[dipl] Kemian tekniikan korkeakoulu / CHEM

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  • Heterosyklien klooraus
    (2025-02-01) Peussa, Pietari
     School of Chemical Engineering | Master's thesis
    Chlorination of heterocycles enables multiple convenient follow-up reactions, like Suzuki or Heck cross-couplings. Chlorinated heterocycles on their own also have a major role in multiple drugs. In this work, the most important chlorinating reagents working by electrophilic aromatic substitution are reviewed and N,N-dichloro-tert-butyl carbamate (Cl2NBoc) is introduced as a new possible chlorinating reagent. Three indole de-rivatives were successfully chlorinated. Also, the uncommon aromatic aminochlo-rination was achieved with a reaction between Cl2NBoc and benzofuran.
  • Utilizing handheld FTIR in Cleaning Verification — Effect of excipients on the identification of ibuprofen
    (2025-02-24) Pystynen, Joona
     School of Chemical Engineering | Master's thesis
    Preventing cross-contamination is crucial in the pharmaceutical industry to ensure patient safety and product quality. Drug residues between batches must be below maximum allowable carry-over (MACO) levels when different products are manufactured with the same equipment. Cleanliness of manufacturing equipment and surfaces is monitored with cleaning verification methods. Typical methods include high-performance liquid chromatography (HPLC) and total organic carbon (TOC), but more rapid, sustainable and cost-effective methods have gained interest in recent years. This study utilized a handheld FTIR device as a new rapid cleaning verification method. The handheld FTIR offers real-time analysis directly from different surfaces, reducing steps between sample analysis and acquiring residual results. Before implementing this method as a validated cleaning verification method, the detection and quantification of APIs must be carefully examined. This study focuses on identifying the potential effects of excipients on the qualitative measurements of ibuprofen. Ibuprofen and five excipients: lactose monohydrate, microcrystalline cellulose, croscarmellose sodium, colloidal silicon dioxide, and magnesium stearate were studied. Ibuprofen’s characteristic peaks: carbonyl group C=O, aromatic C=C and C-H were identified. The study demonstrated that the carbonyl group C=O seen around 1700 cm-1 and the aromatic C=C bond seen around 1500 cm-1 were visible in the spectra of all performed measurements. Using C-H at 3000–2850 cm-1 as an indicator of ibuprofen was not ideal, as lactose, microcrystalline cellulose and croscarmellose sodium absorbed in that region as well. These results show that the handheld FTIR is capable of detecting important characteristic peaks of ibuprofen in the presence of excipients.
  • Analytical and testing methods for assessing pulp performance in Lyocell fiber production
    (2025-01-30) Kultalahti, Ella
     School of Chemical Engineering | Master's thesis
    Cellulose is an abundant and renewable biopolymer found in the cell walls of plants. It is used for producing man-made cellulosic fibers (MMCFs) which are a sustainable alternative to synthetic textile fibers. Different types of MMCFs include for example viscose, cuprammonium rayon and Lyocell. Among these, Lyocell is considered as an environmentally friendly process, as it recycles chemicals and water within the process. The global generation of textile waste continues to rise, yet only 1% of it is currently recycled into new textile fibers. The majority is either incinerated or sent to landfills. Utilizing this waste as a raw material for textile fiber production would support circular economy and reduce the reliance on virgin materials in the textile industry. The goal of this thesis is to identify which pulp and Lyocell dope properties can be used to evaluate the suitability of pulp for Lyocell fiber production. Four different pulps, including commercially used dissolving pulps and recycled textiles, are characterized and Lyocell fibers are produced from them. Fiber and spinning dope properties are studied, and a connection between them and the pulp properties is formed. The results show that intrinsic viscosity and degree of polymerization of the pulp greatly influence spinning dope properties. These, in turn, impact the properties of the Lyocell fibers and efficiency of the fiber production process. When the intrinsic viscosity of the pulp was within the range of 350--450 ml/g, the fiber properties were comparable to commercial Lyocell. The results of this study are valuable for expanding the raw material selection for Lyocell fiber production. The characterization methods used in this work provide a strong foundation for assessing the potential of new types of recycled cellulosic materials as raw material for Lyocell fibers.
  • Wet etching of aluminium nitride and germanium thin films for piezoelectric MEMS
    (2025-02-24) Jääskeläinen, Lumi
     School of Chemical Engineering | Master's thesis
    This master’s thesis focused on the development of wet etching processes for the patterning of single layer piezoelectric AlN in phosphoric acid -based etchant PWS, and double-layer Ge/Ti stack in various hydrogen peroxide solutions. For AlN, the wet etching process was studied through variations in etchant temperature, etching time, and through variation in annealing condition of the film. For Ge/Ti stack, the wet etching process was studied in different etchant solutions and the process capabilities were cross compared at their optimal etch temperatures. The etch results were mainly scrutinized based on their ability to produce residue-free surfaces with minimal undercut. The samples were studied with optical microscope, SEM, and SEM-EDX for residual film and other artefacts, and under-cutting was determined through cross-sectional SEM images. The surface topography of some samples was additionally analysed with tapping mode AFM to evaluate the sample film granularity and surface roughness. With these short loop tests, a highly promising etch process in 85°C PWS was found for annealed AlN, although very limited wafer-to-wafer variability was tested. Around an order of magnitude smaller undercut was observed for annealed AlN in comparison to AlN samples without annealing. The lowered etch rate of annealed AlN was found to be highly dependent on a few nm thick surface layer, which could be removed with a 30 sec CF4-O2 PERIE process. A suitable process was also found for the patterning of Ge/Ti in a peroxide solution with Pure Etch TE series additive, with promising wafer-to-wafer stability across lots. However, slight variation in undercutting was seen when the number of wafers in lot was varied. Additionally, concerning time-dependent oxidation of the deposited amorphous Ge film was discovered, which resulted in significant film loss during Ge oxide removal process.
  • Green aromatics from biomass pyrolysis oils
    (2025-01-23) Lehtinen, Veikka
     School of Chemical Engineering | Master's thesis
    The literature review discusses the production of aromatic hydrocarbons, especial-ly benzene, toluene, and xylene, from biomass pyrolysis oils by catalytic cracking with zeolite catalysts. Focus is on the ZSM-5, its activity to aromatics, and stabil-ity with time on stream. Modifications, such as metal doping, introducing hierar-chical structures and the effect of Silica/Alumina-ratio are investigated. Catalyst stability and how it can be improved is discussed. In the experimental section, various bio-oil feedstocks and catalysts were tested in a catalytic fixed-bed reactor and their activity to aromatic hydrocarbons were evaluated. The effect of metal doping with zinc, Silica/Alumina-ratio, tempera-ture, and weight hourly space velocity were investigated. The results showed that introducing zinc to the ZSM-5 structure increased the rela-tive selectivity to aromatic hydrocarbons in the product liquid, produced from hydrogenated bio-oil. The zinc containing catalysts were also more stable with time on stream compared to parent HZSM-5. Increasing temperature from 400 to 550 ˚C increased the relative selectivity to aromatic hydrocarbons and gaseous hydrocarbons. The effect of space velocity was more varied. Gas production was higher at lower space velocity values and the relative selectivity to BTX was highest at 5 h-1.
  • Cost comparison of converting conventional ammonia process to green
    (2025-02-24) Heikkinen, Pinja
     School of Chemical Engineering | Master's thesis
    The study investigated conversion of a conventional ammonia process to a green process using two methods. An essential part of converting conventional ammonia to green is replacing the SMR process of natural gas with electrolysis-based hydrogen. In this study the use of the biomass biogas SMR process was studied, with the addition of a carbon capture unit and the replacement of the natural gas SMR process by water electrolysis. In addition, greenfield water electrolysis-based ammonia production was studied. The capacity of 340 kilotons per year was used for all processes. The processes were simulated by using Aspen Plus V14 software, followed by cost analyses of the simulation using Aspen Process Economic Analyzer software. CAPEX estimates were made using Aspen Capital Cost Estimator software, after which cost sensitivity analysis was used to calculate sensitivities to react to price changes and results were compared with each other. Based on the results, converting conventional ammonia to green is profitable at average and low electricity prices when by-products can be sold. Changes in the price of electricity significantly affect the price of electrolysis-based ammonia, which causes its profitability at the highest electricity prices compared to natural gas-based ammonia to suffer. However, more profitable than building a new one is converting the process to electrolysis based. The construction of a new electrolysis-based plant is less profitable than the construction of a conventional grey ammonia plant. Biomass-based ammonia was less profitable than natural gas-based ammonia in terms of cost in this study.
  • Predictive Modelling of N-Heteroarene Cross-Couplings
    (2025-01-13) Holopainen, Riku
     School of Chemical Engineering | Master's thesis
    Palladium catalysed cross-couplings of dihalogenated heteroarenes have a natural tendency of proceeding selectively, retaining one halide. In general, site-selectivity is biased to occur at a halide adjacent to a heteroatom. While the synthesis of a single regioisomer is a relatively straightforward process, accessing substitution patterns disfavoured by cross-coupling continues to present a challenge. Unconventional site-selectivity can be achieved through substrate- or catalyst-controlled approaches. Despite catalyst-controlled approaches being at the forefront of research, relatively little is known about the relationship between site-selectivity and a catalyst’s structure. The development of novel reactions for unconventional selectivity has traditionally relied on trial-and-error based experimental work, occasionally supplemented by more systematic methods. However, these are still time and resource intensive processes. From early linear regression models to modern machine learning approaches, chemists have long sought to streamline this process through various computational methods by relating chemical structure to function. This work sought to improve the development of novel reactions involving dihalogenated heteroarenes with the development of predictive models, along with the accompanying tools and workflows. More precisely, a classification model for predicting the regiochemical outcomes of various ligands in palladium catalysed Suzuki–Miyaura cross-couplings was developed. The initial model proved to accurately predict the outcomes of four experimentally verified out-of-sample ligands. After the second round of experiments, it became evident that selecting the correct base-solvent combination is as pivotal as choosing the appropriate ligand. The developed models should not only accelerate the discovery process for heteroarenes, but also the development of models accommodating other substrate classes.
  • Host-guest Chemistry for Restricting Bacterial Quorum Sensing
    (2025-01-30) Rantanen, Rasmus
     School of Chemical Engineering | Master's thesis
    In search of potential solutions to antimicrobial resistance (AMR), supramolecular host molecules have gained significant interest due to their characteristic ability to encapsulate various types of guest molecules. Supramolecular host molecules can be harnessed to restrict bacterial quorum sensing (QS) via encapsulation of N-acyl-homoserine lactones (HSLs). HSLs are the main signaling molecules used by Gram-negative bacteria to control a multitude of processes involved in bacterial virulence. In this work, a systematic study on the association constants between modified and native β-cyclodextrins (β-CDs) and HSLs is conducted. Specifically, this thesis investigates the impact of N-acyl chain length, substitution at C3-site of the N-acyl chain and modification of CD structure on the binding affinity. The studied HSL molecules include C4-HSL, C8-HSL and C12-HSL and their oxo- and hydroxy-substituted counterparts. The cyclodextrins used in this work contain native, amino-modified, trimethyl-ammonium-modified, lysine-modified, dimethyl-modified and trimethyl-modified β-CDs. The association constants are derived via fluorescence-based indicator displacement assays (IDAs) using 2-anilinonaphthalene-6-sulfonic acid (2,6-ANS) as fluorescent probe. HSL binding improves as the N-acyl chain length increases from a four-carbon chain to twelve-carbon chain across the studied CDs. On the other hand, the studied CD modifications do not improve the affinity to HSLs. In fact, the highest association constants are recorded for native β-CD across all the studied HSLs. Finally, the substitutions at C3-site of N-acyl chain yields mixed results. Substitution in C12-HSL increases the affinity, whereas substitution in C8-HSL decreases the affinity to the studied CDs.
  • InGENEous: Teaching Synthetic Biology through a Video Game
    (2025-02-13) Aspi, Aarni
     School of Chemical Engineering | Master's thesis
    Synthetic biology is a rapidly evolving interdisciplinary field that combines principles of biology, engineering and computer science to address global challenges sustainably in various fields such as agriculture or biomedicine. This is accomplished by using engineered DNA sequences to genetically modify organisms with advanced functionalities. Synthetic biology is often demonstrated and taught using BioBricks - standardized DNA sequences that simplify the subject to a broader audience. The purposeful use of video games in science, research and education has grown in popularity due to their accessible, engaging, and feedback-driven nature, which enables players to enter a highly focused and motivated flow state. While video games related to synthetic biology have so far provided in-depth knowledge of specific aspects of the field, none have yet provided the player with a comprehensive understanding of the field as whole. InGENEous, an educational game on synthetic biology, aims to provide a holistic understanding of the field to its players, regardless of their background. The players must solve a variety of real-world problems by designing, building, testing, and learning with the help of BioBricks. In doing so, the game fosters critical thinking, creativity, and an understanding of the interdisciplinary nature of synthetic biology. InGENEous also holds promise as a versatile software tool for research, enabling the players to export their designs and data from the game accurately. This feature facilitates a wide range of research applications and supports crowd-sourced citizen science projects.
  • Solar-assisted Waste Heat Utilisation Coupled with Thermal Energy Storage for Electricity Production: Technical and Economic Assessment
    (2025-02-03) Skorniakov, Ilia
     School of Chemical Engineering | Master's thesis
    The amount of energy dissipated as ultra-low-temperature waste heat constitutes approximately 45% of global primary energy consumption. This waste heat poses environmental risks by increasing local temperatures and imposing unnecessary costs on industries through elevated fuel consumption and equipment maintenance. Thus, addressing this challenge is essential for mitigating climate change and improving the energy efficiency of industrial sites. This thesis reviewed four pathways for waste heat utilisation: conversion of waste heat into useful heat, cooling, electricity, and process integration. Various technologies were examined, including heat pumps, chillers, Rankine cycle modifications, solar thermal collectors, and thermal energy storage systems. Among these options, electricity generation was selected as the desired application, and an innovative setup was proposed. The proposed system upgrades 85°C waste heat from pulp and paper mill to 120°C using solar thermal collectors and converts it into electricity via an organic Rankine cycle, which is sold to the local grid. To ensure consistent operation, the system additionally incorporates two thermal energy storages: one to store waste heat and another to store upgraded heat. A techno-economic assessment of the proposed system was conducted for industrial sites in Finland, Spain, and Greece, using one year of weather and electricity price data. The system’s lifespan is estimated to be 25 years, and the analysis revealed best-case payback periods of 99, 13, and 11 years, respectively, with annual electricity production ranging from 4.5 to 5.5 GWh. However, less than 50% of the available waste heat was utilised. The system’s profitability was found to rely heavily on daily electricity price fluctuations rather than longer-term trends. The proposed setup presents a sustainable, though less profitable, alternative to photovoltaic panels for electricity production in regions with high solar irradiation and electricity prices. Alternatively, in regions with low solar irradiation, the system could be adapted to upgrade waste heat for use in district heating networks, offering a practical and environmentally friendly application for ultra-low temperature waste heat recovery.
  • Recycling the recycled: Transforming Cotton Dust into High-performance Regenerated Cellulose Fibers Using Ioncell® Technology
    (2025-02-24) Delgado, Pau
     School of Chemical Engineering | Master's thesis
    This thesis explores the recycling of cotton waste from the company Recover™ into Ioncell® fibers, demonstrating a proof of concept for converting pre-consumer waste into regenerated cellulose fibers suitable for textile applications. The initial characterization of the cotton dust waste (CoD) established its suitability as a cellulose source, but its high viscosity and molar mass required pre-treatment to reduce the molecular weight for optimal dissolution. The milled and adjusted cotton was dissolved in the ionic liquid, 1,5-diazabicyclo[4.3.0]non-5-enium acetate ([DBNH][OAc]), to prepare a homogeneous spinning dope, which was extruded through a spinneret, and resulted into fibers by the Ioncell® process. The regenerated fibers exhibited excellent mechanical properties and crystallinity, with tenacities that surpassed the industry average for recycled fibers (>50 cN/tex). This work demonstrates the viability of utilizing pre-consumer cotton waste as a raw material for the production of high-performance regenerated fibers, providing an innovative approach to addressing the challenges of textile recycling.
  • Hybridization of Cellulose with Phase Change Materials for Insulation Application: A proof-of-concept case study
    (2025-02-21) Portin, Maria
     School of Chemical Engineering | Master's thesis
    The purpose of this master's thesis was to develop a bio-based phase change material for insulation applications and consider its advantages as renewable and sustainable material. PCMI was developed by hybridization by polyethylene glycol (PEG) and cellulose to create foam insulation material by an air-drying method. This material combines two main characteristics: the foamy and porous structure of an insulator and the phase change ability of PCM. When PEG melts, it normally becomes a liquid. However, in this PCMI material, PEG does not leak out during the melting phase as cellulose provides a supportive matrix and forms hydrogen bonds with PEG. The aim of the project was to produce PCMI materials for scale-up production (1 m^2) and to test how different additives affect the material. The additives used were lignin, biochar, expandable graphite, barium sulphate, and sodium bicarbonate. The PCMI samples were characterized with different methods. The results showed that by increasing the volume of PCMI, the density increased as well as a latent heat capacity. PEG 1000 appeared to be the best choice for building insulation applications due to its suitable operation temperature range (melting point 33-40°C). Its narrow range is optimal for regulating the temperature of living environments for comfort. Thus, PEG 1000 was used in additive samples. The PCMI were lightweight, highly porous with different volumes and thicknesses, which is a desirable in insulation materials. With additives, it was possible to modify the properties of the PEG 1000 PCMI samples for different applications. For example, by adding expandable graphite, the fire-resistance and tensile-strength were increased and by adding biochar, the strength were increased.
  • Hygienic design of steam distribution system in food processing
    (2025-02-23) Kumpulainen, Karri
     School of Chemical Engineering | Master's thesis
    Steam has an essential role in the food industry, serving as a heat transfer medium in various thermal processing applications. A well-designed and hygienic steam system is essential for ensuring food safety, meeting regulatory requirements and maintaining production efficiency. This thesis evaluates the steam system of a food production facility and identifies key areas for improvement, focusing on hygiene and energy efficiency. The theoretical part of the study explores steam purity classifications, contamination risks and best practices for steam system design. The applied part evaluates the current steam system, identifying critical issues that may lead to contamination risks and heat losses. To address these challenges, targeted improvements are proposed to enhance system performance. The results show that improving steam filtration in critical areas and insulating pipeline components can significantly reduce contamination risks and lower operating costs. Additionally, adopting clean steam could be considered a long-term solution, as it would eliminate the risk of chemical contamination and further improve food safety. The findings contribute to a deeper understanding of hygienic steam system design in the food industry and provide practical recommendations for optimizing steam usage in industrial applications.
  • Overproduction of L-tyrosine in yeast
    (2025-02-24) Salminen, Pinja
     School of Chemical Engineering | Master's thesis
    L-tyrosine is an industrially relevant compound and a precursor for many oth-ers. Several strategies to create L-tyrosine overproducing Saccharomyces cere-visiae strains have been reported. This project aimed at reviewing strategies pre-viously found successful and implementing selected modifications in S. cerevisiae CEN.PK113-7D through targeted genome-editing. Using CRISPR-Cas9 technology, mutant versions of the ARO3 and ARO4 were introduced to release the feedback inhibition of the shikimic acid pathway. Additionally, TKL1 was overexpressed to favor the pathway through transketolase in the pentose phosphate pathway for increasing the precursors availability for aromatic amino acid synthesis. The feed-back inhibition relieved point-mutation variants of ARO3 and ARO4 were inte-grated into the genome. TKL1 was overexpressed by changing the native promoter to a strong TDH3 promoter. The engineered strains were analyzed for amino acid accumulation.; L-tyrosine and L-phenylalanine accumulated notably in S. cere-visiae CEN.PK113-7D strain harboring the feedback inhibition relieved mutants of ARO3 and ARO4 while in wild type and TKL1 overexpression strains L-tyrosine and L-phenylalanine were below detection level. The developed strains could be used as pre- optimized platform strains for expressing heterologous pathways having L-tyrosine as a precursor. Such heterologous pathways could allow for sustainable biotechnological production of e.g., hydroquinone whose synthesis is currently oil-based.
  • From biotemplate to wearable sensor: Creating a piezoresistive sensor textile for healthcare applications
    (2025-02-21) Mäkelä, Viivi
     School of Chemical Engineering | Master's thesis
    The field of wearable strain sensors has been a target of extensive research in recent years due to their unique features and diverse application range. However, the conventional strain sensors currently used in healthcare lack many of the measurement criteria required to accurately assess the human body due to its complex structure and dynamic nature. The new generation of flexible and textile-based sensors addresses these shortcomings of the conventional sensors and provide improved platforms for healthcare applications. In this thesis work a highly sensitive piezoresistive yarn which can be incorporated into a wearable sensor textile is developed. The developed sensor combines three different elements from previous research into one novel sensor material that has not been studied before. The substrate used for the sensor is starch-nylon yarn, which is incorporated into a twisted/coiled spring structure and coated with Potato virus A (PVA) and silver nanoparticle (AgNP) template. The development process of creating an optimally performing sensor consisted of first optimizing the coating conditions of the starch-nylon yarn and then testing the properties of different spring structures made from the yarn. By combining the optimized coating protocol with the most suitable spring structure, the highly performing piezoresistive sensor was created. This was followed by validating the sensing performance of the created sensor focusing on similar movement ranges that can be seen in the human body. Subsequently, the textile integration of the sensor was demonstrated by fabricating a sensor textile sample. This thesis work shows that a functional piezoresistive sensor can be created by combining the PVA and AgNP coating with the starch-nylon spring structure. Furthermore, the created sensor shows promising preliminary results for the key performance metrics highlighting its potential to be used as wearable sensor. The sensor exhibits high sensitivity, good detection range, relatively short response and recov-ery times and promising results for durability. This thesis also shows that the sensor can be integrated into a textile, showing its potential to be further explored for wearable healthcare applications. This thesis serves a good starting point for further development of the introduced piezoresistive sensor and provides a new platform that can be utilized in future research.
  • Fabrication and investigation of thermoelectric device based on p-type and n-type CoSbS components
    (2024-12-31) Liu, Hanru
     School of Chemical Engineering | Master's thesis
    Thermoelectric materials have garnered significant interest in recent years due to their promising applications in energy conversion and waste heat recovery. This study systematically investigates the thermoelectric properties of CoSbS-based materials, with a focus on the effects of doping elements (Ge, Ni, Se, Te). By precisely controlling the doping concentration and substitution sites, the impact of these elements on optimizing the Seebeck coefficient and reducing thermal conductivity is thoroughly examined. The results reveal that Co0.9Ni0.1Sb0.9Ge0.1S demonstrates outstanding thermoelectric performance. Furthermore, Se and Te doping effectively reduce lattice thermal conductivity; however, their contributions to improving overall thermoelectric performance remain limited. This study highlights the critical role of optimizing doping sites and concentrations in enhancing the thermoelectric properties of CoSbS-based materials, providing valuable in-sights for the future design and development of high-performance thermoelectric materials. In addition, the methods of assembling thermoelectric devices and corresponding application prospects are also discussed.
  • Novel use of blood products: Using existing omics data from extracellular vesicles from differently activated platelets to fine-tune modelling of functionality
    (2024-12-20) Österberg, Anna
     School of Chemical Engineering | Master's thesis
    Platelets are crucial for hemostasis and, upon activation, release extracellular vesicles (PEVs). PEVs are a heterogeneous population, whose contents vary depending on the platelet-activating stimulus. This study re-analyzed existing omics data of PEVs from differently activated platelets, focusing on their immunomodulatory roles. We validated our findings in vitro using primary cells. Dimensionality reduction techniques, including principal component analysis (PCA) and multi-omics factor analysis (MOFA), were applied. For validation, we established a human macrophage in vitro model and isolated PEVs from differently activated platelets with ultracentrifugation. Our re-analysis revealed that TNF-a secretion in THP-1 cells in vitro differed from previous in vivo results, particularly for PEVs derived from thrombin and collagen coactivated platelets (TC PEVs). Additionally, PEVs derived from platelets activated with rhodocytin through the CLEC-2 receptor (CLEC-2 PEVs) exhibited distinct protein and cytokine profiles. Due to unavailability of the rhodocytin reagent, we could not analyze CLEC-2 PEVs further and therefore, our experiments focused on TC PEVs, using PEVs from unstimulated platelets (US PEVs) as controls. We compared TNF-a secretion in M1 (pro-inflammatory) versus M2 (anti-inflammatory) polarized primary macrophages. Results indicated significantly higher TNF-a secretion in M1 cells compared to M2 cells, highlighting the biological differences between the two cell types. No significant variation between PEV-treated and untreated cells was found. However, we observed donor-dependent variation, so further studies with more biological replicates are needed to validate these findings.
  • Artifical intelligence based prediction of protein complexes formed via transient interactions
    (2024-12-28) Hammarberg, Linnéa
     School of Chemical Engineering | Master's thesis
    Transient protein-protein interactions (tPPIs) are interactions between multiple proteins which swiftly switch between an associated and a dissociated state. Such interactions play a crucial role in many dynamical processes in the cell, such as in the regulatory and signaling pathways. Because of their adaptable nature, tPPIs are attractive targets for the development of novel biomaterials. tPPIs have previously been overlooked, due to their low cellular concentrations as well as being hard to capture both experimentally and with computational methods. As a result, there exists a knowledge gap of the structures and functions of tPPIs. This thesis provides a comprehensive analysis of predicting tPPIs with the front-runner of the AI-driven structure predicting algorithms, AlphaFold (AF). Prior to this work, no publications have addressed AI-driven structure predictions of tPPIs. The AF generated tPPI-models are compared against experimental data when available, and against the output of the protein docking algorithm ClusPro. The AF performance is further validated through molecular dynamics simulations. AF showed to be much less confident about predicting tPPIs than stable protein complexes in general. High sampling should therefore be employed to acquire a wider range of models. The AF generated models did not significantly differ from those predicted by ClusPro, and were also fairly close to the experimentally determined interaction site. Interaction site families were readily identifiable from the sample by isolating and comparing the residues predicted to be in contact. Simulating models from each family with MD, showed that AF is able to predict a range of stable interaction sites. The interaction site features varied among the studied proteins, but the most commonly predicted interaction sites included beta-strand residues and disordered loops for all studied proteins. The detailing of the benefits and limitations of predicting tPPIs with AF presented in this work might aid in the engineering of new tPPI-based biomaterials.
  • Optimization of cell culture models for calpain-2 studies for prostate cancer
    (2024-12-19) Hansson, Cecilia
     School of Chemical Engineering | Master's thesis
    Prostate cancer affects millions of men annually and is the second most leading cause of cancer related death for men. Many patients eventually develop castration-resistant prostate cancer (CRPC), a highly aggressive form that is resistant to standard treat-ments. The protease calpain-2 has shown to contribute to cancer progression. Many studies fail due to a poorly designed in vitro model that does not replicate the tumour microenvironment enough. To achieve reliable study outcomes, the in vitro culturing environment must closely mimic the complex conditions of human tumours. In this Master’s thesis a suitable culturing environment for studies of calpain-2 was investigated. Two widely used prostate cancer cell lines, PC3 and LNCaP, were cultured on two different extracellular matrix mimics (Matrigel and collagen) and compare to cells grown directly on plastic wells. Experiments were performed under hypoxic (0.2% oxygen) and normoxic (21% oxygen) conditions. The objective was to explore how these culture conditions and oxygen levels affect cell behaviour, including phenotype and protein expression. The results underscore the importance of using in vitro mod-els that closely replicate human cancer conditions to gain the meaningful insights. Such approach is essential for advancing future research on calpain-2 and its role in prostate cancer.
  • Cleaning Verification in Pharmaceutical production — Direct measurement of Swab samples with FTIR
    (2024-12-30) Jäntti, Hermanni
     School of Chemical Engineering | Master's thesis
    Cleaning verification in pharmaceutical manufacturing is a crucial step in preventing cross-contamination and its potential adverse effects on patient safety. Cleaning methods go through a documented cleaning validation procedure to ensure they can achieve acceptable level of residue. Traditional cleaning validation methods such as swab sampling combined with time-consuming and environmentally unsustainable analyses like HPLC are widely used. Visual cleanliness is also used to verify cleaning results but due to its challenges and tightening regulation it may become insufficient in the future. The pharmaceutical industry urgently needs a rapid, sensitive and portable method for in situ cleaning verification. Handheld FTIR spectrometer presents a potential method for cleaning verification directly from production surface. Swab sampling remains essential for complex or irregular surfaces where direct FTIR measurement is impractical. This thesis explores the background of cleaning verification regulation and the role of swab sampling. It also explores the principles of FTIR spectroscopy and highlights its current applications in rapid spectroscopy analysis. The experimental work focuses on studying the suitability of various swab materials for measurement with a handheld FTIR spectrometer. Six swab types and five chemically different active pharmaceutical ingredients (APIs) were tested by dipping the swab in API solution and measuring directly with FTIR. The study assessed how the swab materials influenced the spectral background. Cotton swabs were proven as the most suitable for detecting API related absorption bands due to their minimal interference. Cotton swab was used to sample Ibuprofen residues from a stainless-steel surface. Ibuprofen related peaks were successfully detected at concentration as low as 0.4 𝜇𝑔/𝑐𝑚2. While further research and method development are necessary, the results of this thesis demonstrate the significant potential of cotton swabs in FTIR-based cleaning verification.