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  • 1
    ISSN: 1432-1017
    Keywords: Lipid diffusion ; random walk ; multistate random walk ; master equations ; two dimensions
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
    Notes: Abstract We present random walk models for the diffusive motion of lipid probe molecules in a lipid bilayer and calculate the diffusion constants for probes spanning the entire bilayer and for probes extending through one lipid layer only. The “stiffness” of such molecules can explain the observed value of 2/3 for the ratio of these diffusion constants.
    Type of Medium: Electronic Resource
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  • 2
    ISSN: 1432-1017
    Keywords: Chloride pump ; halorhodopsin ; ion translocation ; theoretical model ; cis-trans isomerization
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
    Notes: Abstract The chromophore in halorhodopsin (HR) which acts as a light-driven chloride pump in halobacteria shares many properties with its counterpart in bacteriorhodopsin (BR): (i) a similar retinal protein interaction, (ii) trans to cis isomerization and (iii) similar intermediates of its photocycle. One major difference between the two chromoproteins is that the HR chromophore does not become deprotonated during its photocycle. A mechanism for the photocycle of HR is presented, which, in close analogy to an earlier proposed mechanism for BR, involves the sequence of all-trans → 13-cis, 14s-cis → 13-cis → all-trans isomerizations of the chromophore, a Schiff base of retinal. In contrast to the situation in BR the 13-cis, 14s-cis→13-cis isomerization is induced not by deprotonation of the retinal Schiff base chromophore but rather by the movement of an anion (Cl-) towards the protonated nitrogen of the Schiff's base. The suggested mechanism involves the Schiff base directly in the chloride translocation in halorhodopsin.
    Type of Medium: Electronic Resource
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  • 3
    ISSN: 1432-1017
    Keywords: Bacteriorhodopsin ; vibrational analysis ; retinal
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
    Notes: Abstract We discuss to what extent recent vibrational spectra of 14-2H, 15-2H and 14,15-2H isotopically labelled L550 provide evidence for the occurrence of 13-cis, 14-s-trans or 13-cis, 14-s-cis chromophore structures in bacteriorhodopsin's photocycle. The discussion is based on a quantum chemical (MNDO) vibrational analysis of four molecular fragments as models for the retinal chromophore in bacteriorhodopsin.
    Type of Medium: Electronic Resource
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  • 4
    ISSN: 1432-0770
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Computer Science , Physics
    Notes: Abstract We extend the neural concepts of topological feature maps towards self-organization of auto-associative memory and hierarchical pattern classification. As is well-known, topological maps for statistical data sets store information on the associated probability densities. To extract that information we introduce a recurrent dynamics of signal processing. We show that the dynamics converts a topological map into an auto-associative memory for real-valued feature vectors which is capable to perform a cluster analysis. The neural network scheme thus developed represents a generalization of non-linear matrix-type associative memories. The results naturally lead to the concept of a feature atlas and an associated scheme of self-organized, hierarchical pattern classification.
    Type of Medium: Electronic Resource
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  • 5
    ISSN: 1434-6036
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract We develop a notion of high-T csuperconductivity, which considers that phenomenon as a general property of close to half-filled bands of strongly correlated electrons confined to low-dimensional orbital lattices. Based on Andersons suggestion [1] we initially investigate the Cud electron system of the undoped mother substances of the high-T c superconductors in the framework of the spin 1/2 Heisenberg model. We derive a new representation of the corresponding Hamiltonian in terms of triplet quasi-particles. The triplet representation leads to simple physical pictures for the ‘spin liquid’ state and to a hierarchy of nearly exact variational wave functions for the ground state of the linear chain. These wave functions are employed as vacuum states for doping with holes. Holes are shown to form a conduction band embedded in the Hubbard-Mott insulating phase of strongly correlated electrons. The chemical binding forces among these localized electrons entail a strong attractive pair potential acting between the mobile defects. The generality of the hole-hole attraction and its independence of a strict localization of the electrons in the Hubbard-Mott phase is demonstrated by nearly exact solutions of the Hubbard and Pariser-Parr-Pople models of small regular electron chains at various degrees of electron correlation. It is suggested that this exchange-driven attraction leads to an instability of the free hole gas towards Cooper pair formation.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 110 (1999), S. 10452-10467 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We present a hybrid method for molecular dynamics simulations of solutes in complex solvents as represented, for example, by substrates within enzymes. The method combines a quantum mechanical (QM) description of the solute with a molecular mechanics (MM) approach for the solvent. The QM fragment of a simulation system is treated by ab initio density functional theory (DFT) based on plane-wave expansions. Long-range Coulomb interactions within the MM fragment and between the QM and the MM fragment are treated by a computationally efficient fast multipole method. For the description of covalent bonds between the two fragments, we introduce the scaled position link atom method (SPLAM), which removes the shortcomings of related procedures. The various aspects of the hybrid method are scrutinized through test calculations on liquid water, the water dimer, ethane and a small molecule related to the retinal Schiff base. In particular, the extent to which vibrational spectra obtained by DFT for the solute can be spoiled by the lower quality force field of the solvent is checked, including cases in which the two fragments are covalently joined. The results demonstrate that our QM/MM hybrid method is especially well suited for the vibrational analysis of molecules in condensed phase. © 1999 American Institute of Physics.
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  • 7
    ISSN: 0022-2860
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    Amsterdam : Elsevier
    Journal of Photochemistry 9 (1978), S. 333 
    ISSN: 0047-2670
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 9
    ISSN: 0192-8651
    Keywords: molecular dynamics ; protein dynamics ; fast electrostatics computation ; fast multipole method ; multiple-time-step method ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Within molecular dynamics simulations of protein-solvent systems the exact evaluation of long-range Coulomb interactions is computationally demanding and becomes prohibitive for large systems. Conventional truncation methods circumvent that computational problem, but are hampered by serious artifacts concerning structure and dynamics of the simulated systems. To avoid these artifacts we have developed an efficient and yet sufficiently accurate approximation scheme which combines the structure-adapted multipole method (SAMM) [C. Niedermeier and P. Tavan, J. Chem. Phys., 101, 734 (1994)] with a multiple-time-step method. The computational effort for MD simulations required within our fast multiple-time-step structure-adapted multipole method (FAMUSAMM) scales linearly with the number of particles. For a system with 36,000 atoms we achieve a computational speed-up by a factor of 60 as compared with the exact evaluation of the Coulomb forces. Extended test simulations show that the applied approximations do not seriously affect structural or dynamical properties of the simulated systems.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1729-1749, 1997
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 97 (1992), S. 1865-1875 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A Pariser–Parr–Pople (PPP) Hamiltonian of an 8π electron system of the molecule octatetraene, represented in a configuration-interaction basis (CI basis), is analyzed with respect to the statistical properties of its matrix elements. Based on this analysis we develop an effective Hamiltonian, which represents virtual excitations by a Gaussian orthogonal ensemble (GOE). We also examine numerical approaches which replace the original Hamiltonian by a semistochastically generated CI matrix. In that CI matrix, the matrix elements of high energy excitations are choosen randomly according to distributions reflecting the statistics of the original CI matrix.
    Type of Medium: Electronic Resource
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