Scanning Transmission X-Ray Microscopy

The morphology, size distributions, spatial distributions, and quantitative chemical compositions of co-polymer polyol-reinforcing particles in a polyurethane have been investigated with scanning transmission X-ray microscopy (STXM). A detailed discussion of microscope operating procedures is presented and ways to avoid potential artifacts are discussed. Images at selected photon energies in the C 1s, N 1s and O 1s regions allow unambiguous identification of styrene-acrylonitrile-based (SAN) copolymer and polyisocyanate polyaddition product-based (PIPA) reinforcing particles down to particle sizes at the limit of the spatial resolution (50 nm). Quantitative analysis of the chemical composition of individual reinforcing particles is achieved by fitting C 1s spectra to linear combinations of reference spectra. Regression analyses of sequences of images recorded through the chemically sensitive ranges of the C 1s, N 1s and O 1s spectra are used to generate quantitative compositional maps, which provide a fast and effective means of investigating compositional distributions over a large number of reinforcing particles. The size distribution of all particles determined by STXM is shown to be similar to that determined by TEM. The size distributions of each type of reinforcing particle, which differ considerably, were obtained by analysis of STXM images at chemically selective energies.

During the last two décades, scanning transmission x-ray microscopy (STXM) has evolved into a powerful characterixation tool. For best performance, STXM's are located at undulator sources at synchrotron facilities. The scarcity and expense of undulator sources and associated beamlines limits the number of available STXMs. We have successfully reexamined the use of bending magnets as a source for a STXM and implemented a interferometer controlled STXM with excellent performance at the beamline 5. 3. 2. at the Advanced Light Source. Near the carbon K-edge, periodic features with 30 nm half-period could be resolved with a zone plate that has a 40 nm outermost zone width with an energy resolution corresponding to 100 meV and an intensity of about) MHz. The design and performance of the microscope are described.

Much effort has been devoted in the last decade to determine the effects of the reduced size of nanomaterials in their physico-chemical properties. The study of size-dependent properties of nanosize minerals is now an emerging discipline in the field of mineralogy [Hochella et ...

Sixty-three iron-containing particles from five field campaigns (PELTI, ACE-Asia, MILAGRO (urban location and aloft on NCAR C-130), INTEX-B) were characterized with scanning transmission X-ray microscopy and near-edge X-Ray absorption fine structure Ledge spectroscopy (NEXAFS-STXM). Particle sizes ranged from 0.2 to 4.5 mm and were found in many types of morphologies. Iron was found to exist in many different oxidation states with average Fe(II) to Fe(II) + Fe(III) ratios ranging from 0.0 to 0.73. Twenty-two inclusions and six agglomerations were found. For 29 particles, concurrent (spatially resolved) carbon K-edge absorption spectra were collected; X-ray images suggest that in some instances, there are clear phase barriers between iron and carbonaceous regions in agglomerations and irregular particles. Occurrences of Fe(II) fractions and organic functional group abundances among particles appeared primarily in two clusters, one group high in both values and the other low in both, though consistent correlations between the two variables within each particle were not observed. The reduced form of iron on particle surfaces was observed in 16 particles, possibly suggesting atmospheric processing. For this limited set of particles, neither inferred particle source nor surface processing was by itself a strong predictor of overall Fe(II) fraction, indicating that both are important for variables contributing to the observed Fe(II) fraction in the atmosphere. In addition, seven spherical particles from the ACE-Asia campaign showed an iron shell with an absence of iron toward the core. These particles have carbon spectra characteristics consistent with tarballs described by Posfai et al. (2004), Hand et al. (2005), and Tivanski et al. (2007), which were previously identified as homogeneous carbon spherules. In this work, NEXAFS-STXM has detected heterogeneities in iron distribution and redox state over individual particles, showing the existence of a variety of types of iron particles in the atmosphere. Such information can be useful in improving models of iron particles, including deposition and fate in seawater.

Rare-earth-based (RE) nanolaminates have attracted attention recently because of their complicated magnetism and their potential as precursors for strongly correlated two-dimensional materials. In this work, we synthesized a class of nanolaminates with a Mo 4 RE 4 Al 7 C 3 chemistry, where RE = Ce or Pr. Powder samples of both phases were characterized with respect to structure and composition. Single crystals of Mo 4 Ce 4 Al 7 C 3 were used for magnetization measurements. The crystal structure was investigated by means of x-ray diffraction and scanning transmission electron microscopy. Magnetization analysis reveals a ferromagnetic ground state with a Curie temperature of ∼10.5 K. X-ray absorption near-edge structure provides experimental evidence that Ce is in a mixed-valence state. X-ray magnetic circular dichroism shows that only the Ce atoms with 4f 1 configuration occupying one of the two possible sites are ferromagnetically coupled, with a saturation moment of ∼1.2 μ B per atom. We thus classify Mo 4 Ce 4 Al 7 C 3 as a ferromagnetic, mixed-valence compound.

Aggregation of Aldrich humic acid at pH 4. 3 and after loading with Eu (III)-cations at pH 5. 3 is investigated by scanning transmission X-ray microscopy (STXM). C Is-NEXAFS spectra extracted from STXM image stacks for the low pH aggregates show no significant variation, whereas Eu (III)-humate formation is observed to be accompanied by ségrégation into zones with différent optical densities. Thèse zones exhibit distinctly différent NEXAFS features, indicative of the présence of a separation of organic species or components. Increasing humate aggregate densification over a period of several months is observed. The spectrum of the unloaded HA cannot be reproduced by a superposition of spectra extracted from the segregated humate zones ; there is a distinct métal bonding effect on the molecular states of the functional groups involved in complexation.

Iron and manganese are poorly soluble elements in oxic and alkaline solutions, whereas they are much more soluble under anoxic conditions. As a result, the formation of authigenic mineral phases rich in Fe and/or Mn has traditionally been viewed as diagnostic of global or local anoxic conditions. Here we reveal that some specific cyanobacteria of very small size (< 2 µm, i.e., picocyanobacteria) can biomineralize abundant, authigenic Fe(III)-, Mn(IV)-and Sirich amorphous phases under oxic conditions in an alkaline lake in Mexico. The resulting biominerals cluster as small globules arranged as rings around the division septum of cyanobacterial cells. These rings are enveloped within an organic, likely polysaccharidic envelope and are partially preserved, at least morphologically, upon sedimentation. Based on their 16S rDNA sequence, these cyanobacteria were affiliated with the Synechococcales order. The high Fe and Mn enrichment of the biominerals questions the systematic inference of anoxic conditions based on their detection. Moreover, this process scavenges iron from the water column, an overlooked biological contribution to the Fe cycle. Finally, it reveals a new case of controlled biomineralization of Si-rich phases by bacteria.

Iron (Fe) is an essential trace element required for healthy brain function. Yet, disrupted iron neurochemistry, and the associated formation of aberrantly aggregated protein lesions has been implicated in the development of multiple degenerative brain disorders including Alzheimer's disease (AD). Here, nanoscale resolution soft X-ray spectromicroscopy is used to examine the interaction of β-amyloid (Aβ), a peptide fundamentally implicated in the development of Alzheimer's, and ferric (Fe 3+) iron. Crucially, by probing the carbon K (280-320 eV) and iron L 2,3 (700-740 eV) edges, both the organic and inorganic (iron) sample chemistry was established. The co-aggregation of Aβ and iron is known to influence iron chemistry, resulting in the chemical reduction of Fe 3+ into reactive and potentially toxic ferrous (Fe 2+) and zerooxidation (Fe 0) states. Here, nanoscale (i.e. sub-micron) variations in both iron oxidation state and the organic composition of Aβ were observed, replicating in vitro the diverse iron chemistry documented in amyloid plaques from human brain, with the chemical state of iron linked to the conformation state of Aβ. Furthermore, aggregates were formed that were morphologically and chemically distinct dependent on the treatment of Aβ prior to the addition of ferric iron. These findings support the hypothesis that Aβ is responsible for altering iron neurochemistry, and that this altered chemistry is a factor in neurodegenerative processes documented in AD. The methods applied here, combining nanoscale-resolution imaging and high chemical sensitivity, enabled discovery of the nanoscale heterogeneity in the iron and carbon chemistry of in vitro aggregates, and these approaches have scope for wider application in metallomics. † Electronic supplementary information (ESI) available. See

Atypical low-oxidation-state iron phases in Alzheimer’s disease (AD) pathology are implicated in disease pathogenesis, as they may promote elevated redox activity and convey toxicity. However, the origin of low-oxidation-state iron and the pathways responsible for its formation and evolution remain unresolved. Here we investigate the interaction of the AD peptide β-amyloid (Aβ) with the iron storage protein ferritin, to establish whether interactions between these two species are a potential source of low-oxidation-state iron in AD. Using X-ray spectromicroscopy and electron microscopy we found that the co-aggregation of Aβ and ferritin resulted in the conversion of ferritin’s inert ferric core into more reactive low-oxidation-states. Such findings strongly implicate Aβ in the altered iron handling and increased oxidative stress observed in AD pathogenesis. These amyloid-associated iron phases have biomarker potential to assist with disease diagnosis and staging, and may act as targ...

The origin of anisotropy at the molecular and electronic structure levels in individual β-Ga 2 O 3 nanowires grown along the crystallographic b direction was studied using linearly polarized X-ray absorption imaging at both gallium L 3 and oxygen K edges. The O K-edge spectrum shows significant linear dichroism for the electric field vector of the X-rays oriented parallel and perpendicular to the nanowire long axis. The contributions from the three nonequivalent oxygen sites to the observed spectral anisotropy were elucidated by using FDMNES calculations in the framework of the multiple scattering theory. The role of relevant O and Ga orbitals in the linearly polarized O K-edge absorption was determined based on the point group symmetry arguments. The results of this work suggest mixed covalent and ionic character of the Ga−O bond in individual nanowires, with the dominant contribution of O 2p z orbitals to the absorption spectrum for the electric field vector oriented perpendicular, and O 2p x,y orbitals for the electric field vector oriented parallel to the nanowire long axis. Gallium 4p and d orbitals were found to contribute mostly to the antibonding states. These results improve the understanding of the origin of anisotropy in complex transparent metal oxide nanostructures, and could lead to the prediction of physical properties for different nanowire growth directions.

P K-edge EXAFS spectroscopy has been used to determine the local environment of phosphorus during the hydrolysis of FeCl3 in the presence of phosphate. Measurements were performed on liquid samples and in the fluorescence mode. With the detection geometry adopted during experiments, the self absorption of fluorescence has been quantified and does not appear to be an important phenomenon. Thus no correction was made. In order to clearly identify the neighboring atoms around P, a multiple scattering approach has been used. Multiple scattering seems to be an important phenomenon in PO 4/FeCl3 clusters. P K-edge EXAFS data show that even for very acidic solutions, pH < 1, all the phosphate ions are complexed to Fe. For a P/Fe molar ratio of 0.2 one phosphate progressively bonds one, two, and three irons when n ()[OH]/ [Fe]) increases from 0 to 2.0. At n) 2, one phosphate bridges three iron dimers and two kinds of PO 4-Fe linkages are detected. For P/Fe) 0.5, the number of irons linked to PO4 increases when n increases but does not exceed 2. Thus P K-edge EXAFS spectroscopy combined with a multiple scattering approach allowed us to confirm previous results obtained by EXAFS at the Fe K-edge as well as to describe more precisely the type of linkage between the PO4 tetrahedron and the Fe octahedra.

Reliable basin and petroleum system models (BPSM) require accurate kinetic parameters for the conversion of source-rock kerogen to petroleum. The purpose of this paper is to dispel widespread uncertainty about kinetic input to BPSM by providing guidelines based on interpretation of previously published data for 81 worldwide source rocks containing various kerogen types. • Kinetic response is unrelated to kerogen type as defined by Rock-Eval pyrolysis hydrogen index. Default kinetics in BPSM software may differ from that for the same kerogen type in different study areas. Use default kinetics with caution when appropriate measured kinetics are unavailable. • Measure kinetic parameters using thermally immature equivalents of the source rock, which may require multiple samples because kerogen kinetics can vary laterally and vertically in each source rock. • Descriptions of depositional environment are insufficient to define kerogen type or kinetic response in different basins. • Optimize multiple-run programmed pyrolysis results for both the activation energy (E a) and frequency factor (A). Assuming a universal value of A rather than optimizing both E a and A can yield temperature errors of 20°C or more when extrapolated to geologic time. • Alternative kinetic models to calculate vitrinite reflectance (R o) may be more accurate than Easy%R o for BPSM calibration. In the Aurora-1 and Inigok-1 wells in Alaska, Basin%R o and Easy%R o DL, more accurately replicates the dogleg in vitrinite reflectance versus depth commonly observed in wells at depths corresponding to ∼0.7-1.0% R o .

The study of various oxidation states of chromium with Sargassum sp. is of particular interest since hexavalent chromium is reduced to trivalent chromium in an aqueous solution. In this study, a systematic density functional theory (DFT) calculations were performed to study the interactions of transition metal chromium ion with different oxidation states and spin states with the Sargassum sp. decorated with carboxylate (acetate) at the wB97XD/6-311++ G(d,p) level of theory. The structures and binding energies of chromium metal-carboxylate complexes at various oxidation states and spin states in gas phase were examined. The coordination strength of Cr(VI) with the acetate ligand was predominantly the strongest compared to the other oxidation states. Vibrational frequency analysis, for the homoleptic monomers of tris [Cr III (AC) 3 ] 0 and [Cr VI (AC) 3 ] 3+ complexes, illustrate good harmony with the experimental and theoretical calculated frequencies. Using the time-dependent DFT (TD-DFT) at the level of CAM-B3LYP/6-311++G(d,p), the vertical excitation energies were obtained. The stabilization energies derived using the second order perturbation theory, E ij (2) , of NBO analysis confirmed the greater charge transfer for the observed trends in the metal binding. The calculated binding energies (ΔE) and interactions energies ΣE ij (2) favor the formation of [Cr VI (AC) 3 ] 3+ complexes. The findings of this study identify efficient electronic factors as major contributors to the metal binding affinities, with promising possibilities for the design of metal-ligand complexes and sensing of the metal ions.

We report various synchrotron radiation laboratory based techniques used to characterize cement based materials in nanometer scale. High resolution X-ray transmission imaging combined with a rotational axis allows for rendering of samples in three dimensions revealing volumetric details. Scanning transmission X-ray microscope combines high spatial resolution imaging with high spectral resolution of the incident beam to reveal X-ray absorption near edge structure variations in the material nanostructure. Microdiffraction scans the surface of a sample to map its high order reflection or crystallographic variations with a micron-sized incident beam. High pressure X-ray diffraction measures compressibility of pure phase materials. Unique results of studies using the above tools are discussed-a study of pores, connectivity, and morphology of a 2,000 year old concrete using nanotomography; detection of localized and varying silicate chain depolymerization in Al-substituted tobermorite, and quantification of monosulfate distribution in tricalcium aluminate hydration using scanning transmission X-ray microscopy; detection and mapping of hydration products in high volume fly ash paste using microdiffraction; and determination of mechanical properties of various AFm phases using high pressure X-ray diffraction.

A whole A549 cell and isolated nuclei of HeLa S3 cells in the apoptotic process were investigated by using a scanning transmission X-ray microscope (STXM) in the UVSOR Synchrotron (Okazaki, Japan). Near edge X-ray absorption fine structures (NEXAFS) of DNA and histone in the N K-edge region were measured as reference and their distribution in the nuclei was determined by using these reference spectra. The four stages of the apoptosis were successfully distinguished.

A sample cell for performing computed tomography (CT) was developed. The 3dimensional (3D) structure of polystyrene spheres was observed and the fluctuation of reconstructed linear absorption coefficients (LAC) was 9.3%. To improve the quality of data in 3D spectro-microscopy, required measurement condition is discussed.

This investigation studies the various magnetic behaviors of graphene oxide (GO) and reduced graphene oxides (rGOs) and elucidates the relationship between the chemical states that involve defects therein and their magnetic behaviors in GO sheets. Magnetic hysteresis loop reveals that the GO is ferromagnetic whereas photo-thermal moderately reduced graphene oxide (M-rGO) and heavily reduced graphene oxide (H-rGO) gradually become paramagnetic behavior at room temperature. Scanning transmission X-ray microscopy and corresponding X-ray absorption near-edge structure spectroscopy were utilized to investigate thoroughly the variation of the C 2p(π*) states that are bound with oxygen-containing and hydroxyl groups, as well as the C 2p(σ*)-derived states in flat and wrinkle regions to clarify the relationship between the spatially-resolved chemical states and the magnetism of GO, M-rGO and H-rGO. The results of X-ray magnetic circular dichroism further support the finding that C 2p(σ*)-de...

Interfaces between minerals and water, and minerals and microbes, are chemically complex and have traditionally been considered beyond the capabilities of surface science techniques, except for model systems under controlled laboratory conditions. We report on some advances in soft xray spectroscopy and imaging that make it possible to extract meaningful chemical information about interfaces of specimens that have complex histories, involving environmental exposure. These measurements utilize x-ray absorption spectroscopy, in combination with spatial resolution, in a technique called x-ray spectro-microscopy. Examples are drawn from attempts at Mn and Fe speciation of biologically produced minerals, bio-corrosion deposits, and clays.

Reliable basin and petroleum system models (BPSM) require accurate kinetic parameters for the conversion of source-rock kerogen to petroleum. The purpose of this paper is to dispel widespread uncertainty about kinetic input to BPSM by providing guidelines based on interpretation of previously published data for 81 worldwide source rocks containing various kerogen types. • Kinetic response is unrelated to kerogen type as defined by Rock-Eval pyrolysis hydrogen index. Default kinetics in BPSM software may differ from that for the same kerogen type in different study areas. Use default kinetics with caution when appropriate measured kinetics are unavailable. • Measure kinetic parameters using thermally immature equivalents of the source rock, which may require multiple samples because kerogen kinetics can vary laterally and vertically in each source rock. • Descriptions of depositional environment are insufficient to define kerogen type or kinetic response in different basins. • Optimize multiple-run programmed pyrolysis results for both the activation energy (E a) and frequency factor (A). Assuming a universal value of A rather than optimizing both E a and A can yield temperature errors of 20°C or more when extrapolated to geologic time. • Alternative kinetic models to calculate vitrinite reflectance (R o) may be more accurate than Easy%R o for BPSM calibration. In the Aurora-1 and Inigok-1 wells in Alaska, Basin%R o and Easy%R o DL, more accurately replicates the dogleg in vitrinite reflectance versus depth commonly observed in wells at depths corresponding to ∼0.7-1.0% R o .

The aim of the present study was to investigate the porosity of the Posidonia shale as a potential gas shale and to compare the results with data published on gas shales known to be productive. The characterization of the porosity of clays and shales still poses an analytical challenge, however. Different methods were investigated based on a comparison of four different Posidonia shales, with different degrees of maturity. Both direct microscopical methods as well as indirect methods based on gas adsorption or Hg intrusion were applied. Most of the pores in clays and shales were too small to be detected by any of the existing direct methods. About 80% of the pores were ,30 nm wide. The Posidonia shales, as is the case with most shales, are dominated by mesoporosity (ranging from 20 to 50 mm 3 /g). The mesopore peak representing the average pore diameters could be resolved by Hg intrusion and was found to decrease with increasing maturity which may be explained by increased compaction and/or temperature. This relation, if not applicable to the entire Posidonia shale, may be restricted to a single sedimentary system (e.g. a basin or a sequence). The results of the indirect methods (except for CO 2 microprosity) were comparable and this might be explained by the low macroporosity. The most important question concerning shale-gas production and porosity relates to the pore diameter needed to allow gas migration. Natural gas in micropores may be bound too strongly to liberate it without low pressure/vacuum. For gas production either meso-or macropores may be important. Notably, all methods used for characterization of porosity were performed on dry samples. A nm-scale connectivity determined at an illite-smectite interface pore is not supposed to provide a gas pathway in the water-saturated state. Prediction of the gas-production potential from porosity measurements has not been possible to date, therefore. Taking the organic carbon content, vitrinite reflectance, and comparison of the porosity with that of North American gas shales into account, however, indicates potential for the Posidonia shale which still has to be proven by shale-gas production tests.

Situation in the ocean is even more complicated due to Light scattering data measured in various sites ranging from great polydispersity in sizes, shapes, and properties of aggreopen ocean to coastal and harbor waters have been analyzed. The gating particles. Using a dimensional analysis based on fracdependence of scattered light intensity on scattering vector shows tal scaling relationships, Jiang and Logan (11) calculated two distinctive q regions. This I(q) behavior is consistent with the fractal dimensions of aggregates formed in marine systems. two component model of sea particle size distribution. The average For aggregates formed from differential sedimentation and particle fractal dimensions estimated from these data are 1.7 { shear coagulation they determined 1.61 £ D £ 2.31 and 2.4 0.1 for small q values (q £ 2.5 mm 01) and 2.7 { 0.4 for large £ D £ 3.75, respectively. They were not able to calculate q values. These fractal dimensions correspond to cluster-cluster aggregation of larger (B component) particles due to differential the fractal dimension for aggregates formed from Brownian sedimentation and to shear induced particle-cluster aggregation coagulation by use of the dimensional analysis. However, of smaller (A component) particles. They also agree with the fraccomputer simulations verified experimentally by measuretal properties of microaggregates obtained from the recent simulament of fractal dimensions of a variety of aggregates formed tion of phytoplankton bloom in a mesocosm.

The spatial distribution of the linear dichroic signal associated with aligned-sheets in a microtomed section of a Bombyx mori cocoon silk fiber was derived from scanning transmission X-ray microscopy (STXM). The intense C 1s f π* amide peak at 288.25 eV was found to have negligible dichroic signal in transverse sections but a large dichroic signal in longitudinal sections. This is consistent with other measurements of the orientation of the aligned-sheets in silk fibers, in particular with those obtained by polarized Raman microspectroscopy to which our results are compared. When the dichroic signal strength is mapped at better than 100 nm spatial resolution, microscopic variations are found. Although the magnitude of the dichroic signal changes over a fine spatial scale, the direction of the maximum signal at any position does not change. We interpret the spatial variation of the intensity of the dichroic signal as a map of the quality of local orientation of the-sheets in the fiber. At sufficiently high magnification and resolution, this technique should image individual-sheet crystallites, although the present implementation does not achieve that. A map of the orientation parameter 〈P 2 〉 is derived. The average value of 〈P 2 〉 (-0.20 (0.04) from STXM is smaller than that derived from the analysis of the amide I band in polarized Raman spectra (-0.41 (0.03). This deviation is attributed to the fact that the STXM results also include the signal from unaligned regions of the protein.

Strongly correlated electronic systems such as Transition Metal Oxides often possess various mid-gap states originating from intrinsic defects in these materials. In this paper, we investigate an extremely sharp Photoluminescence (PL) transition originating from such defect states in two widely used perovskites, LaAlO3 and SrTiO3. A detailed study of the PL as a function of temperature and magnetic field has been conducted to understand the behavior and origin of the transition involved. The temperature dependence of the PL peak position for SrTiO3 is observed to be opposite to that in LaAlO3. Our results reveal the presence of a spin/orbital character in these transitions which is evident from the splitting of these defect energy levels under a high magnetic field. These PL transitions have the potential for enabling non-contact thermal and field sensors.

tion of reactive groups on the surface of the particles is During the preparation of silica by acidi®cation of water glass, stochastic, directions of particle–particle bonds are rather primary silica particles form extended and rami®ed aggregates. arbitrary and therefore particle–particle interactions result The growing aggregates form a gel, a tenuous network of intercon- in tenuous aggregates with an amorphous structure. Interac-nected aggregates. After aging and drying of the wet gel, porous tions are not restricted to particle–particle or particle–aggre-silica is obtained. To study the extremely vulnerable aggregates gate bonds, and interactions between aggregates or clustersonly noninvasive methods are allowed. Moreover, because of the of particles are also possible, leading to highly ramified andcolloidal scale many methods based on (atomic or molecular scale) extended aggregates.spectroscopy are not informative. Scanning transmission x-ray mi-Polymerization or particle format...

This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

like to thank him for the valuable input, careful supervision and outstanding support he provided during the course of my studies. Furthermore, I thank Prof. Dr. Brian Horsfield, GFZ, for his work as reviewer of this thesis. I sincerely thank Dr. Bernhard M. Krooss, Dr. Amin Ghanizadeh and Reinhard Fink for introducing me to the petrophysical analytical procedures utilized in this thesis. Their constant support and the resulting fruitful discussions are much appreciated and deepened my understanding of petrophysics significantly. A special gratitude goes to Dr. Benjamin Bruns and Dr. Victoria Sachse for their continuous and tireless support regarding the building of a 3D high resolution basin model. In this context, I thank Schlumberger for providing an academic license of the PetroMod software. I sincerely like to acknowledge and thank my friends, fellows and colleagues at the Institute of Geology and Geochemistry of Petroleum and Coal who accompanied me over the last years and provided an outstanding work environment. My deepest regards go to my wife Charlotte, who constantly and relentlessly supported and encouraged me during the creation of this thesis.

Research Highlights: • Samples rich in vitrodetrinite are common both in marginal and basinal positions • Coaly layers were exclusively found in the Søgne and Cod areas • A correlation of TOC with liptinite percentages indicates enhanced bioproductivity or preservation efficiency • Nitrogen sorption data indicate that the soluble organic matter fraction represents the controlling factor on micro-and mesopores • Small mesopores are mainly associated with the high-molecular weight bituminous fraction, which appears non-porous at SEM-scale • The total inner surface area decreases with thermal maturity ABSTRACT The Upper Jurassic Mandal Fm. of the Central Graben, Norway represents an important source rock that charged major petroleum accumulations in the North Sea, including the giant Ekofisk field. Nevertheless, exploration to date has been less successful than expected in marginal basin position such as the Cod Terrace, the Mandal High or the Søgne Basin, probably due to higher proportions of thermally stable (type III) kerogen. In an attempt to delineate changes in initial kerogen composition from later effects such as delayed expulsion of hydrocarbons, traditional organic petrography and scanning electron microscopy were combined with organic geochemical proxies and gas adsorption tests. The kerogen composition of the Mandal Fm. shows considerable variation. Samples hosting autochthonous coaly layers were found in wells from the Søgne Basin and the Cod Terrace, for which less generative potential was previously postulated. Nevertheless, samples hosting mainly vitrodetrinite were also found in basinal wells. A correlation of total organic carbon contents with liptinite percentages highlights enhanced bioproductivity or preservation efficiency for samples with abundant algal organic matter, that were likely deposited under deeper water and possibly oxygen-depleted conditions. By combining organic geochemical proxies with nitrogen sorption data, it could be proven that in case of the Mandal Fm., the (bituminous) organic matter fraction represents the controlling factor on abundance of micro-and mesopores and hence adsorptive gas retention. The amount of bitumen extractable from the Rock-Eval S2 peak (S2bitumen) shows a strong correlation with the total inner surface area, suggesting that small mesopores (<10-15 nm) are mainly associated with the high-molecular bituminous fraction represented by the S2bitumen, which appears nonporous at SEM-scale. Furthermore, the total inner surface area decreases strongly with thermal maturity, documenting a change in pore characteristics of the organic matter fraction (growth of mesopores and occurrence of macropores) by advancing hydrocarbon generation. Pyrobitumen-rich Upper Visean reference samples at peak oil and early wet gas window maturity show intense sponge-like pyrobitumen-hosted porosity coinciding with a low relative proportion of S2bitumen (high petroleum quality). Pyrobitumen is not affected by solvent extraction, thus not contributing high-molecular weight compounds to the extracted fraction. Such inert meso-to macroporous residues might contribute only relatively little to gas sorption capacity, but might represent important storage space for free gas, as well as flow pathways during expulsion.

This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

Petroleum is retained in shales either in a sorbed state or in a free form within pores and fractures. In shales with oil resource potential, organic matter properties (i.e. richness, quality and thermal maturity) control oil retention in general. In gas shales, organic pores govern gas occurrence. While some pores may originate via secondary cracking reactions, it is still largely unclear as to how these pores originate. Here, we present case histories mainly for two classic shales, the Barnett Shale (Texas, USA) and the Posidonia Shale (Germany). In both cases, shale intervals enriched in free oil or bitumen are not necessarily associated with the layers richest in organic matter, but are instead associated with porous biogenic matrices. However, for the vast bulk of the shale, hydrocarbon retention and porosity evolution are strongly related to changes in kerogen density brought about by swelling and shrinkage as a function of thermal maturation. Secondary organic pores can form only after the maximum kerogen retention (swelling) ability is exceeded (at Tmax around 445 o C, ~0.8%Ro). Shrinkage of kerogen itself leads to the formation of organic nano-pores, and associated porosity increase, in the gas window.

Magnetism in graphene has been found to originate from various defects, e.g., vacancy, edge formation, add-atoms etc. Here, we discuss about an alternate route of achieving magnetism in graphene via grain boundary. During chemical vapor deposition of graphene, several graphene nucleation centers grow independently and face themselves with unusual bonding environment, giving rise to the formation of grain boundaries. We investigate the origin of magnetism in such grain boundaries within first-principles calculations, by letting two nucleation centers interact with each other at their interface. We observe formation of unprecedented point defect, consisting of fused three-membered and larger carbon rings, which induces net magnetization to graphene quantum dots. In case of periodic lattices, the appearance of array of point defects leads to the formation of magnetic grain boundaries. The net magnetization on these defects arises due to the deviation from bipartite characteristics of p...

A non-toxic, fast, low-cost, single step and highly efficient reduction method is proposed in this research for the development of high-quality multilayer graphene film using laser diode. Graphene oxide film is irradiated with a diode laser (808 nm, 6 W) for different exposure times (1, 1.5, 2, 2.5, and 3 min.) to reduce it. Surface damage was observed on the graphene oxide (GO) film for exposure time greater than 3 min and at power 6 W. Different measurement techniques (Raman spectroscopy, Uv-visible absorption, photoluminescence and FTIR) are used to study the optical properties of rGO films. After laser irradiation, the Raman spectra of rGO films showed peaks for the D, G, and 2D bands centered at 1335, 1581, and 2710 cm −1 , respectively. A small increase in the (I D /I G) ratio was observed and showed that greater reduction occurred after the graphene oxide film exposure time of 3 min. The as-prepared film of graphene oxide that showed absorption peak at 235 nm was red-shifted to 270 nm after 3 min of laser diode irradiation for reduction. The PL measurements were performed, where the sample was excited by Ar-ion laser (488 nm) and the PL signal was amplified using lock in techniques. The photoluminescence emission spectrum was measured at different positions on the graphene oxide film reduced for 3 min to show the effect of the energy spatial distribution of the laser diode beam on the rGO film. The maximum PL peaks gradually blue shifted and the peak intensities decreased as the measurements go toward the center of the reduced film. The FT-IR spectrum revealed that there are no hydroxyl, carboxyl, and epoxy groups and new peaks were found assigned to functional groups such as CH 2 , C-H by reducing the graphene oxide with laser diode for 3 min.

The infrared beamline at the Swiss light source uses dipole radiation and is designed to transport light to four experimental stations, A, B, C, D. Branch A is dedicated to far IR work in vacuum; branch B is a micro-spectrometer; branch C is dedicated to high resolution spectroscopy in the gas phase; branch D is a pump and probe setup. This contribution describes the optical layout and provides a brief survey of currently available experimental stations. The beamline is in regular user operation since 2009.

Minerals formed by bio-oxidation of ferrous iron (Fe(II)) at neutral pH, their association with bacterial ultrastructures as well as their impact on the metabolism of iron-oxidizing bacteria remain poorly understood. Here, we investigated iron biomineralization by the anaerobic nitrate-dependent iron-oxidizing bacterium Acidovorax sp. strain BoFeN1 in the presence of dissolved Fe(II) using electron microscopy and Scanning Transmission X-ray Microscopy (STXM). All detected minerals consisted mainly of amorphous iron phosphates, but based on their morphology and localization, three types of precipitates could be discriminated: (1) mineralized filaments at distance from the cells, (2) globules of 100 ± 25 nm in diameter, at the cell surface and (3) a 40-nm thick mineralized layer within the periplasm. All of those phases were shown to be intimately associated with organic molecules. Periplasmic encrustation was accompanied by an accumulation of protein moieties. In the same way, exopolysaccharides were associated with the extracellular mineralized filaments. The evolution of cell encrustation was followed by TEM over the time course of a culture: cell encrustation proceeded progressively, with rapid precipitation in the periplasm (in a few tens of minutes), followed by the formation of surface-bound globules. Moreover, we frequently observed an asymmetric mineral thickening at the cell poles. In parallel, the evolution of iron oxidation was quantified by STXM: iron both contained in the bacteria and in the extracellular precipitates reached complete oxidation within 6 days. While a progressive oxidation of Fe in the bacteria and in the medium could be observed, spatial redox (oxido-reduction state) heterogeneities were detected at the cell poles and in the extracellular precipitates after 1 day. All these findings provide new information to further the understanding of molecular processes involved in iron biomineralization by anaerobic iron-oxidizing bacteria and offer potential signatures of those metabolisms that can be looked for in the geological record.

We report various synchrotron radiation laboratory based techniques used to characterize cement based materials in nanometer scale. High resolution X-ray transmission imaging combined with a rotational axis allows for rendering of samples in three dimensions revealing volumetric details. Scanning transmission X-ray microscope combines high spatial resolution imaging with high spectral resolution of the incident beam to reveal X-ray absorption near edge structure variations in the material nanostructure. Microdiffraction scans the surface of a sample to map its high order reflection or crystallographic variations with a micron-sized incident beam. High pressure X-ray diffraction measures compressibility of pure phase materials. Unique results of studies using the above tools are discussed-a study of pores, connectivity, and morphology of a 2,000 year old concrete using nanotomography; detection of localized and varying silicate chain depolymerization in Al-substituted tobermorite, and quantification of monosulfate distribution in tricalcium aluminate hydration using scanning transmission X-ray microscopy; detection and mapping of hydration products in high volume fly ash paste using microdiffraction; and determination of mechanical properties of various AFm phases using high pressure X-ray diffraction.

Soft x-ray scanning transmission x-ray microscopy allows one to image dry and wet environmental science, biological, polymer, and geochemical specimens on a nanoscale. Recent advances in instrumentation at the X-1A beamline at the National Synchrotron Light Source at Brookhaven National Laboratory are described. Recent results on Nomarski differential phase contrast and first results of investigations at the oxygen K edge and iron L edge of hydrous ferric oxide transformations are presented.

Amazonian Dark Earths (ADE) are a unique type of soils developed through intense anthropogenic activities that transformed the original soils into Anthrosols throughout the Brazilian Amazon Basin. We conducted a comparative molecularlevel investigation of soil organic C (SOC) speciation in ADE (ages between 600 and 8700 years B.P.) and adjacent soils using ultraviolet photo-oxidation coupled with 13 C cross polarization-magic angle spinning nuclear magnetic resonance (CP-MAS NMR), synchrotron-based Fourier transform infrared-attenuated total reflectance (Sr-FTIR-ATR) and C (1s) near edge X-ray absorption fine structure (NEXAFS) spectroscopy to obtain deeper insights into the structural chemistry and sources of refractory organic C compounds in ADE. Our results show that the functional group chemistry of SOC in ADE was considerably different from adjacent soils. The SOC in ADE was enriched with: (i) aromatic-C structures mostly from Hand C-substituted aryl-C, (ii) O-rich organic C forms from carboxylic-C, aldehyde-C, ketonic-C and quinine-C, and (iii) diverse group of refractory aliphatic-C moieties. The SOC in adjacent soils was predominantly composed of O-alkyl-C and methoxyl-C/N-alkyl-C structures and elements of labile aliphatic-C functionalities. Our study suggests that the inherent molecular structures of organic C due to selective accumulation of highly refractory aryl-C structures seems to be the key factor for the biochemical recalcitrance and stability of SOC in ADE. Anthropogenic enrichment with charred carbonaceous residues from biomass-derived black C (BC) is presumed to be the precursor of these recalcitrant polyaromatic structures. Our results also highlight the complementary role that might be played by organic C compounds composed of O-containing organic C moieties and aliphatic-C structures that persisted for millennia in these anthropic soils as additional or secondary sources of chemical recalcitrance of SOC in ADE. These organic C compounds could be the products of: (i) primary recalcitrant biomolecules from non-BC sources or (ii) secondary processes involving microbial mediated oxidative or extracellular neoformation reactions of SOC from BC and non-BC sources; and stabilized through physical inaccessibility to decomposers due to sorption onto the surface or into porous structures of BC particles, selective preservation or through intermolecular interactions involving clay and BC particles.

Humic acid (HA) agglomerates formed in aqueous solutions in the presence of trivalent Eu cations were investigated in situ with a combination of atomic force microscopy (AFM) and scanning transmission X-ray microscopy (STXM). The micromorphologies of both natural HA and a melanoidine based synthetic HA observed by AFM in electrolyte solution are in fair agreement with previous AFM studies on humic substances. STXM micrographs of Eu(III) induced HA agglomeration reveal zones of high and low optical density with markedly distinct C K-NEXAFS, indicative of different humic functionalities. Particulate agglomerates observed by AFM can be correlated to the dense zones, whereas fibrous structures in AFM images can be associated with the low density areas. The Eu cation distribution within the agglomerates cannot be unambiguously deduced from their C K-NEXAFS spectra. The near edge X-ray absorption fine structure spectra can be correlated to a segregation of different HA fractions, possibly due to the presence of humic species with different affinities for metal cation complexation. STXM micrographs of purified Aldrich HA exhibit the presence of other yet unidentified, carbon-rich particles, independent of the addition of Eu(III). Both AFM and STXM results for the synthetic melanoidine based HA demonstrate a homogeneous morphology and chemical structure.