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  • 601. Zhang, Qiong
    et al.
    Bulone, Vincent
    Ågren, Hans
    Tu, Yaoquan
    Örebro universitet, Akademin för naturvetenskap och teknik.
    A molecular dynamics study of the thermal response of crystalline cellulose I beta2011Inngår i: Cellulose (London), ISSN 0969-0239, E-ISSN 1572-882X, Vol. 18, nr 2, s. 207-221Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Molecular dynamics simulations were performed to better understand the atomic details of thermal induced transitions in cellulose I beta. The latest version of the GLYCAM force field series (GLYCAM06) was used for the simulations. The unit cell parameters, density, torsion angles and hydrogen-bonding network of the crystalline polymer were carefully analyzed. The simulated data were validated against the experimental results obtained by X-ray diffraction for the crystal structure of cellulose I beta at room and high temperatures, as well as against the temperature-dependent IR measurements describing the variation of hydrogen bonding patterns. Distinct low and high temperature structures were identified, with a phase transition temperature of 475-500 K. In the high-temperature structure, all the origin chains rotated around the helix axis by about 30A degrees and the conformation of all hydroxymethyl groups changed from tg to either gt on origin chains or gg on center chains. The hydrogen-bonding network was reorganized along with the phase transition. Compared to the previously employed GROMOS 45a4 force field, GLYCAM06 yields data in much better agreement with experimental observations, which reflects that a cautious parameterization of the nonbonded interaction terms in a force field is critical for the correct prediction of the thermal response in cellulose crystals.

  • 602.
    Zhang, Qiong
    et al.
    AlbaNova Univ Ctr, Dept Theoret Chem, Royal Inst Technol, Stockholm, Sweden; Adv Mat Lab, E China Univ Sci & Technol, Shanghai, Peoples R China; Inst Fine Chem, E China Univ Sci & Technol, Shanghai, Peoples R China.
    Tu, Yaoquan
    Örebro universitet, Akademin för naturvetenskap och teknik.
    Tian, He
    Adv Mat Lab, E China Univ Sci & Technol, Shanghai, Peoples R China; Inst Fine Chem, E China Univ Sci & Technol, Shanghai, Peoples R China.
    Zhao, Yanli
    Dept Chem, Northwestern Univ, Evanston IL, USA.
    Stoddart, Fraser J.
    Dept Chem, Northwestern Univ, Evanston IL, USA.
    Ågren, Hans
    AlbaNova Univ Ctr, Dept Theoret Chem, Royal Inst Technol, Stockholm, Sweden; Adv Mat Lab, E China Univ Sci & Technol, Shanghai, Peoples R China; Inst Fine Chem, E China Univ Sci & Technol, Shanghai, Peoples R China.
    Working mechanism for a redox switchable molecular machine based on cyclodextrin: a free energy profiles approach2010Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, nr 19, s. 6561-6566Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    This paper reports the working mechanism for a redox-responsive bistable [2]rotaxane incorporating an alpha-cyclodextrin (alpha-CD) ring (J. Am. Chem. Soc. 2008, 130, 11294-11296), based on free energy profiles obtained from all-atom molecular dynamics simulations. Employing an umbrella sampling technique, the free energy profiles (potential of mean force, PMF) were calculated for the shuttling motion of the alpha-CD ring between a tetrathiafulvalene (TTF) recognition site and a triazole (TZ) unit on the dumbbell of the rotaxane for three oxidation states (0, +1, +2) of the TTF unit. These calculated free energy profiles verified the experimentally observed binding preference for each state. Analysis of the free energy components reveals that, for these alpha-CD-based rotaxanes with charged TTF units, the real driving force for the shuttling in the oxidized states is actually the interactions between water and the rotaxane components, which overwhelms the attractive interactions between the alpha-CD ring and the charged dumbbell. In this work, we put forward a feasible approach to correctly describe the complexation behavior of CD with charged species, that is, free energy profiles obtained from all-atom molecular dynamics simulation.

  • 603.
    Zhang, Ru Bo
    et al.
    Beijing Intitute of Technology.
    Eriksson, Leif A.
    Örebro universitet, Akademin för naturvetenskap och teknik.
    Distinct Hydroxy-Radical-Induced Damage of 3-Uridine Monophosphate in RNA: A Theoretical Study2009Inngår i: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 15, nr 10, s. 2394-2402Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Cutting ties: Strand scission and base release in hydroxy-radical adducts of 3-uridine monophosphate (UMP) have been explored by using density functional theory. The presence of the ribose 2-OH group and the resultant formation of low-barrier hydrogen bonds with oxygen atoms of the 3-phosphate linkage are highly important for hydrogen transfer and the subsequent bond-breakage reactions (see picture).RNA strand scission and base release in 3-uridine monophosphate (UMP), induced by OH radical addition to uracil, is studied at the DFT B3LYP/6-31+G(d,p) level in the gas phase and in solution. In particular, the mechanism of hydrogen-atom transfer subsequent to radical formation, from C2 on the sugar to the C6 site on the base, is explored. The barriers of (C2-)H2a abstraction by the C6 radical site range from 11.2 to 20.0 kcal mol-1 in the gas phase and 14.1 to 21.0 kcal mol-1 in aqueous solution, indicating that the local surrounding governs the hydrogen-abstraction reaction in a stereoselective way. The calculated N1C1 (N1-glycosidic bond) and -phosphate bond strengths show that homolytic and heterolytic bond-breaking processes are largely favored in each case, respectively. The barrier for -phosphate bond rupture is approximately 3.2-4.0 kcal mol-1 and is preferred by 8-12 kcal mol-1 over N1-glycosidic bond cleavage in both the gas phase and solution. The -phosphate bond-rupture reactions are exothermal in the gas phase and solution, whereas N1C1 bond-rupture reactions require both solvation and thermal corrections at 298 K to be energetically favored. The presence of the ribose 2-OH group and its formation of low-barrier hydrogen bonds with oxygen atoms of the 3-phosphate linkage are highly important for hydrogen transfer and the subsequent bond-breakage reactions.

  • 604.
    Zhang, Ru Bo
    et al.
    Sch Sci, Inst Chem Phys, Beijing Inst Technol, Beijing, Peoples R China.
    Eriksson, Leif A.
    Örebro universitet, Akademin för naturvetenskap och teknik. Sch Chem, Natl Univ Ireland, Galway, Ireland.
    Theoretical study on conformational preferences of ribose in 2-thiouridine-the role of the 2 ' OH group2010Inngår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 12, nr 15, s. 3690-3697Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Conformational changes in ribose are well-known to play a significant role in biomolecular identification. The mechanism of selectivity towards C3'-endo conformation (conformer b) in ribose of 2-thiouridine has been studied using DFT (B3LYP) and MP2 methodology, together with 6-31+G(d,p) basis set. The polarity of the C2S2 bond is enhanced due to the orientation of H2' towards the S2 atoms, which leads to a difference in the corresponding bond lengths, the atomic charges and the vO2'H2' stretch vibrations in all the conformers. NBO analysis shows that charge transfer mainly occurs in the C2N3 and C2S2 orbitals. The higher stability of conformer b is attributed to its larger orbital interaction energies within the 2-thiouracil base, and total orbital interaction energies of conformer b. Our conclusion is that the distant electrostatic rather than hydrogen bonding effects between 2'OH and the S2 atoms play the dominant role in the orbital interaction, and enhance the selectivity towards the C3'-endo conformation of ribose.

  • 605. Zhao, Ke
    et al.
    Tu, Yaoquan
    Örebro universitet, Akademin för naturvetenskap och teknik.
    Luo, Yi
    Molecular dynamics and quantum chemistry study on conformations and optical properties of hydrogen bonded dipolar merocyanine dyes2009Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, nr 30, s. 10271-10276Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    An earlier proposed strategy to orient two merocyanine dyes in the desirable head-to-tail parallel fashion through multiple hydrogen bonds has been examined by molecular dynamics simulations and quantum chemical calculations. Two different merocyanine dyes dissolved in chloroform solution under various conditions are simulated by molecular dynamics. It is found that two dipolar units can be well connected through various numbers of hydrogen bonds. Although the probability to form the desirable head-to-tail dimer is unfortunately small even under strong poling electric field and low temperature, the formation of unwanted antiparallel structure has been effectively reduced. Typical hydrogen bonded dimers obtained from molecular dynamics simulations have been studied by hybrid density functional calculations. It is found that only the most probable complex can lead to the optical absorption spectrum that is in close agreement with the corresponding experiments. Calculated results for dipole moments of ground and charge transfer states, as well as first hyperpolarizabilities, of three typical complexes have also been provided.

  • 606.
    Zhao, Xiaocui
    et al.
    Dept Chem, Univ Western Ontario, London ON, Canada.
    Lam, Simon
    Univ Western Ontario, London ON, Canada.
    Jass, Jana
    Örebro universitet, Akademin för naturvetenskap och teknik. Univ Western Ontario, London ON, Canada.
    Ding, Zhifeng
    Dept Chem, Univ Western Ontario, London ON, Canada.
    Scanning electrochemical microscopy of single human urinary bladder cells using reactive oxygen species as probe of inflammatory response2010Inngår i: Electrochemistry communications, ISSN 1388-2481, E-ISSN 1873-1902, Vol. 12, nr 6, s. 773-776Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Scanning electrochemical microscopy of single human bladder (T24) and kidney (A498) epithelial cells after stimulation with heat-killed uropathogenic Escherichia coli GR-12 was investigated for the first time. 124 cells treated with the hk-UPEC in time-lapsed images showed prolonged release of reactive oxygen species (ROS) due to toll-like receptors (TLR4), while A498 cells without TLR4 did not show the ROS increase after the dosage of the same stimulant. This indicates discrete pathways of triggering the inflammatory. It also reveals that ROS can be used as a probe to detect inflammatory response to gram-negative bacteria. (C) 2010 Elsevier B.V. All rights reserved.

  • 607.
    ZILL-E- HUSSNAIN, SYED
    Örebro universitet, Akademin för naturvetenskap och teknik.
    Robot Assisted Video Microscopy for Free-formSurface Inspection2011Independent thesis Advanced level (degree of Master (Two Years)), 20 poäng / 30 hpOppgave
  • 608.
    Åberg, Maria
    Örebro universitet, Akademin för naturvetenskap och teknik.
    Skill and knowledge matrix and evaluation tool for CAD-users at Atlas Copco Rock Drills AB2010Independent thesis Basic level (university diploma), 10 poäng / 15 hpOppgave
  • 609.
    Ålund, Marie
    et al.
    Man-Technology-Environment Research Centre, Örebro University, Örebro, Sweden.
    Arwidsson, Zandra
    Örebro universitet, Institutionen för naturvetenskap och teknik. SAKAB AB, Kumla, Sweden .
    Allard, Bert
    Örebro universitet, Akademin för naturvetenskap och teknik.
    Leaching of metals from contaminated soil with polyhydroxicarboxylic acids of natural origin2009Konferansepaper (Fagfellevurdert)
    Abstract [en]

    The effect of addition of complexing agents, generated from natural products, on the release and redistribution of metals from contaminated soil has been studied. Water soluble humic substances (fulvic acids, FA) generated by leaching of high-molecular weight humic matter (peat) at high pH, and isosaccharinic acid (ISA), generated by degradation of wood (saw-dust) at high pH was used and compared with some synthetic complexing agents representing naturally occurring products: Citric acid (CA), ethylenediamine disuccinic acid (EDDS) and methylglycine diacetic acid (MGDA).

    Four contaminated soils with elevated levels of particularly As, Cr, Cu, Ni and Pb at maximum levels of 1.5, 1.2, 1.7, 0.14 and 3.8 g/kg, respectively (two from shooting-ranges, one from a steel-works site and one from a wood impregnation site) were leached with alkaline solutions (pH 12) containing peat degradation products (1.2 g/l TOC; some 90 % FAs) and wood degradation products (0.7 g/l TOC, some 50-60 % ISA), as well as solutions of CA, EDDS and MGDA (0.25 mM, pH 6-8). Metal releases were analysed after various leaching times: 24 h, 1 week, 5 weeks. Results are related to the total content of metals in the soil (XRF-analysis), total leachable fractions (sequential leaching according to Tessier) and leaching with nitric acid (pH 3).

    A release of some 10 % of the lead inventory and up to 50 % of the copper in one of the soils could be achieved in the FA and ISA leaching systems, while the synthesised agents EDDS and MGDA led to releases of some 60-90 %. The effects of FA and ISA were generally significantly lower than those of the other complexing agents for As, Cr, and Ni, but significantly higher for V (present at the level 40 mg/kg). Thus, a significant enhancement of the release of particularly copper and lead from the contaminated soils by leaching with alkaline (pH 12) leachates of wood and/or peat appears to be feasible.

  • 610.
    Åstrand, Björn
    et al.
    Halmstad University.
    Rögnvaldsson, Thorsteinn
    Halmstad University.
    Bouguerra, Abdelbaki
    Örebro universitet, Akademin för naturvetenskap och teknik.
    Andreasson, Henrik
    Örebro universitet, Akademin för naturvetenskap och teknik.
    Lilienthal, Achim J.
    Örebro universitet, Akademin för naturvetenskap och teknik.
    An Autonomous Robotic System for Load Transportation2009Inngår i: Proceedings of the 4th Swedish Workshop on Autonomous Robotics (SWAR), 2009, s. 56-57Konferansepaper (Fagfellevurdert)
  • 611.
    Öjebo, Erik
    Örebro universitet, Akademin för naturvetenskap och teknik.
    Objekt-relationsmappning i datacentrerad applikation2009Independent thesis Basic level (professional degree), 10 poäng / 15 hpOppgave
    Abstract [sv]

    Denna rapport presenterar en undersökning av sex olika objekt-relationsmappningsramverk, nämligen Entity Framework, LINQ to SQL, NHibernate, Castle ActiveRecord, MyGeneration Doodads och Subsonic. Undersökningen redogör för styrkor och svagheter hos de olika ramverken samt diskuterar när respektive ramverk är lämpligt att använda.

    De ramverk som bedömdes vara mest intressanta var NHibernate och Entity Framework, då de erbjuder flexibel mappning mellan domänmodellen och det underliggande databasschemat samt god tillgång till dokumentation och litteratur.

    Undersökningen användes som grund för att besluta vilket av de aktuella ramverken som skulle användas vid en omskrivning av en existerande applikation för IT-konsultföretaget Sogeti. Det ramverk som ansågs mest lämpligt för applikationen var NHibernate.

  • 612.
    Östrand, Therese
    Örebro universitet, Akademin för naturvetenskap och teknik.
    Analysis of CHS, MEB5.2, PDX1.3 and PR-5 expression in Arabidopsis thaliana ecotypes during UV-B irradiation.2010Independent thesis Advanced level (professional degree), 20 poäng / 30 hpOppgave
  • 613.
    Överstam, Henrik
    et al.
    Örebro universitet, Akademin för naturvetenskap och teknik.
    Johansson, Helena
    Örebro universitet, Akademin för naturvetenskap och teknik.
    Jarl, Magnus
    Örebro universitet, Akademin för naturvetenskap och teknik.
    Temperatures at wire-drawing: simulations and verification efforts2011Inngår i: Hutnik: vol 78, 2011, s. 98-100Konferansepaper (Annet vitenskapelig)
    Abstract [en]

    Temperatures are very important in the wire drawing process. They are hard to measure direct, but a combination of simulations and measurements can give valuable information

10111213 601 - 613 of 613
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