Electronic structure and spectroscopy of nucleic acid bases: Ionization energies, ionization-induced structural changes, and photoelectron spectra (open access)

Electronic structure and spectroscopy of nucleic acid bases: Ionization energies, ionization-induced structural changes, and photoelectron spectra

We report high-level ab initio calculations and single-photon ionization mass spectrometry study of ionization of adenine (A), thymine (T), cytosine (C) and guanine (G). For thymine and adenine, only the lowest-energy tautomers were considered, whereas for cytosine and guanine we characterized five lowest-energy tautomeric forms. The first adiabatic and several vertical ionization energies were computed using equation-of-motion coupled-cluster method for ionization potentials with single and double substitutions. Equilibrium structures of the cationic ground states were characterized by DFT with the {omega}B97X-D functional. The ionization-induced geometry changes of the bases are consistent with the shapes of the corresponding molecular orbitals. For the lowest-energy tautomers, the magnitude of the structural relaxation decreases in the following series G > C > A > T, the respective relaxation energies being 0.41, 0.32, 0.25 and 0.20 eV. The computed adiabatic ionization energies (8.13, 8.89, 8.51-8.67 and 7.75-7.87 eV for A,T,C and G, respectively) agree well with the onsets of the photoionization efficiency (PIE) curves (8.20 {+-} 0.05, 8.95 {+-} 0.05, 8.60 {+-} 0.05 and 7.75 {+-} 0.05 eV). Vibrational progressions for the S{sub 0}-D{sub 0} vibronic bands computed within double-harmonic approximation with Duschinsky rotations are compared with previously reported experimental photoelectron spectra.
Date: August 2, 2010
Creator: Bravaya, Ksenia B.; Kostko, Oleg; Dolgikh, Stanislav; Landau, Arie; Ahmed, Musahid & Krylov, Anna I.
System: The UNT Digital Library
Feature Tracking Using Reeb Graphs (open access)

Feature Tracking Using Reeb Graphs

Tracking features and exploring their temporal dynamics can aid scientists in identifying interesting time intervals in a simulation and serve as basis for performing quantitative analyses of temporal phenomena. In this paper, we develop a novel approach for tracking subsets of isosurfaces, such as burning regions in simulated flames, which are defined as areas of high fuel consumption on a temperature isosurface. Tracking such regions as they merge and split over time can provide important insights into the impact of turbulence on the combustion process. However, the convoluted nature of the temperature isosurface and its rapid movement make this analysis particularly challenging. Our approach tracks burning regions by extracting a temperature isovolume from the four-dimensional space-time temperature field. It then obtains isosurfaces for the original simulation time steps and labels individual connected 'burning' regions based on the local fuel consumption value. Based on this information, a boundary surface between burning and non-burning regions is constructed. The Reeb graph of this boundary surface is the tracking graph for burning regions.
Date: August 2, 2010
Creator: Weber, Gunther H.; Bremer, Peer-Timo; Day, Marcus S.; Bell, John B. & Pascucci, Valerio
System: The UNT Digital Library
Investigating two-photon double ionization of D2 by XUV-Pump -- XUV-Probe experiments at FLASH (open access)

Investigating two-photon double ionization of D2 by XUV-Pump -- XUV-Probe experiments at FLASH

Using a novel split-mirror set-up attached to a Reaction Microscope at the Free electron LASer in Hamburg (FLASH) we demonstrate an XUV-pump -- XUV-probe ((hbar omega = 38 eV) experiment by tracing the ultra-fast nuclear wave-packet motion in the D2+ (1s sigma g-state) with<10 fs time resolution. Comparison with time-dependent calculations yields excellent agreement with the measured vibrational period of 22+-4 fs in D2+, points to the importance of the inter-nuclear distance dependent ionization probability and paves the way to control sequential and non-sequential two-photon double ionization contributions.
Date: August 2, 2010
Creator: Collaboration, FLASH; Jiang, Y.; Rudenko, A.; Perez-Torres, J.; Foucar, L.; Kurka, M. et al.
System: The UNT Digital Library
Separation of High Order Harmonics with Fluoride Windows (open access)

Separation of High Order Harmonics with Fluoride Windows

The lower orders produced in high order harmonic generation can be effciently temporally separated into monochromatic pulses by propagation in a Fluoride window while still preserving their femtosecond pulse duration. We present calculations for MgF2, CaF2, and LiF windows for the third, fifth, and seventh harmonics of 800 nm. We demonstrate the use of this simple and inexpensive technique in a femtosecond pump/probe experiment using the fifth harmonic.
Date: August 2, 2010
Creator: Allison, Tom; van Tilborg, Jeroen; Wright, Travis; Hertlein, Marcus; Falcone, Roger & Belkacem, Ali
System: The UNT Digital Library
Controlling X-rays With Light (open access)

Controlling X-rays With Light

Ultrafast x-ray science is an exciting frontier that promises the visualization of electronic, atomic and molecular dynamics on atomic time and length scales. A largelyunexplored area of ultrafast x-ray science is the use of light to control how x-rays interact with matter. In order to extend control concepts established for long wavelengthprobes to the x-ray regime, the optical control field must drive a coherent electronic response on a timescale comparable to femtosecond core-hole lifetimes. An intense field is required to achieve this rapid response. Here an intense optical control pulse isobserved to efficiently modulate photoelectric absorption for x-rays and to create an ultrafast transparency window. We demonstrate an application of x-ray transparencyrelevant to ultrafast x-ray sources: an all-photonic temporal cross-correlation measurement of a femtosecond x-ray pulse. The ability to control x-ray/matterinteractions with light will create new opportunities at current and next-generation x-ray light sources.
Date: August 2, 2010
Creator: Glover, Ernie; Hertlein, Marcus; Southworth, Steve; Allison, Tom; van Tilborg, Jeroen; Kanter, Elliot et al.
System: The UNT Digital Library
Electrically Controllable Spontaneous Magnetism in Nanoscale Mixed Phase Multiferroics (open access)

Electrically Controllable Spontaneous Magnetism in Nanoscale Mixed Phase Multiferroics

The emergence of enhanced spontaneous magnetic moments in self-assembled, epitaxial nanostructures of tetragonal (T-phase) and rhombohedral phases (R-phase) of the multiferroic BiFeO{sub 3} system is demonstrated. X-ray magnetic circular dichroism based photoemission electron microscopy (PEEM) was applied to investigate the local nature of this magnetism. We find that the spontaneous magnetization of the R-phase is significantly enhanced above the canted antiferromagnetic moment in the bulk phase, as a consequence of a piezomagnetic coupling to the adjacent T-phase and the epitaxial constraint. Reversible electric field control and manipulation of this magnetic moment at room temperature is shown using a combination of piezoresponse force microscopy and PEEM studies.
Date: August 2, 2010
Creator: He, Q.; Chu, Y. H.; Heron, J. T.; Yang, S. Y.; Wang, C. H.; Kuo, C. Y. et al.
System: The UNT Digital Library
Analysis of 14C and 13C in Teeth Provides Precise Birth Dating and Clues to Geographical Origin (open access)

Analysis of 14C and 13C in Teeth Provides Precise Birth Dating and Clues to Geographical Origin

None
Date: August 2, 2010
Creator: Alkass, K.; Buchholz, B. A.; Druid, H. & Spalding, K. L.
System: The UNT Digital Library