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Kinetic modeling and infrared spectroscopy of charge carriers across the plasma-wall interface
(2022)
In this thesis, charge transport at the plasma-wall interface is investigated theoretically, on a semiclassical, microscopic level. Based on the Boltzmann and Poisson equations a set of equations is derived and numerically solved to model charge carriers both within a semiconducting wall and a gaseous plasma in front of it. While the plasma is considered collision-free, within the solid, phonon collisions, as well as recombination processes between conduction band electrons and valence band holes are considered. This results, for the first time, in a self-consistent modeling of both the gaseous electron-ion plasma and the electron-hole plasma in the solid on the same footing. Utilizing specific approximations for different physical scenarios, numerical solutions are presented both for the floating and the electronically contacted (biased) interface. In the latter case, the current voltage characteristic is calculated and shown to heavily depend on the charge kinetics within the wall.
Furthermore, we present optical methods to measure the wall charge noninvasively. These utilize the influence of the deposited surplus charges on the optical reflection coefficient of the surface. By calculating the optical response of these charges, we show that the magnitude of the surface charge can be inferred from the change in the reflectivity of the surface caused by the presence of the plasma. While nonlocal effects are considered, it is shown analytically and numerically that these can be neglected at the scales of the considered physical systems.
An experimental investigation of particle parallel flows has been carried out at Wendelstein 7-X (W7-X), one of the most advanced stellarators in the world. The studies are restricted to the outermost plasma region, the scrape-off layer (SOL), which is shaped to tackle the exhaust problem in vision of future fusion reactors based on plasma magnetic confinement. The aim of the measurements is to set the basis for a physics analysis of the SOL dynamics by obtaining direct information on convective heat transport, together with the assessment of the predominant flow directions of the main plasma ions and of fusion-products or wall-released impurities. In this way, a better comprehension of the interplay between the transport parallel and perpendicular to the SOL field lines can be achieved, contributing to the understanding of the effectiveness of the island divertor configuration.
The chosen instrument for the experimental studies is the Coherence Imaging Spectroscopy (CIS) diagnostic, a camera-based interferometer capable of measuring 2D Doppler particle flows associated with a selected visible line from the plasma. The diagnostic is distinguished by its high time resolution and spatial coverage, allowing the visualisation and measurements of flow velocities for a full module of W7-X simultaneously. A CIS diagnostic has been fully designed for W7-X with an improved level of accuracy achieved thanks to the implementation of a new calibration source, a continuous-wave-emission tunable laser. The laser allowed a full characterization of the diagnostic and a frequent precise calibration, making the CIS system reliable for parallel flow investigations during the operational campaign OP1.2. The validity and importance of the CIS measurements have been further confirmed with dedicated simulation of the SOL plasma parameters by the EMC3-EIRENE code, and by comparisons with other edge diagnostics. The CIS results show the effects related to dynamical changes in the SOL due to impurity gas puffs or the development of a plasma current. Moreover, CIS can be used as a powerful tool to test the limits of the current theoretical models, for example in the case of forward and reversed field experiments.
In this work the mechanisms leading to the generation of the various reactive oxygen and nitrogen species (RONS) in a cold atmospheric plasma (CAP) jet and means to control their composition were studied. The investigated CAP jet kinpen is typically operated with Ar feed gas (pure or with molecular admixtures), driven at a frequency of approximately 1 MHz and features fast ionization waves or guided streamers, traveling at velocities of several km/s. The complex reaction networks were investigated by numerical and experimental techniques. Detailed experimental, analytical and computational investigations on the mass and heat transport in the plasma plume were performed: A novel analytical approach to diffusion in jet flows, the non-dispersive path mapping approximation (NDPM) was developed. The method for the first time allows for an estimation of the ambient species density in the near-field of jets that feature a non-homogeneous flow-field. The NDPM approximation was employed for the evaluation of laser induced fluorescence measurements on OH. Through combining measurements and NDPM approximation, this approach yielded an estimation for the ambient species density at the position of the guided streamers, not only in the laminar, but also in the (standard) turbulent operating regime. Accurate measurements of the temporally averaged ambient species density and temperature in the plasma plume were obtained by quantitative Schlieren measurements. The method yields temperature values with sub-Kelvin accuracy and, through combination with computational fluid dynamics (CFD) simulations, allowed for an estimation of the calorimetric power of the jet. In order to obtain a defined environment for the jet to operate in, a shielding gas device was designed in this work, which creates a gas curtain of defined composition around the plasma plume. The plasma dynamics on the ns timescale was investigated by phase resolved optical measurements. The effect of different shielding compositions ranging from pure N2 to pure O2 on guided streamer propagation was investigated. An electrostatic focusing mechanisms was discovered, which promotes the propagation of guided streamers along the channels formed by a noble gas in the plume of plasma jets operating in electronegative gases (such as air or O2). Two zero-dimensional (volume averaged) models were developed: First, the local processes in the guided streamer were modeled using an electron impact reaction kinetic model, which is closely correlated to densities of metastable argon (Ar*) obtained by laser atom absorption measurements. This first model shows that Ar* is the species which dominantly drives the plasma chemistry in the plasma plume. This is exploited in the second plug-flow reaction kinetics model, which is employed to investigate the formation of long-living RONS and uses an Ar* source term as sole energy input. The model uses the previous experimental data on mass and heat transport and temporal dynamics as input and is in turn verified by quantitative FTIR absorption measurements on O3, NO2, N2O, HNO3 and N2O5 in the far-field of the jet, where large absorption lengths can be achieved using a multi pass cell. For the evaluation of the zero-dimensional model, the time-of-flight of RONS from their generation to reaching the multi pass cell was determined using CFD simulations. The insight gained through this combined experimental-modeling approach on the reaction networks revealed relevant control parameters and enabled adjusting the plasma chemistry towards a desired RONS output. Through choosing appropriate feed-gas admixtures and shielding gas compositions, it is possible to generate an NOx-dominated plasma chemistry, although the jet usually produces a strongly O/O3-dominated chemistry. Understanding and controlling the plasma chemistry of cold atmospheric plasma sources for medical applications is not only essential for research, but is also the key for designing future plasma sources for specific medical applications that yield an optimum efficacy and avoid potential side effects of plasma treatment.
The central aim of this thesis was the investigation of protein/polyanion interaction using circular dichroism (CD) spectroscopy, enzyme immune assay (EIA), isothermal titration calorimetry (ITC) and flow cytometry (FC). A further aim was to understand why an endogenous protein becomes immuno-genic when forming a complex. The focus was on the protein platelet factor (PF4), which gained wide interest in the clinical field, due to its role in the life-threatening, immune-driven, adverse drug effect heparin-induced thrombocytopenia (HIT). PF4 is a small homotetrameric chemokine with several basic amino acids on its surface, forming a positively charged ring. The antibodies that are formed during HIT recognize an epitope exposed on PF4, when it is in a complex with heparin at a certain molar ratio at which, PF4 tetramers are aligned on the heparin and forced into close approximation. The main results and conclusions of the thesis are summarized below: 5.1 Evolutionary Conservation of PF4 (Paper I – PF4/Evolution) By carrying out an amino acid sequence survey we found that the positively charged amino acids contributing to the heparin binding site on the surface of PF4 and related proteins are highly conserved in all vertebrates, including fish species. PF4 interacts with the phospholipid lipid A, the innermost part of the lipopolysaccharide (LPS) of Gram negative bacteria. We showed that the shorter the sugar chain of the O antigen, outer and inner core of the LPS were the more PF4 was binding. The interaction of PF4 with lipid A is inhibited by heparin, suggesting that the amino acids known to contribute to heparin binding are also involved in binding to lipid A. 5.2 PF4 Interaction with Polyanions (PA) of varying Length and Degree of Sulfation (Paper II – PF4/PA) CD spectroscopy was found to be a powerful technique to monitor structural changes of PF4 caused by binding to various clinically relevant polyanions. Therefore PF4 was titrated with different PA to investigate the dependencies: i. impact of the PF4:PA molar ratio, ii. degree of polymerization of the PA and iii. degree of sulfation of the PA. In all cases, exposure of HIT-relevant epitope(s) was only observed for PA that also induced changes in secondary structure of PF4. A comparison of results of an immune ¬assay with CD spectroscopic data showed that the extent of complex anti¬genicity correlates well with the magnitude of changes in PF4 secondary structure, and that the structural changes of PF4 have to exceed a certain threshold to achieve PF4/PA complex antigenicity. These findings allowed us to calculate expectation intervals for complex antigenicity solely using CD spectroscopic data. To our knowledge, this was the first demonstration that the capability of drugs to induce antigenicity of PF4 can be assessed without the necessity of in vivo studies or the use of antibodies obtained from immunized patients specific for the antigens. The antigenicity of PF4 in complex is not restricted to negative charges originating from sulfate groups, PA with phosphate groups are also capable (binding to phospholipids). We investigated inorganic polyphosphates (polyP) with a chain length of 75 Pi and showed that the induced secondary structural changes are even higher compared to the changes induced by the different heparins and that the PF4/P75 complexes are antigenic as well. 5.3 PF4 Interaction with defined oligomeric Heparins (Paper III – PF4/defined Heparins) We tested highly purified, monodisperse heparins. In contrast to the clinically relevant but relatively undefined (high polydispersity index) glycosamino glycans reported in paper II (PF4/PA). The defined heparins induced higher secondary structural changes. Here we showed for the first time that strong conformational changes during PF4/PA complex formation are necessary but not sufficient for to the expression of the anti-PF4/heparin antibody binding site. Also, the size of the complexes is not the only prerequisite for anti-PF4/heparin antibody binding (tested by atomic force microscopy). By ITC we found that antigenicity is only induced if the PF4/PA complex has a high binding enthalpy and the complex formation leads to a negative change in entropy. 5.4 PF4/Polyphosphates (polyP) Complex Antigenicity and Interaction with Escherichia coli (E. coli, Paper IV – PF4/polyP) PolyP with chain lengths of 45 Pi and 75 Pi induced remarkable secondary structural changes in the PF4 molecule, thereby exposing the epitope recognized by anti-PF4/heparin antibodies. The induced conformational changes were similar to the changes induced by the defined heparins. Again a high binding enthalpy was observed but here in connection with a positive change in entropy. Further we showed that polyP (≥45 Pi) enhance PF4 binding to the surface of Gram negative E. coli at intermediate concentration and disrupt the binding at elevated polyP concentrations. The increased amounts of PF4 on the bacterial surface also improved the binding of anti-PF4/heparin antibodies and thereby the phagocytosis of the bacteria by poly¬morpho¬nuclear leucocytes. 5.5 Nucleic acid based Aptamers induce structural Changes in the PF4 Molecule (Paper V – PF4/Aptamer) Nucleic acids are another class of molecules containing phosphate groups. Especially after cell damage their extra¬cellular concentration can be locally quite high (>2 mg/ml). We found that certain aptamers form complexes with PF4 and thereby inducing anti-PF4/aptamer antibodies which cross-react with PF4/heparin complexes. Moreover by CD spectroscopy we showed that the protein C-aptamer caused similar secondary structural changes of PF4 like heparin, but already at much lower concentration. The maximally induced changes by the protein-C aptamer were even higher and persisted over a broader concentration range. 5.6 Protamine Interaction with Heparin (Paper VI – PS/Heparin) After the intensive investigation of the complex formation between PF4 and many different classes of PA we assessed another protein for structural changes upon complex formation with heparin. Protamine (PS) a protein in routinely used in post-cardiac surgery to reverse the anticoagulant effects of heparin was found to unfold but not to refold with increasing concentration of PA in solution. 5.7 Conclusion and Outlook When starting this thesis, it was believed that repetitive structures formed by PF4 on a heparin chain mold the epitope recognized by antibodies inducing HIT. These repetitive structures might exhibit similarities with viral capsids and are therefore recognized by the immune system of some patients. We found that induced by the close approximation PF4 changes its conformation, thereby exposing a neoepitope. The conserved positively charged amino acids of the heparin binding site and the involvement of these amino acids in the binding to lipid A confirm our hypothesis of PF4 as part of an ancient immune-mediated host defense mechanism. As possible consequence of the “primitive mechanism of defense” the highly variable O-antigens of LPS might have significantly contributed to an efficient escape mechanism by hiding the structures that made the bacteria vulnerable. In turn polyP might be an adaption of the host improve pathogen recognition by PF4 and further by antibodies inducing phagocytosis of the PF4-marked objects. Although shown only for PF4 and PS, our findings might be applicable to other proteins that also express epitopes upon changes in their secondary structure. Our physicochemical methods may further be applied: i. to drug development for the prediction of antigenicity induced by polyanionic drugs, ii. to guide the development of synthetic heparins and other polyanion based drugs, e.g. aptamers, that do not lead to HIT and iii. to provide relevant aspects for other biological functions of heparins.
Indoloquinoline derivatives are very interesting compounds for pharmaceutical applications because of their broad spectrum of biological activity. However, phenyl-substituted indoloquinolines suffer from solubility problems in aqueous solution and require the synthesis of better soluble derivatives for their effective application. Therefore, the indoloquinoline derivatives were covalently attached to two different types of cationic aminoalkyl linkers. After having successfully established the synthesis and subsequent purification of the novel derivatives that could be isolated in excellent yields, these ligands were characterized in this thesis with regard to their spectral properties in different environments and their sequence specific binding to different types of nucleic acids with a variety of spectroscopic methods.
Triple helix-forming oligonucleotides (TFOs) are one of the most specific DNA duplex binding agents and offer new perspectives towards oligonucleotide-mediated gene regulation and manipulation. However, the poor thermodynamic stability of DNA triplexes under physiological conditions limits a successful application in the antigene strategy. Thus, the conjugation of TFOs with small triplex-specific binding ligands is a promising approach to stabilize the formed complexes and to enhance their overall binding affinity. The present study focused on the synthesis of novel TFO conjugates with triplex-binding indolo[3,2-b]quinoline derivatives (PIQ) and on their ability to form and stabilize intermolecular triplexes through their recognition of a duplex target. During the course of the work the thermodynamics of conjugate binding and structural aspects of drug-DNA interactions have been characterized by a variety of spectroscopic and calorimetric techniques.