Universität Stuttgart
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Item Open Access Novel X-ray lenses for direct and coherent imaging(2019) Sanli, Umut Tunca; Schütz, Gisela (Prof. Dr.)Item Open Access Silicon integrated dual-mode interferometer with differential outputs(2017) Hoppe, Niklas; Scheck, Pascal; Sweidan, Rami; Diersing, Philipp; Rathgeber, Lotte; Vogel, Wolfgang; Riegger, Benjamin R.; Southan, Alexander; Berroth, ManfredThe dual-mode interferometer (DMI) is an attractive alternative to Mach-Zehnder interferometers for sensor purposes, achieving sensitivities to refractive index changes close to state-of-the-art. Modern designs on silicon-on-insulator (SOI) platforms offer thermally stable and compact devices with insertion losses of less than 1 dB and high extinction ratios. Compact arrays of multiple DMIs in parallel are easy to fabricate due to the simple structure of the DMI. In this work, the principle of operation of an integrated DMI with differential outputs is presented which allows the unambiguous phase shift detection with a single wavelength measurement, rather than using a wavelength sweep and evaluating the optical output power spectrum. Fluctuating optical input power or varying attenuation due to different analyte concentrations can be compensated by observing the sum of the optical powers at the differential outputs. DMIs with two differential single-mode outputs are fabricated in a 250 nm SOI platform, and corresponding measurements are shown to explain the principle of operation in detail. A comparison of DMIs with the conventional Mach-Zehnder interferometer using the same technology concludes this work.Item Open Access Soft materials for acoustic applications(2022) Choi, Eunjin; Fischer, Peer (Prof. Dr.)Ultrasound finds wide application in imaging and testing because ultrasound can penetrate tissue and is benign. Gaseous microbubbles strongly scatter ultrasound and are therefore used as contrast agents. Ultrasound responsive materials can be used for many industrial and biomedical applications. Ultrasound can also be used to exert forces and manipulate particles solution and biological cells. In this thesis, material systems are developed for three application areas: 1) models of human organs for the quantitative evaluation of surgical procedures with ultrasound; 2) the fabrication of soft objects by assembling polymeric particles with ultrasound and the acoustic hologram; and 3) the characterization of antibubbles as novel contrast agents that can carry a fluid load. Organ phantoms serve as tools in medical fields to train and plan medical procedures. However, current organ phantoms miss important features or are not realistic. Current models tend to possess a Young’s modulus that is much higher than that of tissue. Furthermore, many of the current models do not show the correct contrast in a medical imaging setting. This thesis presents high fidelity organ phantoms that possess the correct elasticity, compliance, optical appearance, and correct ultrasound contrast. One model is developed for cystoscopy (CY) of the bladder. Another phantom for the transurethral resection of the prostate (TURP). The quality of the phantoms is validated by medical practitioners. For CY, the execution time of the medical practitioners is recorded to completely map the inside of the bladder phantom while localizing tumor models that have been embedded in the bladder wall. For TURP, the quality of the resection is compared with ultrasound imaging before and after the surgical simulation. Parameters are defined to quantify the success of the procedure. The phantoms developed as part of this thesis have received high satisfaction scores from medical practitioners. The parameters reflect the experience of the surgeons. In assembling soft matter, one challenge is that existing 3D printing methods are slow. In contrast, the use of ultrasound patterns shaped with a recently invented acoustic hologram allows objects to be built at once. In this thesis, polydimethylsiloxane (PDMS) particles have been assembled into two-dimensional shapes with ultrasound. To fix the assembly, the PDMS has been physically functionalized with an initiator using swelling. Suitable swelling solutions have been determined based on their solubility. The stability of the physisorbed initiators is evaluated, and the functionalized PDMS particles are fixed via photopolymerization after assembly in aqueous polyethylene glycol dimethacrylate (PEG-DMA) solutions. The fabrication steps can be repeated to increase the thickness of structures that are mechanically stable. The antibubble is an emerging ultrasound contrast agent. It has an inverse form to a conventional bubble in that a substance in the core is surrounded by a gaseous layer. The antibubble is acoustically responsive and, compared to conventional microbubbles, can carry a much greater load. In this thesis, the structure of antibubbles is examined. In particular, the volume of the load is quantified, and the amount of gas per bubble is estimated. The stability of the core substance against diffusion is investigated and shown to be stable for over 11 h.Item Open Access Degradation study on solid oxide steam electrolysis(2020) Hörlein, Michael Philipp; Friedrich, K. Andreas (Prof. Dr.)Untersuchung der Degradation von Festoxidzellen im Elektrolysebetrieb von Wasserdampf anhand von Variationen der Betriebsbedingungen.Item Open Access Development and investigation of protonic ceramic cells for hydrogen production at intermediate temperatures(2024) Zheng, Haoyu; Thess, André (Prof. Dr.)Item Open Access Electronic transport properties of DNA sensing nanopores : insight from quantum mechanical simulations(2017) Sivaraman, Ganesh; Fyta, Maria (Jun.-Prof. Dr.)The translocation of DNA through nanopores is an intensively studied field as it can lead to a new perspective in DNA sequencing. During this process the DNA is electrophoretically driven through a nanoscale hole in a membrane, and use different sensing schemes to read out the sequence. Within the scope of nanopore sequencing two important sensing schemes relevant to this thesis are: 1.) Tunneling sequencers based on solid state nanopores embedded with gold electrodes 2.) 2D materials beyond graphene For scheme 1, an obvious improvement is to coat the gold electrode with molecules that have high conductance and can form instantaneous hydrogen bond bridges with the translocating polynucleotide thereby improving the transverse current signal. The molecule that we propose is the so called diamondoid which are diamond caged molecules with hydrogen termination. Before applying such a molecule to a nanopore electrode set up, one would like to understand their interaction with DNA and its nucleobases. For this purpose, hydrogen bonded complexes formed between nitrogen doped derivatives of smallest diamondoids (i.e. adamantane derivatives) and nucleobases were investigated using dispersion corrected density functional theory (DFT). Mutated and methylated nucleobases are also taken into consideration in these investigations. DFT calculations revealed that hydrogen bonds are of moderate strength. In addition, starting from the DFT predicted hydrogen bonding configuration for each complex, rotations, and translations along a reference axis was performed to capture variations in the interaction energies along the donor-acceptor groups of the hydrogen bonds. The electronic density of states analysis for the hydrogen bonded complexes revealed distinguishable signatures for each nucleobase, thereby showing the suitability for application in electrodes functionalised with such probe molecules. In the next step, an adamantane derivative is placed on one of the electrode and nucleotides are introduced in such a way that nucleobases form hydrogen bonds with the of the nitrogen group of the adamantane derivatives. Electronic transport calculations were performed for gold electrodes functionalised with 3 different adamantane derivatives. Four pristine nucleotides, one mutated, and one methylated nucleotides were considered. Analysis of the transmission spectra reveal that each of the nucleotides has a unique resonance peak far below the Fermi level. We have also proposed a gating voltage window to sample the resonance peaks of the nucleotide so that they can be distinguished from each other. An alternative to tunneling sequencers would be to use nanopores built in to ultra thin metallic nanoribbons such as graphene. The sequence can be read out from the in-plane current modulation resulting from the local field effect of the translocating nucleotides in the vicinity of the metallic pore edges. But the hydrophobicity of graphene makes it a difficult candidate in aqueous environment. Hence in scheme 2, the aim is to model an ultra thin material that can rectify the hydrophobicity of graphene and can be a very good candidate for current modulation sequencing. Ultra thin MoS2 (2H) monolayer exist as direct band gap semiconductor. Nanopores based on 2H phases have been reported in the literature and are not hydrophobic. By means of chemical exfoliation of the 2H phase, a meta stable 1T phase of MoS2 has also been synthesized by various experimental groups. The 1T phase of MoS2 is metallic. The aim of this thesis is to model a nano-biosensor template based on a hybrid MoS2 monolayer made up of a metallic (1T) phase sandwiched between semiconducting (2H) phase. The sensor that we propose, should have only metallic nanopore edges. As a first step, we have modeled the semiconductor-metal interface, and compared them with experiments. Then an investigation to understand the influence of the increase of the metallic unit on the electronic properties is performed. Since, point defects are highly relevant to electrochemical pore growth, a point sulfur defect analysis is provided to ascertain the weakest point in the sheet. Finally to understand the effect of the interface electronic transport calculations are performed. The transmission spectra reveals a clear asymmetry in the current flow across the interface by means of gating. In the end, the relevance of such a hybrid MoS2 material for nanopore sequencing is discussed.Item Open Access Interfacial mechanics and liquid crystal structure of liquid gallium(2021) Yunusa, Muhammad; Sitti, Metin (Prof. Dr.)This dissertation aims to shed light on the fundamental aspects of supercooled liquid gallium. First, the mechanical properties of the oxide skin encapsulating the supercooled liquid gallium droplet is investigated. By leveraging the supercooling behavior of gallium and the formation of its oxide skin, we characterized the emergence of wrinkling at the interface and adhesion energy between the liquid gallium and rigid substrate. An interfacial energy of 0.238 ± 0.008 J m-2 was measured between gallium droplet and flat glass. Second, seed induced crystallization of supercooled liquid gallium on the different substrate materials revealed the dependence of the kinetics of crystallization on thermal behavior of the substrate. Such approach further elucidates on the importance of interface temperature during crystallization with a preferred orientation. The third part of the dissertation reports an unprecedented liquid crystal structure in supercooled liquid gallium. By the use of techniques applied in liquid crystal (LC) research, observation of LC texture in supercooled liquid gallium was realized. Reflective polarized optical microscopy (R-POM) on liquid gallium sandwiched between glasses treated with rubbed polymers reveals the onset of an anisotropic reflection of possible dimer molecules or clusters at 120°C that increases on cooling and persists down to room temperature or below. On the other hand, when gallium is sandwiched between substrates that align conventional liquid crystal molecules normal to the surface, the reflection is isotropic. This observation of LC structure of a highly electrically conductive supercooled liquid gallium provides an unexpected new field of materials science and liquid crystal research.Item Open Access Impact of repetitive, ultra-short soft X-ray pulses from processing of steel with ultrafast lasers on human cell cultures(2024) Holland, Julian; Lungu, Cristiana; Weber, Rudolf; Emperle, Max; Graf, ThomasUltrafast lasers, with pulse durations below a few picoseconds, are of significant interest to the industry, offering a cutting-edge approach to enhancing manufacturing processes and enabling the fabrication of intricate components with unparalleled accuracy. When processing metals at irradiances exceeding the evaporation threshold of about 10 10 W/cm² these processes can generate ultra-short, soft X-ray pulses with photon energies above 5 keV. This has prompted extensive discussions and regulatory measures on radiation safety. However, the impact of these ultra-short X-ray pulses on molecular pathways in the context of living cells, has not been investigated so far. This paper presents the first molecular characterization of epithelial cell responses to ultra-short soft X-ray pulses, generated during processing of steel with an ultrafast laser. The laser provided pulses of 6.7 ps with a pulse repetition rate of 300 kHz and an average power of 500 W. The irradiance was 1.95 ×10 13 W/cm 2 . Ambient exposure of vitro human cell cultures, followed by imaging of the DNA damage response and fitting of the data to a calibrated model for the absorbed dose, revealed a linear increase in the DNA damage response relative to the exposure dose. This is in line with findings from work using continuous wave soft X-ray sources and suggests that the ultra-short X-ray pulses do not generate additional hazard. This research contributes valuable insights into the biological effects of ultrafast laser processes and their potential implications for user safety.Item Open Access Development of super-specific epigenome editing by targeted allele-specific DNA methylation(2023) Rajaram, Nivethika; Kouroukli, Alexandra G.; Bens, Susanne; Bashtrykov, Pavel; Jeltsch, AlbertBackground. Epigenome editing refers to the targeted reprogramming of genomic loci using an EpiEditor which may consist of an sgRNA/dCas9 complex that recruits DNMT3A/3L to the target locus. Methylation of the locus can lead to a modulation of gene expression. Allele-specific DNA methylation (ASM) refers to the targeted methylation delivery only to one allele of a locus. In the context of diseases caused by a dominant mutation, the selective DNA methylation of the mutant allele could be used to repress its expression but retain the functionality of the normal gene. Results. To set up allele-specific targeted DNA methylation, target regions were selected from hypomethylated CGIs bearing a heterozygous SNP in their promoters in the HEK293 cell line. We aimed at delivering maximum DNA methylation with highest allelic specificity in the targeted regions. Placing SNPs in the PAM or seed regions of the sgRNA, we designed 24 different sgRNAs targeting single alleles in 14 different gene loci. We achieved efficient ASM in multiple cases, such as ISG15, MSH6, GPD1L, MRPL52, PDE8A, NARF, DAP3, and GSPT1, which in best cases led to five to tenfold stronger average DNA methylation at the on-target allele and absolute differences in the DNA methylation gain at on- and off-target alleles of > 50%. In general, loci with the allele discriminatory SNP positioned in the PAM region showed higher success rate of ASM and better specificity. Highest DNA methylation was observed on day 3 after transfection followed by a gradual decline. In selected cases, ASM was stable up to 11 days in HEK293 cells and it led up to a 3.6-fold change in allelic expression ratios. Conclusions. We successfully delivered ASM at multiple genomic loci with high specificity, efficiency and stability. This form of super-specific epigenome editing could find applications in the treatment of diseases caused by dominant mutations, because it allows silencing of the mutant allele without repression of the expression of the normal allele thereby minimizing potential side-effects of the treatment.