Magnetotactic bacteria (MTB) are ubiquitous in aquatic environments. They biomineralize membrane-bound magnetic nanoparticles (magnetosomes), which are magnetically single-domain, single crystals of either magnetite, Fe3O4, or greigite, Fe3S4. The chain is a strong magnetic dipole, which aligns the cell with the earth’s magnetic field (magnetotaxis) and, together with chemical signatures (aerotaxis), is believed to increase the efficiency of the organism in finding an optical oxygen concentration in the sediments. As the simplest organisms, in which biomineralization occurs, magnetotactic bacteria serve as an ideal model to study biomineralization mechanism. In this research, soft X-ray STXM (scanning transmission X-ray microscopy) was used to characterize the chemistry and magnetism of magnetotactic bacteria (MTB) on an individual cell and an individual magnetosome basis. Two types of MTB, Candidatus Magnetovibrio blakemorei strain MV-1 and multicellular magnetotoactic prokaryotes (MMPs) were studied in this project. In addition, ptychography technique, which does not rely on X-ray optics and holds promise for imaging with wavelength-limited resolution, is used to study biomineralization and magnetism of MTB cells. A spatial resolution of 7 nm below 1000 eV is achieved with ptychography, which is the highest in the soft X-ray region so far. Precursor-like and immature magnetosomes in intact MV-1 cells with ptychography are observed and a model for the pathway of magnetosome biomineralization for MV-1 is proposed. Our results demonstrate ptychography offers a superior means to characterize the chemical and magnetic properties of magnetotactic bacteria at the individual magnetosome level.

Dissertation

Doctor of Philosophy (PhD)

Understanding electrically activated processes at electrode-electrolyte interfaces is needed to improve many technologies, including energy conversion, semiconductor devices, bio-sensors, corrosion protection, etc. In-situ spectro-electrochemical studies based on a wide range of spectroscopies are particularly useful. Scanning Transmission X-ray microscopy (STXM) is a synchrotron-based technique which measures near-edge X-ray absorption fine structure (NEXAFS) with high spatial resolution. In addition to information on morphology, STXM also provides chemical state analysis using the X-ray absorption data, which makes in-situ STXM studies of electrochemical process of special interest. This thesis reports ex-situ and in-situ STXM based qualitative and quantitative studies on copper (Cu) electrodeposition and electrostripping. The influence of electrolyte pH on the distribution of Cu(I) and Cu(0) species electrodeposited from aqueous CuSO4 solutions was studied. An instrument capable of performing in-situ flow electrochemical STXM studies was designed and fabricated. The performance of this device was evaluated for in-situ Cu electrodeposition studies. Findings based on ex-situ and in-situ STXM studies are discussed. Suggestions are made for further instrumentation improvements.

Thesis

Master of Science (MSc)

Climate change has propelled the development of alternative power sources that minimize the emission of greenhouse effect gases. Widespread commercialization of polymer electrolyte membrane fuel cell (PEM-FC) technology for transportation and stationary applications requires cost-competitiveness with improved durability and performance. Advantages compared to battery electric vehicles include fast refueling and long distance range. One way to improve performance and minimize costs of PEM-FC involves the optimization of the nanostructure of the catalyst layer. The rate limiting oxygen reduction reaction occurs at a triple-phase interface in the cathode catalyst layer (CL) between the proton conductor perfluorosulfonic acid, PFSA, the Pt catalyst particles decorating the electron conductor carbon support and gaseous O2 available through the porous framework of the carbon support. Visualization and quantitation of the distribution of components in the CL requires microscopy techniques. Electron and X-ray microscopy have been used to characterize the distribution of the PFSA relative to the carbon support and porosity in CLs. Understanding and limiting the analytical impact of radiation damage, which occurs due to the ionizing nature of electrons and X-rays, is needed to improve quantitation, particularly of PFSA. This thesis developed scanning transmission X-ray microscopy (STXM) methods for quantitation of damage due to electron and soft X-ray irradiation in PFSA materials. Chemical damage to PFSA when irradiated by photons and electrons is dominated by fluorine loss and CF2-CF2 amorphization. The quantitative results are used to set maximum dose limits to help optimize characterization and quantitation of PFSA in fuel cell cathode catalyst layers using: analytical electron microscopy, X-ray microscopy, spectromicroscopy, spectrotomography, spectroptychography and spectro-ptycho-tomography.

Thesis

Doctor of Philosophy (PhD)

Polymer electrolyte membrane fuel cells are an alternative, environmentally friendly power source for transportation and stationary applications. Major challenges for mass production include cost competitiveness, improved durability and performance. A key component to enhance the performance and lower costs involves understanding and improving the spatial distribution of the perfluorosulfonic acid (PFSA) polymer in the catalyst layer. The ionizing nature of electrons and X-rays used in microscopy characterization tools challenges PFSA characterization since this material is radiation sensitive. This thesis developed measurement protocols and methods for quantitative studies of radiation damage to PFSA and other polymers using scanning transmission X-ray microscopy. The chemical changes to PFSA films irradiated with photons, electrons and ultraviolet (UV) photons were studied. The quantitative results identify limits to analytical electron and soft X-ray microscopy characterization of PFSA. The results are used to optimize methods for soft X-ray microscopy characterization of…

Proton exchange membrane fuel cells (PEMFC) are a promising green energy resource for automotive applications. The cathode is a key rate limiting component of PEMFC. Typical cathodes are composed of Pt catalyst decorated carbon support particles, mixed with a perfluorosulfonic acid (PFSA) polymer. As the proton conduction medium in the cathode, the distribution of the PFSA ionomer will affect PEMFC efficiency, Pt utilization, and degradation kinetics. Optimization of ionomer loadings and distributions is a major goal of PEMFC research. In this thesis, Scanning transmission X-ray microscopy (STXM) has been used to measure the porosity and component distributions in 3D. Initial studies of PEMFC materials by STXM tomography have been presented. The high energy resolution of STXM collects an extra dimension of component information to be added to the 3 dimension of volume imaging. Multi chemical 3D imaging is defined as 4D imaging. To reduce the radiation damage to PFSA, the compressed sensing (CS) algorithm has been used. The results show that the total radiation damage can be reduced below the critical dose, and better reconstruction results with less measured angles are achieved using CS algorithm. PFSA materials were also measured using ptychography STXM tomography to improve the spatial resolution. The spatial resolution was improved from 30 nm to < 15 nm at ~700 eV. 4D imaging using ptychography STXM tomography is presented. Highly porous materials with functional coatings were also characterized by soft X-ray STXM-spectro-tomography and spectro-ptycho-tomography. The sample were Al2O3 aerogels coated with ZnO or TiO2 by atomic layer deposition (ALD). Quantitative analysis shows the ZnO ALD coatings are non uniform. Comparisons are made to electron microscopy imaging and X-ray fluorescence analysis of the same ZnO/ Al2O3 aerogel material. Together the results provide useful feedback for optimization of ALD coated alumina aerogels.

Thesis

Doctor of Philosophy (PhD)

This thesis presents studies of the X-ray linear dichroism (XLD) in individual single-walled (SW) and multi-walled (MW) carbon nanotubes (CNT) measured by a scanning transmission X-ray microscope (STXM). The C 1s spectra of CNT showed a large XLD at the C 1s→π* transition. The magnitude of the XLD was found to be related to the quality of CNT such that in high quality CNT, it was fairly large and as the quality lowered it decreased. This dichroic effect was used to map defects along individual CNT. In addition, STXM was employed to map chemical components in pristine, purified, and dodecyl functionalized SWCNT bundles to investigate the changes occurring in them due to chemical functionalization. STXM has limited spatial resolution. Thus, electron energy loss spectroscopy (EELS) in a transmission electron microscope (TEM) was used to obtain similar information about CNT, but at much higher spatial resolution. The measurements performed in the scanning transmission electron microscopy (STEM) mode produced signals analogous to the XLD when the orientation of the momentum transfer (q) was resolved. This was achieved by displacing the pattern of electron scattering from CNT relative to the EELS entrance aperture. TEM-EELS was also utilized to map defects in pristine and focused ion beam (FIB) modified CNT.

Doctor of Philosophy (PhD)

Magnetotactic bacteria (MTB) are ubiquitous, multi-phylogenetic bacteria that actively synthesize chains of magnetic, membrane bound; single domain magnetite (Fe₃O₄) or greigite (Fe₃S₄) crystals, termed magnetosomes in order to better navigate to their preferred chemical environment using the Earth’s magnetic field. Discovered in 1963, the field is now focused on understanding magnetosome chain formation and associated processes through genetic studies as well as analytical techniques such as Transmission Electron Microscopy (TEM) and Scanning Transmission X-ray Microscopy – X-ray Magnetic Circular Dichroism (STXM-XMCD). This thesis performed studies on Candidatus Magnetovibrio blakemorei strain MV-1 using STXM at the C 1s, O 1s, Ca 2p and Fe 2p edges. STXM-XMCD was used to determine the magnetism of individual magnetosomes and quantitatively determine magnetic properties such as the magnetic moment of individual chains. A sub-population of MV-1 cells was identified as having anomalous magnetic orientations of magnetosome sub-chains when separated spatial gaps. The frequency of this event and the underlying implications to magnetosome formation are discussed.

Master of Science (MSc)

Scanning transmission x-ray microscopes (STXM) focus monochromatic x-rays into an intense sub-30 nm diameter spot. Samples are then positioned at the focal plane and raster scanned through the spot while the transmitted x-rays are acquired to build up images at x-ray photon energies. In addition, x-ray absorption spectroscopy (XAS) can be performed by recording image sequences over a photon energy range of interest. STXMs excel at characterizing thin sections of inhomogeneous soft matter with their combination of high spatial (<30 nm) and photon energy (<0.1 eV) resolution. However, the overarching theme of this thesis is to apply the intense, tightly focused spot of x-rays to induce spatially resolved chemical and physical changes, and directly pattern materials, primarily thin polymer films. The irradiated areas are then investigated using several types of microscopy (scanning transmission x-ray, atomic force, scanning electron) and XAS. The experiments cover three broad areas: i) Nanofabrication; realization of the smallest possible feature sizes, and fabrication schemes unique to focused x-rays with applications including nanofluidics. ii) Radiation chemistry and physics; investigating the mechanisms of radiation-induced processes such as bond formation/loss, morphological change, carbon contamination, and temperature increase. iii) X-ray optics; the spatial distribution of x-rays at a focal plane can be recorded in a thin polymer film and later read out using an atomic force microscope. Applications include feedback for optics fabrication and enhanced image processing, the ultimate goal being increased spatial resolution.

Doctor of Philosophy (PhD)

Cationic antimicrobial peptides (cAMPs) are of interest as a possible solution to the problem of bacterial resistance to antibiotics. In order to facilitate identification of useful cAMPs, the mechanism of action in killing prokaryotic cells is of interest. Robert Hancock (UBC) has proposed that charge interaction between cAMPs and the negatively-charged bacterial membrane is a major factor that contributes to the disruption of the bacterial membrane. The goal of this thesis is to contribute to the development of a method based on scanning transmission X-ray microscopy (STXM) to investigate the electrostatic interaction hypothesis as the method by which cAMPS interact with negatively charged bacterial membranes, using fluorescence microscopy (FM) as a guide. Methods were developed to generate phase-segregated lipid bilayers as model membranes on the silicon nitride membranes. C 1s, N 1s and O 1s X-ray absorption spectra of 3 lipid species - 1,2-di-(9Z-octadecenoyl)-sn-glycero-3-phosphocholine (DOPC), 1,2-dioctadecanoyl-sn-glycero-3-phosphocholine (DSPC), and 1,2-di-(9Z-octadecenoyl)-3-trimethylammonium-propane (chloride salt) (DOTAP) were obtained to be used as reference standards in future studies. FM and STXM were used to map the saturated and unsaturated domains in dried lipid bilayers exhibiting phase segregation. Attempts were also made to image the lipid bilayers under hydrated conditions using both static and flow cells. Efforts to develop a flow cell for STXM using 3D printing are outlined. The potential to evolve this line of research to enable systematic studies of protein and peptide interactions with lipid bilayers under static and dynamic conditions is discussed.

Thesis

Master of Science (MSc)

Inner-shell electron energy-loss spectroscopy (ISEELS) is an electron impact technique for the examination of inner-shell excitation of matter in the soft X-ray energy range between 20 and 1000 eV. It has long been utilized to study the core-excitation spectra of atoms and small organic or inorganic molecules. This thesis demonstrates the extension of such investigations to large organometallic complexes and organosilicon compounds in the gas phase. Measured under low momentum transfer conditions (>2.5 keV impact energy and small scattering angle, ≤2∙), where the spectra are dominated by electric-dipole-allowed transitions, ISEELS spectra have been recorded for transition metal carbonyls Fe(CO)₅, Fe₂(CO)₉ and CO₂(CO)x; metallocenes Fe(C₅H₅)₂, CH₂CH-C₅H₄FeC₅H₅, C₄H₉-C₅H₄FeC₅H₅ and Co(C₅H₅)₂; mixed-ligand complexes C₅H₅TiCl₃, C₆H₆Cr(CO)₃, organopolysilanes (CH₃)₃SiSi(CH₃)₃ and Si[Si(CH₃)₃]₄ as well as related compounds TiCl₄, C₅H₆ and (C₅H₆)₂. The spectral features have been assigned on the basis of comparison with the spectra of the free ligands and with a few previous studies of related organometallic/organosilicon species, along with extended Hückel molecular orbital calculations. The spectra provide novel insight into how inner-shell excitation spectroscopy reflects the metal-ligand bonding in these complexes and ligand-ligand interaction via the central metal atom. All the O 1s spectra are similar to each other, and the C 1s and metal 2p spectra of related compounds in a series (e.g., carbonyl complexes or metallocene derivatives) also have a similar shape, suggesting similar origins of the spectral features. Small variations through each series have been interpreted in terms of changes in the electronic structure associated with changing substituents. The metal 2p spectra are found to be surprisingly sensitive to the identity of the ligands present in the complexes and/or the character of the metal-ligand bonding. A resonance associated with the Si-Si σ* antibonding molecular orbital is identified at 102.5 eV in the Si 2p spectra of the two organosilicon compounds.

Doctor of Philosophy (PhD)

In contrast to photoabsorption techniques, which are subject to electric dipole selection rules, electron energy loss spectroscopy (EELS) can provide a more complete investigation of atomic and molecular electronic structure. This is due to the added capability of accessing dipole and/or spin forbidden electronic transitions under conditions of significant momentum transfer. This work documents the design, construction and performance of a new, high resolution, variable scattering angle, variable impact energy electron spectrometer (McVAHRES) which has been used to investigate electronic transitions in gas phase atoms and molecules under both dipole and non-dipole conditions. The home-built instrument features a complex electron optics system and a sophisticated, computer-interfaced electronics system which allows a high degree of flexibility with regards to control and acquisition. This permits a wide range of experimental conditions. New spectroscopic studies include the observation of spin-forbidden, C is core excited triplet states in C₂H₄, C₂H₂, and C₆H₆. The momentum transfer dependence of the (C 1sˉ¹, π*) ³π state of CO was also investigated. These results are compared to the results of theoretical calculations. Generalised Oscillator Strengths (GOS) as a function of momentum transfer were derived for the S 2p edge of SF6. This work greatly expands previous results reported in the literature. Finally, an interesting feature was observed in the S 2p spectrum of SF₆, which displays quadrupolar momentum transfer behaviour.

Doctor of Philosophy (PhD)

Title: The Inner Shell Electron Energy Loss Spectra of Some Cyclic Organic Molecules, Author: David C. Newbury, Location: Thode

Inner shell electron energy loss spectroscopy has been used to obtain the core excitation spectra of some cyclic molecules. Recorded under the conditions of small momentum transfer (typically 2.5 keV impact energy and small angle scattering, <5°), the spectra are equivalent to those produced by soft x-ray photoabsorption. The molecules investigated are aromatic (benzene, pyridine, furan and pyrrole), unsaturated (cyclopentene, cyclohexene and cyclo-octatetraene) and saturated (cyclopentane, cyclohexane, tetrahydrofuran, pyrrolfdine and piperdine) species. The heterocyclic species contain a single heteroatom which is either nitrogen (pyridine, pyrrole, pyrrolidine and piperdine) or oxygen (furan and tetrahydrofuran). In all cases the spectra are dominated by shape resonance features. The carbon K-shell and heteroatom K-shell spectra are quite similar indicating the transitions are to a similar set of unoccupied orbitals. In certain cases, condensed phase x-ray 'photoabsorption' spectra (recorded by partial electron yield) were available for the purposes of comparision. Such comparisions are very useful in unambiguously identifing Rydberg, π* and δ* states. As a result the carbon K-shell excitation spectrum of benzene has been reassigned. A previously unidentified class of (1s -> π*(CH2)) transitions has been identified and characterized in the spectra of the saturated molecules. All of the spectra studied show continuum resonances which could be assigned to δ*shape resonances. The saturated cyclic systems show a second continuum resonance which is attributed to the overlap of in-ring atomic orbitals. This feature is strongest in the five membered ring systems with a heteroatom. The relationship between the shape resonance position and bond length is extended to these molecules. In the cases where there is extensive delocalization the simple relationship begins to breakdown.

Thesis

Master of Science (MS)

Detailed information about the energies of the electronically excited and ionized states of atoms and molecules is of central importance to the understanding of the interaction of energetic radiation with matter. Such data permits a more complete understanding of various processes taking place in physics, chemistry or biology, with important areas of application including electron and X-ray microscopy, space physics and chemistry or any other area where energetic radiation is used. This work documents the improvements and performance of a variable scattering angle energy loss spectrometer used to investigate inner-shell electronic spectroscopy of gases and to map generalized oscillator strengths. Wide ranges of impact energy and scattering angle are used to study both electric dipole and non-dipole transitions. New spectroscopic studies include: (i) the observation of the non-dipole "B-state" in SF6 S 2 p edge at very high scattering angle (62°) and at 1550 eV impact energy, where it dominates the spectrum; (ii) the first experimental observation of the C 1s [arrow right] σg * transition in CO2 . Generalized Oscillator Strength (GOS) profiles were mapped systematically for a collection of molecules: in SF6 , the GOS for S 2p and S 2s were extended up to very high momentum transfer, while the GOS for F 1s was mapped here for the first time. GOS curves were also obtained for all edges in CO 2 , COS and CS2 , some of them revealing their shapes for the first time. Where available, the results were compared to theoretical calculations. This work greatly extends previous reported studies of GOS for inner-shell excitation.

Doctor of Philosophy (PhD)