The ONETEP linear-scaling density functional theory program.

We present an overview of the onetep program for linear-scaling density functional theory (DFT) calculations with large basis set (plane-wave) accuracy on parallel computers. The DFT energy is computed from the density matrix, which is constructed from spatially localized orbitals we call Non-orthogonal Generalized Wannier Functions (NGWFs), expressed in terms of periodic sinc (psinc) functions. During the calculation, both the density matrix and the NGWFs are optimized with localization constraints. By taking advantage of localization, onetep is able to perform calculations including thousands of atoms with computational effort, which scales linearly with the number or atoms. The code has a large and diverse range of capabilities, explored in this paper, including different boundary conditions, various exchange-correlation functionals (with and without exact exchange), finite electronic temperature methods for metallic systems, methods for strongly correlated systems, molecular dynamics, vibrational calculations, time-dependent DFT, electronic transport, core loss spectroscopy, implicit solvation, quantum mechanical (QM)/molecular mechanical and QM-in-QM embedding, density of states calculations, distributed multipole analysis, and methods for partitioning charges and interactions between fragments. Calculations with onetep provide unique insights into large and complex systems that require an accurate atomic-level description, ranging from biomolecular to chemical, to materials, and to physical problems, as we show with a small selection of illustrative examples. onetep has always aimed to be at the cutting edge of method and software developments, and it serves as a platform for developing new methods of electronic structure simulation. We therefore conclude by describing some of the challenges and directions for its future developments and applications.

Universal Spin Diffusion Length in Polycrystalline Graphene.

Graphene grown by chemical vapor deposition (CVD) is the most promising material for industrial-scale applications based on graphene monolayers. It also holds promise for spintronics; despite being polycrystalline, spin transport in CVD graphene has been measured over lengths up to 30 µm, which is on par with the best measurements made in single-crystal graphene. These results suggest that grain boundaries (GBs) in CVD graphene, while impeding charge transport, may have little effect on spin transport. However, to date very little is known about the true impact of disordered networks of GBs on spin relaxation. Here, by using first-principles simulations, we derive an effective tight-binding model of graphene GBs in the presence of spin-orbit coupling (SOC), which we then use to evaluate spin transport in realistic morphologies of polycrystalline graphene. The spin diffusion length is found to be independent of the grain size, and it is determined only by the strength of the substrate-induced SOC. This result is consistent with the D'yakonov-Perel' mechanism of spin relaxation in the diffusive regime, but we find that it also holds in the presence of quantum interference. These results clarify the role played by GBs and demonstrate that the average grain size does not dictate the upper limit for spin transport in CVD-grown graphene, a result of fundamental importance for optimizing large-scale graphene-based spintronic devices.

A missense mutation in Katnal1 underlies behavioural, neurological and ciliary anomalies.

Microtubule severing enzymes implement a diverse range of tissue-specific molecular functions throughout development and into adulthood. Although microtubule severing is fundamental to many dynamic neural processes, little is known regarding the role of the family member Katanin p60 subunit A-like 1, KATNAL1, in central nervous system (CNS) function. Recent studies reporting that microdeletions incorporating the KATNAL1 locus in humans result in intellectual disability and microcephaly suggest that KATNAL1 may play a prominent role in the CNS; however, such associations lack the functional data required to highlight potential mechanisms which link the gene to disease symptoms. Here we identify and characterise a mouse line carrying a loss of function allele in Katnal1. We show that mutants express behavioural deficits including in circadian rhythms, sleep, anxiety and learning/memory. Furthermore, in the brains of Katnal1 mutant mice we reveal numerous morphological abnormalities and defects in neuronal migration and morphology. Furthermore we demonstrate defects in the motile cilia of the ventricular ependymal cells of mutants, suggesting a role for Katnal1 in the development of ciliary function. We believe the data we present here are the first to associate KATNAL1 with such phenotypes, demonstrating that the protein plays keys roles in a number of processes integral to the development of neuronal function and behaviour.

Achievements of DFT for the investigation of graphene-related nanostructures.

CONSPECTUS: Graphene-related nanostructures stand out as exceptional materials due to both their wide range of properties and their expanse of interest in both applied and fundamental research. They are good examples of nanoscale materials for which the properties do not necessarily replicate those of the bulk. For the description and the understanding of their properties, it is clear that a general quantum-mechanical approach is mandatory. The remarkable result of density functional theory (DFT) is that the quantum-mechanical description of materials at the ground state is made amenable to simulations at a relatively low computational cost. The knowledge of materials has undergone a revolution after the introduction of DFT as an unrivaled instrument for the investigation of materials properties through computer experiments. Their deeper understanding comes from a variety of tools developed from concepts intrinsically present in DFT, notably the total energy and the charge density. Such tools allow the prediction of a diverse set of physicochemical properties relevant for material scientists. This Account lays out an example-driven tour through the achievements of ground-state DFT applied to the description of graphene-related nanostructures and to the deep understanding of their outstanding properties. After a brief introduction to DFT, the survey starts with the determination of the most basic properties that can be obtained from DFT, that is, band structures, lattice parameters, and spin ground state. Next follows an exploration of how total energies of different systems can give information about relative stability, formation energies, and reaction paths. Exploiting the derivatives of the energy with respect to displacements leads the way toward the extraction of vibrational and mechanical properties. In addition, a close examination of the charge density gives information about charge transfer mechanisms, which can be linked to chemical reactivity. The ground state density and Hamiltonian finally connect to the concepts behind transport phenomena, which drive much of the application-oriented research on graphene and graphene-related nanostructures. In each section, a selection of cases that are of current importance are used to illustrate the use and relevance of DFT-based techniques. In summary, this Account presents an introductory landscape of the possibilities of ground-state DFT for the study of graphene-related nanostructures. The prospect is rich, and the use of DFT for the study of graphene-related nanostructures will continue to be fruitful for the advancement of these and other materials.

A chronological expression profile of gene activity during embryonic mouse brain development.

The brain is a functionally complex organ, the patterning and development of which are key to adult health. To help elucidate the genetic networks underlying mammalian brain patterning, we conducted detailed transcriptional profiling during embryonic development of the mouse brain. A total of 2,400 genes were identified as showing differential expression between three developmental stages. Analysis of the data identified nine gene clusters to demonstrate analogous expression profiles. A significant group of novel genes of as yet undiscovered biological function were detected as being potentially relevant to brain development and function, in addition to genes that have previously identified roles in the brain. Furthermore, analysis for genes that display asymmetric expression between the left and right brain hemispheres during development revealed 35 genes as putatively asymmetric from a combined data set. Our data constitute a valuable new resource for neuroscience and neurodevelopment, exposing possible functional associations between genes, including novel loci, and encouraging their further investigation in human neurological and behavioural disorders.

Almost Perfect Spin Filtering in Graphene-Based Magnetic Tunnel Junctions.

We report on large spin-filtering effects in epitaxial graphene-based spin valves, strongly enhanced in our specific multilayer case. Our results were obtained by the effective association of chemical vapor deposited (CVD) multilayer graphene with a high quality epitaxial Ni(111) ferromagnetic spin source. We highlight that the Ni(111) spin source electrode crystallinity and metallic state are preserved and stabilized by multilayer graphene CVD growth. Complete nanometric spin valve junctions are fabricated using a local probe indentation process, and spin properties are extracted from the graphene-protected ferromagnetic electrode through the use of a reference Al2O3/Co spin analyzer. Strikingly, spin-transport measurements in these structures give rise to large negative tunnel magneto-resistance TMR = -160%, pointing to a particularly large spin polarization for the Ni(111)/Gr interface PNi/Gr, evaluated up to -98%. We then discuss an emerging physical picture of graphene-ferromagnet systems, sustained both by experimental data and ab initio calculations, intimately combining efficient spin filtering effects arising (i) from the bulk band structure of the graphene layers purifying the extracted spin direction, (ii) from the hybridization effects modulating the amplitude of spin polarized scattering states over the first few graphene layers at the interface, and (iii) from the epitaxial interfacial matching of the graphene layers with the spin-polarized Ni surface selecting well-defined spin polarized channels. Importantly, these main spin selection effects are shown to be either cooperating or competing, explaining why our transport results were not observed before. Overall, this study unveils a path to harness the full potential of low Resitance.Area (RA) graphene interfaces in efficient spin-based devices.

Two-dimensional graphene with structural defects: elastic mean free path, minimum conductivity, and Anderson transition.

Quantum transport properties of disordered graphene with structural defects (Stone-Wales and divacancies) are investigated using a realistic π-π* tight-binding model elaborated from ab initio calculations. Mean free paths and semiclassical conductivities are then computed as a function of the nature and density of defects (using an order-N real-space Kubo-Greenwood method). By increasing the defect density, the decay of the semiclassical conductivities is predicted to saturate to a minimum value of 4e2/πh over a large range (plateau) of carrier density (>0.5×10(14) cm(-20). Additionally, strong contributions of quantum interferences suggest that the Anderson localization regime could be experimentally measurable for a defect density as low as 1%.

Specific Lyt 123 cells are involved in protection against Listeria monocytogenes and in delayed-type hypersensitivity to listerial antigens.

Specific anti-Lyt antisera and complement were used to determine the Lyt phenotype of peritoneal exudate T lymphocytes from Listeria monocytogenes-immune mice. It was found that Lyt 123+ T cells are crucially involved both in protection against listerial infection and in delayed-type hypersensitivity (DTH) to listerial antigens. Thus, both functions critically depend on a T-cell subclass phenotypically different from that which mediates DTH to noninfectious antigens and help in antibody formation on the one hand, as well as those T cells mediating cytotoxic reactions on the other.

Effector T lymphocytes in lymphocytic choriomeningitis virus-infected mice. Cytolytic activity of Lyt-23 spleen cells in vitro does not correlate with elimination of infectious virus from spleens.

The T lymphocytes from mice recovering from infection with lymphocytic choriomeningitis virus were selected for subclasses by treatment with anti-Lyt antisera and complement. Lyt-23 cells and mixtures of lyt-1 and Lyt-23 cells caused up to one-half the destruction of cultivated target cells as compared with untreated T lymphocytes; Lyt-1 cells alone were not cytotoxic. Selected and unselected spleen T cells were also inoculated intravenously into previously infected mice. Whereas unselected cells reduced infectious virus in the spleens of the recipients approximately 100-fold, only marginal effects, which were not preferentially associated with one particular subclass, were seen with selected LYT-23 or Lyt-1 lymphocytes or a mixture of both. Apparently the Lyt-23 cells, shown to by cytolytic for infected cells in vitro, did not cause elimination of a measurable quantity of the virus from mice.

Quantitative studies on T cell diversity. I. Determination of the precursor frequencies for two types of streptococcus A-specific helper cells in nonimmune, polyclonally activated splenic T cells.

A limiting-dilution system is described that makes use of T cell growth factor T cell expansion and allows the determination of precursor frequencies for various regulatory and effector T cells in nonimmune, polyclonally, or specifically activated T cell populations. Two different sets, a frequent and a rare set, of T helper cell precursors with specificity for trinitrophenyl-group A streptococcal vaccine, could be identified: the frequent set is of the Lyt-123 phenotype, and is present at frequencies of from 1/1,000 to 1/6,000 splenic T cells. It is only active at low cell numbers, whereas it is completely inactivated at greater cell numbers, presumably by suppressor T cells of lower frequency but greater potency. The rare set is of the Lyt-1 phenotype, is present at frequencies of from 1/10,000 to 1/70,000, and is not sensitive to suppressor cells present within the tested cell numbers. We suggest that the frequent set contains primiary helper cell precursors, whereas the rare set contains helper T memory cells preselected by previous exposure to other antigens. The results are discussed with respect to other reports on the involvement of more than one set of helper cells in antibody production.

Quantitative studies on T cell diversity. II. Determination of the frequencies and Lyt phenotypes of two types of precursor cells for alloreactive cytotoxic T cells in polyclonally and specifically activated splenic T cells.

Two different limiting dilution systems have been applied to compare precursor frequencies of alloreactive cytotoxic T cells (CTL-P) in the polyclonally and specifically activated lymphocyte populations and in selected Lyt T cell subsets. Both systems make use of T cell growth factor for T cell expansion but differ with respect to the activation step in that lymphocytes are either activated directly with allogenetic stimulator cells or are sensitized polyclonally with concanavalin A (Con A) in bulk culture before their expansion under limiting dilution conditions. In polyclonally activated C57BL/6 lymphocyte populations, two types of CTL-P specific for H-2d alloantigens could be identified: a frequent set with a frequency of 1/100-1/300, and a rare set with a frequency of 1/2,000-1/8,000. In contrast, only a single CTL-P set was found in specifically activated populations with a frequency similar to that of the frequent CTL-P found on Con A blasts. In Con A blasts, the frequent at higher cell concentrations by suppressor T cells, whereas rare CTL-P were insensitive to this suppressive mechanism. Whereas in specifically activated T cells, the predominant CTL-P phenotype was Lyt-123, the predominant Lyt phenotypes for the frequent and the rare CTL-P found in Con A blasts were Lyt-123 and Lyt-123, respectively, which suggests that they represent primary and secondary CTL-P, respectively. The results are discussed with respect to previous reports on the involvement of Lyt T cell subsets in the generation of cytotoxic responses and their regulation by T suppressor cells.

The severe combined immunodeficiency (scid) mouse. A laboratory model for the analysis of Lyme arthritis and carditis.

We report that the spirochete B. burgdorferi induces progressive polyarthritis and carditis in mice with severe combined immunodeficiency syndrome (scid) but not in normal C.B-17 mice. The onset and severity of the disease were dependent on (a) the viability; (b) the infectivity; and (c) the dose of inoculated B. burgdorferi organisms. Infective spirochetes were isolated from both blood and joints of inoculated scid mice. These findings suggest that B. burgdorferi-induced chronic arthritis and carditis in mice develops independently of lymphocyte function and makes the scid mouse an attractive laboratory model to study the role of the immune system in experimental Lyme Borreliosis.

In vitro- and ex vivo-derived cytolytic leukocytes from granzyme A x B double knockout mice are defective in granule-mediated apoptosis but not lysis of target cells.

Granzyme (gzm) A and gzmB have been implicated in Fas-independent nucleolytic and cytolytic processes exerted by cytotoxic T (Tc) cells, but the underlying mechanism(s) remains unclear. In this study, we compare the potential of Tc and natural killer (NK) cells of mice deficient in both gzmA and B (gzmAxB-/-) with those from single knockout mice deficient in gzmA (-/-), gzmB (-/-), or perforin (-/-) to induce nuclear damage and lysis in target cells. With the exception of perforin-/-, all in vitro- and ex vivo-derived Tc and NK cell populations from the mutant strains induced 51Cr-release in target cells at levels and with kinetics similar to those of normal mice. This contrasts with their capacity to induce apoptotic nuclear damage in target cells. In gzmAxB-/- mice, Tc/NK-mediated target cell DNA fragmentation was not observed, even after extended incubation periods (10 h), but was normal in gzmA-deficient and only impaired in gzmB-deficient mice in short-term (2-4 h), but not long-term (4-10 h), nucleolytic assays. This suggests that gzmA and B are critical for Tc/NK granule- mediated nucleolysis, with gzmB being the main contributor, while target cell lysis is due solely to perforin and independent of both proteases.

Transcription of granzyme A and B genes is differentially regulated during lymphoid ontogeny.

During development, thymocytes express a number of genes typical for activated peripheral T lymphocytes, including granzymes. We have now analyzed by reverse transcription-polymerase chain reaction (RT-PCR), immunohistochemistry, and cytochemistry fetal liver cells and thymocytes at various developmental stages for the expression of granzyme A-G genes. At days 13-17 of gestation, only granzyme B but none of the other granzymes is expressed in fetal liver. In the most immature, Pgp-1+IL2R alpha-, thymocyte subpopulation mRNAs for granzymes A-C but not for granzymes D-G are detectable. Upon further differentiation via Pgp-1-IL-2R alpha + into more mature Pgp-1-IL-2R alpha- thymocytes the level of expression of granzymes A, B, and C gradually declines reaching its lowest level at the CD4+ 8+ double positive stage. In fetal thymic lobes depleted of lymphoid cells by treatment with deoxyguanosine, no transcripts for granzymes A, B, and C were found indicating that the PCR signals are derived exclusively from early precursor T/natural killer (NK) lineage cells rather than from residual stromal elements. In mature CD4+CD8- and CD4-CD8+ thymocytes, granzyme B mRNA is found at similar levels in both subsets whereas granzyme A mRNA is expressed selectively in the CD4-CD8+ subset. Enzymatic activity of granzyme A was only seen in a fraction of CD4-CD8+ thymocytes negative for heat stable antigen (HSA) but not in the more immature HSA+ fraction of CD4-CD8+ thymocytes. The data suggest that (a) granzyme B is a pro-thymocyte marker for all T/NK lineage cells; (b) granzyme A transcripts are associated with thymocytes with the potential to develop into the CD8+ lineage; and (c) granzyme A enzymatic activity is only expressed in the most mature CD4-CD8+ stage, suggesting that granzyme proteins are not involved in early stages of thymocyte development.

Spin filtering by proximity effects at hybridized interfaces in spin-valves with 2D graphene barriers.

We report on spin transport in state-of-the-art epitaxial monolayer graphene based 2D-magnetic tunnel junctions (2D-MTJs). In our measurements, supported by ab-initio calculations, the strength of interaction between ferromagnetic electrodes and graphene monolayers is shown to fundamentally control the resulting spin signal. In particular, by switching the graphene/ferromagnet interaction, spin transport reveals magneto-resistance signal MR > 80% in junctions with low resistance × area products. Descriptions based only on a simple K-point filtering picture (i.e. MR increase with the number of layers) are not sufficient to predict the behavior of our devices. We emphasize that hybridization effects need to be taken into account to fully grasp the spin properties (such as spin dependent density of states) when 2D materials are used as ultimately thin interfaces. While this is only a first demonstration, we thus introduce the fruitful potential of spin manipulation by proximity effect at the hybridized 2D material / ferromagnet interface for 2D-MTJs.

Granzyme B-induced cell death exerted by ex vivo CTL: discriminating requirements for cell death and some of its signs.

Granzyme B (gzmB) of cytotoxic T lymphocytes (CTL) is essential for recovery from intracellular pathogens, but the molecular basis of its action is still unresolved. Here, we analyzed gzmB-mediated death pathways under physiological conditions using ex vivo virus-immune CTLs that express perf and gzmB, but not gzmA (gzmB(+)CTL). We show that gzmB(+)CTL abrogate target cell proliferation most likely by inducing cell death, independent of caspases and mitochondrial signaling. In addition, the data reveal that gzmB(+)CTL independently induce pro-apoptotic processes either via caspase-3/-7, leading to plasma membrane perturbance and ROS production or via Bid/Bak/Bax, resulting in cytochrome c release and that both pathways elicit loss of DeltaPsi(m). Our data provide evidence for a pleiotropic pro-apoptotic function of gzmB presumably to counteract evasion strategies of pathogens and to control tumors.

Label free noninvasive spatially resolved NaCl concentration measurements using Coherent Anti-Stokes Raman Scattering microscopy applied to butter.

Imaging the microstructure of opaque composite foodstuffs and extracting quantitative chemical information about specific localized components is challenging. Herein, a method has been developed to determine spatially resolved concentrations of aqueous salt and applied to measure salt concentrations of water droplets in butter samples. This was done using Coherent Anti-Stokes Raman Scattering (CARS) microscopy which achieves non-invasive label free imaging based on visualization of specific chemical-bond vibrations. The concentration of salt in the dispersed water droplets in butter was determined based on the relative change in intensity of the CARS-signal at two distinct wavenumbers, which have been shown to be dependent on the inter-molecular coupling of water molecules and salt. The results provide the size and salt concentration distribution of the droplets in the samples. It is further shown that the average salt concentration in the whole sample can correctly be inferred from the concentration measured within the water droplets.

Granzyme B is expressed in mouse mast cells in vivo and in vitro and causes delayed cell death independent of perforin.

Mast cells respond to pathogens and allergens by secreting a vast array of preformed and newly synthesized mediators, including enzymes, vasoactive amines, lipid mediators, cytokines and chemokines, thereby affecting innate and adaptive immune responses and pathogenesis. Here, we present evidence that skin-, but not lung-associated primary mast cells as well as in vitro-differentiated bone marrow-derived mast cells (BMMC) express granzyme (gzm) B, but not gzmA or perforin (perf). GzmB is associated with cytoplasmic granules of BMMC and secreted after Fcepsilon-receptor-mediated activation. BMMC from wild type but not gzmB-deficient mice cause cell death in susceptible adherent target cells, indicating that the perf-independent cytotoxicity of BMMC is executed by gzmB. Furthermore, gzmB induces a disorganization of endothelial cell-cell contacts. The data suggest that activated mast cells contribute, via secreted gzmB, to cell death, increased vascular permeability, leukocyte extravasation and subsequent inflammatory processes in affected tissues.

[Lyme borreliosis: research gaps and research approaches. Results from an interdisciplinary expert meeting at the Robert Koch Institute]. / Lyme-Borreliose: Forschungsbedarf und Forschungsansätze. Ergebnisse eines interdisziplinären Expertentreffens am Robert Koch-Institut.

Lyme borreliosis is currently the most frequent tick-transmitted zoonosis in the northern hemisphere. Germany and other European countries are regarded as highly endemic areas; therefore the burden of disease and consequently the costs for the health systems are considered to be high. This report summarises the results of an interdisciplinary workshop on Lyme borreliosis which aimed to identify research deficits and to prioritise areas which need to be addressed. Research needs have been recognised for different areas: diagnosis, epidemiology, immunology, clinics, ecology and health services research. Examples of research areas which have priority are the standardisation of diagnostic tests, the development of markers to detect an active infection, the improvement of the epidemiological database and the analysis of the burden of disease.

Heat shock protein 70 overexpression affects the response to ultraviolet light in murine fibroblasts. Evidence for increased cell viability and suppression of cytokine release.

To elucidate cellular concepts for protection against ultraviolet (UV) light we investigated the effect of heat shock protein 70 (hsp70) overexpression on cell viability and on the secretion of UV-inducible immunological cytokines. Transfected murine fibrosarcoma cells (WEHI-S), overexpressing hsp70 or a sham transfected control were used. Overexpression of hsp70 was sufficient to markedly increase cell viability upon treatment with UVB (290-320 nm). Since long wave UV (UVA, 320-400 nm) as well as UVB turned out to stimulate the release of O2- radicals we studied the cell viability upon oxidative stress. Hsp70 overexpression increased viability upon treatment with hydrogen peroxide or menadione, but had no influence on UV-induced O2- release. UV-light is known to upregulate immunologic and proinflammatory cytokines such as IL-1 and IL-6. Oxidative stress appeared to exert a similar effect. Hsp70 overexpression markedly decreased the release of IL-6 induced by UVA, UVB and oxidative stress. To test whether the hsp70 mediated suppression is confined to events caused by UV-light we determined IL-1-mediated effects. IL-1-induced IL-6 release was reduced by hsp70 overexpression, whereas the IL-1 mediated activation of nuclear factor kappa B was not affected. Our data suggests that hsp70 plays a central role not only in cell protection against UV-light, but also in the regulation of proinflammatory cytokine release induced by UV-exposure.