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  • 1
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 90 (1989), S. 7184-7194 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We present a computer simulation of the real-time detection of ultrafast electronic decay dynamics in polyatomic molecules with femtosecond laser pulses. The intramolecular non-Born-Oppenheimer quantum dynamics is treated numerically exactly for a two-state three-mode vibronic coupling model representing the conically intersecting S1 and S2 excited states of pyrazine. The pump–probe signal is evaluated in lowest order perturbation theory with respect to the radiation–matter interaction by numerical integration over the pump and probe pulses. We discuss in some detail the dependence of the pump–probe signal on the properties of the laser pulses (frequencies and pulse durations). The calculations predict a dramatic (∼12 000 cm−1) and ultrafast (∼20 fs) red shift of the stimulated-emission signal as well as distinctive quantum beats in the pump–probe signal as a function of the delay time. Both effects are very pronounced and should therefore be relatively easily detectable experimentally. They are expected to be generic features of ultrafast internal-conversion processes in polyatomic molecules.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 59 (1986), S. 1799-1806 
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: An accurate and efficient numerical scheme is presented for calculating electrical conditions inside wire-duct electrostatic precipitators. A Galerkin finite-element method with quadratic interpolation is employed in solving Poisson's equation to yield the electric potential solution. A backward difference method is utilized to compute the space-charge density from the continuity equation. The two methods are iteratively applied until convergence criteria for electric potential and current density are met. Computed potential and electric field values show good agreement with analytic solutions and experimental measurements. Comparisons between the present scheme and a finite-difference scheme show that the finite-element method offers distinct advantages in predicting the electrical characteristics of precipitators.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    Woodbury, NY : American Institute of Physics (AIP)
    Applied Physics Letters 53 (1988), S. 34-36 
    ISSN: 1077-3118
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The effects of oxygen precipitation and surface films (SiO2 vs Si3N4) on P diffusion at 1100 °C in Czochralski silicon have been studied. With a fast precipitation rate, P diffusion under both kinds of films is enhanced because of the supersaturation of Si interstitials caused by oxygen precipitation. The larger enhancement in P diffusion under Si3N4 than that under SiO2 covered with Si3N4 is attributed to the slower recombination velocity of interstitials at the Si3N4/Si interface. P diffusion in a denuded zone behaves like that in float-zone Si until the interstitials generated under that zone arrive at the interface.
    Type of Medium: Electronic Resource
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  • 4
    Publication Date: 2015-12-29
    Description: To interpret molecular dynamics simulations of complex systems, systematic dimensionality reduction methods such as principal component analysis (PCA) represent a well-established and popular approach. Apart from Cartesian coordinates, internal coordinates, e.g., backbone dihedral angles or various kinds of distances, may be used as input data in a PCA. Adopting two well-known model problems, folding of villin headpiece and the functional dynamics of BPTI, a systematic study of PCA using distance-based measures is presented which employs distances between C α -atoms as well as distances between inter-residue contacts including side chains. While this approach seems prohibitive for larger systems due to the quadratic scaling of the number of distances with the size of the molecule, it is shown that it is sufficient (and sometimes even better) to include only relatively few selected distances in the analysis. The quality of the PCA is assessed by considering the resolution of the resulting free energy landscape (to identify metastable conformational states and barriers) and the decay behavior of the corresponding autocorrelation functions (to test the time scale separation of the PCA). By comparing results obtained with distance-based, dihedral angle, and Cartesian coordinates, the study shows that the choice of input variables may drastically influence the outcome of a PCA.
    Electronic ISSN: 1931-9223
    Topics: Chemistry and Pharmacology , Physics
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  • 5
    Publication Date: 2015-12-29
    Description: To interpret molecular dynamics simulations of complex systems, systematic dimensionality reduction methods such as principal component analysis (PCA) represent a well-established and popular approach. Apart from Cartesian coordinates, internal coordinates, e.g., backbone dihedral angles or various kinds of distances, may be used as input data in a PCA. Adopting two well-known model problems, folding of villin headpiece and the functional dynamics of BPTI, a systematic study of PCA using distance-based measures is presented which employs distances between C α -atoms as well as distances between inter-residue contacts including side chains. While this approach seems prohibitive for larger systems due to the quadratic scaling of the number of distances with the size of the molecule, it is shown that it is sufficient (and sometimes even better) to include only relatively few selected distances in the analysis. The quality of the PCA is assessed by considering the resolution of the resulting free energy landscape (to identify metastable conformational states and barriers) and the decay behavior of the corresponding autocorrelation functions (to test the time scale separation of the PCA). By comparing results obtained with distance-based, dihedral angle, and Cartesian coordinates, the study shows that the choice of input variables may drastically influence the outcome of a PCA.
    Print ISSN: 0021-9606
    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
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  • 6
    Publication Date: 2015-02-18
    Description: We examine vibrational energy flow in dehydrated and hydrated villin headpiece subdomain HP36 by master equation simulations. Transition rates used in the simulations are obtained from communication maps calculated for HP36. In addition to energy flow along the main chain, we identify pathways for energy transport in HP36 via hydrogen bonding between residues quite far in sequence space. The results of the master equation simulations compare well with all-atom non-equilibrium simulations to about 1 ps following initial excitation of the protein, and quite well at long times, though for some residues we observe deviations between the master equation and all-atom simulations at intermediate times from about 1–10 ps. Those deviations are less noticeable for hydrated than dehydrated HP36 due to energy flow into the water.
    Print ISSN: 0021-9606
    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
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  • 7
    Publication Date: 2015-02-18
    Description: We examine vibrational energy flow in dehydrated and hydrated villin headpiece subdomain HP36 by master equation simulations. Transition rates used in the simulations are obtained from communication maps calculated for HP36. In addition to energy flow along the main chain, we identify pathways for energy transport in HP36 via hydrogen bonding between residues quite far in sequence space. The results of the master equation simulations compare well with all-atom non-equilibrium simulations to about 1 ps following initial excitation of the protein, and quite well at long times, though for some residues we observe deviations between the master equation and all-atom simulations at intermediate times from about 1–10 ps. Those deviations are less noticeable for hydrated than dehydrated HP36 due to energy flow into the water.
    Electronic ISSN: 1931-9223
    Topics: Chemistry and Pharmacology , Physics
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  • 8
    Publication Date: 2015-07-15
    Description: An additional value of the Avogadro constant was obtained by counting the atoms in isotopically enriched Si spheres. With respect to the previous determination, the spheres were etched and repolished to eliminate metal contaminations and to improve the roundness. In addition, all the input quantities—molar mass, lattice parameter, mass, and volume—were remeasured aiming at a smaller uncertainty. In order to make the values given in Andreas et al. [Metrologia 48 , S1 (2011)] and Azuma et al. [Metrologia 52 , 360 (2015)] usable for a least squares adjustment, we report about the estimate of their correlation.
    Print ISSN: 0047-2689
    Electronic ISSN: 1529-7845
    Topics: Chemistry and Pharmacology , Physics
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  • 9
    Publication Date: 2015-10-08
    Description: Based on extensive ab initio calculations and the time-propagation of the nuclear Schrödinger equation, we study the vibrational relaxation dynamics and resulting spectral signatures of the OH stretch vibration of a hydrogen-bonded complex, HCO 2 − ⋅ H 2 O . Despite their smallness, it has been shown experimentally by Johnson and coworkers that the gas-phase infrared spectra of these types of complexes exhibit much of the complexity commonly observed for hydrogen-bonded systems. That is, the OH stretch band exhibits a significant red shift together with an extreme broadening and a pronounced substructure, which reflects its very strong anharmonicity. Employing an adiabatic separation of time scales between the three intramolecular high-frequency modes of the water molecule and the three most important intermolecular low-frequency modes of the complex, we calculate potential energy surfaces (PESs) of the ground and the first excited states of the high-frequency modes and identify a vibrational conical intersection between the PESs of the OH stretch fundamental and the HOH bend overtone. By performing a time-dependent propagation of the resulting system, we show that the conical intersection affects a coherent population transfer between the two states, the first step of which being ultrafast (60 fs) and irreversible. The subsequent relaxation of vibrational energy into the HOH bend and ground state occurs incoherently but also quite fast (1 ps), although the corresponding PESs are well separated in energy. Owing to the smaller effective mass difference between light and heavy degrees of freedom, the adiabatic ansatz is consequently less significant for vibrations than in the electronic case. Based on the model, we consider several approximations to calculate the measured Ar-tag action spectrum of HCO 2 − ⋅ H 2 O and achieve semiquantitative agreement with the experiment.
    Print ISSN: 0021-9606
    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
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