Spin coating of an evaporating polymer solution

We consider a mathematical model of spin coating of a single polymer blended in a solvent. The model describes the one-dimensional development of the thin layer of the mixture as the layer thins due to flow created by a balance of viscous forces and centrifugal forces and due to evaporation of the solvent. In the model both the diffusivity of the solvent in the polymer and the viscosity of the mixture are very rapidly varying functions of the solvent volume fraction. Guided by numerical solutions an asymptotic analysis reveals a number of different possible behaviours of the thinning layer dependent on the nondimensional parameters describing the system.\ud \ud The main practical interest is in controlling the appearance and development of a ``skin'' on the polymer where the solvent concentration reduces rapidly on the outer surface leaving the bulk of the layer still with high concentrations of solvent. The critical parameters controlling this behaviour are found to be $\epsilon$ the ratio of the diffusion to advection time scales, $\delta$ the ratio of the evaporation to advection time scales and $\exp(\gamma)$, the ratio of the diffusivity of the initial mixture and the pure polymer. In particular, our analysis shows that for very small evaporation with $\delta << \exp(-3/(4\gamma)) \epsilon^{3/4}$ skin formation can be prevented

Computational methods for tracking the evolution of complex bacterial communities

The focus of my PhD thesis was to study evolutionary aspects of host-associated microbial communities. In order to better understand these effects, I developed and applied computational methods to search for protein families that are under selection within metagenomes (Publication I) and applied them to various environments (see the articles “Structure and function of the bacterial root microbiota in wild and domesticated barley", and “Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi”. One consistent finding of these studies was the high selective pressure acting on gene families associated with the bacterial defense system (the so-called CRISPR-Cas system) and families annotated as being related to bacteriophages. To study this CRISPR-phage relationship more closely, I systematically analysed CRISPR cassettes and CRISPR-related genes in samples from the Human Microbiome project (HMP) (Publication II). This resulted in one of the most comprehensive CRISPR collections to date. Further, we found novel sequence characteristics in the CRISPR loci and described the differences in the composition of CRISPR-associated genes in different body habitats and a potential relationship between the CRISPR defence system and the restriction modification system of bacteria. Furthermore, I performed a similar but less extensive search on metagenomic samples from infants: “Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life”. Next, I turned my focus to study microbiome evolution in a gnotobiotic mouse model, since this provided the opportunity to study bacteria evolution on an intermediate scale of complexity. I contributed to the development of the mouse model described in the Manuscript “Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium” and a study comparing the stability of the community between animal facilities “Reproducible colonization of germ-free mice with the Oligo-Mouse-Microbiota in different animal facilities” and to a study focusing on the interaction network of this community. However, my main work with the OMM12 model has been to study community effects and evolution during repeated rounds of AB exposure (unpublished Publication III).Der Schwerpunkt meiner Doktorarbeit lag auf der Untersuchung evolutionärer Aspekte von wirtsassoziierten mikrobiellen Gemeinschaften. Um diese Effekte besser zu verstehen, habe ich computergestützte Methoden entwickelt und angewandt, um nach Proteinfamilien zu suchen, die in Metagenomen (Publikation I) der Selektion unterliegen, und sie auf verschiedene Umgebungen angewandt (siehe die Artikel “Structure and function of the bacterial root microbiota in wild and domesticated barley” und “Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi”. Ein durchgängiges Ergebnis dieser Studien war der hohe Selektionsdruck, der auf Genfamilien wirkt, die mit dem bakteriellen Abwehrsystem (dem sogenannten CRISPR-Cas-System) und Familien, die als mit Bakteriophagen verwandt beschrieben werden, verbunden sind. Um diese CRISPR-Phagen-Beziehung genauer zu untersuchen, analysierte ich systematisch CRISPR-Kassetten und CRISPR-verwandte Gene in Proben aus dem Human Microbiome Project (HMP) (Publikation II). Dies führte zu einer der bisher umfassendsten CRISPR-Sammlungen. Darüber hinaus fanden wir neuartige Sequenzmerkmale in den CRISPR-Loci und beschrieben die Unterschiede in der Zusammensetzung von CRISPR-assoziierten Genen in verschiedenen Körperregionen sowie eine mögliche Beziehung zwischen dem CRISPR-Abwehrsystem und dem Restriktionsmodifikationssystem von Bakterien. Außerdem habe ich eine ähnliche, aber weniger umfangreiche Suche an metagenomischen Proben von Säuglingen durchgeführt: “Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life”. Als Nächstes konzentrierte ich mich auf die Untersuchung der Mikrobiomevolution in einem gnotobiotischen Mausmodell, da dies die Möglichkeit bot, die Evolution von Bakterien auf einer mittleren Komplexitätsebene zu untersuchen. Ich war an der Entwicklung des Mausmodells beteiligt, das im Manuskript "Genom-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium" und eine Studie zum Vergleich der Stabilität der OMM12 Gemeinschaft zwischen Tierhaltungsanlagen “Reproducible colonization of germ-free mice with the Oligo-Mouse-Microbiota in different animal facilities” sowie eine Studie, die sich auf das Interaktionsnetzwerk dieser Gemeinschaft konzentriert. Meine Hauptarbeit mit dem OMM12-Modell bestand jedoch darin, die Auswirkungen und die Entwicklung der Gemeinschaft während wiederholter AB-Expositionen zu untersuchen (unveröffentlichtes Manuscript III)

The theory of the fluctuations in brightness of the Milky Way. III

In this paper the integral equation (derived in Paper I) governing the fluctuations in brightness of the Milky Way is explicitly solved for the case in which the system extends to a finite distance in the direction of the line of sight and when all the clouds are equally transparent, The derived theoretical distributions are illustrated

Schlaf und zirkadiane Rhythmik im Alter

Zusammenfassung: Mit steigendem Alter nimmt die nächtliche Schlafkonsolidierung ab, kurze Nickerchen über den Tag nehmen zu, und die Schlafzeit verschiebt sich in frühere Stunden. Die Schlafregulation hängt von der Interaktion zwischen einem zirkadianen Schrittmacher (biologische Uhr) und dem Schlafhomöostaten (je länger die Wachphase, desto größer der Schlafdruck) ab. Wir konnten an gesunden älteren Personen zeigen, dass sich die Amplitude zirkadianer Rhythmen (z. B. die Melatonin-Sekretion) und die Tiefschlafdauer verringert. Gleichzeitig nimmt die Müdigkeit am Nachmittag zu, wie auch die Tendenz—im Gegensatz zu jüngeren Personen—am frühen Abend einzuschlafen. Da Licht der Hauptzeitgeber ist, um die biologische Uhr zu stabilisieren, brauchen ältere Menschen tagsüber und am Abend genügend Licht und sollten während des Tages keine oder nur kurze Nickerchen machen, um in der Folge den Schlaf in der Nacht zu verbesser

Slip-controlled thin film dynamics

In this study, we present a novel method to assess the slip length and the viscosity of thin films of highly viscous Newtonian liquids. We quantitatively analyse dewetting fronts of low molecular weight polystyrene melts on Octadecyl- (OTS) and Dodecyltrichlorosilane (DTS) polymer brushes. Using a thin film (lubrication) model derived in the limit of large slip lengths, we can extract slip length and viscosity. We study polymer films with thicknesses between 50 nm and 230 nm and various temperatures above the glass transition. We find slip lengths from 100 nm up to 1 micron on OTS and between 300 nm and 10 microns on DTS covered silicon wafers. The slip length decreases with temperature. The obtained values for the viscosity are consistent with independent measurements.Comment: 4 figure

Automated quantification of the impact of the wood-decay fungus Physisporinus vitreus on the cell wall structure of Norway spruce by tomographic microscopy

The visualization and the quantification of microscopic decay patterns are important for the study of the impact of wood-decay fungi in general, as well as for wood-decay fungi and microorganisms with possible applications in biotechnology. In the present work, a method was developed for the automated localization and quantification of microscopic cell wall elements (CWE) of Norway spruce wood such as bordered pits, intrinsic defects, hyphae or alterations induced by white-rot fungus Physisporinus vitreus using high-resolution X-ray computed tomographic microscopy. In addition to classical destructive wood anatomical methods such as light or laser scanning microscopy, this method allows for the first time to compute the properties (e.g., area, orientation and size distribution) of CWE of the tracheids in a sample. This is essential for modeling the influence of microscopic CWE on macroscopic properties such as wood strength and permeabilit

Weaker Ligands Can Dominate an Odor Blend due to Syntopic Interactions

Most odors in natural environments are mixtures of several compounds. Perceptually, these can blend into a new "perfume,” or some components may dominate as elements of the mixture. In order to understand such mixture interactions, it is necessary to study the events at the olfactory periphery, down to the level of single-odorant receptor cells. Does a strong ligand present at a low concentration outweigh the effect of weak ligands present at high concentrations? We used the fruit fly receptor dOr22a and a banana-like odor mixture as a model system. We show that an intermediate ligand at an intermediate concentration alone elicits the neuron's blend response, despite the presence of both weaker ligands at higher concentration, and of better ligands at lower concentration in the mixture. Because all of these components, when given alone, elicited significant responses, this reveals specific mixture processing already at the periphery. By measuring complete dose-response curves we show that these mixture effects can be fully explained by a model of syntopic interaction at a single-receptor binding site. Our data have important implications for how odor mixtures are processed in general, and what preprocessing occurs before the information reaches the brai

Hydrogen Dynamics in Superprotonic CsHSO4

We present a detailed study of proton dynamics in the hydrogen-bonded superprotonic conductor CsHSO4 from first-principles molecular dynamics simulations, isolating the subtle interplay between the dynamics of the O--H chemical bonds, the O...H hydrogen bonds, and the SO4 tetrahedra in promoting proton diffusion. We find that the Grotthus mechanism of proton transport is primarily responsible for the dynamics of the chemical bonds, whereas the reorganization of the hydrogen-bond network is dominated by rapid angular hops in concert with small reorientations of the SO4 tetrahedra. Frequent proton jumping across the O--H...O complex is countered by a high rate of jump reversal, which we show is connected to the dynamics of the SO4 tetrahedra, resulting in a diminished CsHSO4/CsDSO4 isotope effect. We also find evidence of multiple timescales for SO4 reorientation events, leading to distinct diffusion mechanisms along the different crystal lattice directions. Finally, we employ graph-theoretic techniques to characterize the topology of the hydrogen-bond network and demonstrate a clear relationship between certain connectivity configurations and the likelihood for diffusive jump events.Comment: 12 pages, 10 figure