CO adsorption on metal surfaces: a hybrid functional study with plane wave basis set

We present a detailed study of the adsorption of CO on Cu, Rh, and Pt (111) surfaces in top and hollow sites. The study has been performed using the local density approximation, the gradient corrected functional PBE, and the hybrid Hartree-Fock density functionals PBE0 and HSE03 within the framework of generalized Kohn-Sham density functional theory using a plane-wave basis set. As expected, the LDA and GGA functionals show a tendency to favor the hollow sites, at variance with experimental findings that give the top site as the most stable adsorption site. The PBE0 and HSE03 functionals reduce this tendency. In fact, they predict the correct adsorption site for Cu and Rh but fail for Pt. But even in this case, the hybrid functional destabilizes the hollow site by 50 meV compared to the PBE functional. The results of the total energy calculations are presented along with an analysis of the projected density of states.Comment: 32 pages, 6 tables, 3 figures. (Re)Submitted to Phys. Rev. B; LDA results added in the tables; minor changes in the tex

Joint knowledge generation in European R&D networks: Results from a discrete choice modelling perspective

The objective of this study is to explore the determinants of joint knowledge generation within European networks of R&D collaboration. This study distinguishes between two types of joint knowledge generation: scientific and commercially relevant knowledge generation. Joint generation of scientific knowledge is measured by co-authored scientific publications, while joint commercially relevant knowledge is measured by co-owned patents and artefacts. Unit of analysis are dyads of organisations jointly participating in projects of the 5th EU Framework Programme (FP5). The data for carrying out this study is taken from a survey among FP5 participants and the EUPRO database. 23 EU member countries (Bulgaria, Cyprus, Malta and Rumania are excluded) plus Switzerland and Norway are included. Regression methods for discrete choice (logit and probit) are employed to meet the objective. The independent variables taken into consideration encompass the types of organisations involved in the dyad, geographical and cultural obstacles, relational factors and project characteristics. Results show that dyads involving universities have the highest probability not only to jointly generate scientific knowledge but also to jointly generate commercially relevant knowledge, whereas the involvement of an industry organisation results in a low probability for both types of knowledge generation. Perhaps, this can be attributed to the fact that joint knowledge generation entails disclosure of own knowledge, which is actually a task of universities but is problematic for industry organisations. Another important result is that crossing national border has a significant positive rather than negative effect on joint scientific knowledge generation, which is essentially a consequence of how the Framework Programmes had been set up. Similarly, crossing EU-15 external border has a positive effect on joint knowledge generation, indicating that the FPs work well in achieving their aim of supporting the catching up process of CEE countries. But, joint generation of commercially relevant knowledge is negatively influenced by language borders. This can be explained by the fact that the co-development of patentable knowledge or artefacts requires more intensive and complex interactions than to co-author a scientific publication where English is the lingua franca anyway. Results on relational factors and project characteristics satisfy expectations: Duration of collaboration and the existence of previous collaboration have a positive effect on joint knowledge generation, whereas the project size, measured by number of participants, affects joint knowledge generation negatively

Accurate Hartree-Fock energy of extended systems using large Gaussian basis sets

Calculating highly accurate thermochemical properties of condensed matter via wave function-based approaches (such as e.g. Hartree-Fock or hybrid functionals) has recently attracted much interest. We here present two strategies providing accurate Hartree-Fock energies for solid LiH in a large Gaussian basis set and applying periodic boundary conditions. The total energies were obtained using two different approaches, namely a supercell evaluation of Hartree-Fock exchange using a truncated Coulomb operator and an extrapolation toward the full-range Hartree-Fock limit of a Pad\'e fit to a series of short-range screened Hartree-Fock calculations. These two techniques agreed to significant precision. We also present the Hartree-Fock cohesive energy of LiH (converged to within sub-meV) at the experimental equilibrium volume as well as the Hartree-Fock equilibrium lattice constant and bulk modulus.Comment: 7.5 pages, 2 figures, submitted to Phys. Rev. B; v2: typos removed, References adde

Elucidating Surface Structure with Action Spectroscopy

Surface Action Spectroscopy, a vibrational spectroscopy method developed in recent years at the Fritz Haber Institute is employed for structure determination of clean and H2O-dosed (111) magnetite surfaces. Surface structural information is revealed by using the microscopic surface vibrations as a fingerprint of the surface structure. Such vibrations involve just the topmost atomic layers, and therefore the structural information is truly surface related. Our results strongly support the view that regular Fe3O4(111)/Pt(111) is terminated by the so-called Fetet1 termination, that the biphase termination of Fe3O4(111)/Pt(111) consists of FeO and Fe3O4(111) terminated areas, and we show that the method can differentiate between different water structures in H2O-derived adsorbate layers on Fe3O4(111)/Pt(111). With this, we conclude that the method is a capable new member in the set of techniques providing crucial information to elucidate surface structures. The method does not rely on translational symmetry and can therefore also be applied to systems which are not well ordered. Even an application to rough surfaces is possible

Barriers to cross-region research and development collaborations in Europe. Evidence from the fifth European Framework Programme

The focus of this paper is on cross-region R&D collaboration funded by the 5th EU Framework Programme (FP5). The objective is to measure distance, institutional, language and technological barrier effects that may hamper collaborative activities between European regions. Particular emphasis is laid on measuring discrepancies between two types of collaborative R&D activities, those generating output in terms of scientific publications and those that do not. The study area is composed of 255 NUTS-2 regions that cover the pre-2007 member states of the European Union (excluding Malta and Cyprus) as well as Norway and Switzerland. We employ a negative binomial spatial interaction model specification to address the research question, along with an eigenvector spatial filtering technique suggested by Fischer and Griffith (2008) to account for the presence of network autocorrelation in the origin-destination cooperation data. The study provides evidence that the role of geographic distance as collaborative deterrent is significantly lower if collaborations generate scientific output. Institutional barriers do not play a significant role for collaborations with scientific output. Language and technological barriers are smaller but the estimates indicate no significant discrepancies between the two types of collaborative R&D activities that are in focus of this study.Series: Working Papers in Regional Scienc

Ab initio Molecular Dynamics Simulations of the Initial Stages of Solid-electrolyte Interphase Formation on Lithium Ion Battery Graphitic Anodes

The decomposition of ethylene carbonate (EC) during the initial growth of solid-electrolyte interphase (SEI) films at the solvent-graphitic anode interface is critical to lithium ion battery operations. Ab initio molecular dynamics simulations of explicit liquid EC/graphite interfaces are conducted to study these electrochemical reactions. We show that carbon edge terminations are crucial at this stage, and that achievable experimental conditions can lead to surprisingly fast EC breakdown mechanisms, yielding decomposition products seen in experiments but not previously predicted.Comment: 5 pages, 4 figure

Spiral Chain O4 Form of Dense Oxygen

Oxygen is in many ways a unique element: the only known diatomic molecular magnet and the capability of stabilization of the hitherto unexpected O8 cluster structure in its solid form at high pressure. Molecular dissociations upon compression as one of the fundamental problems were reported for other diatomic solids (e.g., H2, I2, Br2, and N2), but it remains elusive for solid oxygen, making oxygen an intractable system. We here report the theoretical prediction on the dissociation of molecular oxygen into a polymeric spiral chain O4 structure (\theta-O4) by using first-principles calypso method on crystal structure prediction. The \theta-O4 stabilizes above 2 TPa and has been observed as the third high pressure phase of sulfur (S-III). We find that the molecular O8 phase remains extremely stable in a large pressure range of 0.008 - 2 TPa, whose breakdown is driven by the pressure-induced instability of a transverse acoustic phonon mode at zone boundary, leading to the ultimate formation of \theta-O4. Remarkably, stabilization of \theta-O4 turns oxygen from a superconductor into an insulator with a wide band gap (approximately 5.9 eV) originating from the sp3-like hybridized orbitals of oxygen and the localization of valence electrons. (This is a pre-print version of the following article: Li Zhu et al, Spiral chain O4 form of dense oxygen, Proc. Natl. Acad. Sci. U.S.A. (2011), doi: 10.1073/pnas.1119375109, which has been published online at http://www.pnas.org/content/early/2011/12/27/1119375109 .)Comment: 13 apages, 3 figure

Band Gap Dependence on Cation Disorder in ZnSnN2Solar Absorber

The band gap of earth-abundant ZnSnN2 can be tuned between 1 and 2 eV by varying the growth conditions and resulting cation disorder. The optical absorption edges and carrier densities fall between model curves for cation-ordered orthorhombic and disordered wurtzite ZnSnN2. Hard X-ray photo­emission spectra suggest different degrees of cation disorder from comparison with hybrid DFT-calculated densities of states

Ribosoomide lagundamine bakterites

Väitekirja elektrooniline versioon ei sisalda publikatsiooneRibosoomid on makromolekulaarsed kompleksid, mis koosnevad kahest suurest ja ühest väikesest RNAst ja paljudest erinevatest valkudest. Ribosoomides sünteesitakse kõik valgud, mida organismis leida võib, ning aktiivsete ribsoomide konsentratsioon (ja seega sünteesi kiirus) limiteerib rakkude kasvu kiirust. Ehk teisisõnu, mida kiiremini sünteesitakse uusi ribosoome, seda kiiremini kasvab ja jaguneb ka rakk. Kuna ribosomaalse RNA süntees hõlmab ca 80% raku RNA sünteesi aktiivsusest ja ribosoomi valgud moodustavad kuni veerandi raku valgumassist on selge, et mitte ainult ribosoomide funktsioon valgusünteesil vaid ka nende metabolism on rakulises majapidamises määrava tähtsusega. Tõepoolest, juba mõnda aega on teada, et aeglaselt kasvavates bakterirakkudes tegeleb enamus raku RNA lagundamise võimekusest värskelt sünteesitud ribosomaalse RNA lagundamisega. Sellegipoolest on viimase 50 aasta vältel üldiselt usutud, et kord juba valmis tehtud ja kokku pakitud ribosoomid on äärmiselt stabiilsed ning, et neid lagundatakse vaid tugeva stressi tingimustes. Samuti on meie teadmised ribosoomide lagundamise molekulaarsetest mehhanismidest bakteris üsnagi piiratud. Käesoleva doktoritöö eesmärk on kirjeldada ribosoomide lagundamist kasvavates soolekepikese (Escherichia coli) rakkudes ja heita valgust ribsoomide lagundamise mehhanismidele, molekulaarsetele radadele ning ensüümidele, mis selles protsessis osalevad. Me avastasime üllatusega, et kuigi ribosoome tõepoolest lagundatakse kasvavates bakterirakkudes, toimub see protsess vaid rakukultuuri kasvu aeglustumise perioodil, mis eelneb statsionaarse kasvufaasi saabumisele. Meil ei õnnestunud tuvastada küpsete ribosoomide lagundamist ei ühtlase kiirusega kasvavates ega ka null-kiirusega kasvavates rakkudes. Võimalik, et ribosoomide lagundamine aitab rakke neid ette valmistades eluks statsionaarses faasis, mil ei vajata suurt valgusünteesi võimekust, küll aga vabu komponente, millest elutingimuste paranedes kiiresti uusi makromolekule tootma hakata. Lisaks leidsime, et osad (kuid mitte kõik) ribosoomi RNAd inaktiveerivad mutatsioonid viivad samuti ribsoomide lagundamisele, kuid miskipärast lagundatakse siis nii mutantseid ning inaktiivseid kui metsiktüüpi ning aktiivseid ribosoome. Jällegi viitab see, et ribsoomide lagundamise eesmärk võiks olla üldise ribosoomide konsentratsiooni alandamine rakus. Kui me lisasime ribsoomide lagundamise katsesüsteemi valgusünteesi pärssivat antibiootikumi kloramfenikool, päästsime me sellega ribosoomid lagundamisest. Seda tulemust võib tõlgendada viisil, et de novo valgusüntees on vajalik ribosoomide lagundamisprogrammi käivitamiseks rakus. Testides ribosoomide lagundamise võime osas bakteritüvesid, kus puuduvad erinevad RNAd lagundavad ensüümid, leidsime kaks ensüümi, mille puudumise korral ribosoome ei lagundatud. Neist esimene, RNaas R, lõhub RNAsid alates nende tagumisest ehk 3’ otsast ning tunneb erilist lõbu kõrge sekundaarstruktuuriga RNA-de hävitamisest. RNaas R on ka eelnevalt näidatud osalevat ribosoomide lagundamisel. Teine ensüüm on seevastu suhteliselt vähetuntud endoribonukleeas nimega YbeY, mis lõikab RNAd katki keskelt, mitte ei lagunda seda otstest. See huvitav valk on arvatud osalevat ribsoomide kokkupakkimise kvaliteedikontrollil, kus ta on vajalik kõige viimases etapis, mil tuntakse ära valgusünteesil ebaõnnestuvad ribosoomid ja suunatakse need lagundamisse. Meie katsed viitavad, et seesama valk võib valla päästa ka töökorras olevate ribosoomide lagundamise, tehes ribosoomi RNAsse esimese lõike ning tekitades sellega kaitsetu 3’ otsa, mida tunneb ära RNaas R, mis omakorda suudab ribosoomi RNA täielikult lagundadaRibosomes are macromolecular complexes that consist of two large and one small RNA and of many different small proteins. The ribosome synthesizes all cellular proteins and the concentration of active ribosomes is rate limiting for cell growth. As synthesis or ribosomal RNA encompasses 80% of cellular RNA synthesis activity and the ribosomal proteins can make up half of the cellular protein mass, it is clear that ribosomal metabolism, including ribosomal degradation, makes a worthy object of study. Nevertheless, during the past half century it has been widely believed that mature ribosomes are quite stable in the cells. The major goal of this dissertation is to describe the degradation of mature ribosomes in growing E. coli cells and to shed light on the molecular mechanism of degradation. We discovered that while mature ribosomes are indeed degraded in cells growing in batch cultures, this process is limited to the slowing of growth phase, which precedes entry into the stationary phase. We were unable to detect degradation during constant-rate growth and during early stationary phase. In addition, we found that some, but not all, ribosome-inactivating mutations in 23S rRNA and 16S rRNA led to degradation of both mutant and wild-type ribosomal RNAs. Thus, unlike in yeast, the ribosome degradation in E. coli is a general process that, once initiated, does not discriminate between active and inactive ribosomes. As ribosome degradation is inhibited by the protein synthesis inhibitor chloramphenicol, we further suggest that de novo protein synthesis might be needed for triggering the degradation program. To pinpoint the enzymes responsible for degradation we tested several strains defective for different RNases. We found two RNases, RNaseR and YbeY, whose deletion saved ribosomes from degradation. RNaseR is a well studied 3’ to 5’ exonuclease whose role in degrading heavily structured RNAs, including the rRNAs, is well established. In contrast YbeY is a potential endonuclease recently implicated in a late step ribosomal quality control, which could well be the initiating endonuclease, whose cut(s) in rRNA would present substrates for RNaseR to further scavenge into mononucleotides