| 1. |
- Bergh, Magnus, 1975-
(författare)
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Interaction of Ultrashort X-ray Pulses with Material
- 2007
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Radiation damage limits the resolution in imaging experiments. Damage is caused by energy deposited into the sample during exposure. Ultrashort and extremely bright X-ray pulses from free-electron lasers (FELs) offer the possibility to outrun key damage processes, and temporarily improve radiation tolerance. Theoretical models indicate that high detail-resolutions could be realized on non-crystalline samples with very short pulses, before plasma expansion.Studies presented here describe the interaction of a very intense and ultrashort X-ray pulse with material, and investigate boundary conditions for flash diffractive imaging both theoretically and experimentally. In the hard X-ray regime, predictions are based on particle simulations with a continuum formulation that accounts for screening from free electrons.First experimental results from the first soft X-ray free-electron laser, the FLASH facility in Hamburg, confirm the principle of flash imaging, and provide the first validation of our theoretical models. Specifically, experiments on nano-fabricated test objects show that an interpretable image can be obtained to high resolution before the sample is vaporized. Radiation intensity in these experiments reached 10^14 W/cm^2, and the temperature of the sample rose to 60000 Kelvin after the 25 femtosecond pulse left the sample. Further experiments with time-delay X-ray holography follow the explosion dynamics over some picoseconds after illumination.Finally, this thesis presents results from biological flash-imaging studies on living cells. The model is based on plasma calculations and fluid-like motions of the sample, supported by the time-delay measurements. This study provides an estimate for the achievable resolutions as function of wavelength and pulse length. The technique was demonstrated by our team in an experiment where living cells were exposed to a single shot from the FLASH soft X-ray laser.
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| 2. |
- Ekeberg, Tomas, 1983-
(författare)
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Flash Diffractive Imaging in Three Dimensions
- 2012
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- During the last years we have seen the birth of free-electron lasers, a new type of light source ten billion times brighter than syncrotrons and able to produce pulses only a few femtoseconds long. One of the main motivations for building these multi-million dollar machines was the prospect of imaging biological samples such as proteins and viruses in 3D without the need for crystallization or staining. This thesis contains some of the first biological results from free-electron lasers.These results include 2D images, both of whole cells and of the giant mimivirus and also con- tains a 3D density map of the mimivirus assembled from diffraction patterns from many virus particles. These are important proof-of-concept experiments but they also mark the point where free-electron lasers start to produce biologically relevant results. The most noteworthy of these results is the unexpectedly non-uniform density distribution of the internals of the mimivirus.We also present Hawk, the only open-source software toolkit for analysing single particle diffraction data. The Uppsala-developed program suite supports a wide range fo algorithms and takes advantage of Graphics Processing Units which makes it very computationally efficient.Last, the problem introduced by structural variability in samples is discussed. This includes a description of the problem and how it can be overcome, and also how it could be turned into an advantage that allows us to image samples in all of their conformational states.
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| 3. |
- Hantke, Max Felix, 1984-
(författare)
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Coherent Diffractive Imaging with X-ray Lasers
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The newly emerging technology of X-ray free-electron lasers (XFELs) has the potential to revolutionise molecular imaging. XFELs generate very intense X-ray pulses and predictions suggest that they may be used for structure determination to atomic resolution even for single molecules. XFELs produce femtosecond pulses that outrun processes of radiation damage and permit the study of structures at room temperature and of structural dynamics.While the first demonstrations of flash X-ray diffractive imaging (FXI) on biological particles were encouraging, they also revealed technical challenges. In this work we demonstrated how some of these challenges can be overcome. We exemplified, with heterogeneous cell organelles, how tens of thousands of FXI diffraction patterns can be collected, sorted, and analysed in an automatic data processing pipeline. We improved image resolution and reduced problems with missing data. We validated, described, and deposited the experimental data in the Coherent X-ray Imaging Data Bank.We demonstrated that aerosol injection can be used to collect FXI data at high hit ratios and with low background. We reduced problems with non-volatile sample contaminants by decreasing aerosol droplet sizes from ~1000 nm to ~150 nm. We achieved this by adapting an electrospray aerosoliser to the Uppsala sample injector. Mie scattering imaging was used as a diagnostic tool to measure positions, sizes, and velocities of individual injected particles.XFEL experiments generate large amounts of data at high rates. Preparation, execution, and data analysis of these experiments benefits from specialised software. In this work we present new open-source software tools that facilitates prediction, online-monitoring, display, and pre-processing of XFEL diffraction data.We hope that this work is a valuable contribution in the quest of transitioning FXI from its first experimental demonstration into a technique that fulfills its potentials.
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| 4. |
- Iwan, Bianca
(författare)
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Creating and Probing Extreme States of Materials : From Gases and Clusters to Biosamples and Solids
- 2012
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Free-electron lasers provide high intensity pulses with femtosecond duration and are ideal tools in the investigation of ultrafast processes in materials. Illumination of any material with such pulses creates extreme conditions that drive the sample far from equilibrium and rapidly convert it into high temperature plasma. The dynamics of this transition is not fully understood and the main goal of this thesis is to further our knowledge in this area.We exposed a variety of materials to X-ray pulses of intensities from 1013 to above 1017 W/cm2. We found that the temporal evolution of the resulting plasmas depends strongly on the wavelength and pulse intensity, as well as on material related parameters, such as size, density, and composition.In experiments on atomic and molecular clusters, we find that cluster size and sample composition influence the destruction pathway. In small clusters a rapid Coulomb explosion takes place while larger clusters undergo a hydrodynamic expansion. We have characterized this transition in methane clusters and discovered a strong isotope effect that promotes the acceleration of deuterium ions relative to hydrogen. Our results also show that ions escaping from exploding xenon clusters are accelerated to several keV energies.Virus particles represent a transition between hetero-nuclear clusters and complex biological materials. We injected single mimivirus particles into the pulse train of an X-ray laser, and recorded coherent diffraction images simultaneously with the fragmentation patterns of the individual particles. We used these results to test theoretical damage models. Correlation between the diffraction patterns and sample fragmentation shows how damage develops after the intense pulse has left the sample.Moving from sub-micron objects to bulk materials gave rise to new phenomena. Our experiments with high-intensity X-ray pulses on bulk, metallic samples show the development of a transient X-ray transparency. We also describe the saturation of photoabsorption during ablation of vanadium and niobium samples.Photon science with extremely strong X-ray pulses is in its infancy today and will require much more effort to gain more knowledge. The work described in this thesis represents some of the first results in this area.
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| 5. |
- R. N. C. Maia, Filipe, 1982-
(författare)
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Ultrafast Coherent X-ray Diffractive Nanoimaging
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- X-ray lasers are creating unprecedented research opportunities in physics,chemistry and biology. The peak brightness of these lasers exceeds presentsynchrotrons by 1010, the coherence degeneracy parameters exceedsynchrotrons by 109, and the time resolution is 105 times better. In theduration of a single flash, the beam focused to a micron-sized spot has the samepower density as all the sunlight hitting the Earth, focused to a millimetresquare. Ultrafast coherent X-ray diffractive imaging (CXDI) with X-ray lasers exploitsthese unique properties of X-ray lasers to obtain high-resolution structures fornon-crystalline biological (and other) objects. In such an experiment, thesample is quickly vaporised, but not before sufficient scattered light can berecorded. The continuous diffraction pattern can then be phased and thestructure of a more or less undamaged sample recovered% (speed of light vs. speed of a shock wave).This thesis presents results from the first ultrafast X-ray diffractive imagingexperiments with linear accelerator-driven free-electron lasers and fromoptically-driven table-top X-ray lasers. It also explores the possibility ofinvestigating phase transitions in crystals by X-ray lasers. An important problem with ultrafast CXDI of small samples such as single proteinmolecules is that the signal from a single measurement will be small, requiringsignal enhancement by averaging over multiple equivalent samples. We present anumerical investigation of the problems, including the case where samplemolecules are not exactly identical, and propose tentative solutions. A new software package (Hawk) has been developed for data processing and imagereconstruction. Hawk is the first publicly available software package in thisarea, and it is released as an open source software with the aspiration offostering the development of this field.
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| 6. |
- van der Schot, Gijs, 1984-
(författare)
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Imaging Living Cells with an X-ray Laser
- 2018
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Imaging living cells at a resolution higher than the resolution of optical microscopy is a significant challenge. Fluorescence microscopy can achieve a degree of super-resolution via labeling cellular components with a fluorescent dye. Reaching nanometer or sub-nanometer resolution requires high-energy radiation with significantly shorter wavelength than that of optical light. X-rays and electrons have the requisite wavelengths and could be suitable for such studies; however, these probes also cause significant radiation damage. A dose in excess of 100,000,000 Gray (Gy, J/kg) would be required to reach nanometer resolution on a cell, and no cell can survive this amount of radiation. As a consequence, much of what we know about cells at high resolution today comes from dead material.Theory predicts that an ultra-short and extremely bright coherent X-ray pulse from an X-ray free-electron laser can outrun key damage processes to deliver a molecular-level snapshot of a cell that is alive at the time of image formation. The principle of ‘diffraction before destruction’ exploits the difference between the speed of light (the X-ray pulse) and the much slower speed of damage formation. The femtosecond pulse ‘freezes’ motion in the cell at physiological temperatures on the time scale of atomic vibrations, offering unprecedented time resolution and a plethora of new experimental possibilities.This thesis describes the first test experiments on imaging living cells with an X-ray laser. I present results in three essential areas of live cell imaging. (i) We have used an aerosol injector to introduce live cyanobacteria into the X-ray focus, and recorded diffraction patterns with extremely low background at very high hit rates. (ii) We demonstrated scattered signal beyond 4 nm resolution in some of these experiments. (iii) The thesis also describes image reconstruction, using a new fully automated pipeline that I developed during my studies. The reconstruction of diffraction patterns was successful for all patterns that did not have saturated pixels. The new software suite, called RedFlamingo, selects exposures with desired properties, can sort them according to sample size, shape, orientation, exposure, the number and type of objects in the beam during the exposure, their distance from each other, and so forth. The software includes validation tools to assess the quality of the reconstructions.
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