Variational Monte Carlo study of the hydrogen electronic structure at ultra-high pressure

Die causa finalis der vorliegenden Arbeit ist das Verständnis des Phasendiagramms von Wasserstoff bei ultrahohen Drücken, welche von nichtleitendem H2 bis hin zu metallischem H reichen. Da die Voraussetzungen für ultrahohen Druck im Labor schwer zu schaffen sind, bilden Computersimulationen ein wichtiges alternatives Untersuchungsinstrument. Allerdings sind solche Berechnungen eine große Herausforderung. Eines der größten Probleme ist die genaue Auswertung des Born-Oppenheimer Potentials, welches sowohl für die nichtleitende als auch für die metallische Phase geeignet sein muss. Außerdem muss es die starken Korrelationen berücksichtigen, die durch die kovalenten H2 Bindungen und die eventuellen Phasenübergänge hervorgerufen werden. Auf dieses Problem haben unsere Anstrengungen abgezielt. Im Kontext von Variationellem Monte Carlo (VMC) ist die Shadow Wave Function (SWF) eine sehr vielversprechende Option. Aufgrund ihrer Flexibilität sowohl lokalisierte als auch delokalisierte Systeme zu beschreiben sowie ihrer Fähigkeit Korrelationen hoher Ordnung zu berücksichtigen, ist sie ein idealer Kandidat für unsere Zwecke. Unglücklicherweise bringt ihre Formulierung ein Vorzeichenproblem mit sich, was die Anwendbarkeit limitiert. Nichtsdestotrotz ist es möglich diese Schwierigkeit zu umgehen indem man die Knotenstruktur a priori festlegt. Durch diesen Formalismus waren wir in der Lage die Beschreibung der Elektronenstruktur von Wasserstoff signifikant zu verbessern, was eine sehr vielversprechende Perspektive bietet. Während dieser Forschung haben wir also die Natur des Vorzeichenproblems untersucht, das sich auf die SWF auswirkt, und dabei ein tieferes Verständnis seines Ursprungs erlangt. Die vorliegende Arbeit ist in vier Kapitel unterteilt. Das erste Kapitel führt VMC und die SWF mit besonderer Ausrichtung auf fermionische Systeme ein. Kapitel 2 skizziert die Literatur über das Phasendiagramm von Wasserstoff bei ultrahohem Druck. Das dritte Kapitel präsentiert die Implementierungen unseres VMC Programms und die erhaltenen Ergebnisse. Zum Abschluss fasst Kapitel 4 unsere Bestrebungen zur Lösung des zur SWF zugehörigen Vorzeichenproblems zusammen.

Insights into transcription enhancer factor 1 (TEF-1) activity from the solution structure of the TEA domain.

Transcription enhancer factor 1 is essential for cardiac, skeletal, and smooth muscle development and uses its N-terminal TEA domain (TEAD) to bind M-CAT elements. Here, we present the first structure of TEAD and show that it is a three-helix bundle with a homeodomain fold. Structural data reveal how TEAD binds DNA. Using structure-function correlations, we find that the L1 loop is essential for cooperative loading of TEAD molecules on to tandemly duplicated M-CAT sites. Furthermore, using a microarray chip-based assay, we establish that known binding sites of the full-length protein are only a subset of DNA elements recognized by TEAD. Our results provide a model for understanding the regulation of genome-wide gene expression during development by TEA/ATTS family of transcription factors.

Pion emission from the T2K replica target: method, results and application

The T2K long-baseline neutrino oscillation experiment in Japan needs precise predictions of the initial neutrino flux. The highest precision can be reached based on detailed measurements of hadron emission from the same target as used by T2K exposed to a proton beam of the same kinetic energy of 30 GeV. The corresponding data were recorded in 2007-2010 by the NA61/SHINE experiment at the CERN SPS using a replica of the T2K graphite target. In this paper details of the experiment, data taking, data analysis method and results from the 2007 pilot run are presented. Furthermore, the application of the NA61/SHINE measurements to the predictions of the T2K initial neutrino flux is described and discussed.

Elucidation of the gas-phase structure of a sugar-modified DNA analogue

Antisense oligonucleotides are medical agents for the treatment of genetic diseases that are designed to interact specifically with mRNA. This interaction either induces enzymatic degradation of the targeted RNA or modifies processing pathways, e.g. by inducing alternative splicing of the pre-mRNA. The latter mechanism applies to the treatment of Duchenne muscular dystrophy with a sugar-modified DNA analogue called tricyclo-DNA (tcDNA). In tcDNA the ribose sugar-moiety is extended to a three-membered ring system, which augments the binding affinity and the selectivity of the antisense oligonucleotide for its target. The advent of chemically modified nucleic acids for antisense therapy presents a challenge to diagnostic tools, which must be able to cope with a variety of structural analogues. Mass spectrometry meets this demand for non-enzyme based sequencing methods ideally, because the technique is largely unaffected by structural modifications of the analyte. Sequence coverage of a fully modified tcDNA 15mer can be obtained in a single tandem mass spectrometric experiment. Beyond sequencing experiments, tandem mass spectrometry was applied to elucidate the gas-phase structure and stability of tcDNA:DNA and tcDNA:RNA hybrid duplexes. Most remarkable is the formation of truncated duplexes upon collision-induced dissociation of these structures. Our data suggest that the cleavage site within the duplex is directed by the modified sugar-moiety. Moreover, the formation of truncated duplexes manifests the exceptional stability of the hybrid duplexes in the gas-phase. This stability arises from the modified sugar-moiety, which locks the tcDNA single strand into a conformation that is similar to RNA in A-form duplexes. The conformational particularity of tcDNA in the gas-phase was confirmed by ion mobility-mass spectrometry experiments on tcDNA, DNA, and RNA.

Preliminary results and documentation of sediment cores CRP2 and CRP-2A from the Ross Sea off Cape Roberts, Antarctica

The site for CRP-2, 14 km east of Cape Roberts (77.006°S; 163.719°E), was selected to overlap the early Miocene strata cored in nearby CRP-1, and to sample deeper into the east-dipping strata near the western margin ofe he Victoria Land Basin to investigate Palaeogene climatic and tectonic history. CRP-2 was cored from 5 to 57 mbsf (metres below the sea floor) (core recovery 91 %), with a deviation resulting in CRP-2A being cored at the same site. CRP-2A reached down to 624mbsf (recovery 95%), and to strata with an age of c. 33-35 Ma. Drilling took place from 16 October to 25 November 1998, on 2.0-2.2 m of sea ice and through 178 m of water. Core fractures and other physical properties, such as sonic velocity, density and magnetic susceptibility, were measured throughout the core. Down-hole logs for these and other properties were run from 63 to 167 mbsf and subsequently from 200 to 623 mbsf, although density and velocity data could be obtained only to 440 mbsf because of hole collapse. Sonic velocity averages c. 2.0 km S-1 for the upper part of the hole, but there is an sharp increase to c. 3.0 km s-1 and also a slight angular unconformity, at 306 mbsf, corresponding most likely to the early/late Oligocene boundary (c. 28-30 Ma). Velocity then increases irregularly to around 3.6 km s-1 at the bottom of the hole, which is estimated to lie 120 m above the V4/V5 boundary. The higher velocities below 306 mbsf probably reflect more extensive carbonate and common pyrite cementation, in patches, nodules, bedding-parallel masses and as vein infills. Dip of the strata also increases down-hole from 3° in the upper 300 in to over 10° at the bottom. Temperature gradient is 21° k-1. Over 2 000 fractures were logged through the hole. Borehole televiewer imagery was obtained for the interval from 200 to 440 mbsf to orient the fractures for stress field analysis. Lithostratigraphical descriptions on a scale of 1:20 are presented for the full length of the core, along with core box images, as a 200 page supplement to this issue. The hole initially passed through a layer of muddy gravel to 5.5 mbsf (Lithological Sub-Unit or LSU 1.1), and then into a Quaternary diatom-bearing clast-rich diamicton to 21 mbsf (LSU 2. l), with an interval of alternating compact diamicton and loose sand, and containing a rich Pliocene foraminiferal fauna, to 27 mbsf (LSU 2.2). The unit beneath this (LSU 3.1) has similar physical properties (sonic velocity, porosity, magnetic susceptibility) and includes diamictites of similar character to those of LSU 2.1 and 2.2, but an early Miocene (c. 19 Ma) diatom assemblage at 28 mbsf (top of LSU 3.1) shows that this sub-unit is part of the older section. The strata beneath 27 mbsf, primary target for the project, extend from early Miocene to perhaps latest Eocene age, and are largely cyclic glacimarine nearshore to offshore sediments. They are described as 41 lithological sub-units and interpreted in terms of 12 recurrent lithofacies. These are 1) mudstone, 2) inter-stratified mudstone and sandstone, 3) muddy very fine to coarse sandstone, 4) well-sorted stratified fine sandstone, 5) moderately to well-sorted, medium-grained sandstone, 6) stratified diamictite, 7) massive diamictite, 8) rhythmically inter-stratified sandstone and mudstone, 9) clast-supported conglomerate, 10) matrix-supported conglomerate, 11) mudstone breccia and 12) volcaniclastic sediment. Sequence stratigraphical analysis has identified 22 unconformity-bounded depositional sequences in pre- Pliocene strata. They typically comprise a four-part architecture involving, in ascending order, 1) a sharp-based coarse-grained unit (Facies 6,7,9 or 10), 2) a fining-upward succession of sandstones (Facies 3 and 4), 3) a mudstone interval (Facies l), in some cases coarsening upward to muddy sandstones (Facies 3), and 4) a sharp-based sandstone dominated succession (mainly Facies 4). The cyclicity recorded by the strata is interpreted in terms of a glacier ice margin retreating and advancing from land to the west, and of rises and falls in sea level. Analysis of sequence periodicity awaits afirmer chronology. However, apreliminary spectral analysis of magnetic susceptibility for a deepwater mudstone within one of the sequences (from 339 to 347 mbsf) reveals ratios between hierarchical levels that are similar to those of the three Milankovitch orbital forcing periodicities. The strata contain a wide range of fossils, the most abundant being marine diatoms. These commonly form up to 5% of the sediment, though in places the core is barren (notably between 300 and 412 mbsf). Fifty samples out of 250 reviewed were studied in detail. The assemblages define ten biostratigraphical zones, some of them based on local or as yet undescribed forms. The assemblages are neritic, and largely planktonic, suggesting that the sea floor was mostly below the photic zone throughout deposition of the corcd sequence. Calcareous nannofossils, representing incursions of ocean surface waters, are much less common (72 out of 183 samples examined) and restricted to mudstone intervals a few tens of metres thick, but are important for dating. Foraminifera are also sparse (73 out of 135 samples) and represented only by calcareous benthic species. Changing assemblages indicate a shift from inshore environments in the early Oligocenc to outer shelf in the late Oligocenc, returning to inshore in the early Miocene. Marine palynomorplis yielded large numbers of well-preserved forms from most of the 116 samples examined. The new in situ assemblagc found last year in CRP-1 is extended down into the late Oligocene and a further new assemblage is found in the early Oligoccnc. Many taxa are new, and cannot us yet contribute to an improved understanding of chronology or ecology. Marine invertebrate macrofossils, mostly molluscs and serpulid tubes, are scattered throughout the core. Preservation is good in mudstones but poor in other lithologies. Climate on land is reflected in the content of terrestrial palynomorphs, which are extremely scarce down to c. 300 mbsf. Some forms are reworked, and others represent a low growing sparse tundra with at least one species of Nothofagus. Beneath this level, a significantly greater diversity and abundance suggests a milder climate and a low diversity woody vegetation in the early Oligocene, but still far short of the richness found in known Eocene strata of the region. Sedimentary facies in the oldest strata also suggest a milder climate in the oldest strata cored, with indications of substantial glacial melt-water discharges, but are typical of a coldcr climate in late Oligocene and early Miocene times. Clast analyses from diamictites reveal weak to random fabrics, suggesting either lack of ice-contact deposition or post-depositional modification, but periods when ice grounded at the drill site are inferred from thin zones of in-situ brecciated rock and soft-sediment folding. These are more common above c. 300 mbsf, perhaps reflecting more extensive glacial advances during deposition of those strata. Erosion of the adjacent Transantarctic Mountains through Jurassic basalt and dolerite-intruded Beacon strata into basement rocks beneath is recorded by petrographical studies of clast and sand grain assemblages. Core below 310 mbsf contains a dominance of fine-grained Jurassic dolerite and basalt fragments along with Beacon-derived coal debris and rounded quartz grains, whereas the strata above this level have a much higher proportion of basement derived granitoids, implying that the large areas of the adjacent mountains had been eroded to basement by the end of the early Oligocene. There is little indication of rift-related volcanism below 310 mbsf. Above this, however, basaltic and trachytic tephras are common, especially from 280 to 200 mbsf, from 150 to 46 mbsf, and in Pliocene LSU 2.2 from 21 to 27 mbsf. The largest volcanic eruptions generated layers of coarse (up to 1 cm) trachytic pumice lapilli between 97 and 114 mbsf. The thickest of these (1.2 m at 112 mbsf) may have produced an eruptive column extending tens of km into the stratosphere. A source within a few tens of km of the drill site is considered most likely. Present age estimates for the pre-Pliocene sequence are based mainly on biostratigraphy (using mainly marine diatoms and to a lesser extent calcareous nannofossils), with the age of the tephra from 112 to 114 mbsf (21.44k0.05 Ma from 84 crystals by Ar-Ar) as a key reference point. Although there are varied and well-preserved microfossil assemblages through most of the sequence (notably of diatoms and marine palynomorphs), they comprise largely taxa either known only locally or as yet undescribed. In addition, sequence stratigraphical analysis and features in the core itself indicate numerous disconformities. The present estimate from diatom assemblages is that the interval from 27 to 130 mbsf is early Miocene in age (c. 19 to 23.5 Ma), consistent with the Ar-Ar age from 112 to 114 mbsf. Diatom assemblages also indicate that the late Oligocene epoch extends from c. 130 to 307 mbsf, which is supported by late Oligocene nannofossils from 130 to 185 mbsf. Strata from 307 to 412 mbsf have no age-diagnostic assemblages, but below this early Oligocene diatoms and nannofossils have been recovered. A nannoflora at the bottom of the hole is consistent with an earliest Oligocene or latest Eocene age. Magnetostratigraphical studies based on about 1000 samples, 700 of which have so far undergone demagnetisation treatment, have provided a polarity stratigraphy of 12 pre-Pliocene magnetozones. Samples above 270 mbsf are of consistently high quality. Below this, magnetic behaviour is more variable. A preliminary age-depth plot using the Magnetic Polarity Time Scale (MPTS) and constrained by biostratigraphical data suggests that episodes of relatively rapid sedimentation took place at CRP-2 during Oligocene times (c. 100 m/My), but that more than half of the record was lost in a few major and many minor disconformities. Age estimates from Sr isotopes in shell debris and further tephra dating are expected to lead to a better comparison with the MPTS. CRP-2/2A has recorded a history of subsidence of the Victoria Land Basin margin that is similar to that found in CIROS-170 km to the south, reflecting stability in both basin and the adjacent mountains in late Cenozoic times, but with slow net accumulation in the middle Cenozoic. The climatic indicators from both drill holes show a similar correspondence, indicating polar conditions for the Quaternary but with sub-polar conditions in the early Miocene-late Oligocene and indications of warmer conditions still in the early Oligocene. Correlation between the CRP-2A core and seismic records shows that seismic units V3 and V4, both widespread in the Victoria Land Basin, represent a period of fluctuating ice margins and glacimarine sedimentation. The next drill hole, CRP-3, is expected to core deep into V5 and extend this record of climate and tectonics still further back in time.

Stable oxygen isotope and Mg/Ca ratios of planktonic foraminifera from the Holocene and the Last Glacial Maximum

We measured oxygen isotopes and Mg/Ca ratios in the surface-dwelling planktonic foraminifer Globigerinoides ruber (white s.s.) and the thermocline dweller Pulleniatina obliquiloculata to investigate upper ocean spatial variability in the Indo-Pacific Warm Pool (IPWP). We focused on three critical time intervals: the Last Glacial Maximum (LGM; 18-21.5 ka), the early Holocene (8-9 ka), and the late Holocene (0-2 ka). Our records from 24 stations in the South China Sea, Timor Sea, Indonesian seas, and western Pacific indicate overall dry and cool conditions in the IPWP during the LGM with a low thermal gradient between surface and thermocline waters. During the early Holocene, sea surface temperatures increased by ~3°C over the entire region, indicating intensification of the IPWP. However, in the eastern Indian Ocean (Timor Sea), the thermocline gradually shoaled from the LGM to early Holocene, reflecting intensification of the subsurface Indonesian Throughflow (ITF). Increased surface salinity in the South China Sea during the Holocene appears related to northward displacement of the monsoonal rain belt over the Asian continent together with enhanced influx of saltier Pacific surface water through the Luzon Strait and freshwater export through the Java Sea. Opening of the freshwater portal through the Java Sea in the early Holocene led to a change in the vertical structure of the ITF from surface- to thermocline-dominated flow and to substantial freshening of Timor Sea thermocline waters.

Stable isotope ratios and foraminiferal abundance of sediment cores from the Western Iberian Margin

Rapid climate changes at the onset of the last deglaciation and during Heinrich Event H4 were studied in detail at IMAGES cores MD95-2039 and MD95-2040 from the Western Iberian margin. A major reorganisation of surface water hydrography, benthic foraminiferal community structure, and deepwater isotopic composition commenced already 540 years before the Last Isotopic Maximum (LIM) at 17.43 cal. ka and within 670 years affected all environments. Changes were initiated by meltwater spill in the Nordic Seas and northern North Atlantic that commenced 100 years before concomitant changes were felt off western Iberia. Benthic foraminiferal associations record the drawdown of deepwater oxygenation during meltwater and subsequent Heinrich Events H1 and H4 with a bloom of dysoxic species. At a water depth of 3380 m, benthic oxygen isotopes depict the influence of brines from sea ice formation during ice-rafting pulses and meltwater spill. The brines conceivably were a source of ventilation and provided oxygen to the deeper water masses. Some if not most of the lower deep water came from the South Atlantic. Benthic foraminiferal assemblages display a multi-centennial, approximately 300-year periodicity of oxygen supply at 2470-m water depth. This pattern suggests a probable influence of atmospheric oscillations on the thermohaline convection with frequencies similar to Holocene climate variations. For Heinrich Events H1 and H4, response times of surface water properties off western Iberia to meltwater injection to the Nordic Seas were extremely short, in the range of a few decades only. The ensuing reduction of deepwater ventilation commenced within 500-600 years after the first onset of meltwater spill. These fast temporal responses lend credence to numerical simulations that indicate ocean-climate responses on similar and even faster time scales.

Soil characteristics and abundance of archaea in samples from the Ross Sea Region, Antarctica

The objective of this study was to examine the presence and diversity of Archaea within mineral and ornithogenic soils from 12 locations across the Ross Sea region. Archaea were not abundant but DNA sufficient for producing 16S rRNA gene clone libraries was extracted from 18 of 51 soil samples, from four locations. A total of 1452 clones were analysed by restriction fragment length polymorphism and assigned to 43 operational taxonomic units from which representatives were sequenced. Archaea were primarily restricted to coastal mineral soils which showed a predominance of Crenarchaeota belonging to group 1.1b (>99% of clones). These clones were assigned to six clusters (A through F), based on shared identity to sequences in the GenBank database. Ordination indicated that soil chemistry and water content determined archaeal community structure. This is the first comprehensive study of the archaeal community in Antarctic soils and as such provides a reference point for further investigation of microbial function in this environment.

Age determination of corals from the North Atlantic and the Tasman Sea

During the past 40,000 years, global climate has moved into and out of a full glacial period, with the deglaciation marked by several millennial-scale rapid climate change events. Here we investigate the ecological response of deep-sea coral communities to both glaciation and these rapid climate change events. We find that the deep-sea coral populations of Desmophyllum dianthus in both the North Atlantic and the Tasmanian seamounts expand at times of rapid climate change. However, during the more stable Last Glacial Maximum, the coral population globally retreats to a more restricted depth range. Holocene populations show regional patterns that provide some insight into what causes these dramatic changes in population structure. The most important factors are likely responses to climatically driven changes in productivity, [O2] and [CO3]2-.

Particle flux studies of sediment traps from the northern and equatorial Indian Ocean

The Asian monsoon system governs seasonality and fundamental environmental characteristics in the study area from which two distinct peculiarities are most notable: upwelling and convective mixing in the Arabian Sea and low surface salinity and stratification in the Bay of Bengal due to high riverine input and monsoonal precipitation. The respective oceanography sets the framework for nutrient availability and productivity. Upwelling ensures high nitrate concentration with temporal/spatial Si limitation; freshwater-induced stratification leads to reduced nitrogen input from the subsurface but Si enrichment in surface waters. Ultimately, both environments support high abundance of diatoms, which play a central role in the export of organic matter. It is speculated that, additional to eddy pumping, nitrogen fixation is a source of N in stratified waters and contributes to the low-d15N signal in sinking particles formed under riverine impact. Organic carbon fluxes are best correlated to opal but not to carbonate, which is explained by low foraminiferal carbonate fluxes within the river-impacted systems. This observation points to the necessity of differentiating between carbonate sources for carbon flux modeling. As evident from a compilation of previously published and new data on labile organic matter composition (amino acids and carbohydrates), organic matter fluxes are mainly driven by direct input from marine production, except the site off Pakistan where sedimentary input of (marine) organic matter is dominant during the NE monsoon. The explanation of apparently different organic carbon export efficiency calls for further investigations of, for example, food web structure and water column processes.