Fully spin-dependent transport of triangular graphene flakes

The magnetic moment and spin-polarized electron transport properties of triangular graphene flakes surrounded by boron nitride sheets (BNC structures) are studied by using first-principles calculations based on density functional theory. Their dependence on the BNC structure is discussed, revealing that small isolated graphene flakes have large magnetic moment. When the BNC structure is suspended between graphene electrodes, the spin-polarized charge density distribution accumulates at the edge of the graphene flakes and no spin polarization is observed in the graphene electrodes. We also found that the BNC structure demonstrates perfectly spin-polarized transport properties in the wide energy window around the Fermi level. Our first-principles results indicate that the BNC structure provides new possibilities to electrically control spin

Effective Superpotentials for SO/Sp with Flavor from Matrix Models

We study matrix models related to $SO/Sp$ gauge theories with flavors. We give the effective superpotentials for gauge theories with arbitrary tree level superpotential up to first instanton level. For quartic tree level superpotential we obtained exact one-cut solution. We also derive Seiberg-Witten curve for these gauge theories from matrix model argument.Comment: 17pp,2 figures, v2;refs added and to appear in MPL

Numerical Study of TAP Metastable States in 3-body Ising Spin Glasses

The distribution of solutions of the Thouless-Anderson-Palmer equation is studied by extensive numerical experiments for fully connected 3-body interaction Ising spin glass models in a level of annealed calculation. A recent study predicted that when the equilibrium state of the system is characterized by one-step replica symmetry breaking, the distribution is described by a Becchi-Rouet-Stora-Tyutin (BRST) supersymmetric solution in the relatively low free energy region, whereas the BRST supersymmetry is broken for higher values of free energy (Crisanti et al., Phys. Rev. B 71 (2005) 094202). Our experiments qualitatively reproduce the discriminative behavior of macroscopic variables predicted by the theoretical assessment.Comment: 13 pages, 4 figure

Novel time-saving first-principles calculation method for electron-transport properties

We present a time-saving simulator within the framework of the density functional theory to calculate the transport properties of electrons through nanostructures suspended between semi-infinite electrodes. By introducing the Fourier transform and preconditioning conjugate-gradient algorithms into the simulator, a highly efficient performance can be achieved in determining scattering wave functions and electron-transport properties of nanostructures suspended between semi-infinite jellium electrodes. To demonstrate the performance of the present algorithms, we study the conductance of metallic nanowires and the origin of the oscillatory behavior in the conductance of an Ir nanowire. It is confirmed that the $s$-$d_{z^2}$ channel of the Ir nanowire exhibits the transmission oscillation with a period of two-atom length, which is also dominant in the experimentally obtained conductance trace

Ferroelectric Phase Transitions in Ultra-thin Films of BaTiO3

We present molecular dynamics simulations of a realistic model of an ultrathin film of BaTiO$_3$ sandwiched between short-circuited electrodes to determine and understand effects of film thickness, epitaxial strain and the nature of electrodes on its ferroelectric phase transitions as a function of temperature. We determine a full epitaxial strain-temperature phase diagram in the presence of perfect electrodes. Even with the vanishing depolarization field, we find that ferroelectric phase transitions to states with in-plane and out-of-plane components of polarization exhibit dependence on thickness; it arises from the interactions of local dipoles with their electrostatic images in the presence of electrodes. Secondly, in the presence of relatively bad metal electrodes which only partly compensate the surface charges and depolarization field, a qualitatively different phase with stripe-like domains is stabilized at low temperature

First-principles accurate total-energy surfaces for polar structural distortions of BaTiO3, PbTiO3, and SrTiO3: consequences to structural transition temperatures

Specific forms of the exchange correlation energy functionals in first-principles density functional theory-based calculations, such as the local density approximation (LDA) and generalized-gradient approximations (GGA), give rise to structural lattice parameters with typical errors of -2% and 2%. Due to a strong coupling between structure and polarization, the order parameter of ferroelectric transitions, they result in large errors in estimation of temperature dependent ferroelectric structural transition properties. Here, we employ a recently developed GGA functional of Wu and Cohen [Phys. Rev. B 73, 235116 (2006)] and determine total-energy surfaces for zone-center distortions of BaTiO3, PbTiO3, and SrTiO3, and compare them with the ones obtained with calculations based on standard LDA and GGA. Confirming that the Wu and Cohen functional allows better estimation of structural properties at 0 K, we determine a new set of parameters defining the effective Hamiltonian for ferroelectric transition in BaTiO3. Using the new set of parameters, we perform molecular-dynamics (MD) simulations under effective pressures p=0.0 GPa, p=-2.0 GPa, and p=-0.005T GPa. The simulations under p=-0.005T GPa, which is for simulating thermal expansion, show a clear improvement in the cubic to tetragonal transition temperature and c/a parameter of its ferroelectric tetragonal phase, while the description of transitions at lower temperatures to orthorhombic and rhombohedral phases is marginally improved. Our findings augur well for use of Wu-Cohen functional in studies of ferroelectrics at nano-scale, particularly in the form of epitaxial films where the properties depend crucially on the lattice mismatch.Comment: 10 pages, 7 figures, 3 tables, resubmitted to PR

Mutational pattern and frequency of induced nucleotide changes in mouse ENU mutagenesis

<p>Abstract</p> <p>Background</p> <p>With the advent of sequence-based approaches in the mutagenesis studies, it is now possible to directly evaluate the genome-wide pattern of experimentally induced DNA sequence changes for a diverse array of organisms. To gain a more comprehensive understanding of the mutational bias inherent in mouse ENU mutagenesis, this study describes a detailed evaluation of the induced mutational pattern obtained from a sequence-based screen of ENU-mutagenized mice.</p> <p>Results</p> <p>Based on a large-scale screening data, we derive the sequence-based estimates of the nucleotide-specific pattern and frequency of ENU-induced base replacement mutation in the mouse germline, which are then combined with the pattern of codon usage in the mouse coding sequences to infer the spectrum of amino acid changes obtained by ENU mutagenesis. We detect a statistically significant difference between the mutational patterns in phenotype- versus sequence-based screens, which presumably reflects differential phenotypic effects caused by different amino acid replacements. We also demonstrate that the mutations exhibit strong strand asymmetry, and that this imbalance is generated by transcription, most likely as a by-product of transcription-coupled DNA repair in the germline.</p> <p>Conclusion</p> <p>The results clearly illustrate the biased nature of ENU-induced mutations. We expect that a precise understanding of the mutational pattern and frequency of induced nucleotide changes would be of practical importance when designing sequence-based screening strategies to generate mutant mouse strains harboring amino acid variants at specific loci. More generally, by enhancing the collection of experimentally induced mutations in unambiguously defined genomic regions, sequence-based mutagenesis studies will further illuminate the molecular basis of mutagenic and repair mechanisms that preferentially produce a certain class of mutational changes over others.</p

First-principles transport calculation method based on real-space finite-difference nonequilibrium Green's function scheme

We demonstrate an efficient nonequilibrium Green's function transport calculation procedure based on the real-space finite-difference method. The direct inversion of matrices for obtaining the self-energy terms of electrodes is computationally demanding in the real-space method because the matrix dimension corresponds to the number of grid points in the unit cell of electrodes, which is much larger than that of sites in the tight-binding approach. The procedure using the ratio matrices of the overbridging boundary-matching technique [Phys. Rev. B {\bf 67}, 195315 (2003)], which is related to the wave functions of a couple of grid planes in the matching regions, greatly reduces the computational effort to calculate self-energy terms without losing mathematical strictness. In addition, the present procedure saves computational time to obtain Green's function of the semi-infinite system required in the Landauer-B\"uttiker formula. Moreover, the compact expression to relate Green's functions and scattering wave functions, which provide a real-space picture of the scattering process, is introduced. An example of the calculated results is given for the transport property of the BN ring connected to (9,0) carbon nanotubes. The wave function matching at the interface reveals that the rotational symmetry of wave functions with respect to the tube axis plays an important role in electron transport. Since the states coming from and going to electrodes show threefold rotational symmetry, the states in the vicinity of the Fermi level, whose wave function exhibits fivefold symmetry, do not contribute to the electron transport through the BN ring.Comment: 34 page

Entropy landscape of solutions in the binary perceptron problem

The statistical picture of the solution space for a binary perceptron is studied. The binary perceptron learns a random classification of input random patterns by a set of binary synaptic weights. The learning of this network is difficult especially when the pattern (constraint) density is close to the capacity, which is supposed to be intimately related to the structure of the solution space. The geometrical organization is elucidated by the entropy landscape from a reference configuration and of solution-pairs separated by a given Hamming distance in the solution space. We evaluate the entropy at the annealed level as well as replica symmetric level and the mean field result is confirmed by the numerical simulations on single instances using the proposed message passing algorithms. From the first landscape (a random configuration as a reference), we see clearly how the solution space shrinks as more constraints are added. From the second landscape of solution-pairs, we deduce the coexistence of clustering and freezing in the solution space.Comment: 21 pages, 6 figures, version accepted by Journal of Physics A: Mathematical and Theoretica

Analysis of the proteome of human airway epithelial secretions.

BACKGROUND: Airway surface liquid, often referred to as mucus, is a thin layer of fluid covering the luminal surface that plays an important defensive role against foreign particles and chemicals entering the lungs. Airway mucus contains various macromolecules, the most abundant being mucin glycoproteins, which contribute to its defensive function. Airway epithelial cells cultured in vitro secrete mucins and nonmucin proteins from their apical surface that mimics mucus production in vivo. The current study was undertaken to identify the polypeptide constituents of human airway epithelial cell secretions to gain a better understanding of the protein composition of respiratory mucus. RESULTS: Fifty-five proteins were identified in the high molecular weight fraction of apical secretions collected from in vitro cultures of well-differentiated primary human airway epithelial cells and isolated under physiological conditions. Among these were MUC1, MUC4, MUC5B, and MUC16 mucins. By proteomic analysis, the nonmucin proteins could be classified as inflammatory, anti-inflammatory, anti-oxidative, and/or anti-microbial. CONCLUSIONS: Because the majority of the nonmucin proteins possess molecular weights less than that selected for analysis, it is theoretically possible that they may associate with the high molecular weight and negatively charged mucins to form a highly ordered structural organization that is likely to be important for maintaining the proper defensive function of airway mucus