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Browsing by master's degree program "Materiaalitutkimuksen maisteriohjelma (Materials Research)"

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  • Flinck, Oliver (2022)
    In this thesis, sputtering of several low- and high-index tungsten surface crystal directions are investigated. The molecular dynamics study is conducted using the primary knock-on atom method, which allows for an equal energy deposition for all surface orientations. The energy is introduced into the system on two different depths, on the surface and on a depth of 1 nm. Additionally to the sputtering yield of each surface orientation, the underlying sputtering process is investigated. Amorphous target materials are often used to compare sputtering yields of polycrystalline materials with simulations. Therefore, an amorphous surface is also investigated to compare it's sputtering yield and process with crystalline surface orientations. When the primary knock-on atom was placed on the surface all surface orientations had a cosine shaped angular distribution with little variation in the sputtering yield for most of the surface orientations. Linear collision sequences were observed to have a large impact on the sputtering yield when the energy was introduced deeper inside the material. In these linear collision sequences the recoils are traveling along the most close packed atom rows in the material. The distance from the origin of the collision cascade to the surface in the direction of the most close packed row is therefore crucial for the sputtering yield of the surface. Surface directions with high angles between this direction and the surface normal hence show a reduction in the sputtering yield. The amorphous material had a little lower sputtering yield than the crystalline materials when the primary knock-on atoms was placed on the surface whereas the difference rose into several orders of magnitude when the energy was given at 1 nm. It is impossible for linear collision sequences to propagate long distances in the amorphous material and therefore the angular distribution in both cases is cosine shaped. The amorphous material has no long range order and was therefore unable to reproduce the linear collision sequences, which are characteristic for the crystalline materials. The difference in the sputtering yield was hence up to several orders of magnitude as a result when the energy was introduced at 1 nm depth.
  • Petrow, Pauliina (2022)
    Acuros XB -annoslaskentamalli on Varianin Eclipse-annossuunnitteluohjelmistoon kehitetty annoslaskenta-algoritmi, joka on tarkoitettu ulkoisen sädehoidon fotoniannoslaskentaan. Sen toiminta perustuu lineaaristen Boltzmannin siirtoyhtälöiden ratkaisemiseen. Acuros XB -algoritmi laskee annoksen kudoksessa, minkä johdosta se pystyy tuottamaan tarkan laskennan myös heterogeenisessa väliaineessa. Algoritmin laskentatarkkuus on verrattavissa Monte Carlo -menetelmän tarkkuuteen, mutta tarvittava laskenta-aika on lyhyempi. Tässä tutkimuksessa konfiguroitiin ja testattiin Acuros XB -algoritmi HUS Syöpäkeskuksen sädehoito-osaston lineaarikiihdyttimille. Lisäksi tutkittiin kahden mittalaitteen, OCTAVIUS Detector 1000 SRS -ionisaatiokammiomatriisin ja SRS MapCHECK -puolijohdeilmaisimen, toimintaa pienillä säteilykentillä eli 2cm x 2cm ja tätä pienemmillä säteilykentillä. Acuros XB -algoritmi konfiguroitiin optimoimalla kolmea parametria: fokuspisteen kokoa, moniliuskarajoittimen dosimetrista aukkoa ja moniliuskarajoittimen läpäisykerrointa. Parametrien optimointi tehtiin vertailemalla mitattuja ja Acuros XB -algoritmilla laskettuja annosjakaumia ja säteilykentän keskiakseliannoksia. Konfigurointiprosessissa huomioitiin erilaiset kenttäkoot ja annossuunnittelutekniikat tutkimalla erikokoisia staattisia säteilykenttiä sekä IMRT (Intensity-Modulated Radiation Therapy)-, VMAT (Volumetric Modulated Arc Therapy)- ja SRS (Stereotactic Radiosurgery)-tekniikoilla toteutettuja kenttäjärjestelyjä. Mittalaitteita vertailtiin tutkimalla kolmen pienen staattisen kentän, kolmen dynaamisen kaarikentän ja kolmen VMAT-tekniikalla toteutetun kenttäjärjestelyn tuottamia annosjakaumia. Acuros XB -algoritmin konfiguroinnin tuloksena HUS Syöpäkeskuksen sädehoito-osaston lineaarikiihdyttimille määritettiin fotonienergiakohtaiset arvot fokuspisteen koolle, moniliuskarajoittimen dosimetriselle aukolle ja moniliuskarajoittimen läpäisykertoimelle, ja algoritmi otettiin kliiniseen käyttöön. Mittalaitteiden vertailun tuloksena havaittiin, että SRS MapCHECK -puolijohdeilmaisin toimi pienillä säteilykentillä paremmin kuin OCTAVIUS Detector 1000 SRS -ionisaatiokammiomatriisi. Mittalaitteiden annosjakaumien analysointiohjelmat kuitenkin käsittelevät mittaustulokset eri tavoin, joten lisätutkimusta voidaan tarvita yksiselitteisen tuloksen saamiseksi.
  • Lasonen, Valtteri (2022)
    Modern semiconductor devices require sophisticated patterning techniques that not only offer excellent resolution but also high throughput, low cost, and low number of errors. And because these devices require several patterning steps, even a slight improvement in a patterning technique can have a huge impact. New patterning technique that has a great potential to be used in many of these patterning steps is area-selective etching of polymers by catalytic decomposition. The catalytic effect can either be an intrinsic property of the underlying material, or materials can be catalytically activated/deactivated to achieve the desired pattern. This new technique is self-aligning and extremely simple, and therefore has a potential to significantly reduce the number of errors and cost, while having excellent resolution and throughput. In the literature review part of this thesis, we will have an overview of different aspects that must be considered when using polymers as thermocatalytically decomposable resists. Polymers are already widely used as resists in several patterning techniques due to an immense number of different polymers available, allowing almost endless possibilities to adjust the properties of the resist. Important polymer properties to consider include adequate gas permeability for the etching gases and the decomposition products, decomposition and degradation mechanisms, reflow, integrity during the patterning and the deposition processes, and adhesion to the substrate. Different catalysts and catalytic decomposition mechanisms of polymers as well as other carbon-containing compounds in different atmospheres are reviewed. Because area-selective etching of polymers is a new technique many challenges are still unknown. Therefore, this thesis is mainly aimed to give ideas and directions for the future research. In the experimental part, several metals and metal oxides were tested for their catalytic effect for decomposing poly(methyl methacrylate) (PMMA) in air and H2-atmosphere. Pt, Ti, and CeO2 were confirmed to have a catalytic effect in air, whereas SiO2 and Al2O3 showed no catalytic effect. In the H2-atmosphere, only Ti and Cu showed some promising catalytic effect, whereas SiO2, Al2O3, CeO2, Pt, W, Ni, and Co did not. Additionally, experiments were conducted to find out how thin CeO2 film has an adequate catalytic effect. And finally, the area-selectivity of this patterning technique was tested in the air atmosphere using CeO2 as a catalytic surface and Al2O3 as a non-catalytic surface.
  • Ojala, Juha (2022)
    Photocatalysis is a versatile method to use solar energy for chemical processes. Photocatalytic materials absorb light to generate energetic electron-hole pairs that can be used for redox reactions in production of hydrogen and other chemicals, degradation of pollutants, and many other applications. BiVO4 is a visible light absorbing oxide semiconductor with a band gap of about 2.4 eV, and it has received a lot of attention as a standalone photocatalyst and as a photoanode material. The literature part of this thesis explores how the electronic structure of semiconductors and the different processes in photocatalysis together affect the efficiency of the method. Semiconductor materials are classified based on their chemical composition and compared by selecting most researched materials as examples. Various strategies to improve the photocatalyst material properties are also discussed. Many strategies, such as nanostructured photocatalysts, benefit from deposition of semiconductor thin films. Atomic layer deposition (ALD), as a highly conformal and controllable chemical vapor deposition method, is an excellent choice for depositing semiconductors and various interfacial layers. The literature review also includes a survey of ALD processes for Bi2O3 and V2O5 and a thorough analysis of the existing BiVO4 ALD processes. From the selection of binary ALD processes, bismuth(III) 2,3-dimethyl-2-butoxide (Bi(dmb)3), tetrakis(ethylmethylamido)-vanadium(IV) (TEMAV), and water were chosen as precursors to develop a new ALD process for BiVO4. The binary processes were combined in various metal precursor ratios both completely mixed in supercycles and as nanolaminates, and the resulting films were annealed to crystallize the BiVO4. X-ray diffraction was used to characterize the crystalline phases of the films, and it was noticed that TEMAV reacts with Bi2O3 to make metallic bismuth, but it is reoxidized by annealing. Composition of the films was investigated with energy dispersive X-ray spectrometry and time-of-flight elastic recoil detection analysis (ToF-ERDA). Some sensitivity to process conditions was observed in the deposition, as the metal stoichiometry varied in unexpected manner between some sets of experiments. ToF-ERDA depth profiles also revealed that mixing of the nanolaminate layers was incomplete with annealing temperatures below 450 °C and with laminate layers over 10 nm in thickness. Scanning electron microscopy was used to study the morphology of the films and revealed a granular, non-continuous structure. The optical properties of the films grown on soda-lime glass were investigated with UV-vis spectrophotometry. The band gaps of the films were estimated to be 2.4–2.5 eV. The nanolaminate approach to depositing the films was deemed the best, as it avoids most of the reduction of bismuth by TEMAV. However, it is still not clear why this process is so sensitive to process conditions. This should be investigated to further optimize the film stoichiometry. The morphology of the films might be improved by using different substrates, but it is not a critical aspect of the process as there are methods to passivate the exposed substrate surface. Overall, this process has potential to deposit excellent BiVO4 films that are suitable for further research pertaining their photocatalytic properties and modifications such as nanostructured or doped photoanodes.
  • De Meulder (2022)
    Amorphous metal oxides have proven to deform in a plastic manner at microscopic scale. In this study the plastic deformation and elastic properties of amorphous metal oxides are studied at microscopic scale using classical molecular dynamics simulations. Amorphous solids differ from crystalline solids by not having a regular lattice nor long range order. In this study the amorphous materials were created in simulations by melt-quenching. The glass transition temperature (Tg) depends on the material and cooling rate. The effect of cooling rate was studied with aluminiumoxide (Al2O3) by creating a simulation cell of 115 200 atoms and melt-quenching it with cooling rates of 1011 , 1012 and 1013 K/s. It was observed that faster cooling rates yield higher Tg. The Al2O3 was cooled to 300 K and 50 K after which the material was stretched. The stress-strain curve of the material showed that samples with higher Tg deforms in plastic manner with smaller stresses. The system stretched at 50 K had higher ultimate tensile strength than the system stretched at 300 K and thus confirming the hypothesis proposed by Frankberg about activating plastic flow with work. In order to see if the plastic phenomena can be generalized to other amorphous metal oxides the tensile simulation was performed also with a-Ga2O3 by creating a simulation cell of 105 000 atoms, melt-quenching it and then stretching. Due to the lack of parameters for Buckingham potential these parameters were fitted with GULP using the elastic properties and crystalline structure of Ga2O3. The elastic properties of Ga2O3 with the fitted potential parameters agreed very well with the literature values. The elongated a-Ga2O3 behaved in a very similar fashion compared to a-Al2O3 cooled with the same cooling rate. Further work is needed to establish the Buckingham potential parameters of a-Ga2O3 by experimen tal work. The potential can also be developed further by using the elastic constants and structures of amorphous a-Ga2O3 in the fitting process, although the potential shows already very promising results.
  • Koitermaa, Roni (2022)
    The complex physical mechanisms involved in the formation of vacuum arcs have been of interest for many decades. Vacuum arcs are relevant in many engineering disciplines, but the physics behind them is not yet fully understood. In recent years, there have been many experimental and computational studies focused on understanding aspects of vacuum arcs. This thesis focuses on further development of a simulation model to describe the physical processes starting from electron emission and leading to the formation of an ionized plasma. The FEMOCS code is extended to include plasma simulation based on previous work on ArcPIC. Emission of electrons and heating of the cathode is simulated using the finite element method, while plasma simulation is performed using the particle-in-cell method. We add evaporation of neutral atoms from the cathode, as well as ionization processes for multiple species of ions. Monte Carlo collisions for elastic, Coulomb, impact ionization, charge exchange and recombination collisions between particles are added. Direct field ionization of neutrals is included to account for ionization at high electric fields. A dynamic weighting scheme is described for adjusting superparticle weights during the simulation. Ion bombardment effects such as bombardment heating and sputtering are added to account for additional supply of neutrals resulting from energetic ions accelerated by the electric field. Finally, we add a circuit model for coupling to an external circuit. A static nanotip is simulated with different parameters to study local field thresholds leading to thermal runaway. We find that our simulations agree with experimental results. The most significant interactions contributing to initial formation of vacuum arcs are identified. We find most neutrals are created via evaporation rather than sputtering. The most important collision for plasma formation is impact ionization of neutrals into Cu+ ions, while higher-order ions are found to play a lesser role. Direct field ionization of neutrals is also found to be significant at high fields on the order of 10 GV/m.
  • Halkoaho, Johannes (2022)
    MRS or magnetic resonance spectroscopy is an imagining technique which can be used to gain information about the metabolite concentration within a certain volume of interest. This can be used for example in brain imagining. The brain consists of three main types of tissue: cerebrospinal fluid, white and gray matter. It is important to know the different volume fractions of these tissues as the resolution in MRS is significantly lower than that of magnetic resonance imagining (MRI). The tissues all have different metabolite profiles and in order to get meaningful data the volume fractions need to be taken into account. This information can be gained from the segmentation of an image formed by using MRI. In this work a software tool was created to find these volume fractions with the input of a .rda file that is created by the scanner and Nifti file. The Nifti file is the image formed by using MRI and the .rda file is the manufacturers raw data format for spectroscopy data which has the relevant information about the volumes of interest. The software tool was created using Python and JavaScript programming languages and different functions of FSL. FSL is a comprehensive library of analysis tools used in brain imaging data processing. The steps for the software tool are: determining the coordinates of the volume of interest in FSL voxel coordinates, creating a mask in the correct orientation and location, removing non-brain tissue from the image using FSL’s tool tailored for that purpose (BET), segmenting the image using FSL’s segmenting tool (FAST), registering the mask on the segmented images and calculating the volume fractions. The software tool was tested on imaging data that was obtained at Meilahti Kolmiosairaala for the purpose of the testing. The testing data set included five different spectroscopy volumes from different parts of the brain and a T1 weighted image. The software tool was given the relevant information about the volume of interest in the form of a .rda file and the T1 weighted image in the form of a Nifti file. The software tool then determined the different volume fractions from all of the five volumes of interest. There is variation on the volume fraction of different brain areas within different brains and it is not possible to have an absolute reference value. The results of the test corresponded to the possible volume fractions that can be expected from the volumes in question.
  • Mäkelä, Ville (2022)
    With their ability to convert chemical energy to electrical energy through electrochemical reactions, rechargeable batteries are widely used to store energy in various applications such as electronic mobile equipment, aerospace aviation, road transportation, power grid, and national defense industry Numerous battery types are available commercially. Lithium ion-based batteries stand out due to several key advantages such as high operating voltage, high specific energy, and long cycle life. They also have a market dominance in a wide range of electric vehicles. However, like all battery technologies, lithium ion-based ones suffer from the effects of aging-induced degradation which can lead to reduced capacity, lifetime, and in some cases even safety hazards. One method of preventing/slowing down these aging reactions is to modify the standard battery materials by using dopants and additives. They are specific impurities purposely introduced into the battery during the manufacturing process. In this master’s thesis, the effect of additives (Mg/Al) on the aging of Li-ion cells was examined by using X-ray absorption spectroscopy, more specifically x-ray absorption near edge structure (XANES). For the experiment, 7 different cells, all containing lithium cobalt oxide as the major component (with 4 having a stoichiometric ration of Li/Co, and 3 being Li-rich), with 5 of them containing Mg/Al as dopants, and 2 containing no dopants were examined using XANES as a function of aging in terms of charge/discharge cycles. The dopants were introduced at different stages of the material preparation, either at the lithiation step or at the synthesis of the precursor. This thesis focuses on the XANES experiment and the data analysis, with extensive literature review on the topic of using additives and dopants. The cells were prepared by the Aalto University. The results showed that of the cells with dopant materials, the cells doped during lithiation stage aged slightly better after cycling than the undoped ones, whereas the cells doped during precursor stage aged worse than the undoped cells. This would suggest that doping might be more effective when done during the lithiation stage.
  • Mäntysaari, Matti (2021)
    This thesis describes the data and data analysis concerning Compton scattering experiments to obtain the Compton profiles of metallic sodium (Na) as a function of temperature. The temperatures used in the experiment were 6 K and 300 K. The purpose of the work was to visualize the effect of temperature in the electron momentum density in a free electron gas. The effects of temperature were expected to be manifested through changes to the Fermi momentum according to the free-electron theory, but also more subtle changes could have been possible owing to possible deviations from the free electron theory. The measurements were done at the European Synchrotron Radiation Facility (Grenoble, France) beamline ID20. The data was analyzed with a help of a program written with Matlab, and it converted the measured Compton spectra from photon energy space to electron momentum space, while applying self-absorption corrections to the data, subtracting background, and normalizing the data using trapezoidal numerical integral to yield final Compton profiles. Results were obtained as valence Compton profiles and their differences between 300 K and 6 K, and compared with the prediction from free-electron gas theory. The Compton profiles followed the predictions of the free-electron gas theory well, although the theoretical profiles had a higher amplitude than the measured profiles. This is a commonly found phenomenon in Compton spectroscopy and assigned to originate from electron-electron correlations. The effect of the temperature in the Compton profiles is in good agreement with the free-electron theory.
  • Tommiska, Oskari (2021)
    Työssäni tutkin mahdollisuutta käyttää akustista ajankääntömenetelmää (time-reversal) teollisen ultraäänipuhdistimen puhdistustehon kohdentamiseen. Akustisella ajankääntömenetelmällä pystytään kohdistamaan painekenttä takaisin alkuperäiseen pisteeseen, tallentamalla ko. pisteestä lähetetyt painesignaalit akustisilla antureilla (etusuunta) ja lähettämällä ne takaisin ajassa käännettyinä (takasuunta). Tässä työssä tutkitun kohdentamismenetelmän perusteena toimii elementtimenetelmällä toteutettu simulaatiomalli, jossa sekä ultraäänipuhdistin, että puhdistettava järjestelmä oli mallinnettu tarkasti. Simulaatiomallin avulla voitiin puhdistettavasta alueesta valita mielivaltainen piste johon halutaan kohdentaa puhdistustehoa. Simuloidun etusuuntaisen ajon tuloksena tuotetut signaalit tuotiin ulos mallista ja takasuuntainen ajo suoritettiin kokeellisessa ympäristössä käyttäen simuloituja signaaleja. Työssä esitetään vertailu simuloidun ja kokeellisen ajankääntömenetelmään perustuvan kohdentamisen tuloksista ja osoitetaan, että simuloiduilla signaaleilla on mahdollista kohdentaa akustista tehoa ennalta valittuun mielivaltaiseen pisteeseen. Lisäksi työssä esitetään analyysi anturien määrän vaikutuksesta kohdentamiskykyyn, tarkastellaan ultraäänipuhdistimen avaruudellista kohdentamiskykyä sekä vahvistetaan simulaatioissa tehdyn lineaarisen oletuksen paikkansapitävyys.
  • Mäkinen, Joni (2022)
    Nonlinear acoustic and electric effects for the purposes of fluid and fluid-fluid interface manipulation find many applications in the literature. Some examples include: electrospinning, electrospraying, ultrasonic sonoreactors, acoustic drop sampling and microfluidic particle manipulation via acoustic streaming. Ultrasound-enhanced electrospinning (USES) is one application in which both an acoustic and an electric field deform the surface of an aqueous polymer solution in order to achieve electrospinning of nanofibers. In this thesis, the nonlinear physics involved in USES are reviewed and applied to a finite element method based model of the system. This work builds on my previous publication on acoustic fountain formation and subsequent electrostatic deformation of a liquid-air interface in USES by also considering the effects of acoustic streaming. Results for acoustic streaming near a liquid-air interface in a case where the acoustic field is also focused around the interface are studied with simulations and compared against experiments. The results display an intricate balance of the shape and strength of the acoustic streaming field as the liquid-air interface simultaneously deforms. This even leads to situations where the streaming field could completely change direction. Finally, simulation predictions for acoustic streaming, fountain formation and electrostatic deformation of liquid-air interface in the USES set-up in its standard configuration are given. This simulation predicts a very weak acoustic streaming field and a smaller contribution from the electric field, compared to the acoustic field, on the interface forces. This implies that in the simulated configuration, the electric field serves more as force to pull the acoustic fountain a bit more in order for the acoustic field to find its new balance and exert an even stronger force than it was able to by itself. The simulation also indicates that for the robust and reproducible operation of USES, and possibly for the resulting nanofibers, one needs to have precise control of the process parameters, acoustic field and surface level, due to the complex nature of the fountain formation.
  • Paajanen, Santeri (2022)
    NMDA receptors are ionotropic glutamate receptors (iGluRs), tetrameric proteins, mediating synaptic transmission in the brain and the whole nervous system. Together with another type of iGluRs, AMPA receptors, they are considered essential for neuronal plasticity and memory. Understanding their dynamics and different kinetics is vital for studying various neurological diseases. The relatively slow dynamics, where the time scales of related processes range up to hundreds of milliseconds, make studying them with Molecular Dynamics (MD) simulations challenging. We developed the Functional Sampling Tool (FST), a novel method for enhancing the sampling of a function of interest. Compared to existing enhanced sampling schemes it strikes a balance between generality and simplicity, minimising the need of user input, while allowing for maximal customisability. Using FST, we studied two processes of the NMDA receptor. By keeping all four ligands bound we simulated a desensitisation pathway, and by removing all four we simulated an inactivation pathway. The tool sampled both, giving a good distribution between open and closed states. The tool also allowed us to change the function in the middle of sampling. With the new function we were able to produce more data, focusing on a certain value range.
  • Heikkilä, Jesse (2022)
    Nanoformation of an active pharmaceutical ingredient (API) in controlled expansion of supercritical solution (CESS®) was studied in situ with a schlieren imaging technique in wide range of pre-expansion and expansion conditions, involving pressures up to 1000 bars. The optical methods allowed measurements on solvent state in the first micro and milliseconds of the expansion. Quantitative values on jet shape and solvent thermodynamic state were obtained for different nozzle configurations. These values, combined with mathematical modelling, enabled tracking the nanoparticle formation along the flow. We also report on the importance of solvent phase behavior demonstrated by three fundamentally different expansion schemes: supercritical (SC) to liquid/gas, SC to gas/liquid, and SC to SC. Scanning electron microscope images of the nanosized API are presented. This shows that one can have controlled particle formation by altering the thermodynamic conditions at the nozzle and changing the expansion path. The results guide the in-house process optimization and offer insight into the physics of supercritical fluid processing.
  • Dursun, Sahin (2021)
    This thesis focuses on the initial measurements and development of a 1.5K target temperature cryostat to contain all quantum standards in the quantum metrological triangle. Currently, the cryostat can reach 4.2K end temperature with a cryocooler to liquefy helium for cooling experiments related to the quantum standards of SI-units which require 1.5K end temperature and the 1.5K cooling circuit is one of the research questions of the thesis for future development of the cryostat. Measurements included cooling cycles in a helium environment for liquefaction, as well as no load conditions. Results of the experimentation conclude that liquefaction was unsuccessful at this stage, but could be achieved with improved temperature control. The thesis is based on experimental work carried out in VTT technical research center of Finland, during the course of which the cryostat was progressively developed towards the future utility of combining experiments that realize the quantum standards of Ampere, voltage and resistance under a single low temperature experimental platform, the unified quantum standard cryostat.
  • Papponen, Joni (2022)
    Imaging done with conventional microscopes is diffraction-limited, which sets a lower limit to the resolution. Features smaller than the resolution cannot be distinguished in images. This limit of the diffraction-limit can be overcome with different setups, such as with imaging through a dielectric microcylinder. With this setup it is possible to reach smaller resolution than with a diffraction-limited system, which is called super-resolution. Propagation of light can be modelled with various simulation methods, such as finite-difference time-domain and ray tracing methods. Finitedifference time-domain method simulates the light as waves which is useful for modelling the propagation of light accurately and take into account the interactions between different waves. Ray tracing method simulates the light as rays which requires approximations to the light’s behaviour. This means that some phenomena cannot be taken into account, which can affect the accuracy of the results. In this thesis the model for simulating super-resolution imaging with microcylinder is studied. The model utilizes the finite-difference timedomain method for modelling the near-field effects of the light propagating through the microcylinder and reflecting back from a sample. The reflected light is recorded on the simulation domain boundaries and a near-field-to-far-field transformation is performed to obtain the far-field corresponding to the recorded fields. The far-field is backward propagated to focus a virtual image of the sample, and the virtual image is then used in ray tracing simulation as a light source to focus it to a real image on a detector.
  • Djurabekova, Amina (2022)
    Energy is an essential input for any non-spontaneous mechanism. In biological organisms, the process of producing energy currency, adenosine triphosphate, is called cellular respiration. It is made of three smaller steps, out of which the last one is oxidative phosphorylation that is responsible for the largest production of adenosine triphosphate molecules in the whole process. Oxidative phosphorylation is performed by the electron transport chain made of five protein complexes, named respiratory complex I-V. Complex I is the first and largest protein complex in the electron transport chain, and it is the least understood. Its primary function is to transfer electrons from nicotinamide adenine dinucleotide to ubiquinone, which is coupled to the pumping of four protons across the mitochondrial inner membrane. Although the overall reaction of complex I is understood, the intricate detail of the mechanism is still largely unknown. There is significance in the details because there are numerous point mutations, which have been strongly correlated with neurogenerative diseases, such as Leigh’s syndrome, and aging. Therefore, a more thorough understanding of its mechanism can give insight into potential target drug development. Complex I is made of 14 highly conserved subunits that can be found in most species that use the electron transport chain. They create an L-shape, where seven subunits are embedded in the inner membrane, the membrane domain, and the others are floating in the mitochondrial matrix, the peripheral arm. In mitochondrial complex I, however, there are in addition around 30 accessory subunits. It has been previously thought that the main mechanism is conducted by the 14 subunits that are found in all species. However, in the past couple of years, it has been shown that accessory subunits can play an important role in the mechanism of mitochondrial complex I. The work presented in this thesis uses a multiscale computational approach to study the effect of three mutations, F89A, Y43A and L42A, from an accessory subunit LYRM6 on the function of complex I. Previous experiments demonstrated that the mutations decreased the overall activity of complex I by 76-86 %. The LYRM6 subunit is located at the pivot of the membrane and periplasmic domains. The results of this study show that the point mutations have a long-range effect on the conformations of three loops from three conserved subunits in this region. The shift in the loop dynamics causes a drop in water occupancy. The observed water pathway is tested for the capability of proton transfer. The findings are demonstrated with the help of molecular dynamics and quantum mechanics/molecular mechanics simulations.
  • Mikkola, Kalle (2022)
    This thesis examines the optical response of tuneable chiral plasmonic nanostructures in linear cross-polarization. Plasmonic gold-silver nanostructures composed of silver-coated gold nanorods, and dynamic DNA origami are investigated because of their optical properties of interest in the visible light wavelength region, and because of their controllable rotational asymmetry, which results in tuneable chirality in dimer structures. These plasmonic nanostructures present optical properties such as circular dichroism and optical rotatory dispersion. In this thesis we establish the relationship between perceived color, spectrometry, circular dichroism and optical rotatory dispersion of the samples, depending on the chiral geometry of the nanostructures within. The motivation is to predict perceived color from the chiral geometry of the nanostructures, which will enable visual detection for biosensing applications. Circular dichroism and optical rotatory dispersion give us detailed knowledge about the polarization state of a sample, but visible light detection and spectrometer measurements are more accessible and portable methods for characterizing the polarization state of a sample. We achieve color modulation from green to blue with the switching of chiral geometry, under cross-polarized white light. This has potential for biosensing applications, based on the perceived color change depending on the chiral geometry of the sample. The DNA origami structures react to the presence of an analyte by changing their chiral geometry. Possible applications in biosensing of analytes can be made more practical if the orientation of the DNA origami template can be determined from the perceived color or the transmission spectra, rather than from the less accessible circular dichroism or optical rotatory dispersion measurements.
  • Lehtinen, Miko (2022)
    Molecular hydrogen is considered as the primary alternative to replace fossil fuels for future energy supply. Hydrogen can be produced sustainably through electrocatalytic hydrogen evolution reaction which is a vital step in water electrolysis. So far, the efficiencies of electrochemical and photoelectrochemical water electrolysis systems are too low to satisfy the demands for hydrogen on a commercial scale. Plasmonic nanostructures containing a plasmonic and a catalytic component hold great promise for enhancing the performance of typical water electrolysis systems through plasmonic photocatalysis utilizing localized surface plasmon resonance excitation. Here, a novel plasmonic-catalytic u@AgPd nanorattle is synthesized, characterized, and investigated for plasmon-enhanced hydrogen evolution reaction to provide new insights into the design of light-assisted water electrolysis systems. The nanorattle exhibited significant improvements of performance towards hydrogen evolution reaction under 427 nm illumination, displaying a near 2-fold current increase and a decreased overpotential of 58 mV at a current density of 10 mAcm-2. The material is evidenced to plasmon-enhance the electrocatalytic performance through a combination of charge transfer and local heating mechanisms.
  • Kinnunen, Moonika (2022)
    In this project, poly(2-methyl-2-oxazoline)-block-poly(2-n-butyl-2-oxazine)-block-poly(2-methyl-2- oxazoline) (PMeOx-b-PnBuOzi-b-PMeOx) and poly(2-methyl-2-oxazoline)-block-poly(2-n-propyl-2- oxazine) (PMeOx-b-PnPrOzi) with block lengths of 35-20-35 and 100-100, respectively, were synthesized. When dispersed in water these thermoresponsive polymers aggregate into micellar aggregates or form hydrogels. Polymers were characterized with 1H-NMR, GPC, and DLS. Age-related macular edema and diabetic macular edema are the most common reasons for blindness in industrialized countries. The triamcinolone acetonide, a corticosteroid used to treat both of these macular edemas, was loaded into the polymeric micelles or hydrogel of synthesized polymers using the thin film method. The loading efficiency for a triblock copolymer ((PMeOx35-b-PnBuOzi20- b-PMeOx35) polymeric micelles was 4 % at the polymer/drug ratio of 10/4 and for a hydrogel (PMeOx100-b-PnPrOzi100) it was 48 % with the same polymer/drug ratio. The properties of the PMeOx100-b-PnPrOzi100 hydrogel formulations with the drug were studied with rheological measurements, DSC, DLS, and GPC of formulations. The formulation showed storage modulus of 3 kPa and the gelation temperature at 16 °C. From the DSC two glass transition temperatures were obtained, Tg1 at around 12 °C and Tg2 at around 74 °C. The particle size distribution of the formulation obtained with DLS showed that there were assumingly micelles or vesicles with a hydrodynamic radius between 20 and 80 nm. The drug release from the hydrogel formulation was studied with the dialysis membrane method and all the drug was released within 24 hours. Both copolymers formed quite unstable formulations with the drug. The results from this study gives information how polyoxazoline- and polyoxazine-based materials can be used to encapsulate and release corticosteroids, such as triamcinolone acetonide. To increase the drug loading capacity and to stabilize formulations, some surfactants for the drug could be tested in the future.
  • Lassila, Petri (2021)
    Lipid-based solid-fat substitutes (such as oleogels) structurally modified using ultrasonic standing waves (USW), have recently been shown to potentially increase oleogel storage-stability. To enable their potential application in food products, pharmaceuticals, and cosmetics, practical and economical production methods are needed compared to previous work, where USW treated oleogel production was limited to 50-500 µL. The purpose of this work is to improve upon the previous procedure of producing structurally modified oleogels via the use of USW by developing a scaled up and convenient approach. To this aim, three different USW chamber prototypes were designed and developed, with common features in mind to: (i) increase process volumes to 10-100 mL, (ii) make the sample extractable from the treatment chamber, (iii) avoid contact between the sample and the ultrasonic transducer. Imaging of the internal structure of USW treated oleogels was used as the determining factor of successful chamber design. The best design was subsequently used to produce USW treated oleogels, of which the bulk mechanical properties were studied using uniaxial compression tests, along with local mechanical properties, investigated using scanning acoustic microscopy. Results elucidated the mechanical behaviour of oleogels as foam-like. Finally, the stability of treated oleogels was compared to control samples using an automated image analysis oil release test. This work enables the effective mechanical-structural manipulation of oleogels in volumes of 10-100 mL, paving the way to possible large-scale lipid-based materials USW treatments.