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Coming dissertations at TekNat

  • Exotic Ribosomal Enzymology

    Author: Josefine Liljeruhm
    Publication date: 2019-02-15 08:42

    This thesis clarifies intriguing enzymology of the ribosome, the multiRNA/multiprotein complex that catalyzes protein synthesis (translation). The large ribosomal RNAs (23S and 16S rRNAs in E. coli) are post-transcriptionally modified by many specific modification enzymes, yet the functions of the modifications remain enigmatic. A deeper insight into two of the 23S rRNA S-adenosyl-methionine-requiring methyltransferase enzymes, RlmM and RlmJ, was given by investigating substrate specificity in vitro. Both enzymes were able to methylate in vitro-transcribed, modification-free, protein-free, 2659-nucleotide-long 23S rRNA. Furthermore, RlmM was able to methylate the 611-nucleotide-long Domain V of the 23S rRNA alone and RlmJ could modify the A2030 with only 25 surrounding nucleotides.

    Translation is evolutionary optimized to incorporate L-amino acids to the exclusion of D-amino acids in the cell. To understand how, and how to engineer around this restriction for pharmacological applications, detailed kinetics of ribosomal dipeptide formation with D- versus L-phenylalanine-tRNA were determined. This was done by varying the concentrations of EF-Tu (...

  • Low-Coordinate Organopnictogens : Synthesis and Optoelectronic properties

    Author: Muhammad Anwar Shameem
    Publication date: 2019-02-13 15:39

    This thesis work is based on the development of novel organopnictogen compounds and the exploration of their potential applications in organic electronics. In particular, incorporation of phosphorus and arsenic into π-conjugated systems is known to modify the optoelectronic properties.

    The first chapter of this thesis is fully devoted to the development of a metal-free synthetic route that allows direct, sequential and stereoselective alkynylation of C,C-dibromophosphaalkenes. The subsequent unusual reactivity of thus synthesized C-mono and C,C-diacetylenicphosphaalkenes with terminal acetylenes afforded highly substituted 1-phoshpha-1,3-butadienes heavier analogue of all carbon 1,3-butadiene motifs. Optimization of the reaction condition favored exclusively the formation of 1-phospha-1,3-butadienes. Unveiling the unique cyclization of the 3-yne 1-phospha-1,3-butadiene gave highly substituted phosphole derivatives. Further, it has been experimentally shown that the P=C unit is essential for this rare cyclization and rearrangement to give π-conjugated phosphole derivatives.

    The second chapter of this thesis work deals with incorporation of...

  • Angle dependent light scattering of functional nanoparticle composites

    Author: JunXin Wang
    Publication date: 2019-02-11 13:25

    Varies functional nanoparticles play crucial roles in energy- and optical- related applications. The incorporation of functional nanoparticles into non-absorbing polymers to form optical absorption and scattering thin films have attracted considerable interest due to a successful selection of particles and matrices, synergistic effects of separation and fixation of particles, and controllable layer thicknesses and structures. To investigate the optical parameters, especially absorption and scattering coefficients of the nanocomposites, it is critical to evaluate and optimize those particle based functional layers.

    In this thesis, we mainly focus on developing approaches for the inversion of scattering and absorption coefficients from optically measured transmittance and reflectance spectra. A two-flux radiative transfer model is robust for this purpose, but its limitation lies in failing to converge the transmittance and reflectance spectra to experimental data owing to the approximation of the completely diffuse scattering patterns. We carried out thorough characterization of angle- and wavelength-resolved light scattering on those nanocomposites with metallic Au,...

  • Statistical processing of Flash X-ray Imaging of protein complexes

    Author: Alberto Pietrini
    Publication date: 2019-02-08 14:18

    Flash X-ray Imaging (FXI) at X-ray Free Electron Lasers (XFELs) is a promising technique that permits the investigation of the 3D structure of molecules without the need for crystallization, by diffracting on single individual sample particles.

    In the past few years, some success has been achieved by using FXI on quite large biological complexes (40 nm-1 μm in diameter size). Still, the desired dream-goal of imaging a single individual of a molecule or a protein complex (<15 nm in diameter size) has not been reached yet. The main issue that prevented us from a complete success has been the low signal strength, almost comparable to background noise. That is particularly true for experiments performed at the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS).

    In this thesis, we provide a brief review of the CXI instrument (focusing on experiments there performed) and present a statistical method to deal with low signal-to-noise ratios. We take into account a variety of biological particles, showing the benefits of estimating a background model from sample data and using that for processing said data. Moreover, we present the results of...

  • Characterization of secreted Giardia intestinalis cysteine proteases

    Author: Jingyi Liu
    Publication date: 2019-02-07 09:03

    Giardia intestinalis, the causative agent of the diarrheal disease giardiasis, is a protozoan parasite that colonizes the upper small intestine of mammals, including humans. It can be divided into eight genotypes or assemblages (A through H) and only assemblage A and B are infective to humans. Giardiasis is a multi-factorial disease but few giardial virulence factors have been identified and characterized.

    In this thesis, we used proteomics to identify the major excretory-secretory products (ESPs) released by Giardia trophozoites of the WB and GS isolates during interaction with intestinal epithelial cells (IECs) in vitro (Paper I). To deepen our understanding of the role of ESPs in giardiasis, we focused on three specific secreted Giardia cysteine proteases (CPs; CP14019, CP16160 and CP16779). All the three CPs are capable of opening the apical junction complexes between IECs to degrade chemokines produced in response to Giardia (Paper II). This can partly explain the induction of symptoms and immunosuppression seen during giardiasis. We further studied the cleavage specificity of these CPs using substrate phage...

  • Evolutionary genomics in Corvids : – From single nucleotides to structural variants

    Author: Matthias H. Weissensteiner
    Publication date: 2019-02-04 12:24

    Heritable genetic variation is the raw material of evolution and can occur in many different forms, from altering single nucleotides to rearranging stretches of millions at once. DNA mutations that result in phenotypic differences are the basis upon which natural selection can act, leading to a shift of the frequency of those mutations.

    In this thesis I aim to comprehensively characterize and quantify genetic variation in a natural system, the songbird genus Corvus.

    First, we expand on previous work from a hybrid zone of different populations of Eurasian crows. All black carrion crows and black-and-grey hooded crows meet in a narrow hybrid zone in central Europe, and also in central and Southeast Asia. Comparing population genetic data acquired from these three hybrid zones yielded no single genetic region as a candidate responsible for phenotypic divergence, yet a parallelism in sets of genes and gene networks was evident.

    Second, we capitalize on varying evolutionary timescales to investigate the driver of the heterogeneous genetic differentiation landscape observed in multiple avian species. Genetic diversity, and thus differentiation, seems to be...

  • Computational Studies of 2D Materials : Application to Energy Storage and Electron Transport in Nanoscale Devices

    Author: Vivekanand Shukla
    Publication date: 2019-01-29 10:18

    The field of two-dimensional (2D) layered materials provides a new platform for studying diverse physical phenomena that are scientifically interesting and relevant for technological applications. Novel applications in electronics and energy storage harness the unique electronic, optical, and mechanical properties of 2D materials for design of crucial components. Atomically thin, with large surface to volume ratio, these materials are attractive for broad applications for hydrogen storage, sensing, batteries and photo-catalysis. Theoretical predictions from atomically resolved computational simulations of 2D materials play a pivotal role in designing and advancing these developments.

    The central topic of this thesis is 2D materials studied using density functional theory and non-equilibrium Green’s function. The electronic structure and transport properties are discussed for several synthesized and predicted 2D materials, with diverse potential applications in nanoscale electronic devices, gas sensing, and electrodes for rechargeable batteries. Lateral and vertical heterostructures have been studied for applications in nanoscale devices such as graphene/hBN...

  • From Strange to Charm : Meson production in electron-positron collisions

    Author: Joachim Pettersson
    Publication date: 2019-01-28 13:43

    Decays of pseudoscalar mesons into a lepton-antilepton pair are very rare within the Standard Model since they cannot proceed via a single photon process. The C-even neutral mesons can be produced in electron-positron collisions by a two-photon intermediate state. Due to the rarity the of Pl+l- decays, measurements of their branching fractions are sensitive to physics beyond the Standard Model. This thesis report the first search for the process e+e-→ηusing the K±K0Sπ±K+0 and K+K-η final states to determine the branching fraction of the time reverse process ηc→e+e-. This study is an extension of the previous measurements of π0→e+e- and η→μ+μ-, and the upper limits set for η→e+e- and η'→μ+μ-. The analysis presented in this thesis uses data...

  • Materials Modelling for Energy Harvesting : From Conversion to Application through Storage

    Author: Amitava Banerjee
    Publication date: 2019-01-24 09:42

    In this Ph.D. thesis, ab initio density functional theory along with molecular dynamics and global optimization methods are used to unveil and understand the structures and properties of energy relevant materials. In this connection, the following applications are considered: i. electrocatalyst for solar fuel production through water splitting, ii. hybrid perovskite solar cell for generation of electrical energy and iii. Battery materials to store the electrical energy. The water splitting mechanism in terms of hydrogen evolution and oxygen evolution reactions (HER and OER) on the catalytic surfaces has been envisaged based on the free energy diagram, named reaction coordinate, of the reaction intermediates. The Ti-functionalized two-dimensional (2D) borophene monolayer has been emerged as a promising material for HER and OER mechanisms as compared to the pristine borophene sheet. Further investigation in the series of this noble metal free monolayer catalyst is 2D Al2C monolayer both in form of pristine and functionalized with nitrogen (N), phosphorous (P), boron (B), and sulphur (S). It has been observed that only B substituted Al2C shows very close to thermoneutral, that...

  • Accumulative Charge Separation in Photocatalysis : From Molecules to Nanoparticles

    Author: Mariia Pavliuk
    Publication date: 2019-01-23 15:55

    Photochemical energy conversion into solar fuel involves steps of light absorption, charge separation and catalysis. Nature has taught us that the effective accumulation of redox equivalents and charge separation are the key steps in sunlight conversion. The focus of this thesis is to unveil photophysical and photochemical processes that lead to accumulative charge separation. The optimization of electron transfer process will be held by minimization of losses via recombination, and extension of the lifetime of the charge separated state by usage of the electron relay.

    The goal is to couple light induced electron transfer process with the multi-electron catalytic process of hydrogen evolution. In this regard, light harvesters (molecules, metal nanostructures) that generate at least two electrons per absorbed photon will be studied. Additionally, semiconductors that generate long-lived charge separated states are utilized to accumulate several redox equivalents necessary for hydrogen evolution.

    The hybrid systems produced by the combination of the advantageous properties of molecules, semiconductors, and metal nanoparticles are under the scope of investigation. Metal...