DFTB+, a software package for efficient approximate density functional theory based atomistic simulations.

DFTB+ is a versatile community developed open source software package offering fast and efficient methods for carrying out atomistic quantum mechanical simulations. By implementing various methods approximating density functional theory (DFT), such as the density functional based tight binding (DFTB) and the extended tight binding method, it enables simulations of large systems and long timescales with reasonable accuracy while being considerably faster for typical simulations than the respective ab initio methods. Based on the DFTB framework, it additionally offers approximated versions of various DFT extensions including hybrid functionals, time dependent formalism for treating excited systems, electron transport using non-equilibrium Green's functions, and many more. DFTB+ can be used as a user-friendly standalone application in addition to being embedded into other software packages as a library or acting as a calculation-server accessed by socket communication. We give an overview of the recently developed capabilities of the DFTB+ code, demonstrating with a few use case examples, discuss the strengths and weaknesses of the various features, and also discuss on-going developments and possible future perspectives.

Psychosocial problems in traumatized refugee families: overview of risks and some recommendations for support services.

This article is an abridged version of a report by an advisory council to the German government on the psychosocial problems facing refugee families from war zones who have settled in Germany. It omits the detailed information contained in the report about matters that are specific to the German health system and asylum laws, and includes just those insights and strategies that may be applicable to assisting refugees in other host countries as well. The focus is on understanding the developmental risks faced by refugee children when they or family members are suffering from trauma-related psychological disorders, and on identifying measures that can be taken to address these risks. The following recommendations are made: recognizing the high level of psychosocial problems present in these families, providing family-friendly living accommodations, teaching positive parenting skills, initiating culture-sensitive interventions, establishing training programs to support those who work with refugees, expanding the availability of trained interpreters, facilitating access to education and health care, and identifying intervention requirements through screening and other measures.

Trends for isolated amino acids and dipeptides: Conformation, divalent ion binding, and remarkable similarity of binding to calcium and lead.

We derive structural and binding energy trends for twenty amino acids, their dipeptides, and their interactions with the divalent cations Ca2+, Ba2+, Sr2+, Cd2+, Pb2+, and Hg2+. The underlying data set consists of more than 45,000 first-principles predicted conformers with relative energies up to ~4 eV (~400 kJ/mol). We show that only very few distinct backbone structures of isolated amino acids and their dipeptides emerge as lowest-energy conformers. The isolated amino acids predominantly adopt structures that involve an acidic proton shared between the carboxy and amino function. Dipeptides adopt one of two intramolecular-hydrogen bonded conformations C5 or . Upon complexation with a divalent cation, the accessible conformational space shrinks and intramolecular hydrogen bonding is prevented due to strong electrostatic interaction of backbone and side chain functional groups with cations. Clear correlations emerge from the binding energies of the six divalent ions with amino acids and dipeptides. Cd2+ and Hg2+ show the largest binding energies-a potential correlation with their known high acute toxicities. Ca2+ and Pb2+ reveal almost identical binding energies across the entire series of amino acids and dipeptides. This observation validates past indications that ion-mimicry of calcium and lead should play an important role in a toxicological context.

Approaching truly freestanding graphene: the structure of hydrogen-intercalated graphene on 6H-SiC(0001).

We measure the adsorption height of hydrogen-intercalated quasifreestanding monolayer graphene on the (0001) face of 6H silicon carbide by the normal incidence x-ray standing wave technique. A density functional calculation for the full (6√3×6√3)-R30° unit cell, based on a van der Waals corrected exchange correlation functional, finds a purely physisorptive adsorption height in excellent agreement with experiments, a very low buckling of the graphene layer, a very homogeneous electron density at the interface, and the lowest known adsorption energy per atom for graphene on any substrate. A structural comparison to other graphenes suggests that hydrogen-intercalated graphene on 6H-SiC(0001) approaches ideal graphene.

The ELPA library: scalable parallel eigenvalue solutions for electronic structure theory and computational science.

Obtaining the eigenvalues and eigenvectors of large matrices is a key problem in electronic structure theory and many other areas of computational science. The computational effort formally scales as O(N(3)) with the size of the investigated problem, N (e.g. the electron count in electronic structure theory), and thus often defines the system size limit that practical calculations cannot overcome. In many cases, more than just a small fraction of the possible eigenvalue/eigenvector pairs is needed, so that iterative solution strategies that focus only on a few eigenvalues become ineffective. Likewise, it is not always desirable or practical to circumvent the eigenvalue solution entirely. We here review some current developments regarding dense eigenvalue solvers and then focus on the Eigenvalue soLvers for Petascale Applications (ELPA) library, which facilitates the efficient algebraic solution of symmetric and Hermitian eigenvalue problems for dense matrices that have real-valued and complex-valued matrix entries, respectively, on parallel computer platforms. ELPA addresses standard as well as generalized eigenvalue problems, relying on the well documented matrix layout of the Scalable Linear Algebra PACKage (ScaLAPACK) library but replacing all actual parallel solution steps with subroutines of its own. For these steps, ELPA significantly outperforms the corresponding ScaLAPACK routines and proprietary libraries that implement the ScaLAPACK interface (e.g. Intel's MKL). The most time-critical step is the reduction of the matrix to tridiagonal form and the corresponding backtransformation of the eigenvectors. ELPA offers both a one-step tridiagonalization (successive Householder transformations) and a two-step transformation that is more efficient especially towards larger matrices and larger numbers of CPU cores. ELPA is based on the MPI standard, with an early hybrid MPI-OpenMPI implementation available as well. Scalability beyond 10,000 CPU cores for problem sizes arising in the field of electronic structure theory is demonstrated for current high-performance computer architectures such as Cray or Intel/Infiniband. For a matrix of dimension 260,000, scalability up to 295,000 CPU cores has been shown on BlueGene/P.

Aquatic modules for bioregenerative life support systems: developmental aspects based on the space flight results of the C.E.B.A.S. MIN-MODULE.

The Closed Equilibrated Biological Aquatic System (C.E.B.A.S.) is an artificial aquatic ecosystem which contains teleost fishes, water snails, ammonia oxidizing bacteria and edible non-gravitropic water plants. It serves as a model for aquatic food production modules which are not seriously affected by microgravity and other space conditions. Its space flight version, the so-called C.E.B.A.S. MINI-MODULE was already successfully tested in the STS-89 and STS-90 (NEUROLAB) missions. It will be flown a third time in space with the STS-107 mission in January 2003. All results obtained so far in space indicate that the basic concept of the system is more than suitable to drive forward its development. The C.E.B.A.S. MINI-MODULE is located within a middeck locker with limited space for additional components. These technical limitations allow only some modifications which lead to a maximum experiment time span of 120 days which is not long enough for scientifically essential multi-generation-experiments. The first necessary step is the development of "harvesting devices" for the different organisms. In the limited space of the plant bioreactor a high biomass production leads to self-shadowing effects which results in an uncontrolled degradation and increased oxygen consumption by microorganisms which will endanger the fishes and snails. It was shown already that the latter reproduce excellently in space and that the reproductive functions of the fish species are not affected. Although the parent-offspring-cannibalism of the ovoviviparous fish species (Xiphophorus helleri) serves as a regulating factor in population dynamics an uncontrolled snail reproduction will also induce an increased oxygen consumption per se and a high ammonia concentration in the water. If harvesting locks can be handled by astronauts in, e. g., 4-week intervals their construction is not very difficult and basic technical solutions are already developed. The second problem is the feeding of the animals. Although C.E.B.A.S.-based aquaculture modules are designed to be closed food loop systems (edible herbivorous fish species and edible water plants) which are already verified on Earth this will not be possible in space without devices in which the animals are fed from a food storage. This has to be done at least once daily which would waste too much crew time when done by astronauts. So, the development of a reliable automated food dispenser has highest priority. Also in this case basic technical solutions are already elaborated. The paper gives a comprehensive overview of the proposed further C.E.B.A.S.-based development of longer-term duration aquatic food production modules.

The "C.E.B.A.S. MINI-MODULE": a self-sustaining closed aquatic ecosystem for spaceflight experimentation.

The C.E.B.A.S. MINI-MODULE is the miniaturized space flight version of the Closed Equilibrated Biological Aquatic System (C.E.B.A.S.). It fits into a large middeck locker tray and is scheduled to be flown in the STS 85 and in the NEUROLAB missions. Its volume is about 9 liters and it consists of two animal tanks, a plant cultivator, and a bacteria filter in a monolithic design. An external sensor unit is connected to a data acquisition/control unit. The system integrates its own biological life support. The CO2 exhaled by the consumers (fishes, snails, microorganisms) is assimilated by water plants (Ceratophyllum demersum) which provide them with oxygen. The products of biomass degradation and excretion (mainly ammonia ions) are converted by bacteria into nitrite and nitrate. The latter is taken up by the plants as a nitrogen source together with other ions like phosphate. The plants convert light energy into chemical energy and their illumination is regulated via the oxygen concentration in the water by the control unit. In ground laboratory tests the system exhibited biological stability up to three month. The buffer capacity of the biological filter system is high enough to eliminate the degradation products of about one half of the dead animal biomass as shown in a "crash test". A test series using the laboratory model of the flight hardware demonstrated the biological stability and technical reliability with mission-identical loading and test duration. A comprehensive biological research program is established for the C.E.B.A.S. MINI-MODULE in which five German and three U.S.-American universities as well as the Russian Academy of Sciences are involved.

Pigment composition and concentrations within the plant (Ceratophyllum demersum L.) component of the STS-89 C.E.B.A.S. Mini-Module spaceflight experiment.

The Closed Equilibrated Biological Aquatic System (C.E.B.A.S.) Mini-Module, a Space Shuttle middeck locker payload which supports a variety of aquatic inhabitants (fish, snails, plants and bacteria) in an enclosed 8.6 L chamber, was tested for its biological stability in microgravity. The aquatic plant, Ceratophyllum demersum L., was critical for the vitality and functioning of this artificial mini-ecosystem. Its photosynthetic pigment concentrations were of interest due to their light harvesting and protective functions. "Post-flight" chlorophyll and carotenoid concentrations within Ceratophyllum apical segments were directly related to the quantities of light received in the experiments, with microgravity exposure (STS-89) failing to account for any significant deviation from ground control studies.

Segregation in strongly ordering compounds: a key role of constitutional defects.

For the example of the B2 CoAl(100) surface, we demonstrate that even slight deviations from an ordered alloy's ideal stoichiometry in a subsurface region or in the bulk can drastically affect its surface composition. By experimental surface analysis and first-principles calculations, we show that Co antisite atoms segregate to the very surface, driven by the same strong interactions which enforce order in the bulk. Our findings are consistent with the lack of antisite segregation we found earlier for the much weaker ordering FeAl(100), and resolve contradictory reports for NiAl(100).

An aquatic ecosystem in space.

NASA: The Closed Equilibrated Biological Aquatic System (CEBAS) Mini-Module experiment was designed to study aquatic ecosystem performance within a middeck locker on the Space Shuttle. CEBAS was flown aboard STS-89 in January 1998 with a population of four pregnant Xiphophorus helleri female fish and eleven adult Biomphalaria glabrata snails in the first compartment and 200 juvenile X. helleri and 48 adult and juvenile B. glabrata in the second compartment. A plant compartment contained eleven snails and 53 g of the aquatic angiosperm Ceratophyllum demersum. During the flight, Ceratophyllum fresh weight increased from 53 g to 117 g. All adult fish and 65 juveniles survived the flight experiment and 37 adult snails and 40 newly laid snail spawn packs were recovered after the flight. Oxygen production and pH were as expected.^ieng

Phylogenetic signals from point mutations and polymorphic Alu insertions.

Allelic frequency data derived from five polymorphic Alu insertion loci and five point mutation polymorphic loci were compared to determine their ability to infer phylogenetic relationships among human populations. While point mutation polymorphisms inferred a monophyletic Caucasian clade that is corroborated by other studies, these data failed to support the generally accepted monophyly of Orientals with native Americans. In addition, there is less statistical bootstrap support for the maximum-likelihood tree derived from the point mutation polymorphisms as compared to those generated from either the Alu insertion data or the combined Alu insertion + point mutation data. The Alu data and the combined Alu insertion + point mutation data inferred a monophyletic relationship among the Oriental and native American populations. The Alu insertion data and the combined Alu insertion + point mutation data also displayed two separate, well defined, tight clusters of the Caucasian and the Oriental + native American populations which was not inferred from the point mutation data. These findings indicate greater phylogenetic information contained in Alu insertion frequencies than in allelic frequencies derived from point-mutations.

The closed equilibrated biological aquatic system: a 12 months test of an artificial aquatic ecosystem.

The Closed Equilibrated Biological Aquatic System" (C.E.B.A.S.) is finally disposed for long-term multi-generation experiments with aquatic organisms in a space station. Therefore a minimum operation time of three months is required. It is verified in three versions of laboratory prototypes. The third one passed successfully a 12 months mid-term test in 1995/96 thus demonstrating its high biological stability. The third version of the C.E.B.A.S. consists of a 100 l animal tank, two plant cultivators with a volume of 15 l each with independent illuminations, a 3.0 l semibiological "mechanical" filter, a 3.0 l bacteria filter, a heating/cooling device and a dummy filter unit. The live-bearing teleost Xiphophorus helleri is the vertebrate and the pulmonate water snail Biomphalana glabrata the invertebrate experimental animal in the system. The rootless higher water plant Ceratophyllum demersum is the producer organism. Ammonia oxidizing bacteria and other microorganisms settle in the filters. A sample data acquisition is combined with temperature and plant illumination control. Besides of the space aspects the C.E.B.A.S. proved to be an extremely suitable tool to investigate the organism and subcomponent interactions in a well defined terrestrial aquatic closed ecosystem by providing physical, chemical and biological data which allow an approach to a comprehensive system analysis. Moreover the C.E.B.A.S. is the base for the development of innovative combined animal-plant aquaculture systems for human nutrition on earth which could be implemented into bioregenerative life support systems with a higher degree of complexity suitable for lunar or planetary bases.

Novel laboratory approaches to multi-purpose aquatic bioregenerative closed-loop food production systems.

Based on the construction principle of the Closed Equilibrated Biological Aquatic System (C.E.B.A.S.) two novel combined animal-plant production systems were developed in laboratory scale the first of which is dedicated to mid-term operation in closed state up to two years. In principle both consist of the "classic" C.E.B.A.S. subcomponents: animal tank (Zoological Component), plant cultivators (Botanical Component), ammonia converting bacteria filter (Microbial Component) and data acquisition/control unit (Electronical Component). The innovative approach in the first system is the utilization of minimally three aquatic plant cultivators for different species. In this one the animal tank has a volume of about 160 liters and is constructed as an "endless-way system" surrounding a central unit containing the heat exchanger and the bacteria filter with volumes of about 1.5 liters each. A suspension plant cultivator (1 liter) for the edible duckweed Wolffia arrhiza is externally connected. The second plant cultivator is a meandric microalgal bioreactor for filamentous green algae. The third plant growth facility is a chamber with about 2.5 liters volume for cultivation of the "traditional" C.E.B.A.S. plant species, the rootless buoyant Ceratophyllum demersum. Both latter units are illuminated with 9 W fluorescent lamps. In the current experiment the animal tank contains the live-bearing teleost fish Xiphophorus helleri and the small pulmonate water snail Biomphalaria glabrata because their physiological adaptation to the closed system conditions is well known from many previous C.E.B.A.S. experiments. The water temperature is maintained at 25 degrees C and the oxygen level is regulated between 4 and 7 mg/l by switching on and off the plant cultivator illuminations according to a suitable pattern thus utilizing solely the oxygen produced by photosynthesis. The animals and the microorganisms of filter and biofilm provide the plants with a sufficient amount of carbon dioxide. Oxygen concentration, pH value, temperature and redox potential are on-line recorded. Ion concentrations and numbers of living germs in the system water are determined twice monthly in the laboratory from samples taken from a special "sample removal module"; the sample volume is automatically replaced from an reservoir container. A rotatory pump produces a water flow of about 38 l/min. For a similar smaller test system with approx. 10 l volume developed from the C.E.B.A.S.-MINI-MODULE a novel indirect solar energy supply is tested which has a buffer capacity to maintain the system for 7 days in darkness under central European climate conditions also in winter. It contains only a single plant cultivator which is operated with Wollfia arrhiza. This lemnacean plant is able to produce large amounts of plant biomass in a short time by vegetative reproduction via daughter fronds. This easy-to-handle apparatus is dedicated to be operative more than 4 month. The experimental animals and microorganisms are the same as in the large system. The paper provides detailed information on the system construction principles and the biological, physical and chemical data of the initial phase of the test runs of both systems with the main focus on the large one.

Aortic and peripheral blood pressure during isometric and dynamic exercise.

The purpose of this study was to compare aortic blood pressure (AOR) to peripheral measurements by the Riva-Rocci/Korotkov (RRK) and Finapres continuous finger pressure (FIN) methods during dynamic and static exercise. A tip manometer was introduced in the ascending aorta after coronary angiography in 7 cardiac patients with good exercise capability. Static exercise was of moderate intensity and led to an increase of average diastolic and systolic AOR of 20 and 18 mmHg, respectively. The corresponding RKK values were 20 and 30 mmHg and the FIN values were 16 and 14 mmHg, respectively. In maximal cycle ergometry the discrepancies were larger, especially in the 4 subjects who reached 80% or more of predicted maximal work load. Diastolic and systolic increases in AOR in these 4 subjects were 12 and 38 mmHg, respectively. The RRK values were 17 and 76 mmHg. Increases in FIN values of 17 and 74 mmHg for diastolic and systolic measurements, respectively, were found. The peripheral FIN and RRK measurements give a systolic increase that is twice as large as that for AOR. It is concluded that RRK and FIN greatly overestimate the load to the cardiovascular system in dynamic exercise. When the cardiovascular load is estimated by the rate-pressure product, RRK produces an increase of 197%, FIN of 181%, while AOR gives an increase of only 133%. This suggests that the present criteria for blood pressure in exercise testing should be critically examined.

The Closed Equilibrated Biological Aquatic System: general concept and aspects of botanical research.

The Closed Equilibrated Biological Aquatic System (CEBAS) consists of four subcomponents which form a closed (artificial) aquatic ecosystem initially designed to study the long-term influence of space conditions on several successive generations of aquatic organisms. Teleost fishes and water snails in the zoological component produce CO2 ammonium ions and waste compounds which can be utilized after ammonium is oxidised in a microbial component by the botanical component consisting of a rootless, aquatic higher plant species which eliminates ions, i.e. nitrate, and produces oxygen for animal respiration. An electronic component serves as a data-acquisition and regulation device for temperature and oxygen-dependent illumination of the plant chamber. A comprehensive interdisciplinary research programme, focused around the CEBAS, is especially well developed in the field of zoology. It covers a ground laboratory and preparations for two scheduled space flight projects, as well as aspects of combined animal-plant food production modules for human nutrition in bioregenerative space life-support systems and for terrestrial production sites. In the botanical research programme, morphological investigations on Ceratophyllum demersum L. performed with light and electron microscopy have demonstrated a gas lacuna system which, in addition to starch grains in the plastids, might regulate the buoyancy of the plant and/or serve as a 'gas skeleton'. Also, a remarkable symmetry in the arrangement of tissues was observed in stems and older leaves. The photosynthetic capacities of Ceratophyllum in the CEBAS-MINI MODULE proved to be more than sufficient for life support, and experiments on nitrate uptake into the plants showed their capacity to utilize ions from the water.

Animal protein production modules in biological life support systems: novel combined aquaculture techniques based on the Closed Equilibrated Biological Aquatic System (C.E.B.A.S.).

Based on the experiences made with the Closed Equilibrated Biological Aquatic System (C.E.B.A.S.) which was primarily developed for long-term and multi-generation experiments with aquatic animals and plants in a space station highly effective fresh water recycling modules were elaborated utilizing a combination of ammonia oxidizing bacteria filters and higher plants. These exhibit a high effectivity to eliminate phosphate and anorganic nitrogen compounds and are, in addition, able to contribute to the oxygen supply of the aquatic animals. The C.E.B.A.S. filter system is able to keep a closed artificial aquatic ecosystem containing teleost fishes and water snails biologically stable for several month and to eliminate waste products deriving from degraded dead fishes without a decrease of the oxygen concentration down to less than 3.5 mg/l at 25 degrees C. More advanced C.E.B.A.S. filter systems, the BIOCURE filters, were also developed for utilization in semiintensive and intensive aquaculture systems for fishes. In fact such combined animal-plant aquaculture systems represent highly effective productions sites for human food if proper plant and fish species are selected. The present papers elucidates ways to novel aquaculture systems in which herbivorous fishes are raised by feeding them with plant biomass produced in the BIOCURE filters and presents the scheme of a modification which utilizes a plant species suitable also for human nutrition. Special attention is paid to the benefits of closed aquaculture system modules which may be integrated into bioregenerative life support systems of a higher complexity for, e.g., lunar or planetary bases including some psychological aspects of the introduction of animal protein production into plant-based life support systems. Moreover, the basic reproductive biological problems of aquatic animal breeding under reduced gravity are explained leading to a disposition of essential research programs in this context.

A controlled aquatic ecological life support system (CAELSS) for combined production of fish and higher plant biomass suitable for integration into a lunar or planetary base.

Based on the construction principle of the already operative Closed Equilibrated Biological Aquatic System (C.E.B.A.S.) the concept of an aquaculture system for combined production of animal and plant biomass was developed. It consists of a tank for intensive fish culture which is equipped with a feeding lock representing also a trap for biomass removal followed by a water recycling system. This is an optimized version of the original C.E.B.A.S. filters adapted to higher water pollutions. It operates in a fully biological mode and is able to convert the high ammonia ion concentrations excreted by the fish gills into nitrite ions. The second biomass production site is a higher plant cultivator with an internal fiber optics light distributor which may utilize of solar energy. The selected water plant is a tropical rootless duckweed of the genus Wolffia which possesses a high capacity in nitrate elimination and is terrestrially cultured as a vegetable for human nutrition in Southeast Asia. It is produced in an improved suspension culture which allows the removal of excess biomass by tangential centrifugation. The plant cultivator is able to supply the whole system with oxygen for respiration and eliminates vice versa the carbon dioxide exhaled by the fish via photosynthesis. A gas exchanger may be used for emergency purposes or to deliver excess oxygen into the environment and may be implemented into the air regeneration system of a closed environment of higher order. The plant biomass is fed into a biomass processor which delivers condensed fresh and dried biomass as pellets. The recovered water is fed back into the aquaculture loop. The fresh plants can be used for human nutrition immediately or can be stored after sterilization in an adequate packing. The dried Wolffia pellets are collected and brought into the fish tank by an automated feeder. In parallel the water from the plant cultivator is driven back to the animal tank by a pump. The special feature of the system described is, however, the used fish species. It is the herbivorous teleost Ctenopharyngodon idellus (Chinese Grass Carp) which can be raised solely with plant biomass. In this case, moreover, it can be useful for the bioregeneration of plant biomass inedible for humans which can be used easily as additional food for the fishes thus resulting in an intensivation of animal protein production. The resupply of removed fish biomass has to be guaranteed by a separate hatchery.

Biological-physical-chemical aspects of a human life support system for a lunar base.

To create a life support system based on biological and physical-chemical processes is the optimum solution providing full-valued conditions for existence and efficient work of people at a lunar base. Long-standing experience in experimental research or closed ecosystems and their components allows us to suggest a realistic functional structure of the lunar base and to estimate qualitatively its parameters. The original restrictions are as follows: 1) the basic source of energy to support the biological processes has to be the solar radiation; 2) the initial amount of basic biological elements forming the turnover of substances (C, O, H, P, K, N) has to be delivered from Earth; 3). Moon materials are not to be used in the biological turnover inside the base; 4) the base is to supply the crew fully with atmosphere and water, and with 90% (A scenario) or 40% (B scenario) of food. Experimental data about the plant productivity under the "Moon" rhythm of light and darkness allow us to suggest that the A scenario requires per one human: plant area--40 m2 irradiated during the lunar day by 250-300 W/m2 PAR producing 1250 g of dry biomass a terrestrial day; a heterotrophic component of "biological incineration" of inedible plant biomass (800 g/day) including the aquaculture of fish to produce animal products and contaminating the environment less than birds and mammals, and the culture of edible mushrooms; a component of physical-chemical correction for the LSS environment including the subsystems of: deep oxidation of organic impurities in the atmosphere and of water, organic wastes of human activity and that biological components (420 g/day) CO2 concentration in "Moon" nights, damping O2 in "Moon" days, etc. The stock of prestored or delivered from Earth substances (food additions, seeds, etc.) to be involved in biological turnover is to be about 50 kg/year per man. Increase of the mass of prestored substances per man up to 220 kg/year would reduce twice the plant area and consumed amount of radiant energy to exclude the components of "biological incineration" and physical-chemical destruction of organic wastes.