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  • 1
    Online Resource
    Online Resource
    Theoretical Biochemistry : Processes and Properties of Biological Systems. (2001)
    San Diego :Elsevier Science & Technology,
    Details
    Keywords: Biochemistry. ; Electronic books.
    Type of Medium: Online Resource
    Pages: 1 online resource (719 pages)
    Edition: 1st ed.
    ISBN: 9780080542706
    Series Statement: Issn Series ; v.Volume 9
    URL: https://ebookcentral.proquest.com/lib/geomar/detail.action?docID=317108
    Language: English
    Note: Cover -- Theoretical Biochemistry: Processes and Properties of Biological Systems -- Copyright Page -- Foreword -- Table of Contents -- Chapter 1. The Structure and Function of Blue Copper Proteins -- 1. Introduction -- 2. Methods -- 3. Geometry -- 4. Electronic spectra -- 5. Reorganisation energies -- 6. Reduction potentials -- 7. Related proteins -- 8. Protein strain -- 9. Concluding remarks -- Chapter 2. Myoglobin -- 1. Introduction -- 2. Conformation and structural dynamics -- 3. Complexes with various ligands -- 4. Photodissociation -- 5. Recombination -- 6. Ligand migration -- Chapter 3. Mechanisms for Enzymatic Reactions Involving Formation or Cleavage of O-O Bonds -- 1. Introduction -- 2. Methods and models -- 3. Formation of O2 -- 4. O-O bond cleavage -- 5. Conclusions -- Chapter 4. Catalytic Reactions of Radical Enzymes -- 1. Introduction -- 2. Methodology -- 3. Galactose oxidase -- 4. Pyruvate formate-lyase -- 5. Ribonucleotide reductase -- 6. Concluding remarks -- Chapter 5. Theoretical Studies of Coenzyme B12-Dependent Carbon- Skeleton Rearrangemems -- 1. Introduction -- 2. Background -- 3. Evaluation of theoretical techniques -- 4. 2-Methyleneglutarate mutase -- 5. Methylmalonyl-CoA mutase -- 6. Glutamate mutase -- 7. Comparison of the models for B12-dependent carbon-skeleton mutases -- 8. The partial-proton-transfer concept -- 9. Conclusions -- Chapter 6. Simulations of Enzymatic Systems: Perspectives from Car- Parrinello Molecular Dynamics Simulations -- 1. Introduction -- 2. Principles of the Car-Parrinello method -- 3. Car-Parrinello modeling of biological systems -- 4. Applications to non-enzymatic systems -- 5. Applications to enzymes -- 6. Outlook -- Chapter 7. Computational Enzymology: Protein Tyrosine Phosphatase Reactions -- 1. Introduction -- 2. Protein tyrosine phosphatase reactions. , 3. The empirical valence bond method -- 4. Reaction free energy profile of the LMPTP -- 5. Substrate trapping in cysteine to serine mutated PTPases -- 6. Prediction of a ligand induced conformational change in the active site of CDC25A -- 7. Kinetic isotope effects in phosphoryl transfer reactions -- Chapter 8. Monte Carlo Simulations of HIV-1 Protease Binding Dynamics and Thermodynamics with Ensembles of Protein Conformations: Incorporating Protein Flexibility in Deciphering Mechanisms of Molecular Recognition -- 1. Structural models for molecular recognition -- 2. Structure-based analysis of HIV-1 protease-inhibitor binding -- 3. Structure-based computational models of ligand-protein binding dynamics and molecular docking -- 4. Computer simulations of ligand-protein binding -- 5. Computer simulations of HIV-1 protease-inhibitor binding dynamics and thermodynamics -- 6. Conclusions -- Chapter 9. Modelling G-Protein Coupled Receptors -- 1. Introduction -- 2. Receptor structure and modelling -- 3. Ligand binding -- 4. Structural changes -- 5. Receptor-G-protein interaction -- 6. GPCR dimerisation -- 7. Conclusions -- Chapter 10. Protein-DNA Interactions in the Initiation of Transcription: The Role of Flexibility and Dynamics of the TATA Recognition Sequence and the TATA Box Binding Protein -- 1. TBP and transcription -- 2. TATA box sequence specific recognition -- 3. Dynamic effects in complex stabilization -- 4. Towards the preinitiation complex assembly -- 5. Concluding remarks -- Chapter 11. A Multi-Component Model for Radiation Damage to DNA from its Constituents -- 1. Introduction -- 2. Characterization of DNA radiation products -- 3. Full DNA studies -- 4. A Multi-component model for DNA radiation damage -- 5. Concluding remarks -- Chapter 12. New Computational Strategies for the Quantum Mechanical Study of Biological Systems in Condensed Phases. , 1. Introduction -- 2. The density functional model -- 3. Vibrational averaging -- 4. Solvent effects -- 5. Applications -- 6. Concluding remarks -- Chapter 13. Modelling Enzyme-Ligand Interactions -- 1. Introduction -- 2. Strategies in enzyme-ligand design -- 3. The enzyme-ligand complex in motion -- 4. A quantum insight into the study of enzyme-ligand interactions -- 5. Conclusions -- Chapter 14. The QM/MM Approach to Enzymatic Reactions -- 1. Introduction -- 2. Theory -- 3. QM/MM methods -- 4. Techniques for reaction modelling -- 5. Practical aspects of modelling enzyme reactions -- 6. Some recent applications -- 7. Conclusions -- Chapter 15. Quinones and Quinoidal Radicals in Photosynthesis -- 1. Introduction -- 2. Tests of computational methods for calculating properties of quinoidal radicals -- 3. Calculated properties of quinoidal radicals important in photosynthesis -- 4. Semiquinone radical anions in plant photosystem II -- 5. Conclusions and future directions -- Author Index -- Subject Index.
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  • 2
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    TANGOSat data for sea ice research (2014)
    In:  EPIC31st ESA SAOCOM Companion Satellite Workshop, ESTEC/ESA, Noordwijk, The Netherlands, 2014-10-01-2014-10-02
    Details
    Publication Date: 2014-10-15
    Description: Compared to widely used C-band SAR imagery, L-band SAR is a valuable complement in monitoring the Arctic and Antarctic sea ice covers, since it is very sensitive to ice deformation structures. The continuous observation of sea ice and the retrieval of sea ice properties from satellite data has received increased attention from the science community after the extreme minimum of summer arctic sea ice extent observed in 2007, which was followed by an even lower minimum in 2012. Also in operational sea ice monitoring there is an interest in investigating the potential of L-band SAR for sea ice mapping, although spatial coverage and timeliness of L-band data provided by recent satellite missions are still a critical issue for operational services. The concept of the TANGOSat mission will it make possible to address the potential of satellite tandems in gaining additional insights into the interaction between longer microwaves and sea ice. In particular the tomographic and bistatic phase may offer possibilities for specific investigations such as depth of scatterers and structures in thick multi-year ice (as found north of Greenland), quantification of ice surface roughness due to the occurrence of deformation structures, potential improvements of ice type classification, or snapshots of ice drift components by using along-track interferometry. In the presentation, different possibilities of investigations will be discussed.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Conference , notRev
    Format: application/pdf
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  • 3
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    SEASTAR: A mission to study ocean submesoscale dynamics and small-scale atmosphere-ocean processes in coastal, shelf and polar seas (2019)
    Frontiers Media
    Details
    Publication Date: 2022-11-10
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in [citation], doi:[doi]. Gommenginger, C., Chapron, B., Hogg, A., Buckingham, C., Fox-Kemper, B., Eriksson, L., Soulat, F., Ubelmann, C., Ocampo-Torres, F., Nardelli, B. B., Griffin, D., Lopez-Dekker, P., Knudsen, P., Andersen, O., Stenseng, L., Stapleton, N., Perrie, W., Violante-Carvalho, N., Schulz-Stellenfleth, J., Woolf, D., Isern-Fontanet, J., Ardhuin, F., Klein, P., Mouche, A., Pascual, A., Capet, X., Hauser, D., Stoffelen, A., Morrow, R., Aouf, L., Breivik, O., Fu, L., Johannessen, J. A., Aksenov, Y., Bricheno, L., Hirschi, J., Martin, A. C. H., Martin, A. P., Nurser, G., Polton, J., Wolf, J., Johnsens, H., Soloviev, A., Jacobs, G. A., Collard, F., Groom, S., Kudryavtsev, V., Wilkin, J., Navarro, V., Babanin, A., Martin, M., Siddorn, J., Saulter, A., Rippeth, T., Emery, B., Maximenko, N., Romeiser, R., Graber, H., Azcarate, A. A., Hughes, C. W., Vandemark, D., da Silva, J., Van Leeuwen, P. J., Naveira-Garabato, A., Gemmrich, J., Mahadevan, A., Marquez, J., Munro, Y., Doody, S., & Burbidge, G. SEASTAR: A mission to study ocean submesoscale dynamics and small-scale atmosphere-ocean processes in coastal, shelf and polar seas. Frontiers in Marine Science, 6, (2019):457, doi:10.3389/fmars.2019.00457.
    Description: High-resolution satellite images of ocean color and sea surface temperature reveal an abundance of ocean fronts, vortices and filaments at scales below 10 km but measurements of ocean surface dynamics at these scales are rare. There is increasing recognition of the role played by small scale ocean processes in ocean-atmosphere coupling, upper-ocean mixing and ocean vertical transports, with advanced numerical models and in situ observations highlighting fundamental changes in dynamics when scales reach 1 km. Numerous scientific publications highlight the global impact of small oceanic scales on marine ecosystems, operational forecasts and long-term climate projections through strong ageostrophic circulations, large vertical ocean velocities and mixed layer re-stratification. Small-scale processes particularly dominate in coastal, shelf and polar seas where they mediate important exchanges between land, ocean, atmosphere and the cryosphere, e.g., freshwater, pollutants. As numerical models continue to evolve toward finer spatial resolution and increasingly complex coupled atmosphere-wave-ice-ocean systems, modern observing capability lags behind, unable to deliver the high-resolution synoptic measurements of total currents, wind vectors and waves needed to advance understanding, develop better parameterizations and improve model validations, forecasts and projections. SEASTAR is a satellite mission concept that proposes to directly address this critical observational gap with synoptic two-dimensional imaging of total ocean surface current vectors and wind vectors at 1 km resolution and coincident directional wave spectra. Based on major recent advances in squinted along-track Synthetic Aperture Radar interferometry, SEASTAR is an innovative, mature concept with unique demonstrated capabilities, seeking to proceed toward spaceborne implementation within Europe and beyond.
    Description: CG and AM received funding from the United Kingdom Centre for Earth Observation Instrumentation SEASTAR+ project (Contract No. RP10G0435A02). PVL was supported by the European Research Council (ERC) CUNDA project 694509 under the European Union Horizon 2020 Research and Innovation Program.
    Keywords: Satellite ; Air sea interactions ; Upper ocean dynamics ; Submesoscale ; Coastal ; Marginal ice zone ; Radar ; Along-track interferometry
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 4
    Electronic Resource
    Electronic Resource
    Accurate density functional theory study of cationic magnesium clusters and Mg+–rare gas interactions (1995)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 103 (1995), S. 1050-1056 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The equilibrium geometries, energetics, and hyperfine coupling constants for a number of charged magnesium clusters and magnesium–rare gas complexes are investigated using gradient corrected density functional theory. In the study of matrix effects, Mg+ and Mg+2 are embedded in matrices with up to 10 neon or argon atoms. For the magnesium ion, we calculate a shift in the isotropic hyperfine coupling constant of 10 G when changing the matrix from Ne to Ar (expt. value: 10.9 G), and for Mg+2 the calculated shift is −0.5 G (expt. value=1.1 G). In the second part of the paper, several different positively charged magnesium clusters with up to six magnesium atoms are optimized, and the resulting geometries, relative energies, and hyperfine coupling constants are compared with experimental data and with previous theoretical studies. Based on the computed averaged hyperfine coupling constants, a reassignment is proposed of the experimentally observed average values (in gauss), −222.5 (Mg+), −105.4 (Mg+2), −69.5 (linear Mg+3), −55.0 (triangular Mg+3), −48.5 (Mg+4), and −34.6 (Mg+5). The corresponding calculated values are −211.6, −100.0, −65.2, −58.7, −48.3, and −33.3 G, respectively. For the hexamer ion, we predict an average hfcc of −28.5 G. © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.469815
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  • 5
    Electronic Resource
    Electronic Resource
    Hybrid DFT-MD simulations of geometry and hyperfine structure of the CCH radical in argon matrices at low temperatures (1996)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 105 (1996), S. 8195-8203 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The thermal motion of the CCH radical embedded in a matrix of solid argon is simulated at 4 and 40 K, using a hybrid density functional theory—molecular dynamics (DFT-MD) approach. The DFT calculations are performed at the B3LYP/6-311G(d,p) level. It is concluded that the CCH molecule when embedded in the Ar matrix favors an oscillating, slightly bent geometric struct- ure, whereas in vacuum the molecule is linear. In the matrix at 4 K, the oscillations lie centered at a CCH bond angle of 170±5°. At 40 K far larger oscillations are noted (up to ±19° bending motion, centered at a 154° CCH angle), due to the increased thermal energy. As a consequence of the vibrational motion, the radical hyperfine structure becomes significantly modified, and agree far better with experimental data than do the linear optimized vacuum geometry results. The B3LYP/6-311G(d,p) computed vibrationally averaged isotropic couplings in an ordered Ar matrix at 4 K are 935, 173 and 42 MHz for C–C–H, respectively, to be compared with the experimental values (Ar matrix, 4 K) 902, 156 and 44 MHz, and the data for the B3LYP/6-311G(d,p) optimized linear structure in vacuum: 1043, 224 and 54 MHz. The present hybrid DFT-MD results also agree well with previous vibronically corrected MRDCI data. © 1996 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.472673
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  • 6
    Electronic Resource
    Electronic Resource
    Re-examination of the hyperfine structure of 14NH2 (1995)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 102 (1995), S. 3674-3678 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The hyperfine structure of the 14NH2 radical is investigated by means of multireference single and double configuration interaction (MRCI) techniques. Particular attention is paid to the dependence of the coupling constants on the basis set, reference space, and configuration selection energy threshold. It is found that convergence can be obtained only if more than 83 reference configurations are included with an energy threshold of at least 10−7 hartree. With up to 126 reference configurations, an energy threshold smaller than 10−8 hartree and an uncontracted (13s8p2d/8s2p) basis set, the MRCI isotropic couplings (27.44 and −68.47 MHz for N and H, respectively) are in very good agreement with experimental data (27.9 and −67.2 MHz, respectively). © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.468597
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  • 7
    Electronic Resource
    Electronic Resource
    On the accuracy of gradient corrected density functional methods for transition metal complexes (1995)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 102 (1995), S. 872-878 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Density functional theory with gradient corrections (DFTG) is applied to a series of second-row transition metal compounds. The mean absolute deviations from experiment for the atomic excitation energies and ionization potential are in the range 0.2–0.4 eV. In comparison with accurate multireference configuration interaction (MR-CI) and parametrized CI with parameter 80 (PCI-80) results for the binding energies of the MCH+2 cations, the mean absolute deviation is 6.7 kcal/mol to be compared with 17.8 kcal/mol at the modified coupled pair functional (MCPF) level. The DFTG result is more sensitive to the choice of asymptote with a mean deviation of 14 kcal/mol if the bonding atomic state is not used as asymptote. Product energies and transition states for the addition of methane to RhXL (X=H, Cl, L=H2O, NH3, PH3, and CO) also show the same trends as the PCI-80 comparison and represent an improvement over the MCPF results. © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.469202
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  • 8
    Electronic Resource
    Electronic Resource
    Growth hormone 24-h serum profiles during pregnancy—lack of pulsatility for the secretion of the placental variant (1989)
    Oxford, UK : Blackwell Publishing Ltd
    BJOG 96 (1989), S. 0 
    Details
    ISSN: 1471-0528
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Medicine
    Notes: Summary. Serum profiles of growth hormone (GW) were recorded for 24 h in women at different stages of normal pregnancy. Two monoclonal antibodies directcd against different epitopes and unaffected by human placental lactogen were used in radioimmunoassays to distinguish the pituitary 22K-GH from the placental GH variant. The ‘normal’ episodic peak activity of GH in non-pregnant and first trimester pregnant women was dramatically changed into a continuous very stable secretion during late pregnancy. This change was first observed at 17 weeks gestation. It is concluded that during the second half of pregnancy, serum measurements of GH reflect a major contribution from a non-cpisodically secreted placental GH variant and a concomitant suppression of pituitary GH. This specific signal, i.e. a continuous GH secretion, may be an important regulator of maternal liver metabolism during pregnancy.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1471-0528.1989.tb03352.x
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  • 9
    Electronic Resource
    Electronic Resource
    Density functional calculations of isotropic hyperfine coupling constants of radical cations (1993)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 99 (1993), S. 9756-9763 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The hyperfine (hf) structures of radical cations are calculated using first principles density functional theory. Within the local spin density (LSD) approximation, the isotropic hyperfine coupling constants (Fermi contact terms) are computed for a set of linear (nonbranched) alkane and alkene radical cations with up to four carbon atoms. The results are as a whole in very good agreement with experimental data, obtained from low temperature matrix isolation electron-spin resonance (ESR) measurements, and with results from previous configuration interaction calculations.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.465457
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  • 10
    Electronic Resource
    Electronic Resource
    Internal motion and the tunneling rates of CH+4 and CD+4 (1995)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 103 (1995), S. 8166-8173 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The thermal motion of CD+4 in the gas phase at 4 and 40 K is studied by means of a molecular dynamics method using the MP2/6-31G(d,p) force field. The thermal motion of CD+4 in the temperature range from 4 to 40 K does not involve a deuterium permutation on the picosecond time scale. The electronic energy fluctuations of CD+4 due to thermal motion are less than 0.7 kcal/mol at 4 K and 1.6 kcal/mol at 40 K, which is less than the energy barrier (3.4 kcal/mol at MP2 level) required for the permutation between two energy minimum C2v structures. On the basis of these calculations it is suggested that the observation of four equivalent hydrogen atoms in the ESR spectrum of CH+4 can be attributed to fast quantum tunneling, with an estimated rate of 4.3×106 s−1 for CH+4 and 1.6×103 s−1 for CD+4. © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.470180
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