High-order density-matrix perturbation theory

We present a simple formalism for the calculation of the derivatives of the electronic density matrix at any order, within density functional theory. Our approach, contrary to previous ones, is not based on the perturbative expansion of the Kohn-Sham wavefunctions. It has the following advantages: (i) it allows a simple derivation for the expression for the high order derivatives of the density matrix; (ii) in extended insulators, the treatment of uniform-electric-field perturbations and of the polarization derivatives is straightforward.Comment: 4 page

Random Graph-Homomorphisms and Logarithmic Degree

A graph homomorphism between two graphs is a map from the vertex set of one graph to the vertex set of the other graph, that maps edges to edges. In this note we study the range of a uniformly chosen homomorphism from a graph G to the infinite line Z. It is shown that if the maximal degree of G is `sub-logarithmic', then the range of such a homomorphism is super-constant. Furthermore, some examples are provided, suggesting that perhaps for graphs with super-logarithmic degree, the range of a typical homomorphism is bounded. In particular, a sharp transition is shown for a specific family of graphs C_{n,k} (which is the tensor product of the n-cycle and a complete graph, with self-loops, of size k). That is, given any function psi(n) tending to infinity, the range of a typical homomorphism of C_{n,k} is super-constant for k = 2 log(n) - psi(n), and is 3 for k = 2 log(n) + psi(n)

The OPERA magnetic spectrometer

The OPERA neutrino oscillation experiment foresees the construction of two magnetized iron spectrometers located after the lead-nuclear emulsion targets. The magnet is made up of two vertical walls of rectangular cross section connected by return yokes. The particle trajectories are measured by high precision drift tubes located before and after the arms of the magnet. Moreover, the magnet steel is instrumented with Resistive Plate Chambers that ease pattern recognition and allow a calorimetric measurement of the hadronic showers. In this paper we review the construction of the spectrometers. In particular, we describe the results obtained from the magnet and RPC prototypes and the installation of the final apparatus at the Gran Sasso laboratories. We discuss the mechanical and magnetic properties of the steel and the techniques employed to calibrate the field in the bulk of the magnet. Moreover, results of the tests and issues concerning the mass production of the Resistive Plate Chambers are reported. Finally, the expected physics performance of the detector is described; estimates rely on numerical simulations and the outcome of the tests described above.Comment: 6 pages, 10 figures, presented at the 2003 IEEE-NSS conference, Portland, OR, USA, October 20-24, 200

Electronic structure and excited state dynamics in a dicyanovinyl-substituted oligothiophene on Au(111)

Dicyanovinyl (DCV)-substituted oligothiophenes are promising donor materials in vacuum-processed small-molecule organic solar cells. Here, we studied the structural and the electronic properties of DCV-dimethyl-pentathiophene (DCV5T-Me2) adsorbed on Au(111) from submonolayer to multilayer coverages. Using a multi-technique experimental approach (low-temperature scanning tunneling microscopy/spectroscopy (STM/STS), atomic force microscopy (AFM), and two-photon photoemission (2PPE) spectroscopy), we determined the energetic position of several affinity levels as well as ionization potentials originating from the lowest unoccupied molecular orbitals (LUMO) and the highest occupied molecular orbitals (HOMO), evidencing a transport gap of 1.4 eV. Proof of an excitonic state was found to be a spectroscopic feature located at 0.6 eV below the LUMO affinity level. With increasing coverage photoemission from excitonic states gains importance. We were able to track the dynamics of several electronically excited states of multilayers by means of femtosecond time-resolved 2PPE. We resolved an intriguing relaxation dynamics involving four processes, ranging from sub-picosecond (ps) to several hundred ps time spans. These show a tendency to increase with increasing coverage. The present study provides important parameters such as energetic positions of transport levels as well as lifetimes of electronically excited states, which are essential for designing organic-molecule-based optoelectronic devices

Total energy global optimizations using non orthogonal localized orbitals

An energy functional for orbital based $O(N)$ calculations is proposed, which depends on a number of non orthogonal, localized orbitals larger than the number of occupied states in the system, and on a parameter, the electronic chemical potential, determining the number of electrons. We show that the minimization of the functional with respect to overlapping localized orbitals can be performed so as to attain directly the ground state energy, without being trapped at local minima. The present approach overcomes the multiple minima problem present within the original formulation of orbital based $O(N)$ methods; it therefore makes it possible to perform $O(N)$ calculations for an arbitrary system, without including any information about the system bonding properties in the construction of the input wavefunctions. Furthermore, while retaining the same computational cost as the original approach, our formulation allows one to improve the variational estimate of the ground state energy, and the energy conservation during a molecular dynamics run. Several numerical examples for surfaces, bulk systems and clusters are presented and discussed.Comment: 24 pages, RevTex file, 5 figures available upon reques

Dual targeting of ptp1b and aldose reductase with marine drug phosphoeleganin: A promising strategy for treatment of type 2 diabetes

An in-depth study on the inhibitory mechanism on protein tyrosine phosphatase 1B (PTP1B) and aldose reductase (AR) enzymes, including analysis of the insulin signalling pathway, of phosphoeleganin, a marine-derived phosphorylated polyketide, was achieved. Phosphoeleganin was demonstrated to inhibit both enzymes, acting respectively as a pure non-competitive inhibitor of PTP1B and a mixed-type inhibitor of AR. In addition, in silico docking analyses to evaluate the interaction mode of phosphoeleganin with both enzymes were performed. Interestingly, this study showed that phosphoeleganin is the first example of a dual inhibitor polyketide extracted from a marine invertebrate, and it could be used as a versatile scaffold structure for the synthesis of new designed multiple ligands

Plasma levels of conjugated bile acids in newborns after a short period of parenteral nutrition.

Background: Patients receiving parenteral nutrition (PN) frequently exhibit liver dysfunction. The authors previously reported that plant sterols of lipid emulsions added to the nutritional solution of newborns receiving PN accumulate in plasma and cell membranes and may contribute to the development of cholestasis. Conjugated bile acids (BA) have been shown to be useful markers of cholestasis. Plasma levels of several BA in newborns were quantified after administration of PN for less than 2 weeks. Methods: Plasma samples from 15 healthy control infants (CN), 22 patients who had received PN for 3-15 days (T1), and 9 patients scheduled to receive PN (T0) were analyzed. After a simple extraction procedure, plasma BA were analyzed by liquid chromatography-tandem mass spectrometry using a quantitative isotope dilution method. Results: The concentrations of BA did not differ significantly between controls and patients before PN (CN vs T0), with the exception of glycocholic acid (GCA; 2.30 ± 2.60 ??M vs 7.29 ± 5.39 ??M, respectively). There was a significant difference in several BA between controls and patients after PN (2.30 ± 2.60 ??M vs 7.61 ± 6.46 ??M for GCA, respectively; 4.02 ± 3.49 ??M vs 11.88 ± 11.05 ??M for taurocholic acid [TCA], respectively; and 4.81 ± 3.49 ??M vs 13.58 ± 12.22 ??M for taurochenodeoxycholic + taurodeoxycholic + tauroursodeoxycholic acids [TCDCA+TDCA+TUDCA], respectively). Conclusions: In newborns receiving PN, a short period of PN is associated with an early increase of some conjugated BA. These results suggest that GCA, TCA, and TCDCA+TDCA+TUDCA levels could be used as early markers of PN-related cholestasis

Quantum ESPRESSO: a modular and open-source software project for quantum simulations of materials

Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). Quantum ESPRESSO stands for "opEn Source Package for Research in Electronic Structure, Simulation, and Optimization". It is freely available to researchers around the world under the terms of the GNU General Public License. Quantum ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively-parallel architectures, and a great effort being devoted to user friendliness. Quantum ESPRESSO is evolving towards a distribution of independent and inter-operable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.Comment: 36 pages, 5 figures, resubmitted to J.Phys.: Condens. Matte

p190 Rho-GTPase activating protein associates with plexins and it is required for semaphorin signalling

Plexins are transmembrane receptors for semaphorins, guiding cell migration and axon extension. Plexin activation leads to the disassembly of integrin-based focal adhesive structures and to actin cytoskeleton remodelling and inhibition of cell migration; however, the underlying molecular mechanisms are unclear. We consistently observe a transient decrease of cellular RhoA-GTP levels upon plexin activation in adherent cells. One of the main effectors of RhoA downregulation is p190, a ubiquitously expressed GTPase activating protein (GAP). We show that, in p190-deficient fibroblasts, the typical functional activities mediated by plexins (such as cell collapse and inhibition of integrin-based adhesion) are blocked or greatly impaired. Notably, the functional response can be rescued in these cells by re-expressing exogenous p190, but not a mutant form specifically lacking RhoGAP activity. We furthermore demonstrate that semaphorin function is blocked in epithelial cells, primary endothelial cells and neuroblasts upon treatment with small interfering RNAs that knockdown p190 expression. Finally, we show that p190 transiently associates with plexins, and its RhoGAP activity is increased in response to semaphorin stimulation. We conclude that p190-RhoGAP is crucially involved in semaphorin signalling to the actin cytoskeleton, via interaction with plexins

Non-linear optical susceptibilities, Raman efficiencies and electrooptic tensors from first-principles density functional perturbation theory

The non-linear response of infinite periodic solids to homogenous electric fields and collective atomic displacements is discussed in the framework of density functional perturbation theory. The approach is based on the 2n + 1 theorem applied to an electric-field-dependent energy functional. We report the expressions for the calculation of the non-linear optical susceptibilities, Raman scattering efficiencies and electrooptic coefficients. Different formulations of third-order energy derivatives are examined and their convergence with respect to the k-point sampling is discussed. We apply our method to a few simple cases and compare our results to those obtained with distinct techniques. Finally, we discuss the effect of a scissors correction on the EO coefficients and non-linear optical susceptibilities