Electronic structure and the glass transition in pnictide and chalcogenide semiconductor alloys. Part II: The intrinsic electronic midgap states

We propose a structural model that treats in a unified fashion both the atomic motions and electronic excitations in quenched melts of pnictide and chalcogenide semiconductors. In Part I (submitted to J. Chem. Phys.), we argued these quenched melts represent aperiodic $pp\sigma$-networks that are highly stable and, at the same time, structurally degenerate. These networks are characterized by a continuous range of coordination. Here we present a systematic way to classify these types of coordination in terms of discrete coordination defects in a parent structure defined on a simple cubic lattice. We identify the lowest energy coordination defects with the intrinsic midgap electronic states in semiconductor glasses, which were argued earlier to cause many of the unique optoelectronic anomalies in these materials. In addition, these coordination defects are mobile and correspond to the transition state configurations during the activated transport above the glass transition. The presence of the coordination defects may account for the puzzling discrepancy between the kinetic and thermodynamic fragility in chalcogenides. Finally, the proposed model recovers as limiting cases several popular types of bonding patterns proposed earlier, including: valence-alternation pairs, hypervalent configurations, and homopolar bonds in heteropolar compounds.Comment: 17 pages, 15 figures, revised version, final version to appear in J. Chem. Phy

The cellular microscopy phenotype ontology

BACKGROUND: Phenotypic data derived from high content screening is currently annotated using free-text, thus preventing the integration of independent datasets, including those generated in different biological domains, such as cell lines, mouse and human tissues. DESCRIPTION: We present the Cellular Microscopy Phenotype Ontology (CMPO), a species neutral ontology for describing phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations. CMPO is compatible with related ontology efforts, allowing for future cross-species integration of phenotypic data. CMPO was developed following a curator-driven approach where phenotype data were annotated by expert biologists following the Entity-Quality (EQ) pattern. These EQs were subsequently transformed into new CMPO terms following an established post composition process. CONCLUSION: CMPO is currently being utilized to annotate phenotypes associated with high content screening datasets stored in several image repositories including the Image Data Repository (IDR), MitoSys project database and the Cellular Phenotype Database to facilitate data browsing and discoverability

The structural properties of the multi-layer graphene/4H-SiC(000-1) system as determined by Surface X-ray Diffraction

We present a structural analysis of the multi-layer graphene-4HSiC(000-1}) system using Surface X-Ray Reflectivity. We show for the first time that graphene films grown on the C-terminated (000-1}) surface have a graphene-substrate bond length that is very short (0.162nm). The measured distance rules out a weak Van der Waals interaction to the substrate and instead indicates a strong bond between the first graphene layer and the bulk as predicted by ab-initio calculations. The measurements also indicate that multi-layer graphene grows in a near turbostratic mode on this surface. This result may explain the lack of a broken graphene symmetry inferred from conduction measurements on this system [C. Berger et al., Science 312, 1191 (2006)].Comment: 9 pages with 6 figure

Role of Boron p-Electrons and Holes in Superconducting MgB2, and other Diborides: A Fully-Relaxed, Full-Potential Electronic Structure Study

We present the results of fully-relaxed, full-potential electronic structure calculations for the new superconductor MgB2, and BeB2, NaB2, and AlB2, using density-functional-based methods. Our results described in terms of (i) density of states (DOS), (ii) band-structure, and (iii) the DOS and the charge density around the Fermi energy EF, clearly show the importance of B p-band for superconductivity. In particular, we show that around EF, the charge density in MgB2, BeB2 and NaB2 is planar and is associated with the B plane. For BeB2 and NaB2, our results indicate qualitative similarities but significant quantitative differences in their electronic structure due to different lattice constants a and c.Comment: 4 pages, 4 figures, Submitted to Phys Rev. Lett. on March 6, 2001; resubmission on April 2

Comparison of aggregate and individual participant data approaches to meta-analysis of randomised trials : An observational study

BACKGROUND: It remains unclear when standard systematic reviews and meta-analyses that rely on published aggregate data (AD) can provide robust clinical conclusions. We aimed to compare the results from a large cohort of systematic reviews and meta-analyses based on individual participant data (IPD) with meta-analyses of published AD, to establish when the latter are most likely to be reliable and when the IPD approach might be required. METHODS AND FINDINGS: We used 18 cancer systematic reviews that included IPD meta-analyses: all of those completed and published by the Meta-analysis Group of the MRC Clinical Trials Unit from 1991 to 2010. We extracted or estimated hazard ratios (HRs) and standard errors (SEs) for survival from trial reports and compared these with IPD equivalents at both the trial and meta-analysis level. We also extracted or estimated the number of events. We used paired t tests to assess whether HRs and SEs from published AD differed on average from those from IPD. We assessed agreement, and whether this was associated with trial or meta-analysis characteristics, using the approach of Bland and Altman. The 18 systematic reviews comprised 238 unique trials or trial comparisons, including 37,082 participants. A HR and SE could be generated for 127 trials, representing 53% of the trials and approximately 79% of eligible participants. On average, trial HRs derived from published AD were slightly more in favour of the research interventions than those from IPD (HRAD to HRIPD ratio = 0.95, p = 0.007), but the limits of agreement show that for individual trials, the HRs could deviate substantially. These limits narrowed with an increasing number of participants (p < 0.001) or a greater number (p < 0.001) or proportion (p < 0.001) of events in the AD. On average, meta-analysis HRs from published AD slightly tended to favour the research interventions whether based on fixed-effect (HRAD to HRIPD ratio = 0.97, p = 0.088) or random-effects (HRAD to HRIPD ratio = 0.96, p = 0.044) models, but the limits of agreement show that for individual meta-analyses, agreement was much more variable. These limits tended to narrow with an increasing number (p = 0.077) or proportion of events (p = 0.11) in the AD. However, even when the information size of the AD was large, individual meta-analysis HRs could still differ from their IPD equivalents by a relative 10% in favour of the research intervention to 5% in favour of control. We utilised the results to construct a decision tree for assessing whether an AD meta-analysis includes sufficient information, and when estimates of effects are most likely to be reliable. A lack of power at the meta-analysis level may have prevented us identifying additional factors associated with the reliability of AD meta-analyses, and we cannot be sure that our results are generalisable to all outcomes and effect measures. CONCLUSIONS: In this study we found that HRs from published AD were most likely to agree with those from IPD when the information size was large. Based on these findings, we provide guidance for determining systematically when standard AD meta-analysis will likely generate robust clinical conclusions, and when the IPD approach will add considerable value

Nature of bonding and electronic structure in MgB2, a boron intercalation superconductor

Chemical bonding and electronic structure of MgB2, a boron-based newly discovered superconductor, is studied using self-consistent band structure techniques. Analysis of the transformation of the band structure for the hypothetical series of graphite - primitive graphite - primitive graphite-like boron - intercalated boron, shows that the band structure of MgB2 is graphite-like, with pi-bands falling deeper than in ordinary graphite. These bands possess a typically delocalized and metallic, as opposed to covalent, character. The in-plane sigma-bands retain their 2D covalent character, but exhibit a metallic hole-type conductivity. The coexistence of 2D covalent in-plane and 3D metallic-type interlayer conducting bands is a peculiar feature of MgB2. We analyze the 2D and 3D features of the band structure of MgB2 and related compounds, and their contributions to conductivity.Comment: 4 pages in revtex, 3 figures in 4 separate EPS file

Superconductivity of metallic boron in MgB_2

Boron in MgB_2 forms layers of honeycomb lattices with magnesium as a space filler. Band structure calculations indicate that Mg is substantially ionized, and the bands at the Fermi level derive mainly from B orbitals. Strong bonding with an ionic component and considerable metallic density of states yield a sizeable electron-phonon coupling. Using the rigid atomic sphere approximation and an analogy to Al, we estimate the coupling constant lambda to be of order 1. Together with high phonon frequencies, which we estimate via zone-center frozen phonon calculations to be between 300 and 700 cm^-1, this produces a high critical temperature, consistent with recent experiments reporting Tc=39 K (J. Akimitsu et al., to be published). Thus MgB_2 can be viewed as an analog of the long sought, but still hypothetical, superconducting metallic hydrogen.Comment: several typos corrected, most importantly, units in the tables fixed and a missing zero in the expression for the resistivity restore

Electronic structure and the glass transition in pnictide and chalcogenide semiconductor alloys. Part I: The formation of the ppσpp\sigma-network

Semiconductor glasses exhibit many unique optical and electronic anomalies. We have put forth a semi-phenomenological scenario (J. Chem. Phys. 132, 044508 (2010)) in which several of these anomalies arise from deep midgap electronic states residing on high-strain regions intrinsic to the activated transport above the glass transition. Here we demonstrate at the molecular level how this scenario is realized in an important class of semiconductor glasses, namely chalcogen and pnictogen containing alloys. Both the glass itself and the intrinsic electronic midgap states emerge as a result of the formation of a network composed of $\sigma$-bonded atomic $p$-orbitals that are only weakly hybridized. Despite a large number of weak bonds, these $pp\sigma$-networks are stable with respect to competing types of bonding, while exhibiting a high degree of structural degeneracy. The stability is rationalized with the help of a hereby proposed structural model, by which $pp\sigma$-networks are symmetry-broken and distorted versions of a high symmetry structure. The latter structure exhibits exact octahedral coordination and is fully covalently-bonded. The present approach provides a microscopic route to a fully consistent description of the electronic and structural excitations in vitreous semiconductors.Comment: 22 pages, 17 figures, revised version, final version to appear in J. Chem. Phy