Self-consistent description of Andreev bound states in Josephson quantum dot devices

We develop a general perturbative framework based on a superconducting atomic limit for the description of Andreev bound states (ABS) in interacting quantum dots connected to superconducting leads. A local effective Hamiltonian for dressed ABS, including both the atomic (or molecular) levels and the induced proximity effect on the dot is argued to be a natural starting point. A self-consistent expansion in single-particle tunneling events is shown to provide accurate results even in regimes where the superconducting gap is smaller than the atomic energies, as demonstrated by a comparison to recent Numerical Renormalization Group calculations. This simple formulation may have bearings for interpreting Andreev spectroscopic experiments in superconducting devices, such as STM measurements on carbon nanotubes, or radiative emission in optical quantum dots.Comment: 12 pages, 11 figures. Last version: we added several extra references, modified two figures, and discussed recent proposals for Andreev spectroscop

Nonparametric instrumental regression with non-convex constraints

This paper considers the nonparametric regression model with an additive error that is dependent on the explanatory variables. As is common in empirical studies in epidemiology and economics, it also supposes that valid instrumental variables are observed. A classical example in microeconomics considers the consumer demand function as a function of the price of goods and the income, both variables often considered as endogenous. In this framework, the economic theory also imposes shape restrictions on the demand function, like integrability conditions. Motivated by this illustration in microeconomics, we study an estimator of a nonparametric constrained regression function using instrumental variables by means of Tikhonov regularization. We derive rates of convergence for the regularized model both in a deterministic and stochastic setting under the assumption that the true regression function satisfies a projected source condition including, because of the non-convexity of the imposed constraints, an additional smallness condition

Determining Protein Complex Connectivity Using a Probabilistic Deletion Network Derived from Quantitative Proteomics

Protein complexes are key molecular machines executing a variety of essential cellular processes. Despite the availability of genome-wide protein-protein interaction studies, determining the connectivity between proteins within a complex remains a major challenge. Here we demonstrate a method that is able to predict the relationship of proteins within a stable protein complex. We employed a combination of computational approaches and a systematic collection of quantitative proteomics data from wild-type and deletion strain purifications to build a quantitative deletion-interaction network map and subsequently convert the resulting data into an interdependency-interaction model of a complex. We applied this approach to a data set generated from components of the Saccharomyces cerevisiae Rpd3 histone deacetylase complexes, which consists of two distinct small and large complexes that are held together by a module consisting of Rpd3, Sin3 and Ume1. The resulting representation reveals new protein-protein interactions and new submodule relationships, providing novel information for mapping the functional organization of a complex

Spectroscopic signatures of a bandwidth-controlled Mott transition at the surface of 1T-TaSe2_2

High-resolution angle-resolved photoemission (ARPES) data show that a metal-insulator Mott transition occurs at the surface of the quasi-two dimensional compound TaSe$_2$. The transition is driven by the narrowing of the Ta $5d$ band induced by a temperature-dependent modulation of the atomic positions. A dynamical mean-field theory calculation of the spectral function of the half-filled Hubbard model captures the main qualitative feature of the data, namely the rapid transfer of spectral weight from the observed quasiparticle peak at the Fermi surface to the Hubbard bands, as the correlation gap opens up.Comment: 4 pages, 4 figures; one modified figure, added referenc

Quantum impurity solvers using a slave rotor representation

We introduce a representation of electron operators as a product of a spin-carry ing fermion and of a phase variable dual to the total charge (slave quantum rotor). Based on this representation, a new method is proposed for solving multi-orbital Anderson quantum impurity models at finite interaction strength U. It consists in a set of coupled integral equations for the auxiliary field Green's functions, which can be derived from a controlled saddle-point in the limit of a large number of field components. In contrast to some finite-U extensions of the non-crossing approximation, the new method provides a smooth interpolation between the atomic limit and the weak-coupling limit, and does not display violation of causality at low-frequency. We demonstrate that this impurity solver can be applied in the context of Dynamical Mean-Field Theory, at or close to half-filling. Good agreement with established results on the Mott transition is found, and large values of the orbital degeneracy can be investigated at low computational cost.Comment: 18 pages, 15 figure

The Out-of-Equilibrium Time-Dependent Gutzwiller Approximation

We review the recently proposed extension of the Gutzwiller approximation, M. Schiro' and M. Fabrizio, Phys. Rev. Lett. 105, 076401 (2010), designed to describe the out-of-equilibrium time-evolution of a Gutzwiller-type variational wave function for correlated electrons. The method, which is strictly variational in the limit of infinite lattice-coordination, is quite general and flexible, and it is applicable to generic non-equilibrium conditions, even far beyond the linear response regime. As an application, we discuss the quench dynamics of a single-band Hubbard model at half-filling, where the method predicts a dynamical phase transition above a critical quench that resembles the sharp crossover observed by time-dependent dynamical mean field theory. We next show that one can actually define in some cases a multi-configurational wave function combination of a whole set of mutually orthogonal Gutzwiller wave functions. The Hamiltonian projected in that subspace can be exactly evaluated and is equivalent to a model of auxiliary spins coupled to non-interacting electrons, closely related to the slave-spin theories for correlated electron models. The Gutzwiller approximation turns out to be nothing but the mean-field approximation applied to that spin-fermion model, which displays, for any number of bands and integer fillings, a spontaneous $Z_2$ symmetry breaking that can be identified as the Mott insulator-to-metal transition.Comment: 25 pages. Proceedings of the Hvar 2011 Workshop on 'New materials for thermoelectric applications: theory and experiment

Metal-insulator transition in the two-orbital Hubbard model at fractional band fillings: Self-energy functional approach

We investigate the infinite-dimensional two-orbital Hubbard model at arbitrary band fillings. By means of the self-energy functional approach, we discuss the stability of the metallic state in the systems with same and different bandwidths. It is found that the Mott insulating phases are realized at commensurate band fillings. Furthermore, it is clarified that the orbital selective Mott phase with one orbital localized and the other itinerant is stabilized even at fractional band fillings in the system with different bandwidths.Comment: 7 pages, 10 figure

Histone H3 Methylation by Set2 Directs Deacetylation of Coding Regions by Rpd3S to Suppress Spurious Intragenic Transcription

SummaryYeast Rpd3 histone deacetylase plays an important role at actively transcribed genes. We characterized two distinct Rpd3 complexes, Rpd3L and Rpd3S, by MudPIT analysis. Both complexes shared a three subunit core and Rpd3L contains unique subunits consistent with being a promoter targeted corepressor. Rco1 and Eaf3 were subunits specific to Rpd3S. Mutants of RCO1 and EAF3 exhibited increased acetylation in the FLO8 and STE11 open reading frames (ORFs) and the appearance of aberrant transcripts initiating within the body of these ORFs. Mutants in the RNA polymerase II-associated SET2 histone methyltransferase also displayed these defects. Set2 functioned upstream of Rpd3S and the Eaf3 methyl-histone binding chromodomain was important for recruitment of Rpd3S and for deacetylation within the STE11 ORF. These data indicate that Pol II-associated Set2 methylates H3 providing a transcriptional memory which signals for deacetylation of ORFs by Rpd3S. This erases transcription elongation-associated acetylation to suppress intragenic transcription initiation

Relationship between gene co-expression and probe localization on microarray slides

BACKGROUND: Microarray technology allows simultaneous measurement of thousands of genes in a single experiment. This is a potentially useful tool for evaluating co-expression of genes and extraction of useful functional and chromosomal structural information about genes. RESULTS: In this work we studied the association between the co-expression of genes, their location on the chromosome and their location on the microarray slides by analyzing a number of eukaryotic expression datasets, derived from the S. cerevisiae, C. elegans, and D. melanogaster. We find that in several different yeast microarray experiments the distribution of the number of gene pairs with correlated expression profiles as a function of chromosomal spacing is peaked at short separations and has two superimposed periodicities. The longer periodicity has a spacing of 22 genes (~42 Kb), and the shorter periodicity is 2 genes (~4 Kb). CONCLUSION: The relative positioning of DNA probes on microarray slides and source plates introduces subtle but significant correlations between pairs of genes. Careful consideration of this spatial artifact is important for analysis of microarray expression data. It is particularly relevant to recent microarray analyses that suggest that co-expressed genes cluster along chromosomes or are spaced by multiples of a fixed number of genes along the chromosome

Mott physics and band topology in materials with strong spin-orbit interaction

Recent theory and experiment have revealed that strong spin-orbit coupling can have dramatic qualitative effects on the band structure of weakly interacting solids. Indeed, it leads to a distinct phase of matter, the topological band insulator. In this paper, we consider the combined effects of spin-orbit coupling and strong electron correlation, and show that the former has both quantitative and qualitative effects upon the correlation-driven Mott transition. As a specific example we take Ir-based pyrochlores, where the subsystem of Ir 5d electrons is known to undergo a Mott transition. At weak electron-electron interaction, we predict that Ir electrons are in a metallic phase at weak spin-orbit interaction, and in a topological band insulator phase at strong spin-orbit interaction. Very generally, we show that with increasing strength of the electron-electron interaction, the effective spin-orbit coupling is enhanced, increasing the domain of the topological band insulator. Furthermore, in our model, we argue that with increasing interactions, the topological band insulator is transformed into a "topological Mott insulator" phase, which is characterized by gapless surface spin-only excitations. The full phase diagram also includes a narrow region of gapless Mott insulator with a spinon Fermi surface, and a magnetically ordered state at still larger electron-electron interaction.Comment: 10+ pages including 3+ pages of Supplementary Informatio