States)

Juang, J. N.; Sun, C. T.

1980-01-01

This paper concerns the development of an identification method required in determining structural parameter variations for systems subjected to an extended exposure to the environment. The concept of structural identifiability of a large scale structural system in the absence of damping is presented. Three criteria are established indicating that a large number of system parameters (the coefficient parameters of the differential equations) can be identified by a few actuators and sensors. An eight-bay-fifteen-story frame structure is used as example. A simple model is employed for analyzing the dynamic response of the frame structure.

Annotating Protein Functional Residues by Coupling High-Throughput Fitness Profile and Homologous-Structure Analysis.

Science.gov (United States)

Du, Yushen; Wu, Nicholas C; Jiang, Lin; Zhang, Tianhao; Gong, Danyang; Shu, Sara; Wu, Ting-Ting; Sun, Ren

2016-11-01

Identification and annotation of functional residues are fundamental questions in protein sequence analysis. Sequence and structure conservation provides valuable information to tackle these questions. It is, however, limited by the incomplete sampling of sequence space in natural evolution. Moreover, proteins often have multiple functions, with overlapping sequences that present challenges to accurate annotation of the exact functions of individual residues by conservation-based methods. Using the influenza A virus PB1 protein as an example, we developed a method to systematically identify and annotate functional residues. We used saturation mutagenesis and high-throughput sequencing to measure the replication capacity of single nucleotide mutations across the entire PB1 protein. After predicting protein stability upon mutations, we identified functional PB1 residues that are essential for viral replication. To further annotate the functional residues important to the canonical or noncanonical functions of viral RNA-dependent RNA polymerase (vRdRp), we performed a homologous-structure analysis with 16 different vRdRp structures. We achieved high sensitivity in annotating the known canonical polymerase functional residues. Moreover, we identified a cluster of noncanonical functional residues located in the loop region of the PB1 β-ribbon. We further demonstrated that these residues were important for PB1 protein nuclear import through the interaction with Ran-binding protein 5. In summary, we developed a systematic and sensitive method to identify and annotate functional residues that are not restrained by sequence conservation. Importantly, this method is generally applicable to other proteins about which homologous-structure information is available. To fully comprehend the diverse functions of a protein, it is essential to understand the functionality of individual residues. Current methods are highly dependent on evolutionary sequence conservation, which is

The influence of plate thickness on the welding residual stresses from submerged arc welding in offshore steel structures

DEFF Research Database (Denmark)

Andreassen, Michael Joachim; Yu, Zhenzhen; Liu, Stephen

2017-01-01

Welding-induced residual tensile stresses and distortion have become a major concern in relation to the structural integrity of welded structures within the offshore wind industry. The stresses have a negative impact on the integrity of the welded joint, as they promote distortion, reduce fatigue...... leading to a better understanding of the distribution and development of the welding residual stresses. This can later be used to optimize the fatigue design, providing a more efficient and improved design. In this context, the current research is expected to benefit the offshore industry by leading...... to an improved design, which consequently may be included in future norms and standards. Submerged Arc Welding (SAW) was used to make a fully penetrated butt weld in 10 mm and 40 mm thick steel plates with the same welding parameters as used in the production procedures. The base material is thermomechanical hot...

A hierarchical structure through imprinting of a polyimide precursor without residual layers

International Nuclear Information System (INIS)

Pai, I-Ting; Hon, Min-Hsiung; Leu, Ing-Chi

2008-01-01

A patterned polyimide without a residual layer is obtained by imprinting with the assistance of a residual solvent. The effects of the wetting behaviors of the poly-amic acid (PAA) solution coated on various surfaces are examined and the formation of hierarchical patterns without residual layers is demonstrated. polydimethylsiloxane (PDMS) and PEI/PDMS are used as imprinting molds with Si and 300 nm SiO 2 /Si as substrates. The results indicate that the various ambits of patterns without a residual layer are formed due to the dewetting phenomena caused by surface tension (Suh 2006 Small 2 832). During imprinting, PDMS with a low surface energy makes the PAA solution flow away from its surface exposing the contact area due to dewetting. Self-organized hierarchical structures are also obtained from this process due to effective dewetting. The present study provides a new approach for fabricating patterns without residual layers and the consequent preparation of hierarchical structures, which is considered to be impossible using the lithographic technique

Model-based leakage localization in drinking water distribution networks using structured residuals

OpenAIRE

Puig Cayuela, Vicenç; Rosich, Albert

2013-01-01

In this paper, a new model based approach to leakage localization in drinking water networks is proposed based on generating a set of structured residuals. The residual evaluation is based on a numerical method based on an enhanced Newton-Raphson algorithm. The proposed method is suitable for water network systems because the non-linearities of the model make impossible to derive analytical residuals. Furthermore, the computed residuals are designed so that leaks are decoupled, which impro...

Annotating Protein Functional Residues by Coupling High-Throughput Fitness Profile and Homologous-Structure Analysis

Directory of Open Access Journals (Sweden)

Yushen Du

2016-11-01

Full Text Available Identification and annotation of functional residues are fundamental questions in protein sequence analysis. Sequence and structure conservation provides valuable information to tackle these questions. It is, however, limited by the incomplete sampling of sequence space in natural evolution. Moreover, proteins often have multiple functions, with overlapping sequences that present challenges to accurate annotation of the exact functions of individual residues by conservation-based methods. Using the influenza A virus PB1 protein as an example, we developed a method to systematically identify and annotate functional residues. We used saturation mutagenesis and high-throughput sequencing to measure the replication capacity of single nucleotide mutations across the entire PB1 protein. After predicting protein stability upon mutations, we identified functional PB1 residues that are essential for viral replication. To further annotate the functional residues important to the canonical or noncanonical functions of viral RNA-dependent RNA polymerase (vRdRp, we performed a homologous-structure analysis with 16 different vRdRp structures. We achieved high sensitivity in annotating the known canonical polymerase functional residues. Moreover, we identified a cluster of noncanonical functional residues located in the loop region of the PB1 β-ribbon. We further demonstrated that these residues were important for PB1 protein nuclear import through the interaction with Ran-binding protein 5. In summary, we developed a systematic and sensitive method to identify and annotate functional residues that are not restrained by sequence conservation. Importantly, this method is generally applicable to other proteins about which homologous-structure information is available.

Maximising municipal solid waste--legume trimming residue mixture degradation in composting by control parameters optimization.

Science.gov (United States)

Cabeza, I O; López, R; Ruiz-Montoya, M; Díaz, M J

2013-10-15

Composting is one of the most successful biological processes for the treatment of the residues enriched in putrescible materials. The optimization of parameters which have an influence on the stability of the products is necessary in order to maximize recycling and recovery of waste components. The influence of the composting process parameters (aeration, moisture, C/N ratio, and time) on the stability parameters (organic matter, N-losses, chemical oxygen demand, nitrate, biodegradability coefficient) of the compost was studied. The composting experiment was carried out using Municipal Solid Waste (MSW) and Legume Trimming Residues (LTR) in 200 L isolated acrylic barrels following a Box-Behnken central composite experimental design. Second-order polynomial models were found for each of the studied compost stability parameter, which accurately described the relationship between the parameters. The differences among the experimental values and those estimated by using the equations never exceeded 10% of the former. Results of the modelling showed that excluding the time, the C/N ratio is the strongest variable influencing almost all the stability parameters studied in this case, with the exception of N-losses which is strongly dependent on moisture. Moreover, an optimized ratio MSW/LTR of 1/1 (w/w), moisture content in the range of 40-55% and moderate to low aeration rate (0.05-0.175 Lair kg(-)(1) min(-1)) is recommended to maximise degradation and to obtain a stable product during co-composting of MSW and LTR. Copyright © 2013 Elsevier Ltd. All rights reserved.

Systematic Review of Uit Parameters on Residual Stresses of Sensitized AA5456 and Field Based Residual Stress Measurements for Predicting and Mitigating Stress Corrosion Cracking

Science.gov (United States)

2014-03-01

University Press, 2009, pp. 820–824. [30] S. Kou, Welding Metallurgy , 2nd ed. Hoboken, NJ: John Wiley and Sons, Inc., 2003. [31] M. N.James et al...around welds in aluminum ship structures both in the laboratory and in the field. Tensile residual stresses are often generated during welding and, in...mitigate and even reverse these tensile residual stresses. This research uses x-ray diffraction to measure residual stresses around welds in AA5456 before

Structural and interaction parameters of thermosensitive native α-elastin biohybrid microgel

Science.gov (United States)

Balaceanu, Andreea; Singh, Smriti; Demco, Dan E.; Möller, Martin

2014-09-01

The structural and water interaction parameters for native, α-elastin biohybrid microgel crosslinked with hydrophilic and hydrophobic crosslinkers are obtained from the volume phase transition temperature behaviour, 1H high-resolution magic-angle sample spinning transverse magnetization relaxation NMR, and modified Flory-Rehner swelling theory. Firstly, considering a homogeneous morphology the number of subchains in the biohybrid microgel, the residual water in deswollen state as a function of crosslink density and the temperature dependence of the Flory biopolymer-water interaction parameters are reported for the biohybrid microgels prepared with hydrophilic (PEG-DGE) and hydrophobic (BS3) crosslinkers. The Flory-Rehner classical approach is subsequently modified taking into account the heterogeneities observed by NMR transverse relaxation measurements. Two differently mobile regions are determined, a hydrophobic domain and a crosslinking domain with relative reduced mobility. For the first time, the influence of chain mobility on the Flory interaction parameter is investigated through a modified Flory state equation. The contributions of amino-acids located in the hydrophobic and crosslinking domains in the polypeptide sequence are separated while analyzing the biopolymer-water interaction.

Uncertainties of Molecular Structural Parameters

International Nuclear Information System (INIS)

Császár, Attila G.

2014-01-01

Full text: The most fundamental property of a molecule is its three-dimensional (3D) structure formed by its constituent atoms (see, e.g., the perfectly regular hexagon associated with benzene). It is generally accepted that knowledge of the detailed structure of a molecule is a prerequisite to determine most of its other properties. What nowadays is a seemingly simple concept, namely that molecules have a structure, was introduced into chemistry in the 19th century. Naturally, the word changed its meaning over the years. Elemental analysis, simple structural formulae, two-dimensional and then 3D structures mark the development of the concept to its modern meaning. When quantum physics and quantum chemistry emerged in the 1920s, the simple concept associating structure with a three-dimensional object seemingly gained a firm support. Nevertheless, what seems self-explanatory today is in fact not so straightforward to justify within quantum mechanics. In quantum chemistry the concept of an equilibrium structure of a molecule is tied to the Born-Oppenheimer approximation but beyond the adiabatic separation of the motions of the nuclei and the electrons the meaning of a structure is still slightly obscured. Putting the conceptual difficulties aside, there are several experimental, empirical, and theoretical techniques to determine structures of molecules. One particular problem, strongly related to the question of uncertainties of “measured” or “computed” structural parameters, is that all the different techniques correspond to different structure definitions and thus yield different structural parameters. Experiments probing the structure of molecules rely on a number of structure definitions, to name just a few: r_0, r_g, r_a, r_s, r_m, etc., and one should also consider the temperature dependence of most of these structural parameters which differ from each other in the way the rovibrational motions of the molecules are treated and how the averaging is

Residual life estimation of cracked aircraft structural components

OpenAIRE

Maksimović, Mirko S.; Vasović, Ivana V.; Maksimović, Katarina S.; Trišović, Nataša; Maksimović, Stevan M.

2018-01-01

The subject of this investigation is focused on developing computation procedure for strength analysis of damaged aircraft structural components with respect to fatigue and fracture mechanics. For that purpose, here will be defined computation procedures for residual life estimation of aircraft structural components such as wing skin and attachment lugs under cyclic loads of constant amplitude and load spectrum. A special aspect of this investigation is based on using of the Strain Energy Den...

Solution structure of the 45-residue ATP-binding peptide of adenylate kinase as determined by 2-D NMR, FTIR, and CD spectroscopy

International Nuclear Information System (INIS)

Fry, D.C.; Byler, D.M.; Susi, H.; Brown, E.M.; Kuby, S.A.; Mildyan, A.S.

1986-01-01

In the X-ray structure of adenylate kinase residues 1-45 exist as 47% α-helix, 29% β-structure (strands and turns) and 24% coil. The solution structure of a synthetic peptide corresponding to residues 1-45, which constitutes the MgATP binding site was studied by 3 independent spectroscopic methods. Globularity of the peptide was shown by its broad NMR resonances which narrow upon denaturation, and by its ability to bind MgATP with similar affinity and conformation as the intact enzyme does. COSY and NOESY NMR methods at 250 and 500 MHz reveal proximities among NH, Cα, and Cβ protons indicative of >20% α-helix, and >20% β-structure. Correlation of regions of secondary structure with the primary sequence by 2D NMR indicates at least one α-helix (res. 23 to 29) and two β-strands (res. 12 to 15 and 34 to 38). The broad amide I band in the deconvoluted FTIR spectrum could be fit as the sum of 4 peaks due to specific secondary structures, yielding ≤=45% α-helix, ≤=40% β-structure and ≥=15% coil. The CD spectrum, from 185-250 nm, interpreted with a 3-parameter basis set, yielded 20 +/- 5% α=helix, and ≤=20% β-structure. The solution structure of peptide 1-45 thus approximates that of residues 1-45 in the crystal

NUMERICAL SIMULATION OF RESIDUAL STRESSES GENERATED IN THE WIRE DRAWING PROCESS FOR DIFFERENT PROCESS PARAMETERS

Directory of Open Access Journals (Sweden)

Juliana Zottis

2014-03-01

Full Text Available The drawing process of steel bars is usually used to check better dimensional accuracy and mechanical properties to the material. In the other hand, the major concern found in manufacturing axes through this process is the appearance of distortion of shape. Such distortions are directly linked to the accumulation of residual stresses generated during the processes. As a result, this paper aims to study the influence of process parameters such as shape of puller, speed and lubrication used in wire drawing analyzing the accumulation of residual stress after the process. The stress analysis was performed by FEM being used two simulation software: Simufact.formingGP and DeformTM. Through these analyzes, it was found that the shape of how the bar is pulled causes a reduction of up to 100 MPa in residual stresses in the center of the bar, which represents an important factor in the study of the possible causes of the distortion. As well as factors speed and homogeneity of lubrication significantly altered the profile of residual stresses in the bar.

Calculation method for residual stress analysis of filament-wound spherical pressure vessels

International Nuclear Information System (INIS)

Knight, C.E. Jr.

1976-01-01

Filament wound spherical pressure vessels may be produced with very high performance factors. These performance factors are a calculation of contained pressure times enclosed volume divided by structure weight. A number of parameters are important in determining the level of performance achieved. One of these is the residual stress state in the fabricated unit. A significant level of an unfavorable residual stress state could seriously impair the performance of the vessel. Residual stresses are of more concern for vessels with relatively thick walls and/or vessels constructed with the highly anisotropic graphite or aramid fibers. A method is established for measuring these stresses. A theoretical model of the composite structure is required. Data collection procedures and techniques are developed. The data are reduced by means of the model and result in the residual stress analysis. The analysis method can be used in process parameter studies to establish the best fabrication procedures

Prediction of welding residual distortions of large structures using a local/global approach

International Nuclear Information System (INIS)

Duan, Y. G.; Bergheau, J. M.; Vincent, Y.; Boitour, F.; Leblond, J. B.

2007-01-01

Prediction of welding residual distortions is more difficult than that of the microstructure and residual stresses. On the one hand, a fine mesh (often 3D) has to be used in the heat affected zone for the sake of the sharp variations of thermal, metallurgical and mechanical fields in this region. On the other hand, the whole structure is required to be meshed for the calculation of residual distortions. But for large structures, a 3D mesh is inconceivable caused by the costs of the calculation. Numerous methods have been developed to reduce the size of models. A local/global approach has been proposed to determine the welding residual distortions of large structures. The plastic strains and the microstructure due to welding are supposed can be determined from a local 3D model which concerns only the weld and its vicinity. They are projected as initial strains into a global 3D model which consists of the whole structure and obviously much less fine in the welded zone than the local model. The residual distortions are then calculated using a simple elastic analysis, which makes this method particularly effective in an industrial context. The aim of this article is to present the principle of the local/global approach then show the capacity of this method in an industrial context and finally study the definition of the local model

Prediction of interface residue based on the features of residue interaction network.

Science.gov (United States)

Jiao, Xiong; Ranganathan, Shoba

2017-11-07

Protein-protein interaction plays a crucial role in the cellular biological processes. Interface prediction can improve our understanding of the molecular mechanisms of the related processes and functions. In this work, we propose a classification method to recognize the interface residue based on the features of a weighted residue interaction network. The random forest algorithm is used for the prediction and 16 network parameters and the B-factor are acting as the element of the input feature vector. Compared with other similar work, the method is feasible and effective. The relative importance of these features also be analyzed to identify the key feature for the prediction. Some biological meaning of the important feature is explained. The results of this work can be used for the related work about the structure-function relationship analysis via a residue interaction network model. Copyright © 2017 Elsevier Ltd. All rights reserved.

Development of residual stress analysis procedure for fitness-for-service assessment of welded structure

International Nuclear Information System (INIS)

Kim, Jong Sung; Jin, Tae Eun; Dong, P.; Prager, M.

2003-01-01

In this study, a state of art review of existing residual stress analysis techniques and representative solutions is presented in order to develop the residual stress analysis procedure for Fitness-For-Service(FFS) assessment of welded structure. Critical issues associated with existing residual stress solutions and their treatments in performing FFS are discussed. It should be recognized that detailed residual stress evolution is an extremely complicated phenomenon that typically involves material-specific thermomechanical/metallurgical response, welding process physics, and structural interactions within a component being welded. As a result, computational procedures can vary significantly from highly complicated numerical techniques intended only to elucidate a small part of the process physics to cost-effective procedures that are deemed adequate for capturing some of the important features in a final residual stress distribution. Residual stress analysis procedure for FFS purposes belongs to the latter category. With this in mind, both residual stress analysis techniques and their adequacy for FFS are assessed based on both literature data and analyses performed in this investigation

Treatment of waste incinerator air-pollution-control residues with FeSO4: Laboratory investigation of design parameters

DEFF Research Database (Denmark)

Jensen, Dorthe Lærke; Christensen, Thomas Højlund; Lundtorp, Kasper

2002-01-01

supplied, the liquid-to-solid ratio of the process, the separation of solids and wastewater, the sequence of material mixing, the possibilities of reuse of water, the feasibility of using secondary (brackish) water, and simple means to improve the wastewater quality. The investigation showed...... that an optimum process configuration could be obtained yielding a stabilised solid product with low leaching of heavy metals and a dischargable wastewater with high contents of salts (in order to remove salts from the solid product) and low concentrations of heavy metals. The amount of iron added to the APC......The key design parameters of a new process for treatment of air-pollution-control (APC) residues (the Ferroxprocess) were investigated in the laboratory. The optimisation involved two different APC-residues from actual incinerator plants. The design parameters considered were: amount of iron oxide...

Recovery and residual stress of SMA wires and applications for concrete structures

International Nuclear Information System (INIS)

Choi, Eunsoo; Cho, Sung-Chul; Park, Taehyo; Hu, Jong Wan; Chung, Young-Soo

2010-01-01

In general, NiTi shape memory alloys are used for applications in civil structures. NiTi SMAs show good superelasticity and shape memory effect properties. However, for application of the shape memory effect, it is desirable for SMAs to show a wide temperature hysteresis, especially for civil structures which are exposed to severe environmental conditions. NiTiNb SMAs, in general, show a wider temperature hysteresis than NiTi SMAs and are more applicable for civil structures. This study examines the temperature hysteresis of NiTiNb and NiTi SMAs, and their recovery and residual stress are investigated. In addition, the tensile behaviors of SMA wires under residual stress are evaluated. This study explains the possible applications for concrete structures with the shape memory effect and illustrates two experimental results of concrete cylinders and reinforced concrete columns. For both tests, SMA wires of NiTiNb and NiTi are used to confine concrete using residual stress. The SMA wire jackets on the concrete cylinders increase the peak strength and the ductility compared to the plain concrete cylinders. In addition, the SMA wire jackets on reinforced concrete columns increase the ductility greatly without flexural strength degradation

Fundamentals of a moderate thermocracking-deep deasphalting combined process of Karamay vacuum residue

Energy Technology Data Exchange (ETDEWEB)

Zhiming, X; Tonghua, L.; Suogi, Z.; Renan, W. [University of Petroleum, State Key Laboratory of Heavy Oil Processing, Beijing (China); Lailong, L.; Zhen, L. [Karamay Petrochemical Company, Petrochemical Research Institute, Karamay (China)

2004-07-01

Thermocracking of heavy oil vacuum residue was carried out to determine the optimum conditions for the thermal cracking of Karamay vacuum residue prior to coke formation. The vacuum residue and the cracked residue after distillation were separated using supercritical fluid extraction and fractionation techniques. Sixteen and thirteen fractions and non-extractable end cuts respectively were separated, and their properties, compositions and average structures determined. Solubility parameters of the end cuts were measured, and those of the fractions calculated. The solubility parameter of the end cut of distilled residue was found to have greatly increased. It was determined that when the difference of the end cut and the extractable fractions amounts to 6.37MPa1/2, in the case of Karamay vacuum residue coke will deposit under thermocracking conditions. Based on the results of a series of solvent deep deasphalting experiments, a scheme for vacuum residue thermocracking and deasphalting of the cracked residue was proposed.

Chemical structure investigation on SFEF fractions of Dagang vacuum residue

Energy Technology Data Exchange (ETDEWEB)

Zhang, Z.; Yan, G.; Zhao, S.; Guo, S. [China Univ. of Petroleum, Beijing (China). State Key Laboratory of Heavy Oil Processing; Zhang, Z. [Beijing Aeronautical Technology Research Center, Beijing (China)

2006-07-01

One of the most important problems in petroleum chemistry is the molecular structure and composition of heavy oil fractions and its importance in applications pertaining to the recovery, refining, and upgrading of petroleum. This paper presented an investigation into the chemical structure on supercritical fluid extraction and fraction (SFEF) factions of Dagang vacuum residue. Dagang vacuum residue was cut into sixteen fractions and a tailing with SFEF instrument. Then, using a chromatography, all SFEF fractions were further separated into four group compositions, notably saturated hydrocarbons, aromatic hydrocarbons, resins and asphaltenes (SARA). Last, the chemical structure was explored through a thorough analysis of the products from the ruthenium ions-catalyzed oxidation (RICO) reaction of those aromatics, resins and asphaltenes. The paper discussed the experiment in terms of samples and chemicals; supercritical fluid extraction and fraction; SARA separation; and RICO. The results and discussions focused on alkyl side chains attached to aromatic carbon; polymethylene bridges connecting two aromatic units; benzenecarboxylic acids an aromatic units; and others. The study has brought to light useful characterization on covalent molecular structure of two typical SFEF fractions, notably the tenth and fifteen fraction. 17 refs., 6 tabs., 16 figs., 1 appendix.

Improved Interaction Potentials for Charged Residues in Proteins

DEFF Research Database (Denmark)

Kepp, Kasper Planeta

2008-01-01

Electrostatic interactions dominate the structure and free energy of biomolecules. To obtain accurate free energies involving charged groups from molecular simulations, OPLS-AA parameters have been reoptimized using Monte Carlo free energy perturbation. New parameters fit a self-consistent, exper......Electrostatic interactions dominate the structure and free energy of biomolecules. To obtain accurate free energies involving charged groups from molecular simulations, OPLS-AA parameters have been reoptimized using Monte Carlo free energy perturbation. New parameters fit a self......, TIP4P or TIP3P; i.e., each water model requires specific water-charged molecule interaction potentials. New models (models 1 and 3) are thus described for both water models. Uncertainties in relative free energies of charged residues are ~2 kcal/mol with the new parameters, due to variations in system...

Effects of interface edge configuration on residual stress in the bonded structures for a divertor application

International Nuclear Information System (INIS)

Kitamura, K.; Nagata, K.; Shibui, M.; Tachikawa, N.; Araki, M.

1998-01-01

Residual stresses in the interface region, that developed at the cool down during the brazing, were evaluated for several bonded structures to assess the mechanical strength of the bonded interface, using thermoelasto-plastic stress analysis. Normal stress components of the residual stresses around the interface edge of graphite-copper (C-Cu) bonded structures were compared for three types of bonded features such as flat-type, monoblock-type and saddle-type. The saddle-type structure was found to be favorable for its relatively low residual stress, easy fabrication accuracy on bonded interface and armor replacement. Residual stresses around the interface edge in three armor materials/copper bonded structures for a divertor plate were also examined for the C-Cu, tungsten-copper (W-Cu) and molybdenum alloy-copper (TZM-Cu), varying the interface wedge angle from 45 to 135 . An optimal bonded configuration for the least value of residual stress was found to have a wedge angle of 45 for the C-Cu, and 135 for both the W-Cu and TZM-Cu bonded ones. (orig.)

Life cycle assessment and residue leaching: The importance of parameter, scenario and leaching data selection

Energy Technology Data Exchange (ETDEWEB)

Allegrini, E., E-mail: elia@env.dtu.dk [Technical University of Denmark, Department of Environmental Engineering, Building 115, 2800 Lyngby (Denmark); Butera, S. [Technical University of Denmark, Department of Environmental Engineering, Building 115, 2800 Lyngby (Denmark); Kosson, D.S. [Vanderbilt University, Department of Civil and Environmental Engineering, Box 1831 Station B, Nashville, TN 37235 (United States); Van Zomeren, A. [Energy Research Centre of the Netherlands (ECN), Department of Environmental Risk Assessment, P.O. Box 1, 1755 ZG Petten (Netherlands); Van der Sloot, H.A. [Hans van der Sloot Consultancy, Dorpsstraat 216, 1721 BV Langedijk (Netherlands); Astrup, T.F. [Technical University of Denmark, Department of Environmental Engineering, Building 115, 2800 Lyngby (Denmark)

2015-04-15

Highlights: • Relevance of metal leaching in waste management system LCAs was assessed. • Toxic impacts from leaching could not be disregarded. • Uncertainty of toxicity, due to background activities, determines LCA outcomes. • Parameters such as pH and L/S affect LCA results. • Data modelling consistency and coverage within an LCA are crucial. - Abstract: Residues from industrial processes and waste management systems (WMSs) have been increasingly reutilised, leading to landfilling rate reductions and the optimisation of mineral resource utilisation in society. Life cycle assessment (LCA) is a holistic methodology allowing for the analysis of systems and products and can be applied to waste management systems to identify environmental benefits and critical aspects thereof. From an LCA perspective, residue utilisation provides benefits such as avoiding the production and depletion of primary materials, but it can lead to environmental burdens, due to the potential leaching of toxic substances. In waste LCA studies where residue utilisation is included, leaching has generally been neglected. In this study, municipal solid waste incineration bottom ash (MSWI BA) was used as a case study into three LCA scenarios having different system boundaries. The importance of data quality and parameter selection in the overall LCA results was evaluated, and an innovative method to assess metal transport into the environment was applied, in order to determine emissions to the soil and water compartments for use in an LCA. It was found that toxic impacts as a result of leaching were dominant in systems including only MSWI BA utilisation, while leaching appeared negligible in larger scenarios including the entire waste system. However, leaching could not be disregarded a priori, due to large uncertainties characterising other activities in the scenario (e.g. electricity production). Based on the analysis of relevant parameters relative to leaching, and on general results

Life cycle assessment and residue leaching: the importance of parameter, scenario and leaching data selection.

Science.gov (United States)

Allegrini, E; Butera, S; Kosson, D S; Van Zomeren, A; Van der Sloot, H A; Astrup, T F

2015-04-01

Residues from industrial processes and waste management systems (WMSs) have been increasingly reutilised, leading to landfilling rate reductions and the optimisation of mineral resource utilisation in society. Life cycle assessment (LCA) is a holistic methodology allowing for the analysis of systems and products and can be applied to waste management systems to identify environmental benefits and critical aspects thereof. From an LCA perspective, residue utilisation provides benefits such as avoiding the production and depletion of primary materials, but it can lead to environmental burdens, due to the potential leaching of toxic substances. In waste LCA studies where residue utilisation is included, leaching has generally been neglected. In this study, municipal solid waste incineration bottom ash (MSWI BA) was used as a case study into three LCA scenarios having different system boundaries. The importance of data quality and parameter selection in the overall LCA results was evaluated, and an innovative method to assess metal transport into the environment was applied, in order to determine emissions to the soil and water compartments for use in an LCA. It was found that toxic impacts as a result of leaching were dominant in systems including only MSWI BA utilisation, while leaching appeared negligible in larger scenarios including the entire waste system. However, leaching could not be disregarded a priori, due to large uncertainties characterising other activities in the scenario (e.g. electricity production). Based on the analysis of relevant parameters relative to leaching, and on general results of the study, recommendations are provided regarding the use of leaching data in LCA studies. Copyright © 2014 Elsevier Ltd. All rights reserved.

Structural parameter identifiability analysis for dynamic reaction networks

DEFF Research Database (Denmark)

Davidescu, Florin Paul; Jørgensen, Sten Bay

2008-01-01

method based on Lie derivatives. The proposed systematic two phase methodology is illustrated on a mass action based model for an enzymatically catalyzed reaction pathway network where only a limited set of variables is measured. The methodology clearly pinpoints the structurally identifiable parameters...... where for a given set of measured variables it is desirable to investigate which parameters may be estimated prior to spending computational effort on the actual estimation. This contribution addresses the structural parameter identifiability problem for the typical case of reaction network models....... The proposed analysis is performed in two phases. The first phase determines the structurally identifiable reaction rates based on reaction network stoichiometry. The second phase assesses the structural parameter identifiability of the specific kinetic rate expressions using a generating series expansion...

The influence of punching process on residual stress and magnetic domain structure of non-oriented silicon steel

International Nuclear Information System (INIS)

Cao, Hongzhi; Hao, Linpo; Yi, Jingwen; Zhang, Xianglin; Luo, Zhonghan; Chen, Shenglin; Li, Rongfeng

2016-01-01

The main purpose of this paper is to investigate the influence of punching process on residual stress and magnetic domain structure. The residual stress in non-oriented silicon steel after punching process was measured by nanoindentation. The maximum depth was kept constant as 300 nm during nanoindentation. The material around indentation region exhibited no significant pile-up deformation. The calculation of residual stress was based on the Suresh theoretical model. Our experimental results show that residual compressive stress was generated around the sheared edge after punching. The width of residual stress affected zone by punching was around 0.4–0.5 mm. After annealing treatment, the residual stress was significantly decreased. Magnetic domain structure was observed according to the Bitter method. The un-annealed sample exhibited complicated domain patterns, and the widths of the magnetic domains varied between 3 µm and 8 µm. Most of the domain patterns of the annealed sample were 180°-domains and 90°-domains, and the widths of the domains decreased to 1–3 µm. - Highlights: • The residual stress distribution on sheared edge was measured. • The residual compressive stress was generated around the sheared edge. • The width of residual stress affected zone was about 0.4–0.5 mm. • The shape and width of the domain structure would be changed by annealing.

Improving sensitivity of residual current transformers to high frequency earth fault currents

Directory of Open Access Journals (Sweden)

Czapp Stanislaw

2017-09-01

Full Text Available For protection against electric shock in low voltage systems residual current devices are commonly used. However, their proper operation can be interfered when high frequency earth fault current occurs. Serious hazard of electrocution exists then. In order to detect such a current, it is necessary to modify parameters of residual current devices, especially the operating point of their current transformer. The authors proposed the modification in the structure of residual current devices. This modification improves sensitivity of residual current devices when high frequency earth fault current occurs. The test of the modified residual current device proved that the authors’ proposition is appropriate.

Toward Structure Prediction for Short Peptides Using the Improved SAAP Force Field Parameters

Directory of Open Access Journals (Sweden)

Kenichi Dedachi

2013-01-01

Full Text Available Based on the observation that Ramachandran-type potential energy surfaces of single amino acid units in water are in good agreement with statistical structures of the corresponding amino acid residues in proteins, we recently developed a new all-atom force field called SAAP, in which the total energy function for a polypeptide is expressed basically as a sum of single amino acid potentials and electrostatic and Lennard-Jones potentials between the amino acid units. In this study, the SAAP force field (SAAPFF parameters were improved, and classical canonical Monte Carlo (MC simulation was carried out for short peptide models, that is, Met-enkephalin and chignolin, at 300 K in an implicit water model. Diverse structures were reasonably obtained for Met-enkephalin, while three folded structures, one of which corresponds to a native-like structure with three native hydrogen bonds, were obtained for chignolin. The results suggested that the SAAP-MC method is useful for conformational sampling for the short peptides. A protocol of SAAP-MC simulation followed by structural clustering and examination of the obtained structures by ab initio calculation or simply by the number of the hydrogen bonds (or the hardness was demonstrated to be an effective strategy toward structure prediction for short peptide molecules.

Model parameter estimations from residual gravity anomalies due to simple-shaped sources using Differential Evolution Algorithm

Science.gov (United States)

Ekinci, Yunus Levent; Balkaya, Çağlayan; Göktürkler, Gökhan; Turan, Seçil

2016-06-01

An efficient approach to estimate model parameters from residual gravity data based on differential evolution (DE), a stochastic vector-based metaheuristic algorithm, has been presented. We have showed the applicability and effectiveness of this algorithm on both synthetic and field anomalies. According to our knowledge, this is a first attempt of applying DE for the parameter estimations of residual gravity anomalies due to isolated causative sources embedded in the subsurface. The model parameters dealt with here are the amplitude coefficient (A), the depth and exact origin of causative source (zo and xo, respectively) and the shape factors (q and ƞ). The error energy maps generated for some parameter pairs have successfully revealed the nature of the parameter estimation problem under consideration. Noise-free and noisy synthetic single gravity anomalies have been evaluated with success via DE/best/1/bin, which is a widely used strategy in DE. Additionally some complicated gravity anomalies caused by multiple source bodies have been considered, and the results obtained have showed the efficiency of the algorithm. Then using the strategy applied in synthetic examples some field anomalies observed for various mineral explorations such as a chromite deposit (Camaguey district, Cuba), a manganese deposit (Nagpur, India) and a base metal sulphide deposit (Quebec, Canada) have been considered to estimate the model parameters of the ore bodies. Applications have exhibited that the obtained results such as the depths and shapes of the ore bodies are quite consistent with those published in the literature. Uncertainty in the solutions obtained from DE algorithm has been also investigated by Metropolis-Hastings (M-H) sampling algorithm based on simulated annealing without cooling schedule. Based on the resulting histogram reconstructions of both synthetic and field data examples the algorithm has provided reliable parameter estimations being within the sampling limits of

Structural transformations in Mn2NiGa due to residual stress

International Nuclear Information System (INIS)

Singh, Sanjay; Maniraj, M.; D'Souza, S. W.; Barman, S. R.; Ranjan, R.

2010-01-01

Powder x-ray diffraction study of Mn 2 NiGa ferromagnetic shape memory alloy shows the existence of a 7M monoclinic modulated structure at room temperature (RT). The structure of Mn 2 NiGa is found to be highly dependent on residual stress. For higher stress, the structure is tetragonal at RT, and for intermediate stress it is 7M monoclinic. However, only when the stress is considerably relaxed, the structure is cubic, as is expected at RT since the martensitic transition temperature is 230 K.

Diverse effects of distance cutoff and residue interval on the performance of distance-dependent atom-pair potential in protein structure prediction.

Science.gov (United States)

Yao, Yuangen; Gui, Rong; Liu, Quan; Yi, Ming; Deng, Haiyou

2017-12-08

As one of the most successful knowledge-based energy functions, the distance-dependent atom-pair potential is widely used in all aspects of protein structure prediction, including conformational search, model refinement, and model assessment. During the last two decades, great efforts have been made to improve the reference state of the potential, while other factors that also strongly affect the performance of the potential have been relatively less investigated. Based on different distance cutoffs (from 5 to 22 Å) and residue intervals (from 0 to 15) as well as six different reference states, we constructed a series of distance-dependent atom-pair potentials and tested them on several groups of structural decoy sets collected from diverse sources. A comprehensive investigation has been performed to clarify the effects of distance cutoff and residue interval on the potential's performance. Our results provide a new perspective as well as a practical guidance for optimizing distance-dependent statistical potentials. The optimal distance cutoff and residue interval are highly related with the reference state that the potential is based on, the measurements of the potential's performance, and the decoy sets that the potential is applied to. The performance of distance-dependent statistical potential can be significantly improved when the best statistical parameters for the specific application environment are adopted.

Residual stress effects on the K parameter of the fracture mechanics

International Nuclear Information System (INIS)

Soares, Maria da Conceiccao B. Vieira; Andrade, Arnaldo H. Paes de

1996-01-01

Compressive residual stresses are beneficial and improve resistance to fracture and crack growth. Residual stresses can be introduced in fabricated components by a variety of means and a number of methods such as laser surface treatment, cold expanded hole, and shot peening. Neutrons diffraction measurements of residual stress were performed at a pulsed neutron source (ISIS, Didcot, UK), on shot peened plates of nickel base superalloy Udimet 720 and titanium alloy IMI 834. The stress intensity factor (K) of residual stress was evaluated by finite element modeling and weight function method. Finite element modeling of a 2D plate with a single edge-notch was applied and, due to symmetry only half of the plate was actually modeled. The stress intensity factor (K) was evaluated for both case of remote tension stress and residual stress. Crack surface overlapping, which is physically unacceptable, was noted for small cracks under residual and boundary lading. Overlap correction was proposed and applied in order to obtain reliable values for (K). (author)

HemeBIND: a novel method for heme binding residue prediction by combining structural and sequence information

Directory of Open Access Journals (Sweden)

Hu Jianjun

2011-05-01

Full Text Available Abstract Background Accurate prediction of binding residues involved in the interactions between proteins and small ligands is one of the major challenges in structural bioinformatics. Heme is an essential and commonly used ligand that plays critical roles in electron transfer, catalysis, signal transduction and gene expression. Although much effort has been devoted to the development of various generic algorithms for ligand binding site prediction over the last decade, no algorithm has been specifically designed to complement experimental techniques for identification of heme binding residues. Consequently, an urgent need is to develop a computational method for recognizing these important residues. Results Here we introduced an efficient algorithm HemeBIND for predicting heme binding residues by integrating structural and sequence information. We systematically investigated the characteristics of binding interfaces based on a non-redundant dataset of heme-protein complexes. It was found that several sequence and structural attributes such as evolutionary conservation, solvent accessibility, depth and protrusion clearly illustrate the differences between heme binding and non-binding residues. These features can then be separately used or combined to build the structure-based classifiers using support vector machine (SVM. The results showed that the information contained in these features is largely complementary and their combination achieved the best performance. To further improve the performance, an attempt has been made to develop a post-processing procedure to reduce the number of false positives. In addition, we built a sequence-based classifier based on SVM and sequence profile as an alternative when only sequence information can be used. Finally, we employed a voting method to combine the outputs of structure-based and sequence-based classifiers, which demonstrated remarkably better performance than the individual classifier alone

Prediction of residues in discontinuous B-cell epitopes using protein 3D structures

DEFF Research Database (Denmark)

Andersen, P.H.; Nielsen, Morten; Lund, Ole

2006-01-01

. We show that the new structure-based method has a better performance for predicting residues of discontinuous epitopes than methods based solely on sequence information, and that it can successfully predict epitope residues that have been identified by different techniques. DiscoTope detects 15...... experimental epitope mapping in both rational vaccine design and development of diagnostic tools, and may lead to more efficient epitope identification....

Effect of using the double layer technique on the microstructure, microhardness and residual stress of welded ASTM A516 GR70 structural steel

International Nuclear Information System (INIS)

Oliveira, George Luiz Gomes de; Miranda, Helio Cordeiro de

2010-01-01

The aim of this work is to evaluate the effect of using the double layer technique on the microstructure, microhardness and residual stresses of welded ASTM A516 Gr70 structural steel. Samples were welded with the same welding parameters and two types of chamfers, while the samples welded using the double layer technique underwent a buttering process on their chamfer face. Residual stress measurement was accomplished through x-ray diffraction, using a mini diffractometer for measurement in field. Metallographic analysis was accomplished in the transverse section of the welded joint, using optic microscopy and scanning electron microscopy. The double layer technique showed that can be used in the welding of ASTM A516 Gr70 steel, because, besides promote a refinement and a drawing back of the CG-HAZ, it increased compressive residual stress in the whole surface of the analyzed samples.(author)

Three-residue turns in alpha/beta-peptides and their application in the design of tertiary structures.

Science.gov (United States)

Sharma, Gangavaram V M; Nagendar, Pendem; Ramakrishna, Kallaganti V S; Chandramouli, Nagula; Choudhary, Madavi; Kunwar, Ajit C

2008-06-02

A new three-residue turn was serendipitously discovered in alpha/beta hybrid peptides derived from alternating C-linked carbo-beta-amino acids (beta-Caa) and L-Ala residues. The three-residue beta-alpha-beta turn at the C termini, nucleated by a helix at the N termini, resulted in helix-turn (HT) supersecondary structures in these peptides. The turn in the HT motif is stabilized by two H bonds-CO(i-2)-NH(i), with a seven-membered pseudoring (gamma turn) in the backward direction, and NH(i-2)-CO(i), with a 13-membered pseudoring in the forward direction (i being the last residue)--at the C termini. The study was extended to generalize the new three-residue turn (beta-alpha-beta) by using different alpha- and beta-amino acids. Furthermore, the HT motifs were efficiently converted, by an extension with helical oligomers at the C termini, into peptides with novel helix-turn-helix (HTH) tertiary structures. However, this resulted in the destabilization of the beta-alpha-beta turn with the concomitant nucleation of another three-residue turn, alpha-beta-beta, which is stabilized by 11- and 15-membered bifurcated H bonds. Extensive NMR spectroscopic studies were carried out to delineate the secondary and tertiary structures in these peptides, which are further supported by molecular dynamics (MD) investigations.

Functional validation of Ca2+-binding residues from the crystal structure of the BK ion channel.

Science.gov (United States)

Kshatri, Aravind S; Gonzalez-Hernandez, Alberto J; Giraldez, Teresa

2018-04-01

BK channels are dually regulated by voltage and Ca 2+ , providing a cellular mechanism to couple electrical and chemical signalling. Intracellular Ca 2+ concentration is sensed by a large cytoplasmic region in the channel known as "gating ring", which is formed by four tandems of regulator of conductance for K + (RCK1 and RCK2) domains. The recent crystal structure of the full-length BK channel from Aplysia californica has provided new information about the residues involved in Ca 2+ coordination at the high-affinity binding sites located in the RCK1 and RCK2 domains, as well as their cooperativity. Some of these residues have not been previously studied in the human BK channel. In this work we have investigated, through site directed mutagenesis and electrophysiology, the effects of these residues on channel activation by voltage and Ca 2+ . Our results demonstrate that the side chains of two non-conserved residues proposed to coordinate Ca 2+ in the A. californica structure (G523 and E591) have no apparent functional role in the human BK Ca 2+ sensing mechanism. Consistent with the crystal structure, our data indicate that in the human channel the conserved residue R514 participates in Ca 2+ coordination in the RCK1 binding site. Additionally, this study provides functional evidence indicating that R514 also interacts with residues E902 and Y904 connected to the Ca 2+ binding site in RCK2. Interestingly, it has been proposed that this interaction may constitute a structural correlate underlying the cooperative interactions between the two high-affinity Ca 2+ binding sites regulating the Ca 2+ dependent gating of the BK channel. This article is part of a Special Issue entitled: Beyond the Structure-Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain. Copyright © 2017 Elsevier B.V. All rights reserved.

Optimisation of process parameters in friction stir welding based on residual stress analysis: a feasibility study

DEFF Research Database (Denmark)

Tutum, Cem Celal; Hattel, Jesper Henri

2010-01-01

The present paper considers the optimisation of process parameters in friction stir welding (FSW). More specifically, the choices of rotational speed and traverse welding speed have been investigated using genetic algorithms. The welding process is simulated in a transient, two......-dimensional sequentially coupled thermomechanical model in ANSYS. This model is then used in an optimisation case where the two objectives are the minimisation of the peak residual stresses and the maximisation of the welding speed. The results indicate that the objectives for the considered case are conflicting......, and this is presented as a Pareto optimal front. Moreover, a higher welding speed for a fixed rotational speed results, in general, in slightly higher stress levels in the tension zone, whereas a higher rotational speed for a fixed welding speed yields somewhat lower peak residual stress, however, a wider tension zone...

Residual stresses

International Nuclear Information System (INIS)

Sahotra, I.M.

2006-01-01

The principal effect of unloading a material strained into the plastic range is to create a permanent set (plastic deformation), which if restricted somehow, gives rise to a system of self-balancing within the same member or reaction balanced by other members of the structure., known as residual stresses. These stresses stay there as locked-in stresses, in the body or a part of it in the absence of any external loading. Residual stresses are induced during hot-rolling and welding differential cooling, cold-forming and extruding: cold straightening and spot heating, fabrication and forced fitting of components constraining the structure to a particular geometry. The areas which cool more quickly develop residual compressive stresses, while the slower cooling areas develop residual tensile stresses, and a self-balancing or reaction balanced system of residual stresses is formed. The phenomenon of residual stresses is the most challenging in its application in surface modification techniques determining endurance mechanism against fracture and fatigue failures. This paper discusses the mechanism of residual stresses, that how the residual stresses are fanned and what their behavior is under the action of external forces. Such as in the case of a circular bar under limit torque, rectangular beam under limt moment, reclaiming of shafts welds and peening etc. (author)

Dynamic response of structures with uncertain parameters

International Nuclear Information System (INIS)

Cai, Z H; Liu, Y; Yang, Y

2010-01-01

In this paper, an interval method for the dynamic response of structures with uncertain parameters is presented. In the presented method, the structural physical and geometric parameters and loads can be considered as interval variables. The structural stiffness matrix, mass matrix and loading vectors are described as the sum of two parts corresponding to the deterministic matrix and the uncertainty of the interval parameters. The interval problem is then transformed into approximate deterministic one. The Laplace transform is used to transform the equations of the dynamic system into linear algebra equations. The Maclaurin series expansion is applied on the modified dynamic equation in order to deal with the linear algebra equations. Numerical examples are studied by the presented interval method for the cases with and without damping. The upper bound and lower bound of the dynamic responses of the examples are compared, and it shows that the presented method is effective.

Improved structural integrity through advances in reliable residual stress measurement: the impact of ENGIN-X

Science.gov (United States)

Edwards, L.; Santisteban, J. R.

The determination of accurate reliable residual stresses is critical to many fields of structural integrity. Neutron stress measurement is a non-destructive technique that uniquely provides insights into stress fields deep within engineering components and structures. As such, it has become an increasingly important tool within engineering, leading to improved manufacturing processes to reduce stress and distortion as well as to the definition of more precise lifing procedures. This paper describes the likely impact of the next generation of dedicated engineering stress diffractometers currently being constructed and the utility of the technique using examples of residual stresses both beneficial and detrimental to structural integrity.

Optimization of the Process Parameters for Controlling Residual Stress and Distortion in Friction Stir Welding

DEFF Research Database (Denmark)

Tutum, Cem Celal; Schmidt, Henrik Nikolaj Blicher; Hattel, Jesper Henri

2008-01-01

In the present paper, numerical optimization of the process parameters, i.e. tool rotation speed and traverse speed, aiming minimization of the two conflicting objectives, i.e. the residual stresses and welding time, subjected to process-specific thermal constraints in friction stir welding......, is investigated. The welding process is simulated in 2-dimensions with a sequentially coupled transient thermo-mechanical model using ANSYS. The numerical optimization problem is implemented in modeFRONTIER and solved using the Multi-Objective Genetic Algorithm (MOGA-II). An engineering-wise evaluation or ranking...

Defining an essence of structure determining residue contacts in proteins.

Science.gov (United States)

Sathyapriya, R; Duarte, Jose M; Stehr, Henning; Filippis, Ioannis; Lappe, Michael

2009-12-01

The network of native non-covalent residue contacts determines the three-dimensional structure of a protein. However, not all contacts are of equal structural significance, and little knowledge exists about a minimal, yet sufficient, subset required to define the global features of a protein. Characterisation of this "structural essence" has remained elusive so far: no algorithmic strategy has been devised to-date that could outperform a random selection in terms of 3D reconstruction accuracy (measured as the Ca RMSD). It is not only of theoretical interest (i.e., for design of advanced statistical potentials) to identify the number and nature of essential native contacts-such a subset of spatial constraints is very useful in a number of novel experimental methods (like EPR) which rely heavily on constraint-based protein modelling. To derive accurate three-dimensional models from distance constraints, we implemented a reconstruction pipeline using distance geometry. We selected a test-set of 12 protein structures from the four major SCOP fold classes and performed our reconstruction analysis. As a reference set, series of random subsets (ranging from 10% to 90% of native contacts) are generated for each protein, and the reconstruction accuracy is computed for each subset. We have developed a rational strategy, termed "cone-peeling" that combines sequence features and network descriptors to select minimal subsets that outperform the reference sets. We present, for the first time, a rational strategy to derive a structural essence of residue contacts and provide an estimate of the size of this minimal subset. Our algorithm computes sparse subsets capable of determining the tertiary structure at approximately 4.8 A Ca RMSD with as little as 8% of the native contacts (Ca-Ca and Cb-Cb). At the same time, a randomly chosen subset of native contacts needs about twice as many contacts to reach the same level of accuracy. This "structural essence" opens new avenues in the

Quadratic residues and non-residues selected topics

CERN Document Server

Wright, Steve

2016-01-01

This book offers an account of the classical theory of quadratic residues and non-residues with the goal of using that theory as a lens through which to view the development of some of the fundamental methods employed in modern elementary, algebraic, and analytic number theory. The first three chapters present some basic facts and the history of quadratic residues and non-residues and discuss various proofs of the Law of Quadratic Reciprosity in depth, with an emphasis on the six proofs that Gauss published. The remaining seven chapters explore some interesting applications of the Law of Quadratic Reciprocity, prove some results concerning the distribution and arithmetic structure of quadratic residues and non-residues, provide a detailed proof of Dirichlet’s Class-Number Formula, and discuss the question of whether quadratic residues are randomly distributed. The text is a valuable resource for graduate and advanced undergraduate students as well as for mathematicians interested in number theory.

Effects of lysine residues on structural characteristics and stability of tau proteins

International Nuclear Information System (INIS)

Lee, Myeongsang; Baek, Inchul; Choi, Hyunsung; Kim, Jae In; Na, Sungsoo

2015-01-01

Pathological amyloid proteins have been implicated in neuro-degenerative diseases, specifically Alzheimer's, Parkinson's, Lewy-body diseases and prion related diseases. In prion related diseases, functional tau proteins can be transformed into pathological agents by environmental factors, including oxidative stress, inflammation, Aβ-mediated toxicity and covalent modification. These pathological agents are stable under physiological conditions and are not easily degraded. This un-degradable characteristic of tau proteins enables their utilization as functional materials to capturing the carbon dioxides. For the proper utilization of amyloid proteins as functional materials efficiently, a basic study regarding their structural characteristic is necessary. Here, we investigated the basic tau protein structure of wild-type (WT) and tau proteins with lysine residues mutation at glutamic residue (Q2K) on tau protein at atomistic scale. We also reported the size effect of both the WT and Q2K structures, which allowed us to identify the stability of those amyloid structures. - Highlights: • Lysine mutation effect alters the structure conformation and characteristic of tau. • Over the 15 layers both WT and Q2K models, both tau proteins undergo fractions. • Lysine mutation causes the increment of non-bonded energy and solvent accessible surface area. • Structural instability of Q2K model was proved by the number of hydrogen bonds analysis.

Effects of lysine residues on structural characteristics and stability of tau proteins

Energy Technology Data Exchange (ETDEWEB)

Lee, Myeongsang; Baek, Inchul; Choi, Hyunsung; Kim, Jae In; Na, Sungsoo, E-mail: nass@korea.ac.kr

2015-10-23

Pathological amyloid proteins have been implicated in neuro-degenerative diseases, specifically Alzheimer's, Parkinson's, Lewy-body diseases and prion related diseases. In prion related diseases, functional tau proteins can be transformed into pathological agents by environmental factors, including oxidative stress, inflammation, Aβ-mediated toxicity and covalent modification. These pathological agents are stable under physiological conditions and are not easily degraded. This un-degradable characteristic of tau proteins enables their utilization as functional materials to capturing the carbon dioxides. For the proper utilization of amyloid proteins as functional materials efficiently, a basic study regarding their structural characteristic is necessary. Here, we investigated the basic tau protein structure of wild-type (WT) and tau proteins with lysine residues mutation at glutamic residue (Q2K) on tau protein at atomistic scale. We also reported the size effect of both the WT and Q2K structures, which allowed us to identify the stability of those amyloid structures. - Highlights: • Lysine mutation effect alters the structure conformation and characteristic of tau. • Over the 15 layers both WT and Q2K models, both tau proteins undergo fractions. • Lysine mutation causes the increment of non-bonded energy and solvent accessible surface area. • Structural instability of Q2K model was proved by the number of hydrogen bonds analysis.

Comparison of Welding Residual Stresses of Hybrid Laser-Arc Welding and Submerged Arc Welding in Offshore Steel Structures

DEFF Research Database (Denmark)

Andreassen, Michael Joachim; Yu, Zhenzhen; Liu, Stephen

2016-01-01

In the offshore industry, welding-induced distortion and tensile residual stresses have become a major concern in relation to the structural integrity of a welded structure. Particularly, the continuous increase in size of welded plates and joints needs special attention concerning welding induced...... residual stresses. These stresses have a negative impact on the integrity of the welded joint as they promote distortion, reduce fatigue life, and contribute to corrosion cracking and premature failure in the weld components. This paper deals with the influence and impact of welding method on the welding...... induced residual stresses. It is also investigated whether the assumption of residual stresses up to yield strength magnitude are present in welded structures as stated in the design guidelines. The fatigue strength for welded joints is based on this assumption. The two welding methods investigated...

Inference of reactive transport model parameters using a Bayesian multivariate approach

Science.gov (United States)

Carniato, Luca; Schoups, Gerrit; van de Giesen, Nick

2014-08-01

Parameter estimation of subsurface transport models from multispecies data requires the definition of an objective function that includes different types of measurements. Common approaches are weighted least squares (WLS), where weights are specified a priori for each measurement, and weighted least squares with weight estimation (WLS(we)) where weights are estimated from the data together with the parameters. In this study, we formulate the parameter estimation task as a multivariate Bayesian inference problem. The WLS and WLS(we) methods are special cases in this framework, corresponding to specific prior assumptions about the residual covariance matrix. The Bayesian perspective allows for generalizations to cases where residual correlation is important and for efficient inference by analytically integrating out the variances (weights) and selected covariances from the joint posterior. Specifically, the WLS and WLS(we) methods are compared to a multivariate (MV) approach that accounts for specific residual correlations without the need for explicit estimation of the error parameters. When applied to inference of reactive transport model parameters from column-scale data on dissolved species concentrations, the following results were obtained: (1) accounting for residual correlation between species provides more accurate parameter estimation for high residual correlation levels whereas its influence for predictive uncertainty is negligible, (2) integrating out the (co)variances leads to an efficient estimation of the full joint posterior with a reduced computational effort compared to the WLS(we) method, and (3) in the presence of model structural errors, none of the methods is able to identify the correct parameter values.

Association of Parameters of Mineral Bone Disorder with Mortality in Patients on Hemodialysis according to Level of Residual Kidney Function.

Science.gov (United States)

Wang, Mengjing; Obi, Yoshitsugu; Streja, Elani; Rhee, Connie M; Lau, Wei Ling; Chen, Jing; Hao, Chuanming; Hamano, Takayuki; Kovesdy, Csaba P; Kalantar-Zadeh, Kamyar

2017-07-07

The relationship between mineral and bone disorders and survival according to residual kidney function status has not been previously studied in patients on hemodialysis. We hypothesized that residual kidney function, defined by renal urea clearance, modifies the association between mineral and bone disorder parameters and mortality. The associations of serum phosphorus, albumin-corrected calcium, intact parathyroid hormone, and alkaline phosphatase with all-cause mortality were examined across three strata (kidney function modified the mortality risk associated with serum phosphorus and intact parathyroid hormone among incident hemodialysis patients. Future studies are needed to examine whether taking account for residual kidney function into the assessment of mortality risk associated with serum phosphorus and intact parathyroid hormone improves patient management and clinical outcomes in the hemodialysis population. Copyright © 2017 by the American Society of Nephrology.

Determination of structural fluctuations of proteins from structure-based calculations of residual dipolar couplings

International Nuclear Information System (INIS)

Montalvao, Rinaldo W.; De Simone, Alfonso; Vendruscolo, Michele

2012-01-01

Residual dipolar couplings (RDCs) have the potential of providing detailed information about the conformational fluctuations of proteins. It is very challenging, however, to extract such information because of the complex relationship between RDCs and protein structures. A promising approach to decode this relationship involves structure-based calculations of the alignment tensors of protein conformations. By implementing this strategy to generate structural restraints in molecular dynamics simulations we show that it is possible to extract effectively the information provided by RDCs about the conformational fluctuations in the native states of proteins. The approach that we present can be used in a wide range of alignment media, including Pf1, charged bicelles and gels. The accuracy of the method is demonstrated by the analysis of the Q factors for RDCs not used as restraints in the calculations, which are significantly lower than those corresponding to existing high-resolution structures and structural ensembles, hence showing that we capture effectively the contributions to RDCs from conformational fluctuations.

Effect of pretreatment on biomass residue structure and the application of pyrolysed and composted biomass residues in soilless culture.

Directory of Open Access Journals (Sweden)

Linna Suo

Full Text Available The changes in the structural characteristics of biomass residues during pyrolysis and composting were investigated. The biomass residues particles were prepared by pyrolysing at temperatures ranging from 350 to 400. For soilless production of the ornamental plant Anthurium andraeanum, pure sphagnum peat moss (P has traditionally been used as the growing medium. This use of P must be reduced, however, because P is an expensive and nonrenewable resource. The current study investigated the use of biomass residues as substitutes for P in A. andraeanum production. Plants were grown for 15 months in 10 soilless media that contained different proportions of pyrolysed corn cobs (PC, composted corn cobs (C, pyrolysed garden wastes (PG, and P. Although the media altered the plant nutrient content, A. andraeanum growth, development, and yield were similar with media consisting of 50% P+50% PC, 50% P+35% PC+15% PG, and 100% P. This finding indicates that, when pyrolysed, organic wastes, which are otherwise an environmental problem, can be used to reduce the requirement for peat in the soilless culture of A. andraeanum.

Immunological parameters and residual feed intake of Nellore heifers

Directory of Open Access Journals (Sweden)

Cleisy Ferreira Nascimento

2012-12-01

Full Text Available The residual feed intake (RFI is a parameter used in the identification of animals with respect to more efficient feed utilization. However, physiological basis are still unknown, however, the interrelationships between nutrition an immunity of the animal can contribute to the investigation of biological phenomena relevant to the RFI, since the defense system to oxidative effects caused by free radicals, is formed by acid polyunsaturated fatty acids, water soluble substances and enzymes, which derive mainly from the use of nutrients in the diet. The objective of this study was to evaluate the immunological parameters of Nellore heifers classified according to RFI. It were evaluated 176 heifers (born between 2008 and 2010, Traditional Nellore herd from Instituto de Zootecnia - Sertãozinho/SP, forming three groups of evaluation, submitted to test post weaning feed efficiency and classified into high (> mean + 0.5 SD, n= 55, medium (± 0.5 SD, n= 65 and low RFI (< mean – 0.5 SD, n= 56. The diet was formulated based on Brachiaria decumbens hay, corn, cottonseed meal and mineral mixture (45:55, forage: concentrate. The weight of the animals were performed in fasting blood samples collected by venipuncture vein, using tubes of 10 ml type vacuntainer with EDTA anticoagulant. In the clinical laboratory, we measured the values of leukocytes (LEU; Targeted (SEG and lymphocytes (LIN. The experimental design was a randomized block design using PROC GLM of SAS, considering the fixed effects of year and the age covariate in the statistical model and the averages compared by Tukey test at 5% probability. There was no significant difference (P>0,005 between variables leukocyte (LEU, SEG and LIN and class of RFI (table 1, indicating that there is no distinction between animals more efficient (low RFI and less efficient (high RFI, for inflammatory and immune responses to oxidative effects. Therefore the variables measured leukocytes not explain the differences

The effect of filler metal thickness on residual stress and creep for stainless-steel plate-fin structure

Energy Technology Data Exchange (ETDEWEB)

Jiang Wenchun [School of Mechanical and Power Engineering, Nanjing University of Technology, Nanjing 210009 (China)], E-mail: jiangwenchun@126.com; Gong Jianming; Chen Hu; Tu, S.T. [School of Mechanical and Power Engineering, Nanjing University of Technology, Nanjing 210009 (China)

2008-08-15

Stainless-steel plate-fin heat exchanger (PFHE) has been used as a high-temperature recuperator in microturbine for its excellent qualities in compact structure, high-temperature and pressure resistance. Plate-fin structure, as the core of PFHE, is fabricated by vacuum brazing. The main component fins and the parting sheets are joined by fusion of a brazing alloy cladded to the surface of parting sheets. Owing to the material mismatching between the filler metal and the base metal, residual stresses can arise and decrease the structure strength greatly. The recuperator serves at high temperature and the creep would happen. The thickness of the filler metal plays an important role in the joint strength. Hence this paper presented a finite element (FE) analysis of the brazed residual stresses and creep for a counterflow stainless-steel plate-fin structure. The effect of the filler metal thickness on residual stress and creep was investigated, which provides a reference for strength design.

Distortion and residual stresses in structures reinforced with titanium straps for improved damage tolerance

International Nuclear Information System (INIS)

Liljedahl, C.D.M.; Fitzpatrick, M.E.; Edwards, L.

2008-01-01

Distortion and residual stresses induced during the manufacturing process of bonded crack retarders have been investigated. Titanium alloy straps were adhesively bonded to an aluminium alloy SENT specimen to promote fatigue crack growth retardation. The effect of three different strap dimensions was investigated. The spring-back of a component when released from the autoclave and the residual stresses are important factors to take into account when designing a selective reinforcement, as this may alter the local aerodynamic characteristics and reduce the crack bridging effect of the strap. The principal problem with residual stresses is that the tensile nature of the residual stresses in the primary aluminium structure has a negative impact on the crack initiation and crack propagation behaviour in the aluminium. The residual stresses were measured with neutron diffraction and the distortion of the specimens was measured with a contour measurement machine. The bonding process was simulated with a three-dimensional FE model. The residual stresses were found to be tensile close to the strap and slightly compressive on the un-bonded side. Both the distortion and the residual stresses increased with the thickness and the width of the strap. Very good agreement between the measured stresses and the measured distortion and the FE simulation was found

Residual stress analysis in carbon fiber-reinforced SiC ceramics

International Nuclear Information System (INIS)

Broda, M.

1998-01-01

Systematic residual stress analyses are reported, carried out in long-fiber reinforced SiC ceramics. The laminated C fiber /SiC matrix specimens used were prepared by polymer pyrolysis, and the structural component specimens used are industrial products. Various diffraction methods have been applied for non-destructive evaluation of residual stress fields, so as to completely detect the residual stresses and their distribution in the specimens. The residual stress fields at the surface (μm) have been measured using characteristic X-radiation and applying the sin 2 ψ method as well as the scatter vector method. For residual stress field analysis in the mass volume (cm), neutron diffraction has been applied. The stress fields in the fiber layers (approx. 250μm) have been measured as a function of their location within the laminated composite by using an energy-dispersive method and synchrotron radiation. By means of the systematic, process-accompanying residual stress and phase analyses, conclusions can be drawn as to possible approaches for optimization of fabrication parameters. (orig./CB) [de

Effects of LSP on micro-structures and residual stresses in a 4 mm CLAM steel weld joints

Energy Technology Data Exchange (ETDEWEB)

Chen, Xizhang, E-mail: chenxizhang@wzu.edu.cn [School of Mechanical and Electrical Engineering, Wenzhou University., Wenzhou 325035 (China); School of Materials Science and Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu (China); Fang, Yuanyuan [School of Materials Science and Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu (China); Zhang, Shuyan; Kelleher, Joe F. [ISIS, Rutherford Appleton Laboratory, Chilton, Didcot OX11 0QX (United Kingdom); Zhou, Jianzhong [School of Mechanical Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu (China)

2015-05-15

The effects of laser shock processing (LSP) on the distribution of residual stress and micro-structure of China Low Activation Martensitic (CLAM) steel weldment were investigated via neutron diffraction and optical microscope (OM). A pair of 4 mm CLAM steel plates joined by GTA welding. Special attention is paid to the generation of high level compressive residual stresses introduced by LSP. Residual stress in longitudinal, normal and transversal direction at weldment surface and longitudinal stress through thickness are evaluated via neutron diffraction. Compressive residual stress after LSP occurred at more than 90% areas within the weld joint, it is almost double the areas of compressive stress compare to weldment surface before LSP. The maximum compressive normal residual stress becomes to −183 MPa after LSP from −63 MPa before LSP. The Modification of surface micro-structures including weld zone (WZ), heat affected zone (HAZ) and base metal (BM) are also discussed. Results to date demonstrate that laser shock processing has been a great potential method for the improvement of mechanical performance of components.

Residual life estimation of electrical insulation system for rotating equipment

International Nuclear Information System (INIS)

Vashishtha, Y.D.; Gupta, A.K.; Bhattacharyya, A.K.; Verma, A.K.

1994-01-01

Residual life assessment gains significance towards the end of designed life for granting plant life extensions and resource planning for costly equipment replacement. A critical review of all the diagnostic techniques presently used to assess either health of insulation system or to infer qualitatively the remaining life for rotating machines is presented. However more emphasis is required on developing quantitative methods. This paper also formulates the experimental plan for progressively censored ageing tests, measurement of partial discharge parameters, micro-structural study for delamination and electrical tree growth and measurement of electrical breakdown strength. Partial discharge (PD) patterns, electrical tree growth and time to failure data shall be taken as training set for the neural network learning which can be useful to predict residual life with only one candidate parameter i.e. PD patterns. (author). 9 refs

Evaluation of residue-residue contact predictions in CASP9

KAUST Repository

Monastyrskyy, Bohdan

2011-01-01

This work presents the results of the assessment of the intramolecular residue-residue contact predictions submitted to CASP9. The methodology for the assessment does not differ from that used in previous CASPs, with two basic evaluation measures being the precision in recognizing contacts and the difference between the distribution of distances in the subset of predicted contact pairs versus all pairs of residues in the structure. The emphasis is placed on the prediction of long-range contacts (i.e., contacts between residues separated by at least 24 residues along sequence) in target proteins that cannot be easily modeled by homology. Although there is considerable activity in the field, the current analysis reports no discernable progress since CASP8.

Microbiological parameters and maturity degree during composting of Posidonia oceanica residues mixed with vegetable wastes in semi-arid pedo-climatic condition.

Science.gov (United States)

Saidi, Neyla; Kouki, Soulwene; M'hiri, Fadhel; Jedidi, Naceur; Mahrouk, Meriam; Hassen, Abdennaceur; Ouzari, Hadda

2009-01-01

The aim of this study was to characterize the biological stability and maturity degree of compost during a controlled pile-composting trial of mixed vegetable residues (VR) collected from markets of Tunis City with residues of Posidonia oceanica (PoR), collected from Tunis beaches. The accumulation in beaches (as well as their removal) constitutes a serious environmental problem in all Mediterranean countries particularly in Tunisia. Aerobic-thermophilic composting is the most reasonable way to profit highly-valuable content of organic matter in these wastes for agricultural purposes. The physical, chemical, and biological parameters were monitored during composting over 150 d. The most appropriate parameters were selected to establish the maturity degree. The main result of this research was the deduction of the following maturity criterion: (a) C/N ratio 80%. These five parameters, considered jointly are indicative of a high maturity degree and thus of a high-quality organic amendment which employed in a rational way, may improve soil fertility and soil quality. The mature compost was relatively rich in N (13.0 g/kg), P (4.74 g/kg) and MgO (15.80 g/kg). Thus composting definitively constitutes the most optimal option to exploit these wastes.

Role of long- and short-range hydrophobic, hydrophilic and charged residues contact network in protein’s structural organization

Directory of Open Access Journals (Sweden)

Sengupta Dhriti

2012-06-01

Full Text Available Abstract Background The three-dimensional structure of a protein can be described as a graph where nodes represent residues and the strength of non-covalent interactions between them are edges. These protein contact networks can be separated into long and short-range interactions networks depending on the positions of amino acids in primary structure. Long-range interactions play a distinct role in determining the tertiary structure of a protein while short-range interactions could largely contribute to the secondary structure formations. In addition, physico chemical properties and the linear arrangement of amino acids of the primary structure of a protein determines its three dimensional structure. Here, we present an extensive analysis of protein contact subnetworks based on the London van der Waals interactions of amino acids at different length scales. We further subdivided those networks in hydrophobic, hydrophilic and charged residues networks and have tried to correlate their influence in the overall topology and organization of a protein. Results The largest connected component (LCC of long (LRN-, short (SRN- and all-range (ARN networks within proteins exhibit a transition behaviour when plotted against different interaction strengths of edges among amino acid nodes. While short-range networks having chain like structures exhibit highly cooperative transition; long- and all-range networks, which are more similar to each other, have non-chain like structures and show less cooperativity. Further, the hydrophobic residues subnetworks in long- and all-range networks have similar transition behaviours with all residues all-range networks, but the hydrophilic and charged residues networks don’t. While the nature of transitions of LCC’s sizes is same in SRNs for thermophiles and mesophiles, there exists a clear difference in LRNs. The presence of larger size of interconnected long-range interactions in thermophiles than mesophiles, even at

Networks of high mutual information define the structural proximity of catalytic sites: implications for catalytic residue identification.

Directory of Open Access Journals (Sweden)

Cristina Marino Buslje

Full Text Available Identification of catalytic residues (CR is essential for the characterization of enzyme function. CR are, in general, conserved and located in the functional site of a protein in order to attain their function. However, many non-catalytic residues are highly conserved and not all CR are conserved throughout a given protein family making identification of CR a challenging task. Here, we put forward the hypothesis that CR carry a particular signature defined by networks of close proximity residues with high mutual information (MI, and that this signature can be applied to distinguish functional from other non-functional conserved residues. Using a data set of 434 Pfam families included in the catalytic site atlas (CSA database, we tested this hypothesis and demonstrated that MI can complement amino acid conservation scores to detect CR. The Kullback-Leibler (KL conservation measurement was shown to significantly outperform both the Shannon entropy and maximal frequency measurements. Residues in the proximity of catalytic sites were shown to be rich in shared MI. A structural proximity MI average score (termed pMI was demonstrated to be a strong predictor for CR, thus confirming the proposed hypothesis. A structural proximity conservation average score (termed pC was also calculated and demonstrated to carry distinct information from pMI. A catalytic likeliness score (Cls, combining the KL, pC and pMI measures, was shown to lead to significantly improved prediction accuracy. At a specificity of 0.90, the Cls method was found to have a sensitivity of 0.816. In summary, we demonstrate that networks of residues with high MI provide a distinct signature on CR and propose that such a signature should be present in other classes of functional residues where the requirement to maintain a particular function places limitations on the diversification of the structural environment along the course of evolution.

Networks of high mutual information define the structural proximity of catalytic sites: implications for catalytic residue identification.

Science.gov (United States)

Marino Buslje, Cristina; Teppa, Elin; Di Doménico, Tomas; Delfino, José María; Nielsen, Morten

2010-11-04

Identification of catalytic residues (CR) is essential for the characterization of enzyme function. CR are, in general, conserved and located in the functional site of a protein in order to attain their function. However, many non-catalytic residues are highly conserved and not all CR are conserved throughout a given protein family making identification of CR a challenging task. Here, we put forward the hypothesis that CR carry a particular signature defined by networks of close proximity residues with high mutual information (MI), and that this signature can be applied to distinguish functional from other non-functional conserved residues. Using a data set of 434 Pfam families included in the catalytic site atlas (CSA) database, we tested this hypothesis and demonstrated that MI can complement amino acid conservation scores to detect CR. The Kullback-Leibler (KL) conservation measurement was shown to significantly outperform both the Shannon entropy and maximal frequency measurements. Residues in the proximity of catalytic sites were shown to be rich in shared MI. A structural proximity MI average score (termed pMI) was demonstrated to be a strong predictor for CR, thus confirming the proposed hypothesis. A structural proximity conservation average score (termed pC) was also calculated and demonstrated to carry distinct information from pMI. A catalytic likeliness score (Cls), combining the KL, pC and pMI measures, was shown to lead to significantly improved prediction accuracy. At a specificity of 0.90, the Cls method was found to have a sensitivity of 0.816. In summary, we demonstrate that networks of residues with high MI provide a distinct signature on CR and propose that such a signature should be present in other classes of functional residues where the requirement to maintain a particular function places limitations on the diversification of the structural environment along the course of evolution.

Automated Modal Parameter Estimation of Civil Engineering Structures

DEFF Research Database (Denmark)

Andersen, Palle; Brincker, Rune; Goursat, Maurice

In this paper the problems of doing automatic modal parameter extraction of ambient excited civil engineering structures is considered. Two different approaches for obtaining the modal parameters automatically are presented: The Frequency Domain Decomposition (FDD) technique and a correlation...

Overview and applicability of residual stress estimation of film-substrate structure

International Nuclear Information System (INIS)

Chou, Tsung-Lin; Yang, Shin-Yueh; Chiang, Kuo-Ning

2011-01-01

Residual stresses arising from thermal mismatch in layered structures rank among the major causes of mechanical failures in light-emitting diodes, integrated circuits, electronic packages, and micro-electro-mechanical systems. Applying analytical solutions to predict or calculate residual stresses' magnitude and distribution in multilayer film-substrate system has been widely adopted by many researchers. These researches are based on multilayer theories of film-substrate systems, such as Suhir's formula, Stoney's equation, and extend Stoney's equations. To discuss and distinguish the characteristics of these approaches, finite element analysis numerical solutions and multilayer theory analytical solutions are compared and analyzed. This encompasses the theories' application spectrum as well as their prediction capability. In addition, this work not only discusses the theories' property and workability but also demonstrate the feasibility of the finite element method (FEM) and bilayer theories in experiment. The experimental result demonstrates that FEM is a reliable approach in predicting the mechanical behavior of multilayer structures. Hence, when calculating or predicting thin film stress using the aforementioned theories, the methodology proposed in this research can be employed to effectively validate the feasibility of these theories.

Modeling coding-sequence evolution within the context of residue solvent accessibility.

Science.gov (United States)

Scherrer, Michael P; Meyer, Austin G; Wilke, Claus O

2012-09-12

Protein structure mediates site-specific patterns of sequence divergence. In particular, residues in the core of a protein (solvent-inaccessible residues) tend to be more evolutionarily conserved than residues on the surface (solvent-accessible residues). Here, we present a model of sequence evolution that explicitly accounts for the relative solvent accessibility of each residue in a protein. Our model is a variant of the Goldman-Yang 1994 (GY94) model in which all model parameters can be functions of the relative solvent accessibility (RSA) of a residue. We apply this model to a data set comprised of nearly 600 yeast genes, and find that an evolutionary-rate ratio ω that varies linearly with RSA provides a better model fit than an RSA-independent ω or an ω that is estimated separately in individual RSA bins. We further show that the branch length t and the transition-transverion ratio κ also vary with RSA. The RSA-dependent GY94 model performs better than an RSA-dependent Muse-Gaut 1994 (MG94) model in which the synonymous and non-synonymous rates individually are linear functions of RSA. Finally, protein core size affects the slope of the linear relationship between ω and RSA, and gene expression level affects both the intercept and the slope. Structure-aware models of sequence evolution provide a significantly better fit than traditional models that neglect structure. The linear relationship between ω and RSA implies that genes are better characterized by their ω slope and intercept than by just their mean ω.

Modeling coding-sequence evolution within the context of residue solvent accessibility

Directory of Open Access Journals (Sweden)

Scherrer Michael P

2012-09-01

Full Text Available Abstract Background Protein structure mediates site-specific patterns of sequence divergence. In particular, residues in the core of a protein (solvent-inaccessible residues tend to be more evolutionarily conserved than residues on the surface (solvent-accessible residues. Results Here, we present a model of sequence evolution that explicitly accounts for the relative solvent accessibility of each residue in a protein. Our model is a variant of the Goldman-Yang 1994 (GY94 model in which all model parameters can be functions of the relative solvent accessibility (RSA of a residue. We apply this model to a data set comprised of nearly 600 yeast genes, and find that an evolutionary-rate ratio ω that varies linearly with RSA provides a better model fit than an RSA-independent ω or an ω that is estimated separately in individual RSA bins. We further show that the branch length t and the transition-transverion ratio κ also vary with RSA. The RSA-dependent GY94 model performs better than an RSA-dependent Muse-Gaut 1994 (MG94 model in which the synonymous and non-synonymous rates individually are linear functions of RSA. Finally, protein core size affects the slope of the linear relationship between ω and RSA, and gene expression level affects both the intercept and the slope. Conclusions Structure-aware models of sequence evolution provide a significantly better fit than traditional models that neglect structure. The linear relationship between ω and RSA implies that genes are better characterized by their ω slope and intercept than by just their mean ω.

Development of residual thermal stress-relieving structure of CFC monoblock target for JT-60SA divertor

Energy Technology Data Exchange (ETDEWEB)

Tsuru, Daigo, E-mail: tsuru.daigo@jaea.go.jp; Sakurai, Shinji; Nakamura, Shigetoshi; Ozaki, Hidetsugu; Seki, Yohji; Yokoyama, Kenji; Suzuki, Satoshi

2015-10-15

Highlights: • We carried out numerical simulations on residual thermal stress of targets for the JT-60SA divertor. • We developed three measures to reduce residual thermal stress. • We proposed two structures of CFC monoblock target for the JT-60SA divertor. • We confirmed the effectiveness of the structure by infrared thermography inspection and high heat flux test. - Abstract: Carbon fibre-reinforced carbon composite (CFC) monoblock target for JT-60SA divertor is under development towards the mass-production. CFC monoblocks, WCu interlayers and a CuCrZr cooling tube at the centre of the monoblocks were bonded by vacuum brazing in a high temperature, to a target. If residual thermal stress due to difference of thermal expansions between CFC and CuCrZr exceeds the maximum allowable stress of the CFC after the bonding, cracks are generated in the CFC monoblock and heat removal capacity of the target degrades. In this paper, new structures of the targets were proposed, to reduce residual thermal stress and to mitigate the degradation of heat removal capacity of the targets. Some measures, including slitting of the CFC monoblock aside of the cooling tube, replacement of the interlayer material and shifting the position of the cooling tube, were implemented. The effectiveness of the measures was evaluated by numerical simulations. Target mock-ups with the proposed structures were manufactured. Infrared thermography inspection and high heat flux test were carried out on the mock-ups in order to evaluate the heat removal capacity.

Structural parameter optimization design for Halbach permanent maglev rail

International Nuclear Information System (INIS)

Guo, F.; Tang, Y.; Ren, L.; Li, J.

2010-01-01

Maglev rail is an important part of the magnetic levitation launch system. Reducing the manufacturing cost of magnetic levitation rail is the key problem for the development of magnetic levitation launch system. The Halbach permanent array has an advantage that the fundamental spatial field is cancelled on one side of the array while the field on the other side is enhanced. So this array used in the design of high temperature superconducting permanent maglev rail could improve the surface magnetic field and the levitation force. In order to make the best use of Nd-Fe-B (NdFeB) material and reduce the cost of maglev rail, the effect of the rail's structural parameters on levitation force and the utilization rate of NdFeB material are analyzed. The optimal ranges of these structural parameters are obtained. The mutual impact of these parameters is also discussed. The optimization method of these structure parameters is proposed at the end of this paper.

Structural parameter optimization design for Halbach permanent maglev rail

Energy Technology Data Exchange (ETDEWEB)

Guo, F., E-mail: guofang19830119@163.co [R and D Center of Applied Superconductivity, Huazhong University of Science and Technology, Wuhan 430074 (China); Tang, Y.; Ren, L.; Li, J. [R and D Center of Applied Superconductivity, Huazhong University of Science and Technology, Wuhan 430074 (China)

2010-11-01

Maglev rail is an important part of the magnetic levitation launch system. Reducing the manufacturing cost of magnetic levitation rail is the key problem for the development of magnetic levitation launch system. The Halbach permanent array has an advantage that the fundamental spatial field is cancelled on one side of the array while the field on the other side is enhanced. So this array used in the design of high temperature superconducting permanent maglev rail could improve the surface magnetic field and the levitation force. In order to make the best use of Nd-Fe-B (NdFeB) material and reduce the cost of maglev rail, the effect of the rail's structural parameters on levitation force and the utilization rate of NdFeB material are analyzed. The optimal ranges of these structural parameters are obtained. The mutual impact of these parameters is also discussed. The optimization method of these structure parameters is proposed at the end of this paper.

Distribution, utilization structure and potential of biomass resources in rural China: With special references of crop residues

Energy Technology Data Exchange (ETDEWEB)

Liu, H [Laboratory of Quantitative Vegetation Ecology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093 (China); Graduate University of Chinese Academy of Sciences, Beijing 100049 (China); Jiang, G M [Laboratory of Quantitative Vegetation Ecology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093 (China); Agronomy Department, Shandong Agricultural University, Tai' an 271018, Shandong Province (China); Zhuang, H Y [National Bio-Energy CO., LTD, No. 26B, Financial Street, Xicheng District, Beijing 100032 (China); Shandong Academy of Sciences, No. 19, Keyuan Road, Ji' nan 250014, Shandong Province (China); Wang, K J [Agronomy Department, Shandong Agricultural University, Tai' an 271018, Shandong Province (China)

2008-06-15

As the largest developing country in the world, China is urgently in short of energy and natural resources. However, biological resources such as crop residues are burnt in the field, which cause serious environmental pollution. Still it is not clear how much storage and potential of these huge crop residues are in China. This paper firstly reported the distribution, utilization structure and potential of crop biomass and provided the tangible information of crop residues in rural China through careful collecting and recalculating data. From 1995 to 2005, China produces some 630 million tons of crop residues per year, 50% of which comes from east and central south of China. The amount of crop residues is 1.3 times of the total yield of crops, 2 times of the total fodder of grassland, which covers 41% of China's territory. Crop residues of corn, wheat and rice amounted to 239, 137 and 116 million tons, respectively, accounting for nearly 80% of the total crop residues. Unfortunately, the utilizing structure is seriously improper for such abundant biomass resources. Although 23% of the crop residues are used for forage, 4% for industry materials and 0.5% for biogas, the large parts are used with lower efficiency or wasted, with 37% being directly combusted by farmers, 15% lost during collection and the rest 20.5% discarded or directly burnt in the field. Reasonable adjustment of the utilizing pattern and popularization of the recycling agriculture are essential out-ways for residues, with the development of the forage industry being the breakthrough point. We suggested that utilizing the abandoned 20.5% of the total residues for forage and combining agriculture and stock raising can greatly improve the farm system and cut down fertilizer pollution. Through the development of forage industries, the use efficiency of crop residues could be largely enhanced. Commercializing and popularizing technologies of biomass gasification and liquefaction might be substitute

Investigation of the structural preference and flexibility of the loop residues in amyloid fibrils of the HET-s prion.

Science.gov (United States)

Dolenc, Jožica; Meier, Beat H; Rusu, Victor H; van Gunsteren, Wilfred F

2016-02-17

The structural variability of a 16-residue loop (residues 246-261) which is in part disordered and connects two layers of the β-solenoid formed by the prion-form of HET-s and its prion domain HET-s(218-289) is investigated using molecular dynamics computer simulation. A system of three HET-s(218-289) molecules in a β-sheet structure as in the fibril is simulated in aqueous solution. The trajectory structures appear to be consistent with the Cα chemical shift data obtained. In order to delineate the influence of the β-sheet core of the fibril upon the structural variability of the loop, the latter is also simulated without the β-sheet core, but with its N- and C-terminal residues restrained at their positions in the fibril. The analysis of the trajectories shows that the structural variability of the loop is restricted by the β-sheet core, least at its N-terminal end and most in the middle of the trimer.

Characterization of the Young's modulus and residual stresses for a sputtered silicon oxynitride film using micro-structures

International Nuclear Information System (INIS)

Dong, Jian; Du, Ping; Zhang, Xin

2013-01-01

Silicon oxynitride (SiON) is an important material to fabricate micro-electro-mechanical system (MEMS) devices due to its composition-dependent tunability in electronic and mechanical properties. In this work, the SiON film with 41.45% silicon, 32.77% oxygen and 25.78% nitrogen content was deposited by RF magnetron sputtering. Two types of optimized micro-structures including micro-cantilevers and micro-rotating-fingers were designed and fabricated using MEMS surface micromachining technology. The micro-cantilever bending tests were conducted using a nanoindenter to characterize the Young's modulus of the SiON film. Owing to the elimination of the residual stress effect on the micro-cantilever structure, higher accuracy in the Young's modulus was achieved from this technique. With the information of Young's modulus of the film, the residual stresses were characterized from the deflection of the micro-rotating-fingers. This structure was able to locally measure a large range of tensile or compressive residual stresses in a thin film with sufficient sensitivities. The results showed that the Young's modulus of the SiON film was 122 GPa and the residual stresses of the SiON film were 327 MPa in the crystallographic orientation of the wafer and 334 MPa in the direction perpendicular to the crystallographic orientation, both in compression. This work presents a comprehensive methodology to measure the Young's modulus and residual stresses of a thin film with improved accuracy, which is promising for applications in mechanical characterization of MEMS devices. - Highlight: • We measured the Young's modulus and residual stress of SiON film by microstructure. • Micro cantilever structure improved the Young's modulus' measurement accuracy. • We explored the reason for the deviations of residual stress value of SiON film

A Refined Model for the Structure of Acireductone Dioxygenase from Klebsiella ATCC 8724 Incorporating Residual Dipolar Couplings

Energy Technology Data Exchange (ETDEWEB)

Pochapsky, Thomas C., E-mail: pochapsk@brandeis.edu; Pochapsky, Susan S.; Ju Tingting [Brandeis University, Department of Chemistry (United States); Hoefler, Chris [Brandeis University, Department of Biochemistry (United States); Liang Jue [Brandeis University, Department of Chemistry (United States)

2006-02-15

Acireductone dioxygenase (ARD) from Klebsiella ATCC 8724 is a metalloenzyme that is capable of catalyzing different reactions with the same substrates (acireductone and O{sub 2}) depending upon the metal bound in the active site. A model for the solution structure of the paramagnetic Ni{sup 2+}-containing ARD has been refined using residual dipolar couplings (RDCs) measured in two media. Additional dihedral restraints based on chemical shift (TALOS) were included in the refinement, and backbone structure in the vicinity of the active site was modeled from a crystallographic structure of the mouse homolog of ARD. The incorporation of residual dipolar couplings into the structural refinement alters the relative orientations of several structural features significantly, and improves local secondary structure determination. Comparisons between the solution structures obtained with and without RDCs are made, and structural similarities and differences between mouse and bacterial enzymes are described. Finally, the biological significance of these differences is considered.

Electron paramagnetic resonance parameters and local structure for ...

Indian Academy of Sciences (India)

HUA-MING ZHANG. 1. , GUANG-DUO LU. 1 ... the above ZFSs, the local structure information for the impurity Gd. 3+ is obtained, i.e., .... parameters, extended X-ray absorption fine-structure (EXAFS) measurements and crystal-field spectrum ...

Leptogenesis and residual CP symmetry

International Nuclear Information System (INIS)

Chen, Peng; Ding, Gui-Jun; King, Stephen F.

2016-01-01

We discuss flavour dependent leptogenesis in the framework of lepton flavour models based on discrete flavour and CP symmetries applied to the type-I seesaw model. Working in the flavour basis, we analyse the case of two general residual CP symmetries in the neutrino sector, which corresponds to all possible semi-direct models based on a preserved Z 2 in the neutrino sector, together with a CP symmetry, which constrains the PMNS matrix up to a single free parameter which may be fixed by the reactor angle. We systematically study and classify this case for all possible residual CP symmetries, and show that the R-matrix is tightly constrained up to a single free parameter, with only certain forms being consistent with successful leptogenesis, leading to possible connections between leptogenesis and PMNS parameters. The formalism is completely general in the sense that the two residual CP symmetries could result from any high energy discrete flavour theory which respects any CP symmetry. As a simple example, we apply the formalism to a high energy S 4 flavour symmetry with a generalized CP symmetry, broken to two residual CP symmetries in the neutrino sector, recovering familiar results for PMNS predictions, together with new results for flavour dependent leptogenesis.

Influence of the residual stresses on crack initiation in brittle materials and structures

International Nuclear Information System (INIS)

Henninger, C.

2007-11-01

Many material assemblies subjected to thermo-mechanical loadings develop thermal residual stresses which modify crack onset conditions. Besides if one of the components has a plastic behaviour, plastic residual deformations may also have a contribution. One of the issues in brittle fracture mechanics is to predict crack onset without any pre-existing defect. Leguillon proposed an onset criterion based on both a Griffth-like energetic condition and a maximum stress criterion. The analysis uses matched asymptotics and the theory of singularity. The good fit between the model and experimental measurements led on homogeneous isotropic materials under pure mechanical loading incited us to take into account residual stresses in the criterion. The comparison between the modified criterion and the experimental measurements carried out on an aluminum/epoxy assembly proves to be satisfying concerning the prediction of failure of the interface between the two components. Besides, it allows, through inversion, identifying the fracture properties of this interface. The modified criterion is also applied to the delamination of the tile/structure interface in the plasma facing components of the Tore Supra tokamak. Indeed thermal and plastic residual stresses appear in the metallic part of these coating tiles. (author)

Parameter study of self-absorption effects in Total Reflection X-ray Fluorescence-X-ray Absorption Near Edge Structure analysis of arsenic

International Nuclear Information System (INIS)

Meirer, F.; Pepponi, G.; Streli, C.; Wobrauschek, P.; Kregsamer, P.; Zoeger, N.; Falkenberg, G.

2008-01-01

Total reflection X-ray Fluorescence (TXRF) analysis in combination with X-ray Absorption Near Edge Structure (XANES) analysis is a powerful method to perform chemical speciation studies at trace element levels. However, when measuring samples with higher concentrations and in particular standards, damping of the oscillations is observed. In this study the influence of self-absorption effects on TXRF-XANES measurements was investigated by comparing measurements with theoretical calculations. As(V) standard solutions were prepared at various concentrations and dried on flat substrates. The measurements showed a correlation between the damping of the oscillations and the As mass deposited. A Monte-Carlo simulation was developed using data of the samples shapes obtained from confocal white light microscopy. The results showed good agreement with the measurements; they confirmed that the key parameters are the density of the investigated atom in the dried residues and the shape of the residue, parameters that combined define the total mass crossed by a certain portion of the incident beam. The study presents a simple approach for an a priori evaluation of the self-absorption in TXRF X-ray absorption studies. The consequences for Extended X-ray Absorption Fine Structure (EXAFS) and XANES measurements under grazing incidence conditions are discussed, leading to the conclusion that the damping of the oscillations seems to make EXAFS of concentrated samples non feasible. For XANES 'fingerprint' analysis samples should be prepared with a deposited mass and sample shape leading to an acceptable absorption for the actual investigation

Residual dipolar couplings : a new technique for structure determination of proteins in solution

NARCIS (Netherlands)

van Lune, Frouktje Sapke

2004-01-01

The aim of the work described in this thesis was to investigate how residual dipolar couplings can be used to resolve or refine the three-dimensional structure of one of the proteins of the phosphoenol-pyruvate phosphotransferase system (PTS), the main transport system for carbohydrates in

The Study of Residual Voltage of Induction Motor and the Influence of Various Parameters on the Residual Voltage

Science.gov (United States)

Zhang, Shuping; Zhao, Chen; Tan, Weipu

2017-05-01

The majority important load of industrial area is mainly composed of induction motor, it is more common that induction motor becomes sluggishness and even tripping due to the lose of power supply or other malfunction in the practical work. In this paper, space vector method is used to establish a reduced order model of induction motor, and then study the changes of motor electromagnetic after losing electricity. Based on motion equations of the rotor and magnetic flux conservation principle, it uses mathematical methods to deduce the expression of rotor current, rotor flux, the stator flux and the residual voltage of stator side. In addition, relying on thermal power plants, it uses the actual data of power plants, takes DIgsilent software to simulate the residual voltage of motor after losing electricity. analyses the influence on the residual voltage with the changes of the moment of inertia, load ratio, initial size of slip and the load characteristic of induction motor. By analysis of these, it has a more detailed understanding about the changes of residual voltage in practical application, in additional, it is more beneficial to put into standby power supply safely and effectively, moreover, reduce the influence of the input process to the whole system.

Development of computer program ENMASK for prediction of residual environmental masking-noise spectra, from any three independent environmental parameters

Energy Technology Data Exchange (ETDEWEB)

Chang, Y.-S.; Liebich, R. E.; Chun, K. C.

2000-03-31

Residual environmental sound can mask intrusive4 (unwanted) sound. It is a factor that can affect noise impacts and must be considered both in noise-impact studies and in noise-mitigation designs. Models for quantitative prediction of sensation level (audibility) and psychological effects of intrusive noise require an input with 1/3 octave-band spectral resolution of environmental masking noise. However, the majority of published residual environmental masking-noise data are given with either octave-band frequency resolution or only single A-weighted decibel values. A model has been developed that enables estimation of 1/3 octave-band residual environmental masking-noise spectra and relates certain environmental parameters to A-weighted sound level. This model provides a correlation among three environmental conditions: measured residual A-weighted sound-pressure level, proximity to a major roadway, and population density. Cited field-study data were used to compute the most probable 1/3 octave-band sound-pressure spectrum corresponding to any selected one of these three inputs. In turn, such spectra can be used as an input to models for prediction of noise impacts. This paper discusses specific algorithms included in the newly developed computer program ENMASK. In addition, the relative audibility of the environmental masking-noise spectra at different A-weighted sound levels is discussed, which is determined by using the methodology of program ENAUDIBL.

PREvaIL, an integrative approach for inferring catalytic residues using sequence, structural, and network features in a machine-learning framework.

Science.gov (United States)

Song, Jiangning; Li, Fuyi; Takemoto, Kazuhiro; Haffari, Gholamreza; Akutsu, Tatsuya; Chou, Kuo-Chen; Webb, Geoffrey I

2018-04-14

Determining the catalytic residues in an enzyme is critical to our understanding the relationship between protein sequence, structure, function, and enhancing our ability to design novel enzymes and their inhibitors. Although many enzymes have been sequenced, and their primary and tertiary structures determined, experimental methods for enzyme functional characterization lag behind. Because experimental methods used for identifying catalytic residues are resource- and labor-intensive, computational approaches have considerable value and are highly desirable for their ability to complement experimental studies in identifying catalytic residues and helping to bridge the sequence-structure-function gap. In this study, we describe a new computational method called PREvaIL for predicting enzyme catalytic residues. This method was developed by leveraging a comprehensive set of informative features extracted from multiple levels, including sequence, structure, and residue-contact network, in a random forest machine-learning framework. Extensive benchmarking experiments on eight different datasets based on 10-fold cross-validation and independent tests, as well as side-by-side performance comparisons with seven modern sequence- and structure-based methods, showed that PREvaIL achieved competitive predictive performance, with an area under the receiver operating characteristic curve and area under the precision-recall curve ranging from 0.896 to 0.973 and from 0.294 to 0.523, respectively. We demonstrated that this method was able to capture useful signals arising from different levels, leveraging such differential but useful types of features and allowing us to significantly improve the performance of catalytic residue prediction. We believe that this new method can be utilized as a valuable tool for both understanding the complex sequence-structure-function relationships of proteins and facilitating the characterization of novel enzymes lacking functional annotations

A computational tool to predict the evolutionarily conserved protein-protein interaction hot-spot residues from the structure of the unbound protein.

Science.gov (United States)

Agrawal, Neeraj J; Helk, Bernhard; Trout, Bernhardt L

2014-01-21

Identifying hot-spot residues - residues that are critical to protein-protein binding - can help to elucidate a protein's function and assist in designing therapeutic molecules to target those residues. We present a novel computational tool, termed spatial-interaction-map (SIM), to predict the hot-spot residues of an evolutionarily conserved protein-protein interaction from the structure of an unbound protein alone. SIM can predict the protein hot-spot residues with an accuracy of 36-57%. Thus, the SIM tool can be used to predict the yet unknown hot-spot residues for many proteins for which the structure of the protein-protein complexes are not available, thereby providing a clue to their functions and an opportunity to design therapeutic molecules to target these proteins. Copyright © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Electrostatics of cysteine residues in proteins: Parameterization and validation of a simple model

Science.gov (United States)

Salsbury, Freddie R.; Poole, Leslie B.; Fetrow, Jacquelyn S.

2013-01-01

One of the most popular and simple models for the calculation of pKas from a protein structure is the semi-macroscopic electrostatic model MEAD. This model requires empirical parameters for each residue to calculate pKas. Analysis of current, widely used empirical parameters for cysteine residues showed that they did not reproduce expected cysteine pKas; thus, we set out to identify parameters consistent with the CHARMM27 force field that capture both the behavior of typical cysteines in proteins and the behavior of cysteines which have perturbed pKas. The new parameters were validated in three ways: (1) calculation across a large set of typical cysteines in proteins (where the calculations are expected to reproduce expected ensemble behavior); (2) calculation across a set of perturbed cysteines in proteins (where the calculations are expected to reproduce the shifted ensemble behavior); and (3) comparison to experimentally determined pKa values (where the calculation should reproduce the pKa within experimental error). Both the general behavior of cysteines in proteins and the perturbed pKa in some proteins can be predicted reasonably well using the newly determined empirical parameters within the MEAD model for protein electrostatics. This study provides the first general analysis of the electrostatics of cysteines in proteins, with specific attention paid to capturing both the behavior of typical cysteines in a protein and the behavior of cysteines whose pKa should be shifted, and validation of force field parameters for cysteine residues. PMID:22777874

Properties of Soil Pore Space Regulate Pathways of Plant Residue Decomposition and Community Structure of Associated Bacteria

Science.gov (United States)

Negassa, Wakene C.; Guber, Andrey K.; Kravchenko, Alexandra N.; Marsh, Terence L.; Hildebrandt, Britton; Rivers, Mark L.

2015-01-01

Physical protection of soil carbon (C) is one of the important components of C storage. However, its exact mechanisms are still not sufficiently lucid. The goal of this study was to explore the influence of soil structure, that is, soil pore spatial arrangements, with and without presence of plant residue on (i) decomposition of added plant residue, (ii) CO2 emission from soil, and (iii) structure of soil bacterial communities. The study consisted of several soil incubation experiments with samples of contrasting pore characteristics with/without plant residue, accompanied by X-ray micro-tomographic analyses of soil pores and by microbial community analysis of amplified 16S–18S rRNA genes via pyrosequencing. We observed that in the samples with substantial presence of air-filled well-connected large (>30 µm) pores, 75–80% of the added plant residue was decomposed, cumulative CO2 emission constituted 1,200 µm C g-1 soil, and movement of C from decomposing plant residue into adjacent soil was insignificant. In the samples with greater abundance of water-filled small pores, 60% of the added plant residue was decomposed, cumulative CO2 emission constituted 2,000 µm C g-1 soil, and the movement of residue C into adjacent soil was substantial. In the absence of plant residue the influence of pore characteristics on CO2 emission, that is on decomposition of the native soil organic C, was negligible. The microbial communities on the plant residue in the samples with large pores had more microbial groups known to be cellulose decomposers, that is, Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes, while a number of oligotrophic Acidobacteria groups were more abundant on the plant residue from the samples with small pores. This study provides the first experimental evidence that characteristics of soil pores and their air/water flow status determine the phylogenetic composition of the local microbial community and directions and magnitudes of soil C

Properties of soil pore space regulate pathways of plant residue decomposition and community structure of associated bacteria.

Science.gov (United States)

Negassa, Wakene C; Guber, Andrey K; Kravchenko, Alexandra N; Marsh, Terence L; Hildebrandt, Britton; Rivers, Mark L

2015-01-01

Physical protection of soil carbon (C) is one of the important components of C storage. However, its exact mechanisms are still not sufficiently lucid. The goal of this study was to explore the influence of soil structure, that is, soil pore spatial arrangements, with and without presence of plant residue on (i) decomposition of added plant residue, (ii) CO2 emission from soil, and (iii) structure of soil bacterial communities. The study consisted of several soil incubation experiments with samples of contrasting pore characteristics with/without plant residue, accompanied by X-ray micro-tomographic analyses of soil pores and by microbial community analysis of amplified 16S-18S rRNA genes via pyrosequencing. We observed that in the samples with substantial presence of air-filled well-connected large (>30 µm) pores, 75-80% of the added plant residue was decomposed, cumulative CO2 emission constituted 1,200 µm C g(-1) soil, and movement of C from decomposing plant residue into adjacent soil was insignificant. In the samples with greater abundance of water-filled small pores, 60% of the added plant residue was decomposed, cumulative CO2 emission constituted 2,000 µm C g(-1) soil, and the movement of residue C into adjacent soil was substantial. In the absence of plant residue the influence of pore characteristics on CO2 emission, that is on decomposition of the native soil organic C, was negligible. The microbial communities on the plant residue in the samples with large pores had more microbial groups known to be cellulose decomposers, that is, Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes, while a number of oligotrophic Acidobacteria groups were more abundant on the plant residue from the samples with small pores. This study provides the first experimental evidence that characteristics of soil pores and their air/water flow status determine the phylogenetic composition of the local microbial community and directions and magnitudes of soil C

Characterization of Active Site Residues of Nitroalkane Oxidase†

Science.gov (United States)

Valley, Michael P.; Fenny, Nana S.; Ali, Shah R.; Fitzpatrick, Paul F.

2010-01-01

The flavoenzyme nitroalkane oxidase catalyzes the oxidation of primary and secondary nitrolkanes to the corresponding aldehydes and ketones plus nitrite. The structure of the enzyme shows that Serl71 forms a hydrogen bond to the flavin N5, suggesting that it plays a role in catalysis. Cys397 and Tyr398 were previously identified by chemical modification as potential active site residues. To more directly probe the roles of these residues, the S171A, S171V, S171T, C397S, and Y398F enzymes have been characterized with nitroethane as substrate. The C397S and Y398 enzymes were less stable than the wild-type enzyme, and the C397S enzyme routinely contained a substoichiometric amount of FAD. Analysis of the steady-state kinetic parameters for the mutant enzymes, including deuterium isotope effects, establishes that all of the mutations result in decreases in the rate constants for removal of the substrate proton by ~5-fold and decreases in the rate constant for product release of ~2-fold. Only the S171V and S171T mutations alter the rate constant for flavin oxidation. These results establish that these residues are not involved in catalysis, but rather are required for maintaining the protein structure. PMID:20056514

NMR structure calculation for all small molecule ligands and non-standard residues from the PDB Chemical Component Dictionary

Energy Technology Data Exchange (ETDEWEB)

Yilmaz, Emel Maden; Güntert, Peter, E-mail: guentert@em.uni-frankfurt.de [Goethe University Frankfurt am Main, Center for Biomolecular Magnetic Resonance, Institute of Biophysical Chemistry (Germany)

2015-09-15

An algorithm, CYLIB, is presented for converting molecular topology descriptions from the PDB Chemical Component Dictionary into CYANA residue library entries. The CYANA structure calculation algorithm uses torsion angle molecular dynamics for the efficient computation of three-dimensional structures from NMR-derived restraints. For this, the molecules have to be represented in torsion angle space with rotations around covalent single bonds as the only degrees of freedom. The molecule must be given a tree structure of torsion angles connecting rigid units composed of one or several atoms with fixed relative positions. Setting up CYANA residue library entries therefore involves, besides straightforward format conversion, the non-trivial step of defining a suitable tree structure of torsion angles, and to re-order the atoms in a way that is compatible with this tree structure. This can be done manually for small numbers of ligands but the process is time-consuming and error-prone. An automated method is necessary in order to handle the large number of different potential ligand molecules to be studied in drug design projects. Here, we present an algorithm for this purpose, and show that CYANA structure calculations can be performed with almost all small molecule ligands and non-standard amino acid residues in the PDB Chemical Component Dictionary.

Characterization of the residual structure in the unfolded state of the Delta 131 Delta fragment of staphylococcal nuclease

DEFF Research Database (Denmark)

Francis, C. J.; Lindorff-Larsen, Kresten; Best, R. B.

2006-01-01

dynamics simulations to characterise the residual structure of the 131 fragment of staphylococcal nuclease under physiological conditions. Our findings indicate that 131 under these conditions shows a tendency to form transiently hydrophobic clusters similar to those present in the native state of wild......The determination of the conformational preferences in unfolded states of proteins constitutes an important challenge in structural biology. We use inter-residue distances estimated from site-directed spin-labeling NMR experimental measurements as ensemble-averaged restraints in all-atom molecular...

PARAMETERS AFFECTING THE STRUCTURAL ANALYSIS OF A TUNNEL STRUCTURE EXPOSED TO FIRE

Directory of Open Access Journals (Sweden)

Omid Pouran

2016-12-01

Full Text Available Behaviour of cut-and-cover tunnels exposed to fire should be analysed by using a realistic structural model that takes account of mechanical and thermal effects on the structure. This has been performed with the aid of Finite Element (FE software package called SOFiSTiK in parallel, for two types of elements as a scope of research project financed by the German Bundesanstalt für Straßenwesen BAST. Since the stiffness of the structure at elevated temperatures is highly affected, a realistic model of structural behaviour of the tunnel could be only achieved by considering the nonlinear analysis of the structure. This has been performed for a 2–cell cut and cover tunnel by taking account of simultaneous reduction of stiffness and strength and the time-dependent increasing indirect effects due to axial constraints and temperature gradients induced by elevated temperatures. The thermal analyses have been performed and the effects were implemented into the structural model by the multi-layered strain model. The stress–strain model proposed by EN 1992-1-2 is implemented for the elevated temperature. Since there was sufficient amount of Polypropylene fibres in the concrete mixtures, modelling of spalling was excluded from the analysis. The critical corresponding stresses and material behaviour are compared and interpreted at different time stages. The main parameters affecting the accuracy and convergence of the results of structural analysis for the used model are identified: defining a realistic fire action, using concrete material model fulfilling the requirements of fire situation in tunnels, defining appropriate time intervals for load implementations. These parameters along with other parameters, which influence the results to a lesser degree, are identified and investigated in this paper.

Effect of gamma radiation on the microbiological and physicochemical parameters and on the phenolic compounds of a fruit residue flour during storage

International Nuclear Information System (INIS)

Aranha, Jessica Bomtorin; Negri, Talita Costa; Martin, José Guilherme Prado; Spoto, Marta Helena Fillet

2017-01-01

Agroindustrial residues have high levels of nutrients, but are little exploited for consumption because they require prior treatment to ensure microbiological safety. Irradiation is an effective process for the reduction of microbial counts with maintenance of the product characteristics. The objective of this study was to evaluate the effect of irradiation on the microbiological quality, physicochemical properties and phenolic compounds of a fruit residue flour during storage. The flour was obtained from dehydrated residues of pineapple, melon, papaya and apple, which were submitted to irradiation doses of (0, 1, 2 and 3 kGy). The microbiological (coliforms, moulds, yeast and Salmonella sp. counts) and physicochemical (pH, titratable acidity, soluble solids, water activity, colour parameters L⁎, a⁎ and b⁎ and phenolic compounds) parameters were evaluated after 0, 7, 14 and 21 days of storage. All the irradiation treatments reduced the microbial count, and the presence of Salmonella sp was not detected in any of the samples. The acidity and pH showed changes during storage. The soluble solids and water activity showed no significant differences between the doses during storage. The phenolic compounds were preserved by the application of irradiation. The colour of the flour samples darkened slightly with irradiation. It was concluded that the most effective doses for the maintenance of the microbiological quality and physicochemical characteristics of the flour were 2 and 3 kGy. (author)

Immobilization of acid digestion residue

International Nuclear Information System (INIS)

Greenhalgh, W.O.; Allen, C.R.

1983-01-01

Acid digestion treatment of nuclear waste is similar to incineration processes and results in the bulk of the waste being reduced in volume and weight to some residual solids termed residue. The residue is composed of various dispersible solid materials and typically contains the resultant radioactivity from the waste. This report describes the immobilization of the residue in portland cement, borosilicate glass, and some other waste forms. Diagrams showing the cement and glass virtification parameters are included in the report as well as process steps and candidate waste product forms. Cement immobilization is simplest and probably least expensive; glass vitrification exhibits the best overall volume reduction ratio

Evaluating two-dimensional skeletal structure parameters using radiological bone morphometric analysis

International Nuclear Information System (INIS)

Asa, Kensuke; Sakurai, Takashi; Kashima, Isamu; Kumasaka, Satsuki

2005-01-01

The objectives of this study was to investigate the reliability of two-dimensional (2D) skeletal structure parameters obtained using radiological bone morphometric analysis. The 2D skeletal parameters in the regions of interest (ROIs) were measured on computed radiography (CR) images of first phalanges from racehorses, using radiological bone morphometric analysis. Cancellous bone blocks were made from the phalanges in the same position as the ROI determined on CR images. Three-dimensional (3D) trabecular parameters were measured using micro-computed tomography (μCT). The correlations between the 2D skeletal parameters and 3D trabecular parameters were evaluated in relation to the measured bone strength. The following 2D skeletal structure parameters were correlated with bone strength (r=0.61-0.69): skeletal perimeter (Sk.Pm), skeletal number (Sk.N), skeletal separation (Sk.Sp), skeletal spacing (Sk.Spac), fractal dimension (FD), and skeletal pattern factor (SkPf). The 3D trabecular structure parameters were closely correlated with bone strength (r=0.74-0.86). The 2D skeletal parameters Sk.N, Sk.Pm, FD, SkPf, and Sk.Spac were correlated with the 3D trabecular parameters (r=0.61-0.70). The 2D skeletal parameters obtained using radiological bone morphometric analysis may be useful indicators of trabecular strength. (author)

Pulsar timing residuals due to individual non-evolving gravitational wave sources

International Nuclear Information System (INIS)

Tong Ming-Lei; Zhao Cheng-Shi; Yan Bao-Rong; Yang Ting-Gao; Gao Yu-Ping

2014-01-01

The pulsar timing residuals induced by gravitational waves from non-evolving single binary sources are affected by many parameters related to the relative positions of the pulsar and the gravitational wave sources. We will analyze the various effects due to different parameters. The standard deviations of the timing residuals will be calculated with a variable parameter fixing a set of other parameters. The orbits of the binary sources will be generally assumed to be elliptical. The influences of different eccentricities on the pulsar timing residuals will also be studied in detail. We find that the effects of the related parameters are quite different, and some of them display certain regularities

Electrostatics of cysteine residues in proteins: parameterization and validation of a simple model.

Science.gov (United States)

Salsbury, Freddie R; Poole, Leslie B; Fetrow, Jacquelyn S

2012-11-01

One of the most popular and simple models for the calculation of pK(a) s from a protein structure is the semi-macroscopic electrostatic model MEAD. This model requires empirical parameters for each residue to calculate pK(a) s. Analysis of current, widely used empirical parameters for cysteine residues showed that they did not reproduce expected cysteine pK(a) s; thus, we set out to identify parameters consistent with the CHARMM27 force field that capture both the behavior of typical cysteines in proteins and the behavior of cysteines which have perturbed pK(a) s. The new parameters were validated in three ways: (1) calculation across a large set of typical cysteines in proteins (where the calculations are expected to reproduce expected ensemble behavior); (2) calculation across a set of perturbed cysteines in proteins (where the calculations are expected to reproduce the shifted ensemble behavior); and (3) comparison to experimentally determined pK(a) values (where the calculation should reproduce the pK(a) within experimental error). Both the general behavior of cysteines in proteins and the perturbed pK(a) in some proteins can be predicted reasonably well using the newly determined empirical parameters within the MEAD model for protein electrostatics. This study provides the first general analysis of the electrostatics of cysteines in proteins, with specific attention paid to capturing both the behavior of typical cysteines in a protein and the behavior of cysteines whose pK(a) should be shifted, and validation of force field parameters for cysteine residues. Copyright © 2012 Wiley Periodicals, Inc.

Structure-based network analysis of activation mechanisms in the ErbB family of receptor tyrosine kinases: the regulatory spine residues are global mediators of structural stability and allosteric interactions.

Directory of Open Access Journals (Sweden)

Kevin A James

Full Text Available The ErbB protein tyrosine kinases are among the most important cell signaling families and mutation-induced modulation of their activity is associated with diverse functions in biological networks and human disease. We have combined molecular dynamics simulations of the ErbB kinases with the protein structure network modeling to characterize the reorganization of the residue interaction networks during conformational equilibrium changes in the normal and oncogenic forms. Structural stability and network analyses have identified local communities integrated around high centrality sites that correspond to the regulatory spine residues. This analysis has provided a quantitative insight to the mechanism of mutation-induced "superacceptor" activity in oncogenic EGFR dimers. We have found that kinase activation may be determined by allosteric interactions between modules of structurally stable residues that synchronize the dynamics in the nucleotide binding site and the αC-helix with the collective motions of the integrating αF-helix and the substrate binding site. The results of this study have pointed to a central role of the conserved His-Arg-Asp (HRD motif in the catalytic loop and the Asp-Phe-Gly (DFG motif as key mediators of structural stability and allosteric communications in the ErbB kinases. We have determined that residues that are indispensable for kinase regulation and catalysis often corresponded to the high centrality nodes within the protein structure network and could be distinguished by their unique network signatures. The optimal communication pathways are also controlled by these nodes and may ensure efficient allosteric signaling in the functional kinase state. Structure-based network analysis has quantified subtle effects of ATP binding on conformational dynamics and stability of the EGFR structures. Consistent with the NMR studies, we have found that nucleotide-induced modulation of the residue interaction networks is not

Residual structure of Streptococcus mutans biofilm following complete disinfection favors secondary bacterial adhesion and biofilm re-development.

Directory of Open Access Journals (Sweden)

Tatsuya Ohsumi

Full Text Available Chemical disinfection of oral biofilms often leaves biofilm structures intact. This study aimed to examine whether the residual structure promotes secondary bacterial adhesion. Streptococcus mutans biofilms generated on resin-composite disks in a rotating disc reactor were disinfected completely with 70% isopropyl alcohol, and were again cultured in the same reactor after resupplying with the same bacterial solution. Specimens were subjected to fluorescence confocal laser scanning microscopy, viable cell counts and PCR-Invader assay in order to observe and quantify secondarily adhered cells. Fluorescence microscopic analysis, particularly after longitudinal cryosectioning, demonstrated stratified patterns of viable cells on the disinfected biofilm structure. Viable cell counts of test specimens were significantly higher than those of controls, and increased according to the amount of residual structure and culture period. Linear regression analysis exhibited a high correlation between viable and total cell counts. It was concluded that disinfected biofilm structures favored secondary bacterial adhesion.

Improvement of hydrogen bond geometry in protein NMR structures by residual dipolar couplings - an assessment of the interrelation of NMR restraints

Energy Technology Data Exchange (ETDEWEB)

Jensen, Pernille Rose; Axelsen, Jacob Bock [University of Copenhagen, Institute of Molecular Biology (Denmark); Lerche, Mathilde Hauge [Amersham Health (Sweden); Poulsen, Flemming M. [University of Copenhagen, Institute of Molecular Biology (Denmark)], E-mail: fmp@apk.molbio.ku.dk

2004-01-15

We have examined how the hydrogen bond geometry in three different proteins is affected when structural restraints based on measurements of residual dipolar couplings are included in the structure calculations. The study shows, that including restraints based solely on {sup 1}H{sup N}-{sup 15}N residual dipolar couplings has pronounced impact on the backbone rmsd and Ramachandran plot but does not improve the hydrogen bond geometry. In the case of chymotrypsin inhibitor 2 the addition of {sup 13}CO-{sup 13}C{sup {alpha}} and {sup 15}N-{sup 13}CO one bond dipolar couplings as restraints in the structure calculations improved the hydrogen bond geometry to a quality comparable to that obtained in the 1.8 A resolution X-ray structure of this protein. A systematic restraint study was performed, in which four types of restraints, residual dipolar couplings, hydrogen bonds, TALOS angles and NOEs, were allowed in two states. This study revealed the importance of using several types of residual dipolar couplings to get good hydrogen bond geometry. The study also showed that using a small set of NOEs derived only from the amide protons, together with a full set of residual dipolar couplings resulted in structures of very high quality. When reducing the NOE set, it is mainly the side-chain to side-chain NOEs that are removed. Despite of this the effect on the side-chain packing is very small when a reduced NOE set is used, which implies that the over all fold of a protein structure is mainly determined by correct folding of the backbone.

Quantitative assessment of Aluminium cast Alloys` structural parameters to optimize ITS properties

Directory of Open Access Journals (Sweden)

L. Kuchariková

2017-01-01

Full Text Available The present work deals with evaluation of eutectic Si (its shape, size, and distribution, dendrite cell size and dendrite arm spacing in aluminium cast alloys which were cast into different moulds (sand and metallic. Structural parameters were evaluated using NIS-Elements image analyser software. This software is imaging analysis software for the evaluation, capture, archiving and automated measurement of structural parameters. The control of structural parameters by NIS Elements shows that optimum mechanical properties of aluminium cast alloys strongly depend on the distribution, morphology, size of eute ctic Si and matrix parameters.

Effect of fermented biogas residue on growth performance, serum biochemical parameters, and meat quality in pigs

Directory of Open Access Journals (Sweden)

Xiang Xu

2017-10-01

Full Text Available Objective This study investigated the effect of fermented biogas residue (FBR of wheat on the performance, serum biochemical parameters, and meat quality in pigs. Methods We selected 128 pigs (the mean initial body weight was 40.24±3.08 kg and randomly allocated them to 4 groups (1 control group and 3 treatment groups with 4 replicates per group and 8 pigs per pen in a randomized complete block design based on initial body weight and sex. The control group received a corn-soybean meal-based diet, the treatment group fed diets containing 5%, 10%, and 15% FBR, respectively (abbreviated as FBR5, FBR10, and FBR15, respectively. Every group received equivalent-energy and nitrogen diets. The test lasted 60 days and was divided into early and late stages. Blood and carcass samples were obtained on 60 d. Meat quality was collected from two pigs per pen. Results During the late stage, the average daily feed intake and average daily gain of the treatment groups was greater than that of the control group (p<0.05. During the entire experiment, the average daily gain of the treatment groups was higher than that of the control group (p<0.05. Fermented biomass residue did not significantly affect serum biochemical parameters or meat quality, but did affect amino acid profiles in pork. The contents of Asp, Arg, Tyr, Phe, Leu, Thr, Ser, Lys, Pro, Ala, essential amino acids, non-essential amino acids, and total amino acids in pork of FBR5 and FBR10 were greater than those of the control group (p<0.05. Conclusion These combined results suggest that feeding FBR could increase the average daily gain and average daily feed intake in pigs and the content of several flavor-promoting amino acids.

Residual generator for cardiovascular anomalies detection

KAUST Repository

Belkhatir, Zehor

2014-06-01

This paper discusses the possibility of using observer-based approaches for cardiovascular anomalies detection and isolation. We consider a lumped parameter model of the cardiovascular system that can be written in a form of nonlinear state-space representation. We show that residuals that are sensitive to variations in some cardiovascular parameters and to abnormal opening and closure of the valves, can be generated. Since the whole state is not easily available for measurement, we propose to associate the residual generator to a robust extended kalman filter. Numerical results performed on synthetic data are provided.

Effect of synthesis parameters on polymethacrylic acid xerogel structures and equilibrium swelling

Science.gov (United States)

Panić, V.; Jovanović, J.; Adnadjević, B.; Velicković, S.

2009-09-01

Hydrogels based on crosslinked polymethacrylic acid were synthesized via free-radical polymerization in aqueous solution, using N,N'-methylene bisacrylamide as a crosslinking agent and 2,2'-azobis-[2-(2-imidazolin-2-yl)propane] dihydrochloride as an initiator. The influence of the reaction parameters (the neutralization degree of methacrylic acid and the initial monomer concentration) on the equilibrium swelling degree, the swelling kinetic parameters and the basic structural properties of xerogels was investigated. The change of synthesis parameters leads to the change of the basic structural parameters of xerogel, as well as the equilibrium swelling degree and the initial swelling rate of the hydrogels. It is found that there are power form relationships between the equilibrium swelling degree, the initial swelling rate and the structural xerogel’s properties and the change of the neutralization degree of monomer, i.e. the monomer concentration. The examined correlations proved that the crosslinking density is the crucial parameter which determines all the other investigated structural and swelling parameters.

Characterization of active site residues of nitroalkane oxidase.

Science.gov (United States)

Valley, Michael P; Fenny, Nana S; Ali, Shah R; Fitzpatrick, Paul F

2010-06-01

The flavoenzyme nitroalkane oxidase catalyzes the oxidation of primary and secondary nitroalkanes to the corresponding aldehydes and ketones plus nitrite. The structure of the enzyme shows that Ser171 forms a hydrogen bond to the flavin N5, suggesting that it plays a role in catalysis. Cys397 and Tyr398 were previously identified by chemical modification as potential active site residues. To more directly probe the roles of these residues, the S171A, S171V, S171T, C397S, and Y398F enzymes have been characterized with nitroethane as substrate. The C397S and Y398 enzymes were less stable than the wild-type enzyme, and the C397S enzyme routinely contained a substoichiometric amount of FAD. Analysis of the steady-state kinetic parameters for the mutant enzymes, including deuterium isotope effects, establishes that all of the mutations result in decreases in the rate constants for removal of the substrate proton by approximately 5-fold and decreases in the rate constant for product release of approximately 2-fold. Only the S171V and S171T mutations alter the rate constant for flavin oxidation. These results establish that these residues are not involved in catalysis, but rather are required for maintaining the protein structure. 2009 Elsevier Inc. All rights reserved.

Modeling the Influence of Process Parameters and Additional Heat Sources on Residual Stresses in Laser Cladding

Science.gov (United States)

Brückner, F.; Lepski, D.; Beyer, E.

2007-09-01

In laser cladding thermal contraction of the initially liquid coating during cooling causes residual stresses and possibly cracks. Preweld or postweld heating using inductors can reduce the thermal strain difference between coating and substrate and thus reduce the resulting stress. The aim of this work is to better understand the influence of various thermometallurgical and mechanical phenomena on stress evolution and to optimize the induction-assisted laser cladding process to get crack-free coatings of hard materials at high feed rates. First, an analytical one-dimensional model is used to visualize the most important features of stress evolution for a Stellite coating on a steel substrate. For more accurate studies, laser cladding is simulated including the powder-beam interaction, the powder catchment by the melt pool, and the self-consistent calculation of temperature field and bead shape. A three-dimensional finite element model and the required equivalent heat sources are derived from the results and used for the transient thermomechanical analysis, taking into account phase transformations and the elastic-plastic material behavior with strain hardening. Results are presented for the influence of process parameters such as feed rate, heat input, and inductor size on the residual stresses at a single bead of Stellite coatings on steel.

Measurement of residual stresses using fracture mechanics weight functions

International Nuclear Information System (INIS)

Fan, Y.

2000-01-01

A residual stress measurement method has been developed to quantify through-the-thickness residual stresses. Accurate measurement of residual stresses is crucial for many engineering structures. Fabrication processes such as welding and machining generate residual stresses that are difficult to predict. Residual stresses affect the integrity of structures through promoting failures due to brittle fracture, fatigue, stress corrosion cracking, and wear. In this work, the weight function theory of fracture mechanics is used to measure residual stresses. The weight function theory is an important development in computational fracture mechanics. Stress intensity factors for arbitrary stress distribution on the crack faces can be accurately and efficiently computed for predicting crack growth. This paper demonstrates that the weight functions are equally useful in measuring residual stresses. In this method, an artificial crack is created by a thin cut in a structure containing residual stresses. The cut relieves the residual stresses normal to the crack-face and allows the relieved residual stresses to deform the structure. Strain gages placed adjacent to the cut measure the relieved strains corresponding to incrementally increasing depths of the cut. The weight functions of the cracked body relate the measured strains to the residual stresses normal to the cut within the structure. The procedure details, such as numerical integration of the singular functions in applying the weight function method, will be discussed

Measurement of residual stresses using fracture mechanics weight functions

International Nuclear Information System (INIS)

Fan, Y.

2001-01-01

A residual stress measurement method has been developed to quantify through-the-thickness residual stresses. Accurate measurement of residual stresses is crucial for many engineering structures. Fabrication processes such as welding and machining generate residual stresses that are difficult to predict. Residual stresses affect the integrity of structures through promoting failures due to brittle fracture, fatigue, stress corrosion cracking, and wear. In this work, the weight function theory of fracture mechanics is used to measure residual stresses. The weight function theory is an important development in computational fracture mechanics. Stress intensity factors for arbitrary stress distribution on the crack faces can be accurately and efficiently computed for predicting crack growth. This paper demonstrates that the weight functions are equally useful in measuring residual stresses. In this method, an artificial crack is created by a thin cut in a structure containing residual stresses. The cut relieves the residual stresses normal to the crack-face and allows the relieved residual stresses to deform the structure. Strain gages placed adjacent to the cut measure the relieved strains corresponding to incrementally increasing depths of the cut. The weight functions of the cracked body relate the measured strains to the residual stresses normal to the cut within the structure. The procedure details, such as numerical integration of the singular functions in applying the weight function method, will be discussed. (author)

DEPENDENCIES TO DETERMINE THE MEASURE OF DAMAGE AND CALCULATION OF RESIDUAL LIFE OF REINFORCED CONCRETE SUPERSTRUCTURE, EXPOSED TO SALT CORROSION

OpenAIRE

SAATOVA NODIRA ZIYAYEVNA

2016-01-01

In this paper we consider the current method of determining the measure of damage of concrete and reinforcement. The proposed dependence measures of damage, convenient for use in predicting the life of structures superstructures.The practical method of calculation determination of residual resource of the exploited superstructures developed. The main source of data for calculating the residual life are the parameters defined by the technical diagnosis.

Repetitive Identification of Structural Systems Using a Nonlinear Model Parameter Refinement Approach

Directory of Open Access Journals (Sweden)

Jeng-Wen Lin

2009-01-01

Full Text Available This paper proposes a statistical confidence interval based nonlinear model parameter refinement approach for the health monitoring of structural systems subjected to seismic excitations. The developed model refinement approach uses the 95% confidence interval of the estimated structural parameters to determine their statistical significance in a least-squares regression setting. When the parameters' confidence interval covers the zero value, it is statistically sustainable to truncate such parameters. The remaining parameters will repetitively undergo such parameter sifting process for model refinement until all the parameters' statistical significance cannot be further improved. This newly developed model refinement approach is implemented for the series models of multivariable polynomial expansions: the linear, the Taylor series, and the power series model, leading to a more accurate identification as well as a more controllable design for system vibration control. Because the statistical regression based model refinement approach is intrinsically used to process a “batch” of data and obtain an ensemble average estimation such as the structural stiffness, the Kalman filter and one of its extended versions is introduced to the refined power series model for structural health monitoring.

Thermogravimetric investigation of the co-combustion between the pyrolysis oil distillation residue and lignite.

Science.gov (United States)

Li, Hao; Xia, Shuqian; Ma, Peisheng

2016-10-01

Co-combustion of lignite with distillation residue derived from rice straw pyrolysis oil was investigated by non-isothermal thermogravimetric analysis (TGA). The addition of distillation residue improved the reactivity and combustion efficiency of lignite, such as increasing the weight loss rate at peak temperature and decreasing the burnout temperature and the total burnout. With increasing distillation residue content in the blended fuels, the synergistic interactions between distillation residue and lignite firstly increased and then decreased during co-combustion stage. Results of XRF, FTIR, (13)C NMR and SEM analysis indicated that chemical structure, mineral components and morphology of samples have great influence on the synergistic interactions. The combustion mechanisms and kinetic parameters were calculated by the Coats Redfern model, suggesting that the lowest apparent activation energy (120.19kJ/mol) for the blended fuels was obtained by blending 60wt.% distillation residue during main co-combustion stage. Copyright © 2016 Elsevier Ltd. All rights reserved.

N-terminal aliphatic residues dictate the structure, stability, assembly, and small molecule binding of the coiled-coil region of cartilage oligomeric matrix protein.

Science.gov (United States)

Gunasekar, Susheel K; Asnani, Mukta; Limbad, Chandani; Haghpanah, Jennifer S; Hom, Wendy; Barra, Hanna; Nanda, Soumya; Lu, Min; Montclare, Jin Kim

2009-09-15

The coiled-coil domain of cartilage oligomeric matrix protein (COMPcc) assembles into a homopentamer that naturally recognizes the small molecule 1,25-dihydroxyvitamin D(3) (vit D). To identify the residues critical for the structure, stability, oligomerization, and binding to vit D as well as two other small molecules, all-trans-retinol (ATR) and curcumin (CCM), here we perform an alanine scanning mutagenesis study. Ten residues lining the hydrophobic pocket of COMPcc were mutated into alanine; of the mutated residues, the N-terminal aliphatic residues L37, L44, V47, and L51 are responsible for maintaining the structure and function. Furthermore, two polar residues, T40 and Q54, within the N-terminal region when converted into alanine improve the alpha-helical structure, stability, and self-assembly behavior. Helical stability, oligomerization, and binding appear to be linked in a manner in which mutations that abolish helical structure and assembly bind poorly to vit D, ATR, and CCM. These results provide not only insight into COMPcc and its functional role but also useful guidelines for the design of stable, pentameric coiled-coils capable of selectively storing and delivering various small molecules.

A proposal of parameter determination method in the residual strength degradation model for the prediction of fatigue life (I)

International Nuclear Information System (INIS)

Kim, Sang Tae; Jang, Seong Soo

2001-01-01

The static and fatigue tests have been carried out to verify the validity of a generalized residual strength degradation model. And a new method of parameter determination in the model is verified experimentally to account for the effect of tension-compression fatigue loading of spheroidal graphite cast iron. It is shown that the correlation between the experimental results and the theoretical prediction on the statistical distribution of fatigue life by using the proposed method is very reasonable. Furthermore, it is found that the correlation between the theoretical prediction and the experimental results of fatigue life in case of tension-tension fatigue data in composite material appears to be reasonable. Therefore, the proposed method is more adjustable in the determination of the parameter than maximum likelihood method and minimization technique

Deamidation of asparagine and glutamine residues in proteins and peptides: structural determinants and analytical methodology

NARCIS (Netherlands)

Bischoff, Rainer; Kolbe, H.V.

1994-01-01

Non-enzymatic deamidation of asparagine and glutamine residues in proteins and peptides are reviewed by first outlining the well-described reaction mechanism involving cyclic imide intermediates, followed by a discussion of structural features which influence the reaction rate. The second and major

Numerical simulation of residual stress in laser based additive manufacturing process

Science.gov (United States)

Kalyan Panda, Bibhu; Sahoo, Seshadev

2018-03-01

Minimizing the residual stress build-up in metal-based additive manufacturing plays a pivotal role in selecting a particular material and technique for making an industrial part. In beam-based additive manufacturing, although a great deal of effort has been made to minimize the residual stresses, it is still elusive how to do so by simply optimizing the processing parameters, such as beam size, beam power, and scan speed. Amid different types of additive manufacturing processes, Direct Metal Laser Sintering (DMLS) process uses a high-power laser to melt and sinter layers of metal powder. The rapid solidification and heat transfer on powder bed endows a high cooling rate which leads to the build-up of residual stresses, that will affect the mechanical properties of the build parts. In the present work, the authors develop a numerical thermo-mechanical model for the measurement of residual stress in the AlSi10Mg build samples by using finite element method. Transient temperature distribution in the powder bed was assessed using the coupled thermal to structural model. Subsequently, the residual stresses were estimated with varying laser power. From the simulation result, it found that the melt pool dimensions increase with increasing the laser power and the magnitude of residual stresses in the built part increases.

Mutational and structural analyses of Caldanaerobius polysaccharolyticus Man5B reveal novel active site residues for family 5 glycoside hydrolases.

Directory of Open Access Journals (Sweden)

Takuji Oyama

Full Text Available CpMan5B is a glycoside hydrolase (GH family 5 enzyme exhibiting both β-1,4-mannosidic and β-1,4-glucosidic cleavage activities. To provide insight into the amino acid residues that contribute to catalysis and substrate specificity, we solved the structure of CpMan5B at 1.6 Å resolution. The structure revealed several active site residues (Y12, N92 and R196 in CpMan5B that are not present in the active sites of other structurally resolved GH5 enzymes. Residue R196 in GH5 enzymes is thought to be strictly conserved as a histidine that participates in an electron relay network with the catalytic glutamates, but we show that an arginine fulfills a functionally equivalent role and is found at this position in every enzyme in subfamily GH5_36, which includes CpMan5B. Residue N92 is required for full enzymatic activity and forms a novel bridge over the active site that is absent in other family 5 structures. Our data also reveal a role of Y12 in establishing the substrate preference for CpMan5B. Using these molecular determinants as a probe allowed us to identify Man5D from Caldicellulosiruptor bescii as a mannanase with minor endo-glucanase activity.

Mutational and structural analyses of Caldanaerobius polysaccharolyticus Man5B reveal novel active site residues for family 5 glycoside hydrolases.

Science.gov (United States)

Oyama, Takuji; Schmitz, George E; Dodd, Dylan; Han, Yejun; Burnett, Alanna; Nagasawa, Naoko; Mackie, Roderick I; Nakamura, Haruki; Morikawa, Kosuke; Cann, Isaac

2013-01-01

CpMan5B is a glycoside hydrolase (GH) family 5 enzyme exhibiting both β-1,4-mannosidic and β-1,4-glucosidic cleavage activities. To provide insight into the amino acid residues that contribute to catalysis and substrate specificity, we solved the structure of CpMan5B at 1.6 Å resolution. The structure revealed several active site residues (Y12, N92 and R196) in CpMan5B that are not present in the active sites of other structurally resolved GH5 enzymes. Residue R196 in GH5 enzymes is thought to be strictly conserved as a histidine that participates in an electron relay network with the catalytic glutamates, but we show that an arginine fulfills a functionally equivalent role and is found at this position in every enzyme in subfamily GH5_36, which includes CpMan5B. Residue N92 is required for full enzymatic activity and forms a novel bridge over the active site that is absent in other family 5 structures. Our data also reveal a role of Y12 in establishing the substrate preference for CpMan5B. Using these molecular determinants as a probe allowed us to identify Man5D from Caldicellulosiruptor bescii as a mannanase with minor endo-glucanase activity.

Identification of crystalline structures using Moessbauer parameters and artificial neural network

International Nuclear Information System (INIS)

Salles, E.O.T.; Souza Junior, P.A. De; Garg, V.K.

1995-01-01

Moessbauer spectroscopy is a useful technique for characterizing the valences, electronic and magnetic states, coordination symmetric and site occupancies of Fe cations. The Moessbauer parameters of Isomer Shift (I.S.) and Quadrupole Splitting (Q.S.) are useful to distinguish paramagnetic ferrous and ferric ions in several substances, while the internal magnetic field provides information on the crystallinity. A correlation is being sought between Moessbauer parameters and several structure properties of some iron-containing minerals using Artificial Neural Networks (ANN). Distinct regions of crystalline structures are defined when any two parameters are plotted, but in several cases superposition of these regions leads to erroneous conclusions. We have tried to eliminate this difficulty by using convenient axes. These axes form n-dimensional vectors as input to our ANN. In recent years ANN has shown to be a powerful technique to solve problems as pattern recognition, optimization, preview ups and downs in stock market, automatic control and identification of a mineral from a Moessbauer spectrum of Moessbauer data bank. Using ANN we have been successful in identification of crystalline structures from plots of Moessbauer spectral parameters of I.S., Q.S., and structure using Moessbauer parameters of I.S., Q.S., and polyhedral volume of a coordination site are presented. (author) 28 refs.; 4 figs.; 2 tabs

Identification of residue pairing in interacting β-strands from a predicted residue contact map.

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Mao, Wenzhi; Wang, Tong; Zhang, Wenxuan; Gong, Haipeng

2018-04-19

Despite the rapid progress of protein residue contact prediction, predicted residue contact maps frequently contain many errors. However, information of residue pairing in β strands could be extracted from a noisy contact map, due to the presence of characteristic contact patterns in β-β interactions. This information may benefit the tertiary structure prediction of mainly β proteins. In this work, we propose a novel ridge-detection-based β-β contact predictor to identify residue pairing in β strands from any predicted residue contact map. Our algorithm RDb 2 C adopts ridge detection, a well-developed technique in computer image processing, to capture consecutive residue contacts, and then utilizes a novel multi-stage random forest framework to integrate the ridge information and additional features for prediction. Starting from the predicted contact map of CCMpred, RDb 2 C remarkably outperforms all state-of-the-art methods on two conventional test sets of β proteins (BetaSheet916 and BetaSheet1452), and achieves F1-scores of ~ 62% and ~ 76% at the residue level and strand level, respectively. Taking the prediction of the more advanced RaptorX-Contact as input, RDb 2 C achieves impressively higher performance, with F1-scores reaching ~ 76% and ~ 86% at the residue level and strand level, respectively. In a test of structural modeling using the top 1 L predicted contacts as constraints, for 61 mainly β proteins, the average TM-score achieves 0.442 when using the raw RaptorX-Contact prediction, but increases to 0.506 when using the improved prediction by RDb 2 C. Our method can significantly improve the prediction of β-β contacts from any predicted residue contact maps. Prediction results of our algorithm could be directly applied to effectively facilitate the practical structure prediction of mainly β proteins. All source data and codes are available at http://166.111.152.91/Downloads.html or the GitHub address of https://github.com/wzmao/RDb2C .

[Structure Parameters and Quality Outcomes of Ambulant Home-care].

Science.gov (United States)

Suhr, Ralf; Raeder, Kathrin; Kuntz, Simone; Strube-Lahmann, Sandra; Latendorf, Antje; Klingelhöfer-Noe, Jürgen; Lahmann, Nils

2018-05-14

So far, there are few data available on the changes of ambulant home-care in Germany over the last decades. Therefore, the aim of this research was to provide structure data on nursing personnel, funding, size, regional differences, and training needs of ambulant home-care services in Germany. In addition, a possible association between structure parameters and quality outcomes for pressure ulcer and malnutrition was investigated. In 2015, a multicenter cross-sectional study was conducted in home-care services in Germany. Structure data from 99 randomly selected home-care services as well as data on pressure ulcers and malnutrition of 903 care-dependent clients were analyzed. The median (home-care services. From a cut-off of 20,000 inhabitants, a region was considered urban. The average prevalence for decubitus and malnutrition (BMIhome-care service, and possible associations with structure parameters were analyzed using a multiple linear regression model. The proportion of registered nurses in non-private (private) home-care services was 60.6% (52.3%). The proportion of employees with a 200- h basic qualification in nursing was higher in private (12.5 vs. 4.7%), small home-care services (14.0 vs. 5.8%) and in urban regions (11.5 vs 5.7%). In average, registered nurses working in small home-care services spent significantly more time per client than the ones working in large services (3.8 vs. 2.9 h/week). The highest need for further training was shown on the subjects of pain, medication and cognitive impairment. No statistically significant correlation could be found between the average decubitus prevalence and structure parameters. Only the association between malnutrition prevalence and the proportion of registered nurses was statistically significant. The present representative study provides structure data on nursing personnel, funding, size, regional differences, and training needs of ambulant home-care services in Germany that could be used as a baseline

Structural insights into cellulolytic and chitinolytic enzymes revealing crucial residues of insect β-N-acetyl-D-hexosaminidase.

Directory of Open Access Journals (Sweden)

Tian Liu

Full Text Available The chemical similarity of cellulose and chitin supports the idea that their corresponding hydrolytic enzymes would bind β-1,4-linked glucose residues in a similar manner. A structural and mutational analysis was performed for the plant cellulolytic enzyme BGlu1 from Oryza sativa and the insect chitinolytic enzyme OfHex1 from Ostrinia furnacalis. Although BGlu1 shows little amino-acid sequence or topological similarity with OfHex1, three residues (Trp(490, Glu(328, Val(327 in OfHex1, and Trp(358, Tyr(131 and Ile(179 in BGlu1 were identified as being conserved in the +1 sugar binding site. OfHex1 Glu(328 together with Trp(490 was confirmed to be necessary for substrate binding. The mutant E328A exhibited a 8-fold increment in K(m for (GlcNAc(2 and a 42-fold increment in K(i for TMG-chitotriomycin. A crystal structure of E328A in complex with TMG-chitotriomycin was resolved at 2.5 Å, revealing the obvious conformational changes of the catalytic residues (Glu(368 and Asp(367 and the absence of the hydrogen bond between E328A and the C3-OH of the +1 sugar. V327G exhibited the same activity as the wild-type, but acquired the ability to efficiently hydrolyse β-1,2-linked GlcNAc in contrast to the wild-type. Thus, Glu(328 and Val(327 were identified as important for substrate-binding and as glycosidic-bond determinants. A structure-based sequence alignment confirmed the spatial conservation of these three residues in most plant cellulolytic, insect and bacterial chitinolytic enzymes.

Study on residual stresses in ultrasonic torsional vibration assisted micro-milling

Science.gov (United States)

Lu, Zesheng; Hu, Haijun; Sun, Yazhou; Sun, Qing

2010-10-01

It is well known that machining induced residual stresses can seriously affect the dimensional accuracy, corrosion and wear resistance, etc., and further influence the longevity and reliability of Micro-Optical Components (MOC). In Ultrasonic Torsional Vibration Assisted Micro-milling (UTVAM), cutting parameters, vibration parameters, mill cutter parameters, the status of wear length of tool flank are the main factors which affect residual stresses. A 2D model of UTVAM was established with FE analysis software ABAQUS. Johnson-Cook's flow stress model and shear failure principle are used as the workpiece material model and failure principle, while friction between tool and workpiece uses modified Coulomb's law whose sliding friction area is combined with sticking friction. By means of FEA, the influence rules of cutting parameters, vibration parameters, mill cutter parameters, the status of wear length of tool flank on residual stresses are obtained, which provides a basis for choosing optimal process parameters and improving the longevity and reliability of MOC.

Phenomenological analysis of the Δ resonance parameters

International Nuclear Information System (INIS)

Vasan, S.S.

1976-01-01

The positions of the poles in the complex energy plane corresponding to the resonances Δ ++ and Δ 0 , and the associated residues, are determined by fitting the π + p and π - p hadronic phase shift data from the CARTER 73 analysis. As an illustration of the use of the Δ pole parameters, their application to the problem of parametrizing the residue function associated with the Δ Regge trajectory is considered. The input for the parametrization is given partly by the pole position and the residue of the Δ(1950), the first recurrence of the Δ(1236). These pole parameters are deduced from fits to the F 37 partial wave data from the AYED 74 phase shift analysis. Together with the Δ(1236) pole parameters, these provide information on the behavior of the Regge residue in the resonance region u less than 0 (in the context of s-channel backward scattering being dominated by u-channel Regge exchanges). Attempts to incorporate this information in parametrizations of the residue by means of real and complex functions lead to the conclusion that both the residue and the trajectory are better represented in the resonance region by complex parametrizations

Neglect Of Parameter Estimation Uncertainty Can Significantly Overestimate Structural Reliability

Directory of Open Access Journals (Sweden)

Rózsás Árpád

2015-12-01

Full Text Available Parameter estimation uncertainty is often neglected in reliability studies, i.e. point estimates of distribution parameters are used for representative fractiles, and in probabilistic models. A numerical example examines the effect of this uncertainty on structural reliability using Bayesian statistics. The study reveals that the neglect of parameter estimation uncertainty might lead to an order of magnitude underestimation of failure probability.

Pyrolysis kinetics and thermodynamic parameters of castor (Ricinus communis) residue using thermogravimetric analysis.

Science.gov (United States)

Kaur, Ravneet; Gera, Poonam; Jha, Mithilesh Kumar; Bhaskar, Thallada

2018-02-01

Castor plant is a fast-growing, perennial shrub from Euphorbiaceae family. More than 50% of the residue is generated from its stems and leaves. The main aim of this work is to study the pyrolytic characteristics, kinetics and thermodynamic properties of castor residue. The TGA experiments were carried out from room temperature to 900 °C under an inert atmosphere at different heating rates of 5, 10, 15, 20, 30 and 40 °C/min. The kinetic analysis was carried using different models namely Kissinger, Flynn-Wall-Ozawa (FWO) and Kissinger-Akahira-Sunose (KAS). The average E ɑ calculated by FWO and KAS methods were 167.10 and 165.86 kJ/mole respectively. Gibbs free energy varied from 150.62-154.33 to 150.59-154.65 kJ/mol for FWO and KAS respectively. The HHV of castor residue was 14.43 MJ/kg, considered as potential feedstock for bio-energy production. Kinetic and thermodynamic results will be useful input for the design of pyrolytic process using castor residue as feedstock. Copyright © 2017 Elsevier Ltd. All rights reserved.

3D reconstruction of the structure of a residual limb for customising the design of a prosthetic socket.

Science.gov (United States)

Shuxian, Zheng; Wanhua, Zhao; Bingheng, Lu

2005-01-01

Aiming at overcoming the limitations of the plaster-casting method in traditional prosthetic socket fabrication, the idea of reconstructing the 3D models for bones and skin of the residual limb is proposed. Given the two-dimensional obtained image through CT scanning, using image processing and reverse engineering techniques, the 3D solid model of the residual limb can be successfully reconstructed. The new approach can reproduce both the internal and the external structure of the residual limb. It can moreover avoid making a positive mould by the way of manual modifications. In addition to this, it can provide a scientific basis for the individualization of prosthetic socket design.

Table of periodic properties of fullerenes based on structural parameters.

Science.gov (United States)

Torrens, Francisco

2004-01-01

The periodic table (PT) of the elements suggests that hydrogen could be the origin of everything else. The construction principle is an evolutionary process that is formally similar to those of Darwin and Oparin. The Kekulé structure count and permanence of the adjacency matrix of fullerenes are related to structural parameters involving the presence of contiguous pentagons p, q and r. Let p be the number of edges common to two pentagons, q the number of vertices common to three pentagons, and r the number of pairs of nonadjacent pentagon edges shared between two other pentagons. Principal component analysis (PCA) of the structural parameters and cluster analysis (CA) of the fullerenes permit classifying them and agree. A PT of the fullerenes is built based on the structural parameters, PCA and CA. The periodic law does not have the rank of the laws of physics. (1) The properties of the fullerenes are not repeated; only, and perhaps, their chemical character. (2) The order relationships are repeated, although with exceptions. The proposed statement is the following: The relationships that any fullerene p has with its neighbor p + 1 are approximately repeated for each period.

Bias-Corrected Estimation of Noncentrality Parameters of Covariance Structure Models

Science.gov (United States)

Raykov, Tenko

2005-01-01

A bias-corrected estimator of noncentrality parameters of covariance structure models is discussed. The approach represents an application of the bootstrap methodology for purposes of bias correction, and utilizes the relation between average of resample conventional noncentrality parameter estimates and their sample counterpart. The…

A new approach for applying residual dipolar couplings as restraints in structure elucidation

International Nuclear Information System (INIS)

Meiler, Jens; Blomberg, Niklas; Nilges, Michael; Griesinger, Christian

2000-01-01

Residual dipolar couplings are useful global structural restraints. The dipolar couplings define the orientation of a vector with respect to the alignment tensor. Although the size of the alignment tensor can be derived from the distribution of the experimental dipolar couplings, its orientation with respect to the coordinate system of the molecule is unknown at the beginning of structure determination. This causes convergence problems in the simulated annealing process. We therefore propose a protocol that translates dipolar couplings into intervector projection angles, which are independent of the orientation of the alignment tensor with respect to the molecule. These restraints can be used during the whole simulated annealing protocol

Analysis of core-periphery organization in protein contact networks reveals groups of structurally and functionally critical residues.

Science.gov (United States)

Isaac, Arnold Emerson; Sinha, Sitabhra

2015-10-01

The representation of proteins as networks of interacting amino acids, referred to as protein contact networks (PCN), and their subsequent analyses using graph theoretic tools, can provide novel insights into the key functional roles of specific groups of residues. We have characterized the networks corresponding to the native states of 66 proteins (belonging to different families) in terms of their core-periphery organization. The resulting hierarchical classification of the amino acid constituents of a protein arranges the residues into successive layers - having higher core order - with increasing connection density, ranging from a sparsely linked periphery to a densely intra-connected core (distinct from the earlier concept of protein core defined in terms of the three-dimensional geometry of the native state, which has least solvent accessibility). Our results show that residues in the inner cores are more conserved than those at the periphery. Underlining the functional importance of the network core, we see that the receptor sites for known ligand molecules of most proteins occur in the innermost core. Furthermore, the association of residues with structural pockets and cavities in binding or active sites increases with the core order. From mutation sensitivity analysis, we show that the probability of deleterious or intolerant mutations also increases with the core order. We also show that stabilization centre residues are in the innermost cores, suggesting that the network core is critically important in maintaining the structural stability of the protein. A publicly available Web resource for performing core-periphery analysis of any protein whose native state is known has been made available by us at http://www.imsc.res.in/ ~sitabhra/proteinKcore/index.html.

Nanometer-scale structure of alkali-soluble bio-macromolecules of maize plant residues explains their recalcitrance in soil.

Science.gov (United States)

Adani, Fabrizio; Salati, Silvia; Spagnol, Manuela; Tambone, Fulvia; Genevini, Pierluigi; Pilu, Roberto; Nierop, Klaas G J

2009-07-01

The quantity and quality of plant litter in the soil play an important role in the soil organic matter balance. Besides other pedo-climatic aspects, the content of recalcitrant molecules of plant residues and their chemical composition play a major role in the preservation of plant residues. In this study, we report that intrinsically resistant alkali-soluble bio-macromolecules extracted from maize plant (plant-humic acid) (plant-HA) contribute directly to the soil organic matter (OM) by its addition and conservation in the soil. Furthermore, we also observed that a high syringyl/guaiacyl (S/G) ratio in the lignin residues comprising the plant tissue, which modifies the microscopic structure of the alkali-soluble plant biopolymers, enhances their recalcitrance because of lower accessibility of molecules to degrading enzymes. These results are in agreement with a recent study, which showed that the humic substance of soil consists of a mixture of identifiable biopolymers obtained directly from plant tissues that are added annually by maize plant residues.

Structure of the protein which gives the mitochondrial ATPase its sensitivity to oligomycin (OSCP). Approach of OSCP structural parameters by neutron scattering and spectroscopic techniques

International Nuclear Information System (INIS)

Dupuis, Alain

1983-01-01

This research thesis reports the study of OSCP structure of beef heart mitochondria. The OSCP is a lysine-rich protein which contains five tyrosine residues exposed to a solvent and no tryptophan residue. The molecular mass is determined by gel electrophoresis. Small angle neutron scattering is used to show that OSCP is an elongated protein. The distribution of residues of amino acids in the protein, and the preferential localisation of lysine residues in equatorial regions of the molecules are noticed by using neutron scattering by OSCP in solution in D 2 O. A preliminary functional study determined the stoichiometry and the dissociation constants with which OSCP interacts with mitochondrial ATPase [fr

Reliability updating based on monitoring of structural response parameters

International Nuclear Information System (INIS)

Leira, B.J.

2016-01-01

Short- and long-term aspects of measuring structural response parameters are addressed. Two specific examples of such measurements are considered for the purpose of illustration and in order to focus the discussion. These examples are taken from the petroleum industry (monitoring of riser response) and from the shipping industry (monitoring of ice-induced strains in a ship hull). Similarities and differences between the two cases are elaborated with respect to which are the most relevant mechanical limit states. Furthermore, main concerns related to reliability levels within a short-term versus long-term time horizon are highlighted. Quantifying the economic benefits of applying monitoring systems is also addressed. - Highlights: • Two examples of structural response monitoring are described. • Application of measurements is discussed in relation to updating of load and structural parameters. • Quantification of the value of response monitoring is made for both of the examples.

Solution NMR structure and inhibitory effect against amyloid-β fibrillation of Humanin containing a D-isomerized serine residue

Energy Technology Data Exchange (ETDEWEB)

Alsanousi, Nesreen [Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Sugiki, Toshihiko, E-mail: sugiki@protein.osaka-u.ac.jp [Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Furuita, Kyoko; So, Masatomo; Lee, Young-Ho; Fujiwara, Toshimichi [Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Kojima, Chojiro, E-mail: kojima-chojiro-xk@ynu.ac.jp [Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5, Hodogaya-ku, Yokohama 240-8501 (Japan)

2016-09-02

Humanin comprising 24 amino acid residues is a bioactive peptide that has been isolated from the brain tissue of patients with Alzheimer's disease. Humanin reportedly suppressed aging-related death of various cells due to amyloid fibrils and oxidative stress. There are reports that the cytoprotective activity of Humanin was remarkably enhanced by optical isomerization of the Ser14 residue from L to D form, but details of the molecular mechanism remained unclear. Here we demonstrated that Humanin D-Ser14 exhibited potent inhibitory activity against fibrillation of amyloid-β and remarkably higher binding affinity for amyloid-β than that of the Humanin wild-type and S14G mutant. In addition, we determined the solution structure of Humanin D-Ser14 by nuclear magnetic resonance (NMR) and showed that D-isomerization of the Ser14 residue enables drastic conformational rearrangement of Humanin. Furthermore, we identified an amyloid-β-binding site on Humanin D-Ser14 at atomic resolution by NMR. These biophysical and high-resolution structural analyses clearly revealed structure–function relationships of Humanin and explained the driving force of the drastic conformational change and molecular basis of the potent anti-amyloid-β fibrillation activity of Humanin caused by D-isomerization of the Ser14 residue. This is the first study to show correlations between the functional activity, tertiary structure, and partner recognition mode of Humanin and may lead to elucidation of the molecular mechanisms of the cytoprotective activity of Humanin. - Highlights: • Humanin D-Ser14 showed the strongest inhibitory activity against Aβ40 fibrillation. • NMR structure of Humanin D-Ser14 was determined in alcohol/water mixture solution. • Humanin D-Ser14 directly bound Aβ40 stronger than Humanin wild-type and Humanin S14G. • Aβ40 and zinc ion binding sites of Humanin D-Ser14 were identified. • Structure around Ser14 of Humanin is critical for Aβ40 binding and

Tyrosine residues modification studied by MALDI-TOF mass spectrometry

International Nuclear Information System (INIS)

Santrucek, Jiri; Strohalm, Martin; Kadlcik, Vojtech; Hynek, Radovan; Kodicek, Milan

2004-01-01

Amino acid residue-specific reactivity in proteins is of great current interest in structural biology as it provides information about solvent accessibility and reactivity of the residue and, consequently, about protein structure and possible interactions. In the work presented tyrosine residues of three model proteins with known spatial structure are modified with two tyrosine-specific reagents: tetranitromethane and iodine. Modified proteins were specifically digested by proteases and the mass of resulting peptide fragments was determined using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. Our results show that there are only small differences in the extent of tyrosine residues modification by tetranitromethane and iodine. However, data dealing with accessibility of reactive residues obtained by chemical modifications are not completely identical with those obtained by nuclear magnetic resonance and X-ray crystallography. These interesting discrepancies can be caused by local molecular dynamics and/or by specific chemical structure of the residues surrounding

The integrity of cracked structures under thermal loading

International Nuclear Information System (INIS)

Townley, C.H.A.

1976-01-01

Previous work by Dowling and Townley on the load-carrying capacity of a cracked structure is extended so that quantitative predictions can be made about failure under thermal loading. Residual stresses can be dealt with in the same way as thermal stresses. It is shown that the tolerance of the structure to thermal stress can be quantified in terms of a parameter which defines the state of the structure. This state parameter can be deduced from the calculated performance of the structure when subjected to an external load. (author)

Precision and Accuracy Parameters in Structured Light 3-D Scanning

Science.gov (United States)

Eiríksson, E. R.; Wilm, J.; Pedersen, D. B.; Aanæs, H.

2016-04-01

Structured light systems are popular in part because they can be constructed from off-the-shelf low cost components. In this paper we quantitatively show how common design parameters affect precision and accuracy in such systems, supplying a much needed guide for practitioners. Our quantitative measure is the established VDI/VDE 2634 (Part 2) guideline using precision made calibration artifacts. Experiments are performed on our own structured light setup, consisting of two cameras and a projector. We place our focus on the influence of calibration design parameters, the calibration procedure and encoding strategy and present our findings. Finally, we compare our setup to a state of the art metrology grade commercial scanner. Our results show that comparable, and in some cases better, results can be obtained using the parameter settings determined in this study.

On how to avoid input and structural uncertainties corrupt the inference of hydrological parameters using a Bayesian framework

Science.gov (United States)

Hernández, Mario R.; Francés, Félix

2015-04-01

One phase of the hydrological models implementation process, significantly contributing to the hydrological predictions uncertainty, is the calibration phase in which values of the unknown model parameters are tuned by optimizing an objective function. An unsuitable error model (e.g. Standard Least Squares or SLS) introduces noise into the estimation of the parameters. The main sources of this noise are the input errors and the hydrological model structural deficiencies. Thus, the biased calibrated parameters cause the divergence model phenomenon, where the errors variance of the (spatially and temporally) forecasted flows far exceeds the errors variance in the fitting period, and provoke the loss of part or all of the physical meaning of the modeled processes. In other words, yielding a calibrated hydrological model which works well, but not for the right reasons. Besides, an unsuitable error model yields a non-reliable predictive uncertainty assessment. Hence, with the aim of prevent all these undesirable effects, this research focuses on the Bayesian joint inference (BJI) of both the hydrological and error model parameters, considering a general additive (GA) error model that allows for correlation, non-stationarity (in variance and bias) and non-normality of model residuals. As hydrological model, it has been used a conceptual distributed model called TETIS, with a particular split structure of the effective model parameters. Bayesian inference has been performed with the aid of a Markov Chain Monte Carlo (MCMC) algorithm called Dream-ZS. MCMC algorithm quantifies the uncertainty of the hydrological and error model parameters by getting the joint posterior probability distribution, conditioned on the observed flows. The BJI methodology is a very powerful and reliable tool, but it must be used correctly this is, if non-stationarity in errors variance and bias is modeled, the Total Laws must be taken into account. The results of this research show that the

Solution structure of the 45-residue MgATP-binding peptide of adenylate kinase as examined by 2-D NMR, FTIR, and CD spectroscopy

International Nuclear Information System (INIS)

Fry, D.C.; Byler, D.M.; Susi, H.; Brown, M.; Kuby, S.A.; Mildvan, A.S.

1988-01-01

The structure of a synthetic peptide corresponding to residues 1-45 of rabbit muscle adenylate kinase has been studied in aqueous solution by two-dimensional NMR, FTIR, and CD spectroscopy. This peptide, which binds MgATP and is believed to represent most of the MgATP-binding site of the enzyme, appears to maintain a conformation similar to that of residues 1-45 in the X-ray structure of intact porcine adenylate kinase, with 42% of the residues of the peptide showing NOEs indicative of phi and psi angles corresponding to those found in the protein. The NMR studies suggest that the peptide is composed of two helical regions of residues 4-7 and 23-29, and three stretches of β-strand at residues 8-15, 30-32, and 35-40, yielding an overall secondary structure consisting of 24% α-helix, 38% β-structure, and 38% aperiodic. Although the resolution-enhanced amide I band of the peptide FTIR spectrum is broad and rather featureless, possible due to disorder, it can be fit by using methods developed on well-characterized globular proteins. The CD spectrum is best fit by assuming the presence of at most 13% α-helix in the peptide, 24 +/- 2% β-structure, and 66 +/- 4% aperiodic. The inability of the high-frequency FTIR and CD methods to detect helices in the amount found by NMR may result from the short helical lengths as well as from static and dynamic disorder in the peptide. Upon binding of MgATP, numerous conformation changes in the backbone of the peptide are detected by NMR, with smaller alterations in the overall secondary structure as assess by CD

A proposed residual stress model for oblique turning

International Nuclear Information System (INIS)

Elkhabeery, M. M.

2001-01-01

A proposed mathematical model is presented for predicting the residual stresses caused by turning. Effects of change in tool free length, cutting speed, feed rate, and the tensile strength of work piece material on the maximum residual stress are investigated. The residual stress distribution in the surface region due to turning under unlubricated condition is determined using a deflection etching technique. To reduce the number of experiments required and build the mathematical model for these variables, Response Surface Methodology (RSM) is used. In addition, variance analysis and an experimental check are conducted to determine the prominent parameters and the adequacy of the model. The results show that the tensile stress of the work piece material, cutting speed, and feed rate have significant effects on the maximum residual stresses. The proposed model, that offering good correlation between the experimental and predicted results, is useful in selecting suitable cutting parameters for the machining of different materials. (author)

Parameter Recovery for the 1-P HGLLM with Non-Normally Distributed Level-3 Residuals

Science.gov (United States)

Kara, Yusuf; Kamata, Akihito

2017-01-01

A multilevel Rasch model using a hierarchical generalized linear model is one approach to multilevel item response theory (IRT) modeling and is referred to as a one-parameter hierarchical generalized linear logistic model (1-P HGLLM). Although it has the flexibility to model nested structure of data with covariates, the model assumes the normality…

Comparison of volumetric and functional parameters in simultaneous cardiac PET/MR: feasibility of volumetric assessment with residual activity from prior PET/CT

Energy Technology Data Exchange (ETDEWEB)

Luecke, C.; Brenneis, B.; Grothoff, M.; Gutberlet, M. [University Leipzig - Heart Center, Department of Diagnostic and Interventional Radiology, Leipzig (Germany); Oppolzer, B.; Werner, P.; Jochimsen, T.; Sattler, B.; Barthel, H.; Sabri, O. [University Hospital Leipzig, Department of Nuclear Medicine, Leipzig (Germany); Foldyna, B. [University Leipzig - Heart Center, Department of Diagnostic and Interventional Radiology, Leipzig (Germany); Massachusetts General Hospital - Harvard Medical School, Cardiac MR PET CT Program, Boston, MA (United States); Lurz, P. [University Leipzig - Heart Center, Clinic for Internal Medicine/Cardiology, Leipzig (Germany); Lehmkuhl, L. [Herz- und Gefaess-Klinik GmbH, Radiologische Klinik, Bad Neustadt (Germany)

2017-12-15

To compare cardiac left ventricular (LV) parameters in simultaneously acquired hybrid fluorine-18-fluorodeoxyglucose ([18F] FDG) positron emission tomography/magnetic resonance imaging (PET/MRI) in patients with residual tracer activity of upstream PET/CT. Twenty-nine patients (23 men, age 58±17 years) underwent cardiac PET/MRI either directly after a non-cardiac PET/CT with homogenous cardiac [18F] FDG uptake (n=20) or for viability assessment (n=9). Gated cardiac [18F] FDG PET and cine MR sequences were acquired simultaneously and evaluated blinded to the cross-imaging results. Image quality (IQ), end-diastolic (LVEDV), end-systolic volume (LVESV), ejection fraction (LVEF) and myocardial mass (LVMM) were measured. Pearson correlation and intraclass correlation coefficient (ICC), regression and a Bland-Altman analysis were assessed. Except LVMM, volumetric and functional LV parameters demonstrated high correlations (LVESV: r=0.97, LVEDV: r=0.95, LVEF: r=0.91, LVMM: r=0.87, each p<0.05), but wide limits of agreement (LOA) for LVEDV (-25.3-82.5ml); LVESV (-33.1-72.7ml); LVEF (-18.9-14.8%) and LVMM (-78.2-43.2g). Intra- and interobserver reliability were very high (ICC≥0.95) for all parameters, except for MR-LVEF (ICC=0.87). PET-IQ (0-3) was high (mean: 2.2±0.9) with significant influence on LVMM calculations only. In simultaneously acquired cardiac PET/MRI data, LVEDV, LVESV and LVEF show good agreement. However, the agreement seems to be limited if cardiac PET/MRI follows PET/CT and only the residual activity is used. (orig.)

Modelling of Tool Wear and Residual Stress during Machining of AISI H13 Tool Steel

Science.gov (United States)

Outeiro, José C.; Umbrello, Domenico; Pina, José C.; Rizzuti, Stefania

2007-05-01

Residual stresses can enhance or impair the ability of a component to withstand loading conditions in service (fatigue, creep, stress corrosion cracking, etc.), depending on their nature: compressive or tensile, respectively. This poses enormous problems in structural assembly as this affects the structural integrity of the whole part. In addition, tool wear issues are of critical importance in manufacturing since these affect component quality, tool life and machining cost. Therefore, prediction and control of both tool wear and the residual stresses in machining are absolutely necessary. In this work, a two-dimensional Finite Element model using an implicit Lagrangian formulation with an automatic remeshing was applied to simulate the orthogonal cutting process of AISI H13 tool steel. To validate such model the predicted and experimentally measured chip geometry, cutting forces, temperatures, tool wear and residual stresses on the machined affected layers were compared. The proposed FE model allowed us to investigate the influence of tool geometry, cutting regime parameters and tool wear on residual stress distribution in the machined surface and subsurface of AISI H13 tool steel. The obtained results permit to conclude that in order to reduce the magnitude of surface residual stresses, the cutting speed should be increased, the uncut chip thickness (or feed) should be reduced and machining with honed tools having large cutting edge radii produce better results than chamfered tools. Moreover, increasing tool wear increases the magnitude of surface residual stresses.

On the residual stress modeling of shot-peened AISI 4340 steel: finite element and response surface methods

Science.gov (United States)

Asgari, Ali; Dehestani, Pouya; Poruraminaie, Iman

2018-02-01

Shot peening is a well-known process in applying the residual stress on the surface of industrial parts. The induced residual stress improves fatigue life. In this study, the effects of shot peening parameters such as shot diameter, shot speed, friction coefficient, and the number of impacts on the applied residual stress will be evaluated. To assess these parameters effect, firstly the shot peening process has been simulated by finite element method. Then, effects of the process parameters on the residual stress have been evaluated by response surface method as a statistical approach. Finally, a strong model is presented to predict the maximum residual stress induced by shot peening process in AISI 4340 steel. Also, the optimum parameters for the maximum residual stress are achieved. The results indicate that effect of shot diameter on the induced residual stress is increased by increasing the shot speed. Also, enhancing the friction coefficient magnitude always cannot lead to increase in the residual stress.

Universal relationship connecting various two-body effective residual interactions

International Nuclear Information System (INIS)

Knuepfer, W.; Huber, M.G.

1976-01-01

Starting from a momentum space analysis of the two-body matrix elements, a relation has been established between the size of the model space actually used in a specific calculation and the relevant properties of the effective residual interaction. It turns out that the two-body transition density acts like a filter function on the Fourier transform of the force; it exhibits a distinct structure which clearly reflects the size and the detailed properties of the configuration space actually used. From an investigation of this filter function an equivalence criterion for different effective residual two-body interactions has been established both for closed and open shell nuclei. This result can be used to construct simple although realistic effective forces. As an example, a model for a separable residual interaction is proposed in which the corresponding parameters are being clearly related to the nuclear radius (i.e., the mass number), to the quantum numbers (i.e., the angular momentum) of the state under consideration and to the size of the configuration space used. For a number of examples this force has been applied successfully for the description of low energy properties of both closed and open shell nuclei

Evaluation of design parameters in soil-structure systems through artificial intelligence

International Nuclear Information System (INIS)

Cremonini, M.G.; Vardanega, C.; Parvis, E.

1989-01-01

This study refers to development of an artificial intelligence tool to evaluate design parameters for a soil-structure system as the foundations of Class 1 buildings of a nuclear power plant (NPP). This is based on an expert analysis of a large amount of information, collected during a comprehensive program of site investigations and laboratory tests and stored on a computer data-bank. The methodology comprises the following steps: organization of the available information on the site characteristics in a data-base; implementation and extensive use of a specific knowledge based expert system (KBES) devoted to both the analysis, interpretation and check of the information in the data-base, and to the evaluation of the design parameters; determination of effective access criteria to the data-base, for purposes of reordering the information and extracting design properties from a large number of experimental data; development of design profiles for both index properties and strength/strain parameters; and final evaluation of the design parameters. Results are obtained in the form of: local and general site stratigraphy; summarized soil index properties, detailing the site setting; static and dynamic stress-strain parameters, G/G max behavior and damping factors; condolidation parameters and OCR ratio; spatial distribution of parameters on site area; identification of specific local conditions; and cross correlation of parameters, thus covering the whole range of design parameters for NPP soil-structure systems

Improved computation method in residual life estimation of structural components

Directory of Open Access Journals (Sweden)

Maksimović Stevan M.

2013-01-01

Full Text Available This work considers the numerical computation methods and procedures for the fatigue crack growth predicting of cracked notched structural components. Computation method is based on fatigue life prediction using the strain energy density approach. Based on the strain energy density (SED theory, a fatigue crack growth model is developed to predict the lifetime of fatigue crack growth for single or mixed mode cracks. The model is based on an equation expressed in terms of low cycle fatigue parameters. Attention is focused on crack growth analysis of structural components under variable amplitude loads. Crack growth is largely influenced by the effect of the plastic zone at the front of the crack. To obtain efficient computation model plasticity-induced crack closure phenomenon is considered during fatigue crack growth. The use of the strain energy density method is efficient for fatigue crack growth prediction under cyclic loading in damaged structural components. Strain energy density method is easy for engineering applications since it does not require any additional determination of fatigue parameters (those would need to be separately determined for fatigue crack propagation phase, and low cyclic fatigue parameters are used instead. Accurate determination of fatigue crack closure has been a complex task for years. The influence of this phenomenon can be considered by means of experimental and numerical methods. Both of these models are considered. Finite element analysis (FEA has been shown to be a powerful and useful tool1,6 to analyze crack growth and crack closure effects. Computation results are compared with available experimental results. [Projekat Ministarstva nauke Republike Srbije, br. OI 174001

Structural and functional characterization of Rpn12 identifies residues required for Rpn10 proteasome incorporation.

Science.gov (United States)

Boehringer, Jonas; Riedinger, Christiane; Paraskevopoulos, Konstantinos; Johnson, Eachan O D; Lowe, Edward D; Khoudian, Christina; Smith, Dominique; Noble, Martin E M; Gordon, Colin; Endicott, Jane A

2012-11-15

The ubiquitin-proteasome system targets selected proteins for degradation by the 26S proteasome. Rpn12 is an essential component of the 19S regulatory particle and plays a role in recruiting the extrinsic ubiquitin receptor Rpn10. In the present paper we report the crystal structure of Rpn12, a proteasomal PCI-domain-containing protein. The structure helps to define a core structural motif for the PCI domain and identifies potential sites through which Rpn12 might form protein-protein interactions. We demonstrate that mutating residues at one of these sites impairs Rpn12 binding to Rpn10 in vitro and reduces Rpn10 incorporation into proteasomes in vivo.

Recent advances in residual stress measurement

International Nuclear Information System (INIS)

Withers, P.J.; Turski, M.; Edwards, L.; Bouchard, P.J.; Buttle, D.J.

2008-01-01

Until recently residual stresses have been included in structural integrity assessments of nuclear pressure vessels and piping in a very primitive manner due to the lack of reliable residual stress measurement or prediction tools. This situation is changing the capabilities of newly emerging destructive (i.e. the contour method) and non-destructive (i.e. magnetic and high-energy synchrotron X-ray strain mapping) residual stress measurement techniques for evaluating ferritic and austenitic pressure vessel components are contrasted against more well-established methods. These new approaches offer the potential for obtaining area maps of residual stress or strain in welded plants, mock-up components or generic test-pieces. The mapped field may be used directly in structural integrity calculations, or indirectly to validate finite element process/structural models on which safety cases for pressurised nuclear systems are founded. These measurement methods are complementary in terms of application to actual plant, cost effectiveness and measurements in thick sections. In each case an exemplar case study is used to illustrate the method and to highlight its particular capabilities

Scoring protein interaction decoys using exposed residues (SPIDER): a novel multibody interaction scoring function based on frequent geometric patterns of interfacial residues.

Science.gov (United States)

Khashan, Raed; Zheng, Weifan; Tropsha, Alexander

2012-08-01

Accurate prediction of the structure of protein-protein complexes in computational docking experiments remains a formidable challenge. It has been recognized that identifying native or native-like poses among multiple decoys is the major bottleneck of the current scoring functions used in docking. We have developed a novel multibody pose-scoring function that has no theoretical limit on the number of residues contributing to the individual interaction terms. We use a coarse-grain representation of a protein-protein complex where each residue is represented by its side chain centroid. We apply a computational geometry approach called Almost-Delaunay tessellation that transforms protein-protein complexes into a residue contact network, or an undirectional graph where vertex-residues are nodes connected by edges. This treatment forms a family of interfacial graphs representing a dataset of protein-protein complexes. We then employ frequent subgraph mining approach to identify common interfacial residue patterns that appear in at least a subset of native protein-protein interfaces. The geometrical parameters and frequency of occurrence of each "native" pattern in the training set are used to develop the new SPIDER scoring function. SPIDER was validated using standard "ZDOCK" benchmark dataset that was not used in the development of SPIDER. We demonstrate that SPIDER scoring function ranks native and native-like poses above geometrical decoys and that it exceeds in performance a popular ZRANK scoring function. SPIDER was ranked among the top scoring functions in a recent round of CAPRI (Critical Assessment of PRedicted Interactions) blind test of protein-protein docking methods. Copyright © 2012 Wiley Periodicals, Inc.

Molecular Determinants Underlying Binding Specificities of the ABL Kinase Inhibitors: Combining Alanine Scanning of Binding Hot Spots with Network Analysis of Residue Interactions and Coevolution.

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Amanda Tse

Full Text Available Quantifying binding specificity and drug resistance of protein kinase inhibitors is of fundamental importance and remains highly challenging due to complex interplay of structural and thermodynamic factors. In this work, molecular simulations and computational alanine scanning are combined with the network-based approaches to characterize molecular determinants underlying binding specificities of the ABL kinase inhibitors. The proposed theoretical framework unveiled a relationship between ligand binding and inhibitor-mediated changes in the residue interaction networks. By using topological parameters, we have described the organization of the residue interaction networks and networks of coevolving residues in the ABL kinase structures. This analysis has shown that functionally critical regulatory residues can simultaneously embody strong coevolutionary signal and high network centrality with a propensity to be energetic hot spots for drug binding. We have found that selective (Nilotinib and promiscuous (Bosutinib, Dasatinib kinase inhibitors can use their energetic hot spots to differentially modulate stability of the residue interaction networks, thus inhibiting or promoting conformational equilibrium between inactive and active states. According to our results, Nilotinib binding may induce a significant network-bridging effect and enhance centrality of the hot spot residues that stabilize structural environment favored by the specific kinase form. In contrast, Bosutinib and Dasatinib can incur modest changes in the residue interaction network in which ligand binding is primarily coupled only with the identity of the gate-keeper residue. These factors may promote structural adaptability of the active kinase states in binding with these promiscuous inhibitors. Our results have related ligand-induced changes in the residue interaction networks with drug resistance effects, showing that network robustness may be compromised by targeted mutations

Molecular Determinants Underlying Binding Specificities of the ABL Kinase Inhibitors: Combining Alanine Scanning of Binding Hot Spots with Network Analysis of Residue Interactions and Coevolution

Science.gov (United States)

Tse, Amanda; Verkhivker, Gennady M.

2015-01-01

Quantifying binding specificity and drug resistance of protein kinase inhibitors is of fundamental importance and remains highly challenging due to complex interplay of structural and thermodynamic factors. In this work, molecular simulations and computational alanine scanning are combined with the network-based approaches to characterize molecular determinants underlying binding specificities of the ABL kinase inhibitors. The proposed theoretical framework unveiled a relationship between ligand binding and inhibitor-mediated changes in the residue interaction networks. By using topological parameters, we have described the organization of the residue interaction networks and networks of coevolving residues in the ABL kinase structures. This analysis has shown that functionally critical regulatory residues can simultaneously embody strong coevolutionary signal and high network centrality with a propensity to be energetic hot spots for drug binding. We have found that selective (Nilotinib) and promiscuous (Bosutinib, Dasatinib) kinase inhibitors can use their energetic hot spots to differentially modulate stability of the residue interaction networks, thus inhibiting or promoting conformational equilibrium between inactive and active states. According to our results, Nilotinib binding may induce a significant network-bridging effect and enhance centrality of the hot spot residues that stabilize structural environment favored by the specific kinase form. In contrast, Bosutinib and Dasatinib can incur modest changes in the residue interaction network in which ligand binding is primarily coupled only with the identity of the gate-keeper residue. These factors may promote structural adaptability of the active kinase states in binding with these promiscuous inhibitors. Our results have related ligand-induced changes in the residue interaction networks with drug resistance effects, showing that network robustness may be compromised by targeted mutations of key mediating

Application of secondary and residual stresses to the assessment of the structural integrity of nuclear power-generating plant

International Nuclear Information System (INIS)

Banahan, B.D.

2008-01-01

the perceived structural integrity. Finally, the future requirements for the residual stresses to be incorporated into structural integrity assessments of ferritic steel nuclear power plant components and structures will be discussed. This will be by reference to various weldment geometries and heat treatment cycles including repair welds and fillet attachment welds. In particular, there is a need for improved measurement techniques and analytical/computer models to provide more realistic three-dimensional stress distributions for a range of weldment geometries. In addition, there is a need to revisit the criteria adopted to establish the initiation fracture toughness of ductile ferritic steels with respect to the attendant redistribution of residual stresses

The influence of common stimulus parameters on distortion product otoacoustic emission fine structure.

Science.gov (United States)

Johnson, Tiffany A; Baranowski, Lauren G

2012-01-01

To determine whether common approaches to setting stimulus parameters influence the depth of fine structure present in the distortion product otoacoustic emission (DPOAE) response. Because the presence of fine structure has been suggested as a possible source of errors, if one of the common parametric approaches results in reduced fine-structure depth, it may be preferred over other approaches. DPOAE responses were recorded in a group of 21 subjects with normal hearing for 1/3-octave intervals surrounding 3 f2s (1, 2, and 4 kHz) at three L2s (30, 45, and 55 dB SPL). For each f2 and L2 combination, L1 and f2/f1 were set according to three commonly used parametric approaches. These included a simple approach, the approach recommended by Kummer et al., and the approach described by Johnson et al. These three approaches primarily differ in the recommended relationship between L1 and L2. For each parametric approach, DPOAE fine structure was evaluated by varying f2 in small steps. Differences in DPOAE level and DPOAE fine-structure depth across f2, L2, and the various stimulus parameters were evaluated using repeated-measures analysis of variance. As expected, significant variations in DPOAE level were observed across the three parametric approaches. For stimulus levels #45 dB SPL, the simple stimuli resulted in lower DPOAE levels than were observed for other approaches. An unexpected finding was that stimulus parameters developed by Johnson et al., which were believed to produce higher DPOAE levels than other approaches, produced the lowest DPOAE levels of the three approaches when f2 = 4 kHz. Significant differences in fine-structure depth were also observed. Greater fine-structure depth was observed with the simple parameters, although this effect was restricted to L2 # 45 dB SPL. When L2 = 55 dB SPL, all three parametric approaches resulted in equivalent fine-structure depth. A significant difference in fine-structure depth across the 3 f2s was also observed. The

Residual strain dependence on the matrix structure in RHQ-Nb3Al wires by neutron diffraction measurement

International Nuclear Information System (INIS)

Jin Xinzhe; Nakamoto, Tatsushi; Tsuchiya, Kiyosumi; Ogitsu, Toru; Yamamoto, Akira; Ito, Takayoshi; Harjo, Stefanus; Kikuchi, Akihiro; Takeuchi, Takao; Hemmi, Tsutomu

2012-01-01

We prepared three types of non-Cu RHQ-Nb 3 Al wire sample with different matrix structures: an all-Ta matrix, a composite matrix of Nb and Ta with a Ta inter-filament, and an all-Nb matrix. Neutron diffraction patterns of the wire samples were measured at room temperature in the J-PARC ‘TAKUMI’. To obtain the residual strains of the materials, we estimated the lattice constant a by multi-peak analysis in the wires. A powder sample of each wire was measured, where the powder was considered to be strain free. The grain size of all the powder samples was below 0.02 mm. For the wire sample with the all-Nb matrix, we also obtained the lattice spacing d by a single-peak analysis. The residual strains of the Nb 3 Al filament were estimated from the two analysis results and were compared. The resulting residual strains obtained from the multi-peak analysis showed a good accuracy with small standard deviation. The multi-peak analysis results for the residual strains of the Nb 3 Al filaments in the three samples (without Cu plating) were all tensile residual strain in the axial direction, of 0.12%, 0.12%, and 0.05% for the all-Ta matrix, the composite matrix, and the all-Nb matrix, respectively. The difference in the residual strain of the Nb 3 Al filament between the composite and all-Nb matrix samples indicates that the type of inter-filament material shows a great effect on the residual strain. In this paper, we report the method of measurement, method of analysis, and results for the residual strain in the three types of non-Cu RHQ-Nb 3 Al wires. (paper)

Geophysical exploration of historical mine dumps for the estimation of valuable residuals

Science.gov (United States)

Martin, Tina; Knieß, Rudolf; Noell, Ursula; Hupfer, Sarah; Kuhn, Kerstin; Günther, Thomas

2015-04-01

Within the project ROBEHA, funded by the German Federal Ministry of Education and Research (033R105) the economic potential of different abandoned dump sites for mine waste in the Harz Mountains was investigated. Two different mining dumps were geophysically and mineralogically analysed in order to characterize the mine dump structure and to estimate the volume of the potential recycling material. The geophysical methods comprised geoelectrics, radar, and spectral induced polarization (SIP). One about 100-year old mining dump containing residues from density separated Ag- and Sb-rich Pb (Zn)-gangue ores was investigated in detail. Like most small-scale mining waste disposal sites this investigated dump is very heterogeneously structured. Therefore, 27 geoelectrical profiles, more than 50 radar profiles, and several SIP profiles were measured and analysed. The results from the radar measurements, registered with the GSSI system and a shielded 200 MHz antenna, show the near surface boundary layer (down to 3-4 m beneath surface) of the waste residuals. These results can be used as pre-information for the inversion process of the geoelectrical data. The geoelectrical results reveal the mineral residues as layers with higher resistivities (> 300 Ohm*m) than the surrounding material. The SIP method found low phase signals (mine dump and other parameters we get a first estimate for the volume of the residues but the economical viability and the environmental impact of the reworking of the dump still needs to be evaluated in detail. The results of the second mine dump, an abandoned Cu and Zn-rich slag heap, show that the slag residues are characterized by higher resistivities and higher phases. A localization of the slag residues which are covered by organic material could be realized applying these geophysical methods.

Influence of intensity parameters of earthquake on response of reinforced concrete structures

Science.gov (United States)

Cherian, Ciby Jacob; Madhavan Pillai, T. M.; Sajith, A. S.

2018-03-01

Earthquake is one of the most frightening and destructive phenomena of nature. The destructive capacity of an earthquake depends on various parameters. Without characterising earthquake time history data to the required intensity parameters, its effect on structures cannot be predicted. The influence of intensity parameter of earthquake on the destructive capacity of a structure is essential in the vibration control scenario also. In the present paper, three reinforced concrete (RC) framed structures with natural frequencies 4.688 Hz, 1.762 Hz, 1.661 Hz are used to investigate the influence between the intensity measures and the response. 20 ground motion time history data were selected with predominant frequency ranging from 1 Hz to 12.5 Hz. Some available intensity measures were used to characterise this data. 3D model of the structure was analysed in ETABSUL 13.1.3 software with diaphragm rigidity at floor level. Modal analysis was used to find the modes and corresponding time periods. Linear time history analysis was done for the three models for all the ground motion data. It is noted that four intensity parameters namely predominant frequency, Peak Ground Acceleration, Velocity Spectrum Intensity, Housner Intensity has an appreciable influence on the response.

Effect of structural relaxation of metallic glasses on positron annihilation parameters

International Nuclear Information System (INIS)

Tian Decheng; Xiong Liangyue; Tang Zhongxun; Xu Yinhua

1987-07-01

The results of a comparative study of positron lifetime and a Doppler broadening line-shape parameter for two metallic glasses are presented. The change of lifetime τ-bar and the S-parameter for these two metallic glasses are shown to have a common feature, i.e. at the initial stage of structural relaxation, τ-bar presents a peak-form as a function of annealing time or temperature while the S-parameter decreases monotonically. A possible mechanism is proposed for explaining the peak-form of τ-bar which has been observed in many metallic glasses; the initial rise and the following decrease of τ-bar are attributed to the homogenization of defects taking place during the structural relaxation. The monotonic behaviour of the S-parameter seems to indicate that the annihilation of positrons in free state with the high momentum core electrons is negligible. (author). 8 refs, 2 figs

Texture, residual stress and structural analysis of thin films using a combined X-ray analysis

International Nuclear Information System (INIS)

Lutterotti, L.; Chateigner, D.; Ferrari, S.; Ricote, J.

2004-01-01

Advanced thin films for today's industrial and research needs require highly specialized methodologies for a successful quantitative characterization. In particular, in the case of multilayer and/or unknown phases a global approach is necessary to obtain some or all the required information. A full approach has been developed integrating novel texture and residual stress methodologies with the Rietveld method (Acta Cryst. 22 (1967) 151) (for crystal structure analysis) and it has been coupled with the reflectivity analysis. The complete analysis can be done at once and offers several benefits: the thicknesses obtained from reflectivity can be used to correct the diffraction spectra, the phase analysis help to identify the layers and to determine the electron density profile for reflectivity; quantitative texture is needed for quantitative phase and residual stress analyses; crystal structure determination benefits of the previous. To achieve this result, it was necessary to develop some new methods, especially for texture and residual stresses. So it was possible to integrate them in the Rietveld, full profile fitting of the patterns. The measurement of these spectra required a special reflectometer/diffractometer that combines a thin parallel beam (for reflectivity) and a texture/stress goniometer with a curved large position sensitive detector. This new diffraction/reflectivity X-ray machine has been used to test the combined approach. Several spectra and the reflectivity patterns have been collected at different tilting angles and processed at once by the special software incorporating the aforementioned methodologies. Some analysis examples will be given to show the possibilities offered by the method

Crystal structure of vanadite: Refinement of anisotropic displacement parameters

Czech Academy of Sciences Publication Activity Database

Laufek, F.; Skála, Roman; Haloda, J.; Císařová, I.

2006-01-01

Roč. 51, 3-4 (2006), s. 271-275 ISSN 1210-8197 Institutional research plan: CEZ:AV0Z30130516 Keywords : anisotropic displacement parameter * crystal structure * single-crystal X-ray refinement * vanadinite Subject RIV: DB - Geology ; Mineralogy

Microscopic structure and properties changes of cassava stillage residue pretreated by mechanical activation.

Science.gov (United States)

Liao, Zhengda; Huang, Zuqiang; Hu, Huayu; Zhang, Yanjuan; Tan, Yunfang

2011-09-01

This study has focused on the pretreatment of cassava stillage residue (CSR) by mechanical activation (MA) using a self-designed stirring ball mill. The changes in surface morphology, functional groups and crystalline structure of pretreated CSR were examined by using scanning electron microscopy (SEM), Fourier transform infrared (FTIR) spectroscopy and X-ray diffraction (XRD) under reasonable conditions. The results showed that MA could significantly damage the crystal structure of CSR, resulting in the variation of surface morphology, the increase of amorphous region ratio and hydrogen bond energy, and the decrease in crystallinity and crystalline size. But no new functional groups generated during milling, and the crystal type of cellulose in CSR still belonged to cellulose I after MA. Copyright © 2011 Elsevier Ltd. All rights reserved.

Variability of Structural and Biomechanical Parameters of Pelophylax Esculentus (Amphibia, Anura Limb Bones

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Broshko Ye. O.

2014-07-01

Full Text Available Variability of Structural and Biomechanical Prameters of Pelophylax esculentus (Amphibia, Anura Limb Bones. Broshko Ye. O. — Structural and biomechanical parameters of Edible Frog, Pelophylax esculentus (Linnaeus, 1758, limb bones, namely, mass, linear dimensions, parameters of the shaft’s cross-sectional shape (cross-sectional area, moments of inertia, radiuses of inertia were investigated. Some coefficients were also estimated: diameters ratio (df/ds, cross-sectional index (ik, principal moments of inertia ratio (Imax/Imin.. Coefficients of variation of linear dimensions (11.9-20.0 % anrelative bone mass (22-35 % were established. Moments of inertia of various bones are more variable (CV = 41.67-56.35 % in relation to radii of inertia (CV = 9.68-14.67 %. Shaft’s cross-sectional shape is invariable in all cases. However, there is high individual variability of structural and biomechanical parameters of P. esculentus limb bones. Variability of parameters was limited by the certain range. We suggest the presence of stable norm in bone structure. Stylopodium bones have the primary biomechanical function among the elements of limb skeleton, because their parameters most clearly responsive to changes in body mass.

Residual stress effects in LMFBR fracture assessment procedures

International Nuclear Information System (INIS)

Hooton, D.G.

1984-01-01

Two post-yield fracture mechanics methods, which have been developed into fully detailed failure assessment procedures for ferritic structures, have been reviewed from the point of view of the manner in which as-welded residual stress effects are incorporated, and comparisons then made with finite element and theoretical models of centre-cracked plates containing residual/thermal stresses in the form of crack-driving force curves. Applying the procedures to austenitic structures, comparisons are made in terms of failure assessment curves and it is recommended that the preferred method for the prediction of critical crack sizes in LMFBR austenitic structures containing as-welded residual stresses is the CEGB-R6 procedure based on a flow stress defined at 3% strain in the parent plate. When the prediction of failure loads in such structures is required, it is suggested that the CEGB-R6 procedure be used with residual/thermal stresses factored to give a maximum total stress of flow stress magnitude

Epimorphisms in Varieties of Residuated Structures

Czech Academy of Sciences Publication Activity Database

Bezhanishvili, G.; Moraschini, Tommaso; Raftery, J.G.

2017-01-01

Roč. 492, 15 December (2017), s. 185-211 ISSN 0021-8693 R&D Projects: GA ČR GA17-04630S Institutional support: RVO:67985807 Keywords : Epimorphism * Brouwerian algebra * Heyting algebra * Esakia space * Residuated lattice * Sugihara monoid * Substructural logic * Intuitionistic logic * Relevance logic * R-mingle * Beth definability Subject RIV: BA - General Mathematics OBOR OECD: Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8) Impact factor: 0.610, year: 2016

Direct methods and residue type specific isotope labeling in NMR structure determination and model-driven sequential assignment

International Nuclear Information System (INIS)

Schedlbauer, Andreas; Auer, Renate; Ledolter, Karin; Tollinger, Martin; Kloiber, Karin; Lichtenecker, Roman; Ruedisser, Simon; Hommel, Ulrich; Schmid, Walther; Konrat, Robert; Kontaxis, Georg

2008-01-01

Direct methods in NMR based structure determination start from an unassigned ensemble of unconnected gaseous hydrogen atoms. Under favorable conditions they can produce low resolution structures of proteins. Usually a prohibitively large number of NOEs is required, to solve a protein structure ab-initio, but even with a much smaller set of distance restraints low resolution models can be obtained which resemble a protein fold. One problem is that at such low resolution and in the absence of a force field it is impossible to distinguish the correct protein fold from its mirror image. In a hybrid approach these ambiguous models have the potential to aid in the process of sequential backbone chemical shift assignment when 13 C β and 13 C' shifts are not available for sensitivity reasons. Regardless of the overall fold they enhance the information content of the NOE spectra. These, combined with residue specific labeling and minimal triple-resonance data using 13 C α connectivity can provide almost complete sequential assignment. Strategies for residue type specific labeling with customized isotope labeling patterns are of great advantage in this context. Furthermore, this approach is to some extent error-tolerant with respect to data incompleteness, limited precision of the peak picking, and structural errors caused by misassignment of NOEs

Theoretical conformational analysis of the bovine adrenal medulla 12 residue peptide molecule

Science.gov (United States)

Akhmedov, N. A.; Tagiyev, Z. H.; Hasanov, E. M.; Akverdieva, G. A.

2003-02-01

The spatial structure and conformational properties of the bovine adrenal medulla 12 residue peptide Tyr1-Gly2-Gly3-Phe4-Met5-Arg6-Arg7-Val8-Gly9-Arg10-Pro11-Glu12 (BAM-12P) molecule were studied by theoretical conformational analysis. It is revealed that this molecule can exist in several stable states. The energy and geometrical parameters for the low-energy conformations are obtained. The conformationally rigid and labile segments of this molecule were revealed.

Uncertainty in dual permeability model parameters for structured soils

Science.gov (United States)

Arora, B.; Mohanty, B. P.; McGuire, J. T.

2012-01-01

Successful application of dual permeability models (DPM) to predict contaminant transport is contingent upon measured or inversely estimated soil hydraulic and solute transport parameters. The difficulty in unique identification of parameters for the additional macropore- and matrix-macropore interface regions, and knowledge about requisite experimental data for DPM has not been resolved to date. Therefore, this study quantifies uncertainty in dual permeability model parameters of experimental soil columns with different macropore distributions (single macropore, and low- and high-density multiple macropores). Uncertainty evaluation is conducted using adaptive Markov chain Monte Carlo (AMCMC) and conventional Metropolis-Hastings (MH) algorithms while assuming 10 out of 17 parameters to be uncertain or random. Results indicate that AMCMC resolves parameter correlations and exhibits fast convergence for all DPM parameters while MH displays large posterior correlations for various parameters. This study demonstrates that the choice of parameter sampling algorithms is paramount in obtaining unique DPM parameters when information on covariance structure is lacking, or else additional information on parameter correlations must be supplied to resolve the problem of equifinality of DPM parameters. This study also highlights the placement and significance of matrix-macropore interface in flow experiments of soil columns with different macropore densities. Histograms for certain soil hydraulic parameters display tri-modal characteristics implying that macropores are drained first followed by the interface region and then by pores of the matrix domain in drainage experiments. Results indicate that hydraulic properties and behavior of the matrix-macropore interface is not only a function of saturated hydraulic conductivity of the macroporematrix interface (Ksa) and macropore tortuosity (lf) but also of other parameters of the matrix and macropore domains.

Water dynamics clue to key residues in protein folding

International Nuclear Information System (INIS)

Gao, Meng; Zhu, Huaiqiu; Yao, Xin-Qiu; She, Zhen-Su

2010-01-01

A computational method independent of experimental protein structure information is proposed to recognize key residues in protein folding, from the study of hydration water dynamics. Based on all-atom molecular dynamics simulation, two key residues are recognized with distinct water dynamical behavior in a folding process of the Trp-cage protein. The identified key residues are shown to play an essential role in both 3D structure and hydrophobic-induced collapse. With observations on hydration water dynamics around key residues, a dynamical pathway of folding can be interpreted.

Structure-Activity Relationship in TLR4 Mutations: Atomistic Molecular Dynamics Simulations and Residue Interaction Network Analysis

Science.gov (United States)

Anwar, Muhammad Ayaz; Choi, Sangdun

2017-03-01

Toll-like receptor 4 (TLR4), a vital innate immune receptor present on cell surfaces, initiates a signaling cascade during danger and bacterial intrusion. TLR4 needs to form a stable hexamer complex, which is necessary to dimerize the cytoplasmic domain. However, D299G and T399I polymorphism may abrogate the stability of the complex, leading to compromised TLR4 signaling. Crystallography provides valuable insights into the structural aspects of the TLR4 ectodomain; however, the dynamic behavior of polymorphic TLR4 is still unclear. Here, we employed molecular dynamics simulations (MDS), as well as principal component and residue network analyses, to decipher the structural aspects and signaling propagation associated with mutations in TLR4. The mutated complexes were less cohesive, displayed local and global variation in the secondary structure, and anomalous decay in rotational correlation function. Principal component analysis indicated that the mutated complexes also exhibited distinct low-frequency motions, which may be correlated to the differential behaviors of these TLR4 variants. Moreover, residue interaction networks (RIN) revealed that the mutated TLR4/myeloid differentiation factor (MD) 2 complex may perpetuate abnormal signaling pathways. Cumulatively, the MDS and RIN analyses elucidated the mutant-specific conformational alterations, which may help in deciphering the mechanism of loss-of-function mutations.

Identification of coevolving residues and coevolution potentials emphasizing structure, bond formation and catalytic coordination in protein evolution.

Directory of Open Access Journals (Sweden)

Daniel Y Little

Full Text Available The structure and function of a protein is dependent on coordinated interactions between its residues. The selective pressures associated with a mutation at one site should therefore depend on the amino acid identity of interacting sites. Mutual information has previously been applied to multiple sequence alignments as a means of detecting coevolutionary interactions. Here, we introduce a refinement of the mutual information method that: 1 removes a significant, non-coevolutionary bias and 2 accounts for heteroscedasticity. Using a large, non-overlapping database of protein alignments, we demonstrate that predicted coevolving residue-pairs tend to lie in close physical proximity. We introduce coevolution potentials as a novel measure of the propensity for the 20 amino acids to pair amongst predicted coevolutionary interactions. Ionic, hydrogen, and disulfide bond-forming pairs exhibited the highest potentials. Finally, we demonstrate that pairs of catalytic residues have a significantly increased likelihood to be identified as coevolving. These correlations to distinct protein features verify the accuracy of our algorithm and are consistent with a model of coevolution in which selective pressures towards preserving residue interactions act to shape the mutational landscape of a protein by restricting the set of admissible neutral mutations.

Residual Generation for the Ship Benchmark Using Structural Approach

DEFF Research Database (Denmark)

Cocquempot, V.; Izadi-Zamanabadi, Roozbeh; Staroswiecki, M

1998-01-01

The prime objective of Fault-tolerant Control (FTC) systems is to handle faults and discrepancies using appropriate accommodation policies. The issue of obtaining information about various parameters and signals, which have to be monitored for fault detection purposes, becomes a rigorous task...... with the growing number of subsystems. The structural approach, presented in this paper, constitutes a general framework for providing information when the system becomes complex. The methodology of this approach is illustrated on the ship propulsion benchmark....

Interplay between Peptide Bond Geometrical Parameters in Nonglobular Structural Contexts

OpenAIRE

Esposito, Luciana; Balasco, Nicole; De Simone, Alfonso; Berisio, Rita; Vitagliano, Luigi

2013-01-01

Several investigations performed in the last two decades have unveiled that geometrical parameters of protein backbone show a remarkable variability. Although these studies have provided interesting insights into one of the basic aspects of protein structure, they have been conducted on globular and water-soluble proteins. We report here a detailed analysis of backbone geometrical parameters in nonglobular proteins/peptides. We considered membrane proteins and two distinct fibrous systems (am...

Site-Mutation of Hydrophobic Core Residues Synchronically Poise Super Interleukin 2 for Signaling: Identifying Distant Structural Effects through Affordable Computations

Directory of Open Access Journals (Sweden)

Longcan Mei

2018-03-01

Full Text Available A superkine variant of interleukin-2 with six site mutations away from the binding interface developed from the yeast display technique has been previously characterized as undergoing a distal structure alteration which is responsible for its super-potency and provides an elegant case study with which to get insight about how to utilize allosteric effect to achieve desirable protein functions. By examining the dynamic network and the allosteric pathways related to those mutated residues using various computational approaches, we found that nanosecond time scale all-atom molecular dynamics simulations can identify the dynamic network as efficient as an ensemble algorithm. The differentiated pathways for the six core residues form a dynamic network that outlines the area of structure alteration. The results offer potentials of using affordable computing power to predict allosteric structure of mutants in knowledge-based mutagenesis.

Compatible topologies and parameters for NMR structure determination of carbohydrates by simulated annealing.

Science.gov (United States)

Feng, Yingang

2017-01-01

The use of NMR methods to determine the three-dimensional structures of carbohydrates and glycoproteins is still challenging, in part because of the lack of standard protocols. In order to increase the convenience of structure determination, the topology and parameter files for carbohydrates in the program Crystallography & NMR System (CNS) were investigated and new files were developed to be compatible with the standard simulated annealing protocols for proteins and nucleic acids. Recalculating the published structures of protein-carbohydrate complexes and glycosylated proteins demonstrates that the results are comparable to the published structures which employed more complex procedures for structure calculation. Integrating the new carbohydrate parameters into the standard structure calculation protocol will facilitate three-dimensional structural study of carbohydrates and glycosylated proteins by NMR spectroscopy.

Evaluation of residue-residue contact prediction in CASP10

KAUST Repository

Monastyrskyy, Bohdan

2013-08-31

We present the results of the assessment of the intramolecular residue-residue contact predictions from 26 prediction groups participating in the 10th round of the CASP experiment. The most recently developed direct coupling analysis methods did not take part in the experiment likely because they require a very deep sequence alignment not available for any of the 114 CASP10 targets. The performance of contact prediction methods was evaluated with the measures used in previous CASPs (i.e., prediction accuracy and the difference between the distribution of the predicted contacts and that of all pairs of residues in the target protein), as well as new measures, such as the Matthews correlation coefficient, the area under the precision-recall curve and the ranks of the first correctly and incorrectly predicted contact. We also evaluated the ability to detect interdomain contacts and tested whether the difficulty of predicting contacts depends upon the protein length and the depth of the family sequence alignment. The analyses were carried out on the target domains for which structural homologs did not exist or were difficult to identify. The evaluation was performed for all types of contacts (short, medium, and long-range), with emphasis placed on long-range contacts, i.e. those involving residues separated by at least 24 residues along the sequence. The assessment suggests that the best CASP10 contact prediction methods perform at approximately the same level, and comparably to those participating in CASP9.

Rigid Residue Scan Simulations Systematically Reveal Residue Entropic Roles in Protein Allostery.

Directory of Open Access Journals (Sweden)

Robert Kalescky

2016-04-01

Full Text Available Intra-protein information is transmitted over distances via allosteric processes. This ubiquitous protein process allows for protein function changes due to ligand binding events. Understanding protein allostery is essential to understanding protein functions. In this study, allostery in the second PDZ domain (PDZ2 in the human PTP1E protein is examined as model system to advance a recently developed rigid residue scan method combining with configurational entropy calculation and principal component analysis. The contributions from individual residues to whole-protein dynamics and allostery were systematically assessed via rigid body simulations of both unbound and ligand-bound states of the protein. The entropic contributions of individual residues to whole-protein dynamics were evaluated based on covariance-based correlation analysis of all simulations. The changes of overall protein entropy when individual residues being held rigid support that the rigidity/flexibility equilibrium in protein structure is governed by the La Châtelier's principle of chemical equilibrium. Key residues of PDZ2 allostery were identified with good agreement with NMR studies of the same protein bound to the same peptide. On the other hand, the change of entropic contribution from each residue upon perturbation revealed intrinsic differences among all the residues. The quasi-harmonic and principal component analyses of simulations without rigid residue perturbation showed a coherent allosteric mode from unbound and bound states, respectively. The projection of simulations with rigid residue perturbation onto coherent allosteric modes demonstrated the intrinsic shifting of ensemble distributions supporting the population-shift theory of protein allostery. Overall, the study presented here provides a robust and systematic approach to estimate the contribution of individual residue internal motion to overall protein dynamics and allostery.

An Additive-Multiplicative Restricted Mean Residual Life Model

DEFF Research Database (Denmark)

Mansourvar, Zahra; Martinussen, Torben; Scheike, Thomas H.

2016-01-01

mean residual life model to study the association between the restricted mean residual life function and potential regression covariates in the presence of right censoring. This model extends the proportional mean residual life model using an additive model as its covariate dependent baseline....... For the suggested model, some covariate effects are allowed to be time-varying. To estimate the model parameters, martingale estimating equations are developed, and the large sample properties of the resulting estimators are established. In addition, to assess the adequacy of the model, we investigate a goodness...

Structural basis for new pattern of conserved amino acid residues related to chitin-binding in the antifungal peptide from the coconut rhinoceros beetle Oryctes rhinoceros.

Science.gov (United States)

Hemmi, Hikaru; Ishibashi, Jun; Tomie, Tetsuya; Yamakawa, Minoru

2003-06-20

Scarabaecin isolated from hemolymph of the coconut rhinoceros beetle Oryctes rhinoceros is a 36-residue polypeptide that has antifungal activity. The solution structure of scarabaecin has been determined from twodimensional 1H NMR spectroscopic data and hybrid distance geometry-simulated annealing protocol calculation. Based on 492 interproton and 10 hydrogen-bonding distance restraints and 36 dihedral angle restraints, we obtained 20 structures. The average backbone root-mean-square deviation for residues 4-35 is 0.728 +/- 0.217 A from the mean structure. The solution structure consists of a two-stranded antiparallel beta-sheet connected by a type-I beta-turn after a short helical turn. All secondary structures and a conserved disulfide bond are located in the C-terminal half of the peptide, residues 18-36. Overall folding is stabilized by a combination of a disulfide bond, seven hydrogen bonds, and numerous hydrophobic interactions. The structural motif of the C-terminal half shares a significant tertiary structural similarity with chitin-binding domains of plant and invertebrate chitin-binding proteins, even though scarabaecin has no overall sequence similarity to other peptide/polypeptides including chitin-binding proteins. The length of its primary structure, the number of disulfide bonds, and the pattern of conserved functional residues binding to chitin in scarabaecin differ from those of chitin-binding proteins in other invertebrates and plants, suggesting that scarabaecin does not share a common ancestor with them. These results are thought to provide further strong experimental evidence to the hypothesis that chitin-binding proteins of invertebrates and plants are correlated by a convergent evolution process.

Characterization of Hospital Residuals

International Nuclear Information System (INIS)

Blanco Meza, A.; Bonilla Jimenez, S.

1997-01-01

The main objective of this investigation is the characterization of the solid residuals. A description of the handling of the liquid and gassy waste generated in hospitals is also given, identifying the source where they originate. To achieve the proposed objective the work was divided in three stages: The first one was the planning and the coordination with each hospital center, in this way, to determine the schedule of gathering of the waste can be possible. In the second stage a fieldwork was made; it consisted in gathering the quantitative and qualitative information of the general state of the handling of residuals. In the third and last stage, the information previously obtained was organized to express the results as the production rate per day by bed, generation of solid residuals for sampled services, type of solid residuals and density of the same ones. With the obtained results, approaches are settled down to either determine design parameters for final disposition whether for incineration, trituration, sanitary filler or recycling of some materials, and storage politics of the solid residuals that allow to determine the gathering frequency. The study concludes that it is necessary to improve the conditions of the residuals handling in some aspects, to provide the cleaning personnel of the equipment for gathering disposition and of security, minimum to carry out this work efficiently, and to maintain a control of all the dangerous waste, like sharp or polluted materials. In this way, an appreciable reduction is guaranteed in the impact on the atmosphere. (Author) [es

[Environment of tryptophan residues in proteins--a factor for stability to oxidative nitrosylation. I. Analysis of primary structure].

Science.gov (United States)

Beda, N V; Nedospasov, A A

2001-01-01

Micellar catalysis under aerobic conditions effectively accelerates oxidative nitrosylation because of solubilization of NO and O2 by protein membranes and hydrophobic nuclei. Nitrosylating intermediates NOx (NO2, N2O3, N2O4) form mainly in the hydrophobic phase, and therefore their solubility in aqueous phase is low and hydrolysis is rapid, local concentration of NOx in the hydrophobic phase being essentially higher than in aqueous. Tryptophan is a hydrophobic residue and can nitrosylate with the formation of isomer N-nitrosotryptophans (NOW). Without denitrosylation mechanism, the accumulation of NOW in proteins of NO-synthesizing organisms would be constant, and long-living proteins would contain essential amounts of NOW, which is however not the case. Using Protein Data Bank (more than 78,000 sequences) we investigated the distribution of tryptophan residues environment (22 residues on each side of polypeptide chain) in proteins with known primary structure. Charged and polar residues (D, H, K, N, Q, R, S) are more incident in the immediate surrounding of tryptophan (-6, -5, -2, -1, 1, 2, 4) and hydrophobic residues (A, F, I, L, V, Y) are more rare than in remote positions. Hence, an essential part of tryptophan residues is situated in hydrophilic environment, which decreases the nitrosylation velocity because of lower NOx concentration in aqueous phase and allows the denitrosylation reactions course via nitrosonium ion transfer on nucleophils of functional groups of protein and low-molecular compounds in aqueous phase.

Structural characterization and magnetic properties of steels subjected to fatigue

International Nuclear Information System (INIS)

Lo, C.C.H.; Tang, F.; Biner, S.B.; Jiles, D.C.

2000-01-01

Studies have been made on the effects of residual stress and microstructure on the variations of magnetic properties of steels during fatigue. Strain-controlled fatigue tests have been conducted on 0.2wt% C steel samples which were (1) cold-worked (2) cold-worked and annealed at 500 deg. C to relieve residual stress, and (3) annealed at 905 deg. C to produce a ferrite/pearlite structure. The changes of surface microstructure were studied by SEM replica technique. The dislocation structures of samples fatigued for different numbers of cycle were studied by TEM. In the initial stage of fatigue coercivity was found to behave differently for samples which have different residual stress levels. In the intermediate stage the magnetic hysteresis parameters became stable as the dislocation cell structure developed in the samples. In the final stage the magnetic parameters decreased dramatically. The decrease rate is related to the propagation rate of fatigue cracks observed in the SEM study, which was found to be dependent on the sample microstructure. The present results indicate that the magnetic inspection technique is able to differentiate the residual stress effects from the fatigue damage induced by cyclic loading, and therefore it is possible to detect the onset of fatigue failure in steel components via measurements of the changes in magnetic properties.--This work was sponsored by the National Science Foundation, under grant number CMS-9532056

Small-scale Forearc Structure from Residual Bathymetry and Vertical Gravity Gradients at the Cocos-North America Subduction Zone offshore Mexico

Science.gov (United States)

Garcia, E. S. M.; Ito, Y.

2017-12-01

The subduction of topographic relief on the incoming plate at subduction zones causes deformation of the plate interface as well as the overriding plate. Whether the resulting geometric irregularities play any role in inhibiting or inducing seismic rupture is a topic of relevance for megathrust earthquake source studies. A method to discern the small-scale structure at subduction zone forearcs was recently developed by Bassett and Watts (2015). Their technique constructs an ensemble average of the trench-perpendicular topography, and the removal of this regional tectonic signal reveals the short-wavelength residual bathymetric anomalies. Using examples from selected areas at the Tonga, Mariana, and Japan subduction zones, they were able to link residual bathymetric anomalies to the subduction of seamount chains, given the similarities in wavelength and amplitude to the morphology of seamounts that have yet to subduct. We focus here on an analysis of forearc structures found in the Mexico segment of the Middle America subduction zone, and their potential mechanical interaction with areas on the plate interface that have been previously identified as source regions for earthquake ruptures and aseismic events. We identified several prominent residual bathymetric anomalies off the Guerrero and Oaxaca coastlines, mainly in the shallow portion of the plate interface and between 15 and 50 kilometers away from the trench axis. The residual amplitude of these bathymetric anomalies is typically in the hundreds of meters. Some of the residual bathymetric anomalies offshore Oaxaca are found landward of seamount chains on the incoming Cocos Plate, suggesting that these anomalies are associated with the prior subduction of seamounts at the margin. We also separated the residual and regional components of satellite-based vertical gravity gradient data using a directional median filter to isolate the possible gravity signals from the seamount edifices.

Analysis of residual swirl in tangentially-fired natural gas-boiler

International Nuclear Information System (INIS)

Hasril Hasini; Muhammad Azlan Muad; Mohd Zamri Yusoff; Norshah Hafeez Shuaib

2010-01-01

This paper describes the investigation on residual swirl flow in a 120 MW natural gas, full-scale, tangential-fired boiler. Emphasis is given towards the understanding of the behavior of the combustion gas flow pattern and temperature distribution as a result of the tangential firing system of the boiler. The analysis was carried out based on three-dimensional computational modeling on full scale boiler with validation from key design parameter as well as practical observation. Actual operating parameters of the actual boiler are taken as the boundary conditions for this modeling. The prediction of total heat flux was found to be in agreement with the key design parameter while the residual swirl predicted at the upper furnace agrees qualitatively with the practical observation. Based on this comparison, detail analysis was carried out for comprehensive understanding on the generation and destruction of the residual swirl behavior in boiler especially those with high capacity. (author)

Regulations and decisions in environmental impact assessment of residues radioactivity content

International Nuclear Information System (INIS)

Santos, Adir Janete Godoy dos

2005-01-01

Surveillance of natural radionuclides in the environment did not have high priority over many years compared to that of man-made radioactivity. There is, however, an increasing interest in such measurements since enhanced exposure to natural radioactivity is receiving the same legal weight as any other radiation exposure. In this context the surveillance of technologically enhanced naturally occurring materials, called TENORM becomes important. In Brazil, the industries of processing and chemical compounds production were developed based on mining, milling, transformation and manufacture of ores from sedimentary origin, ignea or metamorphic, which must determine the radioactive composition of the generated solid wastes and residues. Many solids residues stored in the environment has been of environmental concern facing the industries and environmentalists in Brazil as it presents a potential threat to the surrounding environment and to individuals occupationally exposed. Radiation protection regulations have not been applied yet to these industries, as the Brazilian regulatory agency (Comissao Nacional de Energia Nuclear - CNEN) has only recently published a regulatory guide concerning mining and milling of naturally occurring radioactive materials, which may generate enhanced concentrations of radionuclides. With respect to external and internal exposure to natural radionuclides from the solid residues storage, the nuclides of 232 Th, 235 U and 238 U decay chains are relevant, due to the exposure of workers as well as of members of the public. Radionuclides released from a source can be present as ions, molecules, complexes, mononuclear or polynuclear species, colloids, pseudocolloids, particles or fragments varying in size (nominal molecular mass), structure, morphology, density, valence and charge properties. One of the main points in environmental impact assessment is to identify whether the chemical availability is under influence of these speciation

Adaptation of model proteins from cold to hot environments involves continuous and small adjustments of average parameters related to amino acid composition.

Science.gov (United States)

De Vendittis, Emmanuele; Castellano, Immacolata; Cotugno, Roberta; Ruocco, Maria Rosaria; Raimo, Gennaro; Masullo, Mariorosario

2008-01-07

The growth temperature adaptation of six model proteins has been studied in 42 microorganisms belonging to eubacterial and archaeal kingdoms, covering optimum growth temperatures from 7 to 103 degrees C. The selected proteins include three elongation factors involved in translation, the enzymes glyceraldehyde-3-phosphate dehydrogenase and superoxide dismutase, the cell division protein FtsZ. The common strategy of protein adaptation from cold to hot environments implies the occurrence of small changes in the amino acid composition, without altering the overall structure of the macromolecule. These continuous adjustments were investigated through parameters related to the amino acid composition of each protein. The average value per residue of mass, volume and accessible surface area allowed an evaluation of the usage of bulky residues, whereas the average hydrophobicity reflected that of hydrophobic residues. The specific proportion of bulky and hydrophobic residues in each protein almost linearly increased with the temperature of the host microorganism. This finding agrees with the structural and functional properties exhibited by proteins in differently adapted sources, thus explaining the great compactness or the high flexibility exhibited by (hyper)thermophilic or psychrophilic proteins, respectively. Indeed, heat-adapted proteins incline toward the usage of heavier-size and more hydrophobic residues with respect to mesophiles, whereas the cold-adapted macromolecules show the opposite behavior with a certain preference for smaller-size and less hydrophobic residues. An investigation on the different increase of bulky residues along with the growth temperature observed in the six model proteins suggests the relevance of the possible different role and/or structure organization played by protein domains. The significance of the linear correlations between growth temperature and parameters related to the amino acid composition improved when the analysis was

Standard Errors of Estimated Latent Variable Scores with Estimated Structural Parameters

Science.gov (United States)

Hoshino, Takahiro; Shigemasu, Kazuo

2008-01-01

The authors propose a concise formula to evaluate the standard error of the estimated latent variable score when the true values of the structural parameters are not known and must be estimated. The formula can be applied to factor scores in factor analysis or ability parameters in item response theory, without bootstrap or Markov chain Monte…

Selection of regularization parameter for l1-regularized damage detection

Science.gov (United States)

Hou, Rongrong; Xia, Yong; Bao, Yuequan; Zhou, Xiaoqing

2018-06-01

The l1 regularization technique has been developed for structural health monitoring and damage detection through employing the sparsity condition of structural damage. The regularization parameter, which controls the trade-off between data fidelity and solution size of the regularization problem, exerts a crucial effect on the solution. However, the l1 regularization problem has no closed-form solution, and the regularization parameter is usually selected by experience. This study proposes two strategies of selecting the regularization parameter for the l1-regularized damage detection problem. The first method utilizes the residual and solution norms of the optimization problem and ensures that they are both small. The other method is based on the discrepancy principle, which requires that the variance of the discrepancy between the calculated and measured responses is close to the variance of the measurement noise. The two methods are applied to a cantilever beam and a three-story frame. A range of the regularization parameter, rather than one single value, can be determined. When the regularization parameter in this range is selected, the damage can be accurately identified even for multiple damage scenarios. This range also indicates the sensitivity degree of the damage identification problem to the regularization parameter.

Comparison of the population structure and life-history parameters ...

African Journals Online (AJOL)

Blacktail seabream Diplodus capensis were sampled from proximate (10 km apart) exploited and unexploited areas in southern Angola to compare their population structures and life-history parameters. Females dominated the larger size and older age classes in the unexploited area. In the exploited area the length and ...

Structural analysis on mutation residues and interfacial water molecules for human TIM disease understanding

Science.gov (United States)

2013-01-01

Background Human triosephosphate isomerase (HsTIM) deficiency is a genetic disease caused often by the pathogenic mutation E104D. This mutation, located at the side of an abnormally large cluster of water in the inter-subunit interface, reduces the thermostability of the enzyme. Why and how these water molecules are directly related to the excessive thermolability of the mutant have not been investigated in structural biology. Results This work compares the structure of the E104D mutant with its wild type counterparts. It is found that the water topology in the dimer interface of HsTIM is atypical, having a "wet-core-dry-rim" distribution with 16 water molecules tightly packed in a small deep region surrounded by 22 residues including GLU104. These water molecules are co-conserved with their surrounding residues in non-archaeal TIMs (dimers) but not conserved across archaeal TIMs (tetramers), indicating their importance in preserving the overall quaternary structure. As the structural permutation induced by the mutation is not significant, we hypothesize that the excessive thermolability of the E104D mutant is attributed to the easy propagation of atoms' flexibility from the surface into the core via the large cluster of water. It is indeed found that the B factor increment in the wet region is higher than other regions, and, more importantly, the B factor increment in the wet region is maintained in the deeply buried core. Molecular dynamics simulations revealed that for the mutant structure at normal temperature, a clear increase of the root-mean-square deviation is observed for the wet region contacting with the large cluster of interfacial water. Such increase is not observed for other interfacial regions or the whole protein. This clearly suggests that, in the E104D mutant, the large water cluster is responsible for the subunit interface flexibility and overall thermolability, and it ultimately leads to the deficiency of this enzyme. Conclusions Our study

A coherent structure approach for parameter estimation in Lagrangian Data Assimilation

Science.gov (United States)

Maclean, John; Santitissadeekorn, Naratip; Jones, Christopher K. R. T.

2017-12-01

We introduce a data assimilation method to estimate model parameters with observations of passive tracers by directly assimilating Lagrangian Coherent Structures. Our approach differs from the usual Lagrangian Data Assimilation approach, where parameters are estimated based on tracer trajectories. We employ the Approximate Bayesian Computation (ABC) framework to avoid computing the likelihood function of the coherent structure, which is usually unavailable. We solve the ABC by a Sequential Monte Carlo (SMC) method, and use Principal Component Analysis (PCA) to identify the coherent patterns from tracer trajectory data. Our new method shows remarkably improved results compared to the bootstrap particle filter when the physical model exhibits chaotic advection.

Residual stress in a thick section high strength T-butt weld

International Nuclear Information System (INIS)

Pearce, S.V.; Linton, V.M.; Oliver, E.C.

2008-01-01

Residual stresses in a structure are generated as a result of the various fabrication and welding processes used to make the component. Being able to quantify these residual stresses is a key step in determining the continuing integrity of a structure in service. In this work, the residual stresses around a high strength, quenched and tempered steel T-butt web to curved plate weld have been measured using neutron strain scanning. The results show that the residual stresses near the weld were dominated by the welding residual stresses, while the stresses further from the weld were dominated by the bending residual stresses. The results suggest that the combination of welding-induced residual stress and significant pre-welding residual stress, as in the case of a thick bent section of plate can significantly alter the residual stress profile from that in a flat plate

Influence of Weaving Loom Setting Parameters on Changes of Woven Fabric Structure and Mechanical Properties

Directory of Open Access Journals (Sweden)

Aušra ADOMAITIENĖ

2011-11-01

Full Text Available During the manufacturing of fabric of different raw material there was noticed, that after removing the fabric from weaving loom and after stabilization of fabric structure, the changes of parameters of fabric structure are not regular. During this investigation it was analysed, how weaving loom technological parameters (heald cross moment and initial tension of warp should be chosen and how to predict the changes of fabric structure parameters and its mechanical properties. The dependencies of changes of half-wool fabric structure parameters (weft setting, fabric thickness and projections of fabric cross-section and mechanical properties (breaking force, elongation at break, static friction force and static friction coefficient on weaving loom setting parameters (heald cross moment and initial warp tension were analysed. The orthogonal Box plan of two factors was used, the 3-D dependencies were drawn, and empirical equations of these dependencies were established.http://dx.doi.org/10.5755/j01.ms.17.4.780

FragKB: structural and literature annotation resource of conserved peptide fragments and residues.

Directory of Open Access Journals (Sweden)

Ashish V Tendulkar

Full Text Available BACKGROUND: FragKB (Fragment Knowledgebase is a repository of clusters of structurally similar fragments from proteins. Fragments are annotated with information at the level of sequence, structure and function, integrating biological descriptions derived from multiple existing resources and text mining. METHODOLOGY: FragKB contains approximately 400,000 conserved fragments from 4,800 representative proteins from PDB. Literature annotations are extracted from more than 1,700 articles and are available for over 12,000 fragments. The underlying systematic annotation workflow of FragKB ensures efficient update and maintenance of this database. The information in FragKB can be accessed through a web interface that facilitates sequence and structural visualization of fragments together with known literature information on the consequences of specific residue mutations and functional annotations of proteins and fragment clusters. FragKB is accessible online at http://ubio.bioinfo.cnio.es/biotools/fragkb/. SIGNIFICANCE: The information presented in FragKB can be used for modeling protein structures, for designing novel proteins and for functional characterization of related fragments. The current release is focused on functional characterization of proteins through inspection of conservation of the fragments.

Design optimization of structural parameters in double gate MOSFETs for RF applications

International Nuclear Information System (INIS)

Liang Jiale; Xiao Han; Huang Ru; Wang Pengfei; Wang Yangyuan

2008-01-01

Double gate (DG) MOSFETs have recently attracted much attention for both logic and analog/RF applications. In this paper we focus on the design consideration of DG devices for RF applications. The different influences of key structural parameters on RF characteristics are comprehensively studied and optimized, including body thickness, spacer length and source/drain raised height. The impact of the fluctuation of geometrical parameters of DG devices on RF figures-of-merit are estimated. In addition, different dominance of structural parameters for RF applications is studied in DG devices with different channel lengths. The dependence of RF performance on the gate length downscaling of DG devices is also discussed. The obtained results give the design guidelines for DG devices for RF applications

Effects of shot peening on the residual stress of welded SS400 steel

International Nuclear Information System (INIS)

Lee, Jong Man; Kim, Tae Hyung; Cheong, Seong Kyun; Lee, Seung Ho

2002-01-01

The fatigue life of structures is usually determined by welding zone. The tensile residual stress, which is induced by welding, reduces the fatigue life and fatigue strength of welded structures. If we remove the tensile residual stress or induce the compressive residual stress, the fatigue life of welded structures will be improved. The change of hardness and compressive residual stress of welded zone after shot peening was investigated in this paper. The results show that the hardness was increased by shot peening. The residual stress was reduced by shot peening

Structure of the heterotrimeric PCNA from Sulfolobus solfataricus

International Nuclear Information System (INIS)

Williams, Gareth J.; Johnson, Kenneth; Rudolf, Jana; McMahon, Stephen A.; Carter, Lester; Oke, Muse; Liu, Huanting; Taylor, Garry L.; White, Malcolm F.; Naismith, James H.

2006-01-01

The structure of the heterotrimeric PCNA complex from S. sulfataricus is reported to 2.3 Å. PCNA is a ring-shaped protein that encircles DNA, providing a platform for the association of a wide variety of DNA-processing enzymes that utilize the PCNA sliding clamp to maintain proximity to their DNA substrates. PCNA is a homotrimer in eukaryotes, but a heterotrimer in crenarchaea such as Sulfolobus solfataricus. The three proteins are SsoPCNA1 (249 residues), SsoPCNA2 (245 residues) and SsoPCNA3 (259 residues). The heterotrimeric protein crystallizes in space group P2 1 , with unit-cell parameters a = 44.8, b = 78.8, c = 125.6 Å, β = 100.5°. The crystal structure of this heterotrimeric PCNA molecule has been solved using molecular replacement. The resulting structure to 2.3 Å sheds light on the differential stabilities of the interactions observed between the three subunits and the specificity of individual subunits for partner proteins.

The RING 2.0 web server for high quality residue interaction networks.

Science.gov (United States)

Piovesan, Damiano; Minervini, Giovanni; Tosatto, Silvio C E

2016-07-08

Residue interaction networks (RINs) are an alternative way of representing protein structures where nodes are residues and arcs physico-chemical interactions. RINs have been extensively and successfully used for analysing mutation effects, protein folding, domain-domain communication and catalytic activity. Here we present RING 2.0, a new version of the RING software for the identification of covalent and non-covalent bonds in protein structures, including π-π stacking and π-cation interactions. RING 2.0 is extremely fast and generates both intra and inter-chain interactions including solvent and ligand atoms. The generated networks are very accurate and reliable thanks to a complex empirical re-parameterization of distance thresholds performed on the entire Protein Data Bank. By default, RING output is generated with optimal parameters but the web server provides an exhaustive interface to customize the calculation. The network can be visualized directly in the browser or in Cytoscape. Alternatively, the RING-Viz script for Pymol allows visualizing the interactions at atomic level in the structure. The web server and RING-Viz, together with an extensive help and tutorial, are available from URL: http://protein.bio.unipd.it/ring. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Weakly intrusive low-rank approximation method for nonlinear parameter-dependent equations

KAUST Repository

Giraldi, Loic; Nouy, Anthony

2017-01-01

This paper presents a weakly intrusive strategy for computing a low-rank approximation of the solution of a system of nonlinear parameter-dependent equations. The proposed strategy relies on a Newton-like iterative solver which only requires evaluations of the residual of the parameter-dependent equation and of a preconditioner (such as the differential of the residual) for instances of the parameters independently. The algorithm provides an approximation of the set of solutions associated with a possibly large number of instances of the parameters, with a computational complexity which can be orders of magnitude lower than when using the same Newton-like solver for all instances of the parameters. The reduction of complexity requires efficient strategies for obtaining low-rank approximations of the residual, of the preconditioner, and of the increment at each iteration of the algorithm. For the approximation of the residual and the preconditioner, weakly intrusive variants of the empirical interpolation method are introduced, which require evaluations of entries of the residual and the preconditioner. Then, an approximation of the increment is obtained by using a greedy algorithm for low-rank approximation, and a low-rank approximation of the iterate is finally obtained by using a truncated singular value decomposition. When the preconditioner is the differential of the residual, the proposed algorithm is interpreted as an inexact Newton solver for which a detailed convergence analysis is provided. Numerical examples illustrate the efficiency of the method.

Weakly intrusive low-rank approximation method for nonlinear parameter-dependent equations

KAUST Repository

Giraldi, Loic

2017-06-30

This paper presents a weakly intrusive strategy for computing a low-rank approximation of the solution of a system of nonlinear parameter-dependent equations. The proposed strategy relies on a Newton-like iterative solver which only requires evaluations of the residual of the parameter-dependent equation and of a preconditioner (such as the differential of the residual) for instances of the parameters independently. The algorithm provides an approximation of the set of solutions associated with a possibly large number of instances of the parameters, with a computational complexity which can be orders of magnitude lower than when using the same Newton-like solver for all instances of the parameters. The reduction of complexity requires efficient strategies for obtaining low-rank approximations of the residual, of the preconditioner, and of the increment at each iteration of the algorithm. For the approximation of the residual and the preconditioner, weakly intrusive variants of the empirical interpolation method are introduced, which require evaluations of entries of the residual and the preconditioner. Then, an approximation of the increment is obtained by using a greedy algorithm for low-rank approximation, and a low-rank approximation of the iterate is finally obtained by using a truncated singular value decomposition. When the preconditioner is the differential of the residual, the proposed algorithm is interpreted as an inexact Newton solver for which a detailed convergence analysis is provided. Numerical examples illustrate the efficiency of the method.

Life cycle assessment and residue leaching: The importance of parameter, scenario and leaching data selection

DEFF Research Database (Denmark)

Allegrini, Elisa; Butera, Stefania; Kosson, D.S.

2015-01-01

of systems and products and can be applied to waste management systems to identify environmental benefits and critical aspects thereof. From an LCA perspective, residue utilisation provides benefits such as avoiding the production and depletion of primary materials, but it can lead to environmental burdens......Residues from industrial processes and waste management systems (WMSs) have been increasingly reutilised, leading to landfilling rate reductions and the optimisation of mineral resource utilisation in society. Life cycle assessment (LCA) is a holistic methodology allowing for the analysis......, due to the potential leaching of toxic substances. In waste LCA studies where residue utilisation is included, leaching has generally been neglected. In this study, municipal solid waste incineration bottom ash (MSWI BA) was used as a case study into three LCA scenarios having different system...

Roles of s3 site residues of nattokinase on its activity and substrate specificity.

Science.gov (United States)

Wu, Shuming; Feng, Chi; Zhong, Jin; Huan, Liandong

2007-09-01

Nattokinase (Subtilisin NAT, NK) is a bacterial serine protease with high fibrinolytic activity. To probe their roles on protease activity and substrate specificity, three residues of S3 site (Gly(100), Ser(101) and Leu(126)) were mutated by site-directed mutagenesis. Kinetics parameters of 20 mutants were measured using tetrapeptides as substrates, and their fibrinolytic activities were determined by fibrin plate method. Results of mutation analysis showed that Gly(100) and Ser(101) had reverse steric and electrostatic effects. Residues with bulky or positively charged side chains at position 100 decreased the substrate binding and catalytic activity drastically, while residues with the same characters at position 101 could obviously enhance protease and fibrinolytic activity of NK. Mutation of Leu(126) might impair the structure of the active cleft and drastically decreased the activity of NK. Kinetics studies of the mutants showed that S3 residues were crucial to keep protease activity while they moderately affected substrate specificity of NK. The present study provided some original insight into the P3-S3 interaction in NK and other subtilisins, as well as showed successful protein engineering cases to improve NK as a potential therapeutic agent.

A Qualitative Interpretation of Residual Magnetic Anomaly using ...

African Journals Online (AJOL)

A Qualitative Interpretation of Residual Magnetic Anomaly using Ground ... The magnetic data was collected using a G816 proton precision magnetometer. ... Analysis of residual anomaly graph reveals the existence of some structural features ...

Investigating Resulting Residual Stresses during Mechanical Forming Process

Science.gov (United States)

Akinlabi, Stephen A.; Fatoba, Olawale S.; Mashinini, Peter M.; Akinlabi, Esther T.

2018-03-01

Most manufacturing processes such as machining, welding, heat treatment, laser forming, laser cladding and, laser metal deposition, etc. are subjected to a form of heat or energy to change the geometrical shape thus changing the inherent engineering and structural properties of the material. These changes often cause the development of locked up stresses referred to as residual stresses as a result of these activities. This study reports on the residual stresses developed due to the mechanical forming process to maintain a suitable structural integrity for the formed components. The result of the analysis through the X-ray diffraction confirmed that residual stresses were induced in the manufactured parts and further revealed that residual stresses were compressive in nature as found in the parent material but with values less than the parent material.

Adsorption Property and Mechanism of Oxytetracycline onto Willow Residues

Directory of Open Access Journals (Sweden)

Di Wang

2017-12-01

Full Text Available To elucidate the adsorption property and the mechanism of plant residues to reduce oxytetracycline (OTC, the adsorption of OTC onto raw willow roots (WR-R, stems (WS-R, leaves (WL-R, and adsorption onto desugared willow roots (WR-D, stems (WS-D, and leaves (WL-D were investigated. The structural characterization was analyzed by scanning electron microscopy, Fourier-transform infrared spectra, and an elemental analyzer. OTC adsorption onto the different tissues of willow residues was compared and correlated with their structures. The adsorption kinetics of OTC onto willow residues was found to follow the pseudo-first-order model. The isothermal adsorption process of OTC onto the different tissues of willow residues followed the Langmuir and Freundlich model and the process was also a spontaneous endothermic reaction, which was mainly physical adsorption. After the willow residues were desugared, the polarity decreased and the aromaticity increased, which explained why the adsorption amounts of the desugared willow residues were higher than those of the unmodified residues. These observations suggest that the raw and modified willow residues have great potential as adsorbents to remove organic pollutants.

Type Ia supernova Hubble residuals and host-galaxy properties

International Nuclear Information System (INIS)

Kim, A. G.; Aldering, G.; Aragon, C.; Bailey, S.; Fakhouri, H. K.; Antilogus, P.; Bongard, S.; Canto, A.; Cellier-Holzem, F.; Fleury, M.; Guy, J.; Baltay, C.; Buton, C.; Feindt, U.; Greskovic, P.; Kowalski, M.; Childress, M.; Chotard, N.; Copin, Y.; Gangler, E.

2014-01-01

Kim et al. introduced a new methodology for determining peak-brightness absolute magnitudes of type Ia supernovae from multi-band light curves. We examine the relation between their parameterization of light curves and Hubble residuals, based on photometry synthesized from the Nearby Supernova Factory spectrophotometric time series, with global host-galaxy properties. The K13 Hubble residual step with host mass is 0.013 ± 0.031 mag for a supernova subsample with data coverage corresponding to the K13 training; at <<1σ, the step is not significant and lower than previous measurements. Relaxing the data coverage requirement of the Hubble residual step with the host mass is 0.045 ± 0.026 mag for the larger sample; a calculation using the modes of the distributions, less sensitive to outliers, yields a step of 0.019 mag. The analysis of this article uses K13 inferred luminosities, as distinguished from previous works that use magnitude corrections as a function of SALT2 color and stretch parameters: steps at >2σ significance are found in SALT2 Hubble residuals in samples split by the values of their K13 x(1) and x(2) light-curve parameters. x(1) affects the light-curve width and color around peak (similar to the Δm 15 and stretch parameters), and x(2) affects colors, the near-UV light-curve width, and the light-curve decline 20-30 days after peak brightness. The novel light-curve analysis, increased parameter set, and magnitude corrections of K13 may be capturing features of SN Ia diversity arising from progenitor stellar evolution.

Residual stresses analysis in ball end milling of nickel-based superalloy Inconel 718

Energy Technology Data Exchange (ETDEWEB)

Wang, Junteng; Zhang, Dinghua; Wu, Baohai; Luo, Ming [Key Laboratory of Contemporary Design and Integrated Manufacturing Technology, Northwestern Polytechnical University (China)

2017-11-15

Inconel 718 is widely used in the aviation, space, automotive and biomedical industries because of its outstanding properties. Near-surface residual stresses that are induced by ball end milling in Inconel 718 can be crucial for the performance and service time of the machined parts. In this paper, the influences of cutting conditions, including the use of cutting parameters, cutting fluid and spindle angles, on the residual stresses in the ball end milling process of Inconel 718 alloy were investigated experimentally. X-ray diffraction measurements reveal that residual stress distributions are highly influenced by cutting parameters, especially the depth of cut and cutting speed. The milling operation with cooling induces more compressive stresses trend and the magnitude of the residual stresses increases in the tensile direction with the increase of spindle angles. These cutting induced effects were further discussed with respect to thermal- mechanical coupling theory and some observations made by optical microscopy. From this investigation, it is suggested that the machining process parameters are not the smaller the better for the control of residual stresses in the ball end milling process of Inconel 718. (author)

Structure-independent cross-validation between residual dipolar couplings originating from internal and external orienting media

International Nuclear Information System (INIS)

Barbieri, Renato; Bertini, Ivano; Lee, Yong-Min; Luchinat, Claudio; Velders, Aldrik H.

2002-01-01

Lanthanide-substituted calcium binding proteins are known to partially orient in high magnetic fields. Orientation provides residual dipolar couplings (rdc's). Two of these systems, Tm 3+ - and Dy 3+ -substituted calbindin D 9k , dissolved in an external orienting medium (nonionic liquid crystalline phase) provide rdc values which are the sum of those induced by the lanthanides and by the liquid crystalline phase on the native calcium binding protein. This structure-independent check shows the innocence of the orienting medium with respect to the structure of the protein in solution. Furthermore, the simultaneous use of lanthanide substitution and external orienting media provides a further effective tool to control and tune the orientation tensor

Residual stress concerns in containment analysis

International Nuclear Information System (INIS)

Costantini, F.; Kulak, R. F.; Pfeiffer, P. A.

1997-01-01

The manufacturing of steel containment vessels starts with the forming of flat plates into curved plates. A steel containment structure is made by welding individual plates together to form the sections that make up the complex shaped vessels. The metal forming and welding process leaves residual stresses in the vessel walls. Generally, the effect of metal forming residual stresses can be reduced or virtually eliminated by thermally stress relieving the vesseL In large containment vessels this may not be practical and thus the residual stresses due to manufacturing may become important. The residual stresses could possibly tiect the response of the vessel to internal pressurization. When the level of residual stresses is significant it will affect the vessel's response, for instance the yielding pressure and possibly the failure pressure. The paper will address the effect of metal forming residual stresses on the response of a generic pressure vessel to internal pressurization. A scoping analysis investigated the effect of residual forming stresses on the response of an internally pressurized vessel. A simple model was developed to gain understanding of the mechanics of the problem. Residual stresses due to the welding process were not considered in this investigation

Calculating the mounting parameters for Taylor Spatial Frame correction using computed tomography.

Science.gov (United States)

Kucukkaya, Metin; Karakoyun, Ozgur; Armagan, Raffi; Kuzgun, Unal

2011-07-01

The Taylor Spatial Frame uses a computer program-based six-axis deformity analysis. However, there is often a residual deformity after the initial correction, especially in deformities with a rotational component. This problem can be resolved by recalculating the parameters and inputting all new deformity and mounting parameters. However, this may necessitate repeated x-rays and delay treatment. We believe that error in the mounting parameters is the main reason for most residual deformities. To prevent these problems, we describe a new calculation technique for determining the mounting parameters that uses computed tomography. This technique is especially advantageous for deformities with a rotational component. Using this technique, exact calculation of the mounting parameters is possible and the residual deformity and number of repeated x-rays can be minimized. This new technique is an alternative method to accurately calculating the mounting parameters.

Accuracy of crystal structure error estimates

International Nuclear Information System (INIS)

Taylor, R.; Kennard, O.

1986-01-01

A statistical analysis of 100 crystal structures retrieved from the Cambridge Structural Database is reported. Each structure has been determined independently by two different research groups. Comparison of the independent results leads to the following conclusions: (a) The e.s.d.'s of non-hydrogen-atom positional parameters are almost invariably too small. Typically, they are underestimated by a factor of 1.4-1.45. (b) The extent to which e.s.d.'s are underestimated varies significantly from structure to structure and from atom to atom within a structure. (c) Errors in the positional parameters of atoms belonging to the same chemical residue tend to be positively correlated. (d) The e.s.d.'s of heavy-atom positions are less reliable than those of light-atom positions. (e) Experimental errors in atomic positional parameters are normally, or approximately normally, distributed. (f) The e.s.d.'s of cell parameters are grossly underestimated, by an average factor of about 5 for cell lengths and 2.5 for cell angles. There is marginal evidence that the accuracy of atomic-coordinate e.s.d.'s also depends on diffractometer geometry, refinement procedure, whether or not the structure has a centre of symmetry, and the degree of precision attained in the structure determination. (orig.)

Structure of the ordered hydration of amino acids in proteins: analysis of crystal structures

Energy Technology Data Exchange (ETDEWEB)

Biedermannová, Lada, E-mail: lada.biedermannova@ibt.cas.cz; Schneider, Bohdan [Institute of Biotechnology CAS, Videnska 1083, 142 20 Prague (Czech Republic)

2015-10-27

The hydration of protein crystal structures was studied at the level of individual amino acids. The dependence of the number of water molecules and their preferred spatial localization on various parameters, such as solvent accessibility, secondary structure and side-chain conformation, was determined. Crystallography provides unique information about the arrangement of water molecules near protein surfaces. Using a nonredundant set of 2818 protein crystal structures with a resolution of better than 1.8 Å, the extent and structure of the hydration shell of all 20 standard amino-acid residues were analyzed as function of the residue conformation, secondary structure and solvent accessibility. The results show how hydration depends on the amino-acid conformation and the environment in which it occurs. After conformational clustering of individual residues, the density distribution of water molecules was compiled and the preferred hydration sites were determined as maxima in the pseudo-electron-density representation of water distributions. Many hydration sites interact with both main-chain and side-chain amino-acid atoms, and several occurrences of hydration sites with less canonical contacts, such as carbon–donor hydrogen bonds, OH–π interactions and off-plane interactions with aromatic heteroatoms, are also reported. Information about the location and relative importance of the empirically determined preferred hydration sites in proteins has applications in improving the current methods of hydration-site prediction in molecular replacement, ab initio protein structure prediction and the set-up of molecular-dynamics simulations.

Consensus conference on core radiological parameters to describe lumbar stenosis - an initiative for structured reporting

Energy Technology Data Exchange (ETDEWEB)

Andreisek, Gustav; Winklhofer, Sebastian F.X. [University Hospital Zurich, Department of Radiology, Zurich (Switzerland); Deyo, Richard A. [Oregon Health and Science University, Portland, OR (United States); Jarvik, Jeffrey G. [University of Washington, Seattle, WA (United States); Porchet, Francois [Schulthess Klinik, Zuerich (Switzerland); Steurer, Johann [University Hospital Zurich, Horten Center for patient oriented research and knowledge transfer, Zurich (Switzerland); Collaboration: On behalf of the LSOS working group

2014-12-15

To define radiological criteria and parameters as a minimum standard in a structured radiological report for patients with lumbar spinal stenosis (LSS) and to identify criteria and parameters for research purposes. All available radiological criteria and parameters for LSS were identified using systematic literature reviews and a Delphi survey. We invited to the consensus meeting, and provided data, to 15 internationally renowned experts from different countries. During the meeting, these experts reached consensus in a structured and systematic discussion about a core list of radiological criteria and parameters for standard reporting. We identified a total of 27 radiological criteria and parameters for LSS. During the meeting, the experts identified five of these as core items for a structured report. For central stenosis, these were ''compromise of the central zone'' and ''relation between fluid and cauda equina''. For lateral stenosis, the group agreed that ''nerve root compression in the lateral recess'' was a core item. For foraminal stenosis, we included ''nerve root impingement'' and ''compromise of the foraminal zone''. As a minimum standard, five radiological criteria should be used in a structured radiological report in LSS. Other parameters are well suited for research. (orig.)

Precision and Accuracy Parameters in Structured Light 3-D Scanning

DEFF Research Database (Denmark)

Eiríksson, Eyþór Rúnar; Wilm, Jakob; Pedersen, David Bue

2016-01-01

measure is the established VDI/VDE 2634 (Part 2) guideline using precision made calibration artifacts. Experiments are performed on our own structured light setup, consisting of two cameras and a projector. We place our focus on the influence of calibration design parameters, the calibration procedure...

A Numerical Model for Prediction of Residual Stress Using Rayleigh Waves

International Nuclear Information System (INIS)

Yuan, Mao Dan; Kang, To; Kim, Hak Joon; Song, Sung Jin

2011-01-01

In this work, a numerical model is proposed for the relation between the magnitudes and the depth residual stress with the velocity of Rayleigh wave. Three cases, stress-free, uniform stress and layered stress, are investigated for the change tendency of the Rayleigh wave speed. Using the simulated signal with variation of residual stress magnitude and depth, investigation of the parameters for fitting residual stress and velocity change are performed. The speed change of Rayleigh wave shows a linear relation with the magnitude and an exponential relation with the depth of residual stress. The combination of these two effects could be used for the depth profile evaluation of the residual stress

Using cotton plant residue to produce briquettes

Energy Technology Data Exchange (ETDEWEB)

Coates, W. [University of Arizona, Tucson, AZ (United States). Bioresources Research Facility

2000-07-01

In Arizona, cotton (Gossypium) plant residue left in the field following harvest must be buried to prevent it from serving as an overwintering site for insects such as the pink bollworm. Most tillage operations employed to incorporate the residue into the soil are energy intensive and often degrade soil structure. Trials showed that cotton plant residue could be incorporated with pecan shells to produce commercially acceptable briquettes. Pecan shell briquettes containing cotton residue rather than waste paper were slightly less durable, when made using equivalent weight mixtures and moisture contents. Proximate and ultimate analyses showed the only difference among briquette samples to be a higher ash content in those made using cotton plant residue. Briquettes made with paper demonstrated longer flame out time, and lower ash percentage, compared to those made with cotton plant residue. (author)

Residual thermal stresses in a solid sphere cast from a thermosetting material

Science.gov (United States)

Levitsky, M.; Shaffer, B. W.

1975-01-01

Expressions are developed for the residual thermal stresses in a solid sphere cast from a chemically hardening thermosetting material in a rigid spherical mold. The description of the heat generation rate and temperature variation is derived from a first-order chemical reaction. Solidification is described by the continuous transformation of the material from an inviscid liquidlike state into an elastic solid, with intermediate properties determined by the degree of chemical reaction. Residual stress components are obtained as functions of the parameters of the hardening process and the properties of the hardening material. Variation of the residual stresses with a nondimensionalized reaction rate parameter and the relative compressibility of the hardened material is discussed in detail.

Coupling of order parameters, chirality, and interfacial structures in multiferroic materials.

Science.gov (United States)

Conti, Sergio; Müller, Stefan; Poliakovsky, Arkady; Salje, Ekhard K H

2011-04-13

We study optimal interfacial structures in multiferroic materials with a biquadratic coupling between two order parameters. We discover a new duality relation between the strong coupling and the weak coupling regime for the case of isotropic gradient terms. We analyze the phase diagram depending on the coupling constant and anisotropy of the gradient term, and show that in a certain regime the secondary order parameter becomes activated only in the interfacial region.

Modeling Forest Structural Parameters in the Mediterranean Pines of Central Spain using QuickBird-2 Imagery and Classification and Regression Tree Analysis (CART

Directory of Open Access Journals (Sweden)

José A. Delgado

2012-01-01

Full Text Available Forest structural parameters such as quadratic mean diameter, basal area, and number of trees per unit area are important for the assessment of wood volume and biomass and represent key forest inventory attributes. Forest inventory information is required to support sustainable management, carbon accounting, and policy development activities. Digital image processing of remotely sensed imagery is increasingly utilized to assist traditional, more manual, methods in the estimation of forest structural attributes over extensive areas, also enabling evaluation of change over time. Empirical attribute estimation with remotely sensed data is frequently employed, yet with known limitations, especially over complex environments such as Mediterranean forests. In this study, the capacity of high spatial resolution (HSR imagery and related techniques to model structural parameters at the stand level (n = 490 in Mediterranean pines in Central Spain is tested using data from the commercial satellite QuickBird-2. Spectral and spatial information derived from multispectral and panchromatic imagery (2.4 m and 0.68 m sided pixels, respectively served to model structural parameters. Classification and Regression Tree Analysis (CART was selected for the modeling of attributes. Accurate models were produced of quadratic mean diameter (QMD (R2 = 0.8; RMSE = 0.13 m with an average error of 17% while basal area (BA models produced an average error of 22% (RMSE = 5.79 m2/ha. When the measured number of trees per unit area (N was categorized, as per frequent forest management practices, CART models correctly classified 70% of the stands, with all other stands classified in an adjacent class. The accuracy of the attributes estimated here is expected to be better when canopy cover is more open and attribute values are at the lower end of the range present, as related in the pattern of the residuals found in this study. Our findings indicate that attributes derived from

Parameter identification for structural dynamics based on interval analysis algorithm

Science.gov (United States)

Yang, Chen; Lu, Zixing; Yang, Zhenyu; Liang, Ke

2018-04-01

A parameter identification method using interval analysis algorithm for structural dynamics is presented in this paper. The proposed uncertain identification method is investigated by using central difference method and ARMA system. With the help of the fixed memory least square method and matrix inverse lemma, a set-membership identification technology is applied to obtain the best estimation of the identified parameters in a tight and accurate region. To overcome the lack of insufficient statistical description of the uncertain parameters, this paper treats uncertainties as non-probabilistic intervals. As long as we know the bounds of uncertainties, this algorithm can obtain not only the center estimations of parameters, but also the bounds of errors. To improve the efficiency of the proposed method, a time-saving algorithm is presented by recursive formula. At last, to verify the accuracy of the proposed method, two numerical examples are applied and evaluated by three identification criteria respectively.

Effects of structural error on the estimates of parameters of dynamical systems

Science.gov (United States)

Hadaegh, F. Y.; Bekey, G. A.

1986-01-01

In this paper, the notion of 'near-equivalence in probability' is introduced for identifying a system in the presence of several error sources. Following some basic definitions, necessary and sufficient conditions for the identifiability of parameters are given. The effects of structural error on the parameter estimates for both the deterministic and stochastic cases are considered.

Dissimilar friction stir welds in AA5083-AA6082: The effect of process parameters on residual stress

International Nuclear Information System (INIS)

Steuwer, A.; Peel, M.J.; Withers, P.J.

2006-01-01

The effect of tool traverse and rotation speeds on the residual stresses are quantified for welds between non-age-hardening AA5083 and age-hardening AA6082 and compared to single alloy joints made from each of the two constituents. The residual stresses have been characterised non-destructively by neutron diffraction and synchrotron X-ray diffraction. The region around the weld line was characterised by significant tensile residual stress fields which are balanced by compressive stresses in the parent material. The rotation speed of the tool has been found to have a substantially greater influence than the transverse speed on the properties and residual stresses in the welds, particularly on the AA5083 side where the location of the peak stress moves from the stir zone to beyond the edge of the tool shoulder. The changes in residual stress are related to microstructural and hardness changes as determined in a previous study . In particular the larger stresses under the weld tool on the AA5083 side compared to the AA6082 side are related to a transient reduction in yield stress due to dissolution of the hardening precipitates during welding prior to natural aging after welding

Residual nilpotence and residual solubility of groups

International Nuclear Information System (INIS)

Mikhailov, R V

2005-01-01

The properties of the residual nilpotence and the residual solubility of groups are studied. The main objects under investigation are the class of residually nilpotent groups such that each central extension of these groups is also residually nilpotent and the class of residually soluble groups such that each Abelian extension of these groups is residually soluble. Various examples of groups not belonging to these classes are constructed by homological methods and methods of the theory of modules over group rings. Several applications of the theory under consideration are presented and problems concerning the residual nilpotence of one-relator groups are considered.

Structural interface parameters are discriminatory in recognising near-native poses of protein-protein interactions.

Directory of Open Access Journals (Sweden)

Sony Malhotra

Full Text Available Interactions at the molecular level in the cellular environment play a very crucial role in maintaining the physiological functioning of the cell. These molecular interactions exist at varied levels viz. protein-protein interactions, protein-nucleic acid interactions or protein-small molecules interactions. Presently in the field, these interactions and their mechanisms mark intensively studied areas. Molecular interactions can also be studied computationally using the approach named as Molecular Docking. Molecular docking employs search algorithms to predict the possible conformations for interacting partners and then calculates interaction energies. However, docking proposes number of solutions as different docked poses and hence offers a serious challenge to identify the native (or near native structures from the pool of these docked poses. Here, we propose a rigorous scoring scheme called DockScore which can be used to rank the docked poses and identify the best docked pose out of many as proposed by docking algorithm employed. The scoring identifies the optimal interactions between the two protein partners utilising various features of the putative interface like area, short contacts, conservation, spatial clustering and the presence of positively charged and hydrophobic residues. DockScore was first trained on a set of 30 protein-protein complexes to determine the weights for different parameters. Subsequently, we tested the scoring scheme on 30 different protein-protein complexes and native or near-native structure were assigned the top rank from a pool of docked poses in 26 of the tested cases. We tested the ability of DockScore to discriminate likely dimer interactions that differ substantially within a homologous family and also demonstrate that DOCKSCORE can distinguish correct pose for all 10 recent CAPRI targets.

Genetic parameters for residual feed intake in a random population of Pekin duck

Directory of Open Access Journals (Sweden)

Yunsheng Zhang

2017-02-01

Full Text Available Objective The feed intake (FI and feed efficiency are economically important traits in ducks. To obtain insight into this economically important trait, we designed an experiment based on the residual feed intake (RFI and feed conversion ratio (FCR of a random population Pekin duck. Methods Two thousand and twenty pedigreed random population Pekin ducks were established from 90 males mated to 450 females in two hatches. Traits analyzed in the study were body weight at the 42th day (BW42, 15 to 42 days average daily gain (ADG, 15 to 42 days FI, 15 to 42 days FCR, and 15 to 42 days RFI to assess their genetic inter-relationships. The genetic parameters for feed efficiency traits were estimated using restricted maximum likelihood (REML methodology applied to a sire-dam model for all traits using the ASREML software. Results Estimates heritability of BW42, ADG, FI, FCR, and RFI were 0.39, 0.38, 0.33, 0.38, and 0.41, respectively. The genetic correlation was high between RFI and FI (0.77 and moderate between RFI and FCR (0.54. The genetic correlation was high and moderate between FCR and ADG (−0.80, and between FCR and BW42 (−0.64, and between FCR and FI (0.49, respectively. Conclusion Thus, selection on RFI was expected to improve feed efficiency, and reduce FI. Selection on RFI thus improves the feed efficiency of animals without impairing their FI and increase growth rate.

Fracture mechanics evaluation of heavy welded structures

International Nuclear Information System (INIS)

Sprung, I.; Ericksson, C.W.; Zilberstein, V.A.

1982-01-01

This paper describes some applications of nondestructive examination (NDE) and engineering fracture mechanics to evaluation of flaws in heavy welded structures. The paper discusses not only widely recognized linear elastic fracture mechanics (LEFM) analysis, but also methods of the elastic-plastic fracture mechanics (EPFM), such as COD, J-integral, and Failure Assessment Diagram. Examples are given to highlight the importance of interaction between specialists providing input and the specialists performing the analysis. The paper points out that the critical parameters for as-welded structures when calculated by these methods are conservative since they are based on two pessimistic assumptions: that the magnitude of residual stress is always at the yield strength level, and that the residual stress always acts in the same direction as the applied (mechanical) stress. The suggestion is made that it would be prudent to use the COD or the FAD design curves for a conservative design. The appendix examines a J-design curve modified to include residual stresses

Life cycle analysis of biogas from residues; Livscykelanalys av biogas fraan restprodukter

Energy Technology Data Exchange (ETDEWEB)

Tufvesson, Linda; Lantz, Mikael [Dep. for Miljoe- och Energisystem, Lunds Tekniska Hoegskola, Lund (Sweden)

2012-06-15

The purpose of this study is to carry out life cycle assessments for different biogas systems where biogas is produced from different residues. The investigated residues are distiller's waste, rapeseed cake, whey permeate, concentrated whey permeate, fodder milk, fish residues, bakery residues and glycerol. The environmental impact categories included are climate change, eutrophication, acidification, photochemical ozone creation potential, particles and energy balance. The calculations include emissions from technical systems, especially the energy input in various operations and processes. A general conclusion is that all studied residues are very well suited for production of biogas if there is no demand for them as animal feed today. All biogas systems also reduce the emissions of greenhouse gases compared to petrol and diesel and meet the requirements presented in the EU renewable energy directive (RED). The results of the study also show that the investigated biogas systems are complex and many different parameters affect the result. These parameters are both integrated in the life cycle assessment method, but also in the inventory data used.

Four residues of propeptide are essential for precursor folding of nattokinase.

Science.gov (United States)

Jia, Yan; Cao, Xinhua; Deng, Yu; Bao, Wei; Tang, Changyan; Ding, Hanjing; Zheng, Zhongliang; Zou, Guolin

2014-11-01

Subtilisin propeptide functions as an intramolecular chaperone that guides precursor folding. Nattokinase, a member of subtilisin family, is synthesized as a precursor consisting of a signal peptide, a propeptide, and a subtilisin domain, and the mechanism of its folding remains to be understood. In this study, the essential residues of nattokinase propeptide which contribute to precursor folding were determined. Deletion analysis showed that the conserved regions in propeptide were important for precursor folding. Single-site and multi-site mutagenesis studies confirmed the role of Tyr10, Gly13, Gly34, and Gly35. During stage (i) and (ii) of precursor folding, Tyr10 and Gly13 would form the part of interface with subtilisin domain. While Gly34 and Gly35 connected with an α-helix that would stabilize the structure of propeptide. The quadruple Ala mutation, Y10A/G13A/G34A/G35A, resulted in a loss of the chaperone function for the propeptide. This work showed the essential residues of propeptide for precursor folding via secondary structure and kinetic parameter analyses. © The Author 2014. Published by ABBS Editorial Office in association with Oxford University Press on behalf of the Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences.

Applications of bauxite residue: A mini-review.

Science.gov (United States)

Verma, Ajay S; Suri, Narendra M; Kant, Suman

2017-10-01

Bauxite residue is the waste generated during alumina production by Bayer's process. The amount of bauxite residue (40-50 wt%) generated depends on the quality of bauxite ore used for the processing. High alkalinity and high caustic content in bauxite residue causes environmental risk for fertile soil and ground water contamination. The caustic (NaOH) content in bauxite residue leads to human health risks, like dermal problems and irritation to eyes. Moreover, disposal of bauxite residue requires a large area; such problems can only be minimised by utilising bauxite residue effectively. For two decades, bauxite residue has been used as a binder in cement industries and filler/reinforcement for composite materials in the automobile industry. Valuable metals and oxides, like alumina (Al 2 O 3 ), titanium oxide (TiO 2 ) and iron oxide Fe 2 O 3 , were extracted from bauxite residue to reduce waste. Bauxite residue was utilised in construction and structure industries to make geopolymers. It was also used in the making of glass-ceramics and a coating material. Recently bauxite residue has been utilised to extract rare earth elements like scandium (Sc), yttrium (Y), lanthanum (La), cerium (Ce), neodymium (Nd) and dysprosium (Dy). In this review article, the mineralogical characteristics of bauxite residue are summarised and current progresses on utilisation of bauxite residue in different fields of science and engineering are presented in detail.

IDENTIFICATION OF MODAL PARAMETERS OF VIBRATING STRUCTURES WITH UNKNOWN ORSTOCHASTIC EXCITATION

OpenAIRE

Amaro Baldeón, Roberto; Gardel Kurka, Paulo

2014-01-01

The Vector Autoregressive Moving Average (VARMA) Model is used to identify dynamical characteristics of a structural system in the presence of noise. In order to estimate the parameters of the VARMA Model, the Spliid’s fast algorithm is used. To determine the modal parameters the companion matrix is built with the autoregressive part of the VARMA Model. The performance of this method here discussed is presented by means of simulations, using three degrees of freedom mass-dampingstiffness vibr...

Research on structure and electrical parameters of indium antimonide films

International Nuclear Information System (INIS)

Mukhametniyazova, A.; Konyaeva, V.F.; Sukhanov, S.; Ashirov, A.; Aleksanyan, S.N.

1980-01-01

Results of investigations into the effect of conditions of formation of indium antimonide films prepared by thermal vacuum spraying on their structure, phase composition and electric parameters, are presented. The method of studying the synthesized semiconductor layers on the DRON-0.5 X-ray device with CoKsub(α)-radiation is tested. The dependence of structure, phase composition and electric properties of InSb layers 1+3 μm thick sprayed on ferrite substrates on condensation temperature, is established. Hexagonal InSb modification is found

Research on structure and electrical parameters of indium antimonide films

Energy Technology Data Exchange (ETDEWEB)

Mukhametniyazova, A; Konyaeva, V F; Sukhanov, S; Ashirov, A; Aleksanyan, S N [AN Turkmenskoj SSR, Ashkhabad. Fiziko-Tekhnicheskii Inst.

1980-01-01

Results of investigations into the effect of conditions of formation of indium antimonide films prepared by thermal vacuum spraying on their structure, phase composition and electric parameters, are presented. The method of studying the synthesized semiconductor layers on the DRON-0.5 X-ray device with CoKsub(..cap alpha..)-radiation is tested. The dependence of structure, phase composition and electric properties of InSb layers 1+3 ..mu..m thick sprayed on ferrite substrates on condensation temperature, is established. Hexagonal InSb modification is found.

Pivotal statistics for testing subsets of structural parameters in the IV Regression Model

NARCIS (Netherlands)

Kleibergen, F.R.

2000-01-01

We construct a novel statistic to test hypothezes on subsets of the structural parameters in anInstrumental Variables (IV) regression model. We derive the chi squared limiting distribution of thestatistic and show that it has a degrees of freedom parameter that is equal to the number ofstructural

Residual blood processing by centrifugation, cell salvage or ultrafiltration in cardiac surgery: effects on clinical hemostatic and ex-vivo rheological parameters.

Science.gov (United States)

Vonk, Alexander B; Muntajit, Warayouth; Bhagirath, Pranav; van Barneveld, Laurentius J; Romijn, Johannes W; de Vroege, Roel; Boer, Christa

2012-10-01

The study compared the effects of three blood concentration techniques after cardiopulmonary bypass on clinical hemostatic and ex-vivo rheological parameters. Residual blood of patients undergoing elective cardiac surgery was processed by centrifugation, cell salvage or ultrafiltration, and retransfused (n = 17 per group). Study parameters included blood loss, (free) hemoglobin, hematocrit, fibrinogen and erythrocyte aggregation, deformability and 2,3-diphosphoglycerate content. Patient characteristics were similar between groups. Ultrafiltration was associated with the highest weight of the transfusion bag [649 ± 261 vs. 320 ± 134 g (centrifugation) and 391 ± 158 g (cell salvage); P levels in the transfusion bag. Retransfusion of cell saver blood induced the largest gain in postoperative patient hemoglobin levels when compared to centrifugation and ultrafiltration, and was associated with the largest increase in 2,3-diphosphoglycerate when compared to ultrafiltration (Δ2,3-diphosphoglycerate 1.34 ± 1.92 vs. -0.77 ± 1.56 mmol/l; P = 0.03). Cell salvage is superior with respect to postoperative hemoglobin gain and washout of free hemoglobin when compared to centrifugation or ultrafiltration.

Combining specificity determining and conserved residues improves functional site prediction

Directory of Open Access Journals (Sweden)

Gelfand Mikhail S

2009-06-01

Full Text Available Abstract Background Predicting the location of functionally important sites from protein sequence and/or structure is a long-standing problem in computational biology. Most current approaches make use of sequence conservation, assuming that amino acid residues conserved within a protein family are most likely to be functionally important. Most often these approaches do not consider many residues that act to define specific sub-functions within a family, or they make no distinction between residues important for function and those more relevant for maintaining structure (e.g. in the hydrophobic core. Many protein families bind and/or act on a variety of ligands, meaning that conserved residues often only bind a common ligand sub-structure or perform general catalytic activities. Results Here we present a novel method for functional site prediction based on identification of conserved positions, as well as those responsible for determining ligand specificity. We define Specificity-Determining Positions (SDPs, as those occupied by conserved residues within sub-groups of proteins in a family having a common specificity, but differ between groups, and are thus likely to account for specific recognition events. We benchmark the approach on enzyme families of known 3D structure with bound substrates, and find that in nearly all families residues predicted by SDPsite are in contact with the bound substrate, and that the addition of SDPs significantly improves functional site prediction accuracy. We apply SDPsite to various families of proteins containing known three-dimensional structures, but lacking clear functional annotations, and discusse several illustrative examples. Conclusion The results suggest a better means to predict functional details for the thousands of protein structures determined prior to a clear understanding of molecular function.

Characterization of protein and carbohydrate mid-IR spectral features in crop residues

Science.gov (United States)

Xin, Hangshu; Zhang, Yonggen; Wang, Mingjun; Li, Zhongyu; Wang, Zhibo; Yu, Peiqiang

2014-08-01

To the best of our knowledge, a few studies have been conducted on inherent structure spectral traits related to biopolymers of crop residues. The objective of this study was to characterize protein and carbohydrate structure spectral features of three field crop residues (rice straw, wheat straw and millet straw) in comparison with two crop vines (peanut vine and pea vine) by using Fourier transform infrared spectroscopy (FTIR) technique with attenuated total reflectance (ATR). Also, multivariate analyses were performed on spectral data sets within the regions mainly related to protein and carbohydrate in this study. The results showed that spectral differences existed in mid-IR peak intensities that are mainly related to protein and carbohydrate among these crop residue samples. With regard to protein spectral profile, peanut vine showed the greatest mid-IR band intensities that are related to protein amide and protein secondary structures, followed by pea vine and the rest three field crop straws. The crop vines had 48-134% higher spectral band intensity than the grain straws in spectral features associated with protein. Similar trends were also found in the bands that are mainly related to structural carbohydrates (such as cellulosic compounds). However, the field crop residues had higher peak intensity in total carbohydrates region than the crop vines. Furthermore, spectral ratios varied among the residue samples, indicating that these five crop residues had different internal structural conformation. However, multivariate spectral analyses showed that structural similarities still exhibited among crop residues in the regions associated with protein biopolymers and carbohydrate. Further study is needed to find out whether there is any relationship between spectroscopic information and nutrition supply in various kinds of crop residue when fed to animals.

A quantitative analysis of secondary RNA structure using domination based parameters on trees

Directory of Open Access Journals (Sweden)

Zou Yue

2006-03-01

Full Text Available Abstract Background It has become increasingly apparent that a comprehensive database of RNA motifs is essential in order to achieve new goals in genomic and proteomic research. Secondary RNA structures have frequently been represented by various modeling methods as graph-theoretic trees. Using graph theory as a modeling tool allows the vast resources of graphical invariants to be utilized to numerically identify secondary RNA motifs. The domination number of a graph is a graphical invariant that is sensitive to even a slight change in the structure of a tree. The invariants selected in this study are variations of the domination number of a graph. These graphical invariants are partitioned into two classes, and we define two parameters based on each of these classes. These parameters are calculated for all small order trees and a statistical analysis of the resulting data is conducted to determine if the values of these parameters can be utilized to identify which trees of orders seven and eight are RNA-like in structure. Results The statistical analysis shows that the domination based parameters correctly distinguish between the trees that represent native structures and those that are not likely candidates to represent RNA. Some of the trees previously identified as candidate structures are found to be "very" RNA like, while others are not, thereby refining the space of structures likely to be found as representing secondary RNA structure. Conclusion Search algorithms are available that mine nucleotide sequence databases. However, the number of motifs identified can be quite large, making a further search for similar motif computationally difficult. Much of the work in the bioinformatics arena is toward the development of better algorithms to address the computational problem. This work, on the other hand, uses mathematical descriptors to more clearly characterize the RNA motifs and thereby reduce the corresponding search space. These

A discrete exterior approach to structure-preserving discretization of distributed-parameter port-Hamiltonian systems

NARCIS (Netherlands)

Seslija, Marko; Scherpen, Jacquelien M.A.; van der Schaft, Arjan

2011-01-01

This paper addresses the issue of structure-preserving discretization of open distributed-parameter systems with Hamiltonian dynamics. Employing the formalism of discrete exterior calculus, we introduce simplicial Dirac structures as discrete analogues of the Stokes-Dirac structure and demonstrate

Residual creep life assessment by change of martensitic lath structure in modified 9Cr-1Mo steels

International Nuclear Information System (INIS)

Sawada, Kota; Takeda, Masaaki; Maruyama, Kouichi; Komine, Ryuji; Nagae, Yuji

1998-01-01

Mod.9Cr-1Mo steel has a martensitic lath structure. Recovery of the lath structure takes place in the course of creep. Microstructural degradation due to the recovery results in the acceleration of creep rate and the subsequent failure of a specimen. Change of lath width during creep of the steel was quantitatively investigated to propose a residual life assessment methodology based on the recovery process. Since the steel was tempered at 1053 K, the lath structure is thermally stable at the testing temperatures (848 K - 923 K). However, recovery of lath structure readily takes place during creep, indicating that the recovery is induced by creep deformation. Lath width d increases with creep strain and saturates to a value d s determined by creep stress. The increase of d is faster at a higher stress and temperature. A normalized change in lath width, Δd/Δd s , was introduced to explain the variation of lath growth rate with creep stress and temperature. Δd is the change in lath width from the initial value d 0 , and Δd s is the difference between d s , and d 0 . Δd/Δd s is uniquely related to creep strain ε and the relationship is independent of creep stress as well as creep temperature. This Δd/Δd s -ε relationship obtained by an accelerated creep test at a higher temperature or stress is applicable to any creep condition including service conditions of engineering plants. Creep strain can be evaluated from the measurement of Δd/Δd s based on the Δd/Δd s -ε relationship. A creep curve under any creep condition can readily be calculated by creep data of the steel. Combining these information one can assess residual life of a structural component made of the steel. (author)

Interplay between Peptide Bond Geometrical Parameters in Nonglobular Structural Contexts

Directory of Open Access Journals (Sweden)

Luciana Esposito

2013-01-01

Full Text Available Several investigations performed in the last two decades have unveiled that geometrical parameters of protein backbone show a remarkable variability. Although these studies have provided interesting insights into one of the basic aspects of protein structure, they have been conducted on globular and water-soluble proteins. We report here a detailed analysis of backbone geometrical parameters in nonglobular proteins/peptides. We considered membrane proteins and two distinct fibrous systems (amyloid-forming and collagen-like peptides. Present data show that in these systems the local conformation plays a major role in dictating the amplitude of the bond angle N-Cα-C and the propensity of the peptide bond to adopt planar/nonplanar states. Since the trends detected here are in line with the concept of the mutual influence of local geometry and conformation previously established for globular and water-soluble proteins, our analysis demonstrates that the interplay of backbone geometrical parameters is an intrinsic and general property of protein/peptide structures that is preserved also in nonglobular contexts. For amyloid-forming peptides significant distortions of the N-Cα-C bond angle, indicative of sterical hidden strain, may occur in correspondence with side chain interdigitation. The correlation between the dihedral angles Δω/ψ in collagen-like models may have interesting implications for triple helix stability.

Interplay between peptide bond geometrical parameters in nonglobular structural contexts.

Science.gov (United States)

Esposito, Luciana; Balasco, Nicole; De Simone, Alfonso; Berisio, Rita; Vitagliano, Luigi

2013-01-01

Several investigations performed in the last two decades have unveiled that geometrical parameters of protein backbone show a remarkable variability. Although these studies have provided interesting insights into one of the basic aspects of protein structure, they have been conducted on globular and water-soluble proteins. We report here a detailed analysis of backbone geometrical parameters in nonglobular proteins/peptides. We considered membrane proteins and two distinct fibrous systems (amyloid-forming and collagen-like peptides). Present data show that in these systems the local conformation plays a major role in dictating the amplitude of the bond angle N-C(α)-C and the propensity of the peptide bond to adopt planar/nonplanar states. Since the trends detected here are in line with the concept of the mutual influence of local geometry and conformation previously established for globular and water-soluble proteins, our analysis demonstrates that the interplay of backbone geometrical parameters is an intrinsic and general property of protein/peptide structures that is preserved also in nonglobular contexts. For amyloid-forming peptides significant distortions of the N-C(α)-C bond angle, indicative of sterical hidden strain, may occur in correspondence with side chain interdigitation. The correlation between the dihedral angles Δω/ψ in collagen-like models may have interesting implications for triple helix stability.

Residual stress studies of austenitic and ferritic steels

International Nuclear Information System (INIS)

Chrenko, R.M.

1978-01-01

Residual studies have been made on austenitic and ferritic steels of the types used as structural materials. The residual stress results presented here will include residual stress measurements in the heat-affected zone on butt welded Type 304 stainless steel pipes, and the stresses induced in Type 304 austenitic stainless steel and Type A508 ferritic steel by several surface preparations. Such surface preparation procedures as machining and grinding can induce large directionality effects in the residual stresses determined by X-ray techniques and some typical data will be presented. A brief description is given of the mobile X-ray residual stress apparatus used to obtain most of the data in these studies. (author)

Structural Parameters of Star Clusters: Signal to Noise Effects

Directory of Open Access Journals (Sweden)

Narbutis D.

2015-09-01

Full Text Available We study the impact of photometric signal to noise on the accuracy of derived structural parameters of unresolved star clusters using MCMC model fitting techniques. Star cluster images were simulated as a smooth surface brightness distribution following a King profile convolved with a point spread function. The simulation grid was constructed by varying the levels of sky background and adjusting the cluster’s flux to a specified signal to noise. Poisson noise was introduced to a set of cluster images with the same input parameters at each node of the grid. Model fitting was performed using “emcee” algorithm. The presented posterior distributions of the parameters illustrate their uncertainty and degeneracies as a function of signal to noise. By defining the photometric aperture containing 80% of the cluster’s flux, we find that in all realistic sky background level conditions a signal to noise ratio of ~50 is necessary to constrain the cluster’s half-light radius to an accuracy better than ~20%. The presented technique can be applied to synthetic images simulating various observations of extragalactic star clusters.

A framework for scalable parameter estimation of gene circuit models using structural information

KAUST Repository

Kuwahara, Hiroyuki

2013-06-21

Motivation: Systematic and scalable parameter estimation is a key to construct complex gene regulatory models and to ultimately facilitate an integrative systems biology approach to quantitatively understand the molecular mechanisms underpinning gene regulation. Results: Here, we report a novel framework for efficient and scalable parameter estimation that focuses specifically on modeling of gene circuits. Exploiting the structure commonly found in gene circuit models, this framework decomposes a system of coupled rate equations into individual ones and efficiently integrates them separately to reconstruct the mean time evolution of the gene products. The accuracy of the parameter estimates is refined by iteratively increasing the accuracy of numerical integration using the model structure. As a case study, we applied our framework to four gene circuit models with complex dynamics based on three synthetic datasets and one time series microarray data set. We compared our framework to three state-of-the-art parameter estimation methods and found that our approach consistently generated higher quality parameter solutions efficiently. Although many general-purpose parameter estimation methods have been applied for modeling of gene circuits, our results suggest that the use of more tailored approaches to use domain-specific information may be a key to reverse engineering of complex biological systems. The Author 2013.

A framework for scalable parameter estimation of gene circuit models using structural information

KAUST Repository

Kuwahara, Hiroyuki; Fan, Ming; Wang, Suojin; Gao, Xin

2013-01-01

Motivation: Systematic and scalable parameter estimation is a key to construct complex gene regulatory models and to ultimately facilitate an integrative systems biology approach to quantitatively understand the molecular mechanisms underpinning gene regulation. Results: Here, we report a novel framework for efficient and scalable parameter estimation that focuses specifically on modeling of gene circuits. Exploiting the structure commonly found in gene circuit models, this framework decomposes a system of coupled rate equations into individual ones and efficiently integrates them separately to reconstruct the mean time evolution of the gene products. The accuracy of the parameter estimates is refined by iteratively increasing the accuracy of numerical integration using the model structure. As a case study, we applied our framework to four gene circuit models with complex dynamics based on three synthetic datasets and one time series microarray data set. We compared our framework to three state-of-the-art parameter estimation methods and found that our approach consistently generated higher quality parameter solutions efficiently. Although many general-purpose parameter estimation methods have been applied for modeling of gene circuits, our results suggest that the use of more tailored approaches to use domain-specific information may be a key to reverse engineering of complex biological systems. The Author 2013.

DFTB Parameters for the Periodic Table: Part 1, Electronic Structure.

Science.gov (United States)

Wahiduzzaman, Mohammad; Oliveira, Augusto F; Philipsen, Pier; Zhechkov, Lyuben; van Lenthe, Erik; Witek, Henryk A; Heine, Thomas

2013-09-10

A parametrization scheme for the electronic part of the density-functional based tight-binding (DFTB) method that covers the periodic table is presented. A semiautomatic parametrization scheme has been developed that uses Kohn-Sham energies and band structure curvatures of real and fictitious homoatomic crystal structures as reference data. A confinement potential is used to tighten the Kohn-Sham orbitals, which includes two free parameters that are used to optimize the performance of the method. The method is tested on more than 100 systems and shows excellent overall performance.

A simplified method for random vibration analysis of structures with random parameters

International Nuclear Information System (INIS)

Ghienne, Martin; Blanzé, Claude

2016-01-01

Piezoelectric patches with adapted electrical circuits or viscoelastic dissipative materials are two solutions particularly adapted to reduce vibration of light structures. To accurately design these solutions, it is necessary to describe precisely the dynamical behaviour of the structure. It may quickly become computationally intensive to describe robustly this behaviour for a structure with nonlinear phenomena, such as contact or friction for bolted structures, and uncertain variations of its parameters. The aim of this work is to propose a non-intrusive reduced stochastic method to characterize robustly the vibrational response of a structure with random parameters. Our goal is to characterize the eigenspace of linear systems with dynamic properties considered as random variables. This method is based on a separation of random aspects from deterministic aspects and allows us to estimate the first central moments of each random eigenfrequency with a single deterministic finite elements computation. The method is applied to a frame with several Young's moduli modeled as random variables. This example could be expanded to a bolted structure including piezoelectric devices. The method needs to be enhanced when random eigenvalues are closely spaced. An indicator with no additional computational cost is proposed to characterize the ’’proximity” of two random eigenvalues. (paper)

A pairwise residue contact area-based mean force potential for discrimination of native protein structure

Directory of Open Access Journals (Sweden)

Pezeshk Hamid

2010-01-01

Full Text Available Abstract Background Considering energy function to detect a correct protein fold from incorrect ones is very important for protein structure prediction and protein folding. Knowledge-based mean force potentials are certainly the most popular type of interaction function for protein threading. They are derived from statistical analyses of interacting groups in experimentally determined protein structures. These potentials are developed at the atom or the amino acid level. Based on orientation dependent contact area, a new type of knowledge-based mean force potential has been developed. Results We developed a new approach to calculate a knowledge-based potential of mean-force, using pairwise residue contact area. To test the performance of our approach, we performed it on several decoy sets to measure its ability to discriminate native structure from decoys. This potential has been able to distinguish native structures from the decoys in the most cases. Further, the calculated Z-scores were quite high for all protein datasets. Conclusions This knowledge-based potential of mean force can be used in protein structure prediction, fold recognition, comparative modelling and molecular recognition. The program is available at http://www.bioinf.cs.ipm.ac.ir/softwares/surfield

Identification of Arbitrary Zonation in Groundwater Parameters using the Level Set Method and a Parallel Genetic Algorithm

Science.gov (United States)

Lei, H.; Lu, Z.; Vesselinov, V. V.; Ye, M.

2017-12-01

Simultaneous identification of both the zonation structure of aquifer heterogeneity and the hydrogeological parameters associated with these zones is challenging, especially for complex subsurface heterogeneity fields. In this study, a new approach, based on the combination of the level set method and a parallel genetic algorithm is proposed. Starting with an initial guess for the zonation field (including both zonation structure and the hydraulic properties of each zone), the level set method ensures that material interfaces are evolved through the inverse process such that the total residual between the simulated and observed state variables (hydraulic head) always decreases, which means that the inversion result depends on the initial guess field and the minimization process might fail if it encounters a local minimum. To find the global minimum, the genetic algorithm (GA) is utilized to explore the parameters that define initial guess fields, and the minimal total residual corresponding to each initial guess field is considered as the fitness function value in the GA. Due to the expensive evaluation of the fitness function, a parallel GA is adapted in combination with a simulated annealing algorithm. The new approach has been applied to several synthetic cases in both steady-state and transient flow fields, including a case with real flow conditions at the chromium contaminant site at the Los Alamos National Laboratory. The results show that this approach is capable of identifying the arbitrary zonation structures of aquifer heterogeneity and the hydrogeological parameters associated with these zones effectively.

Discrete exterior geometry approach to structure-preserving discretization of distributed-parameter port-Hamiltonian systems

NARCIS (Netherlands)

Seslija, Marko; van der Schaft, Arjan; Scherpen, Jacquelien M.A.

This paper addresses the issue of structure-preserving discretization of open distributed-parameter systems with Hamiltonian dynamics. Employing the formalism of discrete exterior calculus, we introduce a simplicial Dirac structure as a discrete analogue of the Stokes-Dirac structure and demonstrate

Residual stress and texture in Aluminum doped Zinc Oxide layers deposited by reactive radio frequency magnetron sputtering

Energy Technology Data Exchange (ETDEWEB)

Azanza Ricardo, C.L., E-mail: Cristy.Azanza@ing.unitn.it [Department of Civil, Environmental and Mechanical Engineering, University of Trento, 38123 via Mesiano 77, Trento (Italy); Pastorelli, M.; D' Incau, M. [Department of Civil, Environmental and Mechanical Engineering, University of Trento, 38123 via Mesiano 77, Trento (Italy); Aswath, P. [College of Engineering, University of Texas at Arlington, TX (United States); Scardi, P. [Department of Civil, Environmental and Mechanical Engineering, University of Trento, 38123 via Mesiano 77, Trento (Italy)

2016-04-30

Aluminum doped Zinc Oxide thin films were deposited on standard soda-lime substrates by reactive radio frequency magnetron sputtering. Residual stress and texture were studied by X-ray diffraction, while X-ray Absorption Near Edge Spectroscopy provided information on the Al environment in the best performing thin films. The influence of deposition parameters on structural and microstructural properties is discussed. A correlation between microstructure and residual stress state with electrical and optical properties is proposed. - Highlights: • Al doped ZnO thin films were obtained by reactive radio frequency magnetron sputtering. • Correlation of stresses and texture with electrical and optical properties is shown. • Homogeneous and stress-free thin-films are the best performing ones. • XANES confirmed the doping mechanism and excluded some spurious phases.

The impact of structural error on parameter constraint in a climate model

Science.gov (United States)

McNeall, Doug; Williams, Jonny; Booth, Ben; Betts, Richard; Challenor, Peter; Wiltshire, Andy; Sexton, David

2016-11-01

Uncertainty in the simulation of the carbon cycle contributes significantly to uncertainty in the projections of future climate change. We use observations of forest fraction to constrain carbon cycle and land surface input parameters of the global climate model FAMOUS, in the presence of an uncertain structural error. Using an ensemble of climate model runs to build a computationally cheap statistical proxy (emulator) of the climate model, we use history matching to rule out input parameter settings where the corresponding climate model output is judged sufficiently different from observations, even allowing for uncertainty. Regions of parameter space where FAMOUS best simulates the Amazon forest fraction are incompatible with the regions where FAMOUS best simulates other forests, indicating a structural error in the model. We use the emulator to simulate the forest fraction at the best set of parameters implied by matching the model to the Amazon, Central African, South East Asian, and North American forests in turn. We can find parameters that lead to a realistic forest fraction in the Amazon, but that using the Amazon alone to tune the simulator would result in a significant overestimate of forest fraction in the other forests. Conversely, using the other forests to tune the simulator leads to a larger underestimate of the Amazon forest fraction. We use sensitivity analysis to find the parameters which have the most impact on simulator output and perform a history-matching exercise using credible estimates for simulator discrepancy and observational uncertainty terms. We are unable to constrain the parameters individually, but we rule out just under half of joint parameter space as being incompatible with forest observations. We discuss the possible sources of the discrepancy in the simulated Amazon, including missing processes in the land surface component and a bias in the climatology of the Amazon.

Relating structural parameters to leachability in a glass-bonded ceramic waste form

International Nuclear Information System (INIS)

Frank, S. M.; Johnson, S. G.; Moschetti, T. L.

1998-01-01

Lattice parameters for a crystalline material can be obtained by several methods, notably by analyzing x-ray powder diffraction patterns. By utilizing a computer program to fit a pattern, one can follow the evolution or subtle changes in a structure of a crystalline species in different environments. This work involves such a study for an essential component of the ceramic waste form that is under development at Argonne National Laboratory. Zeolite 4A and zeolite 5A are used to produce two different types of waste forms: a glass-bonded sodalite and a glass-bonded zeolite, respectively. Changes in structure during production of the waste forms are discussed. Specific salt-loadings in the sodalite waste form are related to relative peak intensities of certain reflections in the XRD patterns. Structural parameters for the final waste forms will also be given and related to leachability under standard conditions

Numerical simulation of residual stresses at holes near edges and corners in tempered glass: A parametric study

DEFF Research Database (Denmark)

Pourmoghaddam, Navid; Nielsen, Jens Henrik; Schneider, Jens

2016-01-01

This work presents 3D results of the thermal tempering simulation by the Finite Element Method in order to calculate the residual stresses in the area of the holes near edges and corners of a tem-pered glass plate. A viscoelastic material behavior of the glass is considered for the tempering...... process. The structural relaxation is taken into account using Narayanaswamy’s model. The motiva-tion for this work is to study the effect of the reduction of the hole and edge minimum distances, which are defined according to EN 12150-1. It is the objective of the paper to demonstrate and elucidate...... the influence of the hole and edge distances on the minimal residual compressive stress-es at holes after the tempering process. The residual stresses in the area of the holes are calculat-ed varying the following parameters: the hole diameter, the plate thickness and the interaction between holes and edges...

Effect of textiles structural parameters on surgical healing; a case study

Science.gov (United States)

Marwa, A. Ali

2017-10-01

Medical Textiles is one of the most rapidly expanding sectors in the technical textile market. The huge growth of medical textiles applications was over the last 12 years. “Biomedical Textiles” is a subcategory of medical textiles that narrows the field down to those applications that are intended for active tissue contact, tissue regeneration or surgical implantation. Since the mid-1960s, the current wave of usage is coming as a result of new fibers and new technologies for textile materials construction. “Biotextiles” term include structures composed of textile fibers designed for use in specific biological environments. Medical Textile field was utilizing different materials, textile techniques and structures to provide new medical products with high functionality in the markets. There are other processes that are associated with textiles in terms of the various treatments and finishing. The aim of this article is to draw attention to the medical field in each of Vitro and Vivo trend, and its relation with textile structural parameters, with regard to the fiber material, production techniques, and fabric structures. Also, it is focusing on some cases studies which were applied in our research which produced with different textile parameters. Finally; an overview is presented about modern and innovative applications of the medical textiles.

Residues from waste incineration. Final report

Energy Technology Data Exchange (ETDEWEB)

Astrup, T.; Juul Pedersen, A.; Hyks, J.; Frandsen, F.J.

2009-08-15

The overall objective of the project was to improve the understanding of the formation and characteristics of residues from waste incineration. This was done focusing on the importance of the waste input and the operational conditions of the furnace. Data and results obtained from the project have been discussed in this report according to the following three overall parts: i) mass flows and element distribution, ii) flue gas/particle partitioning and corrosion/deposition aspects, and iii) residue leaching. This has been done with the intent of structuring the discussion while tacitly acknowledging that these aspects are interrelated and cannot be separated. Overall, it was found that the waste input composition had significant impact of the characteristics of the generated residues. A similar correlation between operational conditions and residue characteristics could not be observed. Consequently, the project recommend that optimization of residue quality should focus on controlling the waste input composition. The project results showed that including specific waste materials (and thereby also excluding the same materials) may have significant effects on the residue composition, residue leaching, aerosol and deposit formation.It is specifically recommended to minimize Cl in the input waste. Based on the project results, it was found that a significant potential for optimization of waste incineration exist. (author)

Statistical evaluation of low cycle loading curves parameters for structural materials by mechanical characteristics

International Nuclear Information System (INIS)

Daunys, Mykolas; Sniuolis, Raimondas

2006-01-01

About 300 welded joint materials that are used in nuclear power energy were tested under monotonous tension and low cycle loading in Kaunas University of Technology together with St. Peterburg Central Research Institute of Structural Materials in 1970-2000. The main mechanical, low cycle loading and fracture characteristics of base metals, weld metals and some heat-affected zones of welded joints metals were determined during these experiments. Analytical dependences of low cycle fatigue parameters on mechanical characteristics of structural materials were proposed on the basis of a large number of experimental data, obtained by the same methods and testing equipment. When these dependences are used, expensive low cycle fatigue tests may be omitted and it is possible to compute low cycle loading curves parameters and lifetime for structural materials according to the main mechanical characteristics given in technical manuals. Dependences of low cycle loading curves parameters on mechanical characteristics for several groups of structural materials used in Russian nuclear power energy are obtained by statistical methods and proposed in this paper

Residual stress evaluation and curvature behavior of aluminium 7050 peen forming processed; Avaliacao da tensao residual em aluminio 7050 conformado pelo processo peen forming

Energy Technology Data Exchange (ETDEWEB)

Oliveira, R.R. de; Lima, N.B., E-mail: rolivier@ipen.b, E-mail: nblima@ipen.b [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil); Braga, A.P.V.; Goncalves, M., E-mail: anapaola@ipt.b, E-mail: mgoncalves@ipt.b [Instituto de Pesquisas Tecnologicas (IPT), Sao Paulo, SP (Brazil)

2010-07-01

Shot peening is a superficial cold work process used to increase the fatigue life evaluated by residual stress measurements. The peen forming process is a variant of the shot peening process, where a curvature in the plate is obtained by the compression of the grains near to the surface. In this paper, the influence of the parameters such as: pressure of shot, ball shot size and thickness of aluminum 7050 samples with respect to residual stress profile and resulting arc height was studied. The evaluation of the residual stress profile was obtained by sin{sup 2} {Psi} method. (author)

Structure, microstructure and residual stresses in borided steels

Czech Academy of Sciences Publication Activity Database

Pala, Z.; Mušálek, Radek; Kyncl, J.; Harcuba, P.; Stráský, J.; Kolařík, K.

2013-01-01

Roč. 20, č. 2 (2013), s. 93-95 ISSN 1211-5894. [Struktura 2013 - Kolokvium Krystalografické společnosti. Češkovice (Blansko), 09.09.2013-13.09.2013] Institutional support: RVO:61389021 Keywords : boriding * surface hardening * iron borides * tooth-shaped microstructure * residual stresses Subject RIV: JK - Corrosion ; Surface Treatment of Materials http://www.xray.cz/ms/bul2013-2/s6.pdf

Residual stresses analysis of friction stir welding using one-way FSI simulation

International Nuclear Information System (INIS)

Kang, Sung Wook; Jang, Beom Seon; Song, Ha Cheol

2015-01-01

When certain mechanisms, such as plastic deformations and temperature gradients, occur and are released in a structure, stresses remain because of the shape of the structure and external constraints. These stresses are referred to as residual stresses. The base material locally expands during heating in the welding process. When the welding is completed and cooled to room temperature, the residual stresses are left at nearly the yield strength level. In the case of friction stir welding, the maximum temperature is 80% to 90% of the melting point of the materials. Thus, the residual stresses in the welding process are smaller than those in other fusion welding processes; these stresses have not been considered previously. However, friction stir welding residual stresses are sometimes measured at approximately 70% or above. These residual stresses significantly affect fatigue behavior and lifetime. The present study investigates the residual stress distributions in various welding conditions and shapes of friction stir welding. In addition, the asymmetric feature is considered in temperature and residual stress distribution. Heat transfer analysis is conducted using the commercial computational fluid dynamics program Fluent, and results are used in the finite element structural analysis with the ANSYS Multiphysics software. The calculated residual stresses are compared with experimental values using the X-ray diffraction method.

Relationships between residue Voronoi volume and sequence conservation in proteins.

Science.gov (United States)

Liu, Jen-Wei; Cheng, Chih-Wen; Lin, Yu-Feng; Chen, Shao-Yu; Hwang, Jenn-Kang; Yen, Shih-Chung

2018-02-01

Functional and biophysical constraints can cause different levels of sequence conservation in proteins. Previously, structural properties, e.g., relative solvent accessibility (RSA) and packing density of the weighted contact number (WCN), have been found to be related to protein sequence conservation (CS). The Voronoi volume has recently been recognized as a new structural property of the local protein structural environment reflecting CS. However, for surface residues, it is sensitive to water molecules surrounding the protein structure. Herein, we present a simple structural determinant termed the relative space of Voronoi volume (RSV); it uses the Voronoi volume and the van der Waals volume of particular residues to quantify the local structural environment. RSV (range, 0-1) is defined as (Voronoi volume-van der Waals volume)/Voronoi volume of the target residue. The concept of RSV describes the extent of available space for every protein residue. RSV and Voronoi profiles with and without water molecules (RSVw, RSV, VOw, and VO) were compared for 554 non-homologous proteins. RSV (without water) showed better Pearson's correlations with CS than did RSVw, VO, or VOw values. The mean correlation coefficient between RSV and CS was 0.51, which is comparable to the correlation between RSA and CS (0.49) and that between WCN and CS (0.56). RSV is a robust structural descriptor with and without water molecules and can quantitatively reflect evolutionary information in a single protein structure. Therefore, it may represent a practical structural determinant to study protein sequence, structure, and function relationships. Copyright © 2017 Elsevier B.V. All rights reserved.

Topology Synthesis of Structures Using Parameter Relaxation and Geometric Refinement

Science.gov (United States)

Hull, P. V.; Tinker, M. L.

2007-01-01

Typically, structural topology optimization problems undergo relaxation of certain design parameters to allow the existence of intermediate variable optimum topologies. Relaxation permits the use of a variety of gradient-based search techniques and has been shown to guarantee the existence of optimal solutions and eliminate mesh dependencies. This Technical Publication (TP) will demonstrate the application of relaxation to a control point discretization of the design workspace for the structural topology optimization process. The control point parameterization with subdivision has been offered as an alternative to the traditional method of discretized finite element design domain. The principle of relaxation demonstrates the increased utility of the control point parameterization. One of the significant results of the relaxation process offered in this TP is that direct manufacturability of the optimized design will be maintained without the need for designer intervention or translation. In addition, it will be shown that relaxation of certain parameters may extend the range of problems that can be addressed; e.g., in permitting limited out-of-plane motion to be included in a path generation problem.

Hydrogen bond strengths in phosphorylated and sulfated amino acid residues.

Directory of Open Access Journals (Sweden)

Chaya Rapp

Full Text Available Post-translational modification by the addition of an oxoanion functional group, usually a phosphate group and less commonly a sulfate group, leads to diverse structural and functional consequences in protein systems. Building upon previous studies of the phosphoserine residue (pSer, we address the distinct nature of hydrogen bonding interactions in phosphotyrosine (pTyr and sulfotyrosine (sTyr residues. We derive partial charges for these modified residues and then study them in the context of molecular dynamics simulation of model tripeptides and sulfated protein complexes, potentials of mean force for interacting residue pairs, and a survey of the interactions of modified residues among experimental protein structures. Overall, our findings show that for pTyr, bidentate interactions with Arg are particularly dominant, as has been previously demonstrated for pSer. sTyr interactions with Arg are significantly weaker, even as compared to the same interactions made by the Glu residue. Our work sheds light on the distinct nature of these modified tyrosine residues, and provides a physical-chemical foundation for future studies with the goal of understanding their roles in systems of biological interest.

Coevolution of amino acid residues in the key photosynthetic enzyme Rubisco

Directory of Open Access Journals (Sweden)

Kapralov Maxim V

2011-09-01

Full Text Available Abstract Background One of the key forces shaping proteins is coevolution of amino acid residues. Knowing which residues coevolve in a particular protein may facilitate our understanding of protein evolution, structure and function, and help to identify substitutions that may lead to desired changes in enzyme kinetics. Rubisco, the most abundant enzyme in biosphere, plays an essential role in the process of carbon fixation through photosynthesis, thus facilitating life on Earth. This makes Rubisco an important model system for studying the dynamics of protein fitness optimization on the evolutionary landscape. In this study we investigated the selective and coevolutionary forces acting on large subunit of land plants Rubisco using Markov models of codon substitution and clustering approaches applied to amino acid substitution histories. Results We found that both selection and coevolution shape Rubisco, and that positively selected and coevolving residues have their specifically favored amino acid composition and pairing preference. The mapping of these residues on the known Rubisco tertiary structures showed that the coevolving residues tend to be in closer proximity with each other compared to the background, while positively selected residues tend to be further away from each other. This study also reveals that the residues under positive selection or coevolutionary force are located within functionally important regions and that some residues are targets of both positive selection and coevolution at the same time. Conclusion Our results demonstrate that coevolution of residues is common in Rubisco of land plants and that there is an overlap between coevolving and positively selected residues. Knowledge of which Rubisco residues are coevolving and positively selected could be used for further work on structural modeling and identification of substitutions that may be changed in order to improve efficiency of this important enzyme in crops.

Role of cysteine residues in the structure, stability, and alkane producing activity of cyanobacterial aldehyde deformylating oxygenase.

Directory of Open Access Journals (Sweden)

Yuuki Hayashi

Full Text Available Aldehyde deformylating oxygenase (AD is a key enzyme for alkane biosynthesis in cyanobacteria, and it can be used as a catalyst for alkane production in vitro and in vivo. However, three free Cys residues in AD may impair its catalytic activity by undesired disulfide bond formation and oxidation. To develop Cys-deficient mutants of AD, we examined the roles of the Cys residues in the structure, stability, and alkane producing activity of AD from Nostoc punctiforme PCC 73102 by systematic Cys-to-Ala/Ser mutagenesis. The C71A/S mutations reduced the hydrocarbon producing activity of AD and facilitated the formation of a dimer, indicating that the conserved Cys71, which is located in close proximity to the substrate-binding site, plays crucial roles in maintaining the activity, structure, and stability of AD. On the other hand, mutations at Cys107 and Cys117 did not affect the hydrocarbon producing activity of AD. Therefore, we propose that the C107A/C117A double mutant is preferable to wild type AD for alkane production and that the double mutant may be used as a pseudo-wild type protein for further improvement of the alkane producing activity of AD.

Stabilization of Rocky Flats combustible residues contaminated with plutonium metal and organic solvents

International Nuclear Information System (INIS)

Bowen, S.M.; Cisneros, M.R.; Jacobson, L.L.; Schroeder, N.C.; Ames, R.L.

1998-01-01

This report describes tests on a proposed flowsheet designed to stabilize combustible residues that were generated at the Rocky Flats Environmental Technology Site (RFETS) during the machining of plutonium metal. Combustible residues are essentially laboratory trash contaminated with halogenated organic solvents and plutonium metal. The proposed flowsheet, designed by RFETS, follows a glovebox procedure that includes (1) the sorting and shredding of materials, (2) a low temperature thermal desorption of solvents from the combustible materials, (3) an oxidation of plutonium metal with steam, and (4) packaging of the stabilized residues. The role of Los Alamos National Laboratory (LANL) in this study was to determine parameters for the low temperature thermal desorption and steam oxidation steps. Thermal desorption of carbon tetrachloride (CCl 4 ) was examined using a heated air stream on a Rocky Flats combustible residue surrogate contaminated with CCl 4 . Three types of plutonium metal were oxidized with steam in a LANL glovebox to determine the effectiveness of this procedure for residue stabilization. The results from these LANL experiments are used to recommend parameters for the proposed RFETS stabilization flowsheet

Numerical Simulation of Temperature Field and Residual Stress Distribution for Laser Cladding Remanufacturing

Directory of Open Access Journals (Sweden)

Liang Hua

2014-05-01

Full Text Available A three-dimensional finite element model was employed to simulate the cladding process of Ni-Cr-B-Si coatings on 16MnR steel under different parameters of laser power, scanning speed, and spot diameter. The temperature and residual stress distribution, the depth of the heat affected zone (HAZ, and the optimized parameters for laser cladding remanufacturing technology were obtained. The orthogonal experiment and intuitive analysis on the depth of the HAZ were performed to study the influence of different cladding parameters. A new criterion based on the ratio of the maximum tensile residual stress and fracture strength of the substrate was proposed for optimization of the remanufacturing parameters. The result showed well agreement with that of the HAZ analysis.

Residual Wage Differences by Gender: Bounding the Estimates.

Science.gov (United States)

Sakellariou, Chris N.; Patrinos, Harry A.

1996-01-01

Uses data from the 1986 Canadian labor market activity survey file to derive estimates of residual gender wage gap differences. Investigates these estimates' dependence on experimental design and on assumptions about discrimination-free wage structures. Residual differences persist, even after restricting the sample to a group of highly motivated,…

Two-step method to evaluate equibiaxial residual stress of metal surface based on micro-indentation tests

International Nuclear Information System (INIS)

Nishikawa, Masaaki; Soyama, Hitoshi

2011-01-01

Highlights: → The sensitivity to residual stress was improved by selecting the depth parameter. → Residual stress could be obtained while determining the effect of unknown parameters. → The estimated residual stress agreed well with those of X-ray diffraction. -- Abstract: The present study proposed a method to evaluate the equibiaxial compressive residual stress of a metal surface by means of a depth-sensing indentation method using a spherical indenter. Inverse analysis using the elastic-plastic finite-element model for an indentation test was established to evaluate residual stress from the indentation load-depth curve. The proposed inverse analysis utilizes two indentation test results for a reference specimen whose residual stress is already known and for a target specimen whose residual stress is unknown, in order to exclude the effect of other unknown mechanical properties, such as Young's modulus and yield stress. Residual stress estimated by using the indentation method is almost identical to that measured by X-ray diffraction for indentation loads of 0.49-0.98 N. Therefore, it can be concluded that the proposed method can effectively evaluate residual stress on metal surface.

Specification of indoor climate design parameters at the assessment of moisture protective properties of enclosing structures

Directory of Open Access Journals (Sweden)

Kornienko Sergey Valer’evich

2016-11-01

Full Text Available Due to wide implementation of enveloping structures with increased heat-insulation properties in modern construction here appeared a necessity to assess their moisture conditions. Assessment of moisture conditions of enveloping structures is carried out according to maximum allowable moisture state basing on determining the surface of maximum damping. In relation to it the necessity of additional vapour barrier is checked using moisture balance equation. Though the change of indoor climate parameters in premises is not taken into account in moisture balance equations defined for different seasons. The author improves the method of calculating moisture protective parameters of enclosing structures according to the maximum allowable damping state for a year and a period of moisture accumulation. It is shown in this article that accounting of temperature and relative humidity change of inside air allows specifying calculated parameters of indoor climate in residential and office rooms in assessment of moisture protective properties of enclosing structures for the case of an effective enclosing structure with a façade heat-insulation composite system. Coordinates of the maximum moistened surface of the envelope depends on indoor climate design parameters. It is concluded that the increase of requirements for moisture protection of enclosing structures when using design values of temperature and relative humidity of internal air according to the Russian regulation (SP 50.13330.2012 is not always reasonable. Accounting of changes of indoor climate parameters allows more precise assessment of moisture protective properties of enclosing structures during their design.

SucStruct: Prediction of succinylated lysine residues by using structural properties of amino acids.

Science.gov (United States)

López, Yosvany; Dehzangi, Abdollah; Lal, Sunil Pranit; Taherzadeh, Ghazaleh; Michaelson, Jacob; Sattar, Abdul; Tsunoda, Tatsuhiko; Sharma, Alok

2017-06-15

Post-Translational Modification (PTM) is a biological reaction which contributes to diversify the proteome. Despite many modifications with important roles in cellular activity, lysine succinylation has recently emerged as an important PTM mark. It alters the chemical structure of lysines, leading to remarkable changes in the structure and function of proteins. In contrast to the huge amount of proteins being sequenced in the post-genome era, the experimental detection of succinylated residues remains expensive, inefficient and time-consuming. Therefore, the development of computational tools for accurately predicting succinylated lysines is an urgent necessity. To date, several approaches have been proposed but their sensitivity has been reportedly poor. In this paper, we propose an approach that utilizes structural features of amino acids to improve lysine succinylation prediction. Succinylated and non-succinylated lysines were first retrieved from 670 proteins and characteristics such as accessible surface area, backbone torsion angles and local structure conformations were incorporated. We used the k-nearest neighbors cleaning treatment for dealing with class imbalance and designed a pruned decision tree for classification. Our predictor, referred to as SucStruct (Succinylation using Structural features), proved to significantly improve performance when compared to previous predictors, with sensitivity, accuracy and Mathew's correlation coefficient equal to 0.7334-0.7946, 0.7444-0.7608 and 0.4884-0.5240, respectively. Copyright © 2017 Elsevier Inc. All rights reserved.

A Design of Finite Memory Residual Generation Filter for Sensor Fault Detection

Directory of Open Access Journals (Sweden)

Kim Pyung Soo

2017-04-01

Full Text Available In the current paper, a residual generation filter with finite memory structure is proposed for sensor fault detection. The proposed finite memory residual generation filter provides the residual by real-time filtering of fault vector using only the most recent finite measurements and inputs on the window. It is shown that the residual given by the proposed residual generation filter provides the exact fault for noisefree systems. The proposed residual generation filter is specified to the digital filter structure for the amenability to hardware implementation. Finally, to illustrate the capability of the proposed residual generation filter, extensive simulations are performed for the discretized DC motor system with two types of sensor faults, incipient soft bias-type fault and abrupt bias-type fault. In particular, according to diverse noise levels and windows lengths, meaningful simulation results are given for the abrupt bias-type fault.

Analysis of Parameters Assessment on Laminated Rubber-Metal Spring for Structural Vibration

International Nuclear Information System (INIS)

Salim, M.A.; Putra, A.; Mansor, M.R.; Musthafah, M.T.; Akop, M.Z.; Abdullah, M.A.

2016-01-01

This paper presents the analysis of parameter assessment on laminated rubber-metal spring (LR-MS) for vibrating structure. Three parameters were selected for the assessment which are mass, Young's modulus and radius. Natural rubber materials has been used to develop the LR-MS model. Three analyses were later conducted based on the selected parameters to the LR-MS performance which are natural frequency, location of the internal resonance frequency and transmissibility of internal resonance. Results of the analysis performed were plotted in frequency domain function graph. Transmissibility of laminated rubber-metal spring (LR-MS) is changed by changing the value of the parameter. This occurrence was referred to the theory from open literature then final conclusion has been make which are these parameters have a potential to give an effects and trends for LR-MS transmissibility. (paper)

A Novel Coupled State/Input/Parameter Identification Method for Linear Structural Systems

Directory of Open Access Journals (Sweden)

Zhimin Wan

2018-01-01

Full Text Available In many engineering applications, unknown states, inputs, and parameters exist in the structures. However, most methods require one or two of these variables to be known in order to identify the other(s. Recently, the authors have proposed a method called EGDF for coupled state/input/parameter identification for nonlinear system in state space. However, the EGDF method based solely on acceleration measurements is found to be unstable, which can cause the drift of the identified inputs and displacements. Although some regularization methods can be adopted for solving the problem, they are not suitable for joint input-state identification in real time. In this paper, a strategy of data fusion of displacement and acceleration measurements is used to avoid the low-frequency drift in the identified inputs and structural displacements for linear structural systems. Two numerical examples about a plane truss and a single-stage isolation system are conducted to verify the effectiveness of the proposed modified EGDF algorithm.

Prediction of residue-residue contact matrix for protein-protein interaction with Fisher score features and deep learning.

Science.gov (United States)

Du, Tianchuan; Liao, Li; Wu, Cathy H; Sun, Bilin

2016-11-01

Protein-protein interactions play essential roles in many biological processes. Acquiring knowledge of the residue-residue contact information of two interacting proteins is not only helpful in annotating functions for proteins, but also critical for structure-based drug design. The prediction of the protein residue-residue contact matrix of the interfacial regions is challenging. In this work, we introduced deep learning techniques (specifically, stacked autoencoders) to build deep neural network models to tackled the residue-residue contact prediction problem. In tandem with interaction profile Hidden Markov Models, which was used first to extract Fisher score features from protein sequences, stacked autoencoders were deployed to extract and learn hidden abstract features. The deep learning model showed significant improvement over the traditional machine learning model, Support Vector Machines (SVM), with the overall accuracy increased by 15% from 65.40% to 80.82%. We showed that the stacked autoencoders could extract novel features, which can be utilized by deep neural networks and other classifiers to enhance learning, out of the Fisher score features. It is further shown that deep neural networks have significant advantages over SVM in making use of the newly extracted features. Copyright © 2016. Published by Elsevier Inc.

Dityrosine, 3,4-Dihydroxyphenylalanine (DOPA), and radical formation from tyrosine residues on milk proteins with globular and flexible structures as a result of riboflavin-mediated photo-oxidation

DEFF Research Database (Denmark)

Dalsgaard, Trine Kastrup; Nielsen, Jacob Holm; Brown, Bronwyn

2011-01-01

Riboflavin-mediated photo-oxidative damage to protein Tyr residues has been examined to determine whether protein structure influences competing protein oxidation pathways in single proteins and protein mixtures. EPR studies resulted in the detection of Tyr-derived o-semiquione radicals, with thi......Riboflavin-mediated photo-oxidative damage to protein Tyr residues has been examined to determine whether protein structure influences competing protein oxidation pathways in single proteins and protein mixtures. EPR studies resulted in the detection of Tyr-derived o-semiquione radicals...

Case report of recurrent acute appendicitis in a residual tip.

LENUS (Irish Health Repository)

O'Leary, Donal P

2010-01-01

INTRODUCTION: Residual appendicitis involving the stump of the appendix has been well described in the literature in the past. CASE REPORT: We report the case of a 43 year old male with acute onset of abdominal pain who had undergone an appendicectomy ten years previously. Ultrasound revealed the presence of an inflamed tubular structure. Subsequent laparotomy and histology confirmed that this structure was an inflamed residual appendiceal tip. CONCLUSION: Residual tip appendicitis has not been reported in the literature previously and should be considered in the differential diagnosis of localised peritonitis in a patient with a history of a previous open appendicectomy.

Line-feature-based calibration method of structured light plane parameters for robot hand-eye system

Science.gov (United States)

Qi, Yuhan; Jing, Fengshui; Tan, Min

2013-03-01

For monocular-structured light vision measurement, it is essential to calibrate the structured light plane parameters in addition to the camera intrinsic parameters. A line-feature-based calibration method of structured light plane parameters for a robot hand-eye system is proposed. Structured light stripes are selected as calibrating primitive elements, and the robot moves from one calibrating position to another with constraint in order that two misaligned stripe lines are generated. The images of stripe lines could then be captured by the camera fixed at the robot's end link. During calibration, the equations of two stripe lines in the camera coordinate system are calculated, and then the structured light plane could be determined. As the robot's motion may affect the effectiveness of calibration, so the robot's motion constraints are analyzed. A calibration experiment and two vision measurement experiments are implemented, and the results reveal that the calibration accuracy can meet the precision requirement of robot thick plate welding. Finally, analysis and discussion are provided to illustrate that the method has a high efficiency fit for industrial in-situ calibration.

A framework for scalable parameter estimation of gene circuit models using structural information.

Science.gov (United States)

Kuwahara, Hiroyuki; Fan, Ming; Wang, Suojin; Gao, Xin

2013-07-01

Systematic and scalable parameter estimation is a key to construct complex gene regulatory models and to ultimately facilitate an integrative systems biology approach to quantitatively understand the molecular mechanisms underpinning gene regulation. Here, we report a novel framework for efficient and scalable parameter estimation that focuses specifically on modeling of gene circuits. Exploiting the structure commonly found in gene circuit models, this framework decomposes a system of coupled rate equations into individual ones and efficiently integrates them separately to reconstruct the mean time evolution of the gene products. The accuracy of the parameter estimates is refined by iteratively increasing the accuracy of numerical integration using the model structure. As a case study, we applied our framework to four gene circuit models with complex dynamics based on three synthetic datasets and one time series microarray data set. We compared our framework to three state-of-the-art parameter estimation methods and found that our approach consistently generated higher quality parameter solutions efficiently. Although many general-purpose parameter estimation methods have been applied for modeling of gene circuits, our results suggest that the use of more tailored approaches to use domain-specific information may be a key to reverse engineering of complex biological systems. http://sfb.kaust.edu.sa/Pages/Software.aspx. Supplementary data are available at Bioinformatics online.

Characterization of residual stress as a function of friction stir welding parameters in oxide dispersion strengthened (ODS) steel MA956

Energy Technology Data Exchange (ETDEWEB)

Brewer, L.N., E-mail: lnbrewer1@eng.ua.edu [Naval Postgraduate School (United States); Bennett, M.S.; Baker, B.W. [Naval Postgraduate School (United States); Payzant, E.A.; Sochalski-Kolbus, L.M. [Oak Ridge National Laboratory (United States)

2015-10-28

Friction stir welding (FSW) can generate large residual stresses during solid state joining of oxide dispersion strengthened steels. In this work, a plate of MA956 steel was friction stir welded at three conditions: 500 rpm/25 mm per minute (mmpm), 400 rpm/50 mmpm and 400 rpm/100 mmpm. The residual stresses across these welds were measured using both x-ray and neutron diffraction techniques. The distribution and magnitude of the residual stresses agreed well between the two techniques. Longitudinal residual stresses up to eighty percent of the yield strength were observed for the 400 rpm/100 mmpm condition. The surface residual stresses were somewhat larger on the root side of the weld than on the crown side. Increases in the relative heat input during FSW decreased the measured residual stresses in the stir zone and the thermomechanically affected zone (TMAZ). Increasing the traverse rate while holding the rotational speed fixed increased the residual stress levels. The fatigue strength of the material is predicted to decrease by at least twenty percent with cracking most likely in the TMAZ.

Characterization of residual stress as a function of friction stir welding parameters in oxide dispersion strengthened (ODS) steel MA956

International Nuclear Information System (INIS)

Brewer, L.N.; Bennett, M.S.; Baker, B.W.; Payzant, E.A.; Sochalski-Kolbus, L.M.

2015-01-01

Friction stir welding (FSW) can generate large residual stresses during solid state joining of oxide dispersion strengthened steels. In this work, a plate of MA956 steel was friction stir welded at three conditions: 500 rpm/25 mm per minute (mmpm), 400 rpm/50 mmpm and 400 rpm/100 mmpm. The residual stresses across these welds were measured using both x-ray and neutron diffraction techniques. The distribution and magnitude of the residual stresses agreed well between the two techniques. Longitudinal residual stresses up to eighty percent of the yield strength were observed for the 400 rpm/100 mmpm condition. The surface residual stresses were somewhat larger on the root side of the weld than on the crown side. Increases in the relative heat input during FSW decreased the measured residual stresses in the stir zone and the thermomechanically affected zone (TMAZ). Increasing the traverse rate while holding the rotational speed fixed increased the residual stress levels. The fatigue strength of the material is predicted to decrease by at least twenty percent with cracking most likely in the TMAZ.

High-speed infrared thermography for the measurement of microscopic boiling parameters on micro- and nano-structured surfaces

International Nuclear Information System (INIS)

Park, Youngjae; Kim, Hyungdae; Kim, Hyungmo; Kim, Joonwon

2014-01-01

Micro- and nano-scale structures on boiling surfaces can enhance nucleate boiling heat transfer coefficient (HTC) and critical heat flux (CHF). A few studies were conducted to explain the enhancements of HTC and CHF using the microscopic boiling parameters. Quantitative measurements of microscopic boiling parameters are needed to understand the physical mechanism of the boiling heat transfer augmentation on structured surfaces. However, there is no existing experimental techniques to conveniently measure the boiling parameters on the structured surfaces because of the small (structured surfaces. The visualization results are analyzed to obtain the microscopic boiling parameters. Finally, quantitative microscopic boiling parameters are used to interpret the enhancement of HTC and CHF. In this study, liquid-vapor phase distributions of each surface were clearly visualized by IR thermography during the nucleate boiling phenomena. From the visualization results, following microscopic boiling parameters were quantitatively measured by image processing. - Number density of dry patch, NDP IR thermography technique was demonstrated by nucleate pool boiling experiments with M- and N surfaces. The enhancement of HTC and CHF could be explained by microscopic boiling parameters

Effect of varying geometrical parameters of trapezoidal corrugated-core sandwich structure

Directory of Open Access Journals (Sweden)

Zaid N.Z.M.

2017-01-01

Full Text Available Sandwich structure is an attractive alternative that increasingly used in the transportation and aerospace industry. Corrugated-core with trapezoidal shape allows enhancing the damage resistance to the sandwich structure, but on the other hand, it changes the structural response of the sandwich structure. The aim of this paper is to study the effect of varying geometrical parameters of trapezoidal corrugated-core sandwich structure under compression loading. The corrugated-core specimen was fabricated using press technique, following the shape of trapezoidal shape. Two different materials were used in the study, glass fibre reinforced plastic (GFRP and carbon fibre reinforced plastic (CFRP. The result shows that the mechanical properties of the core in compression loading are sensitive to the variation of a number of unit cells and the core thickness.

Observation of the hot GDR in neutron-deficient thorium evaporation residues

International Nuclear Information System (INIS)

Seitz, J.P.; Back, B.B.; Carpenter, M.P.; Dioszegi, I.; Eisenman, K.; Heckman, P.; Hofman, D.J.; Kelly, M.P.; Khoo, T.L.; Mitsuoka, S.; Nanal, V.; Pennington, T.; Siemssen, R.H.; Thoennessen, M.; Varner, R.L.

2005-01-01

The giant dipole resonance built on excited states was observed in very fissile nuclei in coincidence with evaporation residues. The reaction 48 Ca+ 176 Yb populated evaporation residues of mass A=213-220 with a cross section of ∼200 μb at 259 MeV. The extracted giant dipole resonance parameters are in agreement with theoretical predictions for this mass region

Influence of choice of null network on small-world parameters of structural correlation networks.

Directory of Open Access Journals (Sweden)

S M Hadi Hosseini

Full Text Available In recent years, coordinated variations in brain morphology (e.g., volume, thickness have been employed as a measure of structural association between brain regions to infer large-scale structural correlation networks. Recent evidence suggests that brain networks constructed in this manner are inherently more clustered than random networks of the same size and degree. Thus, null networks constructed by randomizing topology are not a good choice for benchmarking small-world parameters of these networks. In the present report, we investigated the influence of choice of null networks on small-world parameters of gray matter correlation networks in healthy individuals and survivors of acute lymphoblastic leukemia. Three types of null networks were studied: 1 networks constructed by topology randomization (TOP, 2 networks matched to the distributional properties of the observed covariance matrix (HQS, and 3 networks generated from correlation of randomized input data (COR. The results revealed that the choice of null network not only influences the estimated small-world parameters, it also influences the results of between-group differences in small-world parameters. In addition, at higher network densities, the choice of null network influences the direction of group differences in network measures. Our data suggest that the choice of null network is quite crucial for interpretation of group differences in small-world parameters of structural correlation networks. We argue that none of the available null models is perfect for estimation of small-world parameters for correlation networks and the relative strengths and weaknesses of the selected model should be carefully considered with respect to obtained network measures.

Influence of Choice of Null Network on Small-World Parameters of Structural Correlation Networks

Science.gov (United States)

Hosseini, S. M. Hadi; Kesler, Shelli R.

2013-01-01

In recent years, coordinated variations in brain morphology (e.g., volume, thickness) have been employed as a measure of structural association between brain regions to infer large-scale structural correlation networks. Recent evidence suggests that brain networks constructed in this manner are inherently more clustered than random networks of the same size and degree. Thus, null networks constructed by randomizing topology are not a good choice for benchmarking small-world parameters of these networks. In the present report, we investigated the influence of choice of null networks on small-world parameters of gray matter correlation networks in healthy individuals and survivors of acute lymphoblastic leukemia. Three types of null networks were studied: 1) networks constructed by topology randomization (TOP), 2) networks matched to the distributional properties of the observed covariance matrix (HQS), and 3) networks generated from correlation of randomized input data (COR). The results revealed that the choice of null network not only influences the estimated small-world parameters, it also influences the results of between-group differences in small-world parameters. In addition, at higher network densities, the choice of null network influences the direction of group differences in network measures. Our data suggest that the choice of null network is quite crucial for interpretation of group differences in small-world parameters of structural correlation networks. We argue that none of the available null models is perfect for estimation of small-world parameters for correlation networks and the relative strengths and weaknesses of the selected model should be carefully considered with respect to obtained network measures. PMID:23840672

Microarchitecture Parameters Describe Bone Structure and Its Strength Better Than BMD

Directory of Open Access Journals (Sweden)

Tomasz Topoliński

2012-01-01

Full Text Available Introduction and Hypothesis. Some papers have shown that bone mineral density (BMD may not be accurate in predicting fracture risk. Recently microarchitecture parameters have been reported to give information on bone characteristics. The aim of this study was to find out if the values of volume, fractal dimension, and bone mineral density are correlated with bone strength. Methods. Forty-two human bone samples harvested during total hip replacement surgery were cut to cylindrical samples. The geometrical mesh of layers of bone mass obtained from microCT investigation and the volumes of each layer and fractal dimension were calculated. The finite element method was applied to calculate the compression force F causing ε=0.8% strain. Results. There were stronger correlations for microarchitecture parameters with strength than those for bone mineral density. The values of determination coefficient R2 for mean volume and force were 0.88 and 0.90 for mean fractal dimension and force, while for BMD and force the value was 0.53. The samples with bigger mean bone volume of layers and bigger mean fractal dimension of layers (more complex structure presented higher strength. Conclusion. The volumetric and fractal dimension parameters better describe bone structure and strength than BMD.

Safe structural food bolus in elderly: the relevant parameters

OpenAIRE

Vandenberghe-Descamps, Mathilde; Septier, Chantal; Prot, Aurélie; Tournier, Carole; Hennequin, Martine; Vigneau, Evelyne; Feron, Gilles; Labouré, Hélène

2017-01-01

Mastication is essential to prepare food into a bolus ready to be swallowed safely, with no choking risk. Based on food bolus properties, a masticatory normative indicator was developed by Woda et al. (2010) to identify impaired masticatory function within good oral health population. The aim of the present study was to identify relevant parameters of bolus' structure to differentiate safe to unsafe bolus among elderly contrasting by their dental status.93 elderly, 58% with at least 7 posteri...

Model structural uncertainty quantification and hydrologic parameter and prediction error analysis using airborne electromagnetic data

DEFF Research Database (Denmark)

Minsley, B. J.; Christensen, Nikolaj Kruse; Christensen, Steen

Model structure, or the spatial arrangement of subsurface lithological units, is fundamental to the hydrological behavior of Earth systems. Knowledge of geological model structure is critically important in order to make informed hydrological predictions and management decisions. Model structure...... is never perfectly known, however, and incorrect assumptions can be a significant source of error when making model predictions. We describe a systematic approach for quantifying model structural uncertainty that is based on the integration of sparse borehole observations and large-scale airborne...... electromagnetic (AEM) data. Our estimates of model structural uncertainty follow a Bayesian framework that accounts for both the uncertainties in geophysical parameter estimates given AEM data, and the uncertainties in the relationship between lithology and geophysical parameters. Using geostatistical sequential...

Estimating material parameters of a structurally based constitutive relation for skin mechanics

KAUST Repository

Jor, Jessica W. Y.

2010-11-25

This paper presents a structurally based modeling framework to characterize the structure-function relation in skin tissues, based upon biaxial tensile experiments performed in vitro on porcine skin. Equi-axial deformations were imposed by stretching circular skin specimens uniformly along twelve directions, and the resultant loads at the membrane attachment points were measured. Displacement fields at each deformation step were tracked using an image 2D cross-correlation technique. A modeling framework was developed to simulate the experiments, whereby measured forces were applied to finite element models that were created to represent the geometry and structure of the tissue samples. Parameters of a structurally based constitutive relation were then identified using nonlinear optimization. Results showed that the ground matrix stiffness ranged from 5 to 32 kPa, fiber orientation mean from 2 to 13. from the torso midline, fiber undulation mean from 1.04 to 1.34 and collagen fiber stiffness from 48 to 366 MPa. It was concluded that the objective function was highly sensitive to the mean orientation and that a priori information about fiber orientation mean was important for the reliable identification of constitutive parameters. © Springer-Verlag 2010.

Structural Parameters and Strengthening Mechanisms in Cold-Drawn Pearlitic Steel Wires

DEFF Research Database (Denmark)

Zhang, Xiaodan; Godfrey, Andy; Huang, Xiaoxu

2012-01-01

Pearlitic steel wires have a nanoscale structure and a strength which can reach 5 GPa. In order to investigate strengthening mechanisms, structural parameters including interlamellar spacing, dislocation density and cementite decomposition, have been analyzed by transmission electron microscopy...... and high resolution electron microscopy in wires cold drawn up to a strain of 3.7. Three strengthening mechanisms, namely boundary strengthening, dislocation strengthening and solid solution hardening have been analyzed and good agreement has been found between the measured flow stress and the value...

Influence of process parameters and biomass characteristics on the durability of pellets from the pruning residues of Olea europaea L.

Energy Technology Data Exchange (ETDEWEB)

Carone, Maria Teresa; Pantaleo, Antonio; Pellerano, Achille [Department of Engineering and Management of the Agricultural, Livestock and Forest Systems, Faculty of Agriculture, University of Bari, Via Amendola, 165/A, 70126 Bari (Italy)

2011-01-15

The present work aims to investigate the influence of the main process parameters (pressure and temperature) and biomass characteristics (moisture content and particle size) on some mechanical properties (density and durability) of olive tree pruning residues pellets. By means of a lab scale pellet press, able to control process parameters, the biomass, ground with three different hammer mill screen sizes (1, 2 and 4 mm) and conditioned at different moisture contents (5, 10, 15 and 20% w.b.), was pelletized at various process temperatures (60, 90, 120 and 150 C) and pressures (71, 106, 141 and 176 MPa). Compressed sample dimensions and mass were measured in order to calculate pellet density, while compressive strength tests were carried out to estimate the durability of the final biofuel. The relationships between the factor settings and the responses (density, compression strength and modulus of elasticity) were examined by univariate and multivariate statistical analysis. Temperature resulted the most important variable influencing pellet mechanical properties, followed by the initial moisture content and the particle size of the raw material. In particular, high process temperature, low moisture contents and reduced particle sizes allowed obtaining good quality pellets. The effect of compression force resulted scarcely relevant. (author)

Effectiveness of stress release geometries on reducing residual stress in electroforming metal microstructure

Science.gov (United States)

Song, Chang; Du, Liqun; Zhao, Wenjun; Zhu, Heqing; Zhao, Wen; Wang, Weitai

2018-04-01

Micro electroforming, as a mature micromachining technology, is widely used to fabricate metal microdevices in micro electro mechanical systems (MEMS). However, large residual stress in the local positions of the micro electroforming layer often leads to non-uniform residual stress distributions, dimension accuracy defects and reliability issues during fabrication of the metal microdevice. To solve this problem, a novel design method of presetting stress release geometries in the topological structure of the metal microstructure is proposed in this paper. First, the effect of stress release geometries (circular shape, annular groove shape and rivet shape) on the residual stress in the metal microstructure was investigated by finite element modeling (FEM) analysis. Two evaluation parameters, stress concentration factor K T and stress non-uniformity factor δ were calculated. The simulation results show that presetting stress release geometries can effectively reduce and homogenize the residual stress in the metal microstructures were measured metal microstructure. By combined use with stress release geometries of annular groove shape and rivet shape, the stress concentration factor K T and the stress non-uniformity factor δ both decreased at a maximum of 49% and 53%, respectively. Meanwhile, the average residual stress σ avg decreased at a maximum of 20% from  -292.4 MPa to  -232.6 MPa. Then, micro electroforming experiments were carried out corresponding to the simulation models. The residual stresses in the metal microstructures were measured by micro Raman spectroscopy (MRS) method. The results of the experiment proved that the stress non-uniformity factor δ and the average residual stress σ avg also decreased at a maximum with the combination use of annular groove shape and rivet shape stress release geometries, which is in agreement with the results of FEM analysis. The stress non-uniformity factor δ has a maximum decrease of 49% and the

Airborne-Measured Spatially-Averaged Temperature and Moisture Turbulent Structure Parameters Over a Heterogeneous Surface

Science.gov (United States)

Platis, Andreas; Martinez, Daniel; Bange, Jens

2014-05-01

Turbulent structure parameters of temperature and humidity can be derived from scintillometer measurements along horizontal paths of several 100 m to several 10 km. These parameters can be very useful to estimate the vertical turbulent heat fluxes at the surface (applying MOST). However, there are many assumptions required by this method which can be checked using in situ data, e.g. 1) Were CT2 and CQ2 correctly derived from the initial CN2 scintillometer data (structure parameter of density fluctuations or refraction index, respectively)? 2) What is the influence of the surround hetereogeneous surface regarding its footprint and the weighted averaging effect of the scintillometer method 3) Does MOST provide the correct turbulent fluxes from scintillometer data. To check these issues, in situ data from low-level flight measurements are well suited, since research aircraft cover horizontal distances in very short time (Taylor's hypothesis of a frozen turbulence structure can be applyed very likely). From airborne-measured time series the spatial series are calculated and then their structure functions that finally provide the structure parameters. The influence of the heterogeneous surface can be controlled by the definition of certain moving-average window sizes. A very useful instrument for this task are UAVs since they can fly very low and maintain altitude very precisely. However, the data base of such unmanned operations is still quite thin. So in this contribution we want to present turbulence data obtained with the Helipod, a turbulence probe hanging below a manned helicopter. The structure parameters of temperature and moisture, CT2 and CQ2, in the lower convective boundary layer were derived from data measured using the Helipod in 2003. The measurements were carried out during the LITFASS03 campaign over a heterogeneous land surface around the boundary-layer field site of the Lindenberg Meteorological Observatory-Richard-Aßmann-Observatory (MOL) of the

Residual stress in sprayed Ni+5%Al coatings determined by neutron diffraction

CERN Document Server

Matejicek, J; Gnaeupel-Herold, T; Prask, H J

2002-01-01

Coatings of nickel-based alloys are used in numerous high-performance applications. Their properties and lifetimes are influenced by factors such as residual stress. Neutron diffraction is a powerful tool for nondestructive residual stress determination. In this study, through-thickness residual stress profiles in Ni+5%Al coatings on steel substrates were determined. Two examples of significantly different spraying techniques - plasma spraying and cold spraying - are highlighted. Different stress-generation mechanisms are discussed with respect to process parameters and material properties. (orig.)

Order parameters in smectic liquid crystals

International Nuclear Information System (INIS)

Beldon, Stephen M.

2001-01-01

This thesis explores some of the important mechanisms for switching in smectic liquid crystals. It is mainly concerned with the interaction of the electric field and various order parameters in smectic phases. Distortion of these order parameters and also the layer structures associated with smectics are discussed in depth. Initial work is concentrated on the electroclinic effect of commercially available FLC mixtures, where experimental results suggest the presence of non-uniformity in the molecular director profile. Two possible models are suggested assuming a variation of the order parameter θ through the cell. The first model assumes that the smectic layers remain bookshelf-like, and the second that the layers tilt in a vertical chevron structure when a cone angle is induced electroclinically or otherwise. The latter model is the first 'order parameter' model of an electric field induced vertical chevron. The presence of non-uniformity in the director profile is sensed by a method similar to wavelength extinction spectroscopy. Investigations are undertaken on racemic smectic materials with high dielectric biaxiality. Modelling of such a material reveals a new electroclinic effect which shows a discrete second order phase transition on application of a field. It is suggested that a bistable electroclinic effect stabilised with a high frequency ac field may be realised if a residual polarisation is present in the high biaxiality material, and that this might be useful in the displays industry. Experimental investigations of such a material confirm the above effects close to the smectic A-C transition. Finally a higher order smectic phase, the smectic I* phase, is considered. The distortion of the hexagonal bond orientational order is investigated experimentally during application of an electric field. The first dynamic model of the switching process is presented, showing good agreement with the experimental results. It is suggested that the bond orientational

Challenges in parameter identification of large structural dynamic systems

International Nuclear Information System (INIS)

Koh, C.G.

2001-01-01

In theory, it is possible to determine the parameters of a structural or mechanical system by subjecting it to some dynamic excitation and measuring the response. Considerable research has been carried out in this subject area known as the system identification over the past two decades. Nevertheless, the challenges associated with numerical convergence are still formidable when the system is large in terms of the number of degrees of freedom and number of unknowns. While many methods work for small systems, the convergence becomes difficult, if not impossible, for large systems. In this keynote lecture, both classical and non-classical system identification methods for dynamic testing and vibration-based inspection are discussed. For classical methods, the extended Kalman filter (EKF) approach is used. On this basis, a substructural identification method has been developed as a strategy to deal with large structural systems. This is achieved by reducing the problem size, thereby significantly improving the numerical convergence and efficiency. Two versions of this method are presented each with its own merits. A numerical example of frame structure with 20 unknown parameters is illustrated. For non-classical methods, the Genetic Algorithm (GA) is shown to be applicable with relative ease due to its 'forward analysis' nature. The computational time is, however, still enormous for large structural systems due to the combinatorial explosion problem. A model GA method has been developed to address this problem and tested with considerable success on a relatively large system of 50 degrees of freedom, accounting for input and output noise effects. An advantages of this GA-based identification method is that the objective function can be defined in response measured. Numerical studies show that the method is relatively robust, as it does in response measured. Numerical studies show that the method is relatively robust, as it dos not require good initial guess and the

Homology modeling and docking analyses of M. leprae Mur ligases reveals the common binding residues for structure based drug designing to eradicate leprosy.

Science.gov (United States)

Shanmugam, Anusuya; Natarajan, Jeyakumar

2012-06-01

Multi drug resistance capacity for Mycobacterium leprae (MDR-Mle) demands the profound need for developing new anti-leprosy drugs. Since most of the drugs target a single enzyme, mutation in the active site renders the antibiotic ineffective. However, structural and mechanistic information on essential bacterial enzymes in a pathway could lead to the development of antibiotics that targets multiple enzymes. Peptidoglycan is an important component of the cell wall of M. leprae. The biosynthesis of bacterial peptidoglycan represents important targets for the development of new antibacterial drugs. Biosynthesis of peptidoglycan is a multi-step process that involves four key Mur ligase enzymes: MurC (EC:6.3.2.8), MurD (EC:6.3.2.9), MurE (EC:6.3.2.13) and MurF (EC:6.3.2.10). Hence in our work, we modeled the three-dimensional structure of the above Mur ligases using homology modeling method and analyzed its common binding features. The residues playing an important role in the catalytic activity of each of the Mur enzymes were predicted by docking these Mur ligases with their substrates and ATP. The conserved sequence motifs significant for ATP binding were predicted as the probable residues for structure based drug designing. Overall, the study was successful in listing significant and common binding residues of Mur enzymes in peptidoglycan pathway for multi targeted therapy.

RSARF: Prediction of residue solvent accessibility from protein sequence using random forest method

KAUST Repository

Ganesan, Pugalenthi; Kandaswamy, Krishna Kumar Umar; Chou -, Kuochen; Vivekanandan, Saravanan; Kolatkar, Prasanna R.

2012-01-01

Prediction of protein structure from its amino acid sequence is still a challenging problem. The complete physicochemical understanding of protein folding is essential for the accurate structure prediction. Knowledge of residue solvent accessibility gives useful insights into protein structure prediction and function prediction. In this work, we propose a random forest method, RSARF, to predict residue accessible surface area from protein sequence information. The training and testing was performed using 120 proteins containing 22006 residues. For each residue, buried and exposed state was computed using five thresholds (0%, 5%, 10%, 25%, and 50%). The prediction accuracy for 0%, 5%, 10%, 25%, and 50% thresholds are 72.9%, 78.25%, 78.12%, 77.57% and 72.07% respectively. Further, comparison of RSARF with other methods using a benchmark dataset containing 20 proteins shows that our approach is useful for prediction of residue solvent accessibility from protein sequence without using structural information. The RSARF program, datasets and supplementary data are available at http://caps.ncbs.res.in/download/pugal/RSARF/. - See more at: http://www.eurekaselect.com/89216/article#sthash.pwVGFUjq.dpuf

Disorder–order phase transformation in a fluorite-related oxide thin film: In-situ X-ray diffraction and modelling of the residual stress effects

International Nuclear Information System (INIS)

Gaboriaud, R.J.; Paumier, F.; Lacroix, B.

2016-01-01

This work is focused on the transformation of the disordered fluorite cubic-F phase to the ordered cubic-C bixbyite phase, induced by isothermal annealing as a function of the residual stresses resulting from different concentrations of microstructural defects in the yttrium oxide, Y_2O_3. This transformation was studied using in-situ X-ray diffraction and was modelled using Kolmogorov–Johnson–Mehl–Avrami (KJMA) analysis. The degree of the disorder of the oxygen network was associated with the residual stress, which was a key parameter for the stability and the kinetics of the transition of the different phases that were present in the thin oxide film. When the degree of disorder/residual stress level is high, this transition, which occurs at a rather low temperature (300 °C), is interpreted as a transformation of phases that occurs by a complete recrystallization via the nucleation and growth of a new cubic-C structure. Using the KJMA model, we determined the activation energy of the transformation process, which indicates that this transition occurs via a one-dimensional diffusion process. Thus, we present the analysis and modelling of the stress state. When the disorder/residual stress level was low, a transition to the quasi-perfect ordered cubic-C structure of the yttrium oxide appeared at a rather high temperature (800 °C), which is interpreted as a classic recovery mechanism of the cubic-C structure. - Highlights: • Rare earth oxide thin films • XRD analysis • Phase transformation modelling • Residual stress effects • Crystallographic phase stability

Disorder–order phase transformation in a fluorite-related oxide thin film: In-situ X-ray diffraction and modelling of the residual stress effects

Energy Technology Data Exchange (ETDEWEB)

Gaboriaud, R.J.; Paumier, F. [Institut Pprime, Department of Material Sciences, CNRS-University of Poitiers SP2MI-BP 30179, 86962 Futuroscope-Chasseneuil cedex (France); Lacroix, B. [CSIC, Institut de Ciencia de Materiales, University of Sevilla, Avenida Américo Vespucio, 49, 41092 Sevilla (Spain)

2016-02-29

This work is focused on the transformation of the disordered fluorite cubic-F phase to the ordered cubic-C bixbyite phase, induced by isothermal annealing as a function of the residual stresses resulting from different concentrations of microstructural defects in the yttrium oxide, Y{sub 2}O{sub 3}. This transformation was studied using in-situ X-ray diffraction and was modelled using Kolmogorov–Johnson–Mehl–Avrami (KJMA) analysis. The degree of the disorder of the oxygen network was associated with the residual stress, which was a key parameter for the stability and the kinetics of the transition of the different phases that were present in the thin oxide film. When the degree of disorder/residual stress level is high, this transition, which occurs at a rather low temperature (300 °C), is interpreted as a transformation of phases that occurs by a complete recrystallization via the nucleation and growth of a new cubic-C structure. Using the KJMA model, we determined the activation energy of the transformation process, which indicates that this transition occurs via a one-dimensional diffusion process. Thus, we present the analysis and modelling of the stress state. When the disorder/residual stress level was low, a transition to the quasi-perfect ordered cubic-C structure of the yttrium oxide appeared at a rather high temperature (800 °C), which is interpreted as a classic recovery mechanism of the cubic-C structure. - Highlights: • Rare earth oxide thin films • XRD analysis • Phase transformation modelling • Residual stress effects • Crystallographic phase stability.

Bifurcation Observation of Combining Spiral Gear Transmission Based on Parameter Domain Structure Analysis

Directory of Open Access Journals (Sweden)

He Lin

2016-01-01

Full Text Available This study considers the bifurcation evolutions for a combining spiral gear transmission through parameter domain structure analysis. The system nonlinear vibration equations are created with piecewise backlash and general errors. Gill’s numerical integration algorithm is implemented in calculating the vibration equation sets. Based on cell-mapping method (CMM, two-dimensional dynamic domain planes have been developed and primarily focused on the parameters of backlash, transmission error, mesh frequency and damping ratio, and so forth. Solution demonstrates that Period-doubling bifurcation happens as the mesh frequency increases; moreover nonlinear discontinuous jump breaks the periodic orbit and also turns the periodic state into chaos suddenly. In transmission error planes, three cell groups which are Period-1, Period-4, and Chaos have been observed, and the boundary cells are the sensitive areas to dynamic response. Considering the parameter planes which consist of damping ratio associated with backlash, transmission error, mesh stiffness, and external load, the solution domain structure reveals that the system step into chaos undergoes Period-doubling cascade with Period-2m (m: integer periodic regions. Direct simulations to obtain the bifurcation diagram and largest Lyapunov exponent (LE match satisfactorily with the parameter domain solutions.

Influence of MSD crack pattern on the residual strength of flat stiffened sheets

Science.gov (United States)

Nilsson, K.-F.

A parameter study of the residual strength for a multiple site damaged (MSD) stiffened sheet is presented. The analysis is based on an elastic-plastic fracture analysis using the yield-strip model for interaction between a lead crack and the smaller MSD cracks. Two crack growth criteria, one with a pronounced crack growth resistance and one with no crack growth resistance and five different MSD crack patterns, are analysed for different sizes of the lead crack and the smaller MSD cracks. The analysis indicates that the residual strength reduction depends on all these parameters and that MSD may totally erode the crack arrest capability of a tear strap. Another important outcome is that for certain combinations also very small MSD cracks may induce a significant residual strength reduction.

Mode analysis and structure parameter optimization of a novel SiGe-OI rib optical waveguide

Energy Technology Data Exchange (ETDEWEB)

Feng Song; Gao Yong; Yang Yuan [Department of Electronic Engineering, Xi' an University of Technology, Xi' an 710048 (China); Feng Yuchun, E-mail: vonfs@yahoo.com.c [Key Laboratories of Optoelectronic Devices and Systems, Shenzhen University, Shenzhen 518060 (China)

2009-08-15

The mode of a novel SiGe-OI optical waveguide is analyzed, and its single-mode conditions are derived. The Ge content and structure parameters of SiGe-OI optical waveguides are respectively optimized. Under an operation wavelength of 1300 nm, the structures of SiGe-OI rib optical waveguides are built and analyzed with Optiwave software, and the optical field and transmission losses of the SiGe-OI rib optical waveguides are analyzed. The optimization results show that when the structure parameters H, h, W are respectively 500 nm, 250 nm, 500 nm and the Ge content is 5%, the total power loss of SiGe-OI rib waveguides is 0.3683 dB/cm considering the loss of radiation outside the waveguides and materials, which is less than the traditional value of 0.5 dB/cm. The analytical technique for SiGe-OI optical waveguides and structure parameters computed by this paper are proved to be accurate and computationally efficient compared with the beam propagation method (BPM) and the experimental results. (semiconductor devices)

Excitation of magnetic inhomogeneities in three-layer ferromagnetic structure with different parameters of the magnetic anisotropy and exchange

Energy Technology Data Exchange (ETDEWEB)

Ekomasov, E.G., E-mail: EkomasovEG@gmail.com [Bashkir State University, 32, Validy Str., Ufa, 450076 (Russian Federation); Murtazin, R.R. [Bashkir State University, 32, Validy Str., Ufa, 450076 (Russian Federation); Nazarov, V.N. [Institute of Molecule and Crystal Physics Ufa Research Centre of Russian Academy of Sciences, Prospekt Oktyabrya 151, Ufa, 450075 (Russian Federation)

2015-07-01

The generation and evolution of magnetic inhomogeneities, emerging in a thin flat layer with the parameters of the magnetic anisotropy and exchange interaction, with the parameters different from other two thick layers of the three-layer ferromagnetic structure, were investigated. The parameters ranges that determine the possibility of their existence were found. The possibility of the external magnetic field influence on the structure and dynamic properties of localized magnetic inhomogeneities was shown. - Highlights: • The generation of magnetic inhomogeneities in the three-layer ferromagnetic. • The influence of an external field on the parameters of magnetic inhomogeneities. • Numerical study of the structure and dynamics of magnetic inhomogeneities.

Free-Suspension Residual Flexibility Testing of Space Station Pathfinder: Comparison to Fixed-Base Results

Science.gov (United States)

Tinker, Michael L.

1998-01-01

Application of the free-suspension residual flexibility modal test method to the International Space Station Pathfinder structure is described. The Pathfinder, a large structure of the general size and weight of Space Station module elements, was also tested in a large fixed-base fixture to simulate Shuttle Orbiter payload constraints. After correlation of the Pathfinder finite element model to residual flexibility test data, the model was coupled to a fixture model, and constrained modes and frequencies were compared to fixed-base test. modes. The residual flexibility model compared very favorably to results of the fixed-base test. This is the first known direct comparison of free-suspension residual flexibility and fixed-base test results for a large structure. The model correlation approach used by the author for residual flexibility data is presented. Frequency response functions (FRF) for the regions of the structure that interface with the environment (a test fixture or another structure) are shown to be the primary tools for model correlation that distinguish or characterize the residual flexibility approach. A number of critical issues related to use of the structure interface FRF for correlating the model are then identified and discussed, including (1) the requirement of prominent stiffness lines, (2) overcoming problems with measurement noise which makes the antiresonances or minima in the functions difficult to identify, and (3) the use of interface stiffness and lumped mass perturbations to bring the analytical responses into agreement with test data. It is shown that good comparison of analytical-to-experimental FRF is the key to obtaining good agreement of the residual flexibility values.

Influence analysis of structural parameters on electromagnetic properties of HTS linear induction motor

International Nuclear Information System (INIS)

Zhao, J.; Zheng, T.Q.; Zhang, W.; Fang, J.; Liu, Y.M.

2011-01-01

A new type high temperature superconductor linear induction motor is designed and analyzed as a prototype to ensure applicability aimed at industrial motors. Made of Bi-2223/Ag, primary windings are distributed with the double-layer concentrated structure. The motor is analyzed by 2D electromagnetic Finite Element Method to get magnetic field distribution, thrust force, vertical force and so on. The critical current of motor and the electromagnetic force are mostly decided by the leakage flux density of primary slot and by the main magnetic flux and eddy current respectively. The structural parameters of motor have a great influence on the distribution of magnetic field. Under constant currents, the properties of motor are analyzed with different slot widths, slot heights and winding turns. The properties of motor, such as the maximum slot leakage flux density, motor thrust and motor vertical force, are analyzed with different structural parameters.

Stresses and residual stresses optical measurements systems evaluation; Avaliacao de sistemas opticos de medicao de tensoes e tensoes residuais em dutos

Energy Technology Data Exchange (ETDEWEB)

Peixoto Filho, Flavio Tito; Goncalves Junior, Armando Albertazzi [Universidade Federal de Santa Catarina (UFSC), Florianopolis, SC (Brazil). Lab. de Metrologia e Automatizacao (LABMETRO)

2004-07-01

There is always a constant concern about the pipelines' integrity. An important control parameter is the level of total mechanical stresses acting over the pipeline. However, the loading and residual stresses acting on a pipeline are not measured in the field as much as necessary. Technical difficulties and the high cost of the nowadays techniques and the hostile measurement conditions are the main reason for that. An alternative method has been developed at the Universidade Federal de Santa Catarina (UFSC) since 1992. A new optical measurement device is used to measure strains, mechanical stresses and residual stresses acting over the structure. A metrological and functional evaluation of this system is the main focus of this paper. (author)

CHARACTERIZING RESIDUE TRANSFER EFFICIENCIES USING A FLUORESCENT IMAGING TECHNIQUE

Science.gov (United States)

To reduce the uncertainty associated with current estimates of children's exposure to pesticides by dermal contact and indirect ingestion, residue transfer data are required. Prior to conducting exhaustive studies, a screening study to identify the important parameters for chara...

Monitoring early hydration of reinforced concrete structures using structural parameters identified by piezo sensors via electromechanical impedance technique

Science.gov (United States)

Talakokula, Visalakshi; Bhalla, Suresh; Gupta, Ashok

2018-01-01

Concrete is the most widely used material in civil engineering construction. Its life begins when the hydration process is activated after mixing the cement granulates with water. In this paper, a non-dimensional hydration parameter, obtained from piezoelectric ceramic (PZT) patches bonded to rebars embedded inside concrete, is employed to monitor the early age hydration of concrete. The non-dimensional hydration parameter is derived from the equivalent stiffness determined from the piezo-impedance transducers using the electro-mechanical impedance (EMI) technique. The focus of the study is to monitor the hydration process of cementitious materials commencing from the early hours and continue till 28 days using single non-dimensional parameter. The experimental results show that the proposed piezo-based non-dimensional hydration parameter is very effective in monitoring the early age hydration, as it has been derived from the refined structural impedance parameters, obtained by eliminating the PZT contribution, and using both the real and imaginary components of the admittance signature.

Elimination of some unknown parameters and its effect on outlier detection

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Serif Hekimoglu

Full Text Available Outliers in observation set badly affect all the estimated unknown parameters and residuals, that is because outlier detection has a great importance for reliable estimation results. Tests for outliers (e.g. Baarda's and Pope's tests are frequently used to detect outliers in geodetic applications. In order to reduce the computational time, sometimes elimination of some unknown parameters, which are not of interest, is performed. In this case, although the estimated unknown parameters and residuals do not change, the cofactor matrix of the residuals and the redundancies of the observations change. In this study, the effects of the elimination of the unknown parameters on tests for outliers have been investigated. We have proved that the redundancies in initial functional model (IFM are smaller than the ones in reduced functional model (RFM where elimination is performed. To show this situation, a horizontal control network was simulated and then many experiences were performed. According to simulation results, tests for outlier in IFM are more reliable than the ones in RFM.

Effect of projectile structure on evaporation residue yields in incomplete fusion reactions

CERN Document Server

Babu, K S; Sudarshan, K; Shrivastava, B D; Goswami, A; Tomar, B S

2003-01-01

The excitation functions of heavy residues, representing complete and incomplete fusion products, produced in the reaction of sup 1 sup 2 C and sup 1 sup 3 C on sup 1 sup 8 sup 1 Ta have been measured over the projectile energy range of 5 to 6.5 MeV/nucleon by the recoil catcher method and off-line gamma-ray spectrometry. Comparison of the measured excitation functions with those calculated using the PACE2 code based on the statistical model revealed the occurrence of incomplete fusion reactions in the formation of alpha emission products. The fraction of incomplete fusion cross sections in the sup 1 sup 2 C + sup 1 sup 8 sup 1 Ta reaction was found to be higher, by a factor of approx 2, than that in the sup 1 sup 3 C + sup 1 sup 8 sup 1 Ta reaction. The results have been discussed in terms of the effect of alpha cluster structure of the projectile on incomplete fusion reactions.

Alkaline and Organosolv Lignins from Furfural Residue: Structural Features and Antioxidant Activity

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Xue-Fei Cao

2013-12-01

Full Text Available Furfural residue (FR, composed mainly of cellulose and lignin, is an industrial waste produced during furfural manufacture. In this study, dioxane, alkali, ethanol, alkali-ethanol, and alkaline hydrogen peroxide (AHP were used to extract lignins from FR. The structural features of these lignins obtained were characterized by sugar analysis, GPC, UV, FT-IR, and HSQC spectra. As compared to dioxane lignin (DL, other lignins showed lower molecular weights (Mw owing to the partial cleavage of the linkages between lignin units. Results from HSQC spectra revealed that β-O-4' and β-5' were still the major linkages of the FR lignin. Moreover, p-coumaric and ferulic acids were released and co-precipitated in the lignin preparations extracted with alkali and AHP, whereas part of the esters in DL were preserved during the dioxane extraction. Antioxidant activity investigation indicated that the antioxidant property of the alkali and alkali-ethanol lignins was higher than that of the commercial antioxidant, butylated hydroxytoluene.

Neutron diffraction measurements of residual stress in additively manufactured stainless steel

International Nuclear Information System (INIS)

Brown, D.W.; Bernardin, J.D.; Carpenter, J.S.; Clausen, B.; Spernjak, D.; Thompson, J.M.

2016-01-01

Charpy test specimens were additively manufactured (AM) on a single stainless steel plate from a 17–4 class stainless steel using a powder-bed, laser melting technique on an EOS M280 direct metal laser sintering (DMLS) machine. Cross-hatched mesh support structures for the Charpy test specimens were varied in strut width and density to parametrically study their influence on the build stability and accuracy as the DMLS process has been known to generate parts with large amounts of residual stress. Neutron diffraction was used to profile the residual stresses in several of the AM samples before and after the samples were removed from the support structure for the purpose of determining residual stresses. The residual stresses were found to depend very little on the properties of the support structure over the limited range studied here. The largest stress component was in the long direction of each of the samples studied and was roughly 2/3 of the yield stress of the material. The stress field was altered considerably when the specimen was removed from the support structure. It was noted in this study that a single Charpy specimen developed a significant tear between the growth plate and support structure. The presence of the tear in the support structure strongly affected the observed stress field: the asymmetric tear resulted in a significantly asymmetric stress field that propagated through removal of the sample from the base plate. The altered final residual stress state of the sample as well as its observed final shape indicates that the tear initiated during the build and developed without disrupting the fabrication process, suggesting a need for in-situ monitoring.

Neutron diffraction measurements of residual stress in additively manufactured stainless steel

Energy Technology Data Exchange (ETDEWEB)

Brown, D.W.; Bernardin, J.D.; Carpenter, J.S.; Clausen, B.; Spernjak, D.; Thompson, J.M.

2016-12-15

Charpy test specimens were additively manufactured (AM) on a single stainless steel plate from a 17–4 class stainless steel using a powder-bed, laser melting technique on an EOS M280 direct metal laser sintering (DMLS) machine. Cross-hatched mesh support structures for the Charpy test specimens were varied in strut width and density to parametrically study their influence on the build stability and accuracy as the DMLS process has been known to generate parts with large amounts of residual stress. Neutron diffraction was used to profile the residual stresses in several of the AM samples before and after the samples were removed from the support structure for the purpose of determining residual stresses. The residual stresses were found to depend very little on the properties of the support structure over the limited range studied here. The largest stress component was in the long direction of each of the samples studied and was roughly 2/3 of the yield stress of the material. The stress field was altered considerably when the specimen was removed from the support structure. It was noted in this study that a single Charpy specimen developed a significant tear between the growth plate and support structure. The presence of the tear in the support structure strongly affected the observed stress field: the asymmetric tear resulted in a significantly asymmetric stress field that propagated through removal of the sample from the base plate. The altered final residual stress state of the sample as well as its observed final shape indicates that the tear initiated during the build and developed without disrupting the fabrication process, suggesting a need for in-situ monitoring.

PSAIA – Protein Structure and Interaction Analyzer

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Vlahoviček Kristian

2008-04-01

Full Text Available Abstract Background PSAIA (Protein Structure and Interaction Analyzer was developed to compute geometric parameters for large sets of protein structures in order to predict and investigate protein-protein interaction sites. Results In addition to most relevant established algorithms, PSAIA offers a new method PIADA (Protein Interaction Atom Distance Algorithm for the determination of residue interaction pairs. We found that PIADA produced more satisfactory results than comparable algorithms implemented in PSAIA. Particular advantages of PSAIA include its capacity to combine different methods to detect the locations and types of interactions between residues and its ability, without any further automation steps, to handle large numbers of protein structures and complexes. Generally, the integration of a variety of methods enables PSAIA to offer easier automation of analysis and greater reliability of results. PSAIA can be used either via a graphical user interface or from the command-line. Results are generated in either tabular or XML format. Conclusion In a straightforward fashion and for large sets of protein structures, PSAIA enables the calculation of protein geometric parameters and the determination of location and type for protein-protein interaction sites. XML formatted output enables easy conversion of results to various formats suitable for statistic analysis. Results from smaller data sets demonstrated the influence of geometry on protein interaction sites. Comprehensive analysis of properties of large data sets lead to new information useful in the prediction of protein-protein interaction sites.

Genetic control of residual variance of yearling weight in Nellore beef cattle.

Science.gov (United States)

Iung, L H S; Neves, H H R; Mulder, H A; Carvalheiro, R

2017-04-01

There is evidence for genetic variability in residual variance of livestock traits, which offers the potential for selection for increased uniformity of production. Different statistical approaches have been employed to study this topic; however, little is known about the concordance between them. The aim of our study was to investigate the genetic heterogeneity of residual variance on yearling weight (YW; 291.15 ± 46.67) in a Nellore beef cattle population; to compare the results of the statistical approaches, the two-step approach and the double hierarchical generalized linear model (DHGLM); and to evaluate the effectiveness of power transformation to accommodate scale differences. The comparison was based on genetic parameters, accuracy of EBV for residual variance, and cross-validation to assess predictive performance of both approaches. A total of 194,628 yearling weight records from 625 sires were used in the analysis. The results supported the hypothesis of genetic heterogeneity of residual variance on YW in Nellore beef cattle and the opportunity of selection, measured through the genetic coefficient of variation of residual variance (0.10 to 0.12 for the two-step approach and 0.17 for DHGLM, using an untransformed data set). However, low estimates of genetic variance associated with positive genetic correlations between mean and residual variance (about 0.20 for two-step and 0.76 for DHGLM for an untransformed data set) limit the genetic response to selection for uniformity of production while simultaneously increasing YW itself. Moreover, large sire families are needed to obtain accurate estimates of genetic merit for residual variance, as indicated by the low heritability estimates (Box-Cox transformation was able to decrease the dependence of the variance on the mean and decreased the estimates of genetic parameters for residual variance. The transformation reduced but did not eliminate all the genetic heterogeneity of residual variance, highlighting

A Straight-Line Method for Analyzing Residual Drawdowns at an Observation Well

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Mesut Çimen

2015-01-01

Full Text Available Determination of the hydraulic parameters (transmissivity and storage coefficients of a confined aquifer is important for effective groundwater resources. For this purpose, the residual drawdowns have been in use to estimate the aquifer parameters by the classical Theis recovery method. The proposed method of this paper depends on a straight-line through the field data and it helps to calculate the parameters quickly without any need for long-term pumping data. It is based on the expansion series of the Theis well function by consideration of three terms, and this approach is valid for the dimensionless time factor u′=S′r2/4Tt′≤0.2. The method can be applied reliably to extensive and homogeneous confined aquifers resulting in different storage coefficients during the pumping and recovery periods S≠S′. It presents a strength methodology for the parameters decision making from the residual data in the groundwater field of civil engineering.

Residual biomass resources for energy production. Extended abstract

International Nuclear Information System (INIS)

Prevot, G.

2010-06-01

This report covers the whole problematic of energy production from biomass residues in France except the production of biofuels. It is made of two parts. The first one gives an overview of the availability of residual biomass resources, The concept of residue (or waste) is placed in its economic and regulatory context (the major part of the resource cannot be considered as waste without any further potential use). The conditions of availability of the resource for each market segment are identified. The second part describes the conditions for the use of 5 different conversion options of these residues into energy. The logistics constraints for the procurement of the fuel and the intermediate operations to prepare it are briefly summarised. The objective was the identification of key issues in all relevant aspects, without giving too much emphasis to one of them at the expense of another one in order to avoid duplicating the frequent cases of facilities that do not meet environmental and economic targets because the designers of the system have not paid enough attention to a parameter of the system. (author)

Predicting DNA-binding proteins and binding residues by complex structure prediction and application to human proteome.

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Huiying Zhao

Full Text Available As more and more protein sequences are uncovered from increasingly inexpensive sequencing techniques, an urgent task is to find their functions. This work presents a highly reliable computational technique for predicting DNA-binding function at the level of protein-DNA complex structures, rather than low-resolution two-state prediction of DNA-binding as most existing techniques do. The method first predicts protein-DNA complex structure by utilizing the template-based structure prediction technique HHblits, followed by binding affinity prediction based on a knowledge-based energy function (Distance-scaled finite ideal-gas reference state for protein-DNA interactions. A leave-one-out cross validation of the method based on 179 DNA-binding and 3797 non-binding protein domains achieves a Matthews correlation coefficient (MCC of 0.77 with high precision (94% and high sensitivity (65%. We further found 51% sensitivity for 82 newly determined structures of DNA-binding proteins and 56% sensitivity for the human proteome. In addition, the method provides a reasonably accurate prediction of DNA-binding residues in proteins based on predicted DNA-binding complex structures. Its application to human proteome leads to more than 300 novel DNA-binding proteins; some of these predicted structures were validated by known structures of homologous proteins in APO forms. The method [SPOT-Seq (DNA] is available as an on-line server at http://sparks-lab.org.

Influence of residual composition on the structure and properties of extracellular matrix derived hydrogels.

Science.gov (United States)

Claudio-Rizo, Jesús A; Rangel-Argote, Magdalena; Castellano, Laura E; Delgado, Jorge; Mata-Mata, José L; Mendoza-Novelo, Birzabith

2017-10-01

In this work, hydrolysates of extracellular matrix (hECM) were obtained from rat tail tendon (TR), bovine Achilles tendon (TAB), porcine small intestinal submucosa (SIS) and bovine pericardium (PB), and they were polymerized to generate ECM hydrogels. The composition of hECM was evaluated by quantifying the content of sulphated glycosaminoglycans (sGAG), fibronectin and laminin. The polymerization process, structure, physicochemical properties, in vitro degradation and biocompatibility were studied and related to their composition. The results indicated that the hECM derived from SIS and PB were significantly richer in sGAG, fibronectin and laminin, than those derived from TAB and TR. These differences in hECM composition influenced the polymerization and the structural characteristics of the fibrillar gel network. Consequently, the swelling, mechanics and degradation of the hydrogels showed a direct relationship with the remaining composition. Moreover, the cytocompatibility and the secretion of transforming growth factor beta-1 (TGF-β1) by macrophages were enhanced in hydrogels with the highest residual content of ECM biomolecules. The results of this work evidenced the role of the ECM molecules remaining after both decellularization and hydrolysis steps to produce tissue derived hydrogels with structure and properties tailored to enhance their performance in tissue engineering and regenerative medicine applications. Copyright © 2017 Elsevier B.V. All rights reserved.

Strain concentration at structural discontinuities and its quantification by elastic follow-up parameter

International Nuclear Information System (INIS)

Kasahara, Naoto; Takasho, Hideki

1998-12-01

Elevated temperature structural design codes pay attention to strain concentration at structural discontinuities due to creep and plasticity, since it causes to enlarge creep-fatigue damage of material. One of the difficulties to predict strain concentration is its dependency on loading, constitutive equations, and relaxation time. This study investigated fundamental mechanism of strain concentration and its main factors. It was clarified that strain concentration was caused from strain redistribution between elastic and inelastic regions, which can be quantified by the elastic follow-up parameter. As a function of inelastic strain, the elastic follow-up parameter can describe variation of strain concentration during incremental loading and relaxation process, caused by transition of strain distribution from peak strain concentration to secondary stress redistribution. Structures have their own elastic follow-up characteristics as a function of inelastic strain, which is insensitive to constitutive equations. It means that application of inelastic analysis is not difficult to obtain elastic follow-up characteristics. (author)

Control of residual carbon concentration in GaN high electron mobility transistor and realization of high-resistance GaN grown by metal-organic chemical vapor deposition

Energy Technology Data Exchange (ETDEWEB)

He, X.G. [State Key Laboratory on Integrated Optoelectronics, Institute of Semiconductors, Chinese Academy of Sciences, P.O. Box 912, Beijing 100083 (China); Zhao, D.G., E-mail: dgzhao@red.semi.ac.cn [State Key Laboratory on Integrated Optoelectronics, Institute of Semiconductors, Chinese Academy of Sciences, P.O. Box 912, Beijing 100083 (China); Jiang, D.S.; Liu, Z.S.; Chen, P.; Le, L.C.; Yang, J.; Li, X.J. [State Key Laboratory on Integrated Optoelectronics, Institute of Semiconductors, Chinese Academy of Sciences, P.O. Box 912, Beijing 100083 (China); Zhang, S.M.; Zhu, J.J.; Wang, H.; Yang, H. [Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, Suzhou 215125 (China)

2014-08-01

GaN films were grown by metal-organic chemical vapor deposition (MOCVD) under various growth conditions. The influences of MOCVD growth parameters, i.e., growth pressure, ammonia (NH{sub 3}) flux, growth temperature, trimethyl-gallium flux and H{sub 2} flux, on residual carbon concentration ([C]) were systematically investigated. Secondary ion mass spectroscopy measurements show that [C] can be effectively modulated by growth conditions. Especially, it can increase by reducing growth pressure up to two orders of magnitude. High-resistance (HR) GaN epilayer with a resistivity over 1.0 × 10{sup 9} Ω·cm is achieved by reducing growth pressure. The mechanism of the formation of HR GaN epilayer is discussed. An Al{sub x}Ga{sub 1−x}N/GaN high electron mobility transistor structure with a HR GaN buffer layer and an additional low-carbon GaN channel layer is presented, exhibiting a high two dimensional electron gas mobility of 1815 cm{sup 2}/Vs. - Highlights: • Influence of MOCVD parameters on residual carbon concentration in GaN is studied. • GaN layer with a resistivity over 1 × 10{sup 9} Ω·cm is achieved by reducing growth pressure. • High electron mobility transistor (HEMT) structures were prepared. • Control of residual carbon content results in HEMT with high 2-D electron gas mobility.

Explicitly integrating parameter, input, and structure uncertainties into Bayesian Neural Networks for probabilistic hydrologic forecasting

KAUST Repository

Zhang, Xuesong

2011-11-01

Estimating uncertainty of hydrologic forecasting is valuable to water resources and other relevant decision making processes. Recently, Bayesian Neural Networks (BNNs) have been proved powerful tools for quantifying uncertainty of streamflow forecasting. In this study, we propose a Markov Chain Monte Carlo (MCMC) framework (BNN-PIS) to incorporate the uncertainties associated with parameters, inputs, and structures into BNNs. This framework allows the structure of the neural networks to change by removing or adding connections between neurons and enables scaling of input data by using rainfall multipliers. The results show that the new BNNs outperform BNNs that only consider uncertainties associated with parameters and model structures. Critical evaluation of posterior distribution of neural network weights, number of effective connections, rainfall multipliers, and hyper-parameters shows that the assumptions held in our BNNs are not well supported. Further understanding of characteristics of and interactions among different uncertainty sources is expected to enhance the application of neural networks for uncertainty analysis of hydrologic forecasting. © 2011 Elsevier B.V.

Moisture removal of paddy by agricultural residues: basic physical parameters and drying kinetics modeling

Directory of Open Access Journals (Sweden)

Saniso, E.

2007-05-01

Full Text Available The objectives of this research were to study basic physical parameters of three agricultural residues that could be used for prediction of paddy drying kinetics using desiccants, to investigate a suitable methodfor moisture reduction of fresh paddy using 3 absorbents, and to modify the drying model of Inoue et al. for determining the evolution of moisture transfer during the drying period. Rice husk, sago palm rachis andcoconut husk were used as moisture desiccants in these experiments. From the results, it was concluded that the apparent density of all adsorbents was a linear function of moisture content whilst an equilibriummoisture content equation following Hendersonís model gave the best fit to the experimental results. From studying the relationship between moisture ratio and drying time under the condition of drying temperaturesof 30, 50 and 70oC, air flow rate of 1.6 m/s and initial moisture content of absorbents of 15, 20 and 27% dry-basis, it was shown that the moisture ratio decreased when drying time increased. In addition, thethin-layer desiccant drying equation following of the Page model can appropriately explain the evolution of moisture content of paddy over the drying time. The diffusion coefficient of all absorbents, which was in therange of 1x10-8 to 6x10-8 m2/h, was relatively dependent on drying temperature and inversely related to drying time. The diffusivity of coconut husk had the highest value compared to the other absorbents.The simulating modified mathematical model to determine drying kinetics of paddy using absorption technique and the simulated results had good relation to the experimental results for all adsorbents.

The parameters controlling the strength of soil-steel structures

International Nuclear Information System (INIS)

Barkhordari, M. A.; Abdel-Sayed, G.

2001-01-01

The present paper examines the ultimate load carrying capacity of soil-steel structures taking into consideration the sequence of the developments of plastic hinges, their location, and their sustained plastic moment. Non-linear analysis has been conducted using a micro-computer program in which a structural model is applied with the soil replaced by normal and tangential springs acting at the nodal points of a polygon representing the conduit wall. A comparative study has been conducted for the parameters which affect the load carrying capacity of soil-steel structure, leading to the following conclusions: (1) the load carrying capacity of the composite structure is significantly affected by the shear stiffness (or friction) of the surrounding soil; (2) the conduit span may be used when calculating the buckling load rather than the local radius of the conduit wall; (3) circular arches with sector angle of less than 180 d eg have higher load carrying capacity than equivalent re-entrant arches, i.e. arches with sector angle of more than 180 d eg; (4) the buckling load of the conduit is slightly affected by the rigidity of the lower zone of the conduit wall; (5) eccentric application of the load has practically little effect on its load carrying capacity

Residual Defect Density in Random Disks Deposits.

Science.gov (United States)

Topic, Nikola; Pöschel, Thorsten; Gallas, Jason A C

2015-08-03

We investigate the residual distribution of structural defects in very tall packings of disks deposited randomly in large channels. By performing simulations involving the sedimentation of up to 50 × 10(9) particles we find all deposits to consistently show a non-zero residual density of defects obeying a characteristic power-law as a function of the channel width. This remarkable finding corrects the widespread belief that the density of defects should vanish algebraically with growing height. A non-zero residual density of defects implies a type of long-range spatial order in the packing, as opposed to only local ordering. In addition, we find deposits of particles to involve considerably less randomness than generally presumed.

Effects of high-speed homogenization and high-pressure homogenization on structure of tomato residue fibers.

Science.gov (United States)

Hua, Xiao; Xu, Shanan; Wang, Mingming; Chen, Ying; Yang, Hui; Yang, Ruijin

2017-10-01

Tomato residue fibers obtained after derosination and deproteinization were processed by high-speed homogenization (HSH) and high-pressure homogenization (HPH), and their effects on fiber structure was investigated, respectively. Characterizations including particle size distribution, SEM, TEM and XRD were performed. HSH could break raw fibers to small particles of around 60μm, while HPH could reshape fibers to build network structure. Microfibrils were released and their nanostructure consisting of elementary fibrils was observed by TEM. XRD patterns indicated both HSH and HPH could hardly alter the nanostructure of the fibers. Physicochemical properties including expansibility, WHC and OHC were determined. Both HSH and HPH could increase the soluble fiber content by about 8%, but HSH-HPH combined processing did not show better result. Acid (4mol/L HCl) was used in replacement of water medium and the acidic degradation of fibers could be promoted by high speed shearing or high pressure processing. Copyright © 2017 Elsevier Ltd. All rights reserved.

Crystal Structure of the Extended-Spectrum β-Lactamase PER-2 and Insights into the Role of Specific Residues in the Interaction with β-Lactams and β-Lactamase Inhibitors

Science.gov (United States)

Ruggiero, Melina; Kerff, Frédéric; Herman, Raphaël; Sapunaric, Frédéric; Galleni, Moreno; Gutkind, Gabriel; Charlier, Paulette; Sauvage, Eric

2014-01-01

PER-2 belongs to a small (7 members to date) group of extended-spectrum β-lactamases. It has 88% amino acid identity with PER-1 and both display high catalytic efficiencies toward most β-lactams. In this study, we determined the X-ray structure of PER-2 at 2.20 Å and evaluated the possible role of several residues in the structure and activity toward β-lactams and mechanism-based inhibitors. PER-2 is defined by the presence of a singular trans bond between residues 166 to 167, which generates an inverted Ω loop, an expanded fold of this domain that results in a wide active site cavity that allows for efficient hydrolysis of antibiotics like the oxyimino-cephalosporins, and a series of exclusive interactions between residues not frequently involved in the stabilization of the active site in other class A β-lactamases. PER β-lactamases might be included within a cluster of evolutionarily related enzymes harboring the conserved residues Asp136 and Asn179. Other signature residues that define these enzymes seem to be Gln69, Arg220, Thr237, and probably Arg/Lys240A (“A” indicates an insertion according to Ambler's scheme for residue numbering in PER β-lactamases), with structurally important roles in the stabilization of the active site and proper orientation of catalytic water molecules, among others. We propose, supported by simulated models of PER-2 in combination with different β-lactams, the presence of a hydrogen-bond network connecting Ser70-Gln69-water-Thr237-Arg220 that might be important for the proper activity and inhibition of the enzyme. Therefore, we expect that mutations occurring in these positions will have impacts on the overall hydrolytic behavior. PMID:25070104

Protein-protein docking with dynamic residue protonation states.

Directory of Open Access Journals (Sweden)

Krishna Praneeth Kilambi

2014-12-01

Full Text Available Protein-protein interactions depend on a host of environmental factors. Local pH conditions influence the interactions through the protonation states of the ionizable residues that can change upon binding. In this work, we present a pH-sensitive docking approach, pHDock, that can sample side-chain protonation states of five ionizable residues (Asp, Glu, His, Tyr, Lys on-the-fly during the docking simulation. pHDock produces successful local docking funnels in approximately half (79/161 the protein complexes, including 19 cases where standard RosettaDock fails. pHDock also performs better than the two control cases comprising docking at pH 7.0 or using fixed, predetermined protonation states. On average, the top-ranked pHDock structures have lower interface RMSDs and recover more native interface residue-residue contacts and hydrogen bonds compared to RosettaDock. Addition of backbone flexibility using a computationally-generated conformational ensemble further improves native contact and hydrogen bond recovery in the top-ranked structures. Although pHDock is designed to improve docking, it also successfully predicts a large pH-dependent binding affinity change in the Fc-FcRn complex, suggesting that it can be exploited to improve affinity predictions. The approaches in the study contribute to the goal of structural simulations of whole-cell protein-protein interactions including all the environmental factors, and they can be further expanded for pH-sensitive protein design.

Effects of induction heating parameters on controlling residual stress in intermediate size pipes

International Nuclear Information System (INIS)

Rybicki, E.F.; McGuire, P.A.

1981-01-01

Induction heating for stress improvement (IHSI) is a method for reducing the tensile weld induced stresses on the inner surfaces of the girth welded pipes. The process entails inductively heating the outside of a welded pipe while cooling the inner surface with flowing water. A 10-inch schedule 80 Type 304 stainless steel pipe was selected for this study. Residual stresses due to welding were first determined using a finite element computational model. 26 refs

Evaluation of Crops Sensitivity to Atrazine Soil Residual

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E Izadi

2012-02-01

Full Text Available Abstract In order to study the sensitivity of 9 crops to atrazine soil residual, two separate experiments were conducted in field and greenhouse conditions. First experiment was conducted in a field with treated soil by atrazine based on split plot and the results evaluated in greenhouse conditions. Treatments in the field experiment included two organic manure application rates (0 and 50 t/ha as main plots and 2 atrazine application rates (2 and 4 kg/ha atrazine a.i. as sob plots. After corn harvesting soil was sampled at 0-15 cm surface layer in each plots in 15 points, after mixing the samples. Wheat, barley, sugar beet, pea, lens and colza planted in pots at greenhouse. Second experiment conducted in greenhouse conditions for evaluation of atrazine soil residual in completely randomized design. Treatments included atrazine soil residual concentrations (0, 0.2, 0.5, 1, 5, 10 and 15 mg/kg soil and crops included wheat, barley, sugar beet, pea, lens, rape, bean and tomato. Results showed that atrazine residue had no effect on crops growth in field experiment treated with atrazine. It seems that atrazine residue in filed soil is lower that its damage threshold for crops or maybe for its fast removal in field than in control conditions. But in bioassay experiment (greenhouse experiment crops response to atrazine residues were different. Results showed that onion and pea were most susceptible ant tolerant crops between studied species and based of ED50 parameter the other crops tolerance to total residue ranked as: pea< bean< lentil< sugar beet< tomato< barley< wheat< rape< onion. Keywords: Atrazine residue, Pea, Bean, Lentil, Sugar beet, Barley, Wheat, Rape, Tomato

Effects of Bio-char on Soil Microbes in Herbicide Residual Soils

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WANG Gen-lin

2015-10-01

Full Text Available Effects of biological carbon (bio-char on soil microbial community were studied by pot experiments simulating long residual herbicide residues in soil environment, which clarifed the improvement of biochar and its structural properties on soil microenvironment. The results showed that fungi and actinomycetes had the same effect tendency within 0~0.72 mg·kg-1 in clomazone residue which increased the role of stimulation with crop growth process prolonged, especially in high residue treatment, but strong inhibitory effect on bacteria community was occured early which returned to normal until sugar beet growth to fiftieth day. Soil fungi community decreased with bio-char adding, but had no significant difference with the control. When clomazone residue in soil was below 0.24 mg·kg-1, soil actinomycetes community was higher than control without bio-char, bacteria increased first and then reduced after adding carbon as below 0.12 mg·kg-1. Biochar was ‘deep hole’ structure containing C, O, S and other elements. The results showed that a certain concentration clomazone residue in soil would stimulate soil fungi and actinomycetes to grow. After adding the biochar, the inhibition effect of high herbicides residual on bacterial would be alleviated.

Absence of residual structure in the intrinsically disordered regulatory protein CP12 in its reduced state

Energy Technology Data Exchange (ETDEWEB)

Launay, Hélène; Barré, Patrick [Laboratory of integrative Structural and Chemical Biology (iSCB), Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS UMR 7258, INSERM U 1068, Institut Paoli-Calmettes, Aix-Marseille Universités, Marseille 13009 (France); Puppo, Carine [Aix-Marseille Université, Centre National de la Recherche Scientifique, UMR 7281, Laboratoire de Bioénergétique et Ingénierie des Protéines, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20 (France); Manneville, Stéphanie [Laboratory of integrative Structural and Chemical Biology (iSCB), Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS UMR 7258, INSERM U 1068, Institut Paoli-Calmettes, Aix-Marseille Universités, Marseille 13009 (France); Gontero, Brigitte [Aix-Marseille Université, Centre National de la Recherche Scientifique, UMR 7281, Laboratoire de Bioénergétique et Ingénierie des Protéines, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20 (France); Receveur-Bréchot, Véronique, E-mail: veronique.brechot@inserm.fr [Laboratory of integrative Structural and Chemical Biology (iSCB), Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS UMR 7258, INSERM U 1068, Institut Paoli-Calmettes, Aix-Marseille Universités, Marseille 13009 (France)

2016-08-12

The redox switch protein CP12 is a key player of the regulation of the Benson–Calvin cycle. Its oxidation state is controlled by the formation/dissociation of two intramolecular disulphide bridges during the day/night cycle. CP12 was known to be globally intrinsically disordered on a large scale in its reduced state, while being partly ordered in the oxidised state. By combining Nuclear Magnetic Resonance and Small Angle X-ray Scattering experiments, we showed that, contrary to secondary structure or disorder predictions, reduced CP12 is fully disordered, with no transient or local residual structure likely to be precursor of the structures identified in the oxidised active state and/or in the bound state with GAPDH or PRK. These results highlight the diversity of the mechanisms of regulation of conditionally disordered redox switches, and question the stability of oxidised CP12 scaffold. - Highlights: • CP12 is predicted to form two helices in its N-terminal sequence. • Reduced CP12 is disordered as a random coil according to SAXS. • Limited or no transient structures are observed in reduced CP12 by NMR.

Absence of residual structure in the intrinsically disordered regulatory protein CP12 in its reduced state

International Nuclear Information System (INIS)

Launay, Hélène; Barré, Patrick; Puppo, Carine; Manneville, Stéphanie; Gontero, Brigitte; Receveur-Bréchot, Véronique

2016-01-01

The redox switch protein CP12 is a key player of the regulation of the Benson–Calvin cycle. Its oxidation state is controlled by the formation/dissociation of two intramolecular disulphide bridges during the day/night cycle. CP12 was known to be globally intrinsically disordered on a large scale in its reduced state, while being partly ordered in the oxidised state. By combining Nuclear Magnetic Resonance and Small Angle X-ray Scattering experiments, we showed that, contrary to secondary structure or disorder predictions, reduced CP12 is fully disordered, with no transient or local residual structure likely to be precursor of the structures identified in the oxidised active state and/or in the bound state with GAPDH or PRK. These results highlight the diversity of the mechanisms of regulation of conditionally disordered redox switches, and question the stability of oxidised CP12 scaffold. - Highlights: • CP12 is predicted to form two helices in its N-terminal sequence. • Reduced CP12 is disordered as a random coil according to SAXS. • Limited or no transient structures are observed in reduced CP12 by NMR.

Residual stress analysis of a multi-layer thin film structure by destructive (curvature) and non-destructive (x-ray) methods

International Nuclear Information System (INIS)

Chen, P.C.; Oshida, Y.

1989-01-01

Multi-layer thin film which has structure of Cu/Cr/K/Cr/Cu prepared by sputtering process was analyzed for interfacial stresses for as-deposited conditions. This structure was also annealed at 150 degrees C, and 350 degrees C for around 15 min. in a vacuum and cooled slowly down for stress analyses. Equations for residual stress estimations for homogeneous material system using layer removal technique (stress relief) is now applied for inhomogeneous system (multi-layer structure). The results are compared with the data obtained from x-ray diffraction technique by using sin 2 Ψ - 2 θ method, for Cu layer. From the present analyses, the data obtained using layer removal seem to be qualitatively consistent with but not quantitatively in agreement with x-ray method

MyPMFs: a simple tool for creating statistical potentials to assess protein structural models.

Science.gov (United States)

Postic, Guillaume; Hamelryck, Thomas; Chomilier, Jacques; Stratmann, Dirk

2018-05-29

Evaluating the model quality of protein structures that evolve in environments with particular physicochemical properties requires scoring functions that are adapted to their specific residue compositions and/or structural characteristics. Thus, computational methods developed for structures from the cytosol cannot work properly on membrane or secreted proteins. Here, we present MyPMFs, an easy-to-use tool that allows users to train statistical potentials of mean force (PMFs) on the protein structures of their choice, with all parameters being adjustable. We demonstrate its use by creating an accurate statistical potential for transmembrane protein domains. We also show its usefulness to study the influence of the physical environment on residue interactions within protein structures. Our open-source software is freely available for download at https://github.com/bibip-impmc/mypmfs. Copyright © 2018. Published by Elsevier B.V.

Determination of the Nonlinearity Parameter in the TNM Model of Structural Recovery

Science.gov (United States)

Bari, Rozana; Simon, Sindee

Structural recovery of non-equilibrium glassy materials takes place by evolution of volume and enthalpy as the glass attempts to reach to equilibrium. Structural recovery is nonlinear, nonexponential, and depends on thermal history and the process can be described by phenomenological models of structural recovery, such as the Tool-Narayanaswamy-Moynihan (TNM) and the Kovacs-Aklonis-Hutchinson-Ramos (KAHR) models. The goal of the present work is to analyze methods to determine the nonlinearity parameter x and activation energy Δh/R. The methods to determine x includes the inflectional analysis, time-temperature superposition, and two-step temperature jump methods. The activation energy Δh/R can also be obtained by the first two methods. The TNM model is used to simulate structural recovery data, which are then used to test the accuracy of the methods to determine x and Δh/R, with a particular interest in data obtained after cooling at high rates as can be obtained in the Flash DSC. The nonlinearity parameter x by the inflectional analysis and two-step temperature methods are accurate for exponential recovery. However, for real systems with nonexponential relaxation, methods to determine x are not reliable. The activation energy is well estimated by both the time-temperature superposition and inflectional analysis methods, with the former being slightly better.

Order parameters in smectic liquid crystals[Smectics

Energy Technology Data Exchange (ETDEWEB)

Beldon, Stephen M

2001-07-01

This thesis explores some of the important mechanisms for switching in smectic liquid crystals. It is mainly concerned with the interaction of the electric field and various order parameters in smectic phases. Distortion of these order parameters and also the layer structures associated with smectics are discussed in depth. Initial work is concentrated on the electroclinic effect of commercially available FLC mixtures, where experimental results suggest the presence of non-uniformity in the molecular director profile. Two possible models are suggested assuming a variation of the order parameter {theta} through the cell. The first model assumes that the smectic layers remain bookshelf-like, and the second that the layers tilt in a vertical chevron structure when a cone angle is induced electroclinically or otherwise. The latter model is the first 'order parameter' model of an electric field induced vertical chevron. The presence of non-uniformity in the director profile is sensed by a method similar to wavelength extinction spectroscopy. Investigations are undertaken on racemic smectic materials with high dielectric biaxiality. Modelling of such a material reveals a new electroclinic effect which shows a discrete second order phase transition on application of a field. It is suggested that a bistable electroclinic effect stabilised with a high frequency ac field may be realised if a residual polarisation is present in the high biaxiality material, and that this might be useful in the displays industry. Experimental investigations of such a material confirm the above effects close to the smectic A-C transition. Finally a higher order smectic phase, the smectic I* phase, is considered. The distortion of the hexagonal bond orientational order is investigated experimentally during application of an electric field. The first dynamic model of the switching process is presented, showing good agreement with the experimental results. It is suggested that the bond

VMD-SS: A graphical user interface plug-in to calculate the protein secondary structure in VMD program.

Science.gov (United States)

Yahyavi, Masoumeh; Falsafi-Zadeh, Sajad; Karimi, Zahra; Kalatarian, Giti; Galehdari, Hamid

2014-01-01

The investigation on the types of secondary structure (SS) of a protein is important. The evolution of secondary structures during molecular dynamics simulations is a useful parameter to analyze protein structures. Therefore, it is of interest to describe VMD-SS (a software program) for the identification of secondary structure elements and its trajectories during simulation for known structures available at the Protein Data Bank (PDB). The program helps to calculate (1) percentage SS, (2) SS occurrence in each residue, (3) percentage SS during simulation, and (4) percentage residues in all SS types during simulation. The VMD-SS plug-in was designed using TCL script and stride to calculate secondary structure features. The database is available for free at http://science.scu.ac.ir/HomePage.aspx?TabID=13755.

The formation of a native-like structure containing eight conserved hydrophobic residues is rate limiting in two-state protein folding of ACBP

DEFF Research Database (Denmark)

Kragelund, Birthe Brandt; Osmark, Peter; Neergaard, Thomas B.

1999-01-01

The acyl-coenzyme A-binding proteins (ACBPs) contain 26 highly conserved sequence positions. The majority of these have been mutated in the bovine protein, and their influence on the rate of two-state folding and unfolding has been measured. The results identify eight sequence positions, out of 24...... probed, that are critical for fast productive folding. The residues are all hydrophobic and located in the interface between the N- and C-terminal helices. The results suggest that one specific site dominated by conserved hydrophobic residues forms the structure of the productive rate-determining folding...... step and that a sequential framework model can describe the protein folding reaction....

Embrittling effects of residual elements on steels

International Nuclear Information System (INIS)

Brear, J.M.; King, B.L.

1979-01-01

In a review of work related to reheat cracking in nuclear pressure vessel steels, Dhooge et al referred to work of the authors on the relative embrittling parameter for SA533B steels. The poor agreement when these parameters were applied to creep ductility data for SA508 class 2 lead the reviewers to conclude that the relative importance of impurity elements is a function of base alloy composition. The authors briefly describe some of their more recent work which demonstrates that when various mechanical, and other, effects are taken into consideration, the relative effects of the principal residual elements are similar, despite differing base compositions, and that the embrittling parameters derived correlate well with the data for SA Class 2 steel. (U.K.)

Crop residue decomposition, residual soil organic matter and nitrogen mineralization in arable soils with contrasting textures

NARCIS (Netherlands)

Matus, F.J.

1994-01-01

To evaluate the significance of cropping, soil texture and soil structure for the decomposition of ¹⁴C- and ¹⁵N-labelled crop residues, a study was conducted in a sand and a

Detection of secondary structure elements in proteins by hydrophobic cluster analysis.

Science.gov (United States)

Woodcock, S; Mornon, J P; Henrissat, B

1992-10-01

Hydrophobic cluster analysis (HCA) is a protein sequence comparison method based on alpha-helical representations of the sequences where the size, shape and orientation of the clusters of hydrophobic residues are primarily compared. The effectiveness of HCA has been suggested to originate from its potential ability to focus on the residues forming the hydrophobic core of globular proteins. We have addressed the robustness of the bidimensional representation used for HCA in its ability to detect the regular secondary structure elements of proteins. Various parameters have been studied such as those governing cluster size and limits, the hydrophobic residues constituting the clusters as well as the potential shift of the cluster positions with respect to the position of the regular secondary structure elements. The following results have been found to support the alpha-helical bidimensional representation used in HCA: (i) there is a positive correlation (clearly above background noise) between the hydrophobic clusters and the regular secondary structure elements in proteins; (ii) the hydrophobic clusters are centred on the regular secondary structure elements; (iii) the pitch of the helical representation which gives the best correspondence is that of an alpha-helix. The correspondence between hydrophobic clusters and regular secondary structure elements suggests a way to implement variable gap penalties during the automatic alignment of protein sequences.

Prediction of the residual strength of clay using functional networks

Directory of Open Access Journals (Sweden)

S.Z. Khan

2016-01-01

Full Text Available Landslides are common natural hazards occurring in most parts of the world and have considerable adverse economic effects. Residual shear strength of clay is one of the most important factors in the determination of stability of slopes or landslides. This effect is more pronounced in sensitive clays which show large changes in shear strength from peak to residual states. This study analyses the prediction of the residual strength of clay based on a new prediction model, functional networks (FN using data available in the literature. The performance of FN was compared with support vector machine (SVM and artificial neural network (ANN based on statistical parameters like correlation coefficient (R, Nash--Sutcliff coefficient of efficiency (E, absolute average error (AAE, maximum average error (MAE and root mean square error (RMSE. Based on R and E parameters, FN is found to be a better prediction tool than ANN for the given data. However, the R and E values for FN are less than SVM. A prediction equation is presented that can be used by practicing geotechnical engineers. A sensitivity analysis is carried out to ascertain the importance of various inputs in the prediction of the output.

Laser shock peening of Ti-17 titanium alloy: Influence of process parameters

Energy Technology Data Exchange (ETDEWEB)

Cellard, C.; Retraint, D.; Francois, M. [University of Technology of Troyes (UTT), Charles Delaunay Institute, LASMIS, UMR CNRS 6279, 12 Rue Marie Curie, BP2060, 10010 Troyes Cedex (France); Rouhaud, E., E-mail: rouhaud@utt.fr [University of Technology of Troyes (UTT), Charles Delaunay Institute, LASMIS, UMR CNRS 6279, 12 Rue Marie Curie, BP2060, 10010 Troyes Cedex (France); Le Saunier, D. [SNECMA Evry - Corbeil, Route Henry Auguste Desbrueres, 91003 Evry (France)

2012-01-15

Highlights: Black-Right-Pointing-Pointer Laser shock peening parameters studied through a design of experiments. Black-Right-Pointing-Pointer Laser fluence, pulse duration, number of impacts and sample thickness are studied. Black-Right-Pointing-Pointer The observed work hardening is low, the roughness is lightly affected. Black-Right-Pointing-Pointer A significant part of hardness increase is due to compressive residual stresses. Black-Right-Pointing-Pointer High tensile residual stresses can appear on thin laser shocked specimens. - Abstract: The influence of the process parameters of laser shock peening was investigated on specimens made of an aeronautic titanium alloy: Ti-5Al-2Sn-2Zr-4Cr-4Mo (Ti-17). In order to quantify the effect of relevant process parameters, an experimental design was carried out. It is based on a full factorial design with four factors (laser fluence, pulse duration, number of impacts and thickness of the sample) and two levels for each factor. The process is characterised with the following variables: the depth of the impacts, the roughness of the treated surface, the hardening of the material (itself evaluated with the hardness and X-ray diffraction peak width), the residual stresses left in the sample and the global curvature of the sample. It is found that all the parameters have an influence on the residual stresses and that laser shock peening has no influence on roughness and low influence on work-hardening. The variables are then analysed in order to evaluate correlations. The increase in hardness is found to be essentially due to compressive residual stresses, cold work-hardening having only a small effect. In thin specimens, the stress redistribution due to self-equilibrium leads to tensile residual stresses at the treated surface and to large deformations of the specimens.

Model-checking techniques based on cumulative residuals.

Science.gov (United States)

Lin, D Y; Wei, L J; Ying, Z

2002-03-01

Residuals have long been used for graphical and numerical examinations of the adequacy of regression models. Conventional residual analysis based on the plots of raw residuals or their smoothed curves is highly subjective, whereas most numerical goodness-of-fit tests provide little information about the nature of model misspecification. In this paper, we develop objective and informative model-checking techniques by taking the cumulative sums of residuals over certain coordinates (e.g., covariates or fitted values) or by considering some related aggregates of residuals, such as moving sums and moving averages. For a variety of statistical models and data structures, including generalized linear models with independent or dependent observations, the distributions of these stochastic processes tinder the assumed model can be approximated by the distributions of certain zero-mean Gaussian processes whose realizations can be easily generated by computer simulation. Each observed process can then be compared, both graphically and numerically, with a number of realizations from the Gaussian process. Such comparisons enable one to assess objectively whether a trend seen in a residual plot reflects model misspecification or natural variation. The proposed techniques are particularly useful in checking the functional form of a covariate and the link function. Illustrations with several medical studies are provided.

Synchronization of chaotic systems with parameter uncertainties via variable structure control

International Nuclear Information System (INIS)

Etemadi, Shahram; Alasty, Aria; Salarieh, Hassan

2006-01-01

The Letter introduces a robust control design method to synchronize a pair of different uncertain chaotic systems. The technique is based on sliding-mode and variable structure control theories. Comparison of proposed method with previous works is performed during simulations. It is shown that the proposed controller while appearing in a faster response, is able to overcome random uncertainties of all model parameters

Synchronization of chaotic systems with parameter uncertainties via variable structure control

Energy Technology Data Exchange (ETDEWEB)

Etemadi, Shahram [Centre of Excellence in Design, Robotics and Automation (CEDRA), School of Mechanical Engineering, Sharif University of Technology, Tehran (Iran, Islamic Republic of); Alasty, Aria [Centre of Excellence in Design, Robotics and Automation (CEDRA), School of Mechanical Engineering, Sharif University of Technology, Tehran (Iran, Islamic Republic of)]. E-mail: aalasti@sharif.edu; Salarieh, Hassan [Centre of Excellence in Design, Robotics and Automation (CEDRA), School of Mechanical Engineering, Sharif University of Technology, Tehran (Iran, Islamic Republic of)

2006-08-28

The Letter introduces a robust control design method to synchronize a pair of different uncertain chaotic systems. The technique is based on sliding-mode and variable structure control theories. Comparison of proposed method with previous works is performed during simulations. It is shown that the proposed controller while appearing in a faster response, is able to overcome random uncertainties of all model parameters.

Tailoring diffraction technique Rietveld method on residual stress measurements of cold-can oiled 304 stainless steel plates

International Nuclear Information System (INIS)

Parikin; Killen, P.; Anis, M.

2003-01-01

Tailoring of diffraction technique-Rietveld method on residual stress measurements of cold-canailed stainless steel 304 plates assuming the material is isotopic, the residual stress measurements using X-ray powder diffraction is just performed for a plane lying in a large angle. For anisotropic materials, the real measurements will not be represented by the methods. By Utilizing of all diffraction peaks in the observation region, tailoring diffraction technique-Rietveld analysis is able to cover the limitations. The residual stress measurement using X-ray powder diffraction tailored by Rietveld method, in a series of cold-canailed stainless steel 304 plates deforming; 0, 34, 84, 152, 158, 175, and 196 % reduction in thickness, have been reported. The diffraction data were analyzed by using Rietveld structure refinement method. Also, for all cold-canailed stainless steel 304 plates cuplikans, the diffraction peaks are broader than the uncanailed one, indicating that the strains in these cuplikans are inhomogeneous. From an analysis of the refined peak shape parameters, the average root-mean square strain, which describes the distribution of the inhomogeneous strain field, was calculated. Finally, the average residual stresses in cold-canailed stainless steel 304 plates were shown to be a combination effect of hydrostatic stresses of martensite particles and austenite matrix. The average residual stresses were evaluated from the experimentally determined average lattice strains in each phase. It was found the tensile residual stress in a cuplikan was maximum, reaching 442 MPa, for a cuplikan reducing 34% in thickness and minimum for a 196% cuplikan

A Study on Residual Stress Measurements by Using Laser Speckle Interferometry

International Nuclear Information System (INIS)

Rho, Kyung Wan; Kang, Young June; Hong, Seong Jin; Kang, Hyung Soo

1999-01-01

Residual stress is one of the causes which make defects in engineering components and materials. And interest in the measurement of residual stress exists in many industries. There are commonly used methods by which residual stresses are currently measured. But these methods have a little demerits: time consumption and other problems. Therefore we devised a new experimental technique to measure residual stress in materials with a combination of laser speckle pattern interferometry, finite element method and spot heating. The speckle pattern interferometer measures in-plane deformations while the heating provides for very localized stress relief. FEM is used for determining heat temperature and other parameters. The residual stresses are determined by the amount of strain that is measured subsequent to the heating and cool-down of the region being interrogated. A simple model is presented to provide a description of the method. In this paper, the ambiguity problem for the fringe patterns has solved by a phase shifting method

Effect of residual stress on the nanoindentation response of (100) copper single crystal

International Nuclear Information System (INIS)

Zhu, Li-na; Xu, Bin-shi; Wang, Hai-dou; Wang, Cheng-biao

2012-01-01

Experimental measurements were used to investigate the effect of residual stress on the nanoindentation of (100) copper single crystal. Equi-biaxial tensile and compressive stresses were applied to the copper single crystal using a special designed apparatus. It was found that residual stresses greatly affected peak load, curvature of the loading curve, elastically recovered depth, residual depth, indentation work, pile-up amount and contact area. The Suresh and Giannakopoulos and Lee and Kwon methods were used to calculate the residual stresses from load-depth data and morphology observation of nanoindents using atomic force microscopy. Comparison of the obtained results with stress values from strain gage showed that the residual stresses analyzed from the Suresh and Giannakopoulos model agreed well with the applied stresses. -- Highlights: ► Residual stresses greatly affected various nanoindentation parameters. ► The contact area can be accurately measured from AFM observation. ► The residual stresses analyzed from the S and G model agreed well with applied stresses.

Submillimeter residual losses in high-T_c superconductors

Energy Technology Data Exchange (ETDEWEB)

Miller, David [Univ. of California, Berkeley, CA (United States)

1993-09-01

Bolometry was used obtain accurate submillimeter residual loss data for epitaxial films of YBa₂Cu₃O₇ (YBCO), Tl₂Ca₂Ba₂Cu₃O₁₀, Tl₂CaBa₂Cu₂O₈ (TCBCO), and Ba_0.6K_0.4BiO₃ (BKBO). We were able to fit the absorptivity measured for Nb films to an Eliashberg strong coupling calculation; excellent agreement resulted between parameters from best fits and measured Residual Resistivity Ratio. Microwave surface resistance measurements made on the same YBCO and TCBCO films are in excellent agreement with submillimeter measurements. Absorptivities for all YBCO films studied are qualitatively similar, increasing smoothly with frequency, with no gap-like features below the well known absorption edge at 450 cm^-1. Losses in YBCO films were fit to a weakly coupled grain model for the a-b plane conductivity. Strong phonon structure was observed in TCBCO films between 60 and 700 cm^-1 (2 THz and 23 THz); these losses could not be fitted to the simple weakly coupled grain model, in contrast to the case for other high-T_c superconductors where phonon structure observed in ceramics are is absent in epitaxial oriented films and crystals because of electronic screening due to high conductivity of a-b planes. Absorptivity data for the BKBO films all show a strong absorption onset near the BCS tunneling gap of 3.5 k_BT_c. Comparison with strong coupling Eliashberg predictions and of a Kramers-Kronig analysis indicate that the absorption onset is consistent with a superconducting energy gap. Effects of magnetic field on residual losses in YBCO films show a resonant absorption feature in vicinity of predicted

Mapping the residues of protein kinase CK2 implicated in substrate recognition

DEFF Research Database (Denmark)

Sarno, S; Boldyreff, B; Marin, O

1995-01-01

, hampering the calculation of kinetic parameters. In contrast 3 mutants (K74-77A, K79R80K83A and R191,195K198A) phosphorylated the peptide with reduced efficiency accounted for by increased Km and decreased Vmax values. By using derivatives of the RRRADDSDDDDD peptide in which individual aspartyl residues......, respectively. These data support the conclusion that the basic residues present in the p+1 loop of CK2 alpha specifically recognize the acidic determinant adjacent to the C-terminal side of serine, while the specificity determinants located more down-stream are variably recognized by different residues...

Residual stress evaluation and curvature behavior of aluminium 7050 peen forming processed

International Nuclear Information System (INIS)

Oliveira, R.R. de; Lima, N.B.; Braga, A.P.V.; Goncalves, M.

2010-01-01

Shot peening is a superficial cold work process used to increase the fatigue life evaluated by residual stress measurements. The peen forming process is a variant of the shot peening process, where a curvature in the plate is obtained by the compression of the grains near to the surface. In this paper, the influence of the parameters such as: pressure of shot, ball shot size and thickness of aluminum 7050 samples with respect to residual stress profile and resulting arc height was studied. The evaluation of the residual stress profile was obtained by sin 2 Ψ method. (author)

Computational modeling of allosteric regulation in the hsp90 chaperones: a statistical ensemble analysis of protein structure networks and allosteric communications.

Directory of Open Access Journals (Sweden)

Kristin Blacklock

2014-06-01

Full Text Available A fundamental role of the Hsp90 chaperone in regulating functional activity of diverse protein clients is essential for the integrity of signaling networks. In this work we have combined biophysical simulations of the Hsp90 crystal structures with the protein structure network analysis to characterize the statistical ensemble of allosteric interaction networks and communication pathways in the Hsp90 chaperones. We have found that principal structurally stable communities could be preserved during dynamic changes in the conformational ensemble. The dominant contribution of the inter-domain rigidity to the interaction networks has emerged as a common factor responsible for the thermodynamic stability of the active chaperone form during the ATPase cycle. Structural stability analysis using force constant profiling of the inter-residue fluctuation distances has identified a network of conserved structurally rigid residues that could serve as global mediating sites of allosteric communication. Mapping of the conformational landscape with the network centrality parameters has demonstrated that stable communities and mediating residues may act concertedly with the shifts in the conformational equilibrium and could describe the majority of functionally significant chaperone residues. The network analysis has revealed a relationship between structural stability, global centrality and functional significance of hotspot residues involved in chaperone regulation. We have found that allosteric interactions in the Hsp90 chaperone may be mediated by modules of structurally stable residues that display high betweenness in the global interaction network. The results of this study have suggested that allosteric interactions in the Hsp90 chaperone may operate via a mechanism that combines rapid and efficient communication by a single optimal pathway of structurally rigid residues and more robust signal transmission using an ensemble of suboptimal multiple

Swelling kinetics of several residues from Shenhua coal extraction

Energy Technology Data Exchange (ETDEWEB)

Cao, Mei-xia; Shui, Heng-fu; Wang, Zhi-cai [Anhui University of Technology, Maanshan (China). School of Chemistry and Chemical Engineering

2008-08-15

In order to understand the mechanism of swelling and the relation between swelling behavior and solvent extraction, the swelling kinetics of residues from Shenhua coal extracted by CS{sub 2}/NMP with different mixing ratios were studied in different solvents. The result shows that the swelling rates of extraction residues increase along with swelling temperature. The swelling rate in polar solvent NMP is much higher than that in non-polar solvent THN. Solvent extraction has a great effect on the swelling of extraction residues. The swelling activation energy of extraction residues increases and the swelling rate decreases with the increase of extraction yield. The swelling activation energies of extraction residues in NMP and THN are less than 10 kJ/mol, suggesting that the swelling process is controlled by solvent molecular diffusion in coal structure. 22 refs., 2 figs., 7 tabs.

Use of demolition residues construction in soil-lime bricks

International Nuclear Information System (INIS)

Figueiredo, S.S.; Silva, C.G.; Silva, I.A.; Neves, G.A.

2011-01-01

Besides being responsible for several environmental damage caused by its residues, the construction industry is also considered the greatest natural resources consumer. When finely ground, such residues can exhibit cementing properties, which may replace part of the lime used in the manufacture of soil-lime bricks. This study aimed to verify the viability of using demolition residues (DR) in soil-lime bricks without structural function. For this, test specimens were prepared using mixes in a 1:10 ratio of lime:soil and embedding residue in partial replacement of lime in the proportions of 25%, 50% and 75%. The test specimens were submitted to curing periods of 28 and 52 days, then it was determined the compression strength. The results showed that when embedded on moderate percentages, demolition residues construction can be used in the production of soil-lime bricks. (author)

Determination of structural and spectroscopic parameters of 4-hydroxyantipyrine, using DFT method

International Nuclear Information System (INIS)

Catikkas, B.; Aktan, E.

2010-01-01

In this study, structural and vibrational parameters were calculated. First of all, conformational analysis of 4-hydroxyantipyrine was carried out in gas phase. Then, the geometric parameters (bond length, bond angle and tortion angle) of the most stable conformer were calculated and the Infrared and Raman frequencies of fundamental modes were determined. Calculations were made by using DFT B3LYP/6-311+G(d,p) method implemented the Gaussian 03 program. Afterwards, vibrational assignments of the title molecule were calculated by using Scaled Quantum Mechanical (SQM) analysis. In conclusion, calculated values were compared with corresponding experimental results.

Influence of electrospinning parameters on the structural morphology and diameter of electrospun nanofibers

CSIR Research Space (South Africa)

Jacobs, V

2009-11-01

Full Text Available Electrospinning is a simple method of producing nanofibers by introducing electric field into the polymer solutions. We report an experimental investigation on the influence of processing parameters and solution properties on the structural...

Residue preference mapping of ligand fragments in the Protein Data Bank.

Science.gov (United States)

Wang, Lirong; Xie, Zhaojun; Wipf, Peter; Xie, Xiang-Qun

2011-04-25

The interaction between small molecules and proteins is one of the major concerns for structure-based drug design because the principles of protein-ligand interactions and molecular recognition are not thoroughly understood. Fortunately, the analysis of protein-ligand complexes in the Protein Data Bank (PDB) enables unprecedented possibilities for new insights. Herein, we applied molecule-fragmentation algorithms to split the ligands extracted from PDB crystal structures into small fragments. Subsequently, we have developed a ligand fragment and residue preference mapping (LigFrag-RPM) algorithm to map the profiles of the interactions between these fragments and the 20 proteinogenic amino acid residues. A total of 4032 fragments were generated from 71 798 PDB ligands by a ring cleavage (RC) algorithm. Among these ligand fragments, 315 unique fragments were characterized with the corresponding fragment-residue interaction profiles by counting residues close to these fragments. The interaction profiles revealed that these fragments have specific preferences for certain types of residues. The applications of these interaction profiles were also explored and evaluated in case studies, showing great potential for the study of protein-ligand interactions and drug design. Our studies demonstrated that the fragment-residue interaction profiles generated from the PDB ligand fragments can be used to detect whether these fragments are in their favorable or unfavorable environments. The algorithm for a ligand fragment and residue preference mapping (LigFrag-RPM) developed here also has the potential to guide lead chemistry modifications as well as binding residues predictions.

Building X-ray pulsar timing model without the use of radio parameters

Science.gov (United States)

Sun, Hai-feng; Sun, Xiong; Fang, Hai-yan; Shen, Li-rong; Cong, Shao-peng; Liu, Yan-ming; Li, Xiao-ping; Bao, Wei-min

2018-02-01

This paper develops a timing solution for the X-ray pulsar timing model without the use of the initial radio model parameters. First, we address the problem of phase ambiguities for the pre-fit residuals in the construction of pulsar timing model. To improve the estimation accuracy of the pulse time of arrival (TOA), we have deduced the general form of test statistics in Fourier transform, and discussed their estimation performances. Meanwhile, a fast maximum likelihood (FML) technique is presented to estimate the pulse TOA, which outperforms cross correlation (CC) estimator and exhibits a performance comparable with maximum likelihood (ML) estimator in spite of a much less reduced computational complexity. Depending on the strategy of the difference minimum of pre-fit residuals, we present an effective forced phase-connected technique to achieve initial model parameters. Then, we use the observations with the Rossi X-Ray Timing Explorer (RXTE) and X-ray pulsar navigation-I (XPNAV-1) satellites for experimental studies, and discuss main differences for the root mean square (RMS) residuals calculated with the X-ray and radio ephemerides. Finally, a chi-square value (CSV) of pulse profiles is presented as a complementary indicator to the RMS residuals for evaluating the model parameters. The results show that the proposed timing solution is valid and effective, and the obtained model parameters can be a reasonable alternative to the radio ephemeris.

Reduction method for residual stress of welded joint using random vibration

International Nuclear Information System (INIS)

Aoki, Shigeru; Nishimura, Tadashi; Hiroi, Tetsumaro

2005-01-01

Welded joints are used for construction of many structures. Residual stress is induced near the bead caused by locally given heat. Tensile residual stress on the surface may reduce fatigue strength. In this paper, a new method for reduction of residual stress using vibration during welding is proposed. As vibrational load, random vibration, white noise and filtered white noise are used. Two thin plates are butt-welded. Residual stress is measured with a paralleled beam X-ray diffractometer with scintillation counter after removing quenched scale chemically. It is concluded that tensile residual stress near the bead is reduced by using random vibration during welding

Comparison of segmentation techniques to determine the geometric parameters of structured surfaces

International Nuclear Information System (INIS)

MacAulay, Gavin D; Giusca, Claudiu L; Leach, Richard K; Senin, Nicola

2014-01-01

Structured surfaces, defined as surfaces characterized by topography features whose shape is defined by design specifications, are increasingly being used in industry for a variety of applications, including improving the tribological properties of surfaces. However, characterization of such surfaces still remains an issue. Techniques have been recently proposed, based on identifying and extracting the relevant features from a structured surface so they can be verified individually, using methods derived from those commonly applied to standard-sized parts. Such emerging approaches show promise but are generally complex and characterized by multiple data processing steps making performance difficult to assess. This paper focuses on the segmentation step, i.e. partitioning the topography so that the relevant features can be separated from the background. Segmentation is key for defining the geometric boundaries of the individual feature, which in turn affects any computation of feature size, shape and localization. This paper investigates the effect of varying the segmentation algorithm and its controlling parameters by considering a test case: a structured surface for bearing applications, the relevant features being micro-dimples designed for friction reduction. In particular, the mechanisms through which segmentation leads to identification of the dimple boundary and influences dimensional properties, such as dimple diameter and depth, are illustrated. It is shown that, by using different methods and control parameters, a significant range of measurement results can be achieved, which may not necessarily agree. Indications on how to investigate the influence of each specific choice are given; in particular, stability of the algorithms with respect to control parameters is analyzed as a means to investigate ease of calibration and flexibility to adapt to specific, application-dependent characterization requirements. (paper)

Generic GPCR residue numbers - aligning topology maps while minding the gaps

DEFF Research Database (Denmark)

Isberg, Vignir; de Graaf, Chris; Bortolato, Andrea

2015-01-01

Generic residue numbers facilitate comparisons of, for example, mutational effects, ligand interactions, and structural motifs. The numbering scheme by Ballesteros and Weinstein for residues within the class A GPCRs (G protein-coupled receptors) has more than 1100 citations, and the recent crysta...

Improving protein fold recognition by extracting fold-specific features from predicted residue-residue contacts.

Science.gov (United States)

Zhu, Jianwei; Zhang, Haicang; Li, Shuai Cheng; Wang, Chao; Kong, Lupeng; Sun, Shiwei; Zheng, Wei-Mou; Bu, Dongbo

2017-12-01

Accurate recognition of protein fold types is a key step for template-based prediction of protein structures. The existing approaches to fold recognition mainly exploit the features derived from alignments of query protein against templates. These approaches have been shown to be successful for fold recognition at family level, but usually failed at superfamily/fold levels. To overcome this limitation, one of the key points is to explore more structurally informative features of proteins. Although residue-residue contacts carry abundant structural information, how to thoroughly exploit these information for fold recognition still remains a challenge. In this study, we present an approach (called DeepFR) to improve fold recognition at superfamily/fold levels. The basic idea of our approach is to extract fold-specific features from predicted residue-residue contacts of proteins using deep convolutional neural network (DCNN) technique. Based on these fold-specific features, we calculated similarity between query protein and templates, and then assigned query protein with fold type of the most similar template. DCNN has showed excellent performance in image feature extraction and image recognition; the rational underlying the application of DCNN for fold recognition is that contact likelihood maps are essentially analogy to images, as they both display compositional hierarchy. Experimental results on the LINDAHL dataset suggest that even using the extracted fold-specific features alone, our approach achieved success rate comparable to the state-of-the-art approaches. When further combining these features with traditional alignment-related features, the success rate of our approach increased to 92.3%, 82.5% and 78.8% at family, superfamily and fold levels, respectively, which is about 18% higher than the state-of-the-art approach at fold level, 6% higher at superfamily level and 1% higher at family level. An independent assessment on SCOP_TEST dataset showed consistent

Residues from waste incineration. Final report. Rev. ed.

Energy Technology Data Exchange (ETDEWEB)

Astrup, T.; Juul Pedersen, A.; Hyks, J.; Frandsen, F.J.

2010-04-15

The overall objective of the project was to improve the understanding of the formation and characteristics of residues from waste incineration. This was done focusing on the importance of the waste input and the operational conditions of the furnace. Data and results obtained from the project have been discussed in this report according to the following three overall parts: i) mass flows and element distribution, ii) flue gas/particle partitioning and corrosion/deposition aspects, and iii) residue leaching. This has been done with the intent of structuring the discussion while tacitly acknowledging that these aspects are interrelated and cannot be separated. Overall, it was found that the waste input composition had significant impact of the characteristics of the generated residues. A similar correlation between operational conditions and residue characteristics could not be observed. Consequently, the project recommend that optimization of residue quality should focus on controlling the waste input composition. The project results showed that including specific waste materials (and thereby also excluding the same materials) may have significant effects on the residue composition, residue leaching, aerosol and deposit formation.It is specifically recommended to minimize Cl in the input waste. Based on the project results, it was found that a significant potential for optimization of waste incineration exist. (Author)

An analytical method on the surface residual stress for the cutting tool orientation

Science.gov (United States)

Li, Yueen; Zhao, Jun; Wang, Wei

2010-03-01

The residual stress is measured by choosing 8 kinds orientations on cutting the H13 dies steel on the HSM in the experiment of this paper. The measured data shows on that the residual stress exists periodicity for the different rake angle (β) and side rake angle (θ) parameters, further study find that the cutting tool orientations have closed relationship with the residual stresses, and for the original of the machined residual stress on the surface from the cutting force and the axial force, it can be gained the simply model of tool-workpiece force, using the model it can be deduced the residual stress model, which is feasible to calculate the size of residual stress. And for almost all the measured residual stresses are compressed stress, the compressed stress size and the direction could be confirmed by the input data for the H13 on HSM. As the result, the residual stress model is the key for optimization of rake angle (β) and side rake angle (θ) in theory, using the theory the more cutting mechanism can be expressed.

Implementation and Development of the Incremental Hole Drilling Method for the Measurement of Residual Stress in Thermal Spray Coatings

Science.gov (United States)

Valente, T.; Bartuli, C.; Sebastiani, M.; Loreto, A.

2005-12-01

The experimental measurement of residual stresses originating within thick coatings deposited by thermal spray on solid substrates plays a role of fundamental relevance in the preliminary stages of coating design and process parameters optimization. The hole-drilling method is a versatile and widely used technique for the experimental determination of residual stress in the most superficial layers of a solid body. The consolidated procedure, however, can only be implemented for metallic bulk materials or for homogeneous, linear elastic, and isotropic materials. The main objective of the present investigation was to adapt the experimental method to the measurement of stress fields built up in ceramic coatings/metallic bonding layers structures manufactured by plasma spray deposition. A finite element calculation procedure was implemented to identify the calibration coefficients necessary to take into account the elastic modulus discontinuities that characterize the layered structure through its thickness. Experimental adjustments were then proposed to overcome problems related to the low thermal conductivity of the coatings. The number of calculation steps and experimental drilling steps were finally optimized.

Analysis of deuterium relaxation-derived methyl axis order parameters and correlation with local structure