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

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

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

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

X-ray image reconstruction from a diffraction pattern alone

A solution to the inversion problem of scattering would offer aberration-free diffraction-limited 3D images without the resolution and depth-of-field limitations of lens-based tomographic systems. Powerful algorithms are increasingly being used to act as lenses to form such images. Current image reconstruction methods, however, require the knowledge of the shape of the object and the low spatial frequencies unavoidably lost in experiments. Diffractive imaging has thus previously been used to increase the resolution of images obtained by other means. We demonstrate experimentally here a new inversion method, which reconstructs the image of the object without the need for any such prior knowledge.Comment: 5 pages, 3 figures, improved figures and captions, changed titl

Molecular Dynamics Simulations of Temperature Equilibration in Dense Hydrogen

The temperature equilibration rate in dense hydrogen (for both T_{i}>T_{e} and T_i<T_e) has been calculated with molecular dynamics simulations for temperatures between 10 and 600 eV and densities between 10^{20}/cc to 10^{24}/cc. Careful attention has been devoted to convergence of the simulations, including the role of semiclassical potentials. We find that for Coulomb logarithms L>1, a model by Gericke-Murillo-Schlanges (GMS) [Gericke et al., PRE 65, 036418 (2002)] based on a T-matrix method and the approach by Brown-Preston-Singleton [Brown et al., Phys. Rep. 410, 237 (2005)] agrees with the simulation data to within the error bars of the simulation. For smaller Coulomb logarithms, the GMS model is consistent with the simulation results. Landau-Spitzer models are consistent with the simulation data for L>4

Femtosecond x-ray diffraction reveals a liquid–liquid phase transition in phase-change materials

6 pags., 5 figs.In phase-change memory devices, a material is cycled between glassy and crystalline states. The highly temperature-dependent kinetics of its crystallization process enables application in memory technology, but the transition has not been resolved on an atomic scale. Using femtosecond x-ray diffraction and ab initio computer simulations, we determined the time-dependent pair-correlation function of phase-change materials throughout the melt-quenching and crystallization process. We found a liquid–liquid phase transition in the phase-change materials AgInSbTe and GeSb at 660 and 610 kelvin, respectively. The transition is predominantly caused by the onset of Peierls distortions, the amplitude of which correlates with an increase of the apparent activation energy of diffusivity. This reveals a relationship between atomic structure and kinetics, enabling a systematic optimization of the memory-switching kinetics.F.Q., A.K., M.N., and K.S.T. gratefully acknowledge financial support from the German Research Council through the Collaborative Research Center SFB 1242 project 278162697 (“Non-Equilibrium Dynamics of Condensed Matter in the Time Domain”), project C01 (“Structural Dynamics in Impulsively Excited Nanostructures”), and individual grant So408/9-1, as well as the European Union (7th Framework Programme, grant no. 280555 GO FAST). M.J.S., R.M., and M.W. acknowledge financial support from the German Research Council through the Collaborative Research Center SFB 917 (“Nanoswitches”) and individual grant Ma-5339/2-1. M.J.S., I.R., and R.M. also acknowledge the computational resources granted by JARA-HPC from RWTH Aachen University under project nos. JARA0150 and JARA0183. M.T., A.M.L., and D.A.R. were supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, through the Division of Materials Sciences and Engineering under contract no. DE-AC02-76SF00515. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under contract DE-AC52-07NA27344. J.L. acknowledges support from the Swedish Research Council. J.S. acknowledges financial support from the Spanish Ministry of Science, Innovation and Universities through research grant UDiSON (TEC2017-82464-R). P.Z. gratefully acknowledges funding by the Humboldt Foundatio