Multi-Walled Carbon Nanotubes and Poly(lactic acid) Nanocomposite Fibrous Membranes Prepared by Solution Blow Spinning

Nanocomposite fibers based on multi-walled carbon nanotubes (MWCNT) and poly(lactic acid) (PLA) were prepared by solution blow spinning (SBS). Fiber morphology was characterized by scanning electron microscopy (SEM) and optical microscopy (OM). Electrical, thermal, surface and crystalline properties of the spun fibers were evaluated, respectively, by conductivity measurements (4-point probe), thermogravimetric analyses (TGA), differential scanning calorimetry (DSC), contact angle and X-ray diffraction (XRD). OM analysis of the spun mats showed a poor dispersion of MWCNT in the matrix, however dispersion in solution was increased during spinning where droplets of PLA in solution loaded with MWCNT were pulled by the pressure drop at the nozzle, producing PLA fibers filled with MWCNT. Good electrical conductivity and hydrophobicity can be achieved at low carbon nanotube contents. When only 1 wt% MWCNT was added to low-crystalline PLA, surface conductivity of the composites increased from 5 x 10(-8) to 0.46 S/cm. Addition of MWCNT can slightly influence the degree of crystallinity of PLA fibers as studied by XRD and DSC. Thermogravimetric analyses showed that MWCNT loading can decrease the onset degradation temperature of the composites which was attributed to the catalytic effect of metallic residues in MWCNT. Moreover, it was demonstrated that hydrophilicity slightly increased with an increase in MWCNT content. These results show that solution blow spinning can also be used to produce nanocomposite fibers with many potential applications such as in sensors and biosensors.

Multi-pollutants impact on modern cement built heritage

It is well known that the deposition of gaseous pollutants and aerosols plays a major role in causing the deterioration of monuments and built cultural heritage in European cities. Despite of many studies dedicated to the environmental damage of cultural heritage, in case of cement mortars, commonly used in the 20th century architecture, the deterioration due to air multipollutants impact, especially the formation of black crusts, is still not well explored making this issue a challenging area of research. This work centers on cement mortars – environment interactions, focusing on the diagnosis of the damage on the modern built heritage due to air multi-pollutants. For this purpose three sites, exposed to different urban areas in Europe, were selected for sampling and subsequent laboratory analyses: Centennial Hall, Wroclaw (Poland), Chiesa dell'Autostrada del Sole, Florence (Italy), Casa Galleria Vichi, Florence (Italy). The sampling sessions were performed taking into account the height from the ground level and protection from rain run off (sheltered, partly sheltered and exposed areas). The complete characterization of collected damage layer and underlying materials was performed using a range of analytical techniques: optical and scanning electron microscopy, X ray diffractometry, differential and gravimetric thermal analysis, ion chromatography, flash combustion/gas chromatographic analysis, inductively coupled plasma-optical emission spectrometer. The data were elaborated using statistical methods (i.e. principal components analyses) and enrichment factor for cement mortars was calculated for the first time. The results obtained from the experimental activity performed on the damage layers indicate that gypsum, due to the deposition of atmospheric sulphur compounds, is the main damage product at surfaces sheltered from rain run-off at Centennial Hall and Casa Galleria Vichi. By contrast, gypsum has not been identified in the samples collected at Chiesa dell'Autostrada del Sole. This is connected to the restoration works, particularly surface cleaning, regularly performed for the maintenance of the building. Moreover, the results obtained demonstrated the correlation between the location of the building and the composition of the damage layer: Centennial Hall is mainly undergoing to the impact of pollutants emitted from the close coal power stations, whilst Casa Galleria Vichi is principally affected by pollutants from vehicular exhaust in front of the building.

Numerical and analytical approaches to strongly correlated electron systems

In this thesis we consider three different models for strongly correlated electrons, namely a multi-band Hubbard model as well as the spinless Falicov-Kimball model, both with a semi-elliptical density of states in the limit of infinite dimensions d, and the attractive Hubbard model on a square lattice in d=2. In the first part, we study a two-band Hubbard model with unequal bandwidths and anisotropic Hund's rule coupling (J_z-model) in the limit of infinite dimensions within the dynamical mean-field theory (DMFT). Here, the DMFT impurity problem is solved with the use of quantum Monte Carlo (QMC) simulations. Our main result is that the J_z-model describes the occurrence of an orbital-selective Mott transition (OSMT), in contrast to earlier findings. We investigate the model with a high-precision DMFT algorithm, which was developed as part of this thesis and which supplements QMC with a high-frequency expansion of the self-energy. The main advantage of this scheme is the extraordinary accuracy of the numerical solutions, which can be obtained already with moderate computational effort, so that studies of multi-orbital systems within the DMFT+QMC are strongly improved. We also found that a suitably defined Falicov-Kimball (FK) model exhibits an OSMT, revealing the close connection of the Falicov-Kimball physics to the J_z-model in the OSM phase. In the second part of this thesis we study the attractive Hubbard model in two spatial dimensions within second-order self-consistent perturbation theory. This model is considered on a square lattice at finite doping and at low temperatures. Our main result is that the predictions of first-order perturbation theory (Hartree-Fock approximation) are renormalized by a factor of the order of unity even at arbitrarily weak interaction (U->0). The renormalization factor q can be evaluated as a function of the filling n for 00, the q-factor vanishes, signaling the divergence of self-consistent perturbation theory in this limit. Thus we present the first asymptotically exact results at weak-coupling for the negative-U Hubbard model in d=2 at finite doping.

Vibrational spectroscopic and electrochemical investigations of multi-centered heme proteins in biomimetic membrane architectures

Membrane proteins play a major role in every living cell. They are the key factors in the cell’s metabolism and in other functions, for example in cell-cell interaction, signal transduction, and transport of ions and nutrients. Cytochrome c oxidase (CcO), as one of the membrane proteins of the respiratory chain, plays a significant role in the energy transformation of higher organisms. CcO is a multi centered heme protein, utilizing redox energy to actively transport protons across the mitochondrial membrane. One aim of this dissertation is to investigate single steps in the mechanism of the ion transfer process coupled to electron transfer, which are not fully understood. The protein-tethered bilayer lipid membrane is a general approach to immobilize membrane proteins in an oriented fashion on a planar electrode embedded in a biomimetic membrane. This system enables the combination of electrochemical techniques with surface enhanced resonance Raman (SERRS), surface enhanced reflection absorption infrared (SEIRAS), and surface plasmon spectroscopy to study protein mediated electron and ion transport processes. The orientation of the enzymes within the surface confined architecture can be controlled by specific site-mutations, i.e. the insertion of a poly-histidine tag to different subunits of the enzyme. CcO can, thus, be oriented uniformly with its natural electron pathway entry pointing either towards or away from the electrode surface. The first orientation allows an ultra-fast direct electron transfer(ET) into the protein, not provided by conventional systems, which can be leveraged to study intrinsic charge transfer processes. The second orientation permits to study the interaction with its natural electron donor cytochrome c. Electrochemical and SERR measurements show conclusively that the redox site structure and the activity of the surface confined enzyme are preserved. Therefore, this biomimetic system offers a unique platform to study the kinetics of the ET processes in order to clarify mechanistic properties of the enzyme. Highly sensitive and ultra fast electrochemical techniques allow the separation of ET steps between all four redox centres including the determination of ET rates. Furthermore, proton transfer coupled to ET could be directly measured and discriminated from other ion transfer processes, revealing novel mechanistic information of the proton transfer mechanism of cytochrome c oxidase. In order to study the kinetics of the ET inside the protein, including the catalytic center, time resolved SEIRAS and SERRS measurements were performed to gain more insight into the structural and coordination changes of the heme environment. The electrical behaviour of tethered membrane systems and membrane intrinsic proteins as well as related charge transfer processes were simulated by solving the respective sets of differential equations, utilizing a software package called SPICE. This helps to understand charge transfer processes across membranes and to develop models that can help to elucidate mechanisms of complex enzymatic processes.

Spektroelektrochemische Untersuchungen mittels oberflächenverstärkter Infrarotabsorptionsspektroskopie (SEIRAS) an Multi-Redox-Center-Proteinen in einer biomimetischen Membranumgebung

Die optische Eigenschaften sowie der Oberflächenverstärkungseffekt von rauen Metalloberflächen sowie Nanopartikeln wurden intensiv für den infraroten Bereich des Spektrums in der Literatur diskutiert. Für die Präparation solcher Oberflächen gibt es prinzipiell zwei verschiedene Strategien, zum einen können die Nanopartikel zuerst ex-situ synthetisiert werden, der zweite Ansatz beruht darauf, dass die Nanopartikel in-situ hergestellt und aufgewachsen werden. Hierbei wurden beide Ansätze ausgetestet, dabei stellte sich heraus, dass man nur mittels der in-situ Synthese der Goldnanopartikel in der Lage ist nanostrukturierte Oberflächen zu erhalten, welche elektronisch leitfähig sind, nicht zu rau sind, um eine Membranbildung zu ermöglichen und gleichzeitig einen optimalen Oberflächenverstärkungseffekt zeigen. Obwohl keine ideale Form der Nanopartikel mittels der in-situ Synthese erhalten werden können, verhalten sich diese dennoch entsprechend der Theorie des Oberflächenverstärkungseffekts. Optimierungen der Form und Grösse der Nanopartikel führten in dieser Arbeit zu einer Optimierung des Verstärkungseffekts. Solche optimierten Oberflächen konnten einfach reproduziert werden und zeichnen sich durch eine hohe Stabilität aus. Der so erhaltene Oberflächenverstärkungseffekt beträgt absolut 128 verglichen mit dem belegten ATR-Kristall ohne Nanopartikel oder etwa 6 mal, verglichen mit der Oberfläche, die bis jetzt auch in unserer Gruppe verwendet wurde. Daher können nun Spektren erhalten werden, welche ein deutlich besseres Signal zu Rauschverhältnis (SNR) aufweisen, was die Auswertung und Bearbeitung der erhaltenen Spektren deutlich vereinfacht und verkürzt.rnNach der Optimierung der verwendeten Metalloberfläche und der verwendeten Messparameter am Beispiel von Cytochrom C wurde nun an der Oberflächenbelegung der deutlich größeren Cytochrom c Oxidase gearbeitet. Hierfür wurde der DTNTA-Linker ex-situ synthetisiert. Anschließend wurden gemischte Monolagen (self assembeld monolayers) aus DTNTA und DTP hergestellt. Die NTA-Funktionalität ist für die Anbindung der CcO mit der his-tag Technologie verantwortlich. Die Kriterien für eine optimale Linkerkonzentration waren die elektrischen Parameter der Schicht vor und nach Rekonstitution in eine Lipidmembran, sowie Elektronentransferraten bestimmt durch elektrochemische Messungen. Erst mit diesem optimierten System, welches zuverlässig und reproduzierbar funktioniert, konnten weitere Messungen an der CcO begonnen werden. Aus elektrochemischen Messungen war bekannt, dass die CcO durch direkten Elektronentransfer unter Sauerstoffsättigung in einen aktivierten Zustand überführt werden kann. Dieser aktivierte Zustand zeichnet sich durch eine Verschiebung der Redoxpotentiale um etwa 400mV gegenüber dem aus Gleichgewichts-Titrationen bekannten Redoxpotential aus. Durch SEIRAS konnte festgestellt werden, dass die Reduktion bzw. Oxidation aller Redoxzentren tatsächlich bei den in der Cyclovoltammetrie gemessenen Potentialen erfolgt. Außerdem ergaben die SEIRA-Spektren, dass durch direkten Elektronentransfer gravierende Konformationsänderungen innerhalb des Proteins stattfinden. rnBisher war man davon ausgegangen, aufgrund des Elektronentransfers mittels Mediatoren, dass nur minimale Konformationsänderungen beteiligt sind. Vor allem konnte erstmaligrnder aktivierte und nicht aktivierte Zustand der Cytochrom c Oxidase spektroskopisch nachweisen werden.rn

A multi-instrumental approach to the study of equatorial ionosphere over South America

An extensive study of the morphology and the dynamics of the equatorial ionosphere over South America is presented here. A multi parametric approach is used to describe the physical characteristics of the ionosphere in the regions where the combination of the thermospheric electric field and the horizontal geomagnetic field creates the so-called Equatorial Ionization Anomalies. Ground based measurements from GNSS receivers are used to link the Total Electron Content (TEC), its spatial gradients and the phenomenon known as scintillation that can lead to a GNSS signal degradation or even to a GNSS signal ‘loss of lock’. A new algorithm to highlight the features characterizing the TEC distribution is developed in the framework of this thesis and the results obtained are validated and used to improve the performance of a GNSS positioning technique (long baseline RTK). In addition, the correlation between scintillation and dynamics of the ionospheric irregularities is investigated. By means of a software, here implemented, the velocity of the ionospheric irregularities is evaluated using high sampling rate GNSS measurements. The results highlight the parallel behaviour of the amplitude scintillation index (S4) occurrence and the zonal velocity of the ionospheric irregularities at least during severe scintillations conditions (post-sunset hours). This suggests that scintillations are driven by TEC gradients as well as by the dynamics of the ionospheric plasma. Finally, given the importance of such studies for technological applications (e.g. GNSS high-precision applications), a validation of the NeQuick model (i.e. the model used in the new GALILEO satellites for TEC modelling) is performed. The NeQuick performance dramatically improves when data from HF radar sounding (ionograms) are ingested. A custom designed algorithm, based on the image recognition technique, is developed to properly select the ingested data, leading to further improvement of the NeQuick performance.

Search for high mass resonances decaying into electron-positron pairs in proton-proton collisions at sqrt(s) = 7 TeV with the ATLAS detector

The Standard Model of particle physics was developed to describe the fundamental particles, which form matter, and their interactions via the strong, electromagnetic and weak force. Although most measurements are described with high accuracy, some observations indicate that the Standard Model is incomplete. Numerous extensions were developed to solve these limitations. Several of these extensions predict heavy resonances, so-called Z' bosons, that can decay into an electron positron pair. The particle accelerator Large Hadron Collider (LHC) at CERN in Switzerland was built to collide protons at unprecedented center-of-mass energies, namely 7 TeV in 2011. With the data set recorded in 2011 by the ATLAS detector, a large multi-purpose detector located at the LHC, the electron positron pair mass spectrum was measured up to high masses in the TeV range. The properties of electrons and the probability that other particles are mis-identified as electrons were studied in detail. Using the obtained information, a sophisticated Standard Model expectation was derived with data-driven methods and Monte Carlo simulations. In the comparison of the measurement with the expectation, no significant deviations from the Standard Model expectations were observed. Therefore exclusion limits for several Standard Model extensions were calculated. For example, Sequential Standard Model (SSM) Z' bosons with masses below 2.10 TeV were excluded with 95% Confidence Level (C.L.).

Integration of room temperature single electron transistor with CMOS subsystem

The single electron transistor (SET) is a charge-based device that may complement the dominant metal-oxide-semiconductor field effect transistor (MOSFET) technology. As the cost of scaling MOSFET to smaller dimensions are rising and the the basic functionality of MOSFET is encountering numerous challenges at dimensions smaller than 10nm, the SET has shown the potential to become the next generation device which operates based on the tunneling of electrons. Since the electron transfer mechanism of a SET device is based on the non-dissipative electron tunneling effect, the power consumption of a SET device is extremely low, estimated to be on the order of 10^-18J. The objectives of this research are to demonstrate technologies that would enable the mass produce of SET devices that are operational at room temperature and to integrate these devices on top of an active complementary-MOSFET (CMOS) substrate. To achieve these goals, two fabrication techniques are considered in this work. The Focus Ion Beam (FIB) technique is used to fabricate the islands and the tunnel junctions of the SET device. A Ultra-Violet (UV) light based Nano-Imprint Lithography (NIL) call Step-and-Flash- Imprint Lithography (SFIL) is used to fabricate the interconnections of the SET devices. Combining these two techniques, a full array of SET devices are fabricated on a planar substrate. Test and characterization of the SET devices has shown consistent Coulomb blockade effect, an important single electron characteristic. To realize a room temperature operational SET device that function as a logic device to work along CMOS, it is important to know the device behavior at different temperatures. Based on the theory developed for a single island SET device, a thermal analysis is carried out on the multi-island SET device and the observation of changes in Coulomb blockade effect is presented. The results show that the multi-island SET device operation highly depends on temperature. The important parameters that determine the SET operation is the effective capacitance Ceff and tunneling resistance Rt . These two parameters lead to the tunneling rate of an electron in the SET device, Γ. To obtain an accurate model for SET operation, the effects of the deviation in dimensions, the trap states in the insulation, and the background charge effect have to be taken into consideration. The theoretical and experimental evidence for these non-ideal effects are presented in this work.

MULTISCALE EXAMINATION AND MODELING OF ELECTRON TRANSPORT IN NANOSCALE MATERIALS AND DEVICES

For half a century the integrated circuits (ICs) that make up the heart of electronic devices have been steadily improving by shrinking at an exponential rate. However, as the current crop of ICs get smaller and the insulating layers involved become thinner, electrons leak through due to quantum mechanical tunneling. This is one of several issues which will bring an end to this incredible streak of exponential improvement of this type of transistor device, after which future improvements will have to come from employing fundamentally different transistor architecture rather than fine tuning and miniaturizing the metal-oxide-semiconductor field effect transistors (MOSFETs) in use today. Several new transistor designs, some designed and built here at Michigan Tech, involve electrons tunneling their way through arrays of nanoparticles. We use a multi-scale approach to model these devices and study their behavior. For investigating the tunneling characteristics of the individual junctions, we use a first-principles approach to model conduction between sub-nanometer gold particles. To estimate the change in energy due to the movement of individual electrons, we use the finite element method to calculate electrostatic capacitances. The kinetic Monte Carlo method allows us to use our knowledge of these details to simulate the dynamics of an entire device— sometimes consisting of hundreds of individual particles—and watch as a device ‘turns on’ and starts conducting an electric current. Scanning tunneling microscopy (STM) and the closely related scanning tunneling spectroscopy (STS) are a family of powerful experimental techniques that allow for the probing and imaging of surfaces and molecules at atomic resolution. However, interpretation of the results often requires comparison with theoretical and computational models. We have developed a new method for calculating STM topographs and STS spectra. This method combines an established method for approximating the geometric variation of the electronic density of states, with a modern method for calculating spin-dependent tunneling currents, offering a unique balance between accuracy and accessibility.

Forward treatment planning for modulated electron radiotherapy (MERT) employing Monte Carlo methods

PURPOSE This paper describes the development of a forward planning process for modulated electron radiotherapy (MERT). The approach is based on a previously developed electron beam model used to calculate dose distributions of electron beams shaped by a photon multi leaf collimator (pMLC). METHODS As the electron beam model has already been implemented into the Swiss Monte Carlo Plan environment, the Eclipse treatment planning system (Varian Medical Systems, Palo Alto, CA) can be included in the planning process for MERT. In a first step, CT data are imported into Eclipse and a pMLC shaped electron beam is set up. This initial electron beam is then divided into segments, with the electron energy in each segment chosen according to the distal depth of the planning target volume (PTV) in beam direction. In order to improve the homogeneity of the dose distribution in the PTV, a feathering process (Gaussian edge feathering) is launched, which results in a number of feathered segments. For each of these segments a dose calculation is performed employing the in-house developed electron beam model along with the macro Monte Carlo dose calculation algorithm. Finally, an automated weight optimization of all segments is carried out and the total dose distribution is read back into Eclipse for display and evaluation. One academic and two clinical situations are investigated for possible benefits of MERT treatment compared to standard treatments performed in our clinics and treatment with a bolus electron conformal (BolusECT) method. RESULTS The MERT treatment plan of the academic case was superior to the standard single segment electron treatment plan in terms of organs at risk (OAR) sparing. Further, a comparison between an unfeathered and a feathered MERT plan showed better PTV coverage and homogeneity for the feathered plan, with V95% increased from 90% to 96% and V107% decreased from 8% to nearly 0%. For a clinical breast boost irradiation, the MERT plan led to a similar homogeneity in the PTV compared to the standard treatment plan while the mean body dose was lower for the MERT plan. Regarding the second clinical case, a whole breast treatment, MERT resulted in a reduction of the lung volume receiving more than 45% of the prescribed dose when compared to the standard plan. On the other hand, the MERT plan leads to a larger low-dose lung volume and a degraded dose homogeneity in the PTV. For the clinical cases evaluated in this work, treatment plans using the BolusECT technique resulted in a more homogenous PTV and CTV coverage but higher doses to the OARs than the MERT plans. CONCLUSIONS MERT treatments were successfully planned for phantom and clinical cases, applying a newly developed intuitive and efficient forward planning strategy that employs a MC based electron beam model for pMLC shaped electron beams. It is shown that MERT can lead to a dose reduction in OARs compared to other methods. The process of feathering MERT segments results in an improvement of the dose homogeneity in the PTV.

Neutrino physics with multi-ton scale liquid xenon detectors

We study the sensitivity of large-scale xenon detectors to low-energy solar neutrinos, to coherent neutrino-nucleus scattering and to neutrinoless double beta decay. As a concrete example, we consider the xenon part of the proposed DARWIN (Dark Matter WIMP Search with Noble Liquids) experiment. We perform detailed Monte Carlo simulations of the expected backgrounds, considering realistic energy resolutions and thresholds in the detector. In a low-energy window of 2–30 keV, where the sensitivity to solar pp and 7Be-neutrinos is highest, an integrated pp-neutrino rate of 5900 events can be reached in a fiducial mass of 14 tons of natural xenon, after 5 years of data. The pp-neutrino flux could thus be measured with a statistical uncertainty around 1%, reaching the precision of solar model predictions. These low-energy solar neutrinos will be the limiting background to the dark matter search channel for WIMP-nucleon cross sections below ~2X 10-48 cm2 and WIMP masses around 50 GeV c 2, for an assumed 99.5% rejection of electronic recoils due to elastic neutrino-electron scatters. Nuclear recoils from coherent scattering of solar neutrinos will limit the sensitivity to WIMP masses below ~6 GeV c-2 to cross sections above ~4X10-45cm2. DARWIN could reach a competitive half-life sensitivity of 5.6X1026 y to the neutrinoless double beta decay of 136Xe after 5 years of data, using 6 tons of natural xenon in the central detector region.

Modeling Techniques for the High-Resolution Interpretation of Cryo-Electron Microscopy Reconstructions

Essential biological processes are governed by organized, dynamic interactions between multiple biomolecular systems. Complexes are thus formed to enable the biological function and get dissembled as the process is completed. Examples of such processes include the translation of the messenger RNA into protein by the ribosome, the folding of proteins by chaperonins or the entry of viruses in host cells. Understanding these fundamental processes by characterizing the molecular mechanisms that enable then, would allow the (better) design of therapies and drugs. Such molecular mechanisms may be revealed trough the structural elucidation of the biomolecular assemblies at the core of these processes. Various experimental techniques may be applied to investigate the molecular architecture of biomolecular assemblies. High-resolution techniques, such as X-ray crystallography, may solve the atomic structure of the system, but are typically constrained to biomolecules of reduced flexibility and dimensions. In particular, X-ray crystallography requires the sample to form a three dimensional (3D) crystal lattice which is technically di‑cult, if not impossible, to obtain, especially for large, dynamic systems. Often these techniques solve the structure of the different constituent components within the assembly, but encounter difficulties when investigating the entire system. On the other hand, imaging techniques, such as cryo-electron microscopy (cryo-EM), are able to depict large systems in near-native environment, without requiring the formation of crystals. The structures solved by cryo-EM cover a wide range of resolutions, from very low level of detail where only the overall shape of the system is visible, to high-resolution that approach, but not yet reach, atomic level of detail. In this dissertation, several modeling methods are introduced to either integrate cryo-EM datasets with structural data from X-ray crystallography, or to directly interpret the cryo-EM reconstruction. Such computational techniques were developed with the goal of creating an atomic model for the cryo-EM data. The low-resolution reconstructions lack the level of detail to permit a direct atomic interpretation, i.e. one cannot reliably locate the atoms or amino-acid residues within the structure obtained by cryo-EM. Thereby one needs to consider additional information, for example, structural data from other sources such as X-ray crystallography, in order to enable such a high-resolution interpretation. Modeling techniques are thus developed to integrate the structural data from the different biophysical sources, examples including the work described in the manuscript I and II of this dissertation. At intermediate and high-resolution, cryo-EM reconstructions depict consistent 3D folds such as tubular features which in general correspond to alpha-helices. Such features can be annotated and later on used to build the atomic model of the system, see manuscript III as alternative. Three manuscripts are presented as part of the PhD dissertation, each introducing a computational technique that facilitates the interpretation of cryo-EM reconstructions. The first manuscript is an application paper that describes a heuristics to generate the atomic model for the protein envelope of the Rift Valley fever virus. The second manuscript introduces the evolutionary tabu search strategies to enable the integration of multiple component atomic structures with the cryo-EM map of their assembly. Finally, the third manuscript develops further the latter technique and apply it to annotate consistent 3D patterns in intermediate-resolution cryo-EM reconstructions. The first manuscript, titled An assembly model for Rift Valley fever virus, was submitted for publication in the Journal of Molecular Biology. The cryo-EM structure of the Rift Valley fever virus was previously solved at 27Å-resolution by Dr. Freiberg and collaborators. Such reconstruction shows the overall shape of the virus envelope, yet the reduced level of detail prevents the direct atomic interpretation. High-resolution structures are not yet available for the entire virus nor for the two different component glycoproteins that form its envelope. However, homology models may be generated for these glycoproteins based on similar structures that are available at atomic resolutions. The manuscript presents the steps required to identify an atomic model of the entire virus envelope, based on the low-resolution cryo-EM map of the envelope and the homology models of the two glycoproteins. Starting with the results of the exhaustive search to place the two glycoproteins, the model is built iterative by running multiple multi-body refinements to hierarchically generate models for the different regions of the envelope. The generated atomic model is supported by prior knowledge regarding virus biology and contains valuable information about the molecular architecture of the system. It provides the basis for further investigations seeking to reveal different processes in which the virus is involved such as assembly or fusion. The second manuscript was recently published in the of Journal of Structural Biology (doi:10.1016/j.jsb.2009.12.028) under the title Evolutionary tabu search strategies for the simultaneous registration of multiple atomic structures in cryo-EM reconstructions. This manuscript introduces the evolutionary tabu search strategies applied to enable a multi-body registration. This technique is a hybrid approach that combines a genetic algorithm with a tabu search strategy to promote the proper exploration of the high-dimensional search space. Similar to the Rift Valley fever virus, it is common that the structure of a large multi-component assembly is available at low-resolution from cryo-EM, while high-resolution structures are solved for the different components but lack for the entire system. Evolutionary tabu search strategies enable the building of an atomic model for the entire system by considering simultaneously the different components. Such registration indirectly introduces spatial constrains as all components need to be placed within the assembly, enabling the proper docked in the low-resolution map of the entire assembly. Along with the method description, the manuscript covers the validation, presenting the benefit of the technique in both synthetic and experimental test cases. Such approach successfully docked multiple components up to resolutions of 40Å. The third manuscript is entitled Evolutionary Bidirectional Expansion for the Annotation of Alpha Helices in Electron Cryo-Microscopy Reconstructions and was submitted for publication in the Journal of Structural Biology. The modeling approach described in this manuscript applies the evolutionary tabu search strategies in combination with the bidirectional expansion to annotate secondary structure elements in intermediate resolution cryo-EM reconstructions. In particular, secondary structure elements such as alpha helices show consistent patterns in cryo-EM data, and are visible as rod-like patterns of high density. The evolutionary tabu search strategy is applied to identify the placement of the different alpha helices, while the bidirectional expansion characterizes their length and curvature. The manuscript presents the validation of the approach at resolutions ranging between 6 and 14Å, a level of detail where alpha helices are visible. Up to resolution of 12 Å, the method measures sensitivities between 70-100% as estimated in experimental test cases, i.e. 70-100% of the alpha-helices were correctly predicted in an automatic manner in the experimental data. The three manuscripts presented in this PhD dissertation cover different computation methods for the integration and interpretation of cryo-EM reconstructions. The methods were developed in the molecular modeling software Sculptor (http://sculptor.biomachina.org) and are available for the scientific community interested in the multi-resolution modeling of cryo-EM data. The work spans a wide range of resolution covering multi-body refinement and registration at low-resolution along with annotation of consistent patterns at high-resolution. Such methods are essential for the modeling of cryo-EM data, and may be applied in other fields where similar spatial problems are encountered, such as medical imaging.

Nannoplankton of multi-net samples, sediment surface and sediment core samples from the northern Arabian Sea

Recent nannoplankton from the "Meteor"-stations M 242, M 243 and M 245 in the northern Arabian Sea were studied by means of the light and electron microscope, and 19 species were found. The nannoplankton assemblage of the northern Arabian Sea is compared with those of the eastern and western Mediterranean Sea and the Atlantic Ocean. Gephyrocapsa oceanica (Kamptner), Cyclococcolithus leptoporus (Murray & Blackman), Emiliania huxleyi (Lohmann), Helicopontospbaera kamptneri (Hay & Mohler), and Umbilicosphaera mirabilis (Lohmann) are the most common species in the northern Arabian Sea. Reworked nannoplankton and nannoplankton species agglutinated by tintinnids are discussed.

Development of Efficient FPGA-Based Multi-Channel Phase Meters for IR-Interferometers

Infrared (IR) interferometry is a method for measuring the line-electron density of fusion plasmas. The significant performance achieved by FPGAs in solving digital signal processing tasks advocates the use of this type of technology in two-color IR interferometers of modern stellarators, such as the TJ-II (Madrid, Spain) and the future W7-X (Greifswald, Germany). In this work the implementation of a line-average electron density measuring system in an FPGA device is described. Several optimizations for multichannel systems are detailed and test results from the TJ-II as well as from a W7-X prototype are presented.

Integration of III-V materials on Silicon Substrates for Multi-junction Solar Cell Applications

The work presented here aims to reduce the cost of multijunction solar cell technology by developing ways to manufacture them on cheap substrates such as silicon. In particular, our main objective is the growth of III-V semiconductors on silicon substrates for photovoltaic applications. The goal is to create a GaAsP/Si virtual substrates onto which other III-V cells could be integrated with an interesting efficiency potential. This technology involves several challenges due to the difficulty of growing III-V materials on silicon. In this paper, our first work done aimed at developing such structure is presented. It was focused on the development of phosphorus diffusion models on silicon and on the preparation of an optimal silicon surface to grow on it III-V materials.