Forces and atomic relaxations in the pSIC approach with ultrasoft pseudopotentials

We present the scheme that allows for efficient calculations of forces in the framework of pseudopotential self-interaction corrected (pSIC) formulation of the density functional theory. The scheme works with norm conserving and also with ultrasoft pseudopotentials and has been implemented in the plane-wave basis code {\sc quantum espresso}. We have performed tests of the internal consistency of the derived expressions for forces considering ZnO and CeO$_2$ crystals. Further, we have performed calculations of equilibrium geometry for LaTiO$_3$, YTiO$_3$, and LaMnO$_3$ perovskites and also for Re and Mn pairs in silicon. Comparison with standard DFT and DFT+U approaches shows that in the cases where spurious self-interaction matters, the pSIC approach predicts different geometry, very often closer to the experimental data.Comment: 11 pages, 2 figure

Beyond homozygosity mapping: family-control analysis based on Hamming distance for prioritizing variants in exome sequencing

A major challenge in current exome sequencing in autosomal recessive (AR) families is the lack of an effective method to prioritize single-nucleotide variants (SNVs). AR families are generally too small for linkage analysis, and length of homozygous regions is unreliable for identification of causative variants. Various common filtering steps usually result in a list of candidate variants that cannot be narrowed down further or ranked. To prioritize shortlisted SNVs we consider each homozygous candidate variant together with a set of SNVs flanking it. We compare the resulting array of genotypes between an affected family member and a number of control individuals and argue that, in a family, differences between family member and controls should be larger for a pathogenic variant and SNVs flanking it than for a random variant. We assess differences between arrays in two individuals by the Hamming distance and develop a suitable test statistic, which is expected to be large for a causative variant and flanking SNVs. We prioritize candidate variants based on this statistic and applied our approach to six patients with known pathogenic variants and found these to be in the top 2 to 10 percentiles of ranks

On non-completely positive quantum dynamical maps on spin chains

The new arguments based on Majorana fermions indicating that non-completely positive maps can describe open quantum evolution are presented.Comment: published; small change

Raising Bi-O bands above the Fermi energy level of hole-doped Bi2_2Sr2_2CaCu2_2O8+δ_{8+\delta} and other cuprate superconductors

The Fermi surface (FS) of Bi$_2$Sr$_2$CaCu$_2$O$_{8+\delta}$ (Bi2212) predicted by band theory displays Bi-related pockets around the $(\pi,0)$ point, which have never been observed experimentally. We show that when the effects of hole doping either by substituting Pb for Bi or by adding excess O in Bi2212 are included, the Bi-O bands are lifted above the Fermi energy ($E_F$) and the resulting first-principles FS is in remarkable accord with measurements. With decreasing hole-doping the Bi-O bands drop below $E_F$ and the system self-dopes below a critical hole concentration. Computations on other Bi- as well as Tl- and Hg-based compounds indicate that lifting of the cation-derived band with hole doping is a general property of the electronic structures of the cuprates.Comment: 4 pages, 4 figures; PRL (2006, in press

Spin orbit coupling in bulk ZnO and GaN

Using group theory and Kane-like $\mathbf{k\cdot p}$ model together with the L\"owdining partition method, we derive the expressions of spin-orbit coupling of electrons and holes, including the linear-$k$ Rashba term due to the intrinsic structure inversion asymmetry and the cubic-$k$ Dresselhaus term due to the bulk inversion asymmetry in wurtzite semiconductors. The coefficients of the electron and hole Dresselhaus terms of ZnO and GaN in wurtzite structure and GaN in zinc-blende structure are calculated using the nearest-neighbor $sp^3$ and $sp^3s^\ast$ tight-binding models separately.Comment: 9 pages, 6 figures, to be published in J. Appl. Phy

Survey incompleteness and the evolution of the QSO luminosity function

We concentrate on a type of QSO survey which depends on selecting QSO candidates based on combinations of colors. Since QSO's have emission lines and power-law continua, they are expected to yield broadband colors unlike those of stellar photospheres. Previously, the fraction of QSO's expected to be hiding (unselected) within the locus of stellar (U-J, J-F) colors was estimated at about 15 percent. We have now verified that the KK88 survey is at least 11 percent incomplete, but have determined that it may be as much as 34 percent incomplete. The 'missing' QSO's are expected to be predominantly at z less than or = 2.2. We have studied the proper motion and variability properties of all stellar objects with J less than or = 22.5 or F less than or = 21.5 in the SA 57 field which has previously been surveyed with a multicolor QSO search by KK88