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S. Marchesini

Publications and source records attributed to S. Marchesini.

At least 19 recordsLinked to original sources
arXiv2022

In-situ observation of the formation of laser-induced periodic surface structures with extreme spatial and temporal resolution

Irradiation of solid surfaces with intense ultrashort laser pulses represents a unique way of depositing energy into materials. It allows to realize states of extreme electronic excitation and/or very high temperature and pressure, and to drive materials close to and beyond fundamental stability limits. As a consequence, structural changes and phase transitions often occur along unusual pathways and under strongly non-equilibrium conditions. Due to the inherent multiscale nature - both temporally and spatially - of these irreversible processes their direct experimental observation requires techniques that combine high temporal resolution with the appropriate spatial resolution and the capability to obtain good quality data on a single pulse/event basis. In this respect fourth generation light sources, namely short wavelength, short pulse free electron lasers (FELs) are offering new and fascinating possibilities. As an example, this chapter will discuss the results of scattering experiments carried at the FLASH free electron laser at DESY (Hamburg, Germany), which allowed us to resolve laser-induced structure formation at surfaces on the nanometer to sub-micron length scale and in temporal regimes ranging from picoseconds to several nanoseconds with sub-picosecond resolution.

cond-mat.mtrl-sci↗
arXiv2011

Iterative Algorithms for Ptychographic Phase Retrieval

Ptychography promises diffraction limited resolution without the need for high resolution lenses. To achieve high resolution one has to solve the phase problem for many partially overlapping frames. Here we review some of the existing methods for solving ptychographic phase retrieval problem from a numerical analysis point of view, and propose alternative methods based on numerical optimization.

physics.optics↗
arXiv2010

Compressive auto-indexing in femtosecond nanocrystallography

Ultrafast nanocrystallography has the potential to revolutionize biology by enabling structural elucidation of proteins for which it is possible to grow crystals with 10 or fewer unit cells on the side. The success of nanocrystallography depends on robust orientation-determination procedures that allow us to average diffraction data from multiple nanocrystals to produce a three dimensional (3D) diffraction data volume with a high signal-to-noise ratio. Such a 3D diffraction volume can then be phased using standard crystallographic techniques. "Indexing" algorithms used in crystallography enable orientation determination of diffraction data from a single crystal when a relatively large number of reflections are recorded. Here we show that it is possible to obtain the exact lattice geometry from a smaller number of measurements than standard approaches using a basis pursuit solver.

physics.optics↗
arXiv2010

Compressive Phase Contrast Tomography

When x-rays penetrate soft matter, their phase changes more rapidly than their amplitude. In- terference effects visible with high brightness sources creates higher contrast, edge enhanced images. When the object is piecewise smooth (made of big blocks of a few components), such higher con- trast datasets have a sparse solution. We apply basis pursuit solvers to improve SNR, remove ring artifacts, reduce the number of views and radiation dose from phase contrast datasets collected at the Hard X-Ray Micro Tomography Beamline at the Advanced Light Source. We report a GPU code for the most computationally intensive task, the gridding and inverse gridding algorithm (non uniform sampled Fourier transform).

physics.optics↗
arXiv2010

Cryptotomography: reconstructing 3D Fourier intensities from randomly oriented single-shot diffraction patterns

We reconstructed the 3D Fourier intensity distribution of mono-disperse prolate nano-particles using single-shot 2D coherent diffraction patterns collected at DESY's FLASH facility when a bright, coherent, ultrafast X-ray pulse intercepted individual particles of random, unmeasured orientations. This first experimental demonstration of cryptotomography extended the Expansion-Maximization-Compression (EMC) framework to accommodate unmeasured fluctuations in photon fluence and loss of data due to saturation or background scatter. This work is an important step towards realizing single-shot diffraction imaging of single biomolecules.

physics.optics↗
arXiv2008

X-Ray Powder Diffraction from Sub-Micron Crystals of Photosystem-1 Membrane Protein

We demonstrate that powder diffraction data can be collected from sub-micron crystals of a mbrane protein with nearly two orders of magnitude more atoms than the molecules commonly used for powder diffraction. The crystals of photosystem-1 protein were size-selected using a 500 nm pore- size filter and delivered to a soft x-ray beam with a photon energy of 1.5 keV using a dynamically focused micro-jet developed for the serial crystallography experiment at beamline 9.0.1. The 10-micron jet places many such randomly oriented crystals in the x-ray beam simultaneously resulting in a powder diffraction pattern which extends to 28 angstrom resolution with just 200 seconds of x-ray exposure. The use of the jet for particle delivery allows for a thin sample, appropriate for the soft x-rays used, and continuously refreshes the crystals so that radiation damage is not possible. The small size of the crystals requires the use of lower energy photons for increased scattering strength and increased spacing between powder rings. The powder patterns obtained in this way, from abundant nano-crystals, could be used to provide low resolution molecular envelopes if phased using techniques such as compressive sensing which do not require atomic resolution data. The results also serve to test our aerojet injector system, with future application to femtosecond diffraction in Free Electron X-ray Laser schemes, and for Serial Crystallography using a single-file beam of aligned hydrated molecules.

physics.bio-ph↗
arXiv2008

Ab initio compressive phase retrieval

Any object on earth has two fundamental properties: it is finite, and it is made of atoms. Structural information about an object can be obtained from diffraction amplitude measurements that account for either one of these traits. Nyquist-sampling of the Fourier amplitudes is sufficient to image single particles of finite size at any resolution. Atomic resolution data is routinely used to image molecules replicated in a crystal structure. Here we report an algorithm that requires neither information, but uses the fact that an image of a natural object is compressible. Intended applications include tomographic diffractive imaging, crystallography, powder diffraction, small angle x-ray scattering and random Fourier amplitude measurements.

physics.optics↗
arXiv2008

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.

cond-mat.mtrl-sci↗
arXiv2008

Ultrafast, ultrabright, X-ray holography using a uniformly-redundant array

Advances in the development of free-electron lasers offer the realistic prospect of high-resolution imaging to study the nanoworld on the time-scale of atomic motions. We identify X-ray Fourier Transform holography, (FTH) as a promising but, so far, inefficient scheme to do this. We show that a uniformly redundant array (URA) placed next to the sample, multiplies the efficiency of X-ray FTH by more than one thousand (approaching that of a perfect lens) and provides holographic images with both amplitude- and phase-contrast information. The experiments reported here demonstrate this concept by imaging a nano-fabricated object at a synchrotron source, and a bacterial cell at a soft X-ray free-electron-laser, where illumination by a single 15 fs pulse was successfully used in producing the holographic image. We expect with upcoming hard X-ray lasers to achieve considerably higher spatial resolution and to obtain ultrafast movies of excited states of matter.

physics.optics↗
arXiv2007

Phase retrieval and saddle-point optimization

Iterative algorithms with feedback are amongst the most powerful and versatile optimization methods for phase retrieval. Among these, the hybrid input-output algorithm has demonstrated practical solutions to giga-element nonlinear phase retrieval problems, escaping local minima and producing images at resolutions beyond the capabilities of lens-based optical methods. Here, the input-output iteration is improved by a lower dimensional subspace saddle-point optimization.

physics.optics↗
arXiv2006

A unified evaluation of iterative projection algorithms for phase retrieval

Iterative projection algorithms are successfully being used as a substitute of lenses to recombine, numerically rather than optically, light scattered by illuminated objects. Images obtained computationally allow aberration-free diffraction-limited imaging and the possibility of using radiation for which no lenses exist. The challenge of this imaging technique is transfered from the lenses to the algorithms. We evaluate these new computational ``instruments'' developed for the phase retrieval problem, and discuss acceleration strategies.

physics.optics↗
arXiv2005

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.

physics.optics↗
arXiv2005

Phase Aberrations in Diffraction Microscopy

In coherent X-ray diffraction microscopy the diffraction pattern generated by a sample illuminated with coherent x-rays is recorded, and a computer algorithm recovers the unmeasured phases to synthesize an image. By avoiding the use of a lens the resolution is limited, in principle, only by the largest scattering angles recorded. However, the imaging task is shifted from the experiment to the computer, and the algorithm's ability to recover meaningful images in the presence of noise and limited prior knowledge may produce aberrations in the reconstructed image. We analyze the low order aberrations produced by our phase retrieval algorithms. We present two methods to improve the accuracy and stability of reconstructions.

physics.optics↗
arXiv2005

High-resolution ab initio three-dimensional X-ray diffraction microscopy

Coherent X-ray diffraction microscopy is a method of imaging non-periodic isolated objects at resolutions only limited, in principle, by the largest scattering angles recorded. We demonstrate X-ray diffraction imaging with high resolution in all three dimensions, as determined by a quantitative analysis of the reconstructed volume images. These images are retrieved from the 3D diffraction data using no a priori knowledge about the shape or composition of the object, which has never before been demonstrated on a non-periodic object. We also construct 2D images of thick objects with infinite depth of focus (without loss of transverse spatial resolution). These methods can be used to image biological and materials science samples at high resolution using X-ray undulator radiation, and establishes the techniques to be used in atomic-resolution ultrafast imaging at X-ray free-electron laser sources.

physics.optics↗
arXiv2005

An assessment of the resolution limitation due to radiation-damage in x-ray diffraction microscopy

X-ray diffraction microscopy (XDM) is a new form of x-ray imaging that is being practiced at several third-generation synchrotron-radiation x-ray facilities. Although only five years have elapsed since the technique was first introduced, it has made rapid progress in demonstrating high-resolution threedimensional imaging and promises few-nm resolution with much larger samples than can be imaged in the transmission electron microscope. Both life- and materials-science applications of XDM are intended, and it is expected that the principal limitation to resolution will be radiation damage for life science and the coherent power of available x-ray sources for material science. In this paper we address the question of the role of radiation damage. We use a statistical analysis based on the so-called "dose fractionation theorem" of Hegerl and Hoppe to calculate the dose needed to make an image of a lifescience sample by XDM with a given resolution. We conclude that the needed dose scales with the inverse fourth power of the resolution and present experimental evidence to support this finding. To determine the maximum tolerable dose we have assembled a number of data taken from the literature plus some measurements of our own which cover ranges of resolution that are not well covered by reports in the literature. The tentative conclusion of this study is that XDM should be able to image frozen-hydrated protein samples at a resolution of about 10 nm with "Rose-criterion" image quality.

physics.optics↗
arXiv2004

Correction of non-linearity effects in detectors for electron spectroscopy

Using photoemission intensities and a detection system employed by many groups in the electron spectroscopy community as an example, we have quantitatively characterized and corrected detector non-linearity effects over the full dynamic range of the system. Non-linearity effects are found to be important whenever measuring relative peak intensities accurately is important, even in the low-countrate regime. This includes, for example, performing quantitative analyses for surface contaminants or sample bulk stoichiometries, where the peak intensities involved can differ by one or two orders of magnitude, and thus could occupy a significant portion of the detector dynamic range. Two successful procedures for correcting non-linearity effects are presented. The first one yields directly the detector efficiency by measuring a flat-background reference intensity as a function of incident x-ray flux, while the second one determines the detector response from a least-squares analysis of broad-scan survey spectra at different incident x-ray fluxes. Although we have used one spectrometer and detection system as an example, these methodologies should be useful for many other cases.

physics.ins-det↗
arXiv2004

Use of extended and prepared reference objects in experimental Fourier transform X-ray holography

The use of one or more gold nanoballs as reference objects for Fourier Transform holography (FTH) is analysed using experimental soft X-ray diffraction from objects consisting of separated clusters of these balls. The holograms are deconvoluted against ball reference objects to invert to images, in combination with a Wiener filter to control noise. A resolution of ~30nm, smaller than one ball, is obtained even if a large cluster of balls is used as the reference, giving the best resolution yet obtained by X-ray FTH. Methods of dealing with missing data due to a beamstop are discussed. Practical prepared objects which satisfy the FTH condition are suggested, and methods of forming them described.

physics.optics↗