NANDRAD 1.4 building simulation model

NANDRAD is a dynamic building energy simulation program. It calulates heating/cooling requirements and electric power consumption with respect to realistic climatic conditions and dynamic room usage. The model includes one-dimensional spatially resolved heat transport through multi-layered walls and thermal storage of solid components (room furniture/building walls). Consequently, massive constructions forms in the European area are very well represented. Further, NANDRAD calculates geometrical long radiation heat exchange inside the room. Heating systems may be modeled with a high level of geometrical detail, i.e. surface heating systems as part of the wall constructions and radiant heaters inside the room. NANDRAD can be applied for passive building simulation, energy optimization and thermal comfort analysis with respect to a very detailed building representation. In this terms, the model supports the simulation of a large number of zones and walls without need for subgrouping or other model reduction strategies.:1 Introduction 2 NANDRAD multi-zone building model 2.1 Fundamentals 2.2 Building component models 2.3 Building services and usage 2.4 Climatic model 3 Model equations 3.1 Balance equations 3.2 Construction balance boundary conditions 3.3 Construction energy sources/sinks 3.4 Windows 3.5 Ambient environment 3.6 Zone internal loads 3.7 Construction internal heat sources 3.8 Loads on inside interfaces 3.9 Evaluation of thermal comfor

Least Squares Estimation in Multiple Change-Point Models

Change-point analysis is devoted to the detection and estimation of the time of structural changes within a data set of time-ordered observations. In this thesis, we estimate simultaneously multiple change-points by the least squares method and examine asymptotic properties of such estimators. Using argmin theorems, we prove weak and strong consistency under different moment conditions and investigate convergence in distribution. The identification of the limit variable allows us to derive an asymptotic confidence region for the unknown parameters. Based on a simulation study we evaluate these results

Environmental Indicators for the Evaluation of Wood Products in Consideration of Site-Dependent Aspects: A Review and Integrated Approach

On the way towards a more biobased economy, the sustainable use of global wood resources remains a challenge as several trade-offs arise, e.g., from an increased energetic use of wood, an increased use of innovative but probably less recyclable wood composites, or from the need to conserve other forest ecosystem services. The aim of this study is to identify existing environmental indicators and methods for an evaluation of the sustainability of wood products in consideration of all life cycle stages, site-dependent aspects and later use in corporate decision-making. We chose a systematic literature review to answer the research questions explicitly and comprehensively. Qualitative content analysis was used to code indicators and scientific methods according to the Pressure-State-Response (PSR) framework. The sample (N = 118) is characterized by a high number of life cycle assessment (LCA) case studies. In 51% of all studies, the study authors use a combination of different methods. A total of 78 indicators and 20 site-dependent aspects could be identified in the sample. The study findings represent a first step towards a holistic environmental assessment of wood products

Cellular dynamics in Zebrafish optic cup morphogenesis

Organ formation is an important step during development of an organism that combines different scales from the molecular to the tissue level. Many organogenesis phenomena involve epithelial morphogenesis, where sheets of cells undergo rearrangements to form complex architectures – organ precursors, which subsequently develop into mature organs. Timely development of the characteristic architectures of the organ precursors is crucial for successful organogenesis and is determined by the choice of epithelial rearrangements that organise the constituent cells in space and time. However, for many organogenesis events the cellular dynamics underlying such epithelial rearrangements remain elusive. In the work presented here, I investigated the morphogenesis of the hemispherical retinal neuroepithelium (RNE), that serves as an organ precursor of the neural retina. Formation of RNE is an important event in vertebrates that shapes the optic cup and sets the stage for subsequent eye development. I investigated RNE morphogenesis in the developing zebrafish embryo by visualising and investigating the cellular dynamics of the process in vivo. My findings show that the zebrafish RNE is shaped by the combined action of two different epithelial rearrangements – basal shrinkage of the neuroepithelial cells and involution of cells at the rim of the developing optic cup. The basal shrinkage of the neuroepithelial cells bends the neuroepithelial sheet and starts the process of invagination. However, my results show that the major player in RNE morphogenesis is rim involution. Rim involution translocates prospective RNE cells to their designated location in the invaginating layer and contributes to RNE invagination. My work unravelled the so far unknown mechanism of rim involution. I show that the rim cells involute by collective epithelial migration using directed membrane protrusions and dynamic cell-matrix contacts. If rim migration is perturbed, the prospective RNE cells cannot reach the invaginating layer. As a result, these migration-defective cells attain the RNE fate at an ectopic location and disrupt the tissue architecture. Therefore, rim migration coordinates the cellular location with the timing of RNE fate determination and orchestrates RNE morphogenesis in space and time. Overall, my work highlights how morphogenetic processes shape the organ precursor architecture and ensure timely organ formation. These findings provide important insights not only for eye development but also for epithelial morphogenesis and organogenesis in many other systems.Für die Entwicklung eines Organismus ist die Bildung von Organen (Organogenese) von zentraler Bedeutung. Organogenese umfasst Prozesse auf allen Ebenen der Längenskala: von der molekularen Ebene, der Gewebeebene, bis hin zur Ebene des ganzen Organismus. Viele Phänomene der Organogenese beinhalten dabei Veränderungen von Epithelien, bei der sich Schichten von Zellen zu komplexen Strukturen - Organvorläufern - umwandeln. Diese entwickeln sich später zu vollständigen Organen. Die rechtzeitige Entwicklung der charakteristischen Architektur der Organvorläufer ist entscheidend für eine erfolgreiche Organogenese und wird durch die Wahl der epithelialen Umwandlungsprozessen bestimmt, welche die Zellen in Raum und Zeit koordinieren müssen. Für viele dieser Prozesse ist jedoch genau diese zugrundeliegende Zelldynamik unklar. In der hier vorgestellten Arbeit untersuchte ich die Bildung des hemisphärischen retinalen Neuropepithels (RNE). Das RNE ist der Organvorläufer der neuralen Retina, weshalb dessen korrekte Bildung die Voraussetzung für die korrekte Entwicklung der Augen ist. Ich untersuchte die RNE-Morphogenese in sich entwickelnden Zebrafisch-Embryos durch Visualisierung und Untersuchung der zellulären Dynamik der beteiligten Prozesse in vivo. Meine Ergebnisse zeigen, dass das RNE in Zebrafischen durch die kombinierte Umwandlung von zwei verschiedenen Epithelien geformt wird. Zum einen findet eine Verkleinerung des basalen Prozesses der neuroepithelialen Zellen statt, zum anderen die Involution von Randzellen. Die basale Verkleinerung der neuroepithelialen Zellen verbiegt die neuroepitheliale Schicht und führt zur Einstülpung des RNE. Meine Ergebnisse zeigten allerdings, dass Involution von Randzellen noch bedeutsamer für die RNE-Morphogenese ist. Die involution von Randzellen transportiert potenzielle RNE-Zellen in das Neuroepithel und trägt zur RNE-Einstülpung bei. Die Bedeutung meiner Arbeit liegt darin, den bisher unbekannten Mechanismus der Randzell-Involution entdeckt zu haben. Ich zeigte, dass die Randzellen sich aktiv durch kollektive epitheliale Migration bewegen indem sie gerichtete Membranforsätze und dynamische Zell zu Matrix Kontakte etablieren. Wird die Migration der Randzellen inhibiert, so führt dies dazu, dass diese Zellen die eingestülpte RNE Schicht nicht erreichen. Sie landen dann an den falschen Positionen, wo sie die Gewerbearchitektur stören können. Daher koordiniert die Randzellmigration die Position der Zellen und orchestriert die RNE-Morphogenese in Raum und Zeit. Insgesamt zeigt meine Arbeit, wie morphogenetische Prozesse die Organvorläuferarchitektur prägen und eine rechtzeitige Organbildung sicherstellen. Diese Erkenntnisse sind sowohl für das Verständnis der Augenentwicklung, als auch für das der epithelialen Morphogenese und Organogenese in anderen Systemen von großer Bedeutung

Towards next-generation sequencing-based identification of norovirus recognition elements and microfluidic array using phage display technology

Noroviruses are the major cause of acute viral gastroenteritis worldwide. Thus, rapid and reliable pathogen detection and control are crucial to avoid epidemic outbreaks. Peptides which bind to these viruses with high specificity and affinity could serve as small and stable recognition elements in biosensing applications for a point-of-care diagnostic of noroviruses. They can be identified by screening large phage display libraries using the biopanning technique. In the present study, this method was applied to identify norovirus-binding peptide motifs. For this purpose, a biopanning based on column chromatography was established, and three rounds of selections were performed. After the second round, the cosmix-plexing recombination technique was implemented to enhance the chance of obtaining peptides with very high affinity. Biopanning data evaluation was based on next-generation sequencing (NGS), to show that this innovative method can enable a detailed analysis of the complete sequence spectrum obtained during and after biopanning. Highly enriched motifs could be characterized by their large proportion of the amino acids W, K, R, N, and F. Neighbourhood analysis was exemplarily performed for selected motifs, showing that the motifs FAT, RWN, and KWF possessed the fingerprints with the largest differences relative to the original library. This thesis thus presents next-generation sequencing-based analysis tools, which could now be transferred to any other biopanning project. The identified peptide motifs represent promising candidates for a future examination of their norovirus-specific binding. A new option for testing such phage-target interactions in the context of biopanning selections was studied in the second part of the thesis. For this purpose, a phage-based microarray was developed as a miniaturized binding assay. As a prerequisite, the different immobilization behaviour of phages on positively and negatively charged surfaces was studied, and a non-contact printing technique for bacteriophages was developed. Subsequently, the interaction of phages and antibodies directed against phage coat proteins was characterized in enzyme-linked immunosorbent assays, and the protocol was successfully transferred to the non-contact printed phage spots. At the proof-of-concept level, the phage array could finally be integrated into a microfluidic setup, showing a higher signal-to-background ratio relative to the static phage array. These results point the way towards a microfluidic phage array, allowing online monitoring, automation, and parallelisation of the phage array analysis.Noroviren gelten als Hauptursache akuter viraler Magen-Darm-Erkrankungen. Nur eine zeitnahe und verlässliche Detektion und Kontrolle dieser Pathogene kann epidemische Ausbrüche vermeiden. Um dies zu ermöglichen, könnten Peptide, die an diese Viren mit hoher Spezifität und Affinität binden, als kleine und stabile Erkennungselemente in biosensorischen Anwendungen eingesetzt werden. Solche Peptide können mithilfe der Biopanning-Technik identifiziert werden, die auf dem Screening großer Phagen-Display-Bibliotheken beruht. In der vorliegenden Arbeit wurde diese Methode genutzt, um Norovirus-bindende Peptidmotive zu identifizieren. Dazu wurde ein auf Säulenchromatographie basierendes Biopanning entwickelt und drei Selektionsrunden durchgeführt. Die Cosmix-Plexing-Rekombinationstechnik wurde nach der zweiten Runde eingesetzt, um die Wahrscheinlichkeit der Gewinnung hochaffiner Binder zu erhöhen. Die Auswertung der Biopanningdaten erfolgte mittels Hochdurchsatzsequenzierung (Next-Generation Sequencing). Es konnte gezeigt werden, dass diese innovative Methode die detailierte Analyse des kompletten Sequenzspektrums während und nach dem Biopanning ermöglicht. Stark angereicherte Motive konnten durch ihren hohen Anteil an den Aminosäuren W, K, R, N und F charakterisiert werden. Eine Nachbarschaftsanalyse wurde exemplarisch für ausgewählte Motive durchgeführt. Dabei wurden die stärksten Unterschiede im Fingerprint im Vergleich zur Ausgangsbibliothek bei den Motiven FAT, RWN und KWF gefunden. Diese Dissertation stellt damit auf Next-Generation Sequencing basierende Analysetechniken vor, die für weitere Biopanningprojekte übernommen werden können. Die identifizierten Peptidmotive könnten als vielversprechende Kandidaten zukünftig auf ihre Norovirus-spezifische Bindung hin getestet werden. Eine neue Möglichkeit, solche Phagen-Analyt-Interaktionen zu untersuchen, wurde im zweiten Teil der Dissertation untersucht. Dafür wurde als miniaturisierter Bindungsassay ein Phagen-basiertes Mikroarray entwickelt. Als Voraussetzung wurde zunächst das unterschiedliche Immobilisierungsverhalten von Bakteriophagen auf positiv und negativ geladenen Oberflächen untersucht und eine kontaktfreie Drucktechnik für Bakteriophagen etabliert. Anschließend wurde die Interaktion von Phagen und gegen sie gerichteten Antikörpern in Enzym-gekoppelten Immunadsorptionstests charakterisiert und das Protokoll erfolgreich auf die kontaktfrei gedruckten Phagenspots übertragen. Schließlich wurde erstmals die grundsätzliche Möglichkeit gezeigt, das Array in ein mikrofluidisches Setup zu integrieren, was zu einem höheren Signal-zu-Hintergrund-Verhältnis im Vergleich zum statischen Array führte. Diese Ergebnisse zeigen damit den Weg zu einem mikrofluidischen Phagen-Array auf, das sowohl die Möglichkeit des Online-Monitorings als auch der Automatisierung und Parallelisierung der Phagen-Array-Analyse bietet

Structural Bioinformatics to Understand the Origin of the Genetic Code: Structural Motif Detection in Aminoacyl-tRNA Synthetases

One of the most profound open questions in biology is how the genetic code developed. The blueprints for proteins are encoded by triplets of nucleic acids, which in turn require proteins for interpretation and replication. The mere existence of this self-referencing system is a chicken-and-egg dilemma. Aminoacyl-tRNA synthetases are key players in the transfer of genetic information and reflect the earliest episode of life. These enzymes are responsible for loading tRNA molecules with the correct amino acid. Two protein superfamilies of aminoacyl-tRNA synthetases emerged, each responsible for ten amino acids. Despite sequence and structure similarity, the delicate balance between these superfamilies is manifested in two structural motifs, which were identified in the context of this thesis: the Backbone Brackets and the Arginine Tweezers. Both motifs realize constant ligand recognition and can be found in almost all protein structures of aminoacyl-tRNA synthetases. In this thesis, I thoroughly characterized Backbone Brackets and Arginine Tweezers. The specific characteristics of these motifs require high-precision methods for their detection and analysis. However, existing algorithms do not feature an adequate computational representation of structural motifs at the atom level and the support of isofunctional residue mutations. In order to address these limitations, I designed the Fit3D algorithm for template-based and template-free detection of structural motifs. I show that proper computational representation of structural motifs is crucial and improves accuracy up to 26% for a benchmark dataset. Fit3D is a general-purpose tool for structural motif detection in high-resolution protein structure data. In conjunction with the accelerating progress in experimental methods, the demand for such tools will increase rapidly over the next years. I applied Fit3D to structures of aminoacyl-tRNA synthetases to investigate whether Backbone Brackets and Arginine Tweezers are universal building blocks for ligand recognition, and to quantify structural changes upon ligand binding. While the Arginine Tweezers motif is exclusively found in aminoacyl-tRNA synthetases and paralogs, the Backbone Brackets seem to be a general pattern to recognize functional groups of certain ligands. The results show subtle differences in side chain orientation for one structural motif and a backbone shift for the other. This suggests a structural rearrangement to be a general mechanism in some aminoacyl-tRNA synthetases. The detailed level of these analyses would not have been possible without high-precision structural motif detection with Fit3D. The results emphasize the importance of structural motifs, which consist of only a few residues, for the global function of the enzyme. Furthermore, the stunning conservation of the structural motifs located in the core domains of aminoacyl-tRNA synthetases suggests their presence in the earliest predecessors of these enzymes. Both motifs might have played a fundamental role in shaping the genetic code as we know it

Transfer Learning for Soil Spectroscopy Based on Convolutional Neural Networks and Its Application in Soil Clay Content Mapping Using Hyperspectral Imagery

Soil spectra are often measured in the laboratory, and there is an increasing number of large-scale soil spectral libraries establishing across the world. However, calibration models developed from soil libraries are difficult to apply to spectral data acquired from the field or space. Transfer learning has the potential to bridge the gap and make the calibration model transferrable from one sensor to another. The objective of this study is to explore the potential of transfer learning for soil spectroscopy and its performance on soil clay content estimation using hyperspectral data. First, a one-dimensional convolutional neural network (1D-CNN) is used on Land Use/Land Cover Area Frame Survey (LUCAS) mineral soils. To evaluate whether the pre-trained 1D-CNN model was transferrable, LUCAS organic soils were used to fine-tune and validate the model. The fine-tuned model achieved a good accuracy (coefficient of determination (R²) = 0.756, root-mean-square error (RMSE)= 7.07 and ratio of percent deviation (RPD) = 2.26) for the estimation of clay content. Spectral index, as suggested as a simple transferrable feature, was also explored on LUCAS data, but did not performed well on the estimation of clay content. Then, the pre-trained 1D-CNN model was further fine-tuned by field samples collect in the study area with spectra extracted from HyMap imagery, achieved an accuracy of R² = 0.601, RMSE = 8.62 and RPD = 1.54. Finally, the soil clay map was generated with the fine-tuned 1D-CNN model and hyperspectral data

Comparison and Combination of Mobile and Terrestrial Laser Scanning for Natural Forest Inventories

Terrestrial laser scanning (TLS) has been successfully used for three-dimensional (3D) data capture in forests for almost two decades. Beyond the plot-based data capturing capabilities of TLS, vehicle-based mobile laser scanning (MLS) systems have the clear advantage of fast and precise corridor-like 3D data capture, thus providing a much larger coverage within shorter acquisition time. This paper compares and discusses advantages and disadvantages of multi-temporal MLS data acquisition compared to established TLS data recording schemes. In this pilot study on integrated TLS and MLS data processing in a forest, it could be shown that existing TLS data evaluation routines can be used for MLS data processing. Methods of automatic laser scanner data processing for forest inventory parameter determination and quantitative structure model (QSM) generation were tested in two sample plots using data from both scanning methods and from different seasons. TLS in a multi-scan configuration delivers very high-density 3D point clouds, which form a valuable basis for generating high-quality QSMs. The pilot study shows that MLS is able to provide high-quality data for an equivalent determination of relevant forest inventory parameters compared to TLS. Parameters such as tree position, diameter at breast height (DBH) or tree height can be determined from MLS data with an accuracy similar to the accuracy of the parameter derived from TLS data. Results for instance in DBH determination by cylinder fitting yielded a standard deviation of 1.1 cm for trees in TLS data and 3.7 cm in MLS data. However, the resolution of MLS scans was found insufficient for successful QSM generation. The registration of MLS data in forests furthermore requires additional effort in considering effects caused by poor GNSS signal

On-surface synthesis of acenes –: organic nanoelectronic materials explored at a single-molecule level

Acenes are a class of polycyclic aromatic hydrocarbons (PAH) with linearly fused benzene rings. They are widely considered as promising materials for organic and molecular electronics. However, larger molecules of this class possessing more than five rings are chemically extremely reactive and show a very low solubility. Hence, large acenes are difficult to handle, and the experimental data available to date is limited. The aim of this work is to show a very promising protocol of how acenes with different lengths can be stabilized and investigated on metallic surfaces. The experimental approach of on-surface synthesis is explored to generate the respective acenes directly on the metallic substrate via the reduction of suitable precursor molecules. High-resolution scanning probe microscopy (SPM) is employed at a temperature of 5 K to verify the chemical conversion at a single-molecule level. In the first part of this work, the on-surface synthesis of acenes is introduced via the example of tetracene (4-acene) formation on Cu(111). Precursors with 1,4-epoxy moieties preferably adsorb with their oxygen-rich site facing the substrate. Subsequently, they can be deoxygenated via annealing of the substrate or by single-molecule manipulation with the tip of the scanning probe microscope. In both cases, atomic force microscopy (AFM) measurements resolve the planar adsorption geometry of tetracene on the surface with atomic resolution. Based on these findings, scanning tunneling microscopy (STM) is employed to investigate the self-assembly patterns of on-surface generated anthracene (3-acene) and tetracene molecules after synthesis on Au(111). These measurements show intriguing organic nanostructures and supramolecular networks that can form at the metallic interface upon thermally-induced surface reactions. The second part of this thesis focuses on the electronic structure of acenes adsorbed on a metallic substrate. By applying the novel method of on-surface reduction, single and isolated hexacene (6-acene) molecules are investigated on Au(111). Scanning tunneling spectroscopy (STS) measurements indicate a weak interaction with the substrate and reveal five accessible molecular resonances at the organic-metal interface. The differential conductance maps with high spatial resolution at the respective resonant bias values compare well to elastic scattering quantum chemistry-based calculations. Finally, the experimental investigations of Br-substituted precursors show the stabilization of genuine unsubstituted heptacene (7-acene), as confirmed by imaging of the molecular structure via atomic-resolution STM. Accordingly, the precise characterization of this molecule via STS allows more insight into the electronic structure of adsorbed acenes with respect to their length.Acene sind eine Klasse von polyzyklischen aromatischen Kohlenwasserstoffen mit linear kondensierten Benzolringen. Sie gelten weithin als vielversprechende Materialien für die organische und molekulare Elektronik. Jedoch sind die größeren Moleküle dieser Klasse mit mehr als fünf Ringen chemisch extrem reaktiv und zeigen eine sehr geringe Löslichkeit, daher gibt es bisher nur wenige experimentelle Untersuchungen ihrer Eigenschaften. Das Ziel dieser Arbeit ist es, Acene mit unterschiedlichen Längen auf einer metallischen Oberfläche stabilisieren und untersuchen zu können. Dabei wird der experimentelle Ansatz der Oberflächensynthese verfolgt und die jeweiligen Acene durch Reduktion von geeigneten Präkursoren direkt an einer metallischen Grenzfläche hergestellt. Hochauflösende Rastersondenmikroskopie an einzelnen Molekülen bei einer Temperatur von 5K nimmt dabei eine Schlüsselrolle im Nachweis der chemischen Umwandlung auf der Oberfläche ein. Im ersten Teil dieser Arbeit wird die Oberflächensynthese von Acenen am Beispiel von Tetracen (4-Acen) auf Cu(111) eingeführt. Die Ausgangsmoleküle mit funktionellen Gruppen adsorbieren bevorzugt mit ihrer sauerstoffreichen Seite auf dem Substrat und können dort sowohl thermisch als auch mithilfe der Spitze des Rastersondenmikroskops umgewandelt werden. In beiden Fällen wird die planare Adsorptionsgeometrie von Tetracen auf der Oberfläche mittels Rasterkraftmikroskopie mit atomarer Auflösung abgebildet. Darauf aufbauend wird Rastertunnelmikroskopie genutzt, um die Selbstassemblierung von Anthracen (3-Acen) und Tetracen nach der jeweiligen Synthese auf Au(111) zu untersuchen. Die Messungen zeigen unerwartete organische Nanostrukturen und supramolekulare Netzwerke, welche sich an der metallischen Grenzfläche durch die induzierte Oberflächenreduktion bilden können. Der zweite Teil dieser Arbeit beschäftigt sich mit den elektronischen Eigenschaften von adsorbierten Acenen. Durch die neuartige Methode der Oberflächenreduktion können einzelne Hexacene (6-Acen) auf Au(111) untersucht werden. Messungen basierend auf Rastertunnelspektroskopie geben Hinweise auf die schwache Wechselwirkung mit dem Substrat und zeigen fünf molekulare Eigenzustände, die im Experiment zugänglich sind. Die entsprechenden Abbildungen der differentiellen Leitfähigkeiten mit hoher Ortsauflösung sind in guter Übereinstimmung mit einer quantenmechanischen Modellierung. Schließlich wird die Stabilisierung von Heptacen (7-Acen) von Br-substituierten Präkursoren mittels Rastertunnelmikroskopie mit atomarer Auflösung gezeigt. Dadurch kann die elektronische Struktur von adsorbierten Acenen anhand ihrer Länge verglichen werden

Model-free inference of direct network interactions from nonlinear collective dynamics

The topology of interactions in network dynamical systems fundamentally underlies their function. Accelerating technological progress creates massively available data about collective nonlinear dynamics in physical, biological, and technological systems. Detecting direct interaction patterns from those dynamics still constitutes a major open problem. In particular, current nonlinear dynamics approaches mostly require to know a priori a model of the (often high dimensional) system dynamics. Here we develop a model-independent framework for inferring direct interactions solely from recording the nonlinear collective dynamics generated. Introducing an explicit dependency matrix in combination with a block-orthogonal regression algorithm, the approach works reliably across many dynamical regimes, including transient dynamics toward steady states, periodic and non-periodic dynamics, and chaos. Together with its capabilities to reveal network (two point) as well as hypernetwork (e.g., three point) interactions, this framework may thus open up nonlinear dynamics options of inferring direct interaction patterns across systems where no model is known