Coming dissertations at TekNat
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Bending, Twisting and Turning : Protein Modeling and Visualization from a Gauge-Invariance Viewpoint
Proteins in nature fold to one dominant native structure. Despite being a heavily studied field, predicting the native structure from the amino acid sequence and modeling the folding process can still be considered unsolved problems. In this thesis I present a new approach to this problem with methods borrowed from theoretical physics. In the first part I show how it is possible to use a discrete Frenet frame to define the discrete curvature and torsion of the main chain of the protein. This method is then extended to the side chains as well. In particular I show how to use the discrete Frenet frame to produce a statistical distribution of angles that works in similar fashion as the commonly used Ramachandran plot and side chain rotamers. The discrete Frenet frame displays a gauge symmetry, in the choice of basis vectors on the normal plane, that is reminiscent of features of Abelian-Higgs theory. In the second part of the thesis I show how this similarity with Abelian-Higgs theory can be translated into an effective energy for a protein. The loops of the proteins are shown to correspond to solitons so that the whole protein can be constructed by gluing together any number of...
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Purification Processes for Complex Biomacromolecules
This thesis details various techniques and considerations for the purification of complex biomacromolecules.
Initially an α-mannosidase from babaco fruit was purified using anion exchange-, lectin affinity- and size exclusion chromatography. The enzyme was approximately 260-280 kDa in size with an apparent an unusual octagonal stoichiometry and displayed properties similar to other known plant α-mannosidases.
Mucins were fractionated by ion exchange and size exclusion chromatography to assess the properties that govern the mucin surface coating interactions in biomaterial research. Commercially available mucins, of bovine and porcine origin, as wells as crude human mucin were tested. All showed to consist of a population of molecules which differ in size, charge and composition.
The third part of the thesis concerns different aspects of plasmid DNA purification processes.
A two-step method for analysis of plasmid DNA consisting of size exclusion followed by thiophilic adsorption chromatography was evaluated. It allowed determination of the supercoiled plasmid DNA concentration in all process steps without requirement for...
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Growth in Aging Colonies : The Importance of Being Different
The accumulation of rifampicin resistant (RifR) mutants in aging bacterial colonies has previously been attributed to stress-induced mutagenesis. Mutations giving rise to RifR are located in the rpoB gene, coding for the β subunit of RNA polymerase, RpoB. We showed that these mutants accumulate because they grow faster than the wild-type in the aging colonies. We found no evidence of increased mutagenesis in the RifR cells and their distribution, as localized clones in the aging colonies, indicated that they accumulated by selection and growth rather than by an increased rate of mutagenesis. Colony competition experiments with reconstructed strains showed that the RifR mutations were responsible for the growth advantage. We also found that deletion of rpoS, coding for the stationary phase sigma factor (RpoS), also gives a growth advantage on bacterial cells in aging colonies.
We suggest that mutants lacking RpoS, having a different transcription pattern than the wild-type, may override the signals to enter stationary phase together with the rest of the population and instead keep growing for as long as possible. We found that the rpoB mutants...
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On the Formation and Structure of the Ionosphere of Titan
We present results on the ionospheric structure around Titan observed during numerous deep (<1000 km) flybys by the Cassini spacecraft. Our results are based on measurements by the radio and plasma wave science instrument, in particular the Langmuir probe. In addition, data from the magnetometer and electron spectrometer have contributed.
The ionosphere of Titan is created when the atmosphere of the moon becomes ionised. There are several mechanisms that contribute to this, the most important of which are considered to be photoionisation by EUV from the Sun with associated photoelectron ionisation, and particle impact ionisation by electrons and ions from Saturn’s corotating magnetosphere.
We investigate the influence of the solar zenith angle on the electron number density at the ionospheric peak. The results show on average four times more plasma on the dayside compared to the nightside, with typical densities of 2500 – 3500 cm-3 and 400 – 1000 cm-3, respectively. In a complementary study, we make a case study of a nightside flyby and show that the altitude structure of the deep ionosphere is reproducible by a simple electron impact ionisation model. Taken...
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Exploring the Molecular Dynamics of Proteins and Viruses
Knowledge about structure and dynamics of the important biological macromolecules — proteins, nucleic acids, lipids and sugars — helps to understand their function. Atomic-resolution structures of macromolecules are routinely captured with X-ray crystallography and other techniques. In this thesis, simulations are used to explore the dynamics of the molecules beyond the static structures.
Viruses are machines constructed from macromolecules. Crystal structures of them reveal little to no information about their genomes. In simulations of empty capsids, we observed a correlation between the spatial distribution of chloride ions in the solution and the position of RNA in crystals of satellite tobacco necrosis virus (STNV) and satellite tobacco mosaic virus (STMV). In this manner, structural features of the non-symmetric RNA could also be inferred.
The capsid of STNV binds calcium ions on the icosahedral symmetry axes. The release of these ions controls the activation of the virus particle upon infection. Our simulations reproduced the swelling of the capsid upon removal of the ions and we quantified the water permeability of the capsid. The structure and dynamics of...
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Magnetic Order in Artificial Structures
The topic of this thesis is the investigation of the magnetic properties of artificially created magnetic structures. Applying different characterization techniques, ranging from direct imaging methods to reciprocal space techniques, the properties of lithographically patterned arrays of magnetic thin film and multilayer elements are investigated by exploring their magnetic state, extending from the atomic scale up to collective ordering phenomena of nano-magnetic elements.
Laterally patterned amorphous multilayer arrays of combined circular and ellipsoidal islands were investigated. The arrays contain a variety of length scales, ranging from their nanometer scale multilayer structure to their lateral periodicity in the micrometer range. The attributes of these arrays are explored using different techniques, applicable for addressing the magnetization at different length scales, including magneto-optical techniques, micromagnetic simulations and x-ray resonant magnetic scattering.
Arrays of dipole interacting elongated magnetic elements composed of Pd(Fe) thin films were investigated. Pd(Fe) films have a low Curie temperature which can be tuned by the thickness of...
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Understanding the Noise : Spliceosomal snRNA Profiling
The concept of the gene has been constantly challenged by new discoveries in the life sciences. Recent challenging observations include the high frequency of alternative splicing events and the common transcription of non-protein-coding-RNAs (ncRNAs) from the genome. The latter has long been considered noise in biological systems. Multiple lines of evidence from genomic studies indicate that alternative splicing and ncRNA play important roles in expanding proteome diversity in eukaryotes. Here, the aim is to find the link between alternative splicing and ncRNAs by studying the expression profile of the spliceosomal snRNAs (U snRNA).
Spliceosomal snRNAs are essential for pre-mRNA splicing in eukaryotes. They participate in splice site selection, recruitment of protein factors and catalyzing the splicing reaction. Because of this, both the abundance and diversity of U snRNAs were expected to be large. In our study we deeply analyzed the U snRNA population in primates using a combination of bioinformatical, biochemical and high throughput sequencing approaches. This transcriptome profiling has revealed that human, chimpanzee and rhesus have similar U snRNA populations, i.e....
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A Study of Jupiter Trojans
Jupiter Trojan asteroid dynamics have been studied for a long time but it is only within the last decades that the known population has become large enough to make other studies meaningful. In four articles I have been scratching the surface of the unknown Trojan knowledge space.
Paper I presents photometric observations confirming a larger variety in surface redness for the smaller Trojans compared to the larger ones, in line with the groups in the outer main asteroid belt. However, the largest Trojans are significantly redder compared to the largest Cybele and Hilda asteroids.
Paper II is an investigation of the Trojan discovery completeness. The analysis shows that all Trojans down to a limiting absolute magnitude of H=11.5 mag have been discovered. Missing Trojans in the almost discovery-completed section should have inclinations above the mean of the same group. The faintest Trojans are discovery biased due to orbit orientations similar to the Milky Way.
Paper III is a general review of dynamical and physical properties of the discovery-completed sample of Jupiter Trojans found in Paper II. The two Trojan swarms are often treated as being equal, but are...
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Theoretical Studies of Magnetism and Electron Correlation in Solids
This work presents new development and applications of ab-initio simulation tools for material science. Focus lies on materials with strong electronic correlation and strong spin-orbit coupling. Improvements on methods for solving the impurity problem in LDA+DMFT is presented, as well as a reliant method for charge self-consistency in a LMTO based electronic structure code. A new adaptive scheme for Brillouin zone integration is developed, where we show a strong reduction of numerical noise compared to standard techniques. A reformulation of the standard LDA+U method aiming to reduce the number of free parameters is introduced. Fast and realistic reduction of the number of free parameters provides the possibility of high throughput calculations and enabled us to study a large number of compounds. An analysis method for polarization in terms of coupled multipoles, and their corresponding energy contributions is developed and applied. This led to the formulation of Katt's rules, a set of rules complementary to Hund's rules. Katt's rules applies for occupying the orbitals of an electronic shell with strong spin-orbit coupling. The analysis is also used to investigate the...
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Transmission Electron Microscopy of Graphene and Hydrated Biomaterial Nanostructures : Novel Techniques and Analysis
Transmission Electron Microscopy (TEM) on light element materials and soft matters is problematic due to electron irradiation damage and low contrast. In this doctoral thesis techniques were developed to address some of those issues and successfully characterize these materials at high resolution. These techniques were demonstrated on graphene flakes, DNA/magnetic beads and a number of water containing biomaterials. The details of these studies are given below.
A TEM based method was presented for thickness characterization of graphene flakes. For the thickness characterization, the dynamical theory of electron diffraction is used to obtain an analytical expression for the intensity of the transmitted electron beam as a function of thickness. From JEMS simulations (experiments) the absorption constant λ in a low symmetry orientation was found to be ~ 208 nm (225 ± 9 nm). When compared to standard techniques for thickness determination of graphene/graphite, the method has the advantage of being relatively simple, fast and requiring only the acquisition of bright-field (BF) images. Using the proposed method, it is possible to measure the thickness change due to one...