Nuclear Hartree-Fock calculations on parallel computers

Hartree-Fock (HF) calculations have had remarkable success in describing large nuclei at high spin, temperature and deformation. To allow full range of possible deformations, the Skyrme HF equations can be discretized on a three-dimensional mesh. However, such calculations are currently limited by the computational resources provided by traditional supercomputers. To take advantage of recent developments in massively parallel computing technology, we have implemented the LLNL Skyrme-force static and rotational HF codes on Intel's DELTA and GAMMA systems at Caltech.

We decomposed the HF code by assigning a portion of the mesh to each node, with nearest neighbor meshes assigned to nodes connected by communication· channels. This kind of decomposition is well-suited for the DELTA and the GAMMA architecture because the only non-local operations are wave function orthogonalization and the boundary conditions of the Poisson equation for the Coulomb field.

Our first application of the HF code on parallel computers has been the study of identical superdeformed (SD) rotational bands in the Hg region. In the last ten years, many SD rotational bands have been found experimentally. One very surprising feature found in these SD rotational bands is that many pairs of bands in nuclei that differ by one or two mass units have nearly identical deexcitation gamma-ray energies. Our calculations of the five rotational bands in ^(192)Hg and ^(194)Pb show that the filling of specific orbitals can lead to bands with deexcitation gamma-ray energies differing by at most 2 keV in nuclei differing by two mass units and over a range of angular momenta comparable to that observed experimentally. Our calculations of SD rotational bands in the Dy region also show that twinning can be achieved by filling or emptying some specific orbitals.

The interpretation of future precise experiments on atomic parity nonconservation (PNC) in terms of parameters of the Standard Model could be hampered by uncertainties in the atomic and nuclear structure. As a further application of the massively parallel HF calculations, we calculated the proton and neutron densities of the Cesium isotopes from A = 125 to A = 139. Based on our good agreement with experimental charge radii, binding energies, and ground state spins, we conclude that the uncertainties in the ratios of weak charges are less than 10^(-3), comfortably smaller than the anticipated experimental error.

Design, synthesis and characterization of sequence-specific DNA-cleaving metalloproteins

This thesis describes research pursued in two areas, both involving the design and synthesis of sequence specific DNA-cleaving proteins. The first involves the use of sequence-specific DNA-cleaving metalloproteins to probe the structure of a protein-DNA complex, and the second seeks to develop cleaving moieties capable of DNA cleavage through the generation of a non-diffusible oxidant under physiological conditions.

Chapter One provides a brief review of the literature concerning sequence-specific DNA-binding proteins. Chapter Two summarizes the results of affinity cleaving experiments using leucine zipper-basic region (bZip) DNA-binding proteins. Specifically, the NH_2-terminal locations of a dimer containing the DNA binding domain of the yeast transcriptional activator GCN4 were mapped on the binding sites 5'-CTGACTAAT-3' and 5'ATGACTCTT- 3' using affinity cleaving. Analysis of the DNA cleavage patterns from Fe•EDTA-GCN4(222-281) and (226-281) dimers reveals that the NH_2-termini are in the major groove nine to ten base pairs apart and symmetrically displaced four to five base pairs from the central C of the recognition site. These data are consistent with structural models put forward for this class of DNA binding proteins. The results of these experiments are evaluated in light of the recently published crystal structure for the GCN4-DNA complex. Preliminary investigations of affinity cleaving proteins based on the DNA-binding domains of the bZip proteins Jun and Fos are also described.

Chapter Three describes experiments demonstrating the simultaneous binding of GCN4(226-281) and 1-Methylimidazole-2-carboxamide-netropsin (2-ImN), a designed synthetic peptide which binds in the minor groove of DNA at 5'-TGACT-3' sites as an antiparallel, side-by-side dimer. Through the use of Fe•EDTA-GCN4(226-281) as a sequence-specific footprinting agent, it is shown that the dimeric protein GCN4(226-281) and the dimeric peptide 2- ImN can simultaneously occupy their common binding site in the major and minor grooves of DNA, respectively. The association constants for 2-ImN in the presence and in the absence of Fe•EDTA-GCN4(226-281) are found to be similar, suggesting that the binding of the two dimers is not cooperative.

Chapter Four describes the synthesis and characterization of PBA-β-OH-His- Hin(139-190), a hybrid protein containing the DNA-binding domain of Hin recombinase and the putative iron-binding and oxygen-activating domain of the antitumor antibiotic bleomycin. This 54-residue protein, comprising residues 139-190 of Hin recombinase with the dipeptide pyrimidoblamic acid-β-hydroxy-L-histidine (PBA-β-OH-His) at the NH2 terminus, was synthesized by solid phase methods. PBA-β-OH-His-Hin(139- 190) binds specifically to DNA at four distinct Hin binding sites with affinities comparable to those of the unmodified Hin(139-190). In the presence of dithiothreitol (DTT), Fe•PB-β-OH-His-Hin(139-190) cleaves DNA with specificity remarkably similar to that of Fe•EDTA-Hin(139-190), although with lower efficiency. Analysis of the cleavage pattern suggests that DNA cleavage is mediated through a diffusible species, in contrast with cleavage by bleomycin, which occurs through a non-diffusible oxidant.

Darrigolen gramatikaz

Published in 2008.

La alimentación de personas con discapacidades: cumplimiento de las recomendaciones para la ingesta de alimentos y nutrientes

[ES] Las personas con discapacidades son un grupo heterogéneo de población, con una amplia variedad en factores que afectan a sus hábitos alimentarios y a su estado nutricional. Los resultados del presente estudio ponen en evidencia que la alimentación que reciben los pacientes estudiados no cumple las recomendaciones nutricionales establecidas por organismos nacionales e internacionales.

Analyse des Fluchtverhaltens von Fischen auf Schiffsgeräusche mit hydroakustischen Methoden

Investigations on the avoidance reactions of pelagic schooling fish (herring and sprat) released by an approaching fishery vessel were carried out during the 378th cruise of FRC "Solea" from 25 September to 3 October 1995 in the Arkona Sea, southern Baltic. An echosounder system EK 500/BI500 with a 38 kHz transducer mounted on a towed body as weIl as a 120 kHz hull mounted transducer were used. Fish densities were measured synchronously as well as under the ship as at a laterally distances from the ship by the transducer of the towed body. By these means the variation of fish densities up to a certain distance from the ship is possible. The advantage of using an echo integrating system for these measurements is, that it works also for not schooling fish and under conditions where schooling fish disperse (e.g. at night).

New strategies for the total synthesis of aza-propellane natural products

The propellane alkaloids comprise a large class of natural products that possess varying degrees of structural complexity and biological activity. The earliest of these to be isolated was acutumine, a chlorinated alkaloid that has been shown to exhibit selective T-cell cytotoxicity and antiamnesic properties. Alternatively, the hasubanan family of natural products has garnered considerable attention from the synthetic community in part due to its structural similarities to morphine. While these alkaloids have been the subject of numerous synthetic studies over the last forty years, very few enantioselective total syntheses have been reported to date.

As part of a research program directed towards the synthesis of various alkaloid natural products, we have developed a unified strategy for the preparation of the hasubanan and acutumine alkaloids. Specifically, a highly diastereoselective 1,2-addition of organometallic reagents to benzoquinone-derived tert-butanesulfinimines was established, which provides access to enantioenriched 4-aminocyclohexadienone products. This methodology enabled the enantioselective construction of functionalized dihydroindolones, which were found to undergo intramolecular Friedel-Crafts conjugate additions to furnish the propellane cores of several hasubanan alkaloids. As a result of these studies, the first enantioselective total syntheses of 8-demethoxyrunanine and cepharatines A, C, and D were accomplished in 9-11 steps from commercially available starting materials.

More recent efforts have focused on applying the sulfinimine methodology to the synthesis of a more structurally complex propellane alkaloid, acutumine. Extensive studies have determined that a properly functionalized dihydroindolone undergoes a photochemical [2+2] cycloaddition followed by a lactone fragmentation/Dieckmann cyclization to establish the carbocyclic framework of the natural product. The preparation of more appropriately oxidized propellane intermediates is currently under investigation, and is anticipated to facilitate our synthetic endeavors toward acutumine.

硬X射线相衬成像技术

介绍了近年来硬X射线位相衬度成像技术的发展状况，详细论述了X射线干涉相衬、衍射增强相衬，类同轴相衬等几种典型的成像原理。

Electron flow through cytochrome P450

The cytochromes P450 (P450s) are a remarkable class of heme enzymes that catalyze the metabolism of xenobiotics and the biosynthesis of signaling molecules. Controlled electron flow into the thiolate-ligated heme active site allows P450s to activate molecular oxygen and hydroxylate aliphatic C–H bonds via the formation of high-valent metal-oxo intermediates (compounds I and II). Due to the reactive nature and short lifetimes of these intermediates, many of the fundamental steps in catalysis have not been observed directly. The Gray group and others have developed photochemical methods, known as “flash-quench,” for triggering electron transfer (ET) and generating redox intermediates in proteins in the absence of native ET partners. Photo-triggering affords a high degree of temporal precision for the gating of an ET event; the initial ET and subsequent reactions can be monitored on the nanosecond-to-second timescale using transient absorption (TA) spectroscopies. Chapter 1 catalogues critical aspects of P450 structure and mechanism, including the native pathway for formation of compound I, and outlines the development of photochemical processes that can be used to artificially trigger ET in proteins. Chapters 2 and 3 describe the development of these photochemical methods to establish electronic communication between a photosensitizer and the buried P450 heme. Chapter 2 describes the design and characterization of a Ru-P450-BM3 conjugate containing a ruthenium photosensitizer covalently tethered to the P450 surface, and nanosecond-to-second kinetics of the photo-triggered ET event are presented. By analyzing data at multiple wavelengths, we have identified the formation of multiple ET intermediates, including the catalytically relevant compound II; this intermediate is generated by oxidation of a bound water molecule in the ferric resting state enzyme. The work in Chapter 3 probes the role of a tryptophan residue situated between the photosensitizer and heme in the aforementioned Ru-P450 BM3 conjugate. Replacement of this tryptophan with histidine does not perturb the P450 structure, yet it completely eliminates the ET reactivity described in Chapter 2. The presence of an analogous tryptophan in Ru-P450 CYP119 conjugates also is necessary for observing oxidative ET, but the yield of heme oxidation is lower. Chapter 4 offers a basic description of the theoretical underpinnings required to analyze ET. Single-step ET theory is first presented, followed by extensions to multistep ET: electron “hopping.” The generation of “hopping maps” and use of a hopping map program to analyze the rate advantage of hopping over single-step ET is described, beginning with an established rhenium-tryptophan-azurin hopping system. This ET analysis is then applied to the Ru-tryptophan-P450 systems described in Chapter 2; this strongly supports the presence of hopping in Ru-P450 conjugates. Chapter 5 explores the implementation of flash-quench and other phototriggered methods to examine the native reductive ET and gas binding events that activate molecular oxygen. In particular, TA kinetics that demonstrate heme reduction on the microsecond timescale for four Ru-P450 conjugates are presented. In addition, we implement laser flash-photolysis of P450 ferrous–CO to study the rates of CO rebinding in the thermophilic P450 CYP119 at variable temperature. Chapter 6 describes the development and implementation of air-sensitive potentiometric redox titrations to determine the solution reduction potentials of a series of P450 BM3 mutants, which were designed for non-native cyclopropanation of styrene in vivo. An important conclusion from this work is that substitution of the axial cysteine for serine shifts the wild type reduction potential positive by 130 mV, facilitating reduction by biological redox cofactors in the presence of poorly-bound substrates. While this mutation abolishes oxygenation activity, these mutants are capable of catalyzing the cyclopropanation of styrene, even within the confines of an E. coli cell. Four appendices are also provided, including photochemical heme oxidation in ruthenium-modified nitric oxide synthase (Appendix A), general protocols (Appendix B), Chapter-specific notes (Appendix C) and Matlab scripts used for data analysis (Appendix D).

Korngrößenzusammensetzung und Staubanteil von vier für das Vorstrecken von Glasaalen verwendeten kommerziellen Futtern

Vier kommerziell hergestellte und für die Aalaufzucht verwendete Brutaufzuchtfutter der Marken Alma, Skretting, Ecovit und Provimi wurden untersucht. Von ihrer Zusammensetzung her handelt es sich um Forellenbrutfutter mit einem Rohproteingehalt um 50% und einem Fettgehalt zwischen 12 und 15%. Bis auf Ecovit werden alle genannten Futter vom Hersteller auch für die Auzucht von Glasaalen empfohlen.

Elektronische Registrierung von Untersuchungsdaten auf See

Die elektronische Erfassung von auf See gewonnenen Daten direkt bei der Entstehung ist eine wesentliche Voraussetzung zur rationellen Nutzung elektronischer Datenverarbeitungssysteme. Die Online-Erfassung erspart nicht nur den späteren zeitaufwand bei der Übertragung der Daten von handschriftlichen Strichlisten in den Rechner, sondern schließt gleichzeitig dabei u.U. entstehende Fehler aus. Darüberhinaus ermöglicht die direkte Eingabe von gewonnenen Daten eine schnelle vorläufige Sichtung von Ergebnissen und erlaubt dadurch die Anpassung von Untersuchungsprogrammen an die an Ort und Stelle erzielten Resultate.

Modelling soil erosion and transport in the Burrishoole catchment, Newport, Co. Mayo, Ireland

The Burrishoole catchment is situated in County Mayo, on the northwest coast of the Republic of Ireland. Much of the catchment is covered by blanket peat that, in many areas, has become heavily eroded in recent years. This is thought to be due, primarily, to the adverse effects of forestry and agricultural activities in the area. Such activities include ploughing, drainage, the planting and harvesting of trees, and sheep farming, all of which are potentially damaging to such a sensitive landscape if not managed carefully. This article examines the sediment yield and hydrology of the Burrishoole catchment. Flow and sediment concentrations were measured at 8-hourly intervals from 5 February 2001 to 8 November 2001 with an automatic sampler and separate flow gauge, and hourly averages were recorded between 4 July 2002 and 6 September 2002 using an automatic river monitoring system [ARMS]. The authors describe the GIS-based model of soil erosion and transport that was applied to the Burrishoole catchment during this study. The results of these analyses were compared, in a qualitative manner, with the aerial photography available for the Burrishoole catchment to see whether areas that were predicted to contribute large proportions of eroded material to the drainage network corresponded with areas where peat erosion could be identified through photo-interpretation.

Análise comparativa in vivo da detecção de lesões de cárie oclusal e proximal por meio de exame visual (ICDAS), exame radiográfico e transiluminação por fibra ótica (FOTI)

O objetivo do presente trabalho foi avaliar in vivo a detecção de cárie através do exame visual ICDAS, transiluminação por fibra ótica combinado ao ICDAS e exame radiográfico. Um total de 2.279 superfícies proximais e cicatrículas e fissuras em incisivos superiores, pré-molares e molares permanentes e 272 superfícies em molares decíduos em72 escolares (8 a 18 anos) foram avaliadas por um examinador treinado. Os sete escores para detecção de cárie primária do sistema visual ICDAS foram aplicados. Dois equipamentos de transiluminação por fibra ótica foram avaliados: FOTI Schott (SCH), com ponta de fibra ótica com 0,5mm de diâmetro, e FOTI Microlux (MIC), com diâmetro da ponta 3 mm. Durante o exame combinado FOTI/ICDAS, a fibra ótica era utilizada tanto para iluminar quanto para transiluminar a superfície sob avaliação. O exame radiográfico (RX) consistiu de radiografias interproximais posteriores e periapicais anteriores. Os exames foram realizados em consultório odontológico após escovação supervisionada. No primeiro dia de exame, o exame visual utilizando o ICDAS era realizado e em seguida, o exame combinado ao MIC ou SCH. Logo após era realizado o exame radiográfico. Após uma semana, novamente o ICDAS era realizado, e em seguida o exame combinado com o equipamento de FOTI não utilizado na semana anterior. Os exames foram repetidos em 10 pacientes após intervalo mínimo de uma semana para avaliação da reprodutibilidade intra-examinador, a qual apresentou valores de 0,95 (ICDAS), 0,94 (MIC), 0,95 (SCH) e 0,99 (RX) pelo kappa ponderado. Em cicatrículas e fissuras de permanentes, o RX julgou que um número maior de superfícies apresentava lesão em dentina (53) do que os outros métodos (34 a 36); porém não detectou nenhuma lesão em esmalte, as quais foram identificadas pelo ICDAS (94), SCH (107) e MIC (91). Em proximais permanentes, a transiluminação por fibra ótica identificou maior número de proximais como lesão em esmalte - 150 (SCH) e 139 (MIC) - do que o exame visual (106), enquanto o RX identificou somente 43. Em oclusais de decíduos, os quatro métodos julgaram um número aproximadamente similar de superfícies sem lesão (52 a 59) ou com lesão em dentina (21 a 26), assim como para lesões proximais em dentina (31 a 36). Entretanto um número reduzido de lesões proximais decíduas em esmalte foi julgado pelo exame radiográfico (3) em comparação com os outros métodos (15 a 16). Em decíduos, o ICDAS e o FOTI combinado ao exame visual julgaram maior número de lesões proximais em esmalte que o exame radiográfico, sendo que número similar de lesões em dentina foram classificadas pelos quatro métodos em oclusais e proximais de molares decíduos. Em cicatrículas e fissuras de permanentes, tanto o exame visual ICDAS quanto sua combinação aos dois equipamentos de transiluminação apresentaram maior similaridade de superfícies julgadas como lesão em esmalte ou como lesão em dentina, enquanto o exame radiográfico classificou mais superfícies como lesão em dentina e nenhuma como lesão em esmalte. A adição da transiluminação por fibra ótica ao exame visual aumentou em um terço a detecção das lesões cariosas proximais julgadas em dentina pelo ICDAS isoladamente e aproximadamente quadruplicou o número daquelas assim classificadas pela avaliação radiográfica em permanentes.