Development of new approaches for characterising DNA origami-based nanostructures with atomic force microscopy and super-resolution microscopy

DNA nanotechnology has developed a versatile set of methods to utilise DNA self-assembly for the bottom-up construction of arbitrary two- and three-dimensional DNA objects in the nanometre size range, and to functionalise the structures with unprecedented site-specificity with nanoscale objects such as metallic and semiconductor nanoparticles, proteins, fluorescent dyes, or synthetic polymers. The advances in structure assembly have resulted in the application of functional DNA-based nanostructures in a gamut of fields from nanoelectronic circuitry, nanophotonics, sensing, drug delivery, to the use as host structure or calibration standard for different types of microscopy. However, the analytical means for characterising DNA-based nanostructures drag behind these advances. Open questions remain, amongst others in quantitative single-structure evaluation. While techniques such as atomic force microscopy (AFM) or transmission electron microscopy (TEM) offer feature resolution in the range of few nanometres, the number of evaluated structures is often limited by the time-consuming manual data analysis. This thesis has introduced two new approaches to quantitative structure evaluation using AFM and super-resolution fluorescence microscopy (SRM). To obtain quantitative data, semi-automated computational image analysis routines were tailored in both approaches. AFM was used to quantify the attachment yield and placement accuracy of poly(3-tri(ethylene glycol)thiophene)-b-oligodeoxynucleotide diblock copolymers on a rectangular DNA origami. This work has also introduced the first hybrid of DNA origami and a conjugated polymer that uses a highly defined polythiophene derivative synthesised via state-of-the-art Kumada catalyst-transfer polycondensation. Among the AFM-based studies on polymer-origami-hybrids, this was the first to attempt near-single molecule resolution, and the first to introduce computational image analysis. Using the FindFoci tool of the software ImageJ revealed attachment yields per handle between 26 - 33%, and determined a single block copolymer position with a precision of 80 - 90%. The analysis has pointed out parameters that potentially influence the attachment yield such as the handle density and already attached objects. Furthermore, it has suggested interactions between the attached polymer molecules. The multicolour SRM approach used the principles of single-molecule high-resolution co-localisation (SHREC) to evaluate the structural integrity and the deposition side of the DNA origami frame “tPad” based on target distances and angles in a chiral fluorophore pattern the tPads were labelled with. The computatinal routine that was developed for image analysis utilised clustering to identify the patterns in a sample’s signals and to determine their characteristic distances and angles for hundreds of tPads simultaneously. The method excluded noise robustly, and depicted the moderate proportion of intact tPads in the samples correctly. With a registration error in the range of 10 -15 nm after mapping of the colour channels, the precision of a single distance measurements on the origami appeared in the range of 20 - 30 nm. By broadening the scope of computational AFM image analysis and taking on a new SRM approach for structure analysis, this work has presented working approaches towards new tools for quantitative analysis in DNA nanotechnology. Furthermore, the work has presented a new approach to constructing hybrid structures from DNA origami and conjugated polymers, which will open up new possibilities in the construction of nanoelectronic and nanophotonic structures

Mechanochemie

Die Mechanochemie wird als Alternative zu konventionellen Syntheserouten mittlerweile vielfältig eingesetzt. In dieser Arbeit wurden verschiedene Ansätze genutzt, um die mechanochemischen Mechanismen systematisch aufzuklären. Anhand von Modellsystemen (Cokristalle) wurden die mechanochemischen Synthesewege durch in situ-Verfolgung aufgeklärt, die kinetischen sowie thermodynamischen Stabilitäten der Edukte und Produkte ermittelt sowie die Aktivierungsenergie quantitativ abgeschätzt. Die Ergebnisse führten zur Hypothese, dass die mechanochemische Cokristallisation über einen nicht-kristallinen – wahrscheinlich amorphen – Übergangszustand abläuft und ähnlich der Kristallisation aus Lösung ist.Mechanochemistry is a widely used alternative for conventional synthesis methods. In this work, different approaches were considered to evaluate the mechanochemical formation pathways. Based on model systems (cocrystals) the synthesis pathways were elucidated using in situ monitoring techniques and thermodynamic and kinetic aspects were investigated. The activation energy of a mechanochemical reaction was quantitavely estimated. The results lead to the assumption that the mechanochemical cocrystallisation proceeds via a non-crystalline phase and that it is similar to the crystallisation from solution

Activation of retinal microglia rather than microglial cell density correlates with retinal neovascularization in the mouse model of oxygen-induced retinopathy

<p>Abstract</p> <p>Background</p> <p>Retinal neovascularization has been intensively investigated in the mouse model of oxygen-induced retinopathy (OIR). Here, we studied the contribution of microglial cells to vascular regression during the hyperoxic phase and to retinal neovascularization during the hypoxic phase.</p> <p>Methods</p> <p>Mice expressing green fluorescent protein (GFP) under the Cx3cr1 promoter labeling microglial cells were kept in 75% oxygen from postnatal day 7 (P7) to P12. Microglial cell density was quantified at different time points and at different retinal positions in retinal flat mounts. Microglial activation was determined by the switch from ramified to amoeboid cell morphology which correlated with the switch from lectin negative to lectin positive staining of GFP positive cells.</p> <p>Results</p> <p>Microglial cell density was constant in the peripheral region of the retina. In the deep vascular layer of the central region, however, it declined 14 fold from P12 to P14 and recovered afterwards. Activated microglial cells were found in the superficial layer of the central avascular zone from P8 to P12 and from P16 to P18. In addition, hyalocytes were found in the vitreal layer in the central region and their cell density decreased over time.</p> <p>Conclusion</p> <p>Density of microglial cells does not correlate with vascular obliteration or revascularization. But the time course of the activation of microglia indicates that they may be involved in retinal neovascularization during the hypoxic phase.</p

Reliability of a bridge with an orthotropic deck exposed to extreme traffic events

The 11th International Conference on Mathematical Methods in Reliability, HONG KONG, CHINE, 03-/06/2019 - 07/06/2019Predicting reliability levels for critical details of bridges based on limited statistical traffic data is a relevant topic nowadays. That is why the comparison between results from various statistical approaches based on the recorded data for applied traffic actions is the main point of interest of this work. The object of the current study is the famous Millau viaduct, a cable-stayed bridge with the steel orthotropic deck located in Southern France. Values of load effects that are used in analysis are derived from a finite element model of a part of the deck. They are based on data from traffic monitoring that is provided from the bridge Weigh-In-Motion system covering several months of axle loads, distances and speeds of heavy trucks. The methodology is based on a definition of limit state functions based on several statistical distributions in order to assess and compare reliability indexes for the ultimate limit state. It includes a comparison between different approaches of extreme values theory, the methodology proposed in background works for European standards and the design load model. Moreover, this work covers the influence of applied loads of a high amplitude, as global effects, onto stresses from axle loads, as local effects

Assessment of Subsampling Strategies in Microspectroscopy of Environmental Microplastic Samples

The analysis of environmental occurrence of microplastic (MP) particles has gained notable attention within the past decade. An effective risk assessment of MP litter requires elucidating sources of MP particles, their pathways of distribution and, ultimately, sinks. Therefore, sampling has to be done in high frequency, both spatially and temporally, resulting in a high number of samples to analyze. Microspectroscopy techniques, such as FTIR imaging or Raman particle measurements allow an accurate analysis of MP particles regarding their chemical classification and size. However, these methods are time-consuming, which gives motivation to establish subsampling protocols that require measuring less particles, while still obtaining reliable results. The challenge regarding the subsampling of environmental MP samples lies in the heterogeneity of MP types and the relatively low numbers of target particles. Herein, we present a comprehensive assessment of different proposed subsampling methods on a selection of real-world samples from different environmental compartments. The methods are analyzed and compared with respect to resulting MP count errors, which eventually allows giving recommendations for staying within acceptable error margins. Our results are based on measurements with Raman microspectroscopy, but are applicable to any other analysis technique. We show that the subsampling-errors are mainly due to statistical counting errors (i.e., extrapolation from low numbers) and only in edge cases additionally impacted by inhomogeneous distribution of particles on the filters. Keeping the subsampling-errors low can mainly be realized by increasing the fraction of MP particles in the samples

Certified Training: Small Boxes are All You Need

We propose the novel certified training method, SABR, which outperforms existing methods across perturbation magnitudes on MNIST, CIFAR-10, and TinyImageNet, in terms of both standard and certifiable accuracies. The key insight behind SABR is that propagating interval bounds for a small but carefully selected subset of the adversarial input region is sufficient to approximate the worst-case loss over the whole region while significantly reducing approximation errors. SABR does not only establish a new state-of-the-art in all commonly used benchmarks but more importantly, points to a new class of certified training methods promising to overcome the robustness-accuracy trade-off

„Wir bibliotheken“ – neue Wege in der bibliothekarischen Ausbildung: Tagungsbericht zur D-A-CH-S-Tagung „Bibliothek – Qualifikation – Perspektiven“

Bericht zur D-A-CH-S-Tagung „Bibliothek – Qualifikation – Perspektiven“ am 13./14. Februar 2019 an der Ludwig-Maximilians-Universität Münche

Efficient multitasking: parallel versus serial processing of multiple tasks

In the context of performance optimizations in multitasking, a central debate has unfolded in multitasking research around whether cognitive processes related to different tasks proceed only sequentially (one at a time), or can operate in parallel (simultaneously). This review features a discussion of theoretical considerations and empirical evidence regarding parallel versus serial task processing in multitasking. In addition, we highlight how methodological differences and theoretical conceptions determine the extent to which parallel processing in multitasking can be detected, to guide their employment in future research. Parallel and serial processing of multiple tasks are not mutually exclusive. Therefore, questions focusing exclusively on either task-processing mode are too simplified. We review empirical evidence and demonstrate that shifting between more parallel and more serial task processing critically depends on the conditions under which multiple tasks are performed. We conclude that efficient multitasking is reflected by the ability of individuals to adjust multitasking performance to environmental demands by flexibly shifting between different processing strategies of multiple task-component scheduling