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  • 1
    Electronic Resource
    Electronic Resource
    Finite element modeling of the July 12, 1993 Hokkaido Nansei-Oki tsunami (1995)
    Springer
    Pure and applied geophysics 144 (1995), S. 769-801 
    Details
    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
    URL: http://dx.doi.org/10.1007/BF00874394
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    Paper (German National Licenses)
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  • 2
    Electronic Resource
    Electronic Resource
    Simulation of protein conformational freedom as a function of pH: constant-pH molecular dynamics using implicit titration (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 523-544 
    Details
    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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    Paper (German National Licenses)
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