High-Throughput Automated Multi-Target Super-resolution Imaging

Super-resolution microscopy techniques developed through the past few decades enable us to surpass the classical diffraction limit of light, and thus open new doors to investigate the formerly inaccessible world of nanometer-sized objects. Most importantly, by using super-resolution microscopy, one can visualize sub-cellular structures in the range of 10 to 200 nm. At this range, we can investigate exciting problems in biology and medicine by visualizing protein-protein interactions and spatiotemporal analysis of structures of interest on the surface or inside cells. These techniques (collectively known as nanoscopy) have a high impact on understanding and solving biological questions. This dissertation starts with a brief and general description of current super-resolution techniques and then moves toward a multi-target super-resolution imaging strategy using sequential imaging that has benefits over conventional multi-color imaging methods. Sequential microscopy takes advantage of the photo-physical properties of the most suitable dye for a particular technique to achieve the optimal and consistent resolution for each of multiple targets of imaging. For example, for dSTORM imaging, this is currently AlexaFluor647.\ Sequential dSTROM has an advantage for multi-target imaging due to having a single imaging channel which avoids dealing with differential aberration-problems between multiple emission paths unlike other multi-color imaging based methods. We show that sequential imaging method can be facilitated using automated imaging. In this dissertation, a sequential microscope is designed, calibrated, and tested on multiple structures. We show that it can automatically re-find the position of each initially registered cell and can account for sample drift through an entire experiment. The microscope has been used in multiple collaborations with other groups to investigate biological problems of interest. Two labeling strategies that facilitate sequential imaging are described.\ The first strategy is DNA-strand-displacement , which allows imaging of multiple structures in a controlled and time-efficient binding-unbinding scenario. The second strategy is imaging with the small, actin binding peptide Lifeact. Finally, future directions and suggestions are made about how we can further improve the microscope. In the Appendix I provide a guide on how to use and troubleshoot the microscope, how to measure the efficiency of the microscope, as well as how to fix and label cells for optimal imaging and how to prepare various imaging buffers

Visualization of Tensor Fields in Mechanics

Tensors are used to describe complex physical processes in many applications. Examples include the distribution of stresses in technical materials, acting forces during seismic events, or remodeling of biological tissues. While tensors encode such complex information mathematically precisely, the semantic interpretation of a tensor is challenging. Visualization can be beneficial here and is frequently used by domain experts. Typical strategies include the use of glyphs, color plots, lines, and isosurfaces. However, data complexity is nowadays accompanied by the sheer amount of data produced by large-scale simulations and adds another level of obstruction between user and data. Given the limitations of traditional methods, and the extra cognitive effort of simple methods, more advanced tensor field visualization approaches have been the focus of this work. This survey aims to provide an overview of recent research results with a strong application-oriented focus, targeting applications based on continuum mechanics, namely the fields of structural, bio-, and geomechanics. As such, the survey is complementing and extending previously published surveys. Its utility is twofold: (i) It serves as basis for the visualization community to get an overview of recent visualization techniques. (ii) It emphasizes and explains the necessity for further research for visualizations in this context

Application and Optimization of Contact-Guided Replica Exchange Molecular Dynamics

Proteine sind komplexe Makromoleküle, die in lebenden Organismen eine große Vielfalt an wichtigen Aufgaben erfüllen. Proteine können beispielsweise Gene regulieren, Struktur stabilisieren, Zellsignale übertragen, Substanzen transportieren und vieles mehr. Typischerweise sind umfassende Kenntnisse von Struktur und Dynamik eines Proteins erforderlich um dessen physiologische Funktion und Interaktionsmechanismen vollständig zu verstehen. Gewonnene Erkenntnisse sind für Biowissenschaften unerlässlich und können auf viele Bereiche angewendet werden, wie z.B. für Arzneimitteldesign oder zur Krankheitsbehandlung. Trotz des unfassbaren Fortschritts experimenteller Techniken bleibt die Bestimmung einer Proteinstruktur immer noch eine herausfordernde Aufgabe. Außerdem können Experimente nur Teilinformationen liefern und Messdaten können mehrdeutig und schwer zu interpretieren sein. Aus diesem Grund werden häufig Computersimulationen durchgeführt um weitere Erkenntnisse zu liefern und die Lücke zwischen Theorie und Experiment zu schließen. Heute sind viele in-silico Methoden in der Lage genaue Protein Strukturmodelle zu erzeugen, sei es mit einem de novo Ansatz oder durch Verbesserung eines anfänglichen Modells unter Berücksichtigung experimenteller Daten. In dieser Dissertation erforsche ich die Möglichkeiten von Replica Exchange Molekulardynamik (REX MD) als ein physikbasierter Ansatz zur Erzeugung von physikalisch sinnvollen Proteinstrukturen. Dabei lege ich den Fokus darauf möglichst nativähnliche Strukturen zu erhalten und untersuche die Stärken und Schwächen der angewendeten Methode. Ich erweitere die Standardanwendung, indem ich ein kontaktbasiertes Bias-Potential integriere um die Leistung und das Endergebnis von REX zu verbessern. Die Einbeziehung nativer Kontaktpaare, die sowohl aus theoretischen als auch aus experimentellen Quellen abgeleitet werden können, treibt die Simulation in Richtung gewünschter Konformationen und reduziert dementsprechend den notwendigen Rechenaufwand. Während meiner Arbeit führte ich mehrere Studien durch mit dem Ziel, die Anreicherung von nativ-ähnlichen Strukturen zu maximieren, wodurch der End-to-End Prozess von geleitetem REX MD optimiert wird. Jede Studie zielt darauf ab wichtige Aspekte der verwendeten Methode zu untersuchen und zu verbessern: 1) Ich studiere die Auswirkungen verschiedener Auswahlen von Bias-Kontakten, insbesondere die Reichweitenabhängigkeit und den negativen Einfluss von fehlerhaften Kontakten. Dadurch kann ich ermitteln, welche Art von Bias zu einer signifikanten Anreicherung von nativ-ähnlichen Konformationen führen im Vergleich zu regulärem REX. 2) Ich führe eine Parameteroptimierung am verwendeten Bias-Potential durch. Der Vergleich von Ergebnissen aus REX-Simulationen unter Verwendung unterschiedlicher sigmoidförmiger Potentiale weist mir sinnvolle Parameter Bereiche auf, wodurch ich ein ideales Bias-Potenzial für den allgemeinen Anwendungsfall ableiten kann. 3) Ich stelle eine de novo Faltungsmethode vor, die möglichst schnell viele einzigartige Startstrukturen für REX generieren kann. Dabei untersuche ich ausführlich die Leistung dieser Methode und vergleiche zwei verschiedene Ansätze zur Auswahl der Startstruktur. Das Ergebnis von REX wird stark verbessert, falls Strukturen bereits zu Beginn eine große Bandbreite des Konformationsraumes abdecken und gleichzeitig eine geringe Distanz zum angestrebten Zustand aufweisen. 4) Ich untersuche vier komplexe Algorithmusketten, die in der Lage sind repräsentative Strukturen aus großen biomolekularen Ensembles zu extrahieren, welche durch REX erzeugt wurden. Dabei studiere ich ihre Robustheit und Zuverlässigkeit, vergleiche sie miteinander und bewerte ihre erbrachte Leistung numerisch. 5) Basierend auf meiner Erfahrung mit geleitetem REX MD habe ich ein Python-Paket entwickelt um REX-Projekte zu automatisieren und zu vereinfachen. Es ermöglicht einem Benutzer das Entwerfen, Ausführen, Analysieren und Visualisieren eines REX-Projektes in einer interaktiven und benutzerfreundlichen Umgebung

Learning the Structure of Continuous Markov Decision Processes

There is growing interest in artificial, intelligent agents which can operate autonomously for an extended period of time in complex environments and fulfill a variety of different tasks. Such agents will face different problems during their lifetime which may not be foreseeable at the time of their deployment. Thus, the capacity for lifelong learning of new behaviors is an essential prerequisite for this kind of agents as it enables them to deal with unforeseen situations. However, learning every complex behavior anew from scratch would be cumbersome for the agent. It is more plausible to consider behavior to be modular and let the agent acquire a set of reusable building blocks for behavior, the so-called skills. These skills might, once acquired, facilitate fast learning and adaptation of behavior to new situations. This work focuses on computational approaches for skill acquisition, namely which kind of skills shall be acquired and how to acquire them. The former is commonly denoted as skill discovery and the latter as skill learning . The main contribution of this thesis is a novel incremental skill acquisition approach which is suited for lifelong learning. In this approach, the agent learns incrementally a graph-based representation of a domain and exploits certain properties of this graph such as its bottlenecks for skill discovery. This thesis proposes a novel approach for learning a graph-based representation of continuous domains based on formalizing the problem as a probabilistic generative model. Furthermore, a new incremental agglomerative clustering approach for identifying bottlenecks of such graphs is presented. Thereupon, the thesis proposes a novel intrinsic motivation system which enables an agent to intelligently allocate time between skill discovery and skill learning in developmental settings, where the agent is not constrained by external tasks. The results of this thesis show that the resulting skill acquisition approach is suited for continuous domains and can deal with domain stochasticity and different explorative behavior of the agent. The acquired skills are reusable and versatile and can be used in multi-task and lifelong learning settings in high-dimensional problems

VGC 2023 - Unveiling the dynamic Earth with digital methods: 5th Virtual Geoscience Conference: Book of Abstracts

Conference proceedings of the 5th Virtual Geoscience Conference, 21-22 September 2023, held in Dresden. The VGC is a multidisciplinary forum for researchers in geoscience, geomatics and related disciplines to share their latest developments and applications.:Short Courses 9 Workshops Stream 1 10 Workshop Stream 2 11 Workshop Stream 3 12 Session 1 – Point Cloud Processing: Workflows, Geometry & Semantics 14 Session 2 – Visualisation, communication & Teaching 27 Session 3 – Applying Machine Learning in Geosciences 36 Session 4 – Digital Outcrop Characterisation & Analysis 49 Session 5 – Airborne & Remote Mapping 58 Session 6 – Recent Developments in Geomorphic Process and Hazard Monitoring 69 Session 7 – Applications in Hydrology & Ecology 82 Poster Contributions 9