196746 research outputs found
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Topology optimization design of Chladni patterns for vibration mode manipulability
No full textClassical Chladni patterns (CPs) are visual representations of eigenvectors, which have a wide range of applications in vibration analysis, instrument design, particle manipulation and separation. Homogeneous structures often exhibit highly regular CPs, which limits their applicability. Application-oriented CPs are highly desired and can be achieved by inverse designs using topology optimization. This study presents an optimization method for designing prescribed CPs using density-based topological optimization. The optimization problem is formulated to minimize the error between the eigenvectors and the targeted CPs. Numerical results demonstrate that the proposed method can generate design configurations for a targeted CP. Moreover, it also can create novel structural configurations for the simultaneous control of several CPs. The presented method enables the precise customized design of CPs, which further provides more options for application-oriented requirements
Enzyme-loaded rod-like microgel shapes:a step towards the creation of shape-specific microreactors for blood detoxification purposes
No full textRapid removal of toxic substances is crucial to restore the normal functions of our body and ensure survival. Due to their high substrate specificity and catalytic efficiency, enzymes are unique candidates to deplete toxic compounds. While enzymes display several limitations including low stability and high immunogenicity, these can be overcome by entrapping them in a diverse range of carriers. The resulting micro/nanoreactors shield the enzymes from their surroundings, preventing their misfolding or denaturation thus allowing them to conduct their function. The micro/nanoreactors must circulate in the blood stream for extended periods of time to ensure complete depletion of the toxic agents. Surprisingly, while it is widely acknowledged that non-spherical carriers exhibit longer residence time in the bloodstream than their spherical counterparts, so far, all the reported micro/nanoreactors have been assembled with a spherical architecture. Herein, we address this important issue by pioneering the first shape-specific microreactors. We use UV-assisted punching to create rod-like microgel shapes with dimensions of 8 μm × 1 μm × 2 μm and demonstrate their biocompatibility by conducting hemolysis and cell viability assays with a macrophage and an endothelial cell line. Upon encapsulation of the model enzyme β-lactamase, the successful fabrication of rod-shaped microreactors is demonstrated by their ability to convert the yellow nitrocefin substrate into its hydrolyzed product.</p
Unexpected discoveries in the targeted protein degradation of squalene synthase and DCAF15
No full textProtein degradation is a universal process performed by human cells to recycle unused proteins and to adapt to an ever-changing environment. Targeted protein degradation (TPD) is a new approach for the treatment of human diseases, where these normal degradation processes are hijacked. Instead of simply blocking a protein’s function, heterobifunctional or monovalent small molecules are used to redirect a specific protein to the cellular protein degradation machinery. If so-called PROteolysis Targeting Chimeras (PROTACs) or molecular glues are developed successfully, they can eliminate all functions of a protein, including catalytic and scaffolding roles. Thereby, TPD can help to unlock yet untreatable diseases and open up new strategies to uncover new biology.In two separate projects within this thesis, the aim was to apply TPD principles to develop degraders of squalene synthase (SQS) and DDB1 Cul4 Associated Factor 15 (DCAF15), two unrelated proteins. SQS is a metabolic enzyme, catalyzing a key step in cholesterol biosynthesis. I wanted to investigate if chemical degradation of SQS could prevent cholesterol biosynthesis and thereby lower overall cholesterol content in human cancer cells. I identified a small molecule degrader of SQS, which was able to lower amounts of the storage form of cholesterol in cells, cholesterol esters. At the same time, I identified so far unknown stabilizers of SQS, which shielded the protein from its natural turnover. Overall, the work shows that SQS protein levels can be manipulated with diverse chemical structures, which can guide future compound development.DCAF15 is the substrate receptor (SR) component of the Cullin 4 Ring Ligase (CRL4) complex, which is one part of natural cellular protein degradation processes. Recent discoveries strongly implicate DCAF15 in protein aggregation, which is a hallmark of neurodegenerative diseases. By developing the first small molecule degraders of DCAF15, I aimed to test the therapeutic potential of chemically eliminating DCAF15 for the treatment of e.g. Alzheimer’s or Parkinson’s disease. After identifying early leads, I am currently in the process of biologically evaluating our compounds
Dissociation of HeH<sup>+</sup> in the electronic ground state using shaped mid-IR laser pulses
No full textInspired by recent experimental work, we study the control over the laser-driven dissociation of the HeH+ ion in the electronic ground state. Shaped pulses with peak intensities below 1012 W cm−2 are obtained by phase modulation of high-intensity transform-limited femtosecond pulses. We investigate the performance of pulse shaping for a number of shaping parameters targeting both vibrational and rotational excitation pathways. The numerical results show that pulse shaping is most effective at low pulse energies and broad spectral bandwidths, while intense transform-limited pulses with narrow spectral bandwidths maximize dissociation. We show that the control achieved with a quadratic chirped pulse optimized for vibrational ladder climbing, a cascade excitation process of adjacent vibrational levels, is hindered by rotational motion leading to significantly reduced dissociation. Moreover, pulse shaping using higher-order polynomial phase functions is found to provide only a marginal increase in dissociation yields. Our results provide additional insights into the coherent control of bond breaking in diatomic molecules, and demonstrate the efficacy of pulse shaping for a range of pulse energies.</p
Codon-tRNA Coadaptation Bias for Identifying Strong Native Promoters in <i>Komagataella phaffii</i>
No full textPromoters are crucial elements for engineering microbial production strains used in bioprocesses. For the increasingly popular chassis Komagataella phaffii (formerly Pichia pastoris), a limited number of well-characterized promoters constrain the data-driven engineering of production strains. Here, we present an in silico approach for condition-independent de novo identification of strong native promoters. The method relies on tRNA-codon coadaptation of coding sequences in the K. phaffii genome and is based on two complementary scores: the number of effective codons and the tRNA adaptation index. Genes with high codon bias are expected to be translated efficiently and, thus, also be under control of strong promoters. Using this approach, we identified promising strong promoter candidates and experimentally assessed their activity using fluorescent reporter assays characterizing 50 promoters spanning a 76-fold difference in expression levels in a glucose medium. Overall, we report several promoters that should be added to the molecular toolbox for engineering of K. phaffii and present an approach for identifying promoters in microbial genomes
Effect of Electric Fields on Probiotic Cells:Modulation of the Encapsulation, Drying, and Viability
No full textProbiotic cells are microorganisms that have health-promoting properties, which could be exerted providing that the cells are viable. Maintaining their viability, however, is challenging, due to their sensitivity to several factors, such as the pH, the presence of oxygen, and the processing conditions (i.e., heating, freezing).This Ph.D. thesis elucidates different approaches to enhance the viability of probiotic cells by the utilization of electric fields. A literature review on selected studies is initially introduced, regarding the effect of the electric field on the stimulation, the manipulation of surface properties, and the electrophoretic movement of probiotic cells and other bacteria.The first experimental part of this Ph.D. thesis explicates the effect of DC electric field to encapsulate surface-charged and hydrophobic probiotic cells (rod-shaped Bifidobacterium animalis subsp. lactis–BIFIDO, and coccus-shaped Streptococcus thermophilus–ST44) within maltodextrin microcapsules, using electrospray processing. The generated electrostatic forces between the negatively surface-charged probiotic cells and the applied negative polarity on the electrospray nozzle, allowed to control the location of the cells towards the core of the electrosprayed microcapsules. The organization of the cells affected the evaporation of the solvent (water), and subsequently the glass transition temperature (Tg) of the electrosprayed microcapsules, as well as the viability of probiotic cells. The utilization of auxiliary ring-shaped electrodes between the nozzle and the collector, enhanced the electric field strength and controlled the deposition of the capsules on the collector. Numerical simulation, through Finite Element Method (FEM), shed light to the effects of the additional ring-electrodes on the electric field strength and potential distribution, revealing a locally stronger electric field (in the proximity of the collector), that enhanced solvent evaporation, and contributed to higher glass transition temperatures of the microcapsules.In addition to maltodextrin, non-water-soluble compounds, such as ethyl cellulose, were used for the encapsulation of BIFIDO probiotic cells in electrosprayed core–shell microcapsules. Different core compounds (concentrated BIFIDO, BIFIDO–maltodextrin and BIFIDO–glycerol) were tested, with ethyl cellulose (ETC) as a shell material. The ETC microcapsules exhibited relatively low water activity (aw below 0.20) and high BIFIDO viability (109–1011 CFU/g). The electrosprayed microcapsules that contained BIFIDO–glycerol in the core, demonstrated a loss in viable cells of barely 3 log CFU/g, while the non-encapsulated BIFIDO lost approximately 7.57 log CFU/g. Even though the shell matrix was prepared using solvents that typically significantly decrease the viability of probiotics, the results of this study evidently demonstrated that the viability of BIFIDO can be extended by encapsulating within core-shell ETC electrosprayed capsules.Since drying and moisture content are crucial for the long-term storage stability of probiotics, the effect of the ionic wind on the electrohydrodynamic drying (EHD) of probiotics was examined in another study of this thesis. Several parameters, such as the polarity and voltage of the electric field, the collector type, the surrounding temperature and gas, as well as the use of excipient, were found to affect the EHD drying process. BIFIDO were dried by the EHD drying and freeze-drying process, the comparison of which uncovered that the survival of cells and the water evaporation rates were similar, confirming the potential of EHD drying as an alternative drying technology for probiotic cells.Probiotic cells’ long-term stability can also be induced through cell aggregation. The stimulation of probiotic cell aggregation by the application of DC electric fields and combined electric field with standing acoustic waves (SAW), was evaluated in an additional study of this thesis. The sole application of acoustic waves did not trigger any cell aggregation; however, the DC electric field induced the polarization and aggregation of the BIFIDO cells. The aggregation was accelerated (~6 times) when applying simultaneously DC electric field and SAW, due to the accumulation of the cells at the acoustic pressure nodes, followed by the aggregation of the polarized cells by dielectrophoresis (DEP). The synergistic effect of DC electric field and SAW not only facilitated the high aggregation of the cells, but also considerably enhanced the hydrophobicity of BIFIDO cells, without compromising their viability or altering their surface charges.The protective effect of lecithin phospholipids’ coating on the viability of BIFIDO in aqueous media was also investigated. It was demonstrated by FTIR and Raman spectroscopy, that the BIFIDO–lecithin interactions are hydrophobic. Moreover, the effect of lecithin concentration on BIFIDO surface properties (surface charge, hydrophobicity) was also assessed and correlated with the long-term stability of probiotics.Notwithstanding the differences of the explored methods, the aim was consistent; to maintain the probiotic cells viable during processing and storage. In summary, the utilization of electric fields significantly modulated the encapsulation, drying, and aggregation of the probiotic cells, subsequently enhancing their viability, as did theemployment of coating materials
Stochastic optimization of trading strategies in sequential electricity markets
No full textQuantity and price risks determine key uncertainties market participants face in electricity markets with increased volatility, for instance due to high shares of renewables. In the time from day-ahead until real-time, there lies a large variation in best available information, such as between forecasts and realizations of uncertain parameters like renewable feed-in and electricity prices. This uncertainty reflects on both the market outcomes and the quantity of renewable generation, making the determination of sound trading strategies across different market segments a complex task. The scope of the paper is to optimize day-ahead and intraday trading decisions jointly for a portfolio with controllable and intermittent renewable generation under consideration of risk. We include a reserve market, a day-ahead market and an intraday market in stochastic modeling and develop a multi-stage stochastic Mixed Integer Linear Program. We assess the profitability as well as the risk exposure, quantified by the conditional value at risk metric, of trading strategies following different risk preferences. We conclude that a risk-neutral trader mainly relies on the opportunity of higher expected profits in intraday trading, whereas risk can be hedged effectively by trading on the day-ahead. Finally, we show that reserve market participation implies various rationales, including the relation of expected reserve prices among each other, the relation of expected reserve prices to spot market prices, as well as the relation of the spot market prices among each other.</p
Sustainability of corrosion protection for offshore wind turbine towers
No full textWhen coatings industries have ambitions to develop more sustainable products it is important to know what path to follow. Quantitative evaluations in the form of Life Cycle Assessment (LCA) offers guidance for sustainability directions. The direction will depend on the type of coating. This work analyses sustainability performance of protective coatings, using the coating of an offshore wind turbine tower as a case. All steps in the manufacturing are assessed and the relevant environmental impacts are evaluated along the life cycle of the turbine tower. The assessment shows that the vast majority of the impacts, including climate change, originate from manufacturing of the steel. Therefore the durability of the coating system to protect the steel and prolong the lifetime, minimizing the need for repair, etc. should be the main priority for a sustainable direction. The coating system must keep the steel structures corrosion free for at least as long as the designed lifetime, as it is much more costly in terms of environmental impacts to repair or replace steel than to protect it properly from the start. When the protection is secured, the sustainable development path from the present situation where thermal sprayed metal (TSM) is used for galvanic protection of the wind turbine tower, will be to develop:- Coating systems where toxic substances are substituted by less toxic or non-toxic substances.- Coating systems where the thermal sprayed metal (TSM) layer is substituted by zinc-rich epoxy or Zinc silicate coatings.- Coating systems where the organic solvents are substituted by water.- Coating systems which would make it possible to reduce the amount of steel used- Coating systems where the organic binder material is substituted with alternatives with lower carbon footprint- Ease of recycling the structure material for reuse in new structures