Entangled semiflexible polymer networks are usually described by the tube model, although this concept has not been able to explain all experimental observations. One of its major shortcomings is neglecting the thermal fluctuations of the polymers surrounding the examined test filament, such that disentanglement effects are not captured. In this study, we present experimental evidence that correlated constraint release which has been predicted theoretically occurs in entangled, but not in crosslinked semiflexible polymer networks. By tracking single semiflexible DNA nanotubes embedded both in entangled and crosslinked F-actin networks, we observed different reptation dynamics in both systems, emphasizing the need for a revision of the classical tube theory for entangled polymer solutions.

The hydroformylation of olefins is one of the most important homogeneously catalyzed processes in industry to produce bulk chemicals. Despite the high catalytic activities and selectivity’s using rhodium-based homogeneous hydroformylation catalysts, catalyst recovery and recycling from the reaction mixture remain a challenging topic on a process level. Therefore, technical solutions involving alternate approaches with heterogeneous catalysts for the conversion of olefins into aldehydes have been considered and research activities have addressed the synthesis and development of heterogeneous rhodium-based hydroformylation catalysts. Different strategies were pursued by different groups of authors, such as the deposition of molecular rhodium complexes, metallic rhodium nanoparticles and single-atom catalysts on a solid support as well as rhodium complexes present in supported liquids. An overview of the recent developments made in the area of the heterogenization of homogeneous rhodium catalysts and their application in the hydroformylation of short-chain olefins is given. A special focus is laid on the mechanistic understanding of the heterogeneously catalyzed reactions at a molecular level in order to provide a guide for the future design of rhodium-based heterogeneous hydroformylation catalysts.

Ruthenium-based complexes have received much interest as potential metallodrugs. In this work, four RuII complexes bearing a dicarbollide moiety, a carbonyl ligand, and a phenanthroline-based ligand were synthesized and characterized, including single crystal diffraction analysis of compounds 2, 4, and 5 and an observed side product SP1. Complexes 2–5 are air and moisture stable under ambient conditions. They show excellent solubility in organic solvents, but low solubility in water.

Leaves from Combretum collinum Fresen (Combretaceae) are commonly used for the treatment of inflammatory conditions, wound healing and bacterial infections in traditional West African medicine. This research focuses on the characterization of the phenolic profile and lipophilic compounds of leaves extracts of C. collinum. Studies of the in vitro anti-inflammatory activity were performed in TNFα stimulated HaCaT cells and antibacterial activity was evaluated with agar well diffusion and microdilution assays. Antioxidant activity was determined by DPPH and ABTS assays and compared to standards. The phytochemical studies confirmed myricetin-3-O-rhamnoside and myricetin-3-O-glucoside as major components of the leaves extracts, each contributing significantly to the antioxidant activity of the hydrophilic extracts. GC-MS analysis identified 19 substances that were confirmed by comparison with spectral library data and authentic standards. Combretum collinum aqueous leaves extract decreased pro-inflammatory mediators in TNFα stimulated HaCaT cells. Further investigations showed that myricetin-3-O-rhamnoside has an anti-inflammatory effect on IL-8 secretion. In the antimicrobial screening, the largest inhibition zones were found against S. epidermidis, MRSA and S. aureus. MIC values resulted in 275.0 µg/mL for S. epidermidis and 385.5 µg/mL for MRSA. The in vitro anti-inflammatory, antibacterial and antioxidant activity supports topical use of C. collinum leaves extracts in traditional West African medicine.

In our organism, mucous surfaces are important boundaries against the environmental milieu with defined fluxes of metabolites through these surfaces and specific rules for defense reactions. Major mucous surfaces are formed by epithelia of the respiratory system and the digestive tract. The heme peroxidases lactoperoxidase (LPO), myeloperoxidase (MPO), and eosinophil peroxidase (EPO) contribute to immune protection at epithelial surfaces and in secretions. Whereas LPO is secreted from epithelial cells and maintains microbes in surface linings on low level, MPO and EPO are released from recruited neutrophils and eosinophils, respectively, at inflamed mucous surfaces. Activated heme peroxidases are able to oxidize (pseudo)halides to hypohalous acids and hypothiocyanite. These products are involved in the defense against pathogens, but can also contribute to cell and tissue damage under pathological conditions. This review highlights the beneficial and harmful functions of LPO, MPO, and EPO at unperturbed and inflamed mucous surfaces. Among the disorders, special attention is directed to cystic fibrosis and allergic reactions.

Liquid-liquid phase separation (LLPS) has been proposed as the underlying physical principle leading to the formation of membrane-less organelles in eukaryotic cells, following advancements, in the last two decades, in experimental observations owing to progress in confocal microscopy. These organelles can act as compartments in sequestering molecules and tuning rates of biochemical reactions, among a repertoire of functions they serve. Biochemical reactions are constantly in progress in living cells and are driven out of equilibrium due to fuel consumption in the form of ATP or GTP molecules. Free diffusion of reactive molecules through these compartments leads to their spatiotemporal sequestration and automatically implies an interplay between phase separation and chemical reactions. In this work, we are specifically interested to understand how the two processes closely affect each other and applying the understanding to tune better bottom-up design principles for synthetic life, which involves coupling compartmentalization and chemical reactions. The first part of this work is devoted to studying the interplay between phase separation and chemical reactions. To this end, we developed the theory of mass action kinetics of equilibrium and out-of-equilibrium processes occurring at phase equilibrium in a multicomponent mixture. Phase equilibrium is imposed at all times, thus restricting the chemical kinetics to the binodal manifold. We learn more about circumstances in which reaction rates can differ in coexisting phases. Next, we decouple the phase-forming components (scaffolds) and the dilute reactive components (clients), which means that the reactive dilute components respond to the heterogeneous profile in the system set by the scaffold but do not affect it. This allows us to investigate to what extent compartments can affect chemical reactions in terms of their yield at steady state for a bimolecular reaction or initial reaction rate for a nucleation process compared to the absence of compartments. We use the effective droplet model and mass reaction kinetics at phase equilibrium to address the above questions. We can understand better how the properties of reactions can be optimally tuned by compartment size. Following the theoretical developments in the first part of this work, we proceed to use the theoretical model of mass action kinetics at phase equilibrium to study emergent properties of parasitic behavior in a system composed of multiple fuel-driven reaction cycles, which lead to the formation of so-called 'building blocks' which can phase separate. This study also helps us probe the buffering capacity of phase separation. It further provides insights into how the lifetime of reactive 'building blocks' can be tuned via phase separation. Synthetic cells are generally realized by localizing minimalistic reactions in micron-scale water-filled environments, thus mimicking compartmentalization. Here we apply our model to understand how the localization of an autocatalytic process (PEN-DNA reaction) inside proteinosomes affect the reaction rates compared to the reactions in a homogeneous buffer solution. To summarize, we developed theoretical approaches to study the interplay of chemical reactions with compartmentalization and apply such approaches to systems chemistry and synthetic biology experimental studies to unravel how reactions can be controlled through compartmentalization.:1 Introduction 1 1.1 Phase Separation - A brief overview of the development of the field . . . . . . 1 1.2 Thermodynamics of phase separation in a multi-component mixture . . . . . 4 1.2.1 Mean field free energy . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 1.2.2 Other possible free energy considerations: Beyond mean-field . . . . . 7 1.2.3 Exchange chemical potential, chemical activity and osmotic pressure . 8 1.2.4 Thermodynamic instability leads to phase separation . . . . . . . . . 9 1.2.5 Phase equilibrium conditions . . . . . . . . . . . . . . . . . . . . . . . 10 1.2.6 Relaxation dynamics to phase equilibrium . . . . . . . . . . . . . . . . 13 1.3 Thermodynamics of chemical reactions in homogeneous mixtures . . . . . . . 14 1.3.1 Chemical equilibrium conditions . . . . . . . . . . . . . . . . . . . . . 14 1.3.2 Relaxation to chemical equilibrium . . . . . . . . . . . . . . . . . . . . 16 1.4 Thermodynamic equilibrium . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17 1.5 Scope of the thesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 2 Chemical reaction kinetics at phase equilibrium 21 2.1 Kinetics of chemical reactions relaxing to thermodynamic equilibrium . . . . 21 2.1.1 Volume fraction field and phase volume kinetics . . . . . . . . . . . . 22 2.1.2 Diffusive exchange rates between phases . . . . . . . . . . . . . . . . . 22 2.1.3 Reaction rates at phase equilibrium . . . . . . . . . . . . . . . . . . . 23 2.1.4 Properties of chemical reactions at phase equilibrium . . . . . . . . . 24 2.2 Unimolecular chemical reactions in coexisting phases . . . . . . . . . . . . . . 25 2.3 Bimolecular chemical reactions in coexisting phases . . . . . . . . . . . . . . . 27 2.4 Chemical reactions maintained away from chemical equilibrium . . . . . . . . 28 2.4.1 Tie-line selecting curve . . . . . . . . . . . . . . . . . . . . . . . . . . 31 2.5 Summary and Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32 3 Chemical reactions of dilute clients in phase-separated compartments 33 3.1 Thermodynamics of a multicomponent mixture of scaffold and clients . . . . 34 3.1.1 Phase equilibrium conditions: Dilute client limit . . . . . . . . . . . . 35 3.1.2 Relaxation dynamics to phase equilibrium: Dilute client limit . . . . . 38 3.1.3 Chemical equilibrium conditions: Dilute client limit . . . . . . . . . . 40 3.1.4 Relaxation dynamics to chemical equilibrium: Dilute client limit . . . 41 3.2 Applications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42 3.2.1 Two-state transitions controlled by a drop . . . . . . . . . . . . . . . . 43 3.2.2 Bimolecular reaction controlled by a drop . . . . . . . . . . . . . . . . 45 3.2.3 Nucleation reaction controlled by a drop . . . . . . . . . . . . . . . . . 47 3.3 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49 4 Fuel-driven chemical reactions in the dilute phase at phase equilibrium 50 4.1 Chemical reaction network and its properties . . . . . . . . . . . . . . . . . . 51 4.1.1 Observations from individual reaction cycles . . . . . . . . . . . . . . 52 4.1.2 Observations from combined reaction cycles . . . . . . . . . . . . . . . 53 4.2 Kinetic equations at phase equilibrium . . . . . . . . . . . . . . . . . . . . . . 55 4.3 Construction of the ternary phase diagram . . . . . . . . . . . . . . . . . . . . 57 4.4 Mechanism of co-phase separation . . . . . . . . . . . . . . . . . . . . . . . . 58 4.4.1 Composition of droplets . . . . . . . . . . . . . . . . . . . . . . . . . . 60 4.5 Co-phase separation with periodic fueling . . . . . . . . . . . . . . . . . . . . 61 4.6 Effects of activation rate constants on host-parasite identity . . . . . . . . . . 63 4.7 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64 5 Study of enzymatic kinetics in compartmentalized systems 65 5.1 Autocatalytic reactions and their properties . . . . . . . . . . . . . . . . . . . 66 5.2 PEN DNA mass action kinetics . . . . . . . . . . . . . . . . . . . . . . . . . . 67 5.3 Proteinosomes affect the PEN DNA reactions . . . . . . . . . . . . . . . . . . 70 5.4 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71 6 Conclusion and Outlook 72 A Free energy calculations for block charged polymers using RPA 76 B Numerical Methods 79 C Linear first order corrections to scaffold equilibrium volume fractions 83 D Dynamic equations in dilute limit 86 E Spatial solutions 88 F Fitting routine and extracted rate coefficients 90 G Experimental methods 95 H Calibration constants and reaction rate coefficients of PEN DNA study 98 List of figures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106

Azopolymers represent a wide class of polymeric systems in which the azobenzene chromophores are either incorporated into the main chain or covalently attached to it as a part of side chain. Light with an appropriate wavelength induces cyclic trans-cis isomerization, which results in preferred orientation of the trans-isomers perpendicular to the light polarization. Most azopolymer materials directionally deform in the presence of various light polarizations. In this thesis, a study is presented for photoinduced deformations in glassy side-chain azopolymers under different irradiation patterns. In particular, the photodeformations are investigated under homogeneous irradiation with linearly and circularly polarized light, and under inhomogeneous irradiation with intensity and polarization interference patterns. It is proposed to explain these mechanical deformations using the orientation approach, which takes into account the reorientation of the chromophores. Due to the rigid attachment of the chromophores with the main chain, the backbone segments in side-chain azopolymers should reorient into the polarization plane, which is accompanied by appearance of light induced stress. To describe the time evolution of light induced stresses, the side-chain azopolymers are modeled as an ensemble of rigid segments in presence of the effective orientation potential. Implementing the stress in a viscoplastic material model of the finite element software ANSYS, it is shown that a square azopolymer post elongates along the polarization for the linearly polarized light and contracts along the propagation direction for the circularly polarized light. Also, the deformations in the elongated oriented colloids under intensity interference patterns are modeled and it is found that the formation of beads and wave-like structures are in accordance with the experiment. The orientation approach also reproduces the peculiar structures at the edges of thin azopolymer film under polarization interference patterns. Hence, the orientation approach correctly predicts local variations of the light induced stress in each illumination pattern for both initially isotropic and highly oriented materials. With this, it is proved that the orientation approach implements a self-sufficient and convincing mechanism to describe photoinduced deformation in azopolymer materials, which does not rely on the photo-fluidization concept. The viscoplastic material modeling, developed in this thesis, can be used to describe the inscription of intricate surface structures under complex interference patterns.

The relatively new research discipline of Eco-Metabolomics is the application of metabolomics techniques to ecology with the aim to characterise biochemical interactions of organisms across different spatial and temporal scales. Metabolomics is an untargeted biochemical approach to measure many thousands of metabolites in different species, including plants and animals. Changes in metabolite concentrations can provide mechanistic evidence for biochemical processes that are relevant at ecological scales. These include physiological, phenotypic and morphological responses of plants and communities to environmental changes and also interactions with other organisms. Traditionally, research in biochemistry and ecology comes from two different directions and is performed at distinct spatiotemporal scales. Biochemical studies most often focus on intrinsic processes in individuals at physiological and cellular scales. Generally, they take a bottom-up approach scaling up cellular processes from spatiotemporally fine to coarser scales. Ecological studies usually focus on extrinsic processes acting upon organisms at population and community scales and typically study top-down and bottom-up processes in combination. Eco-Metabolomics is a transdisciplinary research discipline that links biochemistry and ecology and connects the distinct spatiotemporal scales. In this review, we focus on approaches to study chemical and biochemical interactions of plants at various ecological levels, mainly plant–organismal interactions, and discuss related examples from other domains. We present recent developments and highlight advancements in Eco-Metabolomics over the last decade from various angles. We further address the five key challenges: (1) complex experimental designs and large variation of metabolite profiles; (2) feature extraction; (3) metabolite identification; (4) statistical analyses; and (5) bioinformatics software tools and workflows. The presented solutions to these challenges will advance connecting the distinct spatiotemporal scales and bridging biochemistry and ecology.

Nicotinamide cofactor-dependent oxidoreductases have become a valuable tool for the synthesis of high value chiral compounds. The feasibility of biocatalytic processes involving these enzymes stands and falls with the efficiency of the regeneration of cofactors. In this study, we describe a novel NADPH regeneration method based on the natural thioredoxin electron delivery system. Thioredoxin 1 (Trx1) and thioredoxin reductase (TR) from Thermus thermophilus were characterized for the dithiol-dependent reduction of NADP+, revealing good catalytic activities and a particularly remarkable thermostability. The TR/Trx1 system was then coupled with two representative NADPH-dependent oxidoreductases, alcohol dehydrogenase and cyclohexanone monooxygenase. Reaction conditions for both systems were optimized for reaction yield and selectivity. The results demonstrate the feasibility of the TR/Trx1-system for its application as NADPH regeneration system.

Silicon has been the fundamental material for most semiconductor devices. As Si devices continue to scale down, there is a growing need to gain a better understanding of the characteristics of Si-based nanostructures and to develop novel fabrication methods for devices with extremely small dimensions. Ion beam implantation as a ubiquitous industrial method is a promising candidate for introducing dopants into semiconductor devices. Although the interactions between ion beams and Si nanostructures have been studied for several decades, many questions still remain unanswered, especially when the size of the target structure and the interaction volume of the incident ion beam have similar extents. Recent studies have demonstrated different potential use cases of ion beam interactions with Si nanostructures, such as Si nanocrystals (SiNCs). One of them is to use SiNCs embedded in a SiO2 layer as the Coulomb blockade for a single electron transistor (SET) device. In this work, we demonstrate the ion beam synthesis of SiNCs, as well as other ion beam interactions with Si-based nanostructures. To build the basic structure of a room-temperature SET, both conventional broad-beam implantation and a focused Ne+ beam from a helium ion microscope (HIM) were used for ion beam mixing. Subsequent annealing using rapid thermal processing (RTP) triggered phase separation and Ostwald ripening, where small nucleated Si clusters merge to form larger ones with the lowest surface free energy. Various ion implantation parameters were tested, along with different conditions during the RTP treatment. The SiNC structures were examined with energy-filtered transmission electron microscopy (EFTEM) to determine the optimum fabrication conditions in terms of ion beam fluence and thermal budget for the RTP treatment. Due to their small size and the resulting quantum confinement, SiNCs also exhibited optical activity, which was confirmed by photoluminescence spectroscopy on both broad-beam irradiated blank wafers and vertical hybrid nanopillar structures with embedded SiNCs. By scanning a laser probe over the sample and integrating the signal close to the emission peak, 1 μm-wide micropads with embedded SiNCs could be spatially resolved and imaged, demonstrating a new method of patterning and visualizing the SiNC emission pattern. To integrate SiNCs into vertical nanopillars for the fabrication of the SET, a fundamental study was conducted on the interaction between ions and vertical Si nanopillars. It was discovered that irradiating vertical Si nanopillars with ion fluence up to 2×1016 cm−2 immediately caused amorphization and plastic deformation due to the ion hammering effect and the viscous flow of Si during the irradiation. However, amorphization could be avoided by heating the substrate to above 350 °C, which promotes dynamic annealing. Several factors, including substrate temperature, ion flux, and nanostructure geometry, determine whether ion irradiation causes amorphization. Furthermore, at sufficiently high substrate temperatures, increasing ion fluence gradually reduced the diameter of the nanopillars due to forward sputtering from ions on the sidewalls. With a fluence up to 8×1016 cm−2 from broad-beam Si+, the diameter of Si nanopillars could be reduced by 50% to approximately 11 nm. Similar experiments were conducted on vertical nano-fin structures, which were thinned down to about 16 nm with Ne+ irradiation from the HIM. However, electrical measurements with scanning spreading resistance microscopy (SSRM) showed that the spreading resistance of the fins increased, even at a lower fluence of 2×1016 cm−2, which was too high for subsequent device integration. Nevertheless, these findings contributed to achieving the CMOS-compatible manufacturability of room-temperature SET devices and furthered our understanding of the fundamentals of ion interactions with Si nanostructures.