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  • 1
    Electronic Resource
    Electronic Resource
    Springer
    Pure and applied geophysics 144 (1995), S. 769-801 
    ISSN: 1420-9136
    Keywords: Hokkaido Nansei-Oki ; tsunami ; finite element modeling ; energy conservation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences , Physics
    Notes: Abstract A fault plane model and a finite element hydrodynamic model are applied to the simulation of the Hokkaido Nansei-Oki tsunami of July 12, 1993. The joint performance of the models is assessed based on the overall ability to reproduce observed tsunami waveforms and to preserve mass and energy during tsunami propagation. While a number of observed characteristics of the waveforms are satisfactorily reproduced (in particular, amplitudes and arrival times at tidal gauges relatively close to the source, and general patterns of energy concentration), others are only marginally so (notably, wave periods at the same gauges, and wave heights along Okushiri); differences between observations and simulations are traceable to both the fault plane and the hydrodynamic models. Nonnegligible losses of energy occur throughout the simulated tsunami propagation. These losses seem to be due to a combination of factors, including numerical damping and possible deficiencies of the shallow water equations in preserving energy.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular evolution 47 (1998), S. 353-362 
    ISSN: 1432-1432
    Keywords: Key words: Protein evolution — Trypsin — Tandem gene duplication — Fourier transform — Repeated segment
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. The trypsin family of serine proteases is one of the most studied protein families, with a wealth of amino acid sequence information available in public databases. Since trypsin-like enzymes are widely distributed in living organisms in nature, likely evolutionary scenarios have been proposed. A novel methodology for Fourier transformation of biological sequences (FOTOBIS) is presented. The methodology is well suited for the identification of the size and extent of short repeats in protein sequences. In the present paper the trypsin family of enzymes is analyzed with FOTOBIS and strong evidence for tandem gene duplication is found. A likely evolutionary path for the development of present-day trypsins involved an intrinsic extensive tandem gene duplication of a small DNA fragment of 15–18 nucleotides, corresponding to five or six amino acids. This ancestral trypsin gene was subsequently duplicated, leading to the earliest version of a full-sized trypsin, from which the contemporary trypsins have developed.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 116 (2002), S. 7766-7768 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A theoretical method has recently been proposed to simulate a system weakly coupled to a proton bath [J. Chem. Phys. 114, 9706 (2001)]. However, as discussed here, the method suffers from several theoretical problems and, in the absence of a more sound justification, should probably be regarded as an empirical approach. © 2002 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 4
    ISSN: 1432-1327
    Keywords: Key words Protein electrostatistics ; Electron-proton coupling ; Redox-Bohr effect ; pKa calculations ; Cytochrome c3
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract  A comparative study of the pH-dependent redox mechanisms of several members of the cytochrome c 3 family has been carried out. In a previous work, the molecular determinants of this dependency (the so-called redox-Bohr effect) were investigated for one species using continuum electrostatic methods to find groups with a titrating range and strength of interaction compatible with a mediating role in the redox-Bohr effect. Here we clarify these aspects in the light of new and improved pK a calculations, our findings supporting the hypothesis of propionate D from heme I being the main effector in the pH-dependent modulation of the cytochrome c 3 redox potentials in all the c 3 molecules studied here. However, the weaker (but significant) role of other titrating groups cannot be excluded, their importance and identity changing with the particular molecule under study. We also calculate the relative redox potentials of the four heme centers among the selected members of the c 3 family, using a continuum electrostatic method that takes into account both solvation and interaction effects. Comparison of the calculated values with available data for the microscopic redox potentials was undertaken, the quality of the agreement being dependent upon the choice of the dielectric constant for the protein interior. We find that high dielectric constants give best correlations, while low values result in better magnitudes for the calculated potentials. The possibility that the crystallographic calcium ion in c 3 from Desulfovibrio gigas may be present in the solution structure was tested, and found to be likely.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    Chichester : Wiley-Blackwell
    International Journal for Numerical Methods in Fluids 22 (1996), S. 815-834 
    ISSN: 0271-2091
    Keywords: vertical discretization ; sigma co-ordinates ; localized sigma co-ordinates ; tidal flow ; numerical experimentation ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: We propose an empirical law for vertical nodal placement in tidal simulations that depends on a single parameter p. The influence of dimensionless numbers on the optimal value of pis analysed through a series of numerical experiments for an individual vertical and a single value of pis found to be adequate for all cases. The proposed law can lead to gains in accuracy of over two orders of magnitude relative to a uniform grid and compares favourably with non-uniform grids previously used in the literature. In practical applications the most effective use of this law may require each vertical to have a different number of nodes. Criteria for the distribution of the total number of nodes among different verticals are also proposed, based on the concept of equalizing errors across the domain. The usefulness of the overall approach is demonstrated through a two-dimensional laterally averaged application to a synthetic estuary.
    Additional Material: 15 Ill.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    Chichester : Wiley-Blackwell
    International Journal for Numerical Methods in Fluids 21 (1995), S. 183-204 
    ISSN: 0271-2091
    Keywords: transport equation ; Eulerian-Lagrangian methods ; stability analysis ; accuracy analysis ; numerical experimentation ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Selected finite element Eulerian-Lagrangian methods for the solution of the transport equation are compared systematically in the relatively simple context of 1D, constant coefficient, conservative problems. A combination of formal analysis and numerical experimentation is used to characterize the stability and accuracy that results from alternative treatments of the concentrations at the feet of the characteristic lines. Within the methods analyzed, those that approach such treatment with the perspective of ‘integration’ rather than ‘interpolation’ tend to have superior accuracy. Exact integration leads to unconditional stability and excellent accuracy. Quadrature integration leads only to conditional stability, but newly derived criteria show that stability restrictions are relatively mild and should not preclude the usefulness of quadrature integration methods in a range of practical applications. While conclusions cannot be extended directly to multiple dimensions and complex flows and geometries, results should provide useful insight to the development and behaviour of specific Eulerian-Lagrangian transport models.
    Additional Material: 13 Ill.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 523-544 
    ISSN: 0887-3585
    Keywords: protonation equilibrium ; protein conformation ; continuum electrostatics ; potential of mean force ; force fields ; mean field theory ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Solution pH is a determinant parameter on protein function and stability, and its inclusion in molecular dynamics simulations is attractive for studies at the molecular level. Current molecular dynamics simulations can consider pH only in a very limited way, through a somewhat arbitrary choice of a set of fixed charges on the titrable sites. Conversely, continuum electrostatic methods that explicitly treat pH effects assume a single protein conformation whose choice is not clearly defined. In this paper we describe a general method that combines both titration and conformational freedom. The method is based on a potential of mean force for implicit titration and combines both usual molecular dynamics and pH-dependent calculations based on continuum methods. A simple implementation of the method, using a mean field approximation, is presented and applied to the bovine pancreatic trypsin inhibitor. We believe that this constant-pH molecular dynamics method, by correctly sampling both charges and conformation, can become a valuable help in the understanding of the dependence of protein function and stability on pH. © 1997 Wiley-Liss Inc.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
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