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

Layer-Resolved Ultrafast XUV Measurement of Hole Transport in a Ni-TiO2-Si Photoanode

Metal-oxide-semiconductor junctions are central to most electronic and optoelectronic devices. Here, the element-specificity of broadband extreme ultraviolet (XUV) ultrafast pulses is used to measure the charge transport and recombination kinetics in each layer of a Ni-TiO2-Si junction. After photoexcitation of silicon, holes are inferred to transport from Si to Ni ballistically in ~100 fs, resulting in spectral shifts in the Ni M2,3 XUV edge that are characteristic of holes and the absence of holes initially in TiO2. Meanwhile, the electrons are observed to remain on Si. After picoseconds, the transient hole population on Ni is observed to back-diffuse through the TiO2, shifting the Ti spectrum to higher oxidation state, followed by electron-hole recombination at the Si-TiO2 interface and in the Si bulk. Electrical properties, such as the hole diffusion constant in TiO2 and the initial hole mobility in Si, are fit from these transient spectra and match well with values reported previously

Coherent X-ray Diffractive Imaging; applications and limitations

The inversion of a diffraction pattern offers aberration-free diffraction-limited 3D images without the resolution and depth-of-field limitations of lens-based tomographic systems, the only limitation being radiation damage. We review our experimental results, discuss the fundamental limits of this technique and future plans.Comment: 7 pages, 8 figure

An integrated genomic analysis of lung cancer reveals loss of DUSP4 in EGFR-mutant tumors.

To address the biological heterogeneity of lung cancer, we studied 199 lung adenocarcinomas by integrating genome-wide data on copy number alterations and gene expression with full annotation for major known somatic mutations in this cancer. This showed non-random patterns of copy number alterations significantly linked to EGFR and KRAS mutation status and to distinct clinical outcomes, and led to the discovery of a striking association of EGFR mutations with underexpression of DUSP4, a gene within a broad region of frequent single-copy loss on 8p. DUSP4 is involved in negative feedback control of EGFR signaling, and we provide functional validation for its role as a growth suppressor in EGFR-mutant lung adenocarcinoma. DUSP4 loss also associates with p16/CDKN2A deletion and defines a distinct clinical subset of lung cancer patients. Another novel observation is that of a reciprocal relationship between EGFR and LKB1 mutations. These results highlight the power of integrated genomics to identify candidate driver genes within recurrent broad regions of copy number alteration and to delineate distinct oncogenetic pathways in genetically complex common epithelial cancers

Piecewise linear discretization of Symbolic Implicit Monte Carlo radiation transport in the difference formulation

We describe a Monte Carlo solution for time dependent photon transport, in the difference formulation with the material in local thermodynamic equilibrium (LTE), that is piecewise linear in its treatment of the material state variable. Our method employs a Galerkin solution for the material energy equation while using Symbolic Implicit Monte Carlo (SIMC) to solve the transport equation. In constructing the scheme, one has the freedom to choose between expanding the material temperature, or the equivalent black body radiation energy density at the material temperature, in terms of finite element basis functions. The former provides a linear treatment of the material energy while the latter provides a linear treatment of the radiative coupling between zones. Subject to the conditional use of a lumped material energy in the vicinity of strong gradients, possible with a linear treatment of the material energy, our approach provides a robust solution for time dependent transport of thermally emitted radiation that can address a wide range of problems. It produces accurate results in the diffusion limit

Layer-resolved ultrafast extreme ultraviolet measurement of hole transport in a Ni-TiO₂-Si photoanode

Metal oxide semiconductor junctions are central to most electronic and optoelectronic devices, but ultrafast measurements of carrier transport have been limited to device-average measurements. Here, charge transport and recombination kinetics in each layer of a Ni-TiO₂-Si junction is measured using the element specificity of broadband extreme ultraviolet (XUV) ultrafast pulses. After silicon photoexcitation, holes are inferred to transport from Si to Ni ballistically in ~100 fs, resulting in characteristic spectral shifts in the XUV edges. Meanwhile, the electrons remain on Si. After picoseconds, the transient hole population on Ni is observed to back-diffuse through the TiO₂, shifting the Ti spectrum to a higher oxidation state, followed by electron-hole recombination at the Si-TiO₂ interface and in the Si bulk. Electrical properties, such as the hole diffusion constant in TiO₂ and the initial hole mobility in Si, are fit from these transient spectra and match well with values reported previously

A novel knockout mouse for the small EDRK-rich factor 2 (Serf2) showing developmental and other deficits

The small EDRK-rich factor 2 (SERF2) is a highly conserved protein that modifies amyloid fibre assembly in vitro and promotes protein misfolding. However, the role of SERF2 in regulating age-related proteotoxicity remains largely unexplored due to a lack of in vivo models. Here, we report the generation of Serf2 knockout mice using an ES cell targeting approach, with Serf2 knockout alleles being bred onto different defined genetic backgrounds. We highlight phenotyping data from heterozygous Serf2^{+/-} mice, including unexpected male-specific phenotypes in startle response and pre-pulse inhibition. We report embryonic lethality in Serf2^{-/-} null animals when bred onto a C57BL/6 N background. However, homozygous null animals were viable on a mixed genetic background and, remarkably, developed without obvious abnormalities. The Serf2 knockout mice provide a powerful tool to further investigate the role of SERF2 protein in previously unexplored pathophysiological pathways in the context of a whole organism

Flow field analysis around pressure shielding structures

The flow field around a series of streamwise rods, referred to as canopies, is investigated using two-dimensional two-component time-resolved particle image velocimetry (PIV) and large eddy simulations (LES) to characterize the changes in the flow field responsible for reducing the low and high-frequency surface pressure fluctuations previously observed. It was found that an axisymmetric turbulent boundary layer (ATBL) develops over the rods, whose thickness grows at a greater rate above the rods than below. This boundary layer reaches the wall below the rods at a point where previously a saturation was found in the low-frequency noise attenuation, revealing that the ATBL is responsible for the low-frequency noise attenuation. The flow is displaced by the presence of the rods, particularly above them, which offset was primarily caused by the blockage of the ATBL. The flow below the rods exhibits the properties of a turbulent boundary layer as its profile still conforms to the logarithmic layer, but the friction velocity was found to drop. This viscous effect was found to be responsible for the high-frequency noise attenuation reported previously