Soft X-ray spectro-ptychography of boron nitride nanobamboos, carbon nanotubes and permalloy nanorods.

Spectro-ptychography offers improved spatial resolution and additional phase spectral information relative to that provided by scanning transmission X-ray microscopes. However, carrying out ptychography at the lower range of soft X-ray energies (e.g. below 200 eV to 600 eV) on samples with weakly scattering signals can be challenging. Here, results of soft X-ray spectro-ptychography at energies as low as 180 eV are presented, and its capabilities are illustrated with results from permalloy nanorods (Fe 2p), carbon nanotubes (C 1s) and boron nitride bamboo nanostructures (B 1s, N 1s). The optimization of low-energy X-ray spectro-ptychography is described and important challenges associated with measurement approaches, reconstruction algorithms and their effects on the reconstructed images are discussed. A method for evaluating the increase in radiation dose when using overlapping sampling is presented.

Calculating absorption dose when X-ray irradiation modifies material quantity and chemistry.

X-ray absorption is a sensitive and versatile tool for chemical speciation. However, when high doses are used, the absorbed energy can change the composition, amount and structure of the native material, thereby changing the aspects of the absorption process on which speciation is based. How can one calculate the dose when X-ray irradiation affects the chemistry and changes the amount of the material? This paper presents an assumption-free approach which can retrieve from the experimental data all dose-sensitive parameters - absorption coefficients, composition (elemental molecular units), material densities - which can then be used to calculate accurate doses as a function of irradiation. This approach is illustrated using X-ray damage to a solid film of a perfluorosulfonic acid fluoropolymer in a scanning transmission soft X-ray microscope. This new approach is compared against existing dose models which calculate the dose by making simplifying assumptions regarding the material quantity, density and chemistry. While the detailed measurements used in this approach go beyond typical methods to experimental analytical X-ray absorption, they provide a more accurate quantitation of radiation dose, and help to understand mechanisms of radiation damage.

Magnetosome magnetite biomineralization in a flagellated protist: evidence for an early evolutionary origin for magnetoreception in eukaryotes.

The most well-recognized magnetoreception behaviour is that of the magnetotactic bacteria (MTB), which synthesize membrane-bounded magnetic nanocrystals called magnetosomes via a biologically controlled process. The magnetic minerals identified in prokaryotic magnetosomes are magnetite (Fe3 O4 ) and greigite (Fe3 S4 ). Magnetosome crystals, regardless of composition, have consistent, species-specific morphologies and single-domain size range. Because of these features, magnetosome magnetite crystals possess specific properties in comparison to abiotic, chemically synthesized magnetite. Despite numerous discoveries regarding MTB phylogeny over the last decades, this diversity is still considered underestimated. Characterization of magnetotactic microorganisms is important as it might provide insights into the origin and establishment of magnetoreception in general, including eukaryotes. Here, we describe the magnetotactic behaviour and characterize the magnetosomes from a flagellated protist using culture-independent methods. Results strongly suggest that, unlike previously described magnetotactic protists, this flagellate is capable of biomineralizing its own anisotropic magnetite magnetosomes, which are aligned in complex aggregations of multiple chains within the cell. This organism has a similar response to magnetic field inversions as MTB. Therefore, this eukaryotic species might represent an early origin of magnetoreception based on magnetite biomineralization. It should add to the definition of parameters and criteria to classify biogenic magnetite in the fossil record.

Misalignment between the magnetic dipole moment and the cell axis in the magnetotactic bacterium Magnetospirillum magneticum AMB-1.

While most quantitative studies of the motion of magnetotactic bacteria rely on the premise that the cells' magnetic dipole moment is aligned with their direction of motility, this assumption has so far rarely been challenged. Here we use phase contrast microscopy to detect the rotational diffusion of non-motile cells of Magnetospirillum magneticum AMB-1 around their magnetic moment, showing that in this species the magnetic dipole moment is, in fact, not exactly aligned with the cell body axis. From the cell rotational trajectories, we are able to infer the misalignment between cell magnetic moment and body axis with a precision of better than 1°, showing that it is, on average, 6°, and can be as high as 20°. We propose a method to correct for this misalignment, and perform a non-biased measurement of the magnetic moment of single cells based on the analysis of their orientation distribution. Using this correction, we show that magnetic moment strongly correlates with cell length. The existence of a range of misalignments between magnetic moment and cell axis in a population implies that the orientation and trajectories of magnetotactic bacteria placed in external magnetic fields is more complex than generally assumed, and might show some important cell-to-cell differences.

Measuring spectroscopy and magnetism of extracted and intracellular magnetosomes using soft X-ray ptychography.

Characterizing the chemistry and magnetism of magnetotactic bacteria (MTB) is an important aspect of understanding the biomineralization mechanism and function of the chains of magnetosomes (Fe3O4 nanoparticles) found in such species. Images and X-ray absorption spectra (XAS) of magnetosomes extracted from, and magnetosomes in, whole Magnetovibrio blakemorei strain MV-1 cells have been recorded using soft X-ray ptychography at the Fe 2p edge. A spatial resolution of 7 nm is demonstrated. Precursor-like and immature magnetosome phases in a whole MV-1 cell were visualized, and their Fe 2p spectra were measured. Based on these results, a model for the pathway of magnetosome biomineralization for MV-1 is proposed. Fe 2p X-ray magnetic circular dichroism (XMCD) spectra have been derived from ptychography image sequences recorded using left and right circular polarization. The shape of the XAS and XMCD signals in the ptychographic absorption spectra of both sample types is identical to the shape and signals measured with conventional bright-field scanning transmission X-ray microscope. A weaker and inverted XMCD signal was observed in the ptychographic phase spectra of the extracted magnetosomes. The XMCD ptychographic phase spectrum of the intracellular magnetosomes differed from the ptychographic phase spectrum of the extracted magnetosomes. These results demonstrate that spectro-ptychography offers a superior means of characterizing the chemical and magnetic properties of MTB at the individual magnetosome level.

Importance of the RpoE Regulon in Maintaining the Lipid Bilayer during Antimicrobial Treatment with the Polycationic Agent, Chlorhexidine.

The emergence of multidrug resistance in bacteria has reached alarming levels. To solve this growing problem, discovery of novel cellular targets or pathways important for antimicrobial resistance is urgently needed. In this study, we explored how the alternative sigma factor, RpoE, protects Escherichia coli O157 against the toxic effects of the polycationic antimicrobial agent, chlorhexidine (CHX). Susceptibility of this organism to CHX was found to directly correlate to the growth rate, with the faster replicating wild-type being more susceptible to CHX than its more slowly replicating ΔrpoE O157 mutant. Once the wild-type and rpoE mutant strains had undergone growth arrest (entered the stationary growth phase), their resistance to CHX became entirely dependent on the functionality of RpoE. The RpoE regulon plays a critical role in maintaining the integrity of the asymmetric lipid bilayer of E. coli, thereby preventing the intracellular accumulation of CHX. Finally, using a single-cell, high-resolution, synchrotron-based approach, we discovered a subpopulation of the rpoE mutant strain with no detectable intracellular CHX, a predominant characteristic of the wild-type CHX-resistant population. This finding reveals a role of phenotypic heterogeneity in antimicrobial resistance.

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.

Effect of UV radiation damage in air on polymer film thickness, studied by soft X-ray spectromicroscopy.

The thicknesses of thin films of polystyrene (PS), poly(methyl methacrylate) (PMMA), and perfluorosulfonic acid (PFSA) were measured by Ultraviolet Spectral Reflectance (UV-SR) and Scanning Transmission X-ray Microscopy (STXM). At high doses, the UV irradiation in air used in the UV-SR method was found to modify the chemical structures of PS and PMMA (but not PFSA), leading to thinning of these polymer films. The chemical changes caused by UV/air radiation damage were characterized by STXM. When UV and X-ray radiation are applied using no-damage conditions, the film thicknesses measured with the two techniques differ by less than 15% for PS and PMMA and less than 5% for PFSA. This is an important result for verifying the quantitation capabilities of STXM. The chemical damage to PS and PMMA is explained by oxygen implantation from air with formation of ozone. The thickness depletion caused by UV/air radiation for PS and PMMA films is exponential with exposure time. Different rates of depletion are linked to surface or bulk driven photo-chemical product erosion. The initial rate of material erosion was found to be constant and non-specific to the studied polymers.

Optimization of Three-Dimensional (3D) Chemical Imaging by Soft X-Ray Spectro-Tomography Using a Compressed Sensing Algorithm.

Soft X-ray spectro-tomography provides three-dimensional (3D) chemical mapping based on natural X-ray absorption properties. Since radiation damage is intrinsic to X-ray absorption, it is important to find ways to maximize signal within a given dose. For tomography, using the smallest number of tilt series images that gives a faithful reconstruction is one such method. Compressed sensing (CS) methods have relatively recently been applied to tomographic reconstruction algorithms, providing faithful 3D reconstructions with a much smaller number of projection images than when conventional reconstruction methods are used. Here, CS is applied in the context of scanning transmission X-ray microscopy tomography. Reconstructions by weighted back-projection, the simultaneous iterative reconstruction technique, and CS are compared. The effects of varying tilt angle increment and angular range for the tomographic reconstructions are examined. Optimization of the regularization parameter in the CS reconstruction is explored and discussed. The comparisons show that CS can provide improved reconstruction fidelity relative to weighted back-projection and simultaneous iterative reconstruction techniques, with increasingly pronounced advantages as the angular sampling is reduced. In particular, missing wedge artifacts are significantly reduced and there is enhanced recovery of sharp edges. Examples of using CS for low-dose scanning transmission X-ray microscopy spectroscopic tomography are presented.

Magnetic Field Landscapes Guiding the Chemisorption of Diamagnetic Molecules.

It is shown that the self-assembly of diamagnetic molecule submonolayers on a surface can be influenced by magnetic stray field landscapes emerging from artificially fabricated magnetic domains and domain walls. The directed local chemisorption of diamagnetic subphthalocyaninatoboron molecules in relation to the artificially created domain pattern is proved by a combination of surface analytical methods: ToF-SIMS, X-PEEM, and NEXAFS imaging. Thereby, a new method to influence self-assembly processes and to produce patterned submonolayers is presented.

Microscopic and spectroscopic analyses of chlorhexidine tolerance in Delftia acidovorans biofilms.

The physicochemical responses of Delftia acidovorans biofilms exposed to the commonly used antimicrobial chlorhexidine (CHX) were examined in this study. A CHX-sensitive mutant (MIC, 1.0 µg ml(-1)) was derived from a CHX-tolerant (MIC, 15.0 µg ml(-1)) D. acidovorans parent strain using transposon mutagenesis. D. acidovorans mutant (MT51) and wild-type (WT15) strain biofilms were cultivated in flow cells and then treated with CHX at sub-MIC and inhibitory concentrations and examined by confocal laser scanning microscopy (CLSM), scanning transmission X-ray microscopy (STXM), and infrared (IR) spectroscopy. Specific morphological, structural, and chemical compositional differences between the CHX-treated and -untreated biofilms of both strains were observed. Apart from architectural differences, CLSM revealed a negative effect of CHX on biofilm thickness in the CHX-sensitive MT51 biofilms relative to those of the WT15 strain. STXM analyses showed that the WT15 biofilms contained two morphochemical cell variants, whereas only one type was detected in the MT51 biofilms. The cells in the MT51 biofilms bioaccumulated CHX to a similar extent as one of the cell types found in the WT15 biofilms, whereas the other cell type in the WT15 biofilms did not bioaccumulate CHX. STXM and IR spectral analyses revealed that CHX-sensitive MT51 cells accumulated the highest levels of CHX. Pretreating biofilms with EDTA promoted the accumulation of CHX in all cells. Thus, it is suggested that a subpopulation of cells that do not accumulate CHX appear to be responsible for greater CHX resistance in D. acidovorans WT15 biofilm in conjunction with the possible involvement of bacterial membrane stability.

Characterization of polymer monoliths containing embedded nanoparticles by scanning transmission X-ray microscopy (STXM).

The structural and chemical homogeneity of monolithic columns is a key parameter for high efficiency stationary phases in liquid chromatography. Improved characterization techniques are needed to better understand the polymer morphology and its optimization. Here the analysis of polymer monoliths by scanning transmission X-ray microscopy (STXM) is presented for the first time. Poly(butyl methacrylate-co-ethyleneglycoldimethacrylate) [poly(BuMA-co-EDMA)] monoliths containing encapsulated divinylbenzene (DVB) nanoparticles were characterized by STXM, which gives a comprehensive, quantitative chemical analysis of the monolith at a spatial resolution of 30 nm. The results are compared with other methods commonly used for the characterization of polymer monoliths [scanning electron microscopy (SEM), transmission electron microscopy (TEM), mercury porosimetry, and nitrogen adsorption]. The technique permitted chemical identification and mapping of the nanoparticles within the polymeric scaffold. Residual surfactant, which was used during the manufacture of the nanoparticles, was also detected. We show that STXM can give more in-depth chemical information for these types of materials and therefore lead to a better understanding of the link between polymer morphology and chromatographic performance.

Spectromicroscopy and coherent diffraction imaging: focus on energy materials applications.

Current and future capabilities of X-ray spectromicroscopy are discussed based on coherence-limited imaging methods which will benefit from the dramatic increase in brightness expected from a diffraction-limited storage ring (DLSR). The methods discussed include advanced coherent diffraction techniques and nanoprobe-based real-space imaging using Fresnel zone plates or other diffractive optics whose performance is affected by the degree of coherence. The capabilities of current systems, improvements which can be expected, and some of the important scientific themes which will be impacted are described, with focus on energy materials applications. Potential performance improvements of these techniques based on anticipated DLSR performance are estimated. Several examples of energy sciences research problems which are out of reach of current instrumentation, but which might be solved with the enhanced DLSR performance, are discussed.

Synchrotron-based chemical nano-tomography of microbial cell-mineral aggregates in their natural, hydrated state.

Chemical nano-tomography of microbial cells in their natural, hydrated state provides direct evidence of metabolic and chemical processes. Cells of the nitrate-reducing Acidovorax sp. strain BoFeN1 were cultured in the presence of ferrous iron. Bacterial reduction of nitrate causes precipitation of Fe(III)-(oxyhydr)oxides in the periplasm and in direct vicinity of the cells. Nanoliter aliquots of cell-suspension were injected into custom-designed sample holders wherein polyimide membranes collapse around the cells by capillary forces. The immobilized, hydrated cells were analyzed by synchrotron-based scanning transmission X-ray microscopy in combination with angle-scan tomography. This approach provides three-dimensional (3D) maps of the chemical species in the sample by employing their intrinsic near-edge X-ray absorption properties. The cells were scanned through the focus of a monochromatic soft X-ray beam at different, chemically specific X-ray energies to acquire projection images of their corresponding X-ray absorbance. Based on these images, chemical composition maps were then calculated. Acquiring projections at different tilt angles allowed for 3D reconstruction of the chemical composition. Our approach allows for 3D chemical mapping of hydrated samples and thus provides direct evidence for the localization of metabolic and chemical processes in situ.

Investigating the effects of L- to D-amino acid substitution and deamidation on the activity and membrane interactions of antimicrobial peptide anoplin.

Isolated from the venom sac of solitary spider wasp, Anoplius samariensis, anoplin is the smallest linear α-helical antimicrobial peptide found naturally with broad spectrum activity against both Gram-positive and Gram-negative bacteria, and little hemolytic activity toward human erythrocytes. Deamidation was found to decrease the peptide's antibacterial properties. In the present work, interactions of amidated (Ano-NH2) and deamidated (Ano-OH) forms of anoplin as well as Ano-NH2 composed of all D-amino acids (D-Ano-NH2) with model cell membranes were investigated by means of Langmuir Blodgett (LB) technique, atomic force microscopy (AFM), X-ray photoemission electron microscopy (X-PEEM) and carboxyfluorescein leakage assay in order to gain a better understanding of the effect of these peptide modifications on membrane binding and lytic properties. According to LB, all three peptides form stable monolayers at the air/water interface with Ano-NH2 occupying a slightly greater area per molecule than Ano-OH. All three forms of the peptide interact preferentially with anionic 1,2-dipalmitoyl-sn-glycero-3-[phospho-rac-(1-glycerol)] (DPPG), rather than zwitterionic 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) lipid monolayer. Peptides form nanoscale clusters in zwitterionic but not in anionic monolayers. Finally, membrane lytic activity of all derivatives was found to depend strongly on membrane composition and lipid/peptide ratio. The results suggest that amidated forms of peptides are likely to possess higher membrane binding affinity due to the increased charge.

Accurate dosimetry in scanning transmission X-ray microscopes via the cross-linking threshold dose of poly(methyl methacrylate).

The sensitivity of various polymers to radiation damage by soft X-rays has been measured previously with scanning transmission X-ray microscopes. However, the critical dose values reported by different groups for the same material differ by more than 100%. Possible sources of this variability are investigated here for poly(methyl methacrylate) (PMMA) using controlled exposure to monochromatic soft X-rays at 300 eV. Radiation sensitivity, judged by several different criteria, was evaluated as a function of dose rate, pre-exposure thermal treatments and X-ray polarization. Both the measured critical dose and the dose required to initiate negative mode (cross-linking) were observed to depend only on dose, not the other factors explored. A method of determining detector efficiency from the dose required to initiate negative mode in PMMA is outlined. This method was applied to many of the soft X-ray STXMs presently operating to derive the efficiencies of their transmitted X-ray detectors in the C 1s absorption-edge region.

Three-dimensional structure and defects in colloidal photonic crystals revealed by tomographic scanning transmission X-ray microscopy.

Self-assembled colloidal crystals have attracted major attention because of their potential as low-cost three-dimensional (3D) photonic crystals. Although a high degree of perfection is crucial for the properties of these materials, little is known about their exact structure and internal defects. In this study, we use tomographic scanning transmission X-ray microscopy (STXM) to access the internal structure of self-assembled colloidal photonic crystals with high spatial resolution in three dimensions for the first time. The positions of individual particles of 236 nm in diameter are identified in three dimensions, and the local crystal structure is revealed. Through image analysis, structural defects, such as vacancies and stacking faults, are identified. Tomographic STXM is shown to be an attractive and complementary imaging tool for photonic materials and other strongly absorbing or scattering materials that cannot be characterized by either transmission or scanning electron microscopy or optical nanoscopy.

Experimental investigation of beam heating in a soft X-ray scanning transmission X-ray microscope.

A variable temperature sample holder with an operational range of 15 to 200 °C and an accuracy of ±1 °C has been fabricated for scanning transmission X-ray microscopes (STXM). Here we describe the device, and use it to image the polycrystalline morphology of solid stearic acid and palmitic acid at temperatures near their respective melting points as a means of checking for possible sample heating caused by the focused X-ray beam. The melting points observed in STXM were identical to those observed by conventional methods within measurement uncertainty, even under the most extreme, high dose rate imaging conditions investigated. The beam-induced temperature rise in the sample is inferred to be below 1 °C for dose rates of up to 2.7 GGy/s.

Probing platinum degradation in polymer electrolyte membrane fuel cells by synchrotron X-ray microscopy.

Synchrotron-based scanning transmission X-ray spectromicroscopy (STXM) was used to characterize the local chemical environment at and around the platinum particles in the membrane (PTIM) which form in operationally tested (end-of-life, EOL) catalyst coated membranes (CCMs) of polymer electrolyte membrane fuel cells (PEM-FC). The band of metallic Pt particles in operationally tested CCM membranes was imaged using transmission electron microscopy (TEM). The cathode catalyst layer in the beginning-of-life (BOL) CCMs was fabricated using commercially available catalysts created from Pt precursors with and without nitrogen containing ligands. The surface composition of these catalyst powders was measured by X-ray Photoelectron Spectroscopy (XPS). The local chemical environment of the PTIM in EOL CCMs was found to be directly related to the Pt precursor used in CCM fabrication. STXM chemical mapping at the N 1s edge revealed a characteristic spectrum at and around the dendritic Pt particles in CCMs fabricated with nitrogen containing Pt-precursors. This N 1s spectrum was identical to that of the cathode and different from the membrane. For CCM samples fabricated without nitrogen containing Pt-precursors the N 1s spectrum at the Pt particles was indistinguishable from that of the adjacent membrane. We interpret these observations to indicate that nitrogenous ligands in the nitrogen containing precursors, or decomposition product(s) from that source, are transported together with the dissolved Pt from the cathode into the membrane as a result of the catalyst degradation process. This places constraints on possible mechanisms for the PTIM band formation process.

Chemical Structure and Distribution in Nickel-Nitrogen-Carbon Catalysts for CO2 Electroreduction Identified by Scanning Transmission X-ray Microscopy.

Atomically dispersed metal-nitrogen-carbon (M-N-C) materials are a class of electrocatalysts for fuel cell and electrochemical CO2 reduction (CO2R) applications. However, it is challenging to characterize the identity and concentration of catalytically active species owing to the structural heterogeneity of M-N-C materials. We utilize scanning transmission X-ray microscopy (STXM) as a correlative spectromicroscopy approach for spatially resolved imaging, identification, and quantification of structures and chemical species in mesoscale regions of nickel-nitrogen-carbon (Ni-N-C) catalysts, thereby elucidating the relationship between Ni content/speciation and CO2R activity/selectivity. STXM results are correlated with conventional characterization approaches relying on either bulk average (X-ray absorption spectroscopy) or spatially localized (scanning transmission electron microscopy with electron energy loss spectroscopy) measurements. This comparison illustrates the advantages of soft X-ray STXM to provide spatially resolved identification and quantification of active structures in Ni-N-C catalysts. The active site structures in these catalysts are identified to be atomically dispersed NiN x /C sites distributed throughout entire catalyst particles. The NiN x /C sites were notably demonstrated by spectroscopy to possess a variety of chemical structures with a spectroscopic signature that most closely resembles nickel(II) tetraphenylporphyrin molecules. The quantification and spatial distribution mapping of atomically dispersed Ni active sites achieved by STXM address a target that was elusive to the scientific community despite its importance in guiding advanced material designs.