Homogenization Approach to Smoothed Molecular Dynamics

In classical Molecular Dynamics a molecular system is modelled by classi-cal Hamiltonian equations of motion. The potential part of the correspond-ing energy function of the system includes contributions of several types of atomic interaction. Among these, some interactions represent the bond structure of the molecule. Particularly these interactions lead to extremely stiff potentials which force the solution of the equations of motion to oscil late on a very small time scale. There is a strong need for eliminating the smallest time scales because they are a severe restriction for numerical long-term simulations of macromolecules. This leads to the idea of just freezing the high frequency degrees of freedom (bond stretching and bond angles) via increasing the stiffness of the strong part of the potential to infinity However, the naive way of doing this via holonomic constraints mistakenly ignores the energy contribution of the fast oscillations. The paper presents a mathematically rigorous discussion of the limit situation of infinite stiffnes

A review of data on abundance, trends in abundance, habitat use and diet of ice-breeding seals in the Southern Ocean

The development of models of marine ecosystems in the Southern Ocean is becoming increasingly important as a means of understanding and managing impacts such as exploitation and climate change. Collating data from disparate sources, and understanding biases or uncertainties inherent in those data, are important first steps for improving ecosystem models. This review focuses on seals that breed in ice habitats of the Southern Ocean (i.e. crabeater seal, Lobodon carcinophaga; Ross seal, Ommatophoca rossii; leopard seal, Hydrurga leptonyx; and Weddell seal, Leptonychotes weddellii). Data on populations (abundance and trends in abundance), distribution and habitat use (movement, key habitat and environmental features) and foraging (diet) are summarised, and potential biases and uncertainties inherent in those data are identified and discussed. Spatial and temporal gaps in knowledge of the populations, habitats and diet of each species are also identified

Data and Services at the Integrated Climate Data Center (ICDC) at the University of Hamburg

KlimawandelEarth observation data obtained from remote sensing sensors and in-situ data archives are fundamental for our current understanding of the Earth’s climate system. Such data are an important pre-requisite for Earth System research and should be easy to access and easy to use. In addition such data should be quality assessed and attached with information about uncertainties and long-term stability. If these data sets are stored in a self-explanatory, easy-to-use format, their usefulness and scientific value increase. This is the guideline for the Integrated Climate Data Center (ICDC) at the Center for Earth System Research and Sustainability (CEN), University of Hamburg. ICDC offers a reliable, quick and easy data access along with expert support for users and data providers. The ICDC provides several types of worldwide accessible in situ and satellite Earth observation data of the atmosphere, ocean, land surface, and cryosphere via the web portal http://icdc.zmaw.de. Recently, data from socio-economic sciences have been integrated into ICDC’s data base to enhance interdisciplinary collaboration. On ICDC’s web portal, each data set has its own page. It contains the data access points, a short data description, information about spatiotemporal coverage and resolution, data quality, important reference documents and contacts, and about how to cite the data set. The data are converted into netCDF or ASCII format. Consistency and quality checks are carried out – often in the framework of international collaborations. Literature studies are conducted to learn about potential limitations or preferred application areas of the data offered. The data sets can be accessed through the web page via FTP, HTTP or OPeNDAP. Using the Live Access Server, users can visualize data as maps, along transects and profiles, zoom into key regions, and create time series. In both fields, visualization and data access, ICDC tries to provide fast response times and high reliability

Effect of chemical disorder on NiMnSb investigated by Appearance Potential Spectroscopy: a theoretical study

The half-Heusler alloy NiMnSb is one of the local-moment ferromagnets with unique properties for future applications. Band structure calculations predict exclusively majority bands at the Fermi level, thus indicating {100%} spin polarization there. As one thinks about applications and the design of functional materials, the influence of chemical disorder in these materials must be considered. The magnetization, spin polarization, and electronic structure are expected to be sensitive to structural and stoichiometric changes. In this contribution, we report on an investigation of the spin-dependent electronic structure of NiMnSb. We studied the influence of chemical disorder on the unoccupied electronic density of states by use of the ab-initio Coherent Potential Approximation method. The theoretical analysis is discussed along with corresponding spin-resolved Appearance Potential Spectroscopy measurements. Our theoretical approach describes the spectra as the fully-relativistic self-convolution of the matrix-element weighted, orbitally resolved density of states.Comment: JPD submitte

The Production and Utilization of GDP-glucose in the Biosynthesis of Trehalose 6-Phosphate by Streptomyces venezuelae

Trehalose-6-phosphate synthase OtsA from streptomycetes is unusual in that it uses GDP-glucose as the donor substrate rather than the more commonly used UDP-glucose. We now confirm that OtsA from Streptomyces venezuelae has such a preference for GDP-glucose and can utilize ADP-glucose to some extent too. A crystal structure of the enzyme shows that it shares twin Rossmann-like domains with the UDP-glucose-specific OtsA from Escherichia coli. However, it is structurally more similar to Streptomyces hygroscopicus VldE, a GDP-valienol-dependent pseudoglycosyltransferase enzyme. Comparison of the donor binding sites reveals that the amino acids associated with the binding of diphosphoribose are almost all identical in these three enzymes. By contrast, the amino acids associated with binding guanine in VldE (Asn, Thr, and Val) are similar in S. venezuelae OtsA (Asp, Ser, and Phe, respectively) but not conserved in E. coli OtsA (His, Leu, and Asp, respectively), providing a rationale for the purine base specificity of S. venezuelae OtsA. To establish which donor is used in vivo, we generated an otsA null mutant in S. venezuelae. The mutant had a cell density-dependent growth phenotype and accumulated galactose 1-phosphate, glucose 1-phosphate, and GDP-glucose when grown on galactose. To determine how the GDP-glucose is generated, we characterized three candidate GDP-glucose pyrophosphorylases. SVEN_3027 is a UDP-glucose pyrophosphorylase, SVEN_ 3972 is an unusual ITP-mannose pyrophosphorylase, and SVEN_2781 is a pyrophosphorylase that is capable of generating GDP-glucose as well as GDP-mannose. We have therefore established how S. venezuelae can make and utilize GDP-glucose in the biosynthesis of trehalose 6-phosphate

Convergence of simple adaptive Galerkin schemes based on h − h/2 error estimators

We discuss several adaptive mesh-refinement strategies based on (h − h/2)-error estimation. This class of adaptivemethods is particularly popular in practise since it is problem independent and requires virtually no implementational overhead. We prove that, under the saturation assumption, these adaptive algorithms are convergent. Our framework applies not only to finite element methods, but also yields a first convergence proof for adaptive boundary element schemes. For a finite element model problem, we extend the proposed adaptive scheme and prove convergence even if the saturation assumption fails to hold in general

Late Maastrichtian carbon isotope stratigraphy and cyclostratigraphy of the Newfoundland Margin (Site U1403, IODP Expedition 342)

Earth’s climate during the Maastrichtian (latest Cretaceous) was punctuated by brief warming and cooling episodes, accompanied by perturbations of the global carbon cycle. Superimposed on a long-term cooling trend, the middle Maastrichtian is characterized by deep-sea warming and relatively high values of stable carbon-isotope ratios, followed by strong climatic variability towards the end of the Cretaceous. A lack of knowledge on the timing of climatic change inhibits our understanding of underlying causal mechanisms. We present an integrated stratigraphy from Integrated Ocean Drilling Program (IODP) Site U1403, providing an expanded deep ocean record from the North Atlantic (Expedition 342, Newfoundland Margin). Distinct sedimentary cyclicity suggests that orbital forcing played a major role in depositional processes, which is confirmed by statistical analyses of high resolution elemental data obtained by X-ray fluorescence (XRF) core scanning. Astronomical calibration reveals that the investigated interval encompasses seven 405-kyr cycles (Ma4051 to Ma4057) and spans the 2.8 Myr directly preceding the Cretaceous/Paleocene (K/Pg) boundary. A high-resolution carbon-isotope record from bulk carbonates allows us to identify global trends in the late Maastrichtian carbon cycle. Low-amplitude variations (up to 0.4‰) in carbon isotopes at Site U1403 match similar scale variability in records from Tethyan and Pacific open-ocean sites. Comparison between Site U1403 and the hemipelagic restricted basin of the Zumaia section (northern Spain), with its own well-established independent cyclostratigraphic framework, is more complex. Whereas the pre-K/Pg oscillations and the negative values of the Mid-Maastrichtian Event (MME) can be readily discerned in both the Zumaia and U1403 records, patterns diverge during a ~ 1 Myr period in the late Maastrichtian (67.8–66.8 Ma), with Site U1403 more reliably reflecting global carbon cycling. Our new carbon isotope record and cyclostratigraphy offer promise for Site U1403 to serve as a future reference section for high-resolution studies of late Maastrichtian paleoclimatic change