From Full stopping to transparency in a holographic model of heavy ion collisions

We numerically simulate planar shock wave collisions in anti-de Sitter space as a model for heavy ion collisions of large nuclei. We uncover a crossover between two different dynamical regimes as a function of the collision energy. At low energies the shocks first stop and then explode in a manner approximately described by hydrodynamics, in close similarity with the Landau model. At high energies the receding fragments move outwards at the speed of light, with a region of negative energy density and negative longitudinal pressure trailing behind them. The rapidity distribution of the energy density at late times around midrapidity is not approximately boost invariant but Gaussian, albeit with a width that increases with the collision energy.

Distributed all-atom simulations of intrinsically unstructured proteins

The Computational Biophysics Group at the Universitat Pompeu Fabra (GRIB-UPF) hosts two unique computational resources dedicated to the execution of large scale molecular dynamics (MD) simulations: (a) the ACMD molecular-dynamics software, used on standard personal computers with graphical processing units (GPUs); and (b) the GPUGRID. net computing network, supported by users distributed worldwide that volunteer GPUs for biomedical research. We leveraged these resources and developed studies, protocols and open-source software to elucidate energetics and pathways of a number of biomolecular systems, with a special focus on flexible proteins with many degrees of freedom. First, we characterized ion permeation through the bactericidal model protein Gramicidin A conducting one of the largest studies to date with the steered MD biasing methodology. Next, we addressed an open problem in structural biology, the determination of drug-protein association kinetics; we reconstructed the binding free energy, association, and dissaciociation rates of a drug like model system through a spatial decomposition and a Makov-chain analysis. The work was published in the Proceedings of the National Academy of Sciences and become one of the few landmark papers elucidating a ligand-binding pathway. Furthermore, we investigated the unstructured Kinase Inducible Domain (KID), a 28-peptide central to signalling and transcriptional response; the kinetics of this challenging system was modelled with a Markovian approach in collaboration with Frank Noe’s group at the Freie University of Berlin. The impact of the funding includes three peer-reviewed publication on high-impact journals; three more papers under review; four MD analysis components, released as open-source software; MD protocols; didactic material, and code for the hosting group.

Configurational statistical model for the damaged structure of silicon oxide after ion implantation

A configurational model for silicon oxide damaged after a high-dose ion implantation of a nonreactive species is presented. Based on statistics of silicon-centered tetrahedra, the model takes into account not only the closest environment of a given silicon atom, but also the second neighborhood, so it is specified whether the oxygen attached to one given silicon is bridging two tetrahedra or not. The frequencies and intensities of infrared vibrational bands have been calculated by averaging over the distributions and these results are in agreement with the ones obtained from infrared experimental spectra. Likewise, the chemical shifts obtained from x-ray photoelectron spectroscopy (XPS) analysis are similar to the reported values for the charge-transfer model of SiOx compounds.

Initial state of ultrarelativistic heavy ion collision

A model for energy, pressure, and flow velocity distributions at the beginning of ultrarelativistic heavy ion collisions is presented, which can be used as an initial condition for hydrodynamic calculations. Our model takes into account baryon recoil for both target and projectile, arising from the acceleration of partons in an effective field F mu nu produced in the collision. The typical field strength (string tension) for RHIC energies is about 512 GeV/fm, which allows us to talk about string ropes. The results show that a quark-gluon plasma forms a tilted disk, such that the direction of the largest pressure gradient stays in the reaction plane, but deviates from both the beam and the usual transverse flow directions. Such initial conditions may lead to the creation of antiflow or third flow component [L. P. Csernai and D. Rhrich, Phys. Rev. Lett. B 458, 454 (1999)].

Characterization of nano-oxide layers fabricated by ion beam oxidation

In this paper, a remote O2 ion source is used for the formation of nano-oxide layers. The oxidation efficiency was measured in CoFe-oxide films, and a decrease of the oxide layer with the pan angle and the oxidation pressure is observed. For the same oxidation pressure, the oxidation efficiency depends on the O2 content in the Ar-O2 plasma. These results were applied in optimizing the fabrication of Al2O3 barrier for tunnel junctions. This method was also used to fabricate junctions with Fe-oxide layers inserted at the Al2O3-CoFe interface. TEM and magnetization data indicate that after anneal at 385°C, a homogeneous ferromagnetic Fe-oxide layer (Fe3O4?) is formed.

Matching stages of heavy-ion collision models

Heavy-ion reactions and other collective dynamical processes are frequently described by different theoretical approaches for the different stages of the process, like initial equilibration stage, intermediate locally equilibrated fluid dynamical stage, and final freeze-out stage. For the last stage, the best known is the Cooper-Frye description used to generate the phase space distribution of emitted, noninteracting particles from a fluid dynamical expansion or explosion, assuming a final ideal gas distribution, or (less frequently) an out-of-equilibrium distribution. In this work we do not want to replace the Cooper-Frye description, but rather clarify the ways of using it and how to choose the parameters of the distribution and, eventually, how to choose the form of the phase space distribution used in the Cooper-Frye formula. Moreover, the Cooper-Frye formula is used in connection with the freeze-out problem, while the discussion of transition between different stages of the collision is applicable to other transitions also. More recently, hadronization and molecular dynamics models have been matched to the end of a fluid dynamical stage to describe hadronization and freeze-out. The stages of the model description can be matched to each other on space-time hypersurfaces (just like through the frequently used freeze-out hypersurface). This work presents a generalized description of how to match the stages of the description of a reaction to each other, extending the methodology used at freeze-out, in simple covariant form which is easily applicable in its simplest version for most applications.

Approval voting ion dichotomous preferences

The aim of this paper is to find normative foundations of Approval Voting. In order to show that Approval Voting is the only social choice function that satisfies anonymity, neutrality, strategy-proofness and strict monotonicity we rely on an intermediate result which relates strategy-proofness of a social choice function to the properties of Independence of Irrelevant Alternatives and monotonicity of the corresponding social welfare function. Afterwards we characterize Approval Voting by means of strict symmetry, neutrality and strict monotonicity and relate this result to May's Theorem. Finally, we show that it is possible to substitute the property of strict monotonicity by the one efficiency of in the second characterization.

Sindicació de contingut a la Web : Els formats RSS i Atom

Aquest projecte centre el seu estudi en els llenguatges de sindicació RSS i Atom, les bases de dades XML natives i el llenguatge de consulta XQUERY.

Els formats per a la sindicació del contingut web : RSS i Atom

En aquesta memòria desenvolupem els conceptes associats al RSS i Atom: què és la web semàntica i la sindicació web, quines són les particularitats del XML i del seu llenguatge de consulta, el XQuery, les característiques dels formats RSS i Atom, i les bases de dades XML natives.

Critical thoughts on computing atom condensed Fukui functions

Different procedures to obtain atom condensed Fukui functions are described. It is shown how the resulting values may differ depending on the exact approach to atom condensed Fukui functions. The condensed Fukui function can be computed using either the fragment of molecular response approach or the response of molecular fragment approach. The two approaches are nonequivalent; only the latter approach corresponds in general with a population difference expression. The Mulliken approach does not depend on the approach taken but has some computational drawbacks. The different resulting expressions are tested for a wide set of molecules. In practice one must make seemingly arbitrary choices about how to compute condensed Fukui functions, which suggests questioning the role of these indicators in conceptual density-functional theory

Selected configuration interaction with truncation energy error and application to the Ne atom

Selected configuration interaction (SCI) for atomic and molecular electronic structure calculations is reformulated in a general framework encompassing all CI methods. The linked cluster expansion is used as an intermediate device to approximate CI coefficients BK of disconnected configurations (those that can be expressed as products of combinations of singly and doubly excited ones) in terms of CI coefficients of lower-excited configurations where each K is a linear combination of configuration-state-functions (CSFs) over all degenerate elements of K. Disconnected configurations up to sextuply excited ones are selected by Brown's energy formula, ΔEK=(E-HKK)BK2/(1-BK2), with BK determined from coefficients of singly and doubly excited configurations. The truncation energy error from disconnected configurations, Δdis, is approximated by the sum of ΔEKS of all discarded Ks. The remaining (connected) configurations are selected by thresholds based on natural orbital concepts. Given a model CI space M, a usual upper bound ES is computed by CI in a selected space S, and EM=E S+ΔEdis+δE, where δE is a residual error which can be calculated by well-defined sensitivity analyses. An SCI calculation on Ne ground state featuring 1077 orbitals is presented. Convergence to within near spectroscopic accuracy (0.5 cm-1) is achieved in a model space M of 1.4× 109 CSFs (1.1 × 1012 determinants) containing up to quadruply excited CSFs. Accurate energy contributions of quintuples and sextuples in a model space of 6.5 × 1012 CSFs are obtained. The impact of SCI on various orbital methods is discussed. Since ΔEdis can readily be calculated for very large basis sets without the need of a CI calculation, it can be used to estimate the orbital basis incompleteness error. A method for precise and efficient evaluation of ES is taken up in a companion paper

Density functional energy decomposition into one- and two-atom contributions

The present work provides a generalization of Mayer's energy decomposition for the density-functional theory (DFT) case. It is shown that one- and two-atom Hartree-Fock energy components in Mayer's approach can be represented as an action of a one-atom potential VA on a one-atom density ρ A or ρ B. To treat the exchange-correlation term in the DFT energy expression in a similar way, the exchange-correlation energy density per electron is expanded into a linear combination of basis functions. Calculations carried out for a number of density functionals demonstrate that the DFT and Hartree-Fock two-atom energies agree to a reasonable extent with each other. The two-atom energies for strong covalent bonds are within the range of typical bond dissociation energies and are therefore a convenient computational tool for assessment of individual bond strength in polyatomic molecules. For nonspecific nonbonding interactions, the two-atom energies are low. They can be either repulsive or slightly attractive, but the DFT results more frequently yield small attractive values compared to the Hartree-Fock case. The hydrogen bond in the water dimer is calculated to be between the strong covalent and nonbonding interactions on the energy scale

Metallic and nonmetallic shine in luster: An elastic ion backscattering study

Luster is a metal glass nanocomposite layer first produced in the Middle East in early Islamic times ( 9th AD) made of metal copper or silver nanoparticles embedded in a silica-based glassy matrix. These nanoparticles are produced by ion exchange between Cu+ and Ag+ and alkaline ions from the glassy matrix and further growth in a reducing atmosphere. The most striking property of luster is its capability of reflecting light like a continuous metal layer and it was unexpectedly found to be linked to one single production parameter: the presence of lead in the glassy matrix composition. The purpose of this article is to describe the characteristics and differences of the nanoparticle layers developed on lead rich and lead free glasses. Copper luster layers obtained using the ancient recipes and methods are analyzed by means of elastic ion backscattering spectroscopy associated with other analytical techniques. The depth profile of the different elements is determined, showing that the luster layer formed in lead rich glasses is 5–6 times thinner and 3–4 times Cu richer. Therefore, the metal nanoparticles are more densely packed in the layer and this fact is related to its higher reflectivity. It is shown that lead influences the structure of the metal nanoparticle layer through the change of the precipitation kinetics