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  • Oxford University Press  (20)
  • American Institute of Physics (AIP)  (9)
  • 2015-2019  (26)
  • 1985-1989  (3)
  • 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
    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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  • 3
    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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  • 4
    Publication Date: 2015-08-20
    Description: Contrasting with birds and mammals, poikilothermic vertebrates often have homomorphic sex chromosomes, possibly resulting from high rates of sex-chromosome turnovers and/or occasional X–Y recombination. Strong support for the latter mechanism was provided by four species of European tree frogs, which inherited from a common ancestor (~5 Ma) the same pair of homomorphic sex chromosomes (linkage group 1, LG1), harboring the candidate sex-determining gene Dmrt1. Here, we test sex linkage of LG1 across six additional species of the Eurasian Hyla radiation with divergence times ranging from 6 to 40 Ma. LG1 turns out to be sex linked in six of nine resolved cases. Mapping the patterns of sex linkage to the Hyla phylogeny reveals several transitions in sex-determination systems within the last 10 My, including one switch in heterogamety. Phylogenetic trees of DNA sequences along LG1 are consistent with occasional X–Y recombination in all species where LG1 is sex linked. These patterns argue against one of the main potential causes for turnovers, namely the accumulation of deleterious mutations on nonrecombining chromosomes. Sibship analyses show that LG1 recombination is strongly reduced in males from most species investigated, including some in which it is autosomal. Intrinsically low male recombination might facilitate the evolution of male heterogamety, and the presence of important genes from the sex-determination cascade might predispose LG1 to become a sex chromosome.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
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  • 5
    Publication Date: 2016-06-24
    Description: The Fifth Assessment Report of the Intergovernmental Panel on Climate Change highlights that climate change and ocean acidification are challenging the sustainable management of living marine resources (LMRs). Formal and systematic treatment of uncertainty in existing LMR projections, however, is lacking. We synthesize knowledge of how to address different sources of uncertainty by drawing from climate model intercomparison efforts. We suggest an ensemble of available models and projections, informed by observations, as a starting point to quantify uncertainties. Such an ensemble must be paired with analysis of the dominant uncertainties over different spatial scales, time horizons, and metrics. We use two examples: (i) global and regional projections of Sea Surface Temperature and (ii) projection of changes in potential catch of sablefish ( Anoplopoma fimbria ) in the 21st century, to illustrate this ensemble model approach to explore different types of uncertainties. Further effort should prioritize understanding dominant, undersampled dimensions of uncertainty, as well as the strategic collection of observations to quantify, and ultimately reduce, uncertainties. Our proposed framework will improve our understanding of future changes in LMR and the resulting risk of impacts to ecosystems and the societies under changing ocean conditions.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
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  • 6
    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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  • 7
    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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  • 8
    Publication Date: 2016-05-12
    Description: Many physical parameters in astrophysics are derived using the ratios of two observed quantities. If the relative uncertainties on measurements are small enough, uncertainties can be propagated analytically using simplifying assumptions, but for large normally distributed uncertainties, the probability distribution of the ratio become skewed, with a modal value offset from that expected in Gaussian uncertainty propagation. Furthermore, the most likely value of a ratio A/B is not equal to the reciprocal of the most likely value of B/A. The effect is most pronounced when the uncertainty on the denominator is larger than that on the numerator. We show that this effect is seen in an analysis of 12 126 spectra from the Sloan Digital Sky Survey (SDSS). The intrinsically fixed ratio of the [O iii ] lines at 4959 and 5007 Å is conventionally expressed as the ratio of the stronger line to the weaker line. Thus, the uncertainty on the denominator is larger, and non-Gaussian probability distributions result. By taking this effect into account, we derive an improved estimate of the intrinsic 5007/4959 ratio. We obtain a value of 3.012 ± 0.008, which is slightly but statistically significantly higher than the theoretical value of 2.98. We further investigate the suggestion that fluxes measured from emission lines in noisy spectra are strongly biased upwards. We were unable to detect this effect in the SDSS line flux measurements, and we could not reproduce the results of Rola and Pelat who first described this bias. We suggest that the magnitude of this effect may depend strongly on the specific fitting algorithm used.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 9
    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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  • 10
    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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