Universität Stuttgart
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Item Open Access Das untere Sprunggelenk als biomechanischer Einflussfaktor : Entwicklung und Anwendung eines IMU-Systems zur Beschreibung der Orientierung der Achsen des Sprunggelenks(2020) Schlechtweg, Sascha; Alt, Wilfried (Prof. Dr.)Item Open Access Knoten für Tragkonstruktionen aus betongefülltem Faser-Kunststoff-Verbund, inspiriert von der Biomechanik pflanzlicher Verzweigungen : Sondierung einer neuen Bauweise für Tragknoten aus geflochtenem Textil und Beton(Stuttgart : Institut für Tragkonstruktionen und Konstruktives Entwerfen, Universität Stuttgart, 2020) Jonas, Florian, A.; Knippers, Jan (Prof. Dr.-Ing.)Item Open Access Der biologische Abbau von hydroxylierten Alkylethern(2018) Woiski, Christine; Engesser, Karl-Heinrich (Prof. Dr. rer. nat. habil.)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 Optische Messsysteme und Ein-Sensor-Bildgebungsverfahren für Biosensoren(2024) Berner, Marcel; Werner, Jürgen H. (Prof. Dr. rer. nat. habil.)Die vorliegende Arbeit präsentiert die Entwicklung mehrerer Messsysteme und -verfahren für optische Biosensoranwendungen. Der erste Teil dieser Arbeit entwirft eine universelle experimentelle Plattform für die Erprobung neuer optischer Biosensorkonzepte nach dem Prinzip der laserinduzierten Fluoreszenz (LIF). Die Plattform unterstützt das europäische Forschungsprojekt Nanodem bei der Entwicklung eines portablen Point-of-Care-Testing-Gerätes (PoCT) zur Live-Überwachung von Immunsuppressivakonzentrationen im Blut von Transplantationspatienten unmittelbar am Patientenbett. Das in dieser Arbeit entwickelte Plattformkonzept umfasst die optoelektronische Fluoreszenzanregung und -detektion, optische Filtersysteme, den fluoreszenten Farbstoff, das Materialsystem der Transducerchips, das Mikrofluidiksystem sowie die Automatisierung der Ablaufsteuerung. Der Ausgangspunkt der Entwicklung ist die Herleitung eines allgemeinen physikalischen Modells für LIF-Systeme, an dem sich die Konstruktion der Plattform orientiert. Das in Kooperation mit der Eberhard Karls Universität Tübingen entworfene Transducerchipkonzept auf der Basis lasergeschnittener Klebebänder gestattet eine hohe Flexibilität bezüglich der Geometrie und des Aufbaus der Transducerchips und unterstützt den Technologietransfer akademischer Forschungsergebnisse in die industrielle Fertigung. Die entworfenen Photodetektorarrays aus amorphem Silizium lassen sich dank leicht adaptierbarer Herstellungsprozesse kosteneffizient auf beliebige Biosensorgeometrien anpassen. Die erreichte spezifische Detektivität D* = 11 × 10^12 Jones der Detektoren liegt dabei auf Augenhöhe mit der von State-of-the-Art-Detektoren aus kristallinem Material. Die erzielte Detektionsgrenze von c_{LOD,exp} = 26 nmol/l. Weiter bestätigen die experimentellen Messdaten das aufgestellte physikalische Modell. Der zweite Teil dieser Arbeit zeigt ein neues optisches Verfahren zur ortsaufgelösten Messung, das eine Vielzahl von Bildpunkten simultan mit nur einem einzigen optischen Sensor beobachtet. Das Verfahren nutzt hierzu ortsaufgelöste Lichtmodulatoren (Spatial Light Modulators - SLMs), um eine ortsabhängige optische Modulation zu erzeugen. Die erzeugten optischen Trägersignale gestatten die Zuordnung der als Summensignal empfangenen Signale zu ihren Ursprungspunkten. Der sogenannte Fourier Spotter macht sich dabei die mathematischen Eigenschaften der Fourier-Transformation zunutze. Durch die Anwendung zueinander phasenverschobener Modulationssignale gestattet der Fourier Spotter zudem die unmittelbare Messung von Helligkeitsdifferenzen zwischen unterschiedlichen Beobachtungspunkten. Dieses differentielle optische Messprinzip ist der Kern eines bereits erteilten Patents des Autors mit der Universität Stuttgart. Das neuartige optische Messprinzip eignet sich für die Integration in optische Biosensor-Verfahren, wie etwa die Einwellenlängenreflektometrie (engl. Single Color Reflectometry - SCORE), welche derzeit noch auf teure Spezialkameras angewiesen sind. Herkömmliche Kamerasysteme erzeugen hohe Datenmengen, deren Auswertung erhebliche Rechenleistung in Anspruch nimmt und damit der Weiterentwicklung hin zu miniaturisierten, portablen Biosensorplattformen entgegensteht. Die vorliegende Arbeit präsentiert einen erfolgreichen experimentellen Machbarkeitsnachweis des Fourier Imagers anhand von Helligkeitsdifferenzmessungen an einem SCORE-Aufbau. Eine zukünftige Erweiterung des Fourier Spotters um ein Zeilenspektrometer erlaubt neben der ortsaufgelösten Beobachtung auch eine simultane Erfassung der optischen Spektren jedes einzelnen beobachteten Punktes. Durch diese hyperspektrale Erweiterung wird die erstmalige Umsetzung einer auf der reflektometrischen Interferenzspektroskopie (RIfS) basierenden mehrkanaligen optischen Biosensorplattform möglich. Der dritte Teil dieser Arbeit verallgemeinert das Prinzip des Fourier Spotters und überführt dieses in ein Ein-Pixel-Kamera-Verfahren - das AM-FDM Imaging (engl. Amplitude Modulated Frequency Division Multiplexing). Das AM-FDM Imaging basiert auf der Anwendung von Näherungsverfahren, die ein Übersprechen zwischen den Trägersignalen minimieren. Das aufgestellte systemtheoretische Modell des AM-FDM Imaging umfasst auch das Fourier Spotting und erlaubt den Vergleich mit Rasterscans sowie bereits bekannten Ein-Pixel-Kamera-Verfahren wie dem Hadamard Imaging. Ist das Signal-zu-Rausch-Verhältnis durch das Rauschen des Detektorsystems begrenzt, so erreicht das AM-FDM Imaging einen sogenannten Multiplexgewinn amult = O(M) in der Größenordnung der Anzahl simultan beobachteter Bildpunkte M. Mit den derzeit eingesetzten Näherungsverfahren erreicht das AM-FDM Imaging hinsichtlich des Signal-zu-Rausch-Verhältnisses, der Anzahl simultan beobachtbarer Bildpunkte und der erzielbaren Bildwiederholrate nicht die Leistungsfähigkeit des bei Ein-Pixel-Imaging-Verfahren vorherrschenden Hadamard Imagings. Die in dieser Arbeit diskutierten Verwandtschaftsverhältnisse des AM-FDM Imagings zu anderen bekannten Ein-Pixel-Kamera-Verfahren legen jedoch die Vermutung nahe, dass ein bisher unbekanntes Näherungsverfahren existiert, das das AM-FDM Imaging mit dem Hadamard Imaging gleichstellt. Die Ergebnisse des systemtheoretischen Modells wurden mittels Simulation in Matlab bestätigt und gelten auch für den Fourier Spotter. Damit zeigen die Ergebnisse auf, dass im SCORE-Anwendungsfall eine Modulation nach dem Prinzip des Hadamard Imagings vorteilhafter ist. Das erteilte Patent zum optisch differentiellen Messverfahren schließt auch eine differentielle Variante des Hadamard Imagings mit ein. Gegenüber der Differenzwertbestimmung aus gemessenen Absolutwerten verdoppelt das differentielle Messverfahren wahlweise das Signal-zu-Rauschleistungs-Verhältnis oder die Bildwiederholrate des Hadamard Imagings.Item Open Access The benefit of muscle-actuated systems : internal mechanics, optimization and learning(Stuttgart : Institut für Modellierung und Simulation Biomechanischer Systeme, Computational Biophysics and Biorobotics, 2023) Wochner, Isabell; Schmitt, Syn (Prof. Dr.)We are facing the challenge of an over-aging and overweight society. This leads to an increasing number of movement disorders and causes the loss of mobility and independence. To address this pressing issue, we need to develop new rehabilitation techniques and design innovative assistive devices. Achieving this goal requires a deeper understanding of the underlying mechanics that control muscle-actuated motion. However, despite extensive studies, the neural control of muscle-actuated motion remains poorly understood. While experiments are valuable and necessary tools to further our understanding, they are often limited by ethical and practical constraints. Therefore, simulating muscle-actuated motion has become increasingly important for testing hypotheses and bridge this knowledge gap. In silico, we can establish cause-effect relationships that are experimentally difficult or even impossible to measure. By changing morphological aspects of the underlying musculoskeletal structure or the neural control strategy itself, simulations are crucial in the quest for a deeper understanding of muscle-actuated motion. The insights gained from these simulations paves the way to develop new rehabilitation techniques, enhance pre-surgical planning, design better assistive devices and improve the performance of current robots. The primary objective of this dissertation is to study the intricate interplay between musculoskeletal dynamics, neural controller and the environment. To achieve this goal, a simulation framework has been developed as part of this thesis, enabling the modeling and control of muscle-actuated motion using both model-based and learning-based methods. By utilizing this framework, musculoskeletal models of the arm, head-neck complex and a simplified whole-body model are investigated in conjunction with various concepts of motor control. The main research questions of this thesis are therefore: 1. How does the neural control strategy select muscle activation patterns to generate the desired movement, and can we use this knowledge to design better assistive devices? 2. How does the musculoskeletal dynamics facilitate the neural control strategy in accomplishing this task of generating desired movements? To address these research questions, this thesis comprises a total of five journal and conference articles. More specifically, contributions I-III of this thesis focus on addressing the first research question which aims to understand how voluntary and reflexive movements can be predicted. First, we investigate various optimality principles using a musculoskeletal arm model to predict point-to-manifold reaching tasks. By using predictive simulations, we demonstrate how the arm would move towards a goal if, for example, our neural control strategy would minimize energy consumption. The main finding of this contribution shows that it is essential to include muscle dynamics and consider tasks with more openly defined targets to draw accurate conclusions about motor control. Through our analysis, we show that a combination of mechanical work, jerk and neuronal stimulation effort best predicts point-reaching when compared to human experiments. Second, we propose a novel method to optimize the design of exoskeleton power units taking into account the load cycle of predicted human movements. To achieve this goal, we employ a forward dynamic simulation of a generic musculoskeletal arm model, which is first scaled to represent different individuals. Next, we predict individual human motions and employ the predicted human torques to scale the electrical power units employing a novel scalability model. By considering the individual user needs and task demands, our approach achieves a lighter and more efficient design. In conclusion, our framework demonstrates the potential to improve the design of individual assistive devices. The third contribution focuses on predicting reflexive movements in response to sudden perturbations of the head-neck complex. To achieve this, we conducted experiments in which volunteers were placed on a table while supporting their heads with a trapdoor. This trapdoor was then suddenly released leading to a downward movement of the head until the reflexive reaction of the muscles stops the head from falling. We analyzed the results of these experiments, presenting characteristic parameters and highlighting differences between separate age and gender groups. Using this data, we also set up benchmark validations for a musculoskeletal head-neck model, including reflex control strategies. Our main findings are that there are large individual differences in reflexive responses between participants and that the perturbation direction significantly affects the reflexive response. Furthermore, we show that this data can be used as a benchmark test to validate musculoskeletal models and different muscle control strategies. While the first three contributions focus on the research question (1), contributions IV-V focus on (2) whether and how the musculoskeletal dynamics facilitate the learning and control task of various movements. We utilize a recently introduced information-theoretic approach called control effort to quantify the minimally required information to perform specific movements. By applying this concept, we can for example quantify how much biological muscles reduce the neuronal information load compared to technical DC-motors. We present a novel optimization algorithm to find this control effort and apply it to point-reaching and walking tasks. The main finding of this contribution is that the musculoskeletal dynamics reduce the control effort required for these movements compared to torque-driven systems. Finally, we hypothesize that the highly nonlinear muscle dynamics not only facilitate the control task but also provide inherent stability that is beneficial for learning from scratch. To test this, we employed various learning strategies for multiple anthropomorphic tasks, including point-reaching, ball-hitting, hopping, and squatting. The results of this investigation demonstrate that using muscle-like actuators improves the data-efficiency of the learning tasks. Additionally, including the muscle dynamics improves the robustness towards hyperparameters and allows for a better generalization towards unknown and unlearned perturbations. In summary, this thesis enhances existing methods to control and learn muscle-actuated motion, quantifies the control effort needed to perform certain movements and demonstrates that the inherent stability of the muscle dynamics facilitates the learning task. The models, control strategies, and experimental data presented in this work aid researchers in science and industry to improve their predictions in various fields such as neuroscience, ergonomics, rehabilitation, passive safety systems, and robotics. This allows us to reverse-engineer how we as humans control movement, uncovering the complex relationship between musculoskeletal dynamics and neural controller.Item Open Access Improving optical measurements, online monitoring, growth modeling, and automated control in microalgae production of Phaeodactylum tricornutum(2024) Yeh, Yen-Cheng; Tovar, Günter E. M. (Prof. Dr.)