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  • 1
    Electronic Resource
    Electronic Resource
    A comparison between the sensitivity behavior of direct and long-lived classical trajectories and quantum wave packets (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 90 (1989), S. 2274-2282 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We compare the sensitivities to initial conditions for both direct (regular) and long-lived (chaotic) trajectories in classical scattering calculations with the corresponding properties of trajectories of position and momentum expectation values for quantum wave packets. The collinear H+H2 reaction is used as an example. The results show that the high sensitivity seen in chaotic trajectories is not reflected in the quantum dynamics. We conclude that it is possible for a classical ensemble consisting of only regular trajectories to respond trajectory by trajectory to perturbations in much the same way as a quantum wave packet. (There will of course be cases that are exceptions to this rule.) The response of an ensemble consisting of chaotic trajectories may on the average be similar to that of a wave packet, but not at the level of individual trajectories. In addition, the sensitivities of these trajectories to variations in the potential are analyzed. We conclude that the large contributions to the sensitivities from particular long-lived trajectories must approximately cancel when an exact ensemble average is taken. An algorithm is presented to smoothly account for the contributions to the sensitivities from these trajectories.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.456021
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  • 2
    Electronic Resource
    Electronic Resource
    The comparative role of potential structure in classical, semiclassical, and quantum mechanics (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 90 (1989), S. 2263-2273 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The corresponding effects of features in the potential on classical, semiclassical, and quantum mechanics are probed using the technique of functional sensitivity analysis. It is shown that the classical and quantum functional sensitivities are equivalent in the classical (small (h-dash-bar)) and harmonic limits. Classical and quantum mechanics are known to react in qualitatively similar ways provided that features on the potential are smooth on the length scale of oscillations in the quantum wave function. By using functional sensitivity analysis, we are able to show in detail how the classical and quantum dynamics differ in the way that they sense the potential. Two examples are given, the first of which is the harmonic oscillator. This problem is well understood by other means but is useful to examine because it illustrates the detailed information about the interaction of the potential and the dynamics which can be provided by functional sensitivity analysis, simplifying the analysis of more complex systems. The second example is the collinear H+H2 reaction. In that case there are a number of detailed and striking differences between the ways that classical and quantum mechanics react to features on the potential. For features which are broad compared to oscillations in the wave function, the two react in qualitatively the same way. The sensitivities are oscillatory, however, and there are phasing differences between the classical and quantum sensitivity functions. This means that using classical mechanics plus experimental data in an inversion scheme intended to find the "true'' potential will necessarily introduce sizeable errors.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.456020
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    Paper (German National Licenses)
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  • 3
    Electronic Resource
    Electronic Resource
    A classical functional sensitivity analysis of the collinear F+H2 reaction (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 90 (1989), S. 2283-2295 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The method of classical functional sensitivity analysis (CFSA) is applied to the collinear F+H2 reaction and its isotopic analogues. The effects of features in the Muckerman 5 (M5) potential upon product vibrational energy are examined using constant energy ensembles (1 and 5 kcal/mol) with H2(v=0) and H2(v=1). The same is done using thermal averaged ensembles at 300, 400, 1000, and 1500 K. Two significant results are reported. First, at low energies and at even relatively high temperatures (1000 K), the region of the potential to which the reactive product vibrational energy is most sensitive is the vicinity of the saddle point. In addition, the sensitivity function is smooth and nonoscillatory there. Second, at high temperatures and energies, the sensitivity function becomes oscillatory in magnitude and sign over the entire interaction region. The implications which these results have for methods which fit a potential to experimental data are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.455969
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  • 4
    Electronic Resource
    Electronic Resource
    Body frame close coupling wave packet approach to gas phase atom–rigid rotor inelastic collisions (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 90 (1989), S. 241-250 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The close coupling wave packet (CCWP) method is formulated in a body-fixed representation for atom–rigid rotor inelastic scattering. For total J〉jmax the computational cost of propagating the coupled channel wave packets in the body frame scales approximately as N3/2 where N is the total number of channels. For large numbers of channels, this will be much more efficient than the space frame CCWP method previously developed which scales approximately as N2 under the same conditions. Timing results are reported for a model system for 25, 64, 144, 256, and 969 channels. The calculations were run with total J=30 and with parameters corresponding to a heavy diatom. The results for some representative transitions are compared to the identical transitions obtained using the space frame formalism. For all values of N, the body frame computations ran faster than the corresponding ones using the space frame, with the ratio increasing to a value of 4.5 for 969 channels. This is a significant improvement which will continue to increase with N, encouraging us to believe that the body frame CCWP method will prove practical for calculating scattering information for more realistic inelastic and reactive systems.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.456526
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    Paper (German National Licenses)
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  • 5
    Electronic Resource
    Electronic Resource
    Classical functional sensitivity analysis of coplanar inelastic scattering for hydrogen + hydrogen and its isotopic analogs (1989)
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 93 (1989), S. 2400-2411 
    Details
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/j100343a038
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    Paper (German National Licenses)
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  • 6
    Electronic Resource
    Electronic Resource
    Do intelligent configuration search techniques outperform random search for large molecules? (1992)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 44 (1992), S. 277-290 
    Details
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We compare three global configuration search methods on a scalable model problem to measure relative performance over a range of molecule sizes. Our model problem is a 2-D polymer composed of atoms connected by rigid rods in which all pairs of atoms interact via Lennard-Jones potentials. The global minimum energy can be calculated analytically. The search methods are all hybrids combining a global sampling algorithm with a local refinement technique. The sampling methods are simulated annealing (SA), genetic algorithms (GA), and random search. Each of these uses a conjugate gradient (CG) routine to perform the local refinement. Both GA and SA perform progressively better relative to random search as the molecule size increases. We also test two other local refinement techniques in addition to CG, coupled to random search as the global method. These are simplex followed by CG and simplex followed by block-truncated Newton. For small problems, the addition of the intermediate simplex step improved the performance of the overall hybrid method. © 1992 John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560440214
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  • 7
    Electronic Resource
    Electronic Resource
    Docking flexible molecules: A case study of three proteins (1995)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 16 (1995), S. 1405-1419 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A genetic algorithm (GA) conformation search method is used to dock a series of flexible molecules into one of three proteins. The proteins examined are thermolysin (tmn), carboxypeptidase A (cpa), and dihydrofolate reductase (dfr). In the latter two proteins, the crystal ligand was redocked. For thermolysin, we docked eight ligands into a protein conformation derived from a single crystal structure. The bound conformations of the other ligands in tmn are known. In the cpa and dfr cases, and in seven of the eight tmn ligands, the GA docking method found conformations within 1.6 Å root mean square (rms) of the relaxed crystal conformation. © 1995 John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540161109
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    Paper (German National Licenses)
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  • 8
    Electronic Resource
    Electronic Resource
    A comparison of a direct search method and a genetic algorithm for conformational searching (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 1142-1151 
    Details
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present results from the application of two conformational searching methods: genetic algorithms (GA) and direct search methods for finding low energy conformations of organic molecules. GAs are in a class of biologically motivated optimization methods that evolve a population of individuals in which individuals who are more “fit” have a higher probability of surviving into subsequent generations. The parallel direct search method (PDS) is a type of pattern search method that uses an adaptive grid to search for minima. Both methods found energies equal to or lower than the energy of the relaxed crystal structure in all cases, at a relatively small cost in CPU time. We suggest that either method would be a good candidate to find 3-D conformations in a large scale screening application. © 1996 by John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
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    Paper (German National Licenses)
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