Individual aerosol particles from an urban background site in Mainz (Germany), a traffic hotspot site in Essen (Germany), the free troposphere in the Swiss Alps (high altitude research station Jungfraujoch), a rural background/marine site on Cyprus (Cyprus Atmospheric Observatory) and a rural background site in the forested area of Odenwald (Germany) were characterised with two different scanning electronmicroscopy techniques, operator controlled (opSEM) and computer controlled (ccSEM). For all samples, about 500 particles were investigated by opSEM, and between 1103 and 6940 particles by ccSEM. Large systematic differences (in some cases a factor up to ~ 20) in the abundance of the various particle groups are observed in the results of the two techniques. These differences are dependent on particle type and size. With ccSEM, information on the mixing state of particles (e.g., presence of heterogeneous inclusions, surface coatings or gradients in chemical composition) cannot be obtained, and particle groups which are recognised by their complex morphology (e.g., soot and fly ash particles) are classified into other particle groups. In addition, highly volatile particles (i.e., particles which evaporate under electron bombardment within seconds) will be overlooked by ccSEM. If these limitations of ccSEM are not considered, normalising the particle group abundances to 100% (a popular practise in many publications) may lead to drastic misinterpretation of the real aerosol composition. OpSEM is indispensable when detailed information of particle composition is required, although it suffers from a much higher expenditure of time. In conclusion, both techniques might be used for singleparticle characterisation as long as drawbacks of each are considered.
Scanning ElectronMicroscopy (SEM) and Transmission electron micro- scopy (TEM) are widely used for studying the physical properties of the thin films. SEM is mainly used for analysis of a surface topography and com- position [45, 46]. TEM is used for studying the interfaces [47, 48], and the structural and dynamic properties of the thin films [49, 50]. SEM resolution is 1 − 20 nm, and TEM resolution reaches 0.05 nm . An advantage of TEM is, that it is capable to get not only an image of the surface, but also diffraction patterns for the same region of the surface. TEM images reflect the periodicity of the crystal lattice since the lattice acts as a phase grating. The interpretation of the images obtained with TEM can be complicated, because it depends on the sample thickness, objective lens defocus and inter- ference effects. However, none of these methods can be used for organic thin film study because high energy electrons are capable to destroy the organic samples. TEM and SEM are widely used in industrial application, where the resolution of tens and hundreds nm is usually required.
Having adapted and described the reconstruction algorithms for low-dose con- ditions, we now turn to analyzing one of many interesting applications: the application to structure determination of single particles. We perform multi- slice simulations with slice++ of three different biological macromolecules with molecular weights ranging from 64 kDa to 4 MDa. We choose the 64 kDa he- moglobin [ 123 ], the 706 kDa 20S proteasome from yeast [ 124 ], and the 4 MDa human ribosome [ 125 ]. Hemoglobin is one of the smallest proteins imaged to date with cryo-EM, 20S proteasome is a typical test-sample because of its sym- metry, and the ribosome is an example for a large non-symmetric particle in the MDa range. We create atomic potential maps using the Matlab code InSili- coTem [ 33 ], with a thickness of 50 nm and at an electron energy of 300 keV. We use the isolated atom superposition approximation, without solving the Poisson- Boltzmann equations for the interaction between the molecule and the ions. We also do not model the amorphousness of the solvent, which was performed in [ 33 ] using molecular dynamics simulations, but was seen to have a negligible effect at very low doses. As described in [ 33 ], we model the imaginary part of the potential via the inelastic mean free path, creating a minimal transmission contrast between the vitreous ice and the protein. Using these potential maps, we simulate a ptychography experiment by cropping three-dimensional slices from the potential at several positions and propagate a coherent incoming wave through the slices using the methods described in [ 28 ] in the slice++ code. The final model for the formation of the intensity on the detector is described in section 1.2.
The method applies to a very broad photon energy since no manipulative optics or sample is needed between the focusing optics and the detector. In particular, the method enables the characterization of hard X-ray pulses measured in far-field of focusing optics without either a need for the unique fabrication process or scanning over a sample up- stream of the detector. The numerical implementation of the method discussed within this thesis shows the feasibility of the iterative method to converge reliably when the specified conditions are met for the given energy that practically allows the method applies to soft and hard x-ray beamlines, solely by a change in the generic geometry of x-ray microscopy proposed within the next chapters. As it will be shown later, for the soft and hard x-ray wave field determination the far field condition to measure diffrac- tion patterns varies in order of few meters. This realization is often compatible with the availabilities provided in most beamlines, such as those reported at the SPB/SFX instrument at the European XFEL for hard x-ray energy range or as an alternative to the softer photon energy at the FLASH beamline BL2.
Another issue that arose during analyzing the ISWI-nucleosome complexes was that the affinity of ISWI was overestimated when analyzed by gel retardation assays (EMSA) compared to in solution measurements (MST). One enormous problem for EM analysis, which derived from this finding, is that upon formation of sufficient ISWI- nucleosome complexes, the grid was over-crowded. For singleparticle analysis, the particles have to be distinguishable, but at those ISWI concentrations, nearly no complexes with the nucleosome were formed. Once the aggregation problematic is solved, one could try to shorten the incubation with the grid to prevent overcrowding. Instead, I focused on increasing the affinity of ISWI to the nucleosome by various ATP analogs and mutations in the ATPase domain. Among the ATP analogs I tested in MST, only one pre-transition state analog ADP·BeFx was able to increase the affinity of ISWI to the nucleosome. Unfortunately, exactly those conditions with an activated ATP mimetic were used to calculate a EM structure of the human ISWI homolog SNF2h (Racki et al., 2009). Another promising candidate is the Walker B mutant of ISWI (E257A), which in presence of ATP should also mimic an ATP bound state of ISWI and showed marginally higher affinity to the nucleosome compared to WT ISWI. Furthermore, the addition of other subunits such as Acf1 and the two histone-fold CHRAC subunits could further increase the affinity and should be analyzed by MST. Finally, the binding affinity results from Thermophoresis measurements could be further complemented with ATPase assays of the various mutants.
The continuous development of new solid-state lighting technologies and devices and a growing demand motivate the search for new nitridosilicate phosphors. However, structure elucidation of such new phosphors often proved difficult and time-consuming, and either large single crystals or phase-pure samples were usually necessary. Commonly, a single-particle-diagnosis approach is used, which enables the determination of luminescence and crystal structures of rather small single crystals up to 10 μm. 19 Yet, many explorative syntheses lead to inhomogeneous and microcrystalline products with crystal size below a few μm. Consequently, structure characterization with conventional single-crystal X-ray diffraction is no longer possible. Here, we apply an approach that combines transmission electronmicroscopy (TEM) and synchrotron microfocus diffraction. This method allows for the analysis of particles with a volume even smaller than 1 μm 3 and furthermore provides the possibility of analyzing the same particle by TEM and X-ray diffraction. 20 In contrast to structure determination by electron crystallography, e.g. with automated electron diffraction tomography (ADT) or rotation electron diffraction (RED), 21-25 this method allows a much more accurate determination of bond lengths, mixed occupancies and displacement parameters. Data acquired with microfocused synchrotron radiation yielded the crystal structure of the novel yellow phosphor La 3 BaSi 5 N 9 O 2 :Ce 3+ discussed in this contribution.
Scanning probe nanolithography has its origins in the microsco- py techniques of atomic force microscopy (AFM) and scanning tunneling microscopy (STM). In both cases, a probe is scanned over a sample and the interaction is used to study the sample properties. For AFM, the atomic force between a sharp tip at the end of a cantilever beam and the sample surface is measured by read-out of the cantilever bending. The STM uses the tunneling current between a tip and the surface to obtain information about the sample surface [106,107]. Scanning probe nanolithog- raphy uses the interaction of such a tip with the sample to nano- structure its surface. For the purpose of this review, scanning probe nanolithography (SPL) refers to the application of these proximity probes for nanolithography of polymeric resists and we therefore focus on electron-based SPL methods. However, we will mention briefly the diversity of SPL methods that take advantage of the multiplicity of probe–sample interaction mech- anisms [108-112]. Static or dynamic ploughing lithography (dSPL), for example, utilizes the mechanical interaction be- tween the tip and the resist, comparable to scratching [113,114]. In thermal SPL (tSPL) a heated AFM tip is used to evaporate the polymer [115,116]. In local anodic oxidation scanning probe lithography (oSPL) [117,118] a water meniscus is formed be- tween the tip and the sample due to an applied voltage. Inside this water meniscus local oxidation of the sample takes place. The resolution is limited for dSPL by the tip size and tilting during the ploughing process, for tSPL by the heat diffusion and for oSPL by the size of the water meniscus and the oxidation reaction. Using tSPL and oSPL, features with sizes in the sub- 10 nm range (dots) and pitches down to 15 nm (oSPL) can be generated [116,117].
population relaxation. Ground state levels of NV center are separated by approximately 0.14 K, thus at room temperature their are equally populated. Optical polarization of the spin results in an non-equilibrium state which exchanges energy with the lattice coming back to equilib- rium. This is why it is also called spin-lattice relaxation. Since energy separation by zero-field splitting is low, the relaxation due to spontaneous emission proportional to the cube of frequency is negligible in contrast to optical transitions. Therefore the main source of relaxation is phonon scattering. Another reason for longitudinal relaxation is interaction of the spin with fluctuating local magnetic fields, which can originate either from surrounding electron or nuclear spins in the lattice or from external spins placed close to the NV center. The latter is more important for this thesis since measurements of spin-lattice relaxation time is utilized to observe presence of a magnetic particle in the vicinity of an NV center. Thermal motion forces spins to fluctuate. If this fluctuating field has effective frequency close to the Larmor frequency of NV center then it can cause a spin flip. It should be noticed that only xy-components of the fluctuating field induce spin flip exactly in the same way how it happens in EPR. However, in contrast to magnetic resonance technique, local field produces random “microwave pulses” defined by thermal motion and thus brings system into thermodynamic equilibrium with the reservoir.
In this dissertation we present a new approach for modeling and tting large structured RNAs into cryo-EM density maps. Our homology modeling approach lead to highly accurate models of the common ribosomal core structure. Combined with cryo-EM and singleparticle analysis we were able to build de novo molecular models for the eukaryotic RNA expansion segments. The models are very similar compared to the recently published crystal structure at 4.5 Å resolution (see section 12.1.3, see Figure 12.1.2), however, structural dierences are evident (see section 12.2.2), which were expected at our resolution of 5.5 Å. Some of our models, like the highly exible ES7 L and ES27 L , are even more complete than the recent crystal structure, but need to be further validated by future high-resolution crystal structures or cryo-EM maps. Taken together, this approach of de novo and homology RNA modeling combined with cryo-EM data is extremely valid for further modeling, for example the few drastically extended and highly exible expansion segments in Drosophila melanogaster or Homo sapiens, which certainly will not be crystallized in the near future. Moreover, the modeling approach can be applied to other large RNA complexes.
Research on carbon nanotubes has progressed rapidly since the first experimental ob- servation of carbon nanotubes, using transmission electronmicroscopy, as reported by Iijima in 1991 . Carbon nanotubes are graphene sheets rolled into hollow cylinders. Owing to their small size, a diameter on the order of nanometers and length on the order of microns, they can be regarded as large molecules or as quasi- one dimensional condensed matter with translational periodicity along their tube axis. The various structures of carbon nanotubes are due to the large variety of possible helical geometries. One of their most significant physical properties is the strong dependence of their electronic structure on their geometry. Although com- posed only from carbon atoms, their electronic band structure is either metallic or semiconducting in nature. This unique property, which depends solely on the com- bination of diameter and chirality, and does not require additional doping, is unique to solid state physics. Further, the energy gap of semiconducting carbon nanotubes can essentially vary continuously only by modifying the nanotube diameter. On this basis, various electronic applications are envisioned, such as: nanotube based- transistors, -sensors, -interconnectors, -field emission displays, -conductive coatings and more [2–8]. Metallic carbon nanotubes are particularly interesting due to their quasi-ballistic electron transport on the µm scale. However, recent experimental findings [9–11] show that the scattering length of electrons in the high-bias regime is more than a hundred times shorter than in the low-bias regime. In the high-bias regime, the accelerated electrons relax by the emission of high energy phonons.
Andrew B Yankovich 1 , Benjamin Berkels 2 , Wolfgang Dahmen 3,4 , Peter Binev 3 and Paul M Voyles 1*
Determining the precise atomic structure of materials’ surfaces, defects, and interfaces is important to help provide the connection between structure and important materials’ properties. Modern scanning transmission electronmicroscopy (STEM) techniques now allow for atomic resolution STEM images to have down to sub-picometer precision in locating positions of atoms, but these high-precision techniques generally require large electron doses, making them less useful for beam-sensitive materials. Here, we show that 1- to 2-pm image precision is possible by non-rigidly registering and averaging a high-angle dark field image series of a 5- to 6-nm Au nanoparticle even though a very coarsely sampled image and decreased exposure time was used to minimize the electron dose. These imaging conditions minimize the damage to the nanoparticle and capture the whole nanoparticle in the same image. The high-precision STEM image reveals bond length contraction around the entire nanoparticle surface, and no bond length variation along a twin boundary that separates the nanoparticle into two grains. Surface atoms at the edges and corners exhibit larger bond length contraction than atoms near the center of surface facets.
When after denaturation and self reannealing [ 8 ], circularly perm uted molecules form hom oduplex circles, two pairs of single-stranded branches cor responding to the term inal repetition appear. The distance between the two pairs of single-stranded branches gives the size o f the shift of the two re annealed single strand molecules due to the p erm u tation. The distribution o f such a perm utation length can give, then, inform ation on the cutting m echa nism of the concatamer.
filter, and were cultivated under simulated microgravity (SMG), using the Clinostat, and under normal Earth gravity (1 g) as a control. Three different A. niger strains were tested: wild-type (N402), melanin mutant (ΔfwnA – MA93.1), and a hyperbranching mutant (ΔracA – MA80.1). Each mutant strain had triplicate samples for each condition (SMG and 1 g) to address the possible mechanisms involved in adapting to the microgravity environment. Each colony sample had a diameter of approx. two centimeters, so three different regions of the colonies were analyzed, corresponding to different stages of development: center, intermediate and rim. Sample preparation was conducted in multiple steps - fixation, dehydration, freeze-fracture, critical point drying, and sputter-coated – before imaging at the electron microscope.
compared with the same strain bearing a plasmid overexpressing either Enterococcus faecalis TetM (+TetM) or one of the TetM variants (Fig. 4D). In the absence of TetM, the wild-type Escherichia coli strain (black circles) is sensitive to tetracycline with a minimal inhibitory concentration (MIC 50 ) of ∼0.6 μg/mL, whereas as before (19), overexpression of Enterococcus faecalis TetM (red circles) raises the MIC 50 by 14-fold to ∼10 μg/mL (Fig. 4D). Although mutation of F516 to alanine (F516A) had a modest affect on TetM activity (MIC 50 ∼3 μg/mL), mutation of F516 to the negatively charged Asp (F516D) led to a complete loss of activity (Fig. 4D), consistent with the importance of F516 for providing a hydrophobic environment to maintain the de- fined conformation of loop III necessary for tetracycline release. Another possible source of stabilization of Loop III is the Fig. 4. Stabilization of loop III in TetM via intra-TetM interactions ensures TetM activity. (A) Relative binding position of TetM triple mutant SPV508-510AAA (orange) and tetracycline (Tet, red; ref. 6). (B) Tyrosine residues Y506 and Y507 of loop III of TetM domain IV (orange) stabilize the conformation of loop III via interactions with G467 of loop II, 16S rRNA residue C1051 and residue E435 of loop I, respectively. (C) Localization of TetM residue F516 within the hy- drophobic pocket formed by loop III. (D) Growth curves of wildtype E. coli strain BL21 (black) in the presence of increasing concentrations of tetracycline (0-128 μg/mL) compared with the wildtype strain harboring a plasmid encoding wildtype TetM (red) and TetM single mutants F516A (green) and F516D (brown). (E) Interaction between the sidechain V510 of loop III of TetM with the invariant tryptophan (W442) located in loop I. (F) as in D but with TetM mutant W442A (orange) and the double mutants W442A/Y506A (brown), W442A/Y507A (green), W442A/S508A (olive), W442A/P509A (blue) and W442A/ V510A (violet). In D and F, the error bars represent the SD from the mean for three independent experiments.
To ensure interoperability with a plethora of cryo-EM tools, Warp allows the user to im- port and export data at several steps in its workflow using widely accepted formats and standards. Raw movie data in the MRC, TIFF and EM formats are supported, and a ‘head- erless’ option allows the user to manually specify properties of an unknown binary for- mat. Data are exported in the widely used MRC format, whereas all metadata are saved in the STAR format, adhering to the conventions established by RELION and adopted by many other tools. All pre-processing steps can be turned off if required. Results obtained with other tools can be imported to skip or benefit from particular algorithms in Warp. For instance, particle positions can be imported to export aligned particle averages, up- date their CTF models with Warp’s local estimates, to obtain a comprehensive overview of the particle distribution in a large project, or to retrain a BoxNet model. Frame align- ment data can be exported to initiate a more accurate, reference-based alignment in RELION 3.0. Micrograph and particle lists adhering to user-selected quality criteria can be quickly prepared and exported. Taken together, Warp is highly flexible and allows for easy interoperation with other cryo-EM data processing tools used by the community.
and the precise orientation of the carbon grid, dividing them into groups of metallic and semiconducting nanotubes [34, 35]. Singe walled carbon nanotubes are more than an order of magnitude thinner than the state of the art in transistor size of modern, silicon based chip technology. Therefore they are a potential link to the miniaturization of electronics and moreover, could be used for quantum information technology in the future. After the first observation of the emission of non-classical light in terms of single photons from individual carbon nanotubes at low temperatures [111, 112, 113], recent improvements in nanotube growth and well-controlled doping extended single photon emission to room tem- perature . A single-walled carbon nanotube is often visualized as a sheet of graphene that is rolled up along a specific vector of the honeycomb lattice of carbon atoms , shown in fig. 5.1a. This “roll-up” vector can be expressed as a linear combination of the two unit vectors of the crystal structure and in this way, all different nanotube chiralities can be classified by the two integer coefficients of the roll-up vector, which is therefore called chiral vector. The first unit vector is parallel to the “zigzag” axis while the second one is parallel to the “armchair” axis. The chiral vector’s angle with the zigzag axis is called the chiral angle, while its length equals the circumference of the tube. Carbon nan- otubes as quasi-1D systems show an electronic density of states with distinct peaks, which are van Hove singularities [34, 35] (fig. 5.1b). The first two optically allowed transitions between corresponding valence and conduction bands, called E 11 and E 22 , mainly deter-
With water as solvent the absorption spectrum reduces to a band at 601 nm with a small shoulder at 700 nm. Furthermore, nearly no fluorescence signal is observed in the region of the former fluorescence spectrum. Depending on the environment 4-PEG-TDI forms aggregates in polar media, such as water. It is known that strong intermolecular forces are responsible for self-association of dyes in solution [53, 54]. 4-PEG-TDI is a relatively rigid molecule with a large planar π–electron system with hydrophobic nature and therefore, has a strong tendency to aggregate in polar solvents. Previous studies have already characterized aggregates of ππ–stacked perylenediimide dyes  and terrylenediimide dyes like WS-TDI in aqueous solution , which has a similar π–electron system as 4-PEG-TDI. In contrast to monomeric species, aggregates in solution exhibit distinct changes in absorption and fluorescence properties. Two known species of dye aggregates exist: H- and J-aggregates. In H-aggregates, the absorption maximum is blue-shifted with respect to the isolated chromophore and the fluorescence is normally quenched . In contrast, J-aggregates show fluorescence and the absorption and emission maxima are red-shifted . In our analysis, we observe a strong blue-shifted absorption spectrum for 4-PEG-TDI. This indicates that 4-PEG-TDI forms H- aggregates in water. In addition a small part of the 4-PEG-TDI molecules may also form J-aggregates which can be responsible for the red-shifted shoulder in the absorption spectrum at 700 nm. However, these aggregates show low fluorescence intensity. Furthermore, previous studies have shown the effect that the fluorescence intensity increased dramatically with high surfactant concentrations, for example, with the nonionic block copolymer surfactant poly(ethylene oxide)-poly-(propylene oxide)-poly-(ethylene oxide) (Pluronic P123) . Experiments showed that P123 forms micelles with a concentration above 0.04 wt%/wt, which leads to an incorporation of the dye molecules into the micelles so that most of the molecules are present in a monomeric form associated with the hydrophobic micelles . Herein, we could observe a similar increase of fluorescence intensity of 4-PEG-TDI in the presence of 20 wt%/wt Pluronic (Figure 3.4b). The corresponding quantum yield of fluorescence is equal to 0.03. Also in this case micelles are formed which incorporate monomeric 4-PEG-TDI molecules and this leads to fluorescence of the dye. All spectral and photophysical data are summarized in Table 3.1.
In 2011, Wang et al. 33 reported enhanced stability of PtNi nanoparticles as a result of surface reorganization after a post annealing treatment. In 2013, Ahmadi et al. 49 did a systematic study of PtNi octahedra under different annealing environments and observed segregation and alloy formation in the nanoparticles using X-ray photoelectron spectroscopy (XPS). In this section, different annealing environments are applied to PtNi-hexapod octahedra and PtNi-alloy octahedra to study microstructural changes and their influence on stability after electrochemical measurements. First, the removal of ligands from the surfaces of PtNi-alloy octahedral is investigated. Alkaline conditions have proved to be useful for cleaning octahedral nanoparticle surfaces, while acid-leaching-based methods have been found to alter their compositional structures 66,67 . In the present study annealing in oxygen and hydrogen is used to remove the ligands (OAm and OAc) to study their influence on the compositions und structures of PtNi-alloy octahedra. Parts of this section are taken from “Tuning the Electrocatalytic Oxygen Reduction Reaction Activity and Stability of Shape-Controlled Pt–Ni Nanoparticles by Thermal Annealing − Elucidating the Surface Atomic Structural and Compositional Changes” 129 , “Shape Stability of Octahedral PtNi Nanocatalysts for Electrochemical Oxygen Reduction Reaction studied by in situ Transmission ElectronMicroscopy” 2 , “Concave curvature facets benefit oxygen electroreduction catalysis on octahedral shaped PtNi nanocatalysts“ 130 and “Transformation of carbon-supported Pt–Ni octahedral electrocatalysts into cubes: toward stable electrocatalysis“ 131 .
In der Vergangenheit wurden Gewebe hauptsächlich mit dem SEM (engl.: scanning electron microscope, konventionelles Rasterelektronenmikroskop) dargestellt. Das SEM wurde aufgrund seines hohen Auflösungvermögens oft zur Darstellung von Ultrastrukturen in der Größenordnung von einigen µm verwendet, zum Beispiel zur Darstellung von Lebersinusoiden (Motta und Porter 1974), zur Interaktion zwischen Blutgefäßen und Podozoyten in der Niere (Kondo 1999) und zur Darstellung von der Gefäßstruktur der Nebenniere (Kikuta und Murakami 1982). Das ESEM hingegen bietet eine Möglichkeit Gewebe in der Übersicht darzustellen. Dies ist mit dem SEM aufgrund der schlechteren Probenerhaltung nur bedingt möglich. In den publizierten Bildern von Geweben, die mit dem SEM aufgenommen wurden, sind die Gewebe weniger plastisch als die ESEM-Aufnahmen. Hierfür gibt es verschiedene Gründe: Im SEM können Aufladungen der Probe entstehen, welche die Bildqualität beeinträchtigen. Die Eindringtiefe der Elektronen ist beim SEM geringer, so entsteht ein Oberflächenbild, da dieses nur von einem SE-Signal erzeugt wird. Außerdem kann die Präparation der Probe, insbesondere durch die Trocknung, zu Artefakten führen. Gerade die Möglichkeit der Darstellung von feuchten Proben im ESEM ist hier von Vorteil. Um diese Unterschiede zu verdeutlichen sind in Abb. 33 im Vergleich die SEM-Aufnahme (Arvidson 1976) und die ESEM-Aufnahme einer Zunge gegenübergestellt.