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Browsing by Author "de Jonge, MD"

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Complex atomic fine structure in the phase domain: exciting opportunities and challenges
(International Union of Crystallography, 2021-08-14) Tran, CQ; Chantler, CT; Kirk, T; Dao, MH; Di Pasquale, P; Ceddia, J; Barnea, Z; de Jonge, MD; Kewish, CM
X-ray Absorption Spectroscopy has been one of the most powerful tools for probing atomic and molecular structures of materials. However, the measured fine structures in the absorption domain do not have adequate dimensionalities to extract three-dimensional structural information of the material of interest. A technique that allows accurate measurements of atomic fine structure in both the absorption and phase domains will open exciting opportunities in a wide range of fundamental and applied research. In this presentation, we will describe a new technique for determining simultaneously the real and imaginary components of the complex atomic form factor. The technique used Fourier Transform Holography with an extended reference and applicable to both crystalline and amorphous samples. Details of an application of the technique in spectroscopy mode to obtain the X-ray Complex Fine Structure across the copper K-edge will be discussed. © The Authors
Direct imaging of endogenous biometal distributions within millimetre-scale organisms at micrometre resolution – x-ray fluorescence tomography
(Australian Microscopy and Microanalysis Society, 2016-02-04) de Jonge, MD; Ruben, G; Mayo, SS; Ryan, CG; Kirkham, R; Howard, DL; Paterson, DJ
First-row transition metals are required for all forms of life on earth. The high reactivity of these elements means that an array of mechanisms has evolved to regulate key processes governing their transport and binding action. Tracking metals within biological tissue is non-trivial; tagging approaches suffer from lack of specificity, and can fail to find strongly-bound species; in addition, tags can interfere with normal biochemistry. Electron microscopy provides stupendous resolution, but probes miniscule volumes due to the short penetration of electrons. With μM sensitivity, X-ray Fluorescence Microscopy (XFM) can probe endogenous metal concentrations at resolutions at the μm length scale. Elemental maps are quantitative. With penetration depth and depth of field well matched at around 0.5 mm, the method can be up-scaled to 3-D visualisations via tomography. Here we report on our application of X-ray fluorescence tomography of Zn, Cu, Fe, and Mn in C. elegans and discuss recent progress in developing self-absorption corrections that will enable accurate mapping of light elements.
High-accuracy transmission and fluorescence XAFS of zinc at 10 K, 50 K, 100 K and 150 K using the hybrid technique
(International Union of Crystallography, 2022-10-24) John, MW; Sier, D; Ekanayake, RSK; Schalken, MJ; Tran, CQ; Johannessen, B; de Jonge, MD; Kappen, P; Chantler, CT
The most accurate measurements of the mass attenuation coefficient for metals at low temperature for the zinc K-edge from 9.5 keV to 11.5 keV at temperatures of 10 K, 50 K, 100 K and 150 K using the hybrid technique are reported. This is the first time transition metal X-ray absorption fine structure (XAFS) has been studied using the hybrid technique and at low temperatures. This is also the first hybrid-like experiment at the Australian Synchrotron. The measured transmission and fluorescence XAFS spectra are compared and benchmarked against each other with detailed systematic analyses. A recent method for modelling self-absorption in fluorescence has been adapted and applied to a solid sample. The XAFS spectra are analysed using eFEFFIT to provide a robust measurement of the evolution of nanostructure, including such properties as net thermal expansion and mean-square relative displacement. This work investigates crystal dynamics, nanostructural evolution and the results of using the Debye and Einstein models to determine atomic positions. Accuracies achieved, when compared with the literature, exceed those achieved by both relative and differential XAFS, and represent a state-of-the-art for future structural investigations. Bond length uncertainties are of the order of 20–40 fm. © Open Access - CC BY 4.0 licence
High-speed free-run ptychography at the Australian Synchrotron
(International Union of Crystallography, 2022-03) Jones, MWM; van Riessen, GA; Phillips, NW; Schrank, CE; Hinsley, GN; Afshar, N; Reinhardt, J; de Jonge, MD; Kewish, CM
Over the last decade ptychography has progressed rapidly from a specialist ultramicroscopy technique into a mature method accessible to non-expert users. However, to improve scientific value ptychography data must reconstruct reliably, with high image quality and at no cost to other correlative methods. Presented here is the implementation of high-speed ptychography used at the Australian Synchrotron on the XFM beamline, which includes a free-run data collection mode where dead time is eliminated and the scan time is optimized. It is shown that free-run data collection is viable for fast and high-quality ptychography by demonstrating extremely high data rate acquisition covering areas up to 352 000 μm2 at up to 140 μm2 s-1, with 13x spatial resolution enhancement compared with the beam size. With these improvements, ptychography at velocities up to 250 μm s-1 is approaching speeds compatible with fast-scanning X-ray fluorescence microscopy. The combination of these methods provides morphological context for elemental and chemical information, enabling unique scientific outcomes. © The Authors - Open Access CC-By Licence
In situ applications of soft x-ray ptychography
(Australian Microscopy and Microanalysis Society, 2016-02-04) van Riessen, GA; James, M; van Riessen, A; Phillips, NW; de Jonge, MD; Kourousias, G; Giamoncelli, A; Bozzini, B
Coherent diffractive imaging (CDI) with synchrotron X-ray beams allows extended objects to be characterised at high spatial resolution (<30 nm) and high energy resolution (0.1 eV). In an implementation of CDI known as ptychography, a far-field diffraction pattern is measured from many overlapping regions as the sample is scanned through a coherent X-ray beam. Quantitative images of an object are then obtained from the far-field intensity pattern through iterative reconstruction algorithms. This provides a unique method of studying the elemental and chemical-state distributions in relatively thick materials and their relationship to nanoscale morphology. The high coherent flux offered by synchrotron X-ray sources can also potentially allow high temporal resolution through the use of emerging detector technology and advanced image reconstruction algorithms. This in turn allows the nanoscale structure of functional materials to be studied under non-equilibrium real-time conditions. In this work, we review recent efforts to apply soft X-ray ptychography to in situ and operando applications at several synchrotron facilities. We emphasise studies of functional materials that are characterised by heterogeneity over a range of relevant length scales, including energy storage materials based on polypyrrole nanocomposites and inorganic, aluminosilicate based ceramics. Finally, a perspective on the future prospects of the method will be given, with particular attention to how experimental challenges can be overcome to achieve the spatiotemporal resolution limits defined by the available coherent flux from synchrotron light sources.
Mechanisms of murine cerebral malaria: multimodal imaging of altered cerebral metabolism and protein oxidation at hemorrhage sites
(American Association for the Advancement of Science, 2015-12-18) Hackett, MJ; Aitken, JB; El-Assaad, F; McQuillan, JA; Carter, EA; Ball, HJ; Tobin, MJ; Paterson, DJ; de Jonge, MD; Siegele, R; Cohen, DD; Vogt, S; Grau, GE; Hunt, NH; Lay, PA
Using a multimodal biospectroscopic approach, we settle several long-standing controversies over the molecular mechanisms that lead to brain damage in cerebral malaria, which is a major health concern in developing countries because of high levels of mortality and permanent brain damage. Our results provide the first conclusive evidence that important components of the pathology of cerebral malaria include peroxidative stress and protein oxidation within cerebellar gray matter, which are colocalized with elevated nonheme iron at the site of microhemorrhage. Such information could not be obtained previously from routine imaging methods, such as electron microscopy, fluorescence, and optical microscopy in combination with immunocytochemistry, or from bulk assays, where the level of spatial information is restricted to the minimum size of tissue that can be dissected. We describe the novel combination of chemical probe–free, multimodal imaging to quantify molecular markers of disturbed energy metabolism and peroxidative stress, which were used to provide new insights into understanding the pathogenesis of cerebral malaria. In addition to these mechanistic insights, the approach described acts as a template for the future use of multimodal biospectroscopy for understanding the molecular processes involved in a range of clinically important acute and chronic (neurodegenerative) brain diseases to improve treatment strategies. 2015 © The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. Distributed under a Creative Commons Attribution Non Commercial Licence 4.0 (CC BY-NC).
Microspectroscopy beamline at the Australian synchrotron: design and capabilities
(XRM Conference, 2008-07) Paterson, DJ; de Jonge, MD; McKinlay, J; Ryan, CG; Cohen, DD
A hard x-ray micro-nanoprobe is being constructed at the Australian Synchrotron [1] to provide sub-micron spatial resolution across an energy range of 4.5–25 keV. The SXM will combine 2D mapping with μ-XRF, μ-XANES and μ-XAFS for elemental and chemical microanalysis. The primary design goal is to achieve sub-100 nm spatial resolution with DE/E ~10-4, and sub-ppm elemental sensitivity. The optical design is a novel “all horizontal” scheme [2]. Interchangeable Fresnel zone plates and Kirkpatrick-Baez mirrors will be used. An advanced fluorescence detector developed by BNL [3] and CSIRO [4] featuring a large solid-angle planar silicon array will enable count rates up to 108 events/sec and real-time processing with deconvoluted image projection. A differential phase contrast detection scheme [5] will be employed for quantitative measurement of soft matter [6]. The Microspectroscopy Beamline will commence operation in late 2008 and will accommodate a diverse range of environmental, biological and materials science applications to cater for the broad requirements of the Australian community. The design, anticipated performance and research applications will be discussed.
Simultaneous X-ray diffraction, crystallography and fluorescence mapping using the Maia detector
(Elsevier, 2018-02-01) Kirkwood, HJ; de Jonge, MD; Muránsky, O; Hofmann, F; Howard, DL; Ryan, CG; van Riessen, GA; Rowles, MR; Paradowska, AM; Abbey, B
Interactions between neighboring grains influence the macroscale behavior of polycrystalline materials, particularly their deformation behavior, damage initiation and propagation mechanisms. However, mapping all of the critical material properties normally requires that several independent measurements are performed. Here we report the first grain mapping of a polycrystalline foil using a pixelated energy-dispersive X-ray area detector, simultaneously measuring X-ray fluorescence and diffraction with the Maia detector in order to determine grain orientation and estimate lattice strain. These results demonstrate the potential of the next generation of X-ray area detectors for materials characterization. By scanning the incident X-ray energy we investigate these detectors as a complete solution for simultaneously mapping the crystallographic and chemical properties of the sample. The extension of these techniques to broadband X-ray sources is also discussed. © 2017 Acta Materialia Inc. Published by Elsevier Ltd.
Simultaneously localising biometals within the high resolution ultrastructure of whole C. elegans
(Australian Microscopy and Microanalysis Society, 2016-02-04) Jones, MWM; McColl, G; van Riessen, GA; Phillips, NW; Vine, D; Abbey, B; de Jonge, MD
Ptychography is a coherent diffraction imaging method where multiple overlapping diffraction frames are combined, providing high resolution images of the electron density of extended objects. Recently, X-ray ptychography has seen many efficiency improvements that allow large areas to be imaged rapidly, making simultaneous X-ray ptychography and fluorescence microscopy experimentally viable. Here we use simultaneous X-ray fluorescence microscopy and ptychography to image entire C. elegans, with sub-micron and sub 100 nm elemental and ultrastructure resolutions respectively. Rapid data collection allowed the entire 1 mm long animal to be imaged in only a few hours. With the information from both techniques, the elemental maps can be viewed in the context of the high resolution ultrastructure, allowing further insights into the localisation of the fluorescent signal.
Spectroscopic analysis of age-related changes in the brain lateral ventricles during ageing
(Australian Nuclear Science and Technology Organisation, 2021-11-24) Hollings, A; Hackett, MJ; Tobin, MJ; Klein, AR; Vongsvivut, JP; de Jonge, MD; Bone, S; Webb, S; Lam, V; Takechi, R; Mamo, J
Alzheimer’s disease is the most common form of dementia and poses significant health and economic concerns. Currently, the disease has no cure, and it is expected that over 1 million people could be affected by 2058 in Australia alone. The content and distribution of metals such as Fe, Cu, Zn is known to change in the ageing brain and thus, increased understanding of the mechanistic role of metal dis-homeostasis may illuminate new therapeutic strategies. The brain lateral ventricles, which play a role in controlling metal and ion transport, have shown increasing levels of copper surrounding their walls with ageing. As a redox active metal, copper can induce oxidative stress which is a process that occurs during Alzheimer’s disease onset and progression. Our research group has been interested in determining whether the age-related elevation of copper surrounding the lateral ventricles is inducing oxidative stress in that region. In this study, we have utilised X-Ray Absorption Spectroscopy (XAS) at the Stanford Synchrotron Radiation Lightsource to analyse different chemical forms of sulfur and measure oxidative stress by analysis of disulfides. Additionally, we used the infrared microscopy beamline at the Australian Synchrotron to identify whether any other markers of oxidative stress were present around the ventricles. Further insights into metal dis-homeostasis and its influence on other biochemical pathways, may help to reveal some of the neurochemical mechanisms involved in progression of Alzheimer’s disease. In turn, this may help pave the way for potential preventative or therapeutic models.
Strontium mineralization of shark vertebrae
(Nature Publishing Group, 2016-07-18) Raoult, VV; Peddemors, VM; Zahra, D; Howell, NR; Howard, DL; de Jonge, MD; Williamson, JE
Determining the age of sharks using vertebral banding is a vital component of management, but the causes of banding are not fully understood. Traditional shark ageing is based on fish otolith ageing methods where growth bands are assumed to result from varied seasonal calcification rates. Here we investigate these assumptions by mapping elemental distribution within the growth bands of vertebrae from six species of sharks representing four different taxonomic orders using scanning x-ray fluorescence microscopy. Traditional visual growth bands, determined with light microscopy, were more closely correlated to strontium than calcium in all species tested. Elemental distributions suggest that vertebral strontium bands may be related to environmental variations in salinity. These results highlight the requirement for a better understanding of shark movements, and their influence on vertebral development, if confidence in age estimates is to be improved. Analysis of shark vertebrae using similar strontium-focused elemental techniques, once validated for a given species, may allow more successful estimations of age on individuals with few or no visible vertebral bands. © 2016 Macmillan Publishers Limited
Studying biological coordination chemistry: a useful role for low latency, energy-dispersive photon counting XRF detectors
(Australian Microscopy and Microanalysis Society, 2016-02-04) James, S; de Jonge, MD; McColl, G; Burke, R; Paterson, DJ; Howard, DL; Hare, D
Day to day cellular function is fundamentally dependent on electron transfer reactions mediated by transition metals, often iron and/or copper. The biological consequences of this metal-catalysed redox chemistry arise from biochemical context generated via the multi-scale organisation of biological systems, i.e. the local concentration of metal → the nature of the donor atoms and bonding environment within the ligand → the location and abundance of the ligand within the cell → the suite of metal-ligand complexes comprising a cell’s metallome → the differences between one cell’s instance of it’s metallome compared to another within and between tissues. Biochemical insight must be anchored to the structural biology of the cell. In this view, understanding metallobiology requires us to interrogate the coordination environment of biological metal-ligand complexes in situ, and the lack of suitable probes limits our appreciation for the role metallobiology plays in health and disease. Ideally, such probes must exhibit extremely high specificity, sensitivity, and spatial resolution; requirements met by scanning X-ray fluorescence microscopy (XFM) and X-ray Emission Near Edge Structure (XENES). Advances in energy-dispersive detector technology have enormously enhanced the efficiency and speed of data acquisition when performing XFM and XENES measurements. When using the Maia detector system installed at the Australian Synchrotron XFM beamline the distribution of biometals can be mapped at rates in excess of 3 M pix / hr. This speed reduces imaging dose whilst maintaining counting statistics. Exploiting these technical advances we have undertaken a multi-pronged assault on characterising elemental distribution and speciation in a variety of whole- organism biological systems, including Caenorhabditis elegans and Drosophila melanogaster. We have utilised projective elemental mapping and 3D visualisations of elemental distributions to assess the distribution of chemical speciation through XENES imaging and tomography. The complementarity of these studies demonstrates that volumetric chemical speciation is achievable with the right instrumentation and approach to measurement but projective imaging can still provide a window into fundamental biological processes. Opportunities and challenges associated with visualizing in situ biometal speciation will be discussed.
X-ray mass attenuation coefficients and imaginary components of the atomic form factor of zinc over the energy range of 7.2-15.2 keV
(American Physical Society, 2010-02) Rae, NA; Chantler, CT; Barnea, Z; de Jonge, MD; Tran, CQ; Hester, JR
The x-ray mass attenuation coefficients of zinc are measured in a high-accuracy experiment between 7.2 and 15.2 keV with an absolute accuracy of 0.044% and 0.197%. This is the most accurate determination of any attenuation coefficient on a bending-magnet beamline and reduces the absolute uncertainty by a factor of 3 compared to earlier work by advances in integrated column density determination and the full-foil mapping technique described herein. We define a relative accuracy of 0.006%, which is not the same as either the precision or the absolute accuracy. Relative accuracy is the appropriate parameter for standard implementation of analysis of near-edge spectra. Values of the imaginary components f″ of the x-ray form factor of zinc are derived. Observed differences between the measured mass attenuation coefficients and various theoretical calculations reach a maximum of about 5% at the absorption edge and up to 2% further than 1 keV away from the edge. The measurements invite improvements in the theoretical calculations of mass attenuation coefficients of zinc. © 2010, American Physical Society

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