1,299 research outputs found
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 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 - 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 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
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