Viser treff 421-440 av 527

    • Five-Photon Absorption and Selective Enhancement of Multiphoton Absorption Processes 

      Friese, Daniel Henrik; Bast, Radovan; Ruud, Kenneth (Journal article; Tidsskriftartikkel; Peer reviewed, 2015-05-12)
      We study one-, two-, three-, four- and five-photon absorption of three centrosymmetric molecules using density functional theory. These calculations are the first ab initio calculations of five-photon absorption. Even- and odd-order absorption processes show different trends in the absorption cross sections. The behaviour of all even-and odd-photon absorption properties shows a semi-quantitative ...
    • Chemo-inspired Genetic Algorithm for Optimizing the Piecewise Aggregate Approximation 

      Muhammad Fuad, Muhammad Marwan (Journal article; Tidsskriftartikkel; Peer reviewed, 2015)
      In a previous work we presented DEWPAA: an improved version of the piecewise aggregate approximation representation method of time series. DEWPAA uses differential evolution to set weights to different segments of the time series according to their information content. In this paper we use a hybrid of bacterial foraging and genetic algorithm (CGA) to set the weights of the different segments in our ...
    • Screening of variable importance for optimizing electrodialytic remediation of heavy metals from polluted harbour sediments 

      Pedersen, Kristine Bondo; Lejon, Tore; Ottosen, Lisbeth M.; Jensen, Pernille E. (Journal article; Tidsskriftartikkel; Peer reviewed, 2015-04-15)
      Using multivariate design and modelling, optimal conditions for electrodialytic remediation (EDR) of heavy metals were determined for polluted harbour sediments from Hammerfest harbour located in the geographic Arctic region of Norway. The comparative importance of the variables; current density, remediation time, light/no light, the liquid-solid ratio and stirring rate of the sediment suspension ...
    • Recombinant expression and purification of an ATP-dependent DNA ligase from Aliivibrio salmonicida 

      Williamson, Adele Kim; Pedersen, Hege (Journal article; Tidsskriftartikkel; Peer reviewed, 2014-05)
      The genome of the psychrophilic fish-pathogen Aliivibrio salmonicida encodes a putative ATP-dependent DNA ligase in addition to a housekeeping NAD-dependent enzyme. In order to study the structure and activity of the ATP dependent ligase in vitro we have undertaken its recombinant production and purification from an Escherichia coli based expression system. Expression and purification of this ...
    • The Spot 42 RNA: A regulatory small RNA with roles in the central metabolism 

      Haugen, Peik; Bækkedal, Cecilie (Journal article; Tidsskriftartikkel; Peer reviewed, 2015-09-01)
      The Spot 42 RNA is a 109 nucleotide long (in Escherichia coli) noncoding small regulatory RNA (sRNA) encoded by the spf (spot fourty-two) gene. spf is found in gamma-proteobacteria and the majority of experimental work on Spot 42 RNA has been performed using E. coli, and recently Aliivibrio salmonicida. In the cell Spot 42 RNA plays essential roles as a regulator in carbohydrate metabolism and uptake, ...
    • A Haar Wavelet-based Multi-resolution Representation Method of Time Series Data 

      Muhammad Fuad, Muhammad Marwan (Peer reviewed; Journal article; Tidsskriftartikkel, 2015-01-10)
      Similarity search of time series can be efficiently handled through a multi-resolution representation scheme which offers the possibility to use pre-computed distances that are calculated and stored at indexing time and then utilized at query time together with filters in the form of exclusion conditions which speed up the search. In this paper we introduce a new multi-resolution representation ...
    • Discovery of Novel Inhibitor Scaffolds against the Metallo-beta-lactamase VIM-2 by Surface Plasmon Resonance (SPR) Based Fragment Screening 

      Christopeit, Tony; Carlsen, Trine Josefine Olsen; Helland, Ronny; Leiros, Hanna-Kirsti S. (Journal article; Tidsskriftartikkel; Peer reviewed, 2015-10-17)
      Metallo-β-lactamase (MBL) inhibitors can restore the function of carbapenem antibiotics and therefore help to treat infections of antibiotic resistant bacteria. In this study, we report novel fragments inhibiting the clinically relevant MBL Verona integron-encoded metallo-β-lactamase (VIM-2). The fragments were identified from a library of 490 fragments using an orthogonal screening approach based ...
    • An optimised method for electrodialytic removal of heavy metals from harbour sediments 

      Pedersen, Kristine Bondo; Jensen, Pernille E.; Ottosen, Lisbeth M.; Lejon, Tore (Journal article; Tidsskriftartikkel; Peer reviewed, 2015-08-10)
      A 2-compartment electrodialytic cell set-up for treatment of solid materials has in many respects proven superior to other types of cells in removing heavy metals from sediments. Most notably, remediation times were shorter, energy consumption was lower and higher removal efficiencies were observed. By employing multivariate modelling and investigating additional experimental variables, the ...
    • Enzyme-adenylate structure of a bacterial ATP-dependent DNA ligase with a minimized DNA-binding surface 

      Williamson, Adele Kim; Rothweiler, Ulli; Leiros, Hanna-Kirsti S. (Journal article; Tidsskriftartikkel; Peer reviewed, 2014-11-01)
      DNA ligases are a structurally diverse class of enzymes which share a common catalytic core and seal breaks in the phosphodiester backbone of double-stranded DNA via an adenylated intermediate. Here, the structure and activity of a recombinantly produced ATP-dependent DNA ligase from the bacterium Psychromonas sp. strain SP041 is described. This minimal-type ligase, like its close homologues, ...
    • Crystal structure of the DNA polymerase III β subunit (β-clamp) from the extremophile Deinococcus radiodurans 

      Niiranen, Laila; Lian, Kjersti; Johnson, Kenneth A; Moe, Elin (Journal article; Tidsskriftartikkel, 2015-02-27)
      Background: Deinococcus radiodurans is an extremely radiation and desiccation resistant bacterium which can tolerate radiation doses up to 5,000 Grays without losing viability. We are studying the role of DNA repair and replication proteins for this unusual phenotype by a structural biology approach. The DNA polymerase III β subunit (β-clamp) acts as a sliding clamp on DNA, promoting the binding ...
    • Structural and biochemical characterization of VIM-26 shows that Leu224 has implications for the substrate specificity of VIM metallo-β-lactamases 

      Leiros, Hanna-Kirsti S.; Edvardsen, Kine Susann Waade; Bjerga, Gro Elin Kjæreng; Samuelsen, Ørjan (Journal article; Tidsskriftartikkel; Peer reviewed, 2015-02-06)
      During the last decades antimicrobial resistance has become a global health problem. Metallo-β-lactamases (MBLs) which are broad-spectrum β-lactamases that inactivate virtually all β-lactams including carbapenems, are contributing to this health problem. In this study a novel MBL variant, termed VIM-26, identified in a Klebsiella pneumoniae isolate was studied. VIM-26 belongs to the Verona ...
    • Four-Component Relativistic Density Functional Theory Calculations of EPR g- and Hyperfine-Coupling Tensors Using Hybrid Functionals: Validation on Transition-Metal Complexes with Large Tensor Anisotropies and Higher-Order Spin-Orbit Effects 

      Gohr, Sebastian; Hrobárik, Peter; Repisky, Michal; Komorovsky, Stanislav; Ruud, Kenneth; Kaupp, Martin (Journal article; Tidsskriftartikkel; Peer reviewed, 2015-12-04)
      The four-component matrix Dirac-Kohn-Sham (mDKS) implementation of EPR g- and hyperfine A-tensor calculations within a restricted kinetic balance framework in the ReSpect code has been extended to hybrid functionals. The methodology is validated for an extended set of small 4d1 and 5d1 [MEXn] q systems, and for a series of larger Ir(II) and Pt(III) d7 complexes (S=1/2) with particularly ...
    • Benchmarking two-photon absorption cross sections: performance of CC2 and CAM-B3LYP 

      Beerepoot, Maarten T. P.; Friese, Daniel Henrik; List, Nanna Holmgaard; Kongsted, Jacob; Ruud, Kenneth (Journal article; Tidsskriftartikkel; Peer reviewed, 2015-06-25)
      We investigate the performance of CC2 and TDDFT/CAM-B3LYP for the calculation of two-photon absorption (TPA) strengths and cross sections and contrast our results to a recent coupled cluster equation-of-motion (EOM-EE-CCSD) benchmark study [K. D. Nanda and A. I. Krylov, J. Chem. Phys., 2015, 142, 064118]. In particular, we investigate whether CC2 TPA strengths are significantly overestimated compared ...
    • Structure, solvent, and relativistic effects on the NMR chemical shifts in square-planar transition-metal complexes: Assessment of DFT approaches 

      Vicha, Jan; Novotny, Jan; Straka, Michal; Repisky, Michal; Ruud, Kenneth; Komorovsky, Stanislav; Marek, Radek (Journal article; Tidsskriftartikkel; Peer reviewed, 2015-08-25)
      The role of various factors (structure, solvent, and relativistic treatment) was evaluated for square-planar 4d and 5d transition-metal complexes. The DFT method for calculating the structures was calibrated using a cluster approach and compared to X-ray geometries, with the PBE0 functional (def2-TZVPP basis set) providing the best results, followed closely by the hybrid TPSSH and the MN12SX ...
    • Investigating the role of residues W228 and Y233 in the structure and activity of the GIM-1 metallo-beta-lactamase. 

      Skagseth, Susann; Carlsen, Trine Josefine Olsen; Bjerga, Gro Elin Kjæreng; Spencer, James; Samuelsen, Ørjan; Leiros, Hanna-Kirsti S. (Journal article; Tidsskriftartikkel; Peer reviewed, 2015-12-07)
      Metallo--lactamases (MBLs) hydrolyze virtually all -lactam antibiotics, including penicillins, cephalosporins, and carbapenems. The worldwide emergence of antibiotic-resistant bacteria harboring MBLs poses an increasing clinical threat. The MBL German imipenemase-1 (GIM-1) possesses an active site that is narrower and more hydrophobic than the active sites of other MBLs. The GIM-1 active-site ...
    • Quantum chemical studies of asymmetric reactions: Historical aspects and recent examples 

      Hopmann, Kathrin Helen (Journal article; Tidsskriftartikkel; Peer reviewed, 2015-02-18)
      Asymmetric catalysis is essential for the synthesis of chiral compounds such as pharmaceuticals, agrochemicals, fragrances, and flavors. For rational improvement of asymmetric reactions, detailed mechanistic insights are required. The usefulness of quantum mechanical (QM) studies for understanding the stereocontrol of asymmetric reactions was first demonstrated around 40 years ago, with impressive ...
    • The immediate global responses of Aliivibrio salmonicida to iron limitations 

      Thode, Sunniva Katharina; Kahlke, Tim; Robertsen, Espen Mikal; Hansen, Hilde; Haugen, Peik (Journal article; Tidsskriftartikkel, 2015-02-04)
      <i>Background</i>: Iron is an essential micronutrient for all living organisms, and virulence and sequestration of iron in pathogenic bacteria are believed to be correlated. As a defence mechanism, potential hosts therefore keep the level of free iron inside the body to a minimum. In general, iron metabolism is well studied for some bacteria (mostly human or animal pathogens). However, this area ...
    • The autoinducer synthases LuxI and AinS are responsible for temperature-dependent AHL production in the fish pathogen Aliivibrio salmonicida 

      Hansen, Hilde; Purohit, Amit Anand; Leiros, Hanna-Kirsti S.; Johansen, Jostein; Kellermann, Stefanie J.; Bjelland, Ane Mohn; Willassen, Nils Peder (Journal article; Tidsskriftartikkel, 2015-03-24)
      Background: Quorum sensing (QS) is a cell-to-cell communication system used by bacteria to regulate activities such as virulence, bioluminescence and biofilm formation. The most common QS signals in Gram-negative bacteria are N-acyl-homoserine lactones (AHLs). Aliivibrio salmonicida is the etiological agent of cold water vibriosis in Atlantic salmon, a disease which occurs mainly during seasons ...
    • Open-ended recursive approach for the calculation of multiphoton absorption matrix elements 

      Friese, Daniel Henrik; Beerepoot, Maarten T. P.; Ringholm, Magnus; Ruud, Kenneth (Journal article; Tidsskriftartikkel; Peer reviewed, 2015-02-11)
      We present an implementation of single residues for response functions to arbitrary order using a recursive approach. Explicit expressions in terms of density-matrix-based response theory for the single residues of the linear, quadratic, cubic, and quartic response functions are also presented. These residues correspond to one-, two-, three- and four-photon transition matrix elements. The newly ...
    • Open-Ended Recursive Calculation of Single Residues of Response Functions for Perturbation-Dependent Basis Sets 

      Friese, Daniel Henrik; Ringholm, Magnus; Gao, Bin; Ruud, Kenneth (Journal article; Tidsskriftartikkel; Peer reviewed, 2015-09-09)
      We present theory, implementation, and applications of a recursive scheme for the calculation of single residues of response functions that can treat perturbations that affect the basis set. This scheme enables the calculation of nonlinear light absorption properties to arbitrary order for other perturbations than an electric field. We apply this scheme for the first treatment of two-photon circular ...