Code assessment and modelling for Design Basis Accident Analysis of the European sodium fast reactor design. Part I: System description, modelling and benchmarking

The new reactor concepts proposed in the Generation IV International Forum (GIF) are conceived to improve the use of natural resources, reduce the amount of high-level radioactive waste and excel in their reliability and safe operation. Among these novel designs sodium fast reactors (SFRs) stand out due to their technological feasibility as demonstrated in several countries during the last decades. As part of the contribution of EURATOM to GIF the CP-ESFR is a collaborative project with the objective, among others, to perform extensive analysis on safety issues involving renewed SFR demonstrator designs. The verification of computational tools able to simulate the plant behaviour under postulated accidental conditions by code-to-code comparison was identified as a key point to ensure reactor safety. In this line, several organizations employed coupled neutronic and thermal-hydraulic system codes able to simulate complex and specific phenomena involving multi-physics studies adapted to this particular fast reactor technology. In the “Introduction” of this paper the framework of this study is discussed, the second section describes the envisaged plant design and the commonly agreed upon modelling guidelines. The third section presents a comparative analysis of the calculations performed by each organisation applying their models and codes to a common agreed transient with the objective to harmonize the models as well as validating the implementation of all relevant physical phenomena in the different system codes.

Translocation and Functional Analysis of Pseudomonas savastanoi pv. savastanoi NCPPB 3335 Type III Secretion System Effectors Reveals Two Novel Effector Families of the Pseudomonas syringae Complex

Pseudomonas savastanoi pv. savastanoi NCPPB 3335 causes olive knot disease and is a model pathogen for exploring bacterial infection of woody hosts. The type III secretion system (T3SS) effector repertoire of this strain includes 31 effector candidates plus two novel candidates identified in this study which have not been reported to translocate into plant cells. In this work, we demonstrate the delivery of seven NCPPB 3335 effectors into Nicotiana tabacum leaves, including three proteins from two novel families of the P. syringae complex effector super-repertoire (HopBK and HopBL), one of which comprises two proteins (HopBL1 and HopBL2) that harbor a SUMO protease domain. When delivered by P. fluorescens heterologously expressing a P. syringae T3SS, all seven effectors were found to suppress the production of defense-associated reactive oxygen species. Moreover, six of these effectors, including the truncated versions of HopAA1 and HopAZ1 encoded by NCPPB 3335, suppressed callose deposition. The expression of HopAZ1 and HopBL1 by functionally effectorless P. syringae pv. tomato DC3000D28E inhibited the hypersensitive response in tobacco and, additionally, expression of HopBL2 by this strain significantly increased its competitiveness in N. benthamiana. DNA sequences encoding HopBL1 and HopBL2 were uniquely detected in a collection of 31 P. savastanoi pv. savastanoi strains and other P. syringae strains isolated from woody hosts, suggesting a relevant role of these two effectors in bacterial interactions with olive and other woody plants.

A linearization-based system reliability method with application to geotechnical analysis

Los análisis de fiabilidad representan una herramienta adecuada para contemplar las incertidumbres inherentes que existen en los parámetros geotécnicos. En esta Tesis Doctoral se desarrolla una metodología basada en una linealización sencilla, que emplea aproximaciones de primer o segundo orden, para evaluar eficientemente la fiabilidad del sistema en los problemas geotécnicos. En primer lugar, se emplean diferentes métodos para analizar la fiabilidad de dos aspectos propios del diseño de los túneles: la estabilidad del frente y el comportamiento del sostenimiento. Se aplican varias metodologías de fiabilidad — el Método de Fiabilidad de Primer Orden (FORM), el Método de Fiabilidad de Segundo Orden (SORM) y el Muestreo por Importancia (IS). Los resultados muestran que los tipos de distribución y las estructuras de correlación consideradas para todas las variables aleatorias tienen una influencia significativa en los resultados de fiabilidad, lo cual remarca la importancia de una adecuada caracterización de las incertidumbres geotécnicas en las aplicaciones prácticas. Los resultados también muestran que tanto el FORM como el SORM pueden emplearse para estimar la fiabilidad del sostenimiento de un túnel y que el SORM puede mejorar el FORM con un esfuerzo computacional adicional aceptable. Posteriormente, se desarrolla una metodología de linealización para evaluar la fiabilidad del sistema en los problemas geotécnicos. Esta metodología solamente necesita la información proporcionada por el FORM: el vector de índices de fiabilidad de las funciones de estado límite (LSFs) que componen el sistema y su matriz de correlación. Se analizan dos problemas geotécnicos comunes —la estabilidad de un talud en un suelo estratificado y un túnel circular excavado en roca— para demostrar la sencillez, precisión y eficiencia del procedimiento propuesto. Asimismo, se reflejan las ventajas de la metodología de linealización con respecto a las herramientas computacionales alternativas. Igualmente se muestra que, en el caso de que resulte necesario, se puede emplear el SORM —que aproxima la verdadera LSF mejor que el FORM— para calcular estimaciones más precisas de la fiabilidad del sistema. Finalmente, se presenta una nueva metodología que emplea Algoritmos Genéticos para identificar, de manera precisa, las superficies de deslizamiento representativas (RSSs) de taludes en suelos estratificados, las cuales se emplean posteriormente para estimar la fiabilidad del sistema, empleando la metodología de linealización propuesta. Se adoptan tres taludes en suelos estratificados característicos para demostrar la eficiencia, precisión y robustez del procedimiento propuesto y se discuten las ventajas del mismo con respecto a otros métodos alternativos. Los resultados muestran que la metodología propuesta da estimaciones de fiabilidad que mejoran los resultados previamente publicados, enfatizando la importancia de hallar buenas RSSs —y, especialmente, adecuadas (desde un punto de vista probabilístico) superficies de deslizamiento críticas que podrían ser no-circulares— para obtener estimaciones acertadas de la fiabilidad de taludes en suelos. Reliability analyses provide an adequate tool to consider the inherent uncertainties that exist in geotechnical parameters. This dissertation develops a simple linearization-based approach, that uses first or second order approximations, to efficiently evaluate the system reliability of geotechnical problems. First, reliability methods are employed to analyze the reliability of two tunnel design aspects: face stability and performance of support systems. Several reliability approaches —the first order reliability method (FORM), the second order reliability method (SORM), the response surface method (RSM) and importance sampling (IS)— are employed, with results showing that the assumed distribution types and correlation structures for all random variables have a significant effect on the reliability results. This emphasizes the importance of an adequate characterization of geotechnical uncertainties for practical applications. Results also show that both FORM and SORM can be used to estimate the reliability of tunnel-support systems; and that SORM can outperform FORM with an acceptable additional computational effort. A linearization approach is then developed to evaluate the system reliability of series geotechnical problems. The approach only needs information provided by FORM: the vector of reliability indices of the limit state functions (LSFs) composing the system, and their correlation matrix. Two common geotechnical problems —the stability of a slope in layered soil and a circular tunnel in rock— are employed to demonstrate the simplicity, accuracy and efficiency of the suggested procedure. Advantages of the linearization approach with respect to alternative computational tools are discussed. It is also found that, if necessary, SORM —that approximates the true LSF better than FORM— can be employed to compute better estimations of the system’s reliability. Finally, a new approach using Genetic Algorithms (GAs) is presented to identify the fully specified representative slip surfaces (RSSs) of layered soil slopes, and such RSSs are then employed to estimate the system reliability of slopes, using our proposed linearization approach. Three typical benchmark-slopes with layered soils are adopted to demonstrate the efficiency, accuracy and robustness of the suggested procedure, and advantages of the proposed method with respect to alternative methods are discussed. Results show that the proposed approach provides reliability estimates that improve previously published results, emphasizing the importance of finding good RSSs —and, especially, good (probabilistic) critical slip surfaces that might be non-circular— to obtain good estimations of the reliability of soil slope systems.

Engineering analysis of ITER In-Vessel Viewing System guide tube

The In Vessel Viewing System (IVVS) will be one of the essential machine diagnostic systems at ITER to provide information about the status of in-vessel and plasma facing components and to evaluate the dust inside the Vacuum Vessel. The current design consists of six scanning probes and their deployment systems, which are placed in dedicated ports at the divertor level. These units are located in resident guiding tubes 10 m long, which allow the IVVS probes to go from their storage location to the scanning position by means of a simple straight translation. Moreover, each resident tube is supported inside the corresponding Vacuum Vessel and Cryostat port extensions, which are part of the primary confinement barrier. As the Vacuum Vessel and the Cryostat will move with respect to each other during operation (especially during baking) and during incidents and accidents (disruptions, vertical displacement events, seismic events), the structural integrity of the resident tube and the surrounding vacuum boundaries would be compromised if the required flexibility and supports are not appropriately assured. This paper focuses on the integration of the present design of the IVVS into the Vacuum Vessel and Cryostat environment. It presents the adopted strategy to withstand all the main interfacing loads without damaging the confinement barriers and the corresponding analysis supporting it.

Analysis of air flow past and through the 2415-3S airfoil for an unmanned aerial vehicle with internal propulsion system

This paper deals with the prediction of velocity fields on the 2415-3S airfoil which will be used for an unmanned aerial vehicle with internal propulsion system and in this way analyze the air flow through an internal duct of the airfoil using computational fluid dynamics. The main objective is to evaluate the effect of the internal air flow past the airfoil and how this affects the aerodynamic performance by means of lift and drag forces. For this purpose, three different designs of the internal duct were studied; starting from the base 2415-3S airfoil developed in previous investigation, basing on the hypothesis of decreasing the flow separation produced when the propulsive airflow merges the external flow, and in this way obtaining the best configuration. For that purpose, an exhaustive study of the mesh sensitivity was performed. It was used a non-structured mesh since the computational domain is three-dimensional and complex. The selected mesh contains approximately 12.5 million elements. Both the computational domain and the numerical solution were made with commercial CAD and CFD software, respectively. Air, incompressible and steady was analyzed. The boundary conditions are in concordance with experimental setup in the AF 6109 wind tunnel. The k-e model is utilized to describe the turbulent flow process as followed in references. Results allowed obtaining velocity contours as well as lift and drag coefficients and also the location of separation and reattachment regions in some cases for zero degrees of angle of attack on the internal and external surfaces of the airfoil. Finally, the selection of the configuration with the best aerodynamic performance was made, selecting the option without curved baffles.

Numerical analysis of air flow past the 2415-3S airfoil for an unmanned aerial vehicle with internal propulsion system

This paper deals with the prediction of pressure and velocity fields on the 2415-3S airfoil which will be used for and unmanned aerial vehicle with internal propulsion system and in this way analyze the air flow through an internal duct of the airfoil using computational fluid dynamics. The main objective is to evaluate the effect of the internal air flow past the airfoil and how this affects the aerodynamic performance by means of lift and drag forces. For this purpose, three different designs of the internal duct were studied; starting from the base 2415-3S airfoil developed in previous investigation, basing on the hypothesis of decreasing the flow separation produced when the propulsive airflow merges the external flow, and in this way obtaining the best configuration. For that purpose, an exhaustive study of the mesh sensitivity was performed. It was used a non-structured mesh since the computational domain is tridimensional and complex. The selected mesh contains approximately 12.5 million elements. Both the computational domain and the numerical solution were made with commercial CAD and CFD software respectively. Air, incompressible and steady was analyzed. The boundary conditions are in concordance with experimental setup in the AF 6109 wind tunnel. The k-ε model is utilized to describe the turbulent flow process as followed in references. Results allowed obtaining pressure and velocity contours as well as lift and drag coefficients and also the location of separation and reattachment regions in some cases for zero degrees of angle of attack on the internal and external surfaces of the airfoil. Finally, the selection of the configuration with the best aerodynamic performance was made, selecting the option without curved baffles.

System theory based hazard analysis applied to the process industry

Chemical process accidents still occur and cost billions of dollars and, what is worse, many human lives. That means that traditional hazard analysis techniques are not enough mainly owing to the increase of complexity and size of chemical plants. In the last years, a new hazard analysis technique has been developed, changing the focus from reliability to system theory and showing promising results in other industries such as aeronautical and nuclear. In this paper, we present an approach for the application of STAMP and STPA analysis developed by Leveson in 2011 to the process industry.

Path-following analysis of the dynamical response of a piecewise-linear capsule system

Acknowledgements The first author has been supported by a Georg Forster Research Fellowship granted by the Alexander von Humboldt Foundation, Germany

Analysis of a peptide hormone–receptor interaction in the yeast two-hybrid system

Interaction between a peptide hormone and extracellular domains of its receptor is a crucial step for initiation of hormone action. We have developed a modification of the yeast two-hybrid system to study this interaction and have used it to characterize the interaction of insulin-like growth factor 1 (IGF-1) with its receptor by using GAL4 transcriptional regulation with a β-galactosidase assay as readout. In this system, IGF-1 and proIGF-1 bound to the cysteine-rich domain, extracellular domain, or entire IGF-1 proreceptor. This interaction was specific. Thus, proinsulin showed no significant interaction with the IGF-1 receptor, while a chimeric proinsulin containing the C-peptide of IGF-1 had an intermediate interaction, consistent with its affinity for the IGF-1 receptor. Over 2000 IGF-1 mutants were generated by PCR and screened for interaction with the color assay. About 40% showed a strong interaction, 20% showed an intermediate interaction, and 40% give little or no signal. Of 50 mutants that were sequenced, several (Leu-5 → His, Glu-9 → Val, Arg-37 → Gly, and Met-59 → Leu) appeared to enhance receptor association, others resulted in weaker receptor interaction (Tyr-31 → Phe and Ile-43 → Phe), and two gave no detectable signal (Leu-14 → Arg and Glu-46 → Ala). Using PCR-based mutagenesis with proinsulin, we also identified a gain of function mutant (proinsulin Leu-17 → Pro) that allowed for a strong IGF-1–receptor interaction. These data demonstrate that the specificity of the interaction between a hormone and its receptor can be characterized with high efficiency in the two-hybrid system and that novel hormone analogues may be found by this method.

A system for functional analysis of Ebola virus glycoprotein

Ebola virus causes hemorrhagic fever in humans and nonhuman primates, resulting in mortality rates of up to 90%. Studies of this virus have been hampered by its extraordinary pathogenicity, which requires biosafety level 4 containment. To circumvent this problem, we developed a novel complementation system for functional analysis of Ebola virus glycoproteins. It relies on a recombinant vesicular stomatitis virus (VSV) that contains the green fluorescent protein gene instead of the receptor-binding G protein gene (VSVΔG*). Herein we show that Ebola Reston virus glycoprotein (ResGP) is efficiently incorporated into VSV particles. This recombinant VSV with integrated ResGP (VSVΔG*-ResGP) infected primate cells more efficiently than any of the other mammalian or avian cells examined, in a manner consistent with the host range tropism of Ebola virus, whereas VSVΔG* complemented with VSV G protein (VSVΔG*-G) efficiently infected the majority of the cells tested. We also tested the utility of this system for investigating the cellular receptors for Ebola virus. Chemical modification of cells to alter their surface proteins markedly reduced their susceptibility to VSVΔG*-ResGP but not to VSVΔG*-G. These findings suggest that cell surface glycoproteins with N-linked oligosaccharide chains contribute to the entry of Ebola viruses, presumably acting as a specific receptor and/or cofactor for virus entry. Thus, our VSV system should be useful for investigating the functions of glycoproteins from highly pathogenic viruses or those incapable of being cultured in vitro.

Activation and Functional Analysis of Janus Kinase 2 in BA/F3 Cells Using the Coumermycin/Gyrase B System

Janus kinase 2 (Jak2) protein tyrosine kinase plays an important role in interleukin-3– or granulocyte–macrophage colony-stimulating factor–mediated signal transduction pathways leading to cell proliferation, activation of early response genes, and inhibition of apoptosis. However, it is unclear whether Jak2 can activate these signaling pathways directly without the involvement of cytokine receptor phosphorylation. To investigate the specific role of Jak2 in the regulation of signal transduction pathways, we generated gyrase B (GyrB)–Jak2 fusion proteins, dimerized through the addition of coumermycin. Coumermycin induced autophosphorylation of GyrB–Jak2 fusion proteins, thus bypassing receptor activation. Using different types of chimeric Jak2 molecules, we observed that although the kinase domain of Jak2 is sufficient for autophosphorylation, the N-terminal regions are essential for the phosphorylation of Stat5 and for the induction of short-term cell proliferation. Moreover, coumermycin-induced activation of Jak2 can also lead to increased levels of c-myc and CIS mRNAs in BA/F3 cells stably expressing the Jak2 fusion protein with the intact N-terminal region. Conversely, activation of the chimeric Jak2 induced neither phosphorylation of Shc or SHP-2 nor activation of the c-fos promoter. Here, we showed that the GyrB–Jak2 system can serve as an excellent model to dissect signals of receptor-dependent and -independent events. We also obtained evidence indicating a role for the N-terminal region of Jak2 in downstream signaling events.

The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant

Arabidopsis thaliana, a small annual plant belonging to the mustard family, is the subject of study by an estimated 7000 researchers around the world. In addition to the large body of genetic, physiological and biochemical data gathered for this plant, it will be the first higher plant genome to be completely sequenced, with completion expected at the end of the year 2000. The sequencing effort has been coordinated by an international collaboration, the Arabidopsis Genome Initiative (AGI). The rationale for intensive investigation of Arabidopsis is that it is an excellent model for higher plants. In order to maximize use of the knowledge gained about this plant, there is a need for a comprehensive database and information retrieval and analysis system that will provide user-friendly access to Arabidopsis information. This paper describes the initial steps we have taken toward realizing these goals in a project called The Arabidopsis Information Resource (TAIR) (www.arabidopsis.org).

rSNP_Guide, a database system for analysis of transcription factor binding to target sequences: application to SNPs and site-directed mutations

rSNP_Guide is a novel curated database system for analysis of transcription factor (TF) binding to target sequences in regulatory gene regions altered by mutations. It accumulates experimental data on naturally occurring site variants in regulatory gene regions and site-directed mutations. This database system also contains the web tools for SNP analysis, i.e., active applet applying weight matrices to predict the regulatory site candidates altered by a mutation. The current version of the rSNP_Guide is supplemented by six sub-databases: (i) rSNP_DB, on DNA–protein interaction caused by mutation; (ii) SYSTEM, on experimental systems; (iii) rSNP_BIB, on citations to original publications; (iv) SAMPLES, on experimentally identified sequences of known regulatory sites; (v) MATRIX, on weight matrices of known TF sites; (vi) rSNP_Report, on characteristic examples of successful rSNP_Tools implementation. These databases are useful for the analysis of natural SNPs and site-directed mutations. The databases are available through the Web, http://wwwmgs.bionet.nsc.ru/mgs/systems/rsnp/.

Expression and analysis of presenilin 1 in a human neuronal system: localization in cell bodies and dendrites.

Mutations in the recently identified presenilin 1 gene on chromosome 14 cause early onset familial Alzheimer disease (FAD). Herein we describe the expression and analysis of the protein coded by presenilin 1 (PS1) in NT2N neurons, a human neuronal model system. PS1 was expressed using recombinant Semliki Forest virions and detected by introduced antigenic tags or antisera to PS1-derived peptides. Immunoprecipitation revealed two major PS1 bands of approximately 43 and 50 kDa, neither of which were N-glycosylated or O-glycosylated. Immunoreactive PS1 was detected in cell bodies and dendrites of NT2N neurons but not in axons or on the cell surface. PS1 was also detected in BHK cells, where it was also intracellular and colocalized with calnexin, a marker for the rough endoplasmic reticulum. A mutant form of PS1 linked to FAD did not differ from the wild-type protein at the light microscopic level. The model system described here will enable studies of the function of PS1 in human neurons and the role of mutant PS1 in FAD.

Lens complementation system for the genetic analysis of growth, differentiation, and apoptosis in vivo.

A genetic approach has been established that combines the advantages of blastocyst complementation with the experimental attributes of the developing lens for the functional analysis of genes governing cellular proliferation, terminal differentiation, and apoptosis. This lens complementation system (LCS) makes use of a mutant mouse strain, aphakia (ak), homozygotes of which fail to develop an ocular lens. We demonstrate that microinjection of wild-type embryonic stem (ES) cells into ak/ak blastocysts produces chimeras with normal ES-cell-derived lenses and that microinjection of Rb-/- ES cells generates an aberrant lens phenotype identical to that obtained through conventional gene targeting methodology. Our determination that a cell autonomous defect underlies the aphakia condition assures that lenses generated through LCS are necessarily ES-cell-derived. LCS provides for the rapid phenotypic analysis of loss-of-function mutations, circumvents the need for germ-line transmission of null alleles, and, most significantly, facilitates the study of essential genes whose inactivation is associated with early lethal phenotypes.