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Deoxyribonucleic acid (DNA) is the carrier of human genetic information and is exposed to environmental influences such as the ultraviolet (UV) fraction of sunlight every day. The photostability of the DNA against UV light is astonishing. Even if the DNA bases have a strong absorption maximum at around 260 nm/4.77 eV, their quantum yield of photoproducts remains very low 1. If the photon energies exceed the ionization energy (IE) of the nucleobases ( ̴ 8-9 eV) 2, the DNA can be severely damaged. Photoexcitation and -ionization reactions occur, which can induce strand breaks in the DNA. The efficiency of the excitation and ionization induced strand breaks in the target DNA sequences are represented by cross sections. If Si as a substrate material is used in the VUV irradiation experiments, secondary electrons with an energy below 3.6 eV are generated from the substrate. This low energy electrons (LEE) are known to induce dissociative electron attachment (DEA) in DNA and with it DNA strand breakage very efficiently. LEEs play an important role in cancer radiation therapy, since they are generated secondarily along the radiation track of ionizing radiation.
In the framework of this thesis, different single stranded DNA sequences were irradiated with 8.44 eV vacuum UV (VUV) light and cross sections for single strand breaks (SSB) were determined. Several sequences were also exposed to secondary LEEs, which additionally contributed to the SSBs. First, the cross sections for SSBs depending on the type of nucleobases were determined. Both types of DNA sequences, mono-nucleobase and mixed sequences showed very similar results upon VUV radiation. The additional influence of secondarily generated LEEs resulted in contrast in a clear trend for the SSB cross sections. In this, the polythymine sequence had the highest cross section for SSBs, which can be explained by strong anionic resonances in this energy range. Furthermore, SSB cross sections were determined as a function of sequence length. This resulted in an increase in the strand breaks to the same extent as the increase in the geometrical cross section. The longest DNA sequence (20 nucleotides) investigated in this series, however, showed smaller cross section values for SSBs, which can be explained by conformational changes in the DNA. Moreover, several DNA sequences that included the radiosensitizers 5-Bromouracil (5BrU) and 8-Bromoadenine (8BrA) were investigated and the corresponding SSB cross sections were determined. It was shown that 5BrU reacts very strongly to VUV radiation leading to high strand break yields, which showed in turn a strong sequence-dependency. 8BrA, on the other hand, showed no sensitization to the applied VUV radiation, since almost no increase in strand breakage yield was observed in comparison to non-modified DNA sequences.
In order to be able to identify the mechanisms of radiation damage by photons, the IEs of certain DNA sequences were further explored using photoionization tandem mass spectrometry. By varying the DNA sequence, both the IEs depending on the type of nucleobase as well as on the DNA strand length could be identified and correlated to the SSB cross sections. The influence of the IE on the photoinduced reaction in the brominated DNA sequences could be excluded.
Nanophotonics is the field of science and engineering aimed at studying the light-matter interactions on the nanoscale. One of the key aspects in studying such optics at the nanoscale is the ability to assemble the material components in a spatially controlled manner. In this work, DNA origami nanostructures were used to self-assemble dye molecules and DNA coated plasmonic nanoparticles. Optical properties of dye nanoarrays, where the dyes were arranged at distances where they can interact by Förster resonance energy transfer (FRET), were systematically studied according to the size and arrangement of the dyes using fluorescein (FAM) as the donor and cyanine 3 (Cy 3) as the acceptor. The optimized design, based on steady-state and time-resolved fluorometry, was utilized in developing a ratiometric pH sensor with pH-inert coumarin 343 (C343) as the donor and pH-sensitive FAM as the acceptor. This design was further applied in developing a ratiometric toxin sensor, where the donor C343 is unresponsive and FAM is responsive to thioacetamide (TAA) which is a well-known hepatotoxin. The results indicate that the sensitivity of the ratiometric sensor can be improved by simply arranging the dyes into a well-defined array. The ability to assemble multiple fluorophores without dye-dye aggregation also provides a strategy to amplify the signal measured from a fluorescent reporter, and was utilized here to develop a reporter for sensing oligonucleotides. By incorporating target capturing sequences and multiple fluorophores (ATTO 647N dye molecules), a reporter for microbead-based assay for non-amplified target oligonucleotide sensing was developed. Analysis of the assay using VideoScan, a fluorescence microscope-based technology capable of conducting multiplex analysis, showed the DNA origami nanostructure based reporter to have a lower limit of detection than a single stranded DNA reporter. Lastly, plasmonic nanostructures were assembled on DNA origami nanostructures as substrates to study interesting optical behaviors of molecules in the near-field. Specifically, DNA coated gold nanoparticles, silver nanoparticles, and gold nanorods, were placed on the DNA origami nanostructure aiming to study surface-enhanced fluorescence (SEF) and surface-enhanced Raman scattering (SERS) of molecules placed in the hotspot of coupled plasmonic structures.
Microbial processing of organic matter (OM) in the freshwater biosphere is a key component of global biogeochemical cycles. Freshwaters receive and process valuable amounts of leaf OM from their terrestrial landscape. These terrestrial subsidies provide an essential source of energy and nutrients to the aquatic environment as a function of heterotrophic processing by fungi and bacteria. Particularly in freshwaters with low in-situ primary production from algae (microalgae, cyanobacteria), microbial turnover of leaf OM significantly contributes to the productivity and functioning of freshwater ecosystems and not least their contribution to global carbon cycling.
Based on differences in their chemical composition, it is believed that leaf OM is less bioavailable to microbial heterotrophs than OM photosynthetically produced by algae. Especially particulate leaf OM, consisting predominantly of structurally complex and aromatic polymers, is assumed highly resistant to enzymatic breakdown by microbial heterotrophs. However, recent research has demonstrated that OM produced by algae promotes the heterotrophic breakdown of leaf OM in aquatic ecosystems, with profound consequences for the metabolism of leaf carbon (C) within microbial food webs. In my thesis, I aimed at investigating the underlying mechanisms of this so called priming effect of algal OM on the use of leaf C in natural microbial communities, focusing on fungi and bacteria.
The works of my thesis underline that algal OM provides highly bioavailable compounds to the microbial community that are quickly assimilated by bacteria (Paper II). The substrate composition of OM pools determines the proportion of fungi and bacteria within the microbial community (Paper I). Thereby, the fraction of algae OM in the aquatic OM pool stimulates the activity and hence contribution of bacterial communities to leaf C turnover by providing an essential energy and nutrient source for the assimilation of the structural complex leaf OM substrate. On the contrary, the assimilation of algal OM remains limited for fungal communities as a function of nutrient competition between fungi and bacteria (Paper I, II). In addition, results provide evidence that environmental conditions determine the strength of interactions between microalgae and heterotrophic bacteria during leaf OM decomposition (Paper I, III). However, the stimulatory effect of algal photoautotrophic activities on leaf C turnover remained significant even under highly dynamic environmental conditions, highlighting their functional role for ecosystem processes (Paper III).
The results of my thesis provide insights into the mechanisms by which algae affect the microbial turnover of leaf C in freshwaters. This in turn contributes to a better understanding of the function of algae in freshwater biogeochemical cycles, especially with regard to their interaction with the heterotrophic community.
In a changing world facing several direct or indirect anthropogenic challenges the freshwater resources are endangered in quantity and quality. An excessive supply of nutrients, for example, can cause disproportional phytoplankton development and oxygen deficits in large rivers, leading to failure of the aims requested by the Water Framework Directive (WFD). Such problems can be observed in many European river catchments including the Elbe basin, and effective measures for improving water quality status are highly appreciated.
In water resources management and protection, modelling tools can help to understand the dominant nutrient processes and to identify the main sources of nutrient pollution in a watershed. They can be effective instruments for impact assessments investigating the effects of changing climate or socio-economic conditions on the status of surface water bodies, and for testing the usefulness of possible protection measures. Due to the high number of interrelated processes, ecohydrological model approaches containing water quality components are more complex than the pure hydrological ones, and their setup and calibration require more efforts. Such models, including the Soil and Water Integrated Model (SWIM), still need some further development and improvement.
Therefore, this cumulative dissertation focuses on two main objectives: 1) the approach-related objectives aiming in the SWIM model improvement and further development regarding nutrient (nitrogen and phosphorus) process description, and 2) the application-related objectives in meso- to large-scale Elbe river basins to support adaptive river basin management in view of possible future changes. The dissertation is based on five scientific papers published in international journals and dealing with these research questions.
Several adaptations were implemented in the model code to improve the representation of nutrient processes including a simple wetland approach, an extended by ammonium nitrogen cycle in the soils, as well as a detailed in-stream module, simulating algal growth, nutrient transformation processes and oxygen conditions in the river reaches, mainly driven by water temperature and light. Although this new approaches created a highly complex ecohydrological model with a large number of additional calibration parameters and rising uncertainty, the calibration and validation of the SWIM model enhanced by the new approaches in selected subcatchment and the entire Elbe river basin delivered satisfactory to good model results in terms of criteria of fit. Thus, the calibrated and validated model provided a sound base for the assessment of possible future changes and impacts in climate, land use and management in the Elbe river (sub)basin(s).
The new enhanced modelling approach improved the applicability of the SWIM model for the WFD related research questions, where the ability to consider biological water quality components (such as phytoplankton) is important. It additionally enhanced its ability to simulate the behaviour of nutrients coming mainly from point sources (e.g. phosphate phosphorus). Scenario results can be used by decision makers and stakeholders to find and understand future challenges and possible adaptation measures in the Elbe river basin.
Poly(vinylidene fluoride-trifluoroethylene) (P(VDF-TrFE)) ferroelectric thin films of different molar ratio have been studied with regard to data memory applications. Therefore, films with thicknesses of 200 nm and less have been spin coated from solution. Observations gained from single layers have been extended to multilayer capacitors and three terminal transistor devices.
Besides conventional hysteresis measurements, the measurement of dielectric non-linearities has been used as a main tool of characterisation. Being a very sensitive and non-destructive method, non-linearity measurements are well suited for polarisation readout and property studies. Samples have been excited using a high quality, single-frequency sinusoidal voltage with an amplitude significantly smaller than the coercive field of the samples. The response was then measured at the excitation frequency and its higher harmonics. Using the measurement results, the linear and non-linear dielectric permittivities ɛ₁, ɛ₂ and ɛ₃ have been determined. The permittivities have been used to derive the temperature-dependent polarisation behaviour as well as the polarisation state and the order of the phase transitions.
The coercive field in VDF-TrFE copolymers is high if compared to their ceramic competitors. Therefore, the film thickness had to be reduced significantly. Considering a switching voltage of 5 V and a coercive field of 50 MV/m, the film thickness has to be 100 nm and below. If the thickness becomes substantially smaller than the other dimensions, surface and interface layer effects become more pronounced. For thicker films of P(VDF-TrFE) with a molar fraction of 56/44 a second-order phase transition without a thermal hysteresis for an ɛ₁(T) temperature cycle has been predicted and observed. This however, could not be confirmed by the measurements of thinner films. A shift of transition temperatures as well as a temperature independent, non-switchable polarisation and a thermal hysteresis for P(VDF-TrFE) 56/44 have been observed. The impact of static electric fields on the polarisation and the phase transition has therefore been studied and simulated, showing that all aforementioned phenomena including a linear temperature dependence of the polarisation might originate from intrinsic electric fields.
In further experiments the knowledge gained from single layer capacitors has been extended to bilayer copolymer thin films of different molar composition. Bilayers have been deposited by succeeding cycles of spin coating from solution. Single layers and their bilayer combination have been studied individually in order to prove the layers stability. The individual layers have been found to be physically stable. But while the bilayers reproduced the main ɛ₁(T) properties of the single layers qualitatively, quantitative numbers could not be explained by a simple serial connection of capacitors. Furthermore, a linear behaviour of the polarisation throughout the measured temperature range has been observed. This was found to match the behaviour predicted considering a constant electric field.
Retention time is an important quantity for memory applications. Hence, the retention behaviour of VDF-TrFE copolymer thin films has been determined using dielectric non-linearities. The polarisation loss in P(VDF-TrFE) poled samples has been found to be less than 20% if recorded over several days. The loss increases significantly if the samples have been poled with lower amplitudes, causing an unsaturated polarisation. The main loss was attributed to injected charges. Additionally, measurements of dielectric non-linearities have been proven to be a sensitive and non-destructive tool to measure the retention behaviour.
Finally, a ferroelectric field effect transistor using mainly organic materials (FerrOFET) has been successfully studied. DiNaphtho[2,3-b:2',3'-f]Thieno[3,2-b]Thiophene (DNTT) has proven to be a stable, suitable organic semiconductor to build up ferroelectric memory devices. Furthermore, an oxidised aluminium bottom electrode and additional dielectric layers, i.e. parylene C, have proven to reduce the leakage current and therefore enhance the performance significantly.
Amorphous calcium carbonate(ACC) is a wide spread biological material found in many organisms, such as sea Urchins and mollusks, where it serves as either a precursor phase for the crystalline biominerals or is stabilized and used in the amorphous state. As ACC readily crystallizes, stabilizers such as anions, cations or macromolecules are often present to avoid or delay unwanted crystallization. Furthermore, additives often control the properties of the materials to suit the specific function needed for the organism. E.g. cystoliths in leaves that scatter light to optimize energy uptake from the sun or calcite/aragonite crystals used in protective shells in mussels and gastropods. Lifetime of the amorphous phase is controlled by the kinetic stability against crystallization. This has often been linked to water which plays a role in the mobility of ions and hence the probability of forming crystalline nuclei to initiate crystallization. However, it is unclear how the water molecules are incorporated within the amorphous phase, either as liquid confined in pores, as structural water binding to the ions or as a mixture of both. It is also unclear how this is perturbed when additives are added, especially Mg2+, one the most common additives found in biogenic samples. Mg2+ are expected to have a strong influence on the water incorporated into ACC, given the high energy barrier to dehydration of magnesium ions compared to calcium ions in solution.
During the last 10-15 years, there has been a large effort to understand the local environment of the ions/molecules and how this affects the properties of the amorphous phase. But only a few aspects of the structure have so far been well-described in literature. The reason for this is partly caused by the low stability of ACC if exposed to air, where it tends to crystallize within minutes and by the limited quantities of ACC produced in traditional synthesis routes. A further obstacle has been the difficulty in modeling the local structure based on experimental data. To solve the problem of stability and sample size, a few studies have used stabilizers such as Mg2+ or OH- and severely dehydrated samples so as to stabilize the amorphous state, allowing for combined neutron and x-ray analysis to be performed. However, so far, a clear description of the local environments of water present in the structure has not been reported.
In this study we show that ACC can be synthesized without any stabilizing additives in quantities necessary for neutron measurements and that accurate models can be derived with the help of empirical-potential structural refinement. These analyses have shown that there is a wide range of local environments for all of the components in the system suggesting that the amorphous phase is highly inhomogeneous, without any phase separation between ions and water. We also showed that the water in ACC is mainly structural and that there is no confined or liquid-like water present in the system. Analysis of amorphous magnesium carbonate also showed that there is a large difference in the local structure of the two cations and that Mg2+ surprisingly interacts with significantly less water molecules then Ca2+ despite the higher dehydration energy. All in all, this shows that the role of water molecules as a structural component of ACC, with a strong binding to cat- and anions probably retard or prevents the crystallization of the amorphous phase.
Future magnetic recording industry needs a high-density data storage technology. However, switching the magnetization of small bits requires high magnetic fields that cause excessive heat dissipation. Therefore, controlling magnetism without applying external magnetic field is an important research topic for potential applications in data storage devices with low power consumption. Among the different approaches being investigated, two of them stand out, namely i) all-optical helicity dependent switching (AO-HDS) and ii) ferroelectric control of magnetism. This thesis aims to contribute towards a better understanding of the physical processes behinds these effects as well as reporting new and exciting possibility for the optical and/or electric control of magnetic properties. Hence, the thesis contains two differentiated chapters of results; the first devoted to AO-HDS on TbFe alloys and the second to the electric field control of magnetism in an archetypal Fe/BaTiO3 system.
In the first part, the scalability of the AO-HDS to small laser spot-sizes of few microns in the ferrimagnetic TbFe alloy is investigated by spatially resolving the magnetic contrast with photo-emission electron microscopy (PEEM) and X-ray magnetic circular dichroism (XMCD). The results show that the AO-HDS is a local effect within the laser spot size that occurs in the ring-shaped region in the vicinity of thermal demagnetization. Within the ring region, the helicity dependent switching occurs via thermally activated domain wall motion. Further, the thesis reports on a novel effect of thickness dependent inversion of the switching orientation. It addresses some of the important questions like the role of laser heating and the microscopic mechanism driving AO-HDS.
The second part of the thesis focuses on the electric field control of magnetism in an artificial multiferroic heterostructure. The sample consists of an Fe wedge with thickness varying between 0:5 nm and 3 nm, deposited on top of a ferroelectric and ferroelastic BaTiO3 [001]-oriented single crystal substrate. Here, the magnetic contrast is imaged via PEEM and XMCD as a function of out-of-plane voltage. The results show the evidence of the electric field control of superparamagnetism mediated by a ferroelastic modification of the magnetic anisotropy. The changes in the magnetoelastic anisotropy drive the transition from the superparamagnetic to superferromagnetic state at localized sample positions.
Synchrotron-based angle-resolved time-of-flight electron spectroscopy for dynamics in dichalogenides
(2018)
In this thesis, we discuss the characterization of orthogroups by so-called disjunctions of identities. The orthogroups are a subclass of the class of completely regular semigroups, a generalization of the concept of a group. Thus there is for all elements of an orthogroup some kind of an inverse element such that both elements commute. Based on a fundamental result by A.H. Clifford, every completely regular semigroup is a semilattice of completely simple semigroups. This allows the description the gross structure of such semigroup. In particular every orthogroup is a semilattice of rectangular groups which are isomorphic to direct products of rectangular bands and groups. Semilattices of rectangular groups coming from various classes are characterized using the concept of an alternative variety, a generalization of the classical idea of a variety by Birkhoff.
After starting with some fundamental definitions and results concerning semigroups, we introduce the concept of disjunctions of identities and summarize some necessary properties. In particular we present some disjunction of identities which is sufficient for a semigroup for being completely regular. Furthermore we derive from this identity some statements concerning Rees matrix semigroups, a possible representation of completely simple semigroups. A main result of this thesis is the general description of disjunctions of identities such that a completely regular semigroup satisfying the described identity is a semilattice of left groups (right groups / groups). In this case the completely regular semigroup is an orthogroup. Furthermore we define various classes of rectangular groups such that there is an exponent taken from a set of pairwise coprime positive integers. An important result is the characterization of the class of all semilattices of particular rectangular groups (taken from the classes defined before) using a set-theoretic minimal set of disjunctions of identities. Additionally we investigate semilattices of groups (so-called Clifford semigroups). For this purpose we consider abelian groups of particular exponents and prove some well-known results from the theory of Clifford semigroups in an alternative way applying the concept of disjunctions of identities. As a practical application of the results concerning semilattices of left zero semigroups and right zero semigroups we identify a particular transformation semigroup. For more detailed information about the product of two arbitrary elements of a semilattice of semigroups we introduce the concept of strong semilattices of semigroups. It is well-known that a semilattice of groups is a strong semilattice of groups. So we can characterize a strong semilattice of groups of particular pairwise coprime exponents by disjunctions of identities. Additionally we describe the class of all strong semilattices of left zero semigroups and right zero semigroups with the help of such kind of identity, and we relate this statement to the theory of normal bands. A possible extension of the already described semilattices of rectangular groups can be achieved by an auxiliary total order (in terms of chains of semigroups). To this end we present a corresponding characterization due to disjunctions of identities which is obviously minimal. A list of open questions which have arisen during the research for this thesis, but left crude, is attached.
Systemic inflammation is a hallmark of cancer cachexia. Among tumor-host interactions, the white adipose tissue (WAT) is an important contributor to inflammation as it suffers morphological reorganization and lipolysis, releasing free fatty acids (FA), bioactive lipid mediators (LM) and pro-inflammatory cytokines, which accentuate the activation of pro-inflammatory signaling pathways and the recruitment of immune cells to the tissue. This project aimed to investigate which inflammatory factors are involved in the local adipose tissue inflammation and what is the influence of such factors upon enzymes involved in FA or LM metabolism in healthy individuals (Control), weight stable gastro-intestinal cancer patients (WSC) and cachectic cancer patients (CC). The results demonstrated that the inflammatory signature of systemic inflammation is different from local adipose tissue inflammation. The systemic inflammation of the cachectic cancer patients was characterized by higher levels of circulating saturated fatty acids (SFA), tumor-necrosis-factor-α (TNF-α), interleukins IL-6, IL-8 and CRP while levels of polyunsaturated fatty acids (PUFAs), especially n3-PUFAs, were lower in CC than in the other groups. In vitro and in adipose tissue explants, pro-inflammatory cytokines and SFAs were shown to increase the chemokines IL-8 and CXCL10 that were found to be augmented in adipose tissue inflammation in CC which was more profound in the visceral adipose tissue (VAT) than in subcutaneous adipose tissue (SAT). Systemic inflammation was negatively associated with the expression of PUFA synthesizing enzymes, though gene and protein expression did hardly differ between groups. The effects of inflammatory factors on enzymes in the whole tissue could have been masked by differentiated modulation of the diverse cell types in the same tissue. In vitro experiments showed that the expression of FA-modifying enzymes such as desaturases and elongases in adipocytes and macrophages was regulated into opposing directions by TNF-α, IL-6, LPS or palmitate. The higher plasma concentration of the pro-resolving LM resolvin D1 in CC cannot compensate the overall inflammatory status and the results indicate that inflammatory cytokines interfere with synthesis pathways of pro-resolving LM. In summary, the data revealed a complex inter-tissue and inter-cellular crosstalk mediated by pro-inflammatory cytokines and lipid compounds enhancing inflammation in cancer cachexia by feed-forward mechanisms.
Various ways of preparing enantiomerically pure 2-amino[6]helicene derivatives were explored. Ni(0) mediated cyclotrimerization of enantiopure triynes provided (M)- and (P)-7,8-bis(p-tolyl)hexahelicene-2-amine in >99% ee as well as its benzoderivative in >99% ee. The stereocontrol was found to be inefficient for a 2- aminobenzo[6]helicene congener with an embedded five-membered ring. Helically chiral imidazolium salts bearing one or two helicene moieties have been synthesized and applied in enantioselective [2+2+2] cyclotrimerization catalyzed by an in situ formed Ni(0)-NHC complex. The synthesis of the first helically chiral Pd- and Ru-NHC complexes and their application in enantioselective catalysis was demonstrated. The latter shows promising results in enantioselective olefin metathesis reactions. A mechanistic proposal for asymmetric ring closing metathesis is provided.
Thematic role assignment and word order preferences in the child language acquisition of Tagalog
(2018)
A critical task in daily communications is identifying who did what to whom in an utterance, or assigning the thematic roles agent and patient in a sentence. This dissertation is concerned with Tagalog-speaking children’s use of word order and morphosyntactic markers for thematic role assignment. It aims to explain children’s difficulties in interpreting sentences with a non-canonical order of arguments (i.e., patient-before-agent) by testing the predictions of the following accounts: the frequency account (Demuth, 1989), the Competition model (MacWhinney & Bates, 1989), and the incremental processing account (Trueswell & Gleitman, 2004). Moreover, the experiments in this dissertation test the influence of a word order strategy in a language like Tagalog, where the thematic roles are always unambiguous in a sentence, due to its verb-initial order and its voice-marking system. In Tagalog’s voice-marking system, the inflection on the verb indicates the thematic role of the noun marked by 'ang.' First, the possible basis for a word order strategy in Tagalog was established using a sentence completion experiment given to adults and 5- and 7-year-old children (Chapter 2) and a child-directed speech corpus analysis (Chapter 3). In general, adults and children showed an agent-before-patient preference, although adults’ preference was also affected by sentence voice. Children’s comprehension was then examined through a self-paced listening and picture verification task (Chapter 3) and an eye-tracking and picture selection task (Chapter 4), where word order (agent-initial or patient-initial) and voice (agent voice or patient voice) were manipulated. Offline (i.e., accuracy) and online (i.e., listening times, looks to the target) measures revealed that 5- and 7-year-old Tagalog-speaking children had a bias to interpret the first noun as the agent. Additionally, the use of word order and morphosyntactic markers was found to be modulated by voice. In the agent voice, children relied more on a word order strategy; while in the patient voice, they relied on the morphosyntactic markers. These results are only partially explained by the accounts being tested in this dissertation. Instead, the findings support computational accounts of incremental word prediction and learning such as Chang, Dell, & Bock’s (2006) model.
How can interactive devices connect with users in the most immediate and intimate way? This question has driven interactive computing for decades. Throughout the last decades, we witnessed how mobile devices moved computing into users’ pockets, and recently, wearables put computing in constant physical contact with the user’s skin. In both cases moving the devices closer to users allowed devices to sense more of the user, and thus act more personal. The main question that drives our research is: what is the next logical step?
Some researchers argue that the next generation of interactive devices will move past the user’s skin and be directly implanted inside the user’s body. This has already happened in that we have pacemakers, insulin pumps, etc. However, we argue that what we see is not devices moving towards the inside of the user’s body, but rather towards the body’s biological “interface” they need to address in order to perform their function.
To implement our vision, we created a set of devices that intentionally borrow parts of the user’s body for input and output, rather than adding more technology to the body.
In this dissertation we present one specific flavor of such devices, i.e., devices that borrow the user’s muscles. We engineered I/O devices that interact with the user by reading and controlling muscle activity. To achieve the latter, our devices are based on medical-grade signal generators and electrodes attached to the user’s skin that send electrical impulses to the user’s muscles; these impulses then cause the user’s muscles to contract.
While electrical muscle stimulation (EMS) devices have been used to regenerate lost motor functions in rehabilitation medicine since the 1960s, in this dissertation, we propose a new perspective: EMS as a means for creating interactive systems.
We start by presenting seven prototypes of interactive devices that we have created to illustrate several benefits of EMS. These devices form two main categories: (1) Devices that allow users eyes-free access to information by means of their proprioceptive sense, such as the value of a variable in a computer system, a tool, or a plot; (2) Devices that increase immersion in virtual reality by simulating large forces, such as wind, physical impact, or walls and heavy objects.
Then, we analyze the potential of EMS to build interactive systems that miniaturize well and discuss how they leverage our proprioceptive sense as an I/O modality. We proceed by laying out the benefits and disadvantages of both EMS and mechanical haptic devices, such as exoskeletons.
We conclude by sketching an outline for future research on EMS by listing open technical, ethical and philosophical questions that we left unanswered.
Spectroscopy at the limit
(2018)
The aim of this doctoral thesis was to establish a technique for the analysis of biomolecules with infrared matrix-assisted laser dispersion (IR-MALDI) ion mobility (IM) spectrometry. The main components of the work were the characterization of the IR-MALDI process, the development and characterization of different ion mobility spectrometers, the use of IR-MALDI-IM spectrometry as a robust, standalone spectrometer and the development of a collision cross-section estimation approach for peptides based on molecular dynamics and thermodynamic reweighting.
First, the IR-MALDI source was studied with atmospheric pressure ion mobility spectrometry and shadowgraphy. It consisted of a metal capillary, at the tip of which a self-renewing droplet of analyte solution was met by an IR laser beam. A relationship between peak shape, ion desolvation, diffusion and extraction pulse delay time (pulse delay) was established. First order desolvation kinetics were observed and related to peak broadening by diffusion, both influenced by the pulse delay. The transport mechanisms in IR-MALDI were then studied by relating different laser impact positions on the droplet surface to the corresponding ion mobility spectra. Two different transport mechanisms were determined: phase explosion due to the laser pulse and electrical transport due to delayed ion extraction. The velocity of the ions stemming from the phase explosion was then measured by ion mobility and shadowgraphy at different time scales and distances from the source capillary, showing an initially very high but rapidly decaying velocity. Finally, the anatomy of the dispersion plume was observed in detail with shadowgraphy and general conclusions over the process were drawn.
Understanding the IR-MALDI process enabled the optimization of the different IM spectrometers at atmospheric and reduced pressure (AP and RP, respectively). At reduced pressure, both an AP and an RP IR-MALDI source were used. The influence of the pulsed ion extraction parameters (pulse delay, width and amplitude) on peak shape, resolution and area was systematically studied in both AP and RP IM spectrometers and discussed in the context of the IR-MALDI process. Under RP conditions, the influence of the closing field and of the pressure was also examined for both AP and RP sources. For the AP ionization RP IM spectrometer, the influence of the inlet field (IF) in the source region was also examined. All of these studies led to the determination of the optimal analytical parameters as well as to a better understanding of the initial ion cloud anatomy.
The analytical performance of the spectrometer was then studied. Limits of detection (LOD) and linear ranges were determined under static and pulsed ion injection conditions and interpreted in the context of the IR-MALDI mechanism. Applications in the separation of simple mixtures were also illustrated, demonstrating good isomer separation capabilities and the advantages of singly charged peaks. The possibility to couple high performance liquid chromatography (HPLC) to IR-MALDI-IM spectrometry was also demonstrated. Finally, the reduced pressure spectrometer was used to study the effect of high reduced field strength on the mobility of polyatomic ions in polyatomic gases.
The last focus point was on the study of peptide ions. A dataset obtained with electrospray IM spectrometry was characterized and used for the calibration of a collision cross-section (CCS) determination method based on molecular dynamics (MD) simulations at high temperature. Instead of producing candidate structures which are evaluated one by one, this semi-automated method uses the simulation as a whole to determine a single average collision cross-section value by reweighting the CCS of a few representative structures. The method was compared to the intrinsic size parameter (ISP) method and to experimental results. Additional MD data obtained from the simulations was also used to further analyze the peptides and understand the experimental results, an advantage with regard to the ISP method. Finally, the CCS of peptide ions analyzed by IR-MALDI were also evaluated with both ISP and MD methods and the results compared to experiment, resulting in a first validation of the MD method. Thus, this thesis brings together the soft ionization technique that is IR-MALDI, which produces mostly singly charged peaks, with ion mobility spectrometry, which can distinguish between isomers, and a collision cross-section determination method which also provides structural information on the analyte at hand.
Basaltic fissure eruptions, such as on Hawai'i or on Iceland, are thought to be driven by the lateral propagation of feeder dikes and graben subsidence. Associated solid earth processes, such as deformation and structural development, are well studied by means of geophysical and geodetic technologies. The eruptions themselves, lava fountaining and venting dynamics, in turn, have been much less investigated due to hazardous access, local dimension, fast processes, and resulting poor data availability.
This thesis provides a detailed quantitative understanding of the shape and dynamics of lava fountains and the morphological changes at their respective eruption sites. For this purpose, I apply image processing techniques, including drones and fixed installed cameras, to the sequence of frames of video records from two well-known fissure eruptions in Hawai'i and Iceland. This way I extract the dimensions of multiple lava fountains, visible in all frames. By putting these results together and considering the acquisition times of the frames I quantify the variations in height, width and eruption velocity of the lava fountains. Then I analyse these time-series in both time and frequency domains and investigate the similarities and correlations between adjacent lava fountains. Following this procedure, I am able to link the dynamics of the individual lava fountains to physical parameters of the magma transport in the feeder dyke of the fountains.
The first case study in this thesis focuses on the March 2011 Pu'u'O'o eruption, Hawai'i, where a continuous pulsating behaviour at all eight lava fountains has been observed. The lava fountains, even those from different parts of the fissure that are closely connected, show a similar frequency content and eruption behaviour. The regular pattern in the heights of lava fountain suggests a controlling process within the magma feeder system like a hydraulic connection in the underlying dyke, affecting or even controlling the pulsating behaviour.
The second case study addresses the 2014-2015 Holuhraun fissure eruption, Iceland. In this case, the feeder dyke is highlighted by the surface expressions of graben-like structures and fault systems. At the eruption site, the activity decreases from a continuous line of fire of ~60 vents to a limited number of lava fountains. This can be explained by preferred upwards magma movements through vertical structures of the pre-eruptive morphology. Seismic tremors during the eruption reveal vent opening at the surface and/or pressure changes in the feeder dyke. The evolving topography of the cinder cones during the eruption interacts with the lava fountain behaviour. Local variations in the lava fountain height and width are controlled by the conduit diameter, the depth of the lava pond and the shape of the crater. Modelling of the fountain heights shows that long-term eruption behaviour is controlled mainly by pressure changes in the feeder dyke.
This research consists of six chapters with four papers, including two first author and two co-author papers. It establishes a new method to analyse lava fountain dynamics by video monitoring. The comparison with the seismicity, geomorphologic and structural expressions of fissure eruptions shows a complex relationship between focussed flow through dykes, the morphology of the cinder cones, and the lava fountain dynamics at the vents of a fissure eruption.
Characterization of altered inflorescence architecture in Arabidopsis thaliana BG-5 x Kro-0 hybrid
(2018)
A reciprocal cross between two A. thaliana accessions, Kro-0 (Krotzenburg, Germany) and BG-5 (Seattle, USA), displays purple rosette leaves and dwarf bushy phenotype in F1 hybrids when grown at 17 °C and a parental-like phenotype when grown at 21 °C. This F1 temperature-dependent-dwarf-bushy phenotype is characterized by reduced growth of the primary stem together with an increased number of branches. The reduced stem growth was the strongest at the first internode. In addition, we found that a temperature switch from 21 °C to 17 °C induced the phenotype only before the formation of the first internode of the stem. Similarly, the F1 dwarf-bushy phenotype could not be reversed when plants were shifted from 17 °C to 21 °C after the first internode was formed. Metabolic analysis showed that the F1 phenotype was associated with a significant upregulation of anthocyanin(s), kaempferol(s), salicylic acid, jasmonic acid and abscisic acid. As it has been previously shown that the dwarf-bushy phenotype is linked to two loci, one on chromosome 2 from Kro-0 and one on chromosome 3 from BG-5, an artificial micro-RNA approach was used to investigate the necessary genes on these intervals. From the results obtained, it was found that two genes, AT2G14120 that encodes for a DYNAMIN RELATED PROTEIN3B and AT2G14100 that encodes a member of the Cytochrome P450 family protein CYP705A13, were necessary for the appearance of the F1 phenotype on chromosome 2. It was also discovered that AT3G61035 that encodes for another cytochrome P450 family protein CYP705A13 and AT3G60840 that encodes for a MICROTUBULE-ASSOCIATED PROTEIN65-4 on chromosome 3 were both necessary for the induction of the F1 phenotype. To prove the causality of these genes, genomic constructs of the Kro-0 candidate genes on chromosome 2 were transferred to BG-5 and genomic constructs of the chromosome 3 candidate genes from BG-5 were transferred to Kro-0. The T1 lines showed that these genes are not sufficient alone to induce the phenotype. In addition to the F1 phenotype, more severe phenotypes were observed in the F2 generations that were grouped into five different phenotypic classes. Whilst seed yield was comparable between F1 hybrids and parental lines, three phenotypic classes in the F2 generation exhibited hybrid breakdown in the form of reproductive failure. This F2 hybrid breakdown was less sensitive to temperature and showed a dose-dependent effect of the loci involved in F1 phenotype. The severest class of hybrid breakdown phenotypes was observed only in the population of backcross with the parent Kro-0, which indicates a stronger contribution of the BG-5 allele when compared to the Kro-0 allele on the hybrid breakdown phenotypes. Overall, the findings of my thesis provide a further understanding of the genetic and metabolic factors underlying altered shoot architecture in hybrid dysfunction.
The Himalayan arc stretches >2500 km from east to west at the southern edge of the Tibetan Plateau, representing one of the most important Cenozoic continent-continent collisional orogens. Internal deformation processes and climatic factors, which drive weathering, denudation, and transport, influence the growth and erosion of the orogen. During glacial times wet-based glaciers sculpted the mountain range and left overdeepend and U-shaped valleys, which were backfilled during interglacial times with paraglacial sediments over several cycles. These sediments partially still remain within the valleys because of insufficient evacuation capabilities into the foreland. Climatic processes overlay long-term tectonic processes responsible for uplift and exhumation caused by convergence. Possible processes accommodating convergence within the orogenic wedge along the main Himalayan faults, which divide the range into four major lithologic units, are debated. In this context, the identification of processes shaping the Earth’s surface on short- and on long-term are crucial to understand the growth of the orogen and implications for landscape development in various sectors along the arc. This thesis focuses on both surface and tectonic processes that shape the landscape in the western Indian Himalaya since late Miocene.
In my first study, I dated well-preserved glacially polished bedrock on high-elevated ridges and valley walls in the upper of the Chandra Valley the by means of 10Be terrestrial cosmogenic radionuclides (TCN). I used these ages and mapped glacial features to reconstruct the extent and timing of Pleistocene glaciation at the southern front of the Himalaya. I was able to reconstruct an extensive valley glacier of ~200 km length and >1000 m thickness. Deglaciation of the Chandra Valley glacier started subsequently to insolation increase on the Northern Hemisphere and thus responded to temperature increase. I showed that the timing this deglaciation onset was coeval with retreat of further midlatitude glaciers on the Northern and Southern Hemispheres. These comparisons also showed that the post-LGM deglaciation very rapid, occurred within a few thousand years, and was nearly finished prior to the Bølling/Allerød interstadial.
A second study (co-authorship) investigates how glacial advances and retreats in high mountain environments impact the landscape. By 10Be TCN dating and geomorphic mapping, we obtained maximal length and height of the Siachen Glacier within the Nubra Valley. Today the Shyok and Nubra confluence is backfilled with sedimentary deposits, which are attributed to the valley blocking of the Siachen Glacier 900 m above the present day river level. A glacial dam of the Siachen Glacier blocked the Shyok River and lead to the evolution of a more than 20 km long lake. Fluvial and lacustrine deposits in the valley document alternating draining and filling cycles of the lake dammed by the Siachen Glacier. In this study, we can show that glacial incision was outpacing fluvial incision.
In the third study, which spans the million-year timescale, I focus on exhumation and erosion within the Chandra and Beas valleys. In this study the position and discussed possible reasons of rapidly exhuming rocks, several 100-km away from one of the main Himalayan faults (MFT) using Apatite Fission Track (AFT) thermochronometry. The newly gained AFT ages indicate rapid exhumation and confirm earlier studies in the Chandra Valley. I assume that the rapid exhumation is most likely related to uplift over subsurface structures. I tested this hypothesis by combining further low-temperature thermochronometers from areas east and west of my study area. By comparing two transects, each parallel to the Beas/Chandra Valley transect, I demonstrate similarities in the exhumation pattern to transects across the Sutlej region, and strong dissimilarities in the transect crossing the Dhauladar Range. I conclude that the belt of rapid exhumation terminates at the western end of the Kullu-Rampur window. Therewith, I corroborate earlier studies suggesting changes in exhumation behavior in the western Himalaya. Furthermore, I discussed several causes responsible for the pronounced change in exhumation patterns along strike: 1) the role of inherited pre-collisional features such as the Proterozoic sedimentary cover of the Indian basement, former ridges and geological structures, and 2) the variability of convergence rates along the Himalayan arc due to an increased oblique component towards the syntaxis.
The combination of field observations (geological and geomorphological mapping) and methods to constrain short- and long-term processes (10Be, AFT) help to understand the role of the individual contributors to exhumation and erosion in the western Indian Himalaya. With the results of this thesis, I emphasize the importance of glacial and tectonic processes in shaping the landscape by driving exhumation and erosion in the studied areas.
In this thesis we provide a construction of the operator framework starting from the functional formulation of group field theory (GFT). We define operator algebras on Hilbert spaces whose expectation values in specific states provide correlation functions of the functional formulation. Our construction allows us to give a direct relation between the ingredients of the functional GFT and its operator formulation in a perturbative regime. Using this construction we provide an example of GFT states that can not be formulated as states in a Fock space and lead to math- ematically inequivalent representations of the operator algebra. We show that such inequivalent representations can be grouped together by their symmetry properties and sometimes break the left translation symmetry of the GFT action. We interpret these groups of inequivalent representations as phases of GFT, similar to the classification of phases that we use in QFT’s on space-time.
Neuroinflammatory and neurodegenerative diseases such as Parkinson's (PD) and multiple sclerosis (MS) often result in a severe impairment of the patient´s quality of life. Effective therapies for the treatment are currently not available, which results in a high socio-economic burden. Due to the heterogeneity of the disease subtypes, stratification is particularly difficult in the early phase of the disease and is mainly based on clinical parameters such as neurophysiological tests and central nervous imaging. Due to good accessibility and stability, blood and cerebrospinal fluid metabolite markers could serve as surrogates for neurodegenerative processes. This can lead to an improved mechanistic understanding of these diseases and further be used as "treatment response" biomarkers in preclinical and clinical development programs. Therefore, plasma and CSF metabolite profiles will be identified that allow differentiation of PD from healthy controls, association of PD with dementia (PDD) and differentiation of PD subtypes such as akinetic rigid and tremor dominant PD patients. In addition, plasma metabolites for the diagnosis of primary progressive MS (PPMS) should be investigated and tested for their specificity to relapsing-remitting MS (RRMS) and their development during PPMS progression.
By applying untargeted high-resolution metabolomics of PD patient samples and in using random forest and partial least square machine learning algorithms, this study identified 20 plasma metabolites and 14 CSF metabolite biomarkers. These differentiate against healthy individuals with an AUC of 0.8 and 0.9 in PD, respectively. We also identify ten PDD specific serum metabolites, which differentiate against healthy individuals and PD patients without dementia with an AUC of 1.0, respectively. Furthermore, 23 akinetic-rigid specific plasma markers were identified, which differentiate against tremor-dominant PD patients with an AUC of 0.94 and against healthy individuals with an AUC of 0.98. These findings also suggest more severe disease pathology in the akinetic-rigid PD than in tremor dominant PD. In the analysis of MS patient samples a partial least square analysis yielded predictive models for the classification of PPMS and resulted in 20 PPMS specific metabolites. In another MS study unknown changes in human metabolism were identified after administration of the multiple sclerosis drug dimethylfumarate, which is used for the treatment of RRMS. These results allow to describe and understand the hitherto completely unknown mechanism of action of this new drug and to use these findings for the further development of new drugs and targets against RRMS.
In conclusion, these results have the potential for improved diagnosis of these diseases and improvement of mechanistic understandings, as multiple deregulated pathways were identified. Moreover, novel Dimethylfumarate targets can be used to aid drug development and treatment efficiency. Overall, metabolite profiling in combination with machine learning identified as a promising approach for biomarker discovery and mode of action elucidation.
Numbers are omnipresent in daily life. They vary in display format and in their meaning so that it does not seem self-evident that our brains process them more or less easily and flexibly. The present thesis addresses mental number representations in general, and specifically the impact of finger counting on mental number representations. Finger postures that result from finger counting experience are one of many ways to convey numerical information. They are, however, probably the one where the numerical content becomes most tangible. By investigating the role of fingers in adults’ mental number representations the four presented studies also tested the Embodied Cognition hypothesis which predicts that bodily experience (e.g., finger counting) during concept acquisition (e.g., number concepts) stays an immanent part of these concepts. The studies focussed on different aspects of finger counting experience. First, consistency and further details of spontaneously used finger configurations were investigated when participants repeatedly produced finger postures according to specific numbers (Study 1). Furthermore, finger counting postures (Study 2), different finger configurations (Study 2 and 4), finger movements (Study 3), and tactile finger perception (Study 4) were investigated regarding their capability to affect number processing. Results indicated that active production of finger counting postures and single finger movements as well as passive perception of tactile stimulation of specific fingers co-activated associated number knowledge and facilitated responses towards corresponding magnitudes and number symbols. Overall, finger counting experience was reflected in specific effects in mental number processing of adult participants. This indicates that finger counting experience is an immanent part of mental number representations.
Findings are discussed in the light of a novel model. The MASC (Model of Analogue and Symbolic Codes) combines and extends two established models of number and magnitude processing. Especially a symbolic motor code is introduced as an essential part of the model. It comprises canonical finger postures (i.e., postures that are habitually used to represent numbers) and finger-number associations. The present findings indicate that finger counting functions both as a sensorimotor magnitude and as a symbolic representational format and that it thereby directly mediates between physical and symbolic size. The implications are relevant both for basic research regarding mental number representations and for pedagogic practices regarding the effectiveness of finger counting as a means to acquire a fundamental grasp of numbers.
Synthesis of artificial building blocks for sortase-mediated ligation and their enzymatic linkage
(2018)
The enzyme Sortase A catalyzes the formation of a peptide bond between the recognition sequence LPXTG and an oligoglycine. While manifold ligations between proteins and various biomolecules, proteins and small synthetic molecules as well as proteins and surfaces have been reported, the aim of this thesis was to investigate the sortase-catalyzed linkage between artificial building blocks. Hence, this could pave the way for the use of sortase A for tasks from a chemical point of view and maybe even materials science.
For the proof of concept, the studied systems were kept as simple as possible at first by choosing easily accessible silica NPs and commercially available polymers. These building blocks were functionalized with peptide motifs for sortase-mediated ligation. Silica nanoparticles were synthesized with diameters of 60 and 200 nm and surface modified with C=C functionalities. Then, peptides bearing a terminal cysteine were covalently linked by means of a thiol-ene reaction. 60 nm SiO2 NPs were functionalized with pentaglycines, while peptides with LPETG motif were linked to 200 nm silica particles. Polyethyleneglycol (PEG) and poly(N isopropylacrylamide) (PNIPAM) were likewise functionalized with peptides by thiol-ene reaction between cysteine residues and C=C units in the polymer end groups. Hence, G5-PEG and PNIPAM-LPETG conjugates were obtained. With this set of building blocks, NP–polymer hybrids, NP–NP, and polymer–polymer structures were generated by sortase-mediated ligation and the product formation shown by transmission electron microscopy, MALDI-ToF mass spectrometry and dynamic light scatting, among others. Thus, the linkage of these artificial building blocks by the enzyme sortase A could be demonstrated.
However, when using commercially available polymers, the purification of the polymer–peptide conjugates was impossible and resulted in a mixture containing unmodified polymer. Therefore, strategies were developed for the own synthesis of pure peptide-polymer and polymer-peptide conjugates as building blocks for sortase-mediated ligation. The designed routes are based on preparing polymer blocks via RAFT polymerization from CTAs that are attached to N- or C-terminus, respectively, of a peptide. GG-PNIPAM was synthesized through attachment of a suitable RAFT CTA to Fmoc-GG in an esterification reaction, followed by polymerization of NIPAM and cleavage of the Fmoc protection group. Furthermore, several peptides were synthesized by solid-phase peptide synthesis. The linkage of a RAFT CTA (or
polymerization initiator) to the N-terminus of a peptide can be conducted in an automated fashion as last step in a peptide synthesizer. The synthesis of such a conjugate couldn’t be realized in the time frame of this thesis, but many promising strategies exist to continue this strategy using different coupling reagents. Such polymer building blocks can be used to synthesize protein-polymer conjugates catalyzed by sortase A and the approach can be carried on to the synthesis of block copolymers by using polymer blocks with peptide motifs on both ends.
Although the proof of concept demonstrated in this thesis only shows examples that can be also synthesized by exclusively chemical techniques, a toolbox of such building blocks will enable the future formation of new materials and pave the way for the application of enzymes in materials science. In addition to nanoparticle systems and block copolymers, this also includes combination with protein-based building blocks to form hybrid materials. Hence, sortase could become an enzymatic tool that complements established chemical linking technologies and provides specific peptide motifs that are orthogonal to all existing chemical functional groups.
In the present work, we use symbolic regression for automated modeling of dynamical systems. Symbolic regression is a powerful and general method suitable for data-driven identification of mathematical expressions. In particular, the structure and parameters of those expressions are identified simultaneously.
We consider two main variants of symbolic regression: sparse regression-based and genetic programming-based symbolic regression. Both are applied to identification, prediction and control of dynamical systems.
We introduce a new methodology for the data-driven identification of nonlinear dynamics for systems undergoing abrupt changes. Building on a sparse regression algorithm derived earlier, the model after the change is defined as a minimum update with respect to a reference model of the system identified prior to the change. The technique is successfully exemplified on the chaotic Lorenz system and the van der Pol oscillator. Issues such as computational complexity, robustness against noise and requirements with respect to data volume are investigated.
We show how symbolic regression can be used for time series prediction. Again, issues such as robustness against noise and convergence rate are investigated us- ing the harmonic oscillator as a toy problem. In combination with embedding, we demonstrate the prediction of a propagating front in coupled FitzHugh-Nagumo oscillators. Additionally, we show how we can enhance numerical weather predictions to commercially forecast power production of green energy power plants.
We employ symbolic regression for synchronization control in coupled van der Pol oscillators. Different coupling topologies are investigated. We address issues such as plausibility and stability of the control laws found. The toolkit has been made open source and is used in turbulence control applications.
Genetic programming based symbolic regression is very versatile and can be adapted to many optimization problems. The heuristic-based algorithm allows for cost efficient optimization of complex tasks.
We emphasize the ability of symbolic regression to yield white-box models. In contrast to black-box models, such models are accessible and interpretable which allows the usage of established tool chains.
The Sun is the nearest star to the Earth. It consists of an interior and an atmosphere. The convection zone is the outermost layer of the solar interior. A flux rope may emerge as a coherent structure from the convection zone into the solar atmosphere or be formed by magnetic reconnection in the atmosphere. A flux rope is a bundle of magnetic field lines twisting around an axis field line, creating a helical shape by which dense filament material can be supported against gravity. The flux rope is also considered as the key structure of the most energetic phenomena in the solar system, such as coronal mass ejections (CMEs) and flares. These magnetic flux ropes can produce severe geomagnetic storms. In particular, to improve the ability to forecast space weather, it is important to enrich our knowledge about the dynamic formation of flux ropes and the underlying physical mechanisms that initiate their eruption, such as a CME.
A confined eruption consists of a filament eruption and usually an associated are, but does not evolve into a CME; rather, the moving plasma is halted in the solar corona and usually seen to fall back. The first detailed observations of a confined filament eruption were obtained on 2002 May 27by the TRACE satellite in the 195 A band. So, in the Chapter 3, we focus on a flux rope instability model. A twisted flux rope can become unstable by entering the kink instability regime. We show that the kink instability, which occurs if the twist of a flux rope exceeds a critical value, is capable of initiating of an eruption. This model is tested against the well observed confined eruption on 2002 May 27 in a parametric magnetohydrodynamic (MHD) simulation study that comprises all phases of the event. Very good agreement with the essential observed properties is obtained, only except for a relatively poor matching of the initial filament height.
Therefore, in Chapter 4, we submerge the center point of the flux rope deeper below the photosphere to obtain a flatter coronal rope section and a better matching with the initial height profile of the erupting filament. This implies a more realistic inclusion of the photospheric line tying. All basic assumptions and the other parameter settings are kept the same as in Chapter 3. This complement of the parametric study shows that the flux rope instability model can yield an even better match with the observational data. We also focus in Chapters 3 and 4 on the magnetic reconnection during the confined eruption, demonstrating that it occurs in two distinct locations and phases that correspond to the observed brightenings and changes of topology, and consider the fate of the erupting flux, which can reform a (less twisted) flux rope.
The Sun also produces series of homologous eruptions, i.e. eruptions which occur repetitively in the same active region and are of similar morphology. Therefore, in Chapter 5, we employ the reformed flux rope as a new initial condition, to investigate the possibility of subsequent homologous eruptions. Free magnetic energy is built up by imposing motions in the bottom boundary, such as converging motions, leading to flux cancellation. We apply converging motions in the sunspot area, such that a small part of the flux from the sunspots with different polarities is transported toward the polarity inversion line (PIL) and cancels with each other. The reconnection associated with the cancellation process forms more helical magnetic flux around the reformed flux rope, which leads to a second and a third eruption. In this study, we obtain the first MHD simulation results of a homologous sequence of eruptions that show a transition from a confined to two ejective eruptions, based on the reformation of a flux rope after each eruption.
The topic of this thesis is the experimental investigation of evaporating thin films on planar solid substrates and the enrichment, the crystal growth and Marangoni flows near the three phase line in the case of partially wetting mixtures of volatile and non volatile liquids. In short, it deals with the properties of planar liquid films and with those of thin liquid sections near the three phase contact line. In both cases the liquid looses continuously one component by evaporation. One topic is the rupture behavior of ultra-thin films of binary mixtures of a volatile solvent and a nonvolatile solute. It is studied how the thickness at which the film ruptures is related to the solute crystallization at the liquid/ substrate interface as soon as the solute reaches supersaturation. A universal relation between the rupture thickness and the saturation behaviour is presented. The second research subject are individual nanoparticles embedded in molecularly thin films at planar substrates. It is found that the nanoparticles cause an unexpectedly large film surface distortion (meniscus). This distortion can be measured quantitatively by conventional reflective microscopy although the nanoparticles are much smaller than the Rayleigh diffraction limit. Investigations with binary mixtures of volatile solvents and non-volatile solutes (polymers) aim at a better understanding/prediction of the final solute coverage, the timeresolved film thinning, the time-resolved solvent evaporation, and the evolution of the solute concentration within the thinning film. A quantiative theoretical description of the experimental findings is derived. Experiments of completely miscible binary mixtures of volatile liquids, which individually form continuous planar films show unexpectedly that films of mixtures are not necessarily continuous and planar. Rather, they may form surface
undulations or even rupture. This is explained with surface Marangoni flows. A new method for the exceptionally fast fabrication (mm/min) of ultralong aligned diphenylalanin single crystals via dip casting is presented. It is shown how the specific evaporation conditions at the three phase line can be used for a controlled peptide crystal growth process. It is further demonstrated how the confinement inside a smalll capillary affects the peptide crystallization and how this can be understood (and used).
In the thesis there are constructed new quantizations for pseudo-differential boundary value problems (BVPs) on manifolds with edge. The shape of operators comes from Boutet de Monvel’s calculus which exists on smooth manifolds with boundary. The singular case, here with edge and boundary, is much more complicated. The present approach simplifies the operator-valued symbolic structures by using suitable Mellin quantizations on infinite stretched model cones of wedges with boundary. The Mellin symbols themselves are, modulo smoothing ones, with asymptotics, holomorphic in the complex Mellin covariable. One of the main results is the construction of parametrices of elliptic elements in the corresponding operator algebra, including elliptic edge conditions.
Modeling and data analysis of large-scale atmosphere dynamics associated with extreme weather
(2018)
In the last decades the frequency and intensity of extreme weather events like heat waves and heavy rainfall have increased and are at least partly linked to global warming. These events can have a strong impact on agricultural and economic production and, thereby, on society. Thus, it is important to improve our understanding of the physical processes leading to those extreme events in order to provide accurate near-term and long-term forecasts. Thermodynamic drivers associated with global warming are well understood, but dynamical aspects of the atmosphere much less so. The dynamical aspects, while less important than the thermodynamic drivers in regards to large-scale and long-time averaged effects, play a critical role in the formation of extremes.
The overall aim of this thesis is to improve our understanding of patterns, variability and trends in the global atmospheric circulation under a changing climate. In particular, in this dissertation I developed two new data-driven methods to quantitatively describe the dynamics of jet streams, Hadley cells and storm tracks. In addition, I introduce and validate a new statistical-dynamical atmosphere model that can be used to efficiently model the large-scale circulation.
First, I developed a scheme based on the Dijkstra ‘shortest-path’ algorithm to identify jet stream cores. Using reanalysis data, I found a significant change in jet stream strength and position over the last decades: Specifically, a decrease in wind speeds and a spatial shift toward the poles. This work also shows that the splitting or merging of the polar front jet stream and the subtropical jet stream depends on the season and longitudinal position. In a follow-up study, I analyzed trends in the latitudinal position of the poleward edge of the Hadley cell and subtropical jet stream core for all longitudes. These trends depend strongly on longitude and thus the impacts of tropical expansion might be pronounced in some regions and absent in others.
The second approach was to develop an empirical forecast method for European and Mediterranean winter precipitation. This prediction algorithm innovatively incorporates the spatial patterns of predictors in autumn using clustering analyses. I identified the most important precursors (snow cover in Eurasia, Barents and Kara sea ice concentrations as well as sea surface temperature in the Atlantic and Mediterranean region) for the precipitation prediction. This forecast algorithm had higher forecast skills than conventionally employed methods such as Canonical Correlation Analysis or operational systems using climate models.
The last approach was to examine the atmospheric circulation using the novel statisticaldynamical atmosphere model Aeolus. First, I validated the model’s depiction of the largescale circulation in terms of Hadley circulation, jet streams, storm tracks and planetary waves. To do so, I performed a parameter optimization using simulated annealing. Next, I investigated the sensitivity of the large-scale circulation to three different temperature components: global mean temperature, meridional temperature gradient and zonal temperature gradient. The model experiment showed that the strength of the Hadley cell, storm tracks and jet streams depend almost linearly on both the global mean temperature and the meridional temperature gradient, whereas the zonal temperature gradient is shown to have little or no influence. The magnitude of planetary waves is clearly affected by all three temperature components. Finally, the width of the Hadley cell behaves nonlinearly with respect to all three temperature components.
These findings might have profound consequences for climate modeling of the Mediterranean region. The latitudinal poleward trend of the Hadley cell edge position might become stronger under climate change according to the results with Aeolus. These changes would lead to a substantial reduction of the winter precipitation in the Mediterranean region. In this case seasonal empirical forecast methods, like the clustering-based prediction scheme, will play an important role for forecasting seasonal droughts in advance such that water managers and politicians can mitigate impacts.
The continuously increasing pollution of aquatic environments with microplastics (plastic particles < 5 mm) is a global problem with potential implications for organisms of all trophic levels. For microorganisms, trillions of these floating microplastics particles represent a huge surface area for colonization. Due to the very low biodegradability, microplastics remain years to centuries in the environment and can be transported over thousands of kilometers together with the attached organisms. Since also pathogenic, invasive, or otherwise harmful species could be spread this way, it is essential to study microplastics-associated communities.
For this doctoral thesis, eukaryotic communities were analyzed for the first time on microplastics in brackish environments and compared to communities in the surrounding water and on the natural substrate wood. With Illumina MiSeq high-throughput sequencing, more than 500 different eukaryotic taxa were detected on the microplastics samples. Among them were various green algae, dinoflagellates, ciliates, fungi, fungal-like protists and small metazoans such as nematodes and rotifers. The most abundant organisms was a dinoflagellate of the genus Pfiesteria, which could include fish pathogenic and bloom forming toxigenic species. Network analyses revealed that there were numerous interaction possibilities among prokaryotes and eukaryotes in microplastics biofilms. Eukaryotic community compositions on microplastics differed significantly from those on wood and in water, and compositions were additionally distinct among the sampling locations. Furthermore, the biodiversity was clearly lower on microplastics in comparison to the diversity on wood or in the surrounding water.
In another experiment, a situation was simulated in which treated wastewater containing microplastics was introduced into a freshwater lake. With increasing microplastics concentrations, the resulting bacterial communities became more similar to those from the treated wastewater. Moreover, the abundance of integrase I increased together with rising concentrations of microplastics. Integrase I is often used as a marker for anthropogenic environmental pollution and is further linked to genes conferring, e.g., antibiotic resistance.
This dissertation gives detailed insights into the complexity of prokaryotic and eukaryotic communities on microplastics in brackish and freshwater systems. Even though microplastics provide novel microhabitats for various microbes, they might also transport toxigenic, pathogenic, antibiotic-resistant or parasitic organisms; meaning their colonization can pose potential threats to humans and the environment. Finally, this thesis explains the urgent need for more research as well as for strategies to minimize the global microplastic pollution.
Monoclonal antibodies (mAbs) are an innovative group of drugs with increasing clinical importance in oncology, combining high specificity with generally low toxicity. There are, however, numerous challenges associated with the development of mAbs as therapeutics. Mechanistic understanding of factors that govern the pharmacokinetics (PK) of mAbs is critical for drug development and the optimisation of effective therapies; in particular, adequate dosing strategies can improve patient quality life and lower drug cost. Physiologically-based PK (PBPK) models offer a physiological and mechanistic framework, which is of advantage in the context of animal to human extrapolation. Unlike for small molecule drugs, however, there is no consensus on how to model mAb disposition in a PBPK context. Current PBPK models for mAb PK hugely vary in their representation of physiology and parameterisation. Their complexity poses a challenge for their applications, e.g., translating knowledge from animal species to humans.
In this thesis, we developed and validated a consensus PBPK model for mAb disposition taking into account recent insights into mAb distribution (antibody biodistribution coefficients and interstitial immunoglobulin G (IgG) pharmacokinetics) to predict tissue PK across several pre-clinical species and humans based on plasma data only. The model allows to a priori predict target-independent (unspecific) mAb disposition processes as well as mAb disposition in concentration ranges, for which the unspecific clearance (CL) dominates target-mediated CL processes. This is often the case for mAb therapies at steady state dosing.
The consensus PBPK model was then used and refined to address two important problems:
1) Immunodeficient mice are crucial models to evaluate mAb efficacy in cancer therapy. Protection from elimination by binding to the neonatal Fc receptor is known to be a major pathway influencing the unspecific CL of both, endogenous and therapeutic IgG. The concentration of endogenous IgG, however, is reduced in immunodeficient mouse models, and this effect on unspecific mAb CL is unknown, yet of great importance for the extrapolation to human in the context of mAb cancer therapy.
2) The distribution of mAbs into solid tumours is of great interest. To comprehensively investigate mAb distribution within tumour tissue and its implications for therapeutic efficacy, we extended the consensus PBPK model by a detailed tumour distribution model incorporating a cell-level model for mAb-target interaction. We studied the impact of variations in tumour microenvironment on therapeutic efficacy and explored the plausibility of different mechanisms of action in mAb cancer therapy.
The mathematical findings and observed phenomena shed new light on therapeutic utility and dosing regimens in mAb cancer treatment.
The highly conserved protein complex containing the Target of Rapamycin (TOR) kinase is known to integrate intra- and extra-cellular stimuli controlling nutrient allocation and cellular growth. This thesis describes three studies aimed to understand how TOR signaling pathway influences carbon and nitrogen metabolism in Chlamydomonas reinhardtii. The first study presents a time-resolved analysis of the molecular and physiological features across the diurnal cycle. The inhibition of TOR leads to 50% reduction in growth followed by nonlinear delays in the cell cycle progression. The metabolomics analysis showed that the growth repression is mainly driven by differential carbon partitioning between anabolic and catabolic processes. Furthermore, the high accumulation of nitrogen-containing compounds indicated that TOR kinase controls the carbon to nitrogen balance of the cell, which is responsible for biomass accumulation, growth and cell cycle progression. In the second study the cause of the high accumulation of amino acids is explained. For this purpose, the effect of TOR inhibition on Chlamydomonas was examined under different growth regimes using stable 13C- and 15N-isotope labeling. The data clearly showed that an increased nitrogen uptake is induced within minutes after the inhibition of TOR. Interestingly, this increased N-influx is accompanied by increased activities of nitrogen assimilating enzymes. Accordingly, it was concluded that TOR inhibition induces de-novo amino acid synthesis in Chlamydomonas. The recognition of this novel process opened an array of questions regarding potential links between central metabolism and TOR signaling. Therefore a detailed phosphoproteomics study was conducted to identify the potential substrates of TOR pathway regulating central metabolism. Interestingly, some of the key enzymes involved in carbon metabolism as well as amino acid synthesis exhibited significant changes in the phosphosite intensities immediately after TOR inhibition. Altogether, these studies provide a) detailed insights to metabolic response of Chlamydomonas to TOR inhibition, b) identification of a novel process causing rapid upshifts in amino acid levels upon TOR inhibition and c) finally highlight potential targets of TOR signaling regulating changes in central metabolism. Further biochemical and molecular investigations could confirm these observations and advance the understanding of growth signaling in microalgae.
Over the last decades mechanisms of recognition of morphologically complex words have been extensively examined in order to determine whether all word forms are stored and retrieved from the mental lexicon as wholes or whether they are decomposed into their morphological constituents such as stems and affixes. Most of the research in this domain focusses on English. Several factors have been argued to affect morphological processing including, for instance, morphological structure of a word (e.g., existence of allomorphic stem alternations) and its linguistic nature (e.g., whether it is a derived word or an inflected word form). It is not clear, however, whether processing accounts based on experimental evidence from English would hold for other languages. Furthermore, there is evidence that processing mechanisms may differ across various populations including children, adult native speakers and language learners. Recent studies claim that processing mechanisms could also differ between older and younger adults (Clahsen & Reifegerste, 2017; Reifegerste, Meyer, & Zwitserlood, 2017).
The present thesis examined how properties of the morphological structure, types of linguistic operations involved (i.e., the linguistic contrast between inflection and derivation) and characteristics of the particular population such as older adults (e.g., potential effects of ageing as a result of the cognitive decline or greater experience and exposure of older adults) affect initial, supposedly automatic stages of morphological processing in Russian and German. To this end, a series of masked priming experiments was conducted.
In experiments on Russian, the processing of derived -ost’ nouns (e.g., glupost’ ‘stupidity’) and of inflected forms with and without allomorphic stem alternations in 1P.Sg.Pr. (e.g., igraju – igrat’ ‘to play’ vs. košu – kosit’ ‘to mow’) was examined. The first experiment on German examined and directly compared processing of derived -ung nouns (e.g., Gründung ‘foundation’) and inflected -t past participles (e.g., gegründet ‘founded’), whereas the second one investigated the processing of regular and irregular plural forms (-s forms such as Autos ‘cars’ and -er forms such as Kinder ‘children’, respectively).
The experiments on both languages have shown robust and comparable facilitation effects for derived words and regularly inflected forms without stem changes (-t participles in German, forms of -aj verbs in Russian). Observed morphological priming effects could be clearly distinguished from purely semantic or orthographic relatedness between words. At the same time, we found a contrast between forms with and without allomorphic stem alternations in Russian and regular and irregular forms in German, with significantly more priming for unmarked stems (relative to alternated ones) and significantly more priming for regular (compared) word forms. These findings indicate the relevance of morphological properties of a word for initial stages of processing, contrary to claims made in the literature holding that priming effects are determined by surface form and meaning overlap only. Instead, our findings are more consistent with approaches positing a contrast between combinatorial, rule-based and lexically-stored forms (Clahsen, Sonnenstuhl, & Blevins, 2003).
The doctoral dissertation also addressed the role of ageing and age-related cognitive changes on morphological processing. The results obtained on this research issue are twofold. On the one hand, the data demonstrate effects of ageing on general measures of language performance, i.e., overall longer reaction times and/or higher accuracy rates in older than younger individuals. These findings replicate results from previous studies, which have been linked to the general slowing of processing speed at older age and to the larger vocabularies of older adults. One the other hand, we found that more specific aspects of language processing appear to be largely intact in older adults as revealed by largely similar morphological priming effects for older and younger adults. These latter results indicate that initial stages of morphological processing investigated here by means of the masked priming paradigm persist in older age. One caveat should, however, be noted. Achieving the same performance as a younger individual in a behavioral task may not necessarily mean that the same neural processes are involved. Older people may have to recruit a wider brain network than younger individuals, for example. To address this and related possibilities, future studies should examine older people’s neural representations and mechanisms involved in morphological processing.
The prediction of the ground shaking that can occur at a site of interest due to an earthquake is crucial in any seismic hazard analysis. Usually, empirically derived ground-motion prediction equations (GMPEs) are employed within a logic-tree framework to account for this step. This is, however, challenging if the area under consideration has only low seismicity and lacks enough recordings to develop a region-specific GMPE. It is then usual practice to adapt GMPEs from data-rich regions (host area) to the area with insufficient ground-motion recordings (target area). Host GMPEs must be adjusted in such a way that they will capture the specific ground-motion characteristics of the target area. In order to do so, seismological parameters of the target region have to be provided as, for example, the site-specific attenuation factor kappa0. This is again an intricate task if data amount is too sparse to derive these parameters.
In this thesis, I explore methods that can facilitate the selection of non-endemic GMPEs in a logic-tree analysis or their adjustment to a data-poor region. I follow two different strategies towards this goal.
The first approach addresses the setup of a ground-motion logic tree if no indigenous GMPE is available. In particular, I propose a method to derive an optimized backbone model that captures the median ground-motion characteristics in the region of interest. This is done by aggregating several foreign GMPEs as weighted components of a mixture model in which the weights are inferred from observed data. The approach is applied to Northern Chile, a region for which no indigenous GMPE existed at the time of the study. Mixture models are derived for interface and intraslab type events using eight subduction zone GMPEs originating from different parts of the world. The derived mixtures provide satisfying results in terms of average residuals and average sample log-likelihoods. They outperform all individual non-endemic GMPEs and are comparable to a regression model that was specifically derived for that area.
The second approach is concerned with the derivation of the site-specific attenuation factor kappa0. kappa0 is one of the key parameters in host-to-target adjustments of GMPEs but is hard to derive if data amount is sparse. I explore methods to estimate kappa0 from ambient seismic noise. Seismic noise is, in contrast to earthquake recordings, continuously available. The rapidly emerging field of seismic interferometry gives the possibility to infer velocity and attenuation information from the cross-correlation or deconvolution of long noise recordings. The extraction of attenuation parameters from diffuse wavefields is, however, not straightforward especially not for frequencies above 1 Hz and at shallow depth. In this thesis, I show the results of two studies. In the first one, data of a small-scale array experiment in Greece are used to derive Love wave quality factors in
the frequency range 1-4 Hz. In a second study, frequency dependent quality factors of S-waves (5-15 Hz) are estimated by deconvolving noise recorded in a borehole and at a co-located surface station in West Bohemia/Vogtland. These two studies can be seen as preliminary steps towards the estimation of kappa0 from seismic noise.
Physical computing covers the design and realization of interactive objects and installations and allows learners to develop concrete, tangible products of the real world, which arise from their imagination. This can be used in computer science education to provide learners with interesting and motivating access to the different topic areas of the subject in constructionist and creative learning environments. However, if at all, physical computing has so far mostly been taught in afternoon clubs or other extracurricular settings. Thus, for the majority of students so far there are no opportunities to design and create their own interactive objects in regular school lessons.
Despite its increasing popularity also for schools, the topic has not yet been clearly and sufficiently characterized in the context of computer science education. The aim of this doctoral thesis therefore is to clarify physical computing from the perspective of computer science education and to adequately prepare the topic both content-wise and methodologically for secondary school teaching. For this purpose, teaching examples, activities, materials and guidelines for classroom use are developed, implemented and evaluated in schools.
In the theoretical part of the thesis, first the topic is examined from a technical point of view. A structured literature analysis shows that basic concepts used in physical computing can be derived from embedded systems, which are the core of a large field of different application areas and disciplines. Typical methods of physical computing in professional settings are analyzed and, from an educational perspective, elements suitable for computer science teaching in secondary schools are extracted, e. g. tinkering and prototyping. The investigation and classification of suitable tools for school teaching show that microcontrollers and mini computers, often with extensions that greatly facilitate the handling of additional components, are particularly attractive tools for secondary education. Considering the perspectives of science, teachers, students and society, in addition to general design principles, exemplary teaching approaches for school education and suitable learning materials are developed and the design, production and evaluation of a physical computing construction kit suitable for teaching is described.
In the practical part of this thesis, with “My Interactive Garden”, an exemplary approach to integrate physical computing in computer science teaching is tested and evaluated in different courses and refined based on the findings in a design-based research approach. In a series of workshops on physical computing, which is based on a concept for constructionist professional development that is developed specifically for this purpose, teachers are empowered and encouraged to develop and conduct physical computing lessons suitable for their particular classroom settings. Based on their in-class experiences, a process model of physical computing teaching is derived. Interviews with those teachers illustrate that benefits of physical computing, including the tangibility of crafted objects and creativity in the classroom, outweigh possible drawbacks like longer preparation times, technical difficulties or difficult assessment. Hurdles in the classroom are identified and possible solutions discussed.
Empirical investigations in the different settings reveal that “My Interactive Garden” and physical computing in general have a positive impact, among others, on learner motivation, fun and interest in class and perceived competencies.
Finally, the results from all evaluations are combined to evaluate the design principles for physical computing teaching and to provide a perspective on the development of decision-making aids for physical computing activities in school education.
Health effects, attributed to the environmental pollution resulted from using solvents such as benzene, are relatively unexplored among petroleum workers, personal use, and laboratory researchers. Solvents can cause various health problems, such as neurotoxicity, immunotoxicity, and carcinogenicity. As such it can be absorbed via epidermal or respiratory into the human body resulting in interacting with molecules that are responsible for biochemical and physiological processes of the brain.
Owing to the ever-growing demand for finding a solution, an Ionic liquid can use as an alternative solvent. Ionic liquids are salts in a liquid state at low temperature (below 100 C), or even at room temperature. Ionic liquids impart a unique architectural platform, which has been interesting because of their unusual properties that can be tuned by simple ways such as mixing two ionic liquids.
Ionic liquids not only used as reaction solvents but they became a key developing for novel applications based on their thermal stability, electric conductivity with very low vapor pressure in contrast to the conventional solvents.
In this study, ionic liquids were used as a solvent and reactant at the same time for the novel nanomaterials synthesis for different applications including solar cells, gas sensors, and water splitting.
The field of ionic liquids continues to grow, and become one of the most important branches of science. It appears to be at a point where research and industry can work together in a new way of thinking for green chemistry and sustainable production.
New bio-based polymers
(2018)
Redox-responsive polymers, such as poly(disulfide)s, are a versatile class of polymers with potential applications including gene- and drug-carrier systems. Their degradability under reductive conditions allows for a controlled response to the different redox states that are present throughout the body. Poly(disulfide)s are typically synthesized by step growth polymerizations. Step growth polymerizations, however, may suffer from low conversions and therefore low molar masses, limiting potential applications. The purpose of this thesis was therefore to find and investigate new synthetic routes towards the synthesis of amino acid-based poly(disulfide)s.
The different routes in this thesis include entropy-driven ring opening polymerizations of novel macrocyclic monomers, derived from cystine derivatives. These monomers were obtained with overall yields of up to 77% and were analyzed by mass spectrometry as well as by 1D and 2D NMR spectroscopy. The kinetics of the entropy-driven ring-opening metathesis polymerization (ED-ROMP) were thoroughly investigated in dependence of temperature, monomer concentration, and catalyst concentration. The polymerization was optimized to yield poly(disulfide)s with weight average molar masses of up to 80 kDa and conversions of ~80%, at the thermodynamic equilibrium. Additionally, an alternative metal free polymerization, namely the entropy-driven ring-opening disulfide metathesis polymerization (ED-RODiMP) was established for the polymerization of the macrocyclic monomers. The effect of different solvents, concentrations and catalyst loadings on the polymerization process and its kinetics were studied. Polymers with very high weight average molar masses of up to 177 kDa were obtained. Moreover, various post-polymerization reactions were successfully performed.
This work provides the first example of the homopolymerization of endo-cyclic disulfides by ED-ROMP and the first substantial study into the kinetics of the ED-RODiMP process.
Time-dependent correlation function based methods to study optical spectroscopy involving electronic transitions can be traced back to the work of Heller and coworkers. This intuitive methodology can be expected to be computationally efficient and is applied in the current work to study the vibronic absorption, emission, and resonance Raman spectra of selected organic molecules. Besides, the "non-standard" application of this approach to photoionization processes is also explored. The application section consists of four chapters as described below.
In Chapter 4, the molar absorptivities and vibronic absorption/emission spectra of perylene and several of its N-substituted derivatives are investigated. By systematically varying the number and position of N atoms, it is shown that the presence of nitrogen heteroatoms has a negligible effect on the molecular structure and geometric distortions upon electronic transitions, while spectral properties are more sensitive: In particular the number of N atoms is important while their position is less decisive. Thus, N-substitution can be used to fine-tune the optical properties of perylene-based molecules.
In Chapter 5, the same methods are applied to study the vibronic absorption/emission and resonance Raman spectra of a newly synthesized donor-acceptor type molecule. The simulated absorption/emission spectra agree fairly well with experimental data, with discrepancies being attributed to solvent effects. Possible modes which may dominate the fine-structure in the vibronic spectra are proposed by analyzing the correlation function with the aid of Raman and resonance Raman spectra.
In the next two chapters, besides the above types of spectra, the methods are extended to study photoelectron spectra of several small diamondoid-related systems (molecules, radicals, and cations). Comparison of the photoelectron spectra with available experimental data suggests that the correlation function based approach can describe ionization processes reasonably well. Some of these systems, cationic species in particular, exhibit somewhat peculiar optical behavior, which presents them as possible candidates for functional devices.
Correlation function based methods in a more general sense can be very versatile. In fact, besides the above radiative processes, formulas for non-radiative processes such as internal conversion have been derived in literature. Further implementation of the available methods is among our next goals.
Biological invasions are the dispersal and following establishment of species outside their native habitat. Due to globalisation, connectivity of regions and climate changes the number of invasive species and their successful establishment is rising. The impact of these species is mostly negative, can induce community and habitat alterations, and is one main cause for biodiversity loss. This impact is particularly high and less researched in aquatic systems and microbial organisms and despite the high impact, the knowledge about overall mechanisms and specific factors affecting invasions are not fully understood. In general, the characteristics of the habitat, native community and invader determine the invasiveness.
In this thesis, I aimed to provide a better understanding of aquatic invasions focusing on the invader and its traits and identity. This thesis used a set of 12 strains of the invasive cyanobacterium <i>Cylindrospermopsis raciborskii</i> to examine the effect and impact of the invaders’ identity and genetic diversity. Further, the effect of timing on the invasion potential and success was determined, because aquatic systems in particular undergo seasonal fluctuations.
Most studies revealed a higher invasion success with increasing genetic diversity. Here, the increase of the genetic diversity, by either strain richness or phylogenetic dissimilarity, is not firstly driving the invasion, but the strain-identity. The high variability among the strains in traits important for invasions led to the highly varying strain-specific invasion success. This success was most dependent on nitrogen uptake and efficient resource use. The lower invasion success into communities comprising further N-fixing species indicates <i>C. raciborskii</i> can use this advantage only without the presence of competitive species. The relief of grazing pressure, which is suggested to be more important in aquatic invasions, was only promoting the invasion when unselective and larger consumers were present. High abundances of unselective consumers hampered the invasion success.
This indicates a more complex and temporal interplay of competitive and consumptive resistance mechanisms during the invasion process. Further, the fluctuation abundance and presence of competitors (= primary producers) and consumers (= zooplankton) in lakes can open certain ‘invasion windows’.
Remarkably, the composition of the resident community was also strain-specific affected and altered, independent of a high or low invasion success. Prior, this was only documented on the species level. Further, investigations on the population of invasive strains can reveal more about the invasion patterns and how multiple strain invasions change resident communities.
The present dissertation emphasises the importance of invader-addition experiments with a community context and the importance of the strain-level for microbial invasions and in general, e.g. for community assemblies and the outcome of experiments. The strain-specific community changes, also after days, may explain some sudden changes in communities, which have not been explained yet. This and further knowledge may also facilitate earlier and less cost-intensive management to step in, because these species are rarely tracked until they reach a high abundance or bloom, because of their small size.
Concluded for <i>C. raciborskii</i>, it shows that this species is no ‘generalistic’ invader and its invasion success depends more on the competitor presence than grazing pressure. This may explain its, still unknown, invasion pattern, as <i>C. raciborskii</i> is not found in all lakes of a region.
Human actuation
(2018)
Ever since the conception of the virtual reality headset in 1968, many researchers have argued that the next step in virtual reality is to allow users to not only see and hear, but also feel virtual worlds. One approach is to use mechanical equipment to provide haptic feedback, e.g., robotic arms, exoskeletons and motion platforms. However, the size and the weight of such mechanical equipment tends to be proportional to its target’s size and weight, i.e., providing human-scale haptic feedback requires human-scale equipment, often restricting them to arcades and lab environments.
The key idea behind this dissertation is to bypass mechanical equipment by instead leveraging human muscle power. We thus create software systems that orchestrate humans in doing such mechanical labor—this is what we call human actuation. A potential benefit of such systems is that humans are more generic, flexible, and versatile than machines. This brings a wide range of haptic feedback to modern virtual reality systems.
We start with a proof-of-concept system—Haptic Turk, focusing on delivering motion experiences just like a motion platform. All Haptic Turk setups consist of a user who is supported by one or more human actuators. The user enjoys an interactive motion simulation such as a hang glider experience, but the motion is generated by those human actuators who manually lift, tilt, and push the user’s limbs or torso. To get the timing and force right, timed motion instructions in a format familiar from rhythm games are generated by the system.
Next, we extend the concept of human actuation from 3-DoF to 6-DoF virtual reality where users have the freedom to walk around. TurkDeck tackles this problem by orchestrating a group of human actuators to reconfigure a set of passive props on the fly while the user is progressing in the virtual environment. TurkDeck schedules human actuators by their distances from the user, and instructs them to reconfigure the props to the right place on the right time using laser projection and voice output.
Our studies in Haptic Turk and TurkDeck showed that human actuators enjoyed the experience but not as much as users. To eliminate the need of dedicated human actuators, Mutual Turk makes everyone a user by exchanging mechanical actuation between two or more users. Mutual Turk’s main functionality is that it orchestrates the users so as to actuate props at just the right moment and with just the right force to produce the correct feedback in each other's experience.
Finally, we further eliminate the need of another user, making human actuation applicable to single-user experiences. iTurk makes the user constantly reconfigure and animate otherwise passive props. This allows iTurk to provide virtual worlds with constantly varying or even animated haptic effects, even though the only animate entity present in the system is the user. Our demo experience features one example each of iTurk’s two main types of props, i.e., reconfigurable props (the foldable board from TurkDeck) and animated props (the pendulum).
We conclude this dissertation by summarizing the findings of our explorations and pointing out future directions. We discuss the development of human actuation compare to traditional machine actuation, the possibility of combining human and machine actuators and interaction models that involve more human actuators.
In this work, different strategies for the construction of biohybrid photoelectrodes are investigated and have been evaluated according to their intrinsic catalytic activity for the oxidation of the cofactor NADH or for the connection with the enzymes PQQ glucose dehydrogenase (PQQ-GDH), FAD-dependent glucose dehydrogenase (FAD-GDH) and fructose dehydrogenase (FDH). The light-controlled oxidation of NADH has been analyzed with InGaN/GaN nanowire-modified electrodes. Upon illumination with visible light the InGaN/GaN nanowires generate an anodic photocurrent, which increases in a concentration-dependent manner in the presence of NADH, thus allowing determination of the cofactor. Furthermore, different approaches for the connection of enzymes to quantum dot (QD)-modified electrodes via small redox molecules or redox polymers have been analyzed and discussed. First, interaction studies with diffusible redox mediators such as hexacyanoferrate(II) and ferrocenecarboxylic acid have been performed with CdSe/ZnS QD-modified gold electrodes to build up photoelectrochemical signal chains between QDs and the enzymes FDH and PQQ-GDH. In the presence of substrate and under illumination of the electrode, electrons are transferred from the enzyme via the redox mediators to the QDs. The resulting photocurrent is dependent on the substrate concentration and allows a quantification of the fructose and glucose content in solution. A first attempt with immobilized redox mediator, i.e. ferrocenecarboxylic acid chemically coupled to PQQ-GDH and attached to QD-modified gold electrodes, reveal the potential to build up photoelectrochemical signal chains even without diffusible redox mediators in solution. However, this approach results in a significant deteriorated photocurrent response compared to the situation with diffusing mediators. In order to improve the photoelectrochemical performance of such redox mediator-based, light-switchable signal chains, an osmium complex-containing redox polymer has been evaluated as electron relay for the electronic linkage between QDs and enzymes. The redox polymer allows the stable immobilization of the enzyme and the efficient wiring with the QD-modified electrode. In addition, a 3D inverse opal TiO2 (IO-TiO2) electrode has been used for the integration of PbS QDs, redox polymer and FAD-GDH in order to increase the electrode surface. This results in a significantly improved photocurrent response, a quite low onset potential for the substrate oxidation and a broader glucose detection range as compared to the approach with ferrocenecarboxylic acid and PQQ-GDH immobilized on CdSe/ZnS QD-modified gold electrodes. Furthermore, IO-TiO2 electrodes are used to integrate sulfonated polyanilines (PMSA1) and PQQ-GDH, and to investigate the direct interaction between the polymer and the enzyme for the light-switchable detection of glucose. While PMSA1 provides visible light excitation and ensures the efficient connection between the IO-TiO2 electrode and the biocatalytic entity, PQQ-GDH enables the oxidation of glucose. Here, the IO-TiO2 electrodes with pores of approximately 650 nm provide a suitable interface and morphology, which is required for a stable and functional assembly of the polymer and enzyme. The successful integration of the polymer and the enzyme can be confirmed by the formation of a glucose-dependent anodic photocurrent. In conclusion, this work provides insights into the design of photoelectrodes and presents different strategies for the efficient coupling of redox enzymes to photoactive entities, which allows for light-directed sensing and provides the basis for the generation of power from sun light and energy-rich compounds.
Synthesis, assembly and thermo-responsivity of polymer-functionalized magnetic cobalt nanoparticles
(2018)
This thesis mainly covers the synthesis, surface modification, magnetic-field-induced assembly and thermo-responsive functionalization of superparamagnetic Co NPs initially stabilized by hydrophobic small molecules oleic acid (OA) and trioctylphosphine oxide (TOPO), as well as the synthesis of both superparamagnetic and ferromagnetic Co NPs by using end-functionalized-polystyrene as stabilizer.
Co NPs, due to their excellent magnetic and catalytic properties, have great potential application in various fields, such as ferrofluids, catalysis, and magnetic resonance imaging (MRI). Superparamagnetic Co NPs are especially interesting, since they exhibit zero coercivity. They get magnetized in an external magnetic field and reach their saturation magnetization rapidly, but no magnetic moment remains after removal of the applied magnetic field. Therefore, they do not agglomerate in the body when they are used in biomedical applications. Normally, decomposition of metallic precursors at high temperature is one of the most important methods in preparation of monodisperse magnetic NPs, providing tunability in size and shape. Hydrophobic ligands like OA, TOPO and oleylamine are often used to both control the growth of NPs and protect them from agglomeration. The as-prepared magnetic NPs can be used in biological applications as long as they are transferred into water. Moreover, their supercrystal assemblies have the potential for high density data storage and electronic devices. In addition to small molecules, polymers can also be used as surfactants for the synthesis of ferromagnetic and superparamagnetic NPs by changing the reaction conditions. Therefore, chapter 2 gives an overview on the basic concept of synthesis, surface modification and self-assembly of magnetic nanoparticles. Various examples were used to illustrate the recent work.
The hydrophobic Co NPs synthesized with small molecules as surfactants limit their biological applications, which require a hydrophilic or aqueous environment. Surface modification (e.g., ligand exchange) is a general idea for either phase transition or surface-functionalization. Therefore, in chapter 3, a ligand exchange process was conducted to functionalize the surface of Co NPs. PNIPAM is one of the most popular smart polymers and its lower critical solution temperature (LCST) is around 32 °C, with a reversible change in the conformation structure between hydrophobic and hydrophilic. The novel nanocomposites of superparamagnetic Co NPs and thermo-responsive PNIPAM are of great interest. Thus, well-defined superparamagnetic Co NPs were firstly synthesized through the thermolysis of cobalt carbonyl by using OA and TOPO as surfactants. A functional ATRP initiator, containing an amine (as anchoring group) and a 2-bromopropionate group (SI-ATRP initiator), was used to replace the original ligands. This process is rapid and facial for efficient surface functionalization and afterwards the Co NPs can be dispersed into polar solvent DMF without aggregation. FT-IR spectroscopy showed that the TOPO was completely replaced, but a small amount of OA remained on the surface. A TGA measurement allowed the calculation of the grafting density of the initiator as around 3.2 initiator/nm2. Then, the surface-initiated ATRP was conducted for the polymerization of NIPAM on the surface of Co NPs and rendered the nanocomposites water-dispersible. A temperature-dependent dynamic light scattering study showed the aggregation behavior of PNIPAM-coated Co NPs upon heating and this process was proven to be reversible. The combination of superparamagnetic and thermo-responsive properties in these hybrid nanoparticles is promising for future applications e.g. in biomedicine.
In chapter 4, the magnetic-field-induced assembly of superparamagnetic cobalt nanoparticles both on solid substrates and at liquid-air interface was investigated. OA- and TOPO-coated Co NPs were synthesized via the thermolysis of cobalt carbonyl and dispersed into either hexane or toluene. The Co NP dispersion was dropped onto substrates (e.g., TEM grid, silicon wafer) and at liquid-air (water-air or ethylene glycol-air) interface. Due to the attractive dipolar interaction, 1-D chains formed in the presence of an external magnetic field. It is known that the concentration and the strength of the magnetic field can affect the assembly behavior of superparamagnetic Co NPs. Therefore, the influence of these two parameters on the morphology of the assemblies was studied. The formed 1-D chains were shorter and flexible at either lower concentration of the Co NP dispersion or lower strength of the external magnetic field due to thermal fluctuation. However, by increasing either the concentration of the NP dispersion or the strength of the applied magnetic field, these chains became longer, thicker and straighter. The reason could be that a high concentration led to a high fraction of short dipolar chains, and their interaction resulted in longer and thicker chains under applied magnetic field. On the other hand, when the magnetic field increased, the induced moments of the magnetic nanoparticles became larger, which dominated over the thermal fluctuation. Thus, the formed short chains connected to each other and grew in length. Thicker chains were also observed through chain-chain interaction. Furthermore, the induced moments of the NPs tended to direct into one direction with increased magnetic field, thus the chains were straighter. In comparison between the assembly on substrates, at water-air interface and at ethylene glycol-air interface, the assembly of Co NPs in hexane dispersion at ethylene glycol-air interface showed the most regular and homogeneous chain structures due to the better spreading of the dispersion on ethylene glycol subphase than on water subphase and substrates. The magnetic-field-induced assembly of superparamagnetic nanoparticles could provide a powerful approach for applications in data storage and electronic devices.
Chapter 5 presented the synthesis of superparamagnetic and ferromagnetic cobalt nanoparticles through a dual-stage thermolysis of cobalt carbonyl (Co2(CO)8) by using polystyrene as surfactant. The amine end-functionalized polystyrene surfactants with different molecular weight were prepared via atom transfer radical polymerization technique. The molecular weight determination of polystyrene was conducted by gel permeation chromatography (GPC) and matrix-assisted laser desorption/ionization time-of-flight (MALDI-ToF) mass spectrometry techniques. The results showed that, when the molecular weight distribution is low (Mw/Mn < 1.2), the measurement by GPC and MALDI-ToF MS provided nearly similar results. For example, the molecular weight of 10600 Da was obtained by MALDI-ToF MS, while GPC gave 10500 g/mol (Mw/Mn = 1.17). However, if the polymer is poly distributed, MALDI-ToF MS cannot provide an accurate value. This was exemplified for a polymer with a molecular weight of 3130 Da measured by MALDI-TOF MS, while GPC showed 2300 g/mol (Mw/Mn = 1.38). The size, size distribution and magnetic properties of the hybrid particles were different by changing either the molecular weight or concentration of the polymer surfactants. The analysis from TEM characterization showed that the size of cobalt nanoparticles stabilized with polystyrene of lower molecular weight (Mn = 2300 g/mol) varied from 12–22 nm, while the size with middle (Mn = 4500 g/mol) and higher molecular weight (Mn = 10500 g/mol) of polystyrene-coated cobalt nanoparticles showed little change. Magnetic measurements exhibited that the small cobalt particles (12 nm) were superparamagnetic, while larger particles (21 nm) were ferromagnetic and assembled into 1-D chains. The grafting density calculated from thermogravimetric analysis showed that a higher grafting density of polystyrene was obtained with lower molecular weight (Mn = 2300 g/mol) than those with higher molecular weight (Mn = 10500 g/mol). Due to the larger steric hindrance, polystyrene with higher molecular weight cannot form a dense shell on the surface of the nanoparticles, which resulted in a lower grafting density. Wide angle X-ray scattering measurements revealed the epsilon cobalt crystalline phases of both superparamagnetic Co NPs coated with polystyrene (Mn = 2300 g/mol) and ferromagnetic Co NPs coated with polystyrene (Mn = 10500 g/mol). Furthermore, a stability study showed that PS-Co NPs prepared with higher polymer concentration and polymer molecular weight exhibited a better stability.
Plants are unable to move away from unwanted environments and therefore have to locally adapt to changing conditions. Arabidopsis thaliana (Arabidopsis), a model organism in plant biology, has been able to rapidly colonize a wide spectrum of environments with different biotic and abiotic challenges. In recent years, natural variation in Arabidopsis has shown to be an excellent resource to study genes underlying adaptive traits and hybridization’s impact on natural diversity. Studies on Arabidopsis hybrids have provided information on the genetic basis of hybrid incompatibilities and heterosis, as well as inheritance patterns in hybrids. However, previous studies have focused mainly on global accessions and yet much remains to be known about variation happening within a local growth habitat. In my PhD, I investigated the impact of heterozygosity at a local collection site of Arabidopsis and its role in local adaptation. I focused on two different projects, both including hybrids among Arabidopsis individuals collected around Tübingen in Southern Germany. The first project sought to understand the impact of hybridization on metabolism and growth within a local Arabidopsis collection site. For this, the inheritance patterns in primary and secondary metabolism, together with rosette size of full diallel crosses among seven parents originating from Southern Germany were analyzed. In comparison to primary metabolites, compounds from secondary metabolism were more variable and showed pronounced non-additive inheritance patterns. In addition, defense metabolites, mainly glucosinolates, displayed the highest degree of variation from the midparent values and were positively correlated with a proxy for plant size.
In the second project, the role of ACCELERATED CELL DEATH 6 (ACD6) in the defense response pathway of Arabidopsis necrotic hybrids was further characterized. Allelic interactions of ACD6 have been previously linked to hybrid necrosis, both among global and local Arabidopsis accessions. Hence, I characterized the early metabolic and ionic changes induced by ACD6, together with marker gene expression assays of physiological responses linked to its activation. An upregulation of simple sugars and metabolites linked to non-enzymatic antioxidants and the TCA cycle were detected, together with putrescine and acids linked to abiotic stress responses. Senescence was found to be induced earlier in necrotic hybrids and cytoplasmic calcium signaling was unaffected in response to temperature. In parallel, GFP-tagged constructs of ACD6 were developed.
This work therefore gave novel insights on the role of heterozygosity in natural variation and adaptation and expanded our current knowledge on the physiological and molecular responses associated with ACD6 activation.
This publication based thesis, which consists of seven published articles, summarizes my contributions to the research field of laser excited ultrafast structural dynamics. The coherent and incoherent lattice dynamics on microscopic length scales are detected by ultrashort optical and X-ray pulses. The understanding of the complex physical processes is essential for future improvements of technological applications. For this purpose, tabletop soruces and large scale facilities, e.g. synchrotrons, are employed to study structural dynamics of longitudinal acoustic strain waves and heat transport. The investigated effects cover timescales from hundreds of femtoseconds up to several microseconds.
The main part of this thesis is dedicated to the investigation of tailored phonon wave packets propagating in perovskite nanostructures. Tailoring is achieved either by laser excitation of nanostructured bilayer samples or by a temporal series of laser pulses. Due to the propagation of longitudinal acoustic phonons, the out-of-plane lattice spacing of a thin film insulator-metal bilayer sample is modulated on an ultrafast timescale. This leads to an ultrafast modulation of the X-ray diffraction efficiency which is employed as a phonon Bragg switch to shorten hard X-ray pulses emitted from a 3rd generation synchrotron.
In addition, we have observed nonlinear mixing of high amplitude phonon wave packets which originates from an anharmonic interatomic potential. A chirped optical pulse sequence excites a narrow band phonon wave packet with specific momentum and energy. The second harmonic generation of these phonon wave packets is followed by ultrafast X-ray diffraction. Phonon upconversion takes place because the high amplitude phonon wave packet modulates the acoustic properties of the crystal which leads to self steepening and to the successive generation of higher harmonics of the phonon wave packet.
Furthermore, we have demonstrated ultrafast strain in direction parallel to the sample surface. Two consecutive so-called transient grating excitations displaced in space and time are used to coherently control thermal gradients and surface acoustic modes. The amplitude of the coherent and incoherent surface excursion is disentangled by time resolved X-ray reflectivity measurements. We calibrate the absolute amplitude of thermal and acoustic surface excursion with measurements of longitudinal phonon propagation. In addition, we develop a diffraction model which allows for measuring the surface excursion on an absolute length scale with sub-Äangström precision. Finally, I demonstrate full coherent control of an excited surface deformation by amplifying and suppressing thermal and coherent excitations at the surface of a laser-excited Yttrium-manganite sample.
Plastic pollution is ubiquitous on the planet since several millions of tons of plastic waste enter aquatic ecosystems each year. Furthermore, the amount of plastic produced is expected to increase exponentially shortly. The heterogeneity of materials, additives and physical characteristics of plastics are typical of these emerging contaminants and affect their environmental fate in marine and freshwaters. Consequently, plastics can be found in the water column, sediments or littoral habitats of all aquatic ecosystems. Most of this plastic debris will fragment as a product of physical, chemical and biological forces, producing particles of small size. These particles (< 5mm) are known as “microplastics” (MP). Given their high surface-to-volume ratio, MP stimulate biofouling and the formation of biofilms in aquatic systems.
As a result of their unique structure and composition, the microbial communities in MP biofilms are referred to as the “Plastisphere.” While there is increasing data regarding the distinctive composition and structure of the microbial communities that form part of the plastisphere, scarce information exists regarding the activity of microorganisms in MP biofilms. This surface-attached lifestyle is often associated with the increase in horizontal gene transfer (HGT) among bacteria. Therefore, this type of microbial activity represents a relevant function worth to be analyzed in MP biofilms. The horizontal exchange of mobile genetic elements (MGEs) is an essential feature of bacteria. It accounts for the rapid evolution of these prokaryotes and their adaptation to a wide variety of environments. The process of HGT is also crucial for spreading antibiotic resistance and for the evolution of pathogens, as many MGEs are known to contain antibiotic resistance genes (ARGs) and genetic determinants of pathogenicity.
In general, the research presented in this Ph.D. thesis focuses on the analysis of HGT and heterotrophic activity in MP biofilms in aquatic ecosystems. The primary objective was to analyze the potential of gene exchange between MP bacterial communities vs. that of the surrounding water, including bacteria from natural aggregates. Moreover, the thesis addressed the potential of MP biofilms for the proliferation of biohazardous bacteria and MGEs from wastewater treatment plants (WWTPs) and associated with antibiotic resistance. Finally, it seeks to prove if the physiological profile of MP biofilms under different limnological conditions is divergent from that of the water communities. Accordingly, the thesis is composed of three independent studies published in peer-reviewed journals. The two laboratory studies were performed using both model and environmental microbial communities. In the field experiment, natural communities from freshwater ecosystems were examined.
In Chapter I, the inflow of treated wastewater into a temperate lake was simulated with a concentration gradient of MP particles. The effects of MP on the microbial community structure and the occurrence of integrase 1 (int 1) were followed. The int 1 is a marker associated with mobile genetic elements and known as a proxy for anthropogenic effects on the spread of antimicrobial resistance genes. During the experiment, the abundance of int1 increased in the plastisphere with increasing MP particle concentration, but not in the surrounding water. In addition, the microbial community on MP was more similar to the original wastewater community with increasing microplastic concentrations. Our results show that microplastic particles indeed promote persistence of standard indicators of microbial anthropogenic pollution in natural waters.
In Chapter II, the experiments aimed to compare the permissiveness of aquatic bacteria towards model antibiotic resistance plasmid pKJK5, between communities that form biofilms on MP vs. those that are free-living. The frequency of plasmid transfer in bacteria associated with MP was higher when compared to bacteria that are free-living or in natural aggregates. Moreover, comparison increased gene exchange occurred in a broad range of phylogenetically-diverse bacteria. The results indicate a different activity of HGT in MP biofilms, which could affect the ecology of aquatic microbial communities on a global scale and the spread of antibiotic resistance.
Finally, in Chapter III, physiological measurements were performed to assess whether microorganisms on MP had a different functional diversity from those in water. General heterotrophic activity such as oxygen consumption was compared in microcosm assays with and without MP, while diversity and richness of heterotrophic activities were calculated by using Biolog® EcoPlates. Three lakes with different nutrient statuses presented differences in MP-associated biomass build up. Functional diversity profiles of MP biofilms in all lakes differed from those of the communities in the surrounding water, but only in the oligo-mesotrophic lake MP biofilms had a higher functional richness compared to the ambient water. The results support that MP surfaces act as new niches for aquatic microorganisms and can affect global carbon dynamics of pelagic environments.
Overall, the experimental works presented in Chapters I and II support a scenario where MP pollution affects HGT dynamics among aquatic bacteria. Among the consequences of this alteration is an increase in the mobilization and transfer efficiency of ARGs. Moreover, it supposes that changes in HGT can affect the evolution of bacteria and the processing of organic matter, leading to different catabolic profiles such as demonstrated in Chapter III. The results are discussed in the context of the fate and magnitude of plastic pollution and the importance of HGT for bacterial evolution and the microbial loop, i.e., at the base of aquatic food webs. The thesis supports a relevant role of MP biofilm communities for the changes observed in the aquatic microbiome as a product of intense human intervention.