The upper-atmosphere extension of the ICON general circulation model (version: Ua-icon-1.0)

How the upper-atmosphere branch of the circulation contributes to and interacts with the circulation of the middle and lower atmosphere is a research area with many open questions. Inertia-gravity waves, for instance, have moved in the focus of research as they are suspected to be key features in driving and shaping the circulation. Numerical atmospheric models are an important pillar for this research. We use the ICOsahedral Non-hydrostatic (ICON) general circulation model, which is a joint development of the Max Planck Institute for Meteorology (MPI-M) and the German Weather Service (DWD), and provides, e.g., local mass conservation, a flexible grid nesting option, and a non-hydrostatic dynamical core formulated on an icosahedral-triangular grid. We extended ICON to the upper atmosphere and present here the two main components of this new configuration named UA-ICON: an extension of the dynamical core from shallow- to deep-atmosphere dynamics and the implementation of an upper-atmosphere physics package. A series of idealized test cases and climatological simulations is performed in order to evaluate the upper-atmosphere extension of ICON. © Author(s) 2019

Journal Staff

Discoba (Excavata) is an ancient group of eukaryotes with great morphological and ecological diversity. Unlike the other major divisions of Discoba (Jakobida and Euglenozoa), little is known about the mitochondrial DNAs(mtDNAs) of Heterolobosea. We have assembled a complete mtDNA genome from the aggregating heterolobosean amoeba, Acrasis kona, which consists of a single circular highly AT-rich (83.3%) molecule of 51.5 kb. Unexpectedly, A. kona mtDNA is missing roughly 40% of the protein-coding genes and nearly half of the transfer RNAs found in the only other sequenced heterolobosean mtDNAs, those of Naegleria spp. Instead, over a quarter of A. kona mtDNA consists of novel open reading frames. Eleven of the 16 protein-coding genes missing from A. kona mtDNA were identified in its nuclear DNA and polyA RNA, and phylogenetic analyses indicate that at least 10 of these 11 putative nuclear-encoded mitochondrial (NcMt) proteins arose by direct transfer from the mitochondrion. Acrasis kona mtDNA also employs C-to-U type RNA editing, and 12 homologs of DYW-type pentatricopeptide repeat (PPR) proteins implicated in plant organellar RNA editing are found in A. kona nuclear DNA. A mapping of mitochondrial gene content onto a consensus phylogeny reveals a sporadic pattern of relative stasis and rampant gene loss in Discoba. Rampant loss occurred independently in the unique common lineage leading to Heterolobosea + Tsukubamonadida and later in the unique lineage leading to Acrasis. Meanwhile, mtDNA gene content appears to be remarkably stable in the Acrasis sister lineage leading to Naegleria and in their distant relatives Jakobida

Photodissociation of Conformer-Selected Ubiquitin Ions Reveals Site-Specific Cis/Trans Isomerization of Proline Peptide Bonds

Ultraviolet photodissociation (UVPD) of gas-phase proteins has attracted increased attention in recent years. This growing interest is largely based on the fact that, in contrast to slow heating techniques such as collision induced dissociation (CID), the cleavage propensity after absorption of UV light is distributed over the entire protein sequence, which can lead to a very high sequence coverage as required in typical top-down proteomics applications. However, in the gas phase, proteins can adopt a multitude of distinct and sometimes coexisting conformations, and it is not clear how this three-dimensional structure affects the UVPD fragmentation behavior. Using ion mobility–UVPD–mass spectrometry in conjunction with molecular dynamics simulations, we provide the first experimental evidence that UVPD is sensitive to the higher order structure of gas-phase proteins. Distinct UVPD spectra were obtained for different extended conformations of 11+ ubiquitin ions. Assignment of the fragments showed that the majority of differences arise from cis/trans isomerization of one particular proline peptide bond. Seen from a broader perspective, these data highlight the potential of UVPD to be used for the structural analysis of proteins in the gas phas

Shape and Interaction Decoupling for Colloidal Pre-Assembly

Creating materials with a structural hierarchy that is independently controllable at a range of scales requires breaking naturally occurring hierarchies. Breaking natural hierarchies is possible if building block attributes can be decoupled from the structure of pre-assembled, mesoscale building blocks that form the next level in the structural hierarchy. Here, we show that pre-assembled colloidal structures achieving geometric and interaction decoupling can be prepared in emulsions of silica superballs, which are cubic-like particles with rounded edges. We show that, for clusters of up to nine particles, colloidal superballs pack consistently like spheres, despite the presence of shape anisotropy and facets in the cubic-like particles. We compare our results with clusters prepared with magnetic superballs and find good qualitative agreement, suggesting that the cluster geometries are solely determined by the shape of the constituent particles. Our findings demonstrate that highly shape-anisotropic building blocks, under suitable conditions, can be pre-assembled into structures that are not found in bulk, thereby achieving a decoupling that can be further exploited for hierarchical materials development.Comment: 22 pages, 7 figure

Savor the Cryosphere

This article provides concise documentation of the ongoing retreat of glaciers, along with the implications that the ice loss presents, as well as suggestions for geoscience educators to better convey this story to both students and citizens. We present the retreat of glaciers—the loss of ice—as emblematic of the recent, rapid contraction of the cryosphere. Satellites are useful for assessing the loss of ice across regions with the passage of time. Ground-based glaciology, particularly through the study of ice cores, can record the history of environmental conditions present during the existence of a glacier. Repeat photography vividly displays the rapid retreat of glaciers that is characteristic across the planet. This loss of ice has implications to rising sea level, greater susceptibility to dryness in places where people rely upon rivers delivering melt water resources, and to the destruction of natural environmental archives that were held within the ice. Warming of the atmosphere due to rising concentrations of greenhouse gases released by the combustion of fossil fuels is causing this retreat. We highlight multimedia productions that are useful for teaching this story effectively. As geoscience educators, we attempt to present the best scholarship as accurately and eloquently as we can, to address the core challenge of conveying the magnitude of anthropogenic impacts, while also encouraging optimistic determination on the part of students, coupled to an increasingly informed citizenry. We assert that understanding human perturbation of nature, then choosing to engage in thoughtful science-based decision-making, is a wise choice. This topic comprised “Savor the Cryosphere,” a Pardee Keynote Symposium at the 2015 Annual Meeting in Baltimore, Maryland, USA, for which the GSA recorded supporting interviews and a webinar

History of Plio-Pleistocene Climate in the Northeastern Atlantic, Deep Sea Drilling Project Hole 552A

DSDP Hole 552A, cored with the HPC on Hatton Drift, represents an almost complete and undisturbed sediment section spanning the late Neogene and Quaternary. Lithologic, faunal, isotopic, and paleomagnetic analyses indicate that the section represents the most complete deep sea record of climatic evolution hitherto recovered at high latitudes in the northern hemisphere. A glacial record of remarkable resolution for the late Pliocene and Pleistocene is provided by oxygen and carbon isotope ratios in benthic foraminifers. In the upper part of the section, the whole of the standard oxygen isotope record of the past million years is well preserved. The onset of ice-rafting and glacial-interglacial alternations occurs at about 2.4 m.y. ago

Native like helices in a specially designed β peptide in the gas phase

In the natural peptides, helices are stabilized by hydrogen bonds that point backward along the sequence direction. Until now, there is only little evidence for the existence of analogous structures in oligomers of conformationally unrestricted β amino acids. We specifically designed the β peptide Ac-(β2hAla)6-LysH+ to form native like helical structures in the gas phase. The design follows the known properties of the peptide Ac-Ala6-LysH+ that forms a α helix in isolation. We perform ion-mobility mass-spectrometry and vibrational spectroscopy in the gas phase, combined with state-of-the-art density-functional theory simulations of these molecular systems in order to characterize their structure. We can show that the straightforward exchange of alanine residues for the homologous β amino acids generates a system that is generally capable of adopting native like helices with backward oriented H-bonds. By pushing the limits of theory and experiments, we show that one cannot assign a single preferred structure type due to the densely populated energy landscape and present an interpretation of the data that suggests an equilibrium of three helical structures

Spatially valid proprioceptive cues improve the detection of a visual stimulus

Vision and proprioception are the main sensory modalities that convey hand location and direction of movement. Fusion of these sensory signals into a single robust percept is now well documented. However, it is not known whether these modalities also interact in the spatial allocation of attention, which has been demonstrated for other modality pairings. The aim of this study was to test whether proprioceptive signals can spatially cue a visual target to improve its detection. Participants were instructed to use a planar manipulandum in a forward reaching action and determine during this movement whether a near-threshold visual target appeared at either of two lateral positions. The target presentation was followed by a masking stimulus, which made its possible location unambiguous, but not its presence. Proprioceptive cues were given by applying a brief lateral force to the participant’s arm, either in the same direction (validly cued) or in the opposite direction (invalidly cued) to the on-screen location of the mask. The d′ detection rate of the target increased when the direction of proprioceptive stimulus was compatible with the location of the visual target compared to when it was incompatible. These results suggest that proprioception influences the allocation of attention in visual spac

History of oceanic front development in the New Zealand sector of the Southern Ocean during the Cenozoic--a synthesis

The New Zealand sector of the Southern Ocean (NZSSO) has opened about the Indian-Pacific spreading ridge throughout the Cenozoic. Today the NZSSO is characterised by broad zonal belts of antarctic (cold), subantarctic (cool), and subtropical (warm) surface-water masses separated by prominent oceanic fronts: the Subtropical Front (STF) c. 43deg.S, Subantarctic Front (SAF) c. 50deg.S, and Antarctic Polar Front (AAPF) c. 60deg.S. Despite a meagre database, the broad pattern of Cenozoic evolution of these fronts is reviewed from the results of Deep Sea Drilling Project-based studies of sediment facies, microfossil assemblages and diversity, and stable isotope records, as well as from evidence in onland New Zealand Cenozoic sequences. Results are depicted schematically on seven paleogeographic maps covering the NZSSO at 10 m.y. intervals through the Cenozoic. During the Paleocene and most of the Eocene (65-35 Ma), the entire NZSSO was under the influence of warm to cool subtropical waters, with no detectable oceanic fronts. In the latest Eocene (c. 35 Ma), a proto-STF is shown separating subantarctic and subtropical waters offshore from Antarctica, near 65deg.S paleolatitude. During the earliest Oligocene, this front was displaced northwards by development of an AAPF following major global cooling and biotic turnover associated with ice sheet expansion to sea level on East Antarctica. Early Oligocene full opening (c. 31 Ma) of the Tasmanian gateway initiated vigorous proto-circum-Antarctic flow of cold/cool waters, possibly through a West Antarctic seaway linking the southern Pacific and Atlantic Oceans, including detached northwards "jetting" onto the New Zealand plateau where condensation and unconformity development was widespread in cool-water carbonate facies. Since this time, a broad tripartite division of antarctic, subantarctic, and subtropical waters has existed in the NZSSO, including possible development of a proto-SAF within the subantarctic belt. In the Early-early Middle Miocene (25-15 Ma), warm subtropical waters expanded southwards into the northern NZSSO, possibly associated with reduced ice volume on East Antarctica but particularly with restriction of the Indonesian gateway and redirection of intensified warm surface flows southwards into the Tasman Sea, as well as complete opening of the Drake gateway by 23 Ma allowing more complete decoupling of cool circum-Antarctic flow from the subtropical waters. During the late Middle-Late Miocene (15-5 Ma), both the STF and SAF proper were established in their present relative positions across and about the Campbell Plateau, respectively, accompanying renewed ice buildup on East Antarctica and formation of a permanent ice sheet on West Antarctica, as well as generally more expansive and intensified circum-Antarctic flow. The ultimate control on the history of oceanic front development in the NZSSO has been plate tectonics through its influence on the paleogeographic changes of the Australian-New Zealand-Antarctic continents and their intervening oceanic basins, the timing of opening and closing of critical seaways, the potential for submarine ridges and plateaus to exert some bathymetric control on the location of fronts, and the evolving ice budget on the Antarctic continent. The broad trends of the Cenozoic climate curve for New Zealand deduced from fossil evidence in the uplifted marine sedimentary record correspond well to the principal paleoceanographic events controlling the evolution and migration of the oceanic fronts in the NZSSO

Primordial non-Gaussianity in the Bispectrum of the Halo Density Field

The bispectrum vanishes for linear Gaussian fields and is thus a sensitive probe of non-linearities and non-Gaussianities in the cosmic density field. Hence, a detection of the bispectrum in the halo density field would enable tight constraints on non-Gaussian processes in the early Universe and allow inference of the dynamics driving inflation. We present a tree level derivation of the halo bispectrum arising from non-linear clustering, non-linear biasing and primordial non-Gaussianity. A diagrammatic description is developed to provide an intuitive understanding of the contributing terms and their dependence on scale, shape and the non-Gaussianity parameter fNL. We compute the terms based on a multivariate bias expansion and the peak-background split method and show that non-Gaussian modifications to the bias parameters lead to amplifications of the tree level bispectrum that were ignored in previous studies. Our results are in a good agreement with published simulation measurements of the halo bispectrum. Finally, we estimate the expected signal to noise on fNL and show that the constraint obtainable from the bispectrum analysis significantly exceeds the one obtainable from the power spectrum analysis.Comment: 34 pages, 15 figures, (v3): matches JCAP published versio