Transmission Soft X-ray Microscopy Research Articles

Significant Enhancement in Light Output of Photonic-Crystal-Based YAG:Ce Scintillator for Soft X-Ray Detectors

Because of its high light output, Gd <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> S:Tb (P43) phosphor powder is widely used in scintillator detectors for scanning transmission soft X-ray microscopy. However, the long decay time (>1 ms) of P43 phosphor powder limits the image scanning speed. Inorganic scintillators such as YAG:Ce are very suitable for fast scanning imaging due to their short decay time (tens of nanoseconds). Nevertheless, its light output is lower than that of P43 phosphor powder. Patterning photonic crystals (PhCs) on the output surface of an inorganic scintillator is a simple and efficient method to enhance its light output. In this article, we use a soft X-ray interference lithography technique to produce a large-area pattern of nanoscale PhCs on a 200-μm -thickness and 1-in-diameter YAG:Ce scintillator. Measurement of the enhancement ratio was performed on the soft X-ray beamline (BL08U1A) at the Shanghai Synchrotron Radiation Facility. The results show that the light output of the PhC-patterned YAG:Ce scintillator with air coupling is approximately 2.8 times higher than that of the unpatterned YAG:Ce scintillator. Meanwhile, the time-resolved emission with optical excitation showed that the PhC structures did not affect the spontaneous emission rate in the internal of scintillator crystal. This enhancement of the light output indicates that the PhC-patterned YAG:Ce scintillator is a good candidate for soft X-ray detection.

Magnetite magnetosome biomineralization in Magnetospirillum magneticum strain AMB-1: A time course study

Magnetotactic bacteria are a highly studied group of diverse prokaryotes that biomineralize chains of magnetosomes, single domain, single crystal magnetic nanoparticles of magnetite or greigite, enclosed by a lipid bilayer membrane whose synthesis is under strict genetic control. In addition to characterizing the genetics and physicochemical properties of both cultured and uncultured environmental species, there have been a number of investigations using a time course approach to determine the chemical pathway of magnetite biomineralization in these organisms. In time course studies, cells of MTB are typically grown in the absence of iron so they cannot make magnetite, and then provided with iron in culture medium which initiates the biomineralization of magnetosome chains over a subsequent time period. Results from previous time course studies are not consistent with one another, differing with regard to the nature of chemical intermediates and the rate of establishment of magnetosome chains. In this work we report a time course study of Magnetospirillum magneticum strain AMB-1 over a 48h (hour) period, using transmission electron microscopy (TEM) and soft X-ray scanning transmission X-ray microscopy (STXM) at the Fe L-edge. STXM provides capability to measure X-ray absorption spectra (XAS) and map chemical species with ∼25nm spatial resolution and thus gives detailed results on the chemistry of individual particles in single cells. An evolution of the iron oxide speciation, from a more Fe(III)-rich species, possibly α-hematite (Fe2O3), to magnetite (Fe3O4), was observed in the early stages, with evidence for the presence of the Fe(III)-rich character persisting up to 24 h. The spectromicroscopy (X-ray absorption, XAS and X-ray magnetic circular dichroism, XMCD) and TEM results show that biomineralization occurs in a stepwise fashion. First, very small particles, with no measurable magnetization, are produced at different sites in the cell without significant chain formation. The Fe L3 spectra of these early stage particles typically differ from magnetite with an additional signal at 708.4 eV that is consistent with α-hematite. By 6–8h the particles are more numerous, partial chain formation is evident, and the L3 spectrum is very similar to that of magnetite. By 24 h particles-in-chains are the dominant motif and magnetism with the moment along the chain is established. By 48 h the cells are essentially the same as cells grown in Fe-rich medium.

Quantitative Distribution of DNA, RNA, Histone and Proteins Other than Histone in Mammalian Cells, Nuclei and a Chromosome at High Resolution Observed by Scanning Transmission Soft X-Ray Microscopy (STXM).

Soft X-ray microscopy was applied to study the quantitative distribution of DNA, RNA, histone, and proteins other than histone (represented by BSA) in mammalian cells, apoptotic nuclei, and a chromosome at spatial resolutions of 100 to 400 nm. The relative distribution of closely related molecules, such as DNA and RNA, was discriminated by the singular value decomposition (SVD) method using aXis2000 software. Quantities of nucleic acids and proteins were evaluated using characteristic absorption properties due to the 1s–π * transition of N=C in nucleic acids and amide in proteins, respectively, in the absorption spectra at the nitrogen K absorption edge. The results showed that DNA and histone were located in the nucleus. By contrast, RNA was clearly discriminated and found mainly in the cytoplasm. Interestingly, in a chromosome image, DNA and histone were found in the center, surrounded by RNA and proteins other than histone. The amount of DNA in the chromosome was estimated to be 0.73 pg, and the content of RNA, histone, and proteins other than histone, relative to DNA, was 0.48, 0.28, and 4.04, respectively. The method we present in this study could be a powerful approach for the quantitative molecular mapping of biological samples at high resolution.

Carbon-coated montmorillonite nanocomposite for the removal of chromium(VI) from aqueous solutions.

A carbon-coated montmorillonite nanocomposite (CMt), obtained by hydrothermal carbonization of montmorillonite suspension in glucose, was used to remove Cr(VI) from aqueous solutions. The distribution and speciation of Cr immobilized by CMt were assessed by transmission electron microscopy with energy-dispersive X-ray analysis, X-ray absorption near edge structure (XANES), and scanning transmission soft X-ray microscopy (STXM). The variation in the functional groups and molecular structures of CMt was also investigated. The capacity of CMt for adsorbing Cr(VI) was markedly superior to that of the parent montmorillonite, showing maximum uptake of 100 and 12.4 mg g-1 at pH 2 and 8, respectively. The Cr K-edge XANES and STXM analyses indicated that Cr(VI) was reduced to Cr(III) under both acidic and alkaline conditions, while a Cr(OH)3 precipitate and Cr(III)-acetate complex were the predominant species present on the CMt surface. The Fourier transform infrared spectroscopy and C K-edge XANES further suggested that the phenolic groups in CMt could serve as electron donors, facilitating Cr(VI) reduction. The combined results indicate that electrostatic attraction, Cr(VI) reduction, complexation, and precipitation are involved in the removal of Cr(VI) by CMt.

Discrimination of DNA and RNA distribution in a mammalian cell by scanning transmission soft X-ray microscopy.

Soft X-ray spectromicroscopy was applied to study the distribution of DNA and RNA in a mammalian cell at the spatial resolution of 400 nm. The relative distribution of DNA and RNA was examined by the SVD (singular value decomposition) method in aXis2000 program using combined full spectra of DNA and RNA at the absorption edge regions of carbon, nitrogen and oxygen. The absorption of nucleic acid was evaluated using 1s-π* transitions in the NEXAFS spectra at the nitrogen K absorption edge and distributed to DNA and RNA according to the relative level obtained above. The present results revealed the usefulness of the SVD method to discriminate closely related molecules such as DNA and RNA.

Redox-Chemistry of Environmental Biofilms Probed on the Submicron Scale by in-situ Electrochemistry Scanning Transmission (soft) X-ray Microscopy

Redox-Chemistry of Environmental Biofilms Probed on the Submicron Scale by in-situ Electrochemistry Scanning Transmission (soft) X-ray Microscopy

Quantitative analysis of mammalian chromosome by scanning transmission soft X-ray microscopy

Soft X-ray spectromicroscopy was applied to study the quantitative distribution of DNA and protein in a mammalian chromosome at the spatial resolution of 100 nm. The quantities of DNA and protein were evaluated using 1s-π* transition in the NEXAFS spectra at the nitrogen K absorption edge. DNA was not uniformly distributed in the chromosome and DNA/protein ratio was less than 0.497. The present analysis revealed the clues to identify other molecules that contribute to the absorption spectrum of the sample. The results suggested that accumulation of the absorption spectra of relevant molecules would support the refinement of the analysis.

Electric current control of creation and annihilation of sub-100 nm magnetic bubbles examined by full-field transmission soft X-ray microscopy

The effect of electric current pulses on a sub-100 nm magnetic bubble state in a symmetric Pt/Co multilayer was directly observed using a full-field transmission soft X-ray microscope (MTXM). Field-induced evolution of the magnetic stripe domains into isolated bubbles with their sizes down to 100 nm was imaged under varying external magnetic fields. Electric current pulses were then applied to the created magnetic bubbles, and it was observed that the bubbles could be either created or annihilated by the current pulse depending on the strength of applied magnetic field. The results suggest that the Joule heating plays a critical role in the formation and/or elimination of the bubbles and skyrmions. Finally, the schematic phase diagram for the creation and annihilation of bubbles is presented, suggesting an optimized scheme with the combination of magnetic field and electric current necessary to utilize skyrmions in the practical devices.

Scanning X-ray microscopy with large solid angle X-ray fluorescence detection at the XUV beamline P04, DESY

The presented scanning transmission X-ray microscope (STXM), built on top of a modular platform, combines soft X-ray transmission and fluorescence microscopy with high detection efficiency and high spatial resolution. The setups user concept as well as the large solid angle (> 1 sr) of the integrated Silicon-drift-detector are unique characteristics of this endstation. In combination with the soft X-ray beamline P04 at PETRA III (DESY), it delivers a new type of nanoscope, providing a high flexibility and very low acquisition times.

Selenite removal from groundwater by zero-valent iron (ZVI) in combination with oxidants

We recently demonstrated common oxidants simply coupled with ZVI to continuously drive the accelerated Fe0 corrosion and hence achieve fast and very efficient removal of heavy metals and metalloids from groundwater. In this study, we aimed first to answer a basic question of the oxidant dosage theoretically required to sequester a certain amount of selenite. The specific ratio of oxidant dosage to Se(IV) removal, which reflected the theoretically minimal oxidant dosage required to sequester one mole of Se(IV), was almost independent of the initial Se(IV) concentration but significantly affected by the difference in oxidant species. To sequester one mole of Se(IV), the minimum dosage of the required oxidant was calculated to be 3.94–4.09 for NaClO, 3.90–4.33 for H2O2, and 3.29–3.54 for KMnO4, respectively. Simultaneous aeration increased the removal efficiency of Se(IV) and substantially reduced the required dosage of oxidants. To form a strong contrast with very limited Se(IV) removal by ZVI alone, the coupling of NaClO and H2O2 into the ZVI system remarkably enhanced the performance of Se(IV) removal during the long term fixed-bed experiments with a real groundwater background. The ZVI columns coupled by NaClO and H2O2 steadily treated 10,000 volumes (BV) of real groundwater. X-ray adsorption near edge structure (XANES) demonstrated that more than 85% of the selenium was reduced to Se0 and Se2−, with Se0 as the dominant selenium species sequestered in the solid phase. Synchrotron-based scanning transmission soft X-ray microscopy (STXM) explicitly revealed the ubiquitous spatial distribution of selenium in the corrosion products and hence demonstrated a high accessibility of these corrosion products to selenite.

First-principles X-ray absorption dose calculation for time-dependent mass and optical density.

A dose integral of time-dependent X-ray absorption under conditions of variable photon energy and changing sample mass is derived from first principles starting with the Beer-Lambert (BL) absorption model. For a given photon energy the BL dose integral D(e, t) reduces to the product of an effective time integral T(t) and a dose rate R(e). Two approximations of the time-dependent optical density, i.e. exponential A(t) = c + aexp(-bt) for first-order kinetics and hyperbolic A(t) = c + a/(b + t) for second-order kinetics, were considered for BL dose evaluation. For both models three methods of evaluating the effective time integral are considered: analytical integration, approximation by a function, and calculation of the asymptotic behaviour at large times. Data for poly(methyl methacrylate) and perfluorosulfonic acid polymers measured by scanning transmission soft X-ray microscopy were used to test the BL dose calculation. It was found that a previous method to calculate time-dependent dose underestimates the dose in mass loss situations, depending on the applied exposure time. All these methods here show that the BL dose is proportional to the exposure time D(e, t) ≃ K(e)t.

Quantitative study of mammalian cells by scanning transmission soft X-ray microscopy

Molecular distribution in mammalian cells was studied by soft X-ray scanning transmission microscopy with respect to the quantitative aspect of analysis. NEXAFS profiles at the C, N and O K-absorption edges were combined and used for the analysis. For the estimation of quantity for nucleic acids and proteins, NEXAFS profiles of DNA and bovine serum albumin (BSA) at the N K-absorption edge were applied assuming that those were their representatives. The method has a potential to explore the other molecular components than nucleic acids and proteins.

Discharge products of ionic liquid-based Li-O2 batteries observed by energy dependent soft x-ray transmission microscopy

Abstract Products deposited on an O 2 -cathode discharged in ionic liquid electrolytes are analyzed by transmission soft X-ray microscopy (TXM) and compared to ether-based electrolytes, showing differences in morphology and chemical compositions. With both solvents we observe Li 2 O 2 and LiO 2 primary products in similar proportions. However, while as previously observed in tetraglyme an important reactivity takes place producing significant amount of carbonates, in ionic liquid-based electrolytes the formation of carbonates was almost negligible, confirming higher stability. Only when sample is intentionally air exposed before analysis, significant amounts of carbonates came up. However, LiOH crystallites are clearly recognized with the ionic liquid electrolyte. The abundance of these crystallites depends on both the LiTFSI concentration and the storage time of discharged electrodes, suggesting that they result from the reaction of water trace with primary discharge products.

3D membrane segmentation and quantification of intact thick cells using cryo soft X-ray transmission microscopy: A pilot study.

Structural analysis of biological membranes is important for understanding cell and sub-cellular organelle function as well as their interaction with the surrounding environment. Imaging of whole cells in three dimension at high spatial resolution remains a significant challenge, particularly for thick cells. Cryo-transmission soft X-ray microscopy (cryo-TXM) has recently gained popularity to image, in 3D, intact thick cells (∼10μm) with details of sub-cellular architecture and organization in near-native state. This paper reports a new tool to segment and quantify structural changes of biological membranes in 3D from cryo-TXM images by tracking an initial 2D contour along the third axis of the microscope, through a multi-scale ridge detection followed by an active contours-based model, with a subsequent refinement along the other two axes. A quantitative metric that assesses the grayscale profiles perpendicular to the membrane surfaces is introduced and shown to be linearly related to the membrane thickness. Our methodology has been validated on synthetic phantoms using realistic microscope properties and structure dimensions, as well as on real cryo-TXM data. Results demonstrate the validity of our algorithms for cryo-TXM data analysis.

Observation of asymmetric distributions of magnetic singularities across magnetic multilayers

Whereas a great deal of work is being devoted to magnetic singularities in two-dimensional (2D) systems (surfaces, interfaces, films) due to their possible applications, much less is known about their properties along the perpendicular direction. Here, we report on a pronounced asymmetry of the in-depth distribution of meronlike magnetic textures, which are magnetic singularities similar to \textonehalf{} skyrmions, in magnetic layers. Meron textures are observed to be distributed in two groups defined by their topology. One of them resides almost exclusively at the top surface of the film and the other at the bottom one. This observation has been brought to light with element-specific magnetic transmission soft x-ray microscopy. Micromagnetic simulations reveal that closure domains are at the origin of this asymmetry. The result might be of general interest for controlling magnetic three-dimensional (3D) architectures.

Table-top water-window soft X-ray microscope using a Z-pinching capillary discharge source

The development and demonstration of a table-top transmission soft X-ray (SXR) microscope, using a laboratory incoherent capillary discharge source has been carried out. This Z-pinching capillary discharge water-window SXR source, is a first of its kind to be used for high spatial resolution microscopy at λ = 2.88 nm (430 eV) . A grazing incidence ellipsoidal condenser mirror is used for focusing of the SXR radiation at the sample plane. The Fresnel zone plate objective lens is used for imaging of the sample onto a back-illuminated (BI) CCD camera. The achieved half-pitch spatial resolution of the microscope approaches 100 nm, as demonstrated by the knife-edge test. Details about the source, and the construction of the microscope are presented and discussed. Additionally, the SXR images of various samples, proving applicability of such microscope for observation of objects in the nanoscale, are shown.

Nanobubbles at Hydrophilic Particle-Water Interfaces.

The puzzling persistence of nanobubbles breaks Laplace's law for bubbles, which is of great interest for promising applications in surface processing, H2 and CO2 storage, water treatment, and drug delivery. So far, nanobubbles have mostly been reported on hydrophobic planar substrates with atomic flatness. It remains a challenge to quantify nanobubbles on rough and irregular surfaces because of the lack of a characterization technique that can detect both the nanobubble morphology and chemical composition inside individual nanobubble-like objects. Here, by using synchrotron-based scanning transmission soft X-ray microscopy (STXM) with nanometer resolution, we discern nanoscopic gas bubbles of >25 nm with direct in situ proof of O2 inside the nanobubbles at a hydrophilic particle-water interface under ambient conditions. We find a stable cloud of O2 nanobubbles at the diatomite particle-water interface hours after oxygen aeration and temperature variation. The in situ technique may be useful for many surface nanobubble-related studies such as material preparation and property manipulation, phase equilibrium, nucleation kinetics, and relationships with chemical composition within the confined nanoscale space. The oxygen nanobubble clouds may be important in modifying particle-water interfaces and offering breakthrough technologies for oxygen delivery in sediment and/or deep water environments.

Chromium immobilization by extra- and intraradical fungal structures of arbuscular mycorrhizal symbioses

Arbuscular mycorrhizal (AM) fungi can enhance plant Cr tolerance through immobilizing Cr in mycorrhizal roots. However, the detailed processes and mechanisms are unclear. The present study focused on cellular distribution and speciation of Cr in both extraradical mycelium (ERM) and mycorrhizal roots exposed to Cr(VI) by using field emission scanning electron microscopy equipped with energy dispersive X-ray spectrometer (FE-SEM-EDS), scanning transmission soft X-ray microscopy (STXM) and X-ray absorption fine structure (XAFS) spectroscopy techniques. We found that amounts of particles (possibly extracellular polymeric substances, EPS) were produced on the AM fungal surface upon Cr(VI) stress, which contributed greatly to Cr(VI) reduction and immobilization. With EDS of the surface of AM fungi exposed to various Cr(VI) levels, a positive correlation between Cr and P was revealed, suggesting that phosphate groups might act as counter ions of Cr(III), which was also confirmed by the XAFS analysis. Besides, STXM and XAFS analyses showed that Cr(VI) was reduced to Cr(III) in AM fungal structures (arbuscules, intraradical mycelium, etc.) and cell walls in mycorrhizal roots, and complexed possibly with carboxyl groups or histidine analogues. The present work provided evidence of Cr immobilization on fungal surface and in fungal structures in mycorrhizal roots at a cellular level, and thus unraveled the underlying mechanisms by which AM symbiosis immobilize Cr.

A single probe for imaging photons, electrons and physical forces

The combination of complementary measurement techniques has become a frequent approach to improve scientific knowledge. Pairing of the high lateral resolution scanning force microscopy (SFM) with the spectroscopic information accessible through scanning transmission soft x-ray microscopy (STXM) permits assessing physical and chemical material properties with high spatial resolution. We present progress from the NanoXAS instrument towards using an SFM probe as an x-ray detector for STXM measurements. Just by the variation of one parameter, the SFM probe can be utilised to detect either sample photo-emitted electrons or transmitted photons. This allows the use of a single probe to detect electrons, photons and physical forces of interest. We also show recent progress and demonstrate the current limitations of using a high aspect ratio coaxial SFM probe to detect photo-emitted electrons with very high lateral resolution. Novel probe designs are proposed to further progress in using an SFM probe as a STXM detector.

Nanoscale characterization of local structures and defects in photonic crystals using synchrotron-based transmission soft X-ray microscopy.

For the structural characterization of the polystyrene (PS)-based photonic crystals (PCs), fast and direct imaging capabilities of full field transmission X-ray microscopy (TXM) were demonstrated at soft X-ray energy. PS-based PCs were prepared on an O2-plasma treated Si3N4 window and their local structures and defects were investigated using this label-free TXM technique with an image acquisition speed of ~10 sec/frame and marginal radiation damage. Micro-domains of face-centered cubic (FCC (111)) and hexagonal close-packed (HCP (0001)) structures were dominantly found in PS-based PCs, while point and line defects, FCC (100), and 12-fold symmetry structures were also identified as minor components. Additionally, in situ observation capability for hydrated samples and 3D tomographic reconstruction of TXM images were also demonstrated. This soft X-ray full field TXM technique with faster image acquisition speed, in situ observation, and 3D tomography capability can be complementally used with the other X-ray microscopic techniques (i.e., scanning transmission X-ray microscopy, STXM) as well as conventional characterization methods (e.g., electron microscopic and optical/fluorescence microscopic techniques) for clearer structure identification of self-assembled PCs and better understanding of the relationship between their structures and resultant optical properties.