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Quantifying the Flux of Charged Molecules through Bacterial Membrane Proteins
No full textGram-negative bacterial cell envelope acts as the first line of defence against various antibacterial compounds. Antibiotics need to penetrate the outer membrane barrier of the cell envelope to reach their target site. Hydrophilic antibiotics such as β-lactams including penicillins, carbapenems are known to utilize water-filled protein channels such as OmpF and OmpC which are present in the outer membrane to diffuse inside the bacterial cell. Any modification of these channel proteins can often limit the permeation of antibiotics across an outer cell membrane of bacteria.
This thesis highlights a permeation assay based on conventional electrophysiology. The method mainly includes the application of concentration gradients of charged molecules with unequal electrophoretic mobilities of the ions through a membrane channel. The unbalanced flux further creates an electrostatic potential which offers a direct evidence over relative ion fluxes. The experimental method applied here includes measuring zero-voltage-currents and the single channel conductance. Furthermore, we elucidated the chemical stability of ampicillin over its interaction with OmpF. The interaction of OmpF single porin with ampicillin and its primary degradation product, penicilloic-acid was compared. The modulation of ion currents in the presence of ampicillin and penicilloic-acid were analysed. We also investigated the permeation of ampicillin, penicilloic-acid, and benzylpenicillin through OmpF using an electrophysiological zero-current-potential assay under tri-ionic conditions. Further, using channel FhuA 1-160 in which the “cork” domain closing the channel had been removed we expanded the pore diameter by copying the amino acid sequence of two β-strands in a step-wise manner increasing the total number of β -strands from 22 to 34. The pore size of the respective expanded channel protein was characterized by single-channel conductance
Resting State EEG Classification for Motor Learning Skills Using Echo State Networks
No full textEEG records the electrical activities from the scalp surface via electrodes. As a
modern medical imaging technique, it has been proven to be useful in many different
fields. Clinical diagnosis, psychotherapy, brain-computer interfaces and
the pharmaceutical industry all have benefited from the insights that one can
glean from EEG measurements.
However, there exist various difficulties such as uniqueness of individuals, large
volume of data and influences of artifacts that prevent us from extracting useful
information from those measurements, and thus more involved analytical tools
are needed. Recurrent Neural Networks are particularly suitable for dealing
with EEG because these networks can capture the critical spatiotemporal characteristics
that EEG contains.
In this project, we successfully applied Echo State Networks to classify the
people’s motor learning skills, given the resting state EEG recording. We also
discovered some evidence for the existence of different neurological groups with
respect to people’s motor learning skills
Auroral Field-Aligned Currents: Analysis, Structure, and Dynamics
No full textAurora is the most visible result of the dynamic processes associated to the magnetosphere-ionosphere coupling at high altitudes. Field-aligned currents (FACs) are the main coupling agent that mediate the energy and momentum transfer between the magnetospheric and ionospheric plasma. FACs are directly connected to auroral structures covering a large range of temporal and spatial scales, as well as various geometries. The observed spatial scales of FACs range from small scales (0.1-1 km) up to mesoscales and large scales (10-100 km and more).
The first goal of the thesis is to extend basic analysis methods, by tailoring them to a multiscale approach, appropriate for the study of the complex FACs associated with aurora. We introduce the multiscale FAC analyzer, based on multiscale minimum variance analysis (MVA) of the FAC signatures. This technique relies on performing the classical MVA continuously and over a range of scales, by varying the width of the analysis window, and provides multiscale information on the planarity and orientation of the FACs. The derivative of the largest eigenvalue of the magnetic variance matrix with respect to the width of the analysis window provides the location and thickness of the planar FACs.
The second goal is to develop an analysis technique that integrates multiple measurements taken from different observation platforms in order to investigate the dynamics of quasi-periodic FACs. We introduce a new approach to examine the azimuthal (east-west) dynamics of quasi-periodic FACs based on the analysis of the Doppler shifts between different observation points (on ground and in space). This technique provides information on the dependence of the wavelength (or propagation velocity) on the wavefront propagation direction of the FACs. The examination of conjugate data from high- and low-altitude satellites, as well as from ground, makes if possible to cross-check the Doppler analysis and to further constrain the azimuthal motion
Decision Support for Continuous Casting Planning
No full textThe tasks of steel production planning and control have a major impact on the logistics target achievement and therefore on the competitiveness of the company. The planning process is known to be extremely difficult, with various incompatible local constraints at the different production stages. As a consequence, only limited amount of constraints can be respected in higher planning levels. Detailed production planning at the different production stages has the task to derive production programs that are able to respect all local constraints and at the same time lead to appropriate target achievement. Current approaches developed for detailed continuous casting planning are not able to quickly provide alternative solutions and therewith enable decision support for conflicting objectives.
Within this thesis, the detailed continuous casting problem is presented in detail. A new approach to decompose the problem is described. With this decomposition, the problem can be treated as a single machine scheduling problem and effective meta heuristics developed for similar problems can be exploited. Further, with the chosen decomposition it is possible to respect the consumption of hot metal within the scheduling of charges. This important practical constraint could not be respected within the continuous casting problem in the past. Besides the hot metal consumption, setup families and maximum batch sizes are considered in the scheduling model. MILP models are presented for the different extensions of the basic scheduling model. A iterated local search procedure is presented and the effective is shown based on the comparison with a commercial solver.
The findings obtained from the scheduling research is transferred into a decision support system for the detailed continuous casting planning. Based on an industry case study, the application of the developed tool is presented on a real industry situation
On Dephasing and Exciton Transfer in Light-Harvesting Complexes
No full textPhotosynthesis is the main energy source in plants, algae and different types of bacteria, such as purple and green sulphur bacteria. The primary step in photosynthesis is represented by the photo excitation of the light harvesting (LH) pigment present in the organism. Subsequently, the excitation delocalizes among the pigments due to the electronic couplings between them. The excitation energy is then transferred to neighboring LH systems and finally to the reaction center (RC) where charge separation occurs. During the last decades many studies have been carried out in order to understand the optical and the exciton transfer properties of the LH complexes. Nevertheless, a full understanding has not yet been achieved. In particular, the experimentally-observed long-lived coherences as well as dephasing processes have attracted the attention of the scientific community in recent years. The present thesis aims at contributing to the understanding of these processes. To this end, different methods have been employed, such as molecular dynamics simulations, quantum-chemistry methods and wave packet dynamics calculations. The combination of these methods allows a more detailed theoretical description of the studied LH systems. The dephasing phenomenon is discussed in the first half of the thesis. In this work, an analytic and a numerical methodology has been developed to relate it to the energy gap fluctuation. This formalism has been applied to the case of both single pigments and whole complexes. It can be concluded that a universal relation exists between these two entities, independently from the system and from the method used to obtain such quantities. The second half of this thesis consists of combined molecular dynamics and quantum approaches applied to different systems. Three different LH systems are discussed and compared in detail and the photo-active part of a bio-inspired solar cell is studied
Geometric Properties of Gabor Frames and Their Applications to the Phase Retrieval Problem
No full textIn this thesis we address questions arising in two different research areas of mathematics, namely, in the area of Gabor frames in finite dimensions, belonging to the field of applied harmonic analysis, and phase retrieval problem, belonging to the field of signal processing. Our work is inspired by phase retrieval problem, which is motivated by real world applications, such as optics, speech recognition, astronomical imaging, quantum mechanics, and wireless communication. At the same time, study of this problem leads to beautiful and insightful mathematics on the intersection of different fields. The focus of this thesis is the investigation of geometric properties of Gabor frames and their role in the phase retrieval problem in the case of time-frequency structured frames. Even though phase retrieval problem has been studied for a long time, until recently very little was known about how to achieve stable and efficient reconstruction. Nowadays, the case when the measurement frame is a Gaussian frame with independent frame vectors is sufficiently well studied. At the same time very little is known about the case of structured, application relevant frames. The main reason for this is that some geometric properties of structured frames are not yet fully understood. In our work, we investigate such frame properties as optimal frame bounds and frame order statistics in the case of Gabor frames with random windows. The obtained results allow us to conclude that the properties of Gabor frames with random windows are often quite similar to the properties of Gaussian frames with independent vectors, which are optimal for many applications. We also design an efficient phase retrieval algorithm from nearly optimal number of time-frequency structured measurements and show its robustness in the case when measurements are corrupted by additive noise. Robustness analysis of the constructed algorithm turns out to be also closely linked to the geometric properties of Gabor frames
Analysis of Automatic Identification System Data for Maritime Safety
No full textThe Automatic Identification System (AIS) has been globally introduced to increase the maritime safety. When introducing AIS two very high frequency (VHF) channels have been reserved worldwide allowing maritime entities to transmit individual data. The automatically exchanged data provided by shipborne AIS may include the speed of a vessel, its course, heading, rate of turn or its Global Positioning System (GPS) position. Modern bridge devices are connected to AIS allowing to decode and visually represent received AIS data.
Due to the AIS data density, variety and the low effort required to obtain AIS data they have become a research object within the past years. Because of the meaning of AIS data for the maritime field and related research this thesis evaluates AIS data for maritime safety. Hence, a comprehensive analysis of AIS data is part of this work. This analysis gives an essential overview about how shipborne AIS systems are currently configured and used. AIS data attributes relevant for vessel movement prediction and their availability are evaluated and discussed. Furthermore, the AIS reporting intervals are evaluated in detail. With respect to the graphical representation of AIS data on radar systems so far not visually encoded AIS data attributes have been identified in this thesis. An expert group gave feedback about the relevance of these attributes with respect to maritime safety. In addition, visual encodings for these attributes are proposed which have also been judged by the expert group.
Since human error has been identified as the main maritime incident reason a full mission bridge simulator has been used for an integration of live AIS data within this thesis. Moreover, an interactive history-based vessel movement prediction algorithm is proposed within this thesis. The prediction outcome including uncertainty is visualized to the user in a way that mariners are supported in performing collision avoidance
Towards Flexiformal Mathematics
No full textThe application of computer-based methods to mathematics, while meaningful, is constrained by the fact the most mathematical knowledge exists in forms that can only be understood by humans.
In order for it to be also understood by machines, those aspects of mathematical knowledge that are relevant for machine-driven applications need to be made explicit.
One important aspect of mathematics is the underlying semantics which can be made understandable to machines by formalizing it.
Formalization makes explicit the implicit definitions and inference steps that occur naturally in mathematical documents.
But, despite numerous attempts, only a small fragment of mathematics has been formalized because formalization is prohibitively expensive.
Furthermore, existing formalized mathematics typically lacks in other aspects such as presentation information and narrative structure that are common in mathematics and critical for human-oriented practical applications.
Therefore, existing applications for formal mathematics are mostly limited to verification so there is little practical incentive for formalization.
Relying on the idea of flexiformality we propose flexiformalizing mathematics which addresses the bottlenecks discussed above in two ways.
First, by allowing content of flexible formality, it minimizes the starting cost of flexiformalization compared to formalization.
Second, by co-representing the narration, structure and meaning of mathematical knowledge it forms a basis for not only machine processing but also for building practical, human-oriented applications.
We call the result of flexiformalization as described here flexiformal knowledge and we believe mathematical knowledge is fundamentally flexiformal
The Retrotransposon Silencing Complex (RSC) is a key repressor of retrotransposons in Dictyostelium discoideum
No full textAbout 10% of the compact genome of Dictyostelium discoideum comprise of transposable elements (TEs). The active TEs, are highly mutagenic, and they potentially negatively impact the fitness of their host. Dictyostelium’s RNAi machinery and their components, serve as a toolkit indispensable to tightly regulate the activity of TEs. In a recent study, it has been shown that out of three identified RdRPs in the social amoeba (RrpA, RrpB and RrpC), only RrpC plays an important role in the silencing of the most prominent retrotransposon, DIRS-1. Laser scanning microscopy analysis of cells overexpressing RdRP GFP-fusion proteins allowed to describe RrpA and RrpB as nuclear proteins co-localizing with the triple methylated lysine on histone 3 and HcpA, a homologue of Heterochromatin protein 1. In contrast to RrpA and RrpB, the RrpC was found exclusively in the cytoplasm, which correlates with previous findings that DIRS-1-related siRNAs accumulate in the same cellular compartment. The extensive proteomic study of RdRPs, on the side, led to the development of a method to purify the endogenous AgnA protein, a putative interaction partner of RrpC. Moreover, it has been shown, that AgnA binds 21 nt long RNAs. In all likelihood these small RNAs direct the putative complex, formed by RrpC and AgnA, later called Retrotransposon Silencing Complex (RSC) to their targets. Moreover, both parts of the putative RSC plays a crucial role in silencing of DIRS-1 and Skipper. The retrotransposition competency of DIRS-1 and Skipper was monitored by genetically traceable synthetic TEs used in retrotransposition assays. Extending the observation that DIRS-1 and Skipper are silenced by post-transcriptional gene silencing trough the RSC activity, this thesis provides also first indications that Skipper, is also repressed at the level of chromatin via transcriptional gene silencing. This process, RNA-mediated heterochromatisation, appears to involve the activity of RrpA
Production of Biofuels from Microalgae
No full textThe incredible increase in world population, which could reach nine billion by 2050, and the rapid progress of globalization in recent decades have put pressure on the food and energy sectors. The resources currently available for energy production are insufficient to meet future demand. These facts are pushing governments and scientific organizations all over the world to search for alternative renewable energy sources.
Microalgae present an ideal, resurgent resource for the production of biofuels, especially biodiesel and biogas, because their lipid productivity is greater than that of other terrestrial food crops. However, from a biotechnological point of view, the use of microalgae requires further investigation and development to be economically viable, particularly in regard to cost and biomass production.
The most important step in the use of microalgae for biofuel production is strain selection. The optimal strain must be able to withstand outdoor conditions and survive seasonality. Four related manuscripts were prepared during my Ph.D. project. Two of them have been published, one has been submitted for publication, and the fourth is ready for submission. Together, they focus on new strategies for strain selection, lipid production increase, lipid vesicles detection and imaging, total cost reduction strategies, biodiesel production from promising strains, and biogas production from the remaining microalgal residues.
From a practical perspective, only a few microalgal species have been investigated for pharmaceutical and industrial applications. Throughout my Ph.D. project, I have identified microalgal strains able to grow at high temperature and under light stress, as a step toward the development of sustainable microalgal fuels. The four manuscripts that have resulted from my project are described below.
In the first manuscript, entitled “Isolation and characterization of thermo-tolerant Egyptian marine microalgae as proposed candidates for biodiesel pro