Biomolecular imaging and electronic damage using X-ray free-electron lasers

Proposals to determine biomolecular structures from diffraction experiments using femtosecond X-ray free-electron laser (XFEL) pulses involve a conflict between the incident brightness required to achieve diffraction-limited atomic resolution and the electronic and structural damage induced by the illumination. Here we show that previous estimates of the conditions under which biomolecular structures may be obtained in this manner are unduly restrictive, because they are based on a coherent diffraction model that is not appropriate to the proposed interaction conditions. A more detailed imaging model derived from optical coherence theory and quantum electrodynamics is shown to be far more tolerant of electronic damage. The nuclear density is employed as the principal descriptor of molecular structure. The foundations of the approach may also be used to characterize electrodynamical processes by performing scattering experiments on complex molecules of known structure.Comment: 16 pages, 2 figure

Local entanglement and confinement transitions in the random transverse-field Ising model on the pyrochlore lattice

We use numerical linked cluster expansions (NLC) and exact diagonalization to study confinement transitions out of the quantum spin liquid phase in the pyrochlore-lattice Ising antiferromagnet with random transverse fields. We calculate entanglement entropies associated with local regions defined by single tetrahedron to observe these transitions. The randomness-induced confinement transition is marked by a sharp reduction in the local entanglement and a concomitant increase in Ising correlations. In NLC, it is studied through the destruction of loop resonances due to random transverse-fields. The confining phase is characterized by a distribution of local entanglement entropies, which persists to large random fields

SPEDEN: Reconstructing single particles from their diffraction patterns

Speden is a computer program that reconstructs the electron density of single particles from their x-ray diffraction patterns, using a single-particle adaptation of the Holographic Method in crystallography. (Szoke, A., Szoke, H., and Somoza, J.R., 1997. Acta Cryst. A53, 291-313.) The method, like its parent, is unique that it does not rely on ``back'' transformation from the diffraction pattern into real space and on interpolation within measured data. It is designed to deal successfully with sparse, irregular, incomplete and noisy data. It is also designed to use prior information for ensuring sensible results and for reliable convergence. This article describes the theoretical basis for the reconstruction algorithm, its implementation and quantitative results of tests on synthetic and experimentally obtained data. The program could be used for determining the structure of radiation tolerant samples and, eventually, of large biological molecular structures without the need for crystallization.Comment: 12 pages, 10 figure

Munur á afkomu kvæma af íslensku birki í 14-ára tilraun á Miðnesheiði.

Afforestation in southwest Iceland is hindered by eroded, infertile soils and salt deposition from strong oceanic winds. A trial plot of 25 provenances of native downy birch collected throughout Iceland was established in 1998 near Keflavik International Airport to identify the best adapted stock. Seedlings were fertilized in the early years; in 2003 lupine was transplanted into the plot. In 2012, the 25 provenances differed significantly in growth and survival. Both seedling height and survival correlated with latitude of provenance origin, but not with longitude, elevation, or distance from the Keflavik plot. Southern provenances performed better than other regions, with Thórsmörk best in both growth and survival. Local provenances were poorer in performance than many other southern provenances. For afforestation with downy birch, it is recommended that high-performing provenances be planted with initial artificial fertilization, accompanied by simultaneous seeding of lupine.Á Reykjanesskaga stendur ófrjósemi jarðvegs og sterkir hafvindar með saltákomu skógrækt fyrir þrifum. Árið 1998 var komið á fót samanburðartilraun við Keflavíkurflugvöll, með 25 kvæmum af íslensku birki víðsvegar að af landinu, í þeim tilgangi að finna kvæmi sem best væru aðlöguð svæðinu. Borið var á trjáplönturnar í tilrauninni fyrstu árin eftir gróðursetningu. Árið 2003 voru lúpínuplöntur gróðursettar innan um birkið. Fjórtán árum eftir gróðursetningu (2012) reyndist marktækur munur í vexti og lifun kvæmanna. Bæði hæð gróðursettra plantna og lifun þeirra tengdust breiddargráðu upprunastaðar. Engin tengsl voru á milli hæðar og lifunar annars vegar og lengdargráðu, hæðar yfir sjávarmáli og fjarlægð frá tilraunastaðnum við Keflavíkurflugvöll hins vegar. Sunnlensk kvæmi reyndust betur en kvæmi úr öðrum landshlutum og var hæð og lifun kvæmisins Þórsmörk best. Staðarkvæmi þrifust verr en önnur sunnlensk kvæmi. Þegar rækta á birkiskóg á ófrjósömum jarðvegi á Suðurnesjum, er mælt með því að leggja áherslu á þau kvæmi sem sýnt hafa besta frammistöðu í tilrauninni. Einnig er mælt með að bera á plöntur fyrstu ár eftir gróðursetningu og um leið að sá lúpínu.Peer Reviewe

Displacement and emission currents from PLZT 8/65/35 and 4/95/5 excited by a negative voltage pulse at the rear electrode

It is shown that non-prepoled PLZT ceramics, both in ferroelectric and antiferroelectric phase, emit intense current bursts when a negative exciting voltage is applied to the rear surface of the cathode. The spontaneous polarization induced in the bulk by applying the field through the cathode disk, creates a sheet of negative charge on the diode boundary of the ferroelectric. This, in turn, induces such a high electric field at the diode dielectric surface that electrons are ejected out from the ceramic surface into the vacuum. The coherent behaviour of the displacement and emitted current shows clearly that the emission is due to a variation of spontaneous polarization. A second effect generated by the application of the high voltage pulse at the rear side is the formation of a surface plasma. Applying a positive voltage to the anode, electrons are readily transferred through the diode gap

Progress in Three-Dimensional Coherent X-Ray Diffraction Imaging

The Fourier inversion of phased coherent diffraction patterns offers images without the resolution and depth-of-focus limitations of lens-based tomographic systems. We report on our recent experimental images inverted using recent developments in phase retrieval algorithms, and summarize efforts that led to these accomplishments. These include ab-initio reconstruction of a two-dimensional test pattern, infinite depth of focus image of a thick object, and its high-resolution (~10 nm resolution) three-dimensional image. Developments on the structural imaging of low density aerogel samples are discussed.Comment: 5 pages, X-Ray Microscopy 2005, Himeji, Japa

Ultrafast self-gating Bragg diffraction of exploding nanocrystals in an X-ray laser

In structural determination of crystalline proteins using intense femtosecond X-ray lasers, damage processes lead to loss of structural coherence during the exposure. We use a nonthermal description for the damage dynamics to calculate the ultrafast ionization and the subsequent atomic displacement. These effects degrade the Bragg diffraction on femtosecond time scales and gate the ultrafast imaging. This process is intensity and resolution dependent. At high intensities the signal is gated by the ionization affecting low resolution information first. At lower intensities, atomic displacement dominates the loss of coherence affecting high-resolution information. We find that pulse length is not a limiting factor as long as there is a high enough X-ray flux to measure a diffracted signal

Electron Emission from Ferroelectric/Antiferroelectric Cathodes Excited by Short High-Voltage Pulses

Un-prepoled Lead Zirconate Titanate Lanthanum doped-PLZT ferroelectric cathodes have emitted intense current pulses under the action of a high voltage pulse of typically 8 kV/cm for PLZT of 8/65/35 composition and 25 kV/cm for PLZT of 4/95/5 composition. In the experiments described in this paper, the exciting electric field applied to the sample is directed from the rear surface towards the emitting surface. The resulting emission is due to an initial field emission from the metal of the grid deposited over the emitting surface with the consequent plasma formation and the switching of ferroelectric domains. These electrons may be emitted directly form the crystal or from the plasma. This emission requires the material in ferroelectric phase. In fact, PLZT cathodes of the 8/65/35 type, that is with high Titanium content, showing ferroelectric-paraelectric phase sequence, emit at room temperature, while PLZT cathodes of the 4/95/5 type, that is with low Titanium content, having antiferro-ferro-paraelectric phase sequence, emit strongly at a temperature higher than 130°C

Three-dimensional coherent X-ray diffraction imaging of a ceramic nanofoam: determination of structural deformation mechanisms

Ultra-low density polymers, metals, and ceramic nanofoams are valued for their high strength-to-weight ratio, high surface area and insulating properties ascribed to their structural geometry. We obtain the labrynthine internal structure of a tantalum oxide nanofoam by X-ray diffractive imaging. Finite element analysis from the structure reveals mechanical properties consistent with bulk samples and with a diffusion limited cluster aggregation model, while excess mass on the nodes discounts the dangling fragments hypothesis of percolation theory.Comment: 8 pages, 5 figures, 30 reference