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  • 1
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 103 (1995), S. 4097-4128 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A new formalism for quantum functional sensitivity analysis (QFSA) of atom–diatom reactions in the gas phase is developed within a version of Manolopoulos et al.'s [J. Chem. Phys. 93, 403 (1990)] log-derivative Kohn variational method containing contracted translational basis functions. A reference energy, Emid, is introduced to define boundary translational functions which completely remove all scattering energy dependence from the basis functions. This greatly facilitates scattering calculations for a range of energies about Emid without having to recalculate any of the so-called "stiffness'' matrix elements. Our new approach to QFSA is applied to study the sensitivity of the H+H2, D+H2, and H+D2 reaction probabilities to the Boothroyd–Keogh–Martin–Peterson (BKMP) potential energy surface. The transition probability sensitivities of both D+H2 and H+D2 are very similar to those of H+H2 at low energies, but at higher energies, the sensitivities of the H+D2 reaction differ from those of the other two isotopomers. Isotopomers that have very similar reaction probability profiles also have very similar sensitivities to the potential. All three isotopomers exhibit a large region of positive sensitivity at the top of the barrier for an approximately 0.1 to 0.2 eV energy range above threshold. For these energies (∼0.3 to 0.5 eV above the barrier), it is possible to increase the reaction probability with slight increases in barrier height. Sensitivity results from our new code have also provided a wealth of information about (i) how small, localized changes in the potential affect product state distributions, resonance features, and reactivity; and (ii) where the dynamics is most sensitive to inaccuracies in the potential. Comparisons are also made of transition probabilities and sensitivities on the BKMP surface to those of other potential energy surfaces. © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 3
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A new approach to calculating quantum functional sensitivity maps of transition probabilities is described in this paper. This approach is based on the log-derivative version of the Kohn variational principle and is applied here to the collinear H+H2 hydrogen exchange reaction. The sensitivity maps provide detailed quantitative information about how variations in the potential energy surface affect the state-to-state transition probabilities. The key issues investigated are (i) the evolution of sensitivity structure in the 0.30–1.50 eV range of total energy; (ii) the comparison of sensitivity structure on the Porter–Karplus, the Liu–Siegbahn–Truhlar–Horowitz, and the double-many-body-expansion potential energy surfaces; and (iii) the range of linearity for first order sensitivity predictions.
    Type of Medium: Electronic Resource
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  • 4
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Two sensitivity-analysis techniques are used to show how one can predict observables on new or perturbed potential energy surfaces (PES) without doing any additional dynamics calculations on the new PESs. Both techniques require the computation of the observable (O) and its sensitivity to variations in the potential (δO/δV) on just one surface. The first approach uses a simple first order expansion of the observable with respect to δV. The second approach uses a nonlinear least-squares fit of particular features in the observable, and then uses the same functional form to predict the observable on a different PES but with a modified set of fitting parameters. The new fitting parameters are related to the old via a functional Taylor expansion. Both approaches work well when variations in the potential are small. When the potential difference is large, the second approach gives reasonable results even in cases where the first approach is giving spurious predictions. These ideas are tested for the collinear H+H2 reaction within the framework of quantum reactive scattering. The log-derivative version of the Kohn variational principle is used for the scattering calculations.
    Type of Medium: Electronic Resource
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  • 5
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The effects of features in the potential energy surface on the collinear H+H2 reaction rate coefficient are investigated by the method of quantum functional sensitivity analysis (QFSA). The calculations use QFSA to connect features in the microscopic realm, with their response upon macroscopic quantities of chemical interest, via the intermediary sensitivities of the reactive transition probabilities. While the sensitivities of the individual transition probabilities show considerable structure, there is an attendant loss of structure in the rate coefficient sensitivities because of the thermal averaging. For the range of temperatures used in our study (200–2400 K), the most important region of the potential energy surface is found to be not at the top of the barrier, but rather at the lower energy shoulders of the barrier. There are also regions near the barrier where an increase in the potential surface actually increases the reaction rate! The effects of using different underlying potentials [the Porter–Karplus (PK2), Liu–Siegbahn–Truhlar–Horowitz (LSTH), and double many-body expansion (DMBE) surfaces] on the nature of the results were also compared. The absolute sensitivity magnitudes on the PK2 surface vary considerably from the other two, but the relative change in the rate coefficient is about the same on all three surfaces. Furthermore, the identified regions of importance on the potential surfaces remain essentially the same. The reactive scattering calculations were performed with the log-derivative version of the Kohn variational principle.
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  • 6
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: . The phorbol ester TPA (phorbol 12-myristate 13-acetate) substitutes for CO2 as an agonist for transforming Trypanosoma cruzi epimastigotes to the metacyclic trypomastigote stage in a starvation medium consisting of phosphate buffered saline + 10 mM proline, 10 mM sodium acetate and 0.035% NaHCO3. Since TPA is thought to stimulate protein kinase C by mimicking the activity of the secondary messenger diacylglycerol, the above result suggested that T. cruzi metacyclogenesis could be activated by a Ca2+-dependent protein kinase C signal induction pathway. Accordingly, cytosolic calcium flux ([Ca2+]i) in epimastigotes, activated with 5% CO2 or TPA (10-7 M), was measured with the Ca2+ molecular probe, fluo-3AM. In addition, [Ca2+]i was measured in cells incubated with putative metacyclogenic agonists (e.g. proline, glutamate, bioamines, ionophores and catecholamines). None of the compounds studied, except for EGTA, affected cytosolic Ca2+ levels. Control assays with 11 μM thapsigargin, which mobilizes noncytoplasmic Ca2+ stores by inhibiting endoplasmic reticulum Ca2+-ATPase. validated our fluorometric assay procedure. Although thapsigargin significantly increases cytoplasmic Ca2+ fluorescence, it has no effect on transformation. The protein kinase C inhibitors staurosporine, H-7 and HA 1004 were tested for their effect on T. cruzi metacyclogenesis. Low concentrations of staurosporine and HA 1004 significantly elevated Pent strain transformation while H-7 had no effect on Peru strain metacyclogenesis. Inhibitor H-7 did significantly depress CL transformation. the results indicate that induction of T. cruzi metacyclic trypomastigote formation by CO2 and TPA is not accompanied by changes in cytosolic Ca2+ and do not provide supporting evidence for participation of a protein kinase C-mediated phosphoinositide cascade in metacyclogenesis.
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  • 7
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 87 (1987), S. 1648-1652 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A method is described for Monte Carlo path integration that is valid for real time propagation. More specifically, it is shown how matrix elements of the complex-time propagator e−βcH, βc=β/2+it/(h-dash-bar), can be evaluated by straightforward Monte Carlo for values t(very-much-greater-than)β(h-dash-bar)/2. The key feature is that one distorts the path of the integration variables so that the kinetic energy part of the integrand is real. This in turn means that the paths are complex valued, but it is shown that, at least for barrier-type potentials, this causes no difficulties.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 85 (1986), S. 1826-1839 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A new, systematic method for selecting the most important basis functions by using an artificial intelligence tree pruning algorithm is introduced. The technique can be applied to any physical problem which gives rise to coupled equations but is applicable in general to any problem which could benefit from an orderly exploration of linked alternatives in a decision tree. The method is applied here to select the most important states for modeling the multiphoton dynamics of a general vibrating–rotating spherical top molecule. The optimal paths selected by the branch-and-bound search algorithm augmented with dynamic programming are investigated in detail with respect to what information about the dynamics they may contain.
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  • 9
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 85 (1986), S. 1840-1847 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The role of rotational states in IR multiphoton excitation (MPE) is examined for a model spherical top molecule. While the common belief that inclusion of rotational states can enhance MPE by overcoming anharmonic detunings and increasing the number of pathways for excitation is correct for some systems, it is shown that the simultaneous increase in deexcitation pathways can lead to significant rotational heating of lower vibrational bands, and therefore, to a deenhancement of MPE for other systems. The problem of diagonalizing prohibitively large matrices is circumvented by using an artificial intelligence tree pruning algorithm to select the most important basis states for the multiphoton dynamics.
    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 84 (1986), S. 4997-5006 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The energy spectrum in the stochastic region for a model Hamiltonian of two strongly coupled modes is calculated by diagonalizing small matrices which do not provide the Hylleraas–Undheim–MacDonald variational energy upper bounds. In addition, a method for selecting the most important basis functions by artificial intelligence algorithms is utilized. The energy convergence is determined by the Hazi–Taylor stabilization method and by the nearest-neighbor-spacing distribution function which measures the local fluctuations in the spectrum.
    Type of Medium: Electronic Resource
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