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  • 1
    Digitale Medien
    Digitale Medien
    Principal coordinate analysis on a protein model (1999)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 110 (1999), S. 10606-10622 
    Details
    ISSN: 1089-7690
    Quelle: AIP Digital Archive
    Thema: Physik , Chemie und Pharmazie
    Notizen: A well-studied 46-bead protein model is the vehicle for examining principal coordinate analysis as a tool for interpreting topographies of complex potential surfaces. This study compares the effectiveness of several definitions of the comparison variable for revealing information about topographies. The extent of the information is ascertained by comparing the results of the various forms of principal coordinate analysis with results obtained from construction of interconnected monotonic sequences of linked stationary points (IMSLiSP) on the same surface. The conclusion is that the most powerful formulation of principal coordinate analyses for understanding protein folding and, in general, topographies of complex potentials, uses the changes in the set of interparticle distances as the definition of the comparison vector. However, even with this choice, the more efficient principal coordinate analysis is not able to reveal the extent of information contained in a more cumbersome IMSLiSP analysis. © 1999 American Institute of Physics.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1063/1.478992
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  • 2
    Digitale Medien
    Digitale Medien
    Dynamics of Xe Atoms in NaA Zeolites and the 129Xe Chemical Shift (1995)
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 99 (1995), S. 2459-2468 
    Details
    Quelle: ACS Legacy Archives
    Thema: Chemie und Pharmazie , Physik
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1021/j100009a003
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  • 3
    Digitale Medien
    Digitale Medien
    Molecular Geometry and the Rotational Potential Surface in Perfluoro(isopropyl methyl ether) (1995)
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 99 (1995), S. 3473-3477 
    Details
    Quelle: ACS Legacy Archives
    Thema: Chemie und Pharmazie , Physik
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1021/j100011a012
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  • 4
    Digitale Medien
    Digitale Medien
    Ab Initio Investigation of the Conformational Energies, Rotational Barriers, Molecular Structures, Vibrational Frequencies, and Dipole Moments of Aldehydes and Ketones (1995)
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 99 (1995), S. 10511-10520 
    Details
    Quelle: ACS Legacy Archives
    Thema: Chemie und Pharmazie , Physik
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1021/j100026a013
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  • 5
    Digitale Medien
    Digitale Medien
    Confined Clusters of Rare Gas Atoms: Structures and Phases (1995)
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 99 (1995), S. 15557-15564 
    Details
    Quelle: ACS Legacy Archives
    Thema: Chemie und Pharmazie , Physik
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1021/j100042a034
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  • 6
    Digitale Medien
    Digitale Medien
    Finite-time thermodynamics: Exergy and optimization of time-constrained processes (1994)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 76 (1994), S. 629-636 
    Details
    ISSN: 1089-7550
    Quelle: AIP Digital Archive
    Thema: Physik
    Notizen: The criterion of thermodynamic ideality is introduced. It is the ratio of actual rate of entropy production to the minimal rate of entropy production. It is closely related to the exergy approach but incorporates the irreversible losses due to finite-time and nonzero rates. No explicit reference need be made to the average values of the thermodynamic potentials of the environment. The regimes with minimal entropy production for the system where chemical reaction occurs and for the set of parallel heat engines are found.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1063/1.358425
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  • 7
    Digitale Medien
    Digitale Medien
    Simulation of mutation: Influence of a "side group" on global minimum structure and dynamics of a protein model (1999)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 111 (1999), S. 3753-3760 
    Details
    ISSN: 1089-7690
    Quelle: AIP Digital Archive
    Thema: Physik , Chemie und Pharmazie
    Notizen: The 46-bead, three-color model of a β-barrel-forming protein is modified by the addition of a single side group, represented by a bead which may be hydrophilic or hydrophobic. Molecular dynamics and quenching simulations show how the nature and location of the bead influence both the structure at the global minimum of internal energy and the relaxation processes by which the system finds its minima. The most drastic effects occur with a hydrophobic side group in the middle of a sequence of hydrophobes. © 1999 American Institute of Physics.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1063/1.479678
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  • 8
    Digitale Medien
    Digitale Medien
    Regularity in chaotic reaction paths. I. Ar6 (1999)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 110 (1999), S. 9160-9173 
    Details
    ISSN: 1089-7690
    Quelle: AIP Digital Archive
    Thema: Physik , Chemie und Pharmazie
    Notizen: We scrutinize the saddle crossings of a simple cluster of six atoms to show (a) that it is possible to choose a coordinate system in which the transmission coefficient for the classical reaction path is unity at all energies up to a moderately high energy, above which the transition state is chaotic; (b) that at energies just more than sufficient to allow passage across the saddle, all or almost all the degrees of freedom of the system are essentially regular in the region of the transition state; and (c) that the degree of freedom associated with the reaction coordinate remains essentially regular through the region of the transition state, even to moderately high energies. Microcanonical molecular dynamics simulation of Ar6 bound by pairwise Lennard-Jones potentials reveals the mechanics of passage. We use Lie canonical perturbation theory to construct the nonlinear transformation to a hyperbolic coordinate system which reveals these regularities. This transform "rotates away" the recrossings and nonregular behavior, especially of the motion along the reaction coordinate, leaving a coordinate and a corresponding dividing surface in phase space which minimize recrossings and mode–mode mixing in the transition state region. The action associated with the reactive mode tends to be an approximate invariant of motion through the saddle crossings throughout a relatively wide range of energy. Only at very low energies just above the saddle could any other approximate invariants of motion be found for the other, nonreactive modes. No such local invariants appeared at energies at which the modes are all chaotic and coupled to one another. © 1999 American Institute of Physics.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1063/1.478838
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  • 9
    Digitale Medien
    Digitale Medien
    Phase coexistence in clusters: An "experimental" isobar and an elementary model (1997)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 106 (1997), S. 6456-6459 
    Details
    ISSN: 1089-7690
    Quelle: AIP Digital Archive
    Thema: Physik , Chemie und Pharmazie
    Notizen: This work examines the temperature dependence of the coexistence ratios of phaselike forms of atomic clusters of two kinds, a homogeneous cluster bound by pairwise Lennard–Jones forces that simulates Ar55, and a binary, ionic cluster simulating (KCl)32. Two methods have been used: isothermal molecular dynamics and a simple analytical model based on highly simplified densities of states. The phase behavior of the alkali halide cluster is well represented by a two-level density of states, a nondegenerate lower level, and a highly degenerate upper level. The phase behavior of the argon cluster needs an intermediate level of moderate degeneracy to reproduce the three-phase behavior of the simulations. © 1997 American Institute of Physics.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1063/1.473636
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  • 10
    Digitale Medien
    Digitale Medien
    Self-organization and mismatch tolerance in protein folding: General theory and an application (2000)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 112 (2000), S. 5212-5222 
    Details
    ISSN: 1089-7690
    Quelle: AIP Digital Archive
    Thema: Physik , Chemie und Pharmazie
    Notizen: The folding of a protein is a process both expeditious and robust. The analysis of this process presented here uses a coarse, discretized representation of the evolving form of the backbone chain, based on its torsional states. This coarse description consists of discretizing the torsional coordinates modulo the Ramachandran basins in the local softmode dynamics. Whenever the representation exhibits "contact patterns" that correspond to topological compatibilities with particular structural forms, secondary and then tertiary, the elements constituting the pattern are effectively entrained by a reduction of their rates of exploration of their discretized configuration space. The properties "expeditious and robust" imply that the folding protein must have some tolerance to both torsional "frustrated" and side-chain contact mismatches which may occur during the folding process. The energy-entropy consequences of the staircase or funnel topography of the potential surface should allow the folding protein to correct these mismatches, eventually. This tolerance lends itself to an iterative pattern-recognition-and-feedback description of the folding process that reflects mismatched local torsional states and hydrophobic/polar contacts. The predictive potential of our algorithm is tested by application to the folding of bovine pancreatic trypsin inhibitor (BPTI), a protein whose ability to form its active structure is contingent upon its frustration tolerance. © 2000 American Institute of Physics.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1063/1.481076
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