Computational chemistry studies of wood-derived lignans

This thesis is based on computational chemistry studies on lignans, focusing on the naturally occurring lignan hydroxymatairesinol (HMR) (Papers I II) and on TADDOL-like conidendrin-based chiral 1,4-diol ligands (LIGNOLs) (Papers III V). A complete quantum chemical conformational analysis on HMR was previously conducted by Dr. Antti Taskinen. In the works reported in this thesis, HMR was further studied by classical molecular dynamics (MD) simulations in aqueous solution including torsional angle analysis, quantum chemical solvation e ect study by the COnductorlike Screening MOdel (COSMO), and hydrogen bond analysis (Paper I), as well as from a catalytic point of view including protonation and deprotonation studies at di erent levels of theory (Paper II). The computational LIGNOL studies in this thesis constitute a multi-level deterministic structural optimization of the following molecules: 1,1-diphenyl (2Ph), two diastereomers of 1,1,4-triphenyl (3PhR, 3PhS), 1,1,4,4-tetraphenyl (4Ph) and 1,1,4,4-tetramethyl (4Met) 1,4-diol (Paper IV) and a conformational solvation study applying MD and COSMO (Paper V). Furthermore, a computational study on hemiketals in connection with problems in the experimental work by Docent Patrik Eklund's group synthesizing the LIGNOLs based on natural products starting from HMR, is shortly described (Paper III).

Feasibility studies of the weldability of structural steels used in the offshore environment

The rising demand for oil and gas has made it very necessary for the oil and gas industries to explore the offshore. There is a huge resources which is available in the offshore. The search for oil and gas is faced with greater challenges because of the nature of the marine environment as it poses difficult and harsh conditions for the construction of offshore structures. The major problem of the construction of offshore structure is the ability to produce a sound weld that gives the whole structure the structural integrity needed to withstand the harsh environmental conditions. This research work presents the performance of typical offshore steels with improved weldability. The ability of reducing the carbon content of thermo-mechanically rolled steels down to 0.08% makes it possible to achieve good weldability, toughness and strength for high strength steels used in offshore applications. Importantly, the ideal welding procedure should be strictly followed as recommended. The fabrication process is as important as the welding procedure in achieving a sound weld which is free of weld defects such as hydrogen induced cracking, lamellar tearing and solidification cracking. This research work also considers the corrosion as it affects offshore structure and necessary measures to mitigate the problem caused by corrosion.

Studies of Solar Activity with Emphasis on Quasi-Periodic Oscillations

In this thesis mainly long quasi-periodic solar oscillations in various solar atmospheric structures are discussed, based on data obtained at several wavelengths, focussing, however, mainly on radio frequencies. Sunspot (Articles II and III) and quiet Sun area (QSA) (Article I) oscillations are investigated along with quasi-periodic pulsations (QPP) in a flaring event with wide-range radio spectra (Article IV). Various oscillation periods are detected; 3–15, 35–70 and 90 minutes (QSA), 10-60 and 80-130 minutes (in sunspots at various radio frequencies), 3-5, 10-23, 220-240, 340 and 470 minutes (in sunspots at photosphere) and 8-12 and 15-17 seconds (in a solar flare at radio frequencies). Some of the oscillation periods are detected for the first time, while some of them have been confirmed earlier by other research groups. Solar oscillations can provide more information on the nature of various solar structures. This thesis presents the physical mechanisms of some solar structure oscillations. Two different theoretical approaches are chosen; magnetohydrodynamics (MHD) and the shallow sunspot model. These two theories can explain a wide range of solar oscillations from a few seconds up to some hours. Various wave modes in loop structures cause solar oscillations (<45 minutes) both in sunspots and quiet Sun areas. Periods lasting more than 45 minutes in the sunspots (and a fraction of the shorter periods) are related to sunspot oscillations as a whole. Sometimes similar oscillation periods are detected both in sunspot area variations and respectively in magnetic field strength changes. This result supports a concept that these oscillations are related to sunspot oscillations as a whole. In addition, a theory behind QPPs at radio frequencies in solar flares is presented. The thesis also covers solar instrumentation and data sources. Additionally, the data processing methods are presented. As the majority of the investigations in this thesis focus on radio frequencies, also the most typical radio emission mechanisms are presented. The main structures of the Sun, which are related to solar oscillations, are also presented. Two separate projects are included in this thesis. Solar cyclicity is studied using the extensively large solar radio map archieve from Metsähovi Radio Observatory (MRO) at 37 GHz, between 1978 and 2011 (Article V) covering two full solar cycles. Also, some new solar instrumentation (Article VI) was developed during this thesis.

Circular Spectropolarimetric Studies of DQ White Dwarfs

This thesis summarizes studies of a class of white dwarfs (WDs) called DQ WDs. White dwarfs are the remnants of ordinary stars like our Sun that have run out of nuclear fuel. WDs are classified according to the composition of their atmosphere and DQ WDs have an atmosphere made of helium and carbon. The carbon comes in either atomic or molecular form and in some cases the strong spectral absorption features cover the entire optical wavelength region. The research presented here utilizes spectropolarimetry, which is an observational technique that combines spectroscopy and polarization. Separately these allow to study the composition of a target and the inhomogeneous distribution of matter in the target. Put together they form a powerful tool to probe the physical properties in the atmosphere of a star. It is espacially good for detecting magnetic fields. The papers in this thesis describe efforts to do a survey of DQ white dwarfs with spectropolarimetry in order to search for magnetic fields in them. Paper I describes the discovery of a new magnetic cool DQ white dwarf, GJ841B. Initial modeling of molecular features on DQ WDs showed inconsistencies with observations. The first possible solution to this problem was stellar spots on these WDs. To investigate the matter, two DQ WDs were monitored for photometric variability that could arise from the presence of such spots. Paper II summarizes this short campaign and reports the negative results. Paper III reports observations of the rest of the objects in our survey. The paper includes the discovery of polarization from another cool DQ white dwarf, bringing the total of known magnetic cool DQs to three. Unfortunately the model used in this thesis cannot, in its present state, be used to model these objects nor are the observations of high enough spectroscopic resolution to do so.

Unidirectional fiber-reinforced composite as an oral implant abutment material: Experimental studies of E-glass fiber/BisGMA-TEGDMA polymer in vitro

Fiber-reinforced composites (FRCs) are a new group of non-metallic biomaterials showing a growing popularity in many dental and medical applications. As an oral implant material, FRC is biocompatible in bone tissue environment. Soft tissue integration to FRC polymer material is unclear. This series of in vitro studies aimed at evaluating unidirectional E-glass FRC polymer in terms of mechanical, chemical, and biological properties in an attempt to develop a new non-metallic oral implant abutment alternative. Two different types of substrates were investigated: (a) Plain polymer (BisGMA 50%–TEGDMA 50%) and (b) Unidirectional FRC. The mechanical behavior of high fiber-density FRCs was assessed using a three-point bending test. Surface characterization was performed using scanning electron and spinning disk confocal microscopes. The surface wettability/energy was determined using sessile drop method. The blood response, including blood-clotting ability and platelet morphology was evaluated. Human gingival fibroblast cell responses - adhesion kinetics, adhesion strength, and proliferation activity - were studied in cell culture environment using routine test conditions. A novel tissue culture method was developed and used to evaluate porcine gingival tissue graft attachment and growth on the experimental composite implants. The analysis of the mechanical properties showed that there is a direct proportionality in the relationship between E-glass fiber volume fraction and toughness, modulus of elasticity, and load bearing capacity; however, flexural strength did not show significant improvement when high fiber-density FRC is used. FRCs showed moderate hydrophilic properties owing to the presence of exposed glass fibers on the polymer surface. Blood-clotting time was shorter on FRC substrates than on plain polymer. The FRC substrates also showed higher platelet activation state than plain polymer substrates. Fibroblast cell adhesion strength and proliferation rate were highly pronounced on FRCs. A tissue culture study revealed that gingival epithelium and connective tissue established an immediate close contact with both plain polymer and FRC implants. However, FRC seemed to guide epithelial migration outwards from the tissue/implant interface. Due to the anisotropic and hydrophilic nature of FRC, it can be concluded that this material enhances biological events related with soft tissue integration on oral implant surface.

Spectroscopic Studies of III-V Semiconductor Materials for Improved Devices

Defects in semiconductor crystals and at their interfaces usually impair the properties and the performance of devices. These defects include, for example, vacancies (i.e., missing crystal atoms), interstitials (i.e., extra atoms between the host crystal sites), and impurities such as oxygen atoms. The defects can decrease (i) the rate of the radiative electron transition from the conduction band to the valence band, (ii) the amount of charge carriers, and (iii) the mobility of the electrons in the conduction band. It is a common situation that the presence of crystal defects can be readily concluded as a decrease in the luminescence intensity or in the current flow for example. However, the identification of the harmful defects is not straightforward at all because it is challenging to characterize local defects with atomic resolution and identification. Such atomic-scale knowledge is however essential to find methods for reducing the amount of defects in energy-efficient semiconductor devices. The defects formed in thin interface layers of semiconductors are particularly difficult to characterize due to their buried and amorphous structures. Characterization methods which are sensitive to defects often require well-defined samples with long range order. Photoelectron spectroscopy (PES) combined with photoluminescence (PL) or electrical measurements is a potential approach to elucidate the structure and defects of the interface. It is essential to combine the PES with complementary measurements of similar samples to relate the PES changes to changes in the interface defect density. Understanding of the nature of defects related to III-V materials is relevant to developing for example field-effect transistors which include a III-V channel, but research is still far from complete. In this thesis, PES measurements are utilized in studies of various III-V compound semiconductor materials. PES is combined with photoluminescence measurements to study the SiO2/GaAs, SiNx/GaAs and BaO/GaAs interfaces. Also the formation of novel materials InN and photoluminescent GaAs nanoparticles are studied. Finally, the formation of Ga interstitial defects in GaAsN is elucidated by combining calculational results with PES measurements.

Surface studies of limestones and dolostones : characterisation using various techniques and batch dissolution experiments with hydrochloric acid solutions

In this thesis, stepwise titration with hydrochloric acid was used to obtain chemical reactivities and dissolution rates of ground limestones and dolostones of varying geological backgrounds (sedimentary, metamorphic or magmatic). Two different ways of conducting the calculations were used: 1) a first order mathematical model was used to calculate extrapolated initial reactivities (and dissolution rates) at pH 4, and 2) a second order mathematical model was used to acquire integrated mean specific chemical reaction constants (and dissolution rates) at pH 5. The calculations of the reactivities and dissolution rates were based on rate of change of pH and particle size distributions of the sample powders obtained by laser diffraction. The initial dissolution rates at pH 4 were repeatedly higher than previously reported literature values, whereas the dissolution rates at pH 5 were consistent with former observations. Reactivities and dissolution rates varied substantially for dolostones, whereas for limestones and calcareous rocks, the variation can be primarily explained by relatively large sample standard deviations. A list of the dolostone samples in a decreasing order of initial reactivity at pH 4 is: 1) metamorphic dolostones with calcite/dolomite ratio higher than about 6% 2) sedimentary dolostones without calcite 3) metamorphic dolostones with calcite/dolomite ratio lower than about 6% The reactivities and dissolution rates were accompanied by a wide range of experimental techniques to characterise the samples, to reveal how different rocks changed during the dissolution process, and to find out which factors had an influence on their chemical reactivities. An emphasis was put on chemical and morphological changes taking place at the surfaces of the particles via X-ray Photoelectron Spectroscopy (XPS) and Scanning Electron Microscopy (SEM). Supporting chemical information was obtained with X-Ray Fluorescence (XRF) measurements of the samples, and Inductively Coupled Plasma-Mass Spectrometry (ICP-MS) and Inductively Coupled Plasma-Optical Emission Spectrometry (ICP-OES) measurements of the solutions used in the reactivity experiments. Information on mineral (modal) compositions and their occurrence was provided by X-Ray Diffraction (XRD), Energy Dispersive X-ray analysis (EDX) and studying thin sections with a petrographic microscope. BET (Brunauer, Emmet, Teller) surface areas were determined from nitrogen physisorption data. Factors increasing chemical reactivity of dolostones and calcareous rocks were found to be sedimentary origin, higher calcite concentration and smaller quartz concentration. Also, it is assumed that finer grain size and larger BET surface areas increase the reactivity although no certain correlation was found in this thesis. Atomic concentrations did not correlate with the reactivities. Sedimentary dolostones, unlike metamorphic ones, were found to have porous surface structures after dissolution. In addition, conventional (XPS) and synchrotron based (HRXPS) X-ray Photoelectron Spectroscopy were used to study bonding environments on calcite and dolomite surfaces. Both samples are insulators, which is why neutralisation measures such as electron flood gun and a conductive mask were used. Surface core level shifts of 0.7 ± 0.1 eV for Ca 2p spectrum of calcite and 0.75 ± 0.05 eV for Mg 2p and Ca 3s spectra of dolomite were obtained. Some satellite features of Ca 2p, C 1s and O 1s spectra have been suggested to be bulk plasmons. The origin of carbide bonds was suggested to be beam assisted interaction with hydrocarbons found on the surface. The results presented in this thesis are of particular importance for choosing raw materials for wet Flue Gas Desulphurisation (FGD) and construction industry. Wet FGD benefits from high reactivity, whereas construction industry can take advantage of slow reactivity of carbonate rocks often used in the facades of fine buildings. Information on chemical bonding environments may help to create more accurate models for water-rock interactions of carbonates.

Numerical Studies of Dark Energy Models and Observations

The cosmological standard view is based on the assumptions of homogeneity, isotropy and general relativistic gravitational interaction. These alone are not sufficient for describing the current cosmological observations of accelerated expansion of space. Although general relativity is extremely accurately tested to describe the local gravitational phenomena, there is a strong demand for modifying either the energy content of the universe or the gravitational interaction itself to account for the accelerated expansion. By adding a non-luminous matter component and a constant energy component with negative pressure, the observations can be explained with general relativity. Gravitation, cosmological models and their observational phenomenology are discussed in this thesis. Several classes of dark energy models that are motivated by theories outside the standard formulation of physics were studied with emphasis on the observational interpretation. All the cosmological models that seek to explain the cosmological observations, must also conform to the local phenomena. This poses stringent conditions for the physically viable cosmological models. Predictions from a supergravity quintessence model was compared to Supernova 1a data and several metric gravity models were studied with local experimental results. Polytropic stellar configurations of solar, white dwarf and neutron stars were numerically studied with modified gravity models. The main interest was to study the spacetime around the stars. The results shed light on the viability of the studied cosmological models.

Computational studies of deformation in stainless steel rings due to torch heating

A support ring of AISI 304L stainless steel that holds vertical, parallel wires arranged in a circle forming a cylinder is studied. The wires are attached to the ring with heat-induced shrinkage. When the ring is heated with a torch the heat affected zone tries to expand while the adjacent cool structure obstructs the expansion causing upsetting. During cooling, the ring shrinks smaller than its original size clamping the wires. The most important requirement for the ring is that it should be as round as possible and the deformations should occur as overall shrinkage in the ring diameter. A three-dimensional nonlinear transient sequential thermo-structural Abaqus model is used together with a Fortran code that enters the heat flux to each affected element. The local and overall deformations in one ring inflicted by the heating are studied with a small amount of inspection on residual stresses. A variety of different cases are chosen to be studied with the model constructed to provide directional knowledge; torch flux with the means of speed, location of the wires, heating location and structural factors. The decrease of heating speed increases heat flux that rises the temperature increasing shrinkage. In a single progressive heating uneven distribution of shrinkage appears to the start/end region that can be partially fixed with using speeded heating’s to strengthen the heating of that region. Location of the wires affect greatly to the caused shrinkage unlike heating location. The ring structure affects also greatly to the shrinkage; smaller diameter, bigger ring height, thinner thickness and greater number of wires increase shrinkage.

Magnetization studies of polystyrene/multiwall carbon nanotube composite films

Lappeenranta University of Technology School of Technology Technical Physics Evgenii Zhukov MAGNETIZATION STUDIES OF POLYSTYRENE/MULTIWALL CARBON NANOTUBE COMPOSITE FILMS Master’s thesis 2015 55 pages, 41 pictures, 9 Tables. Examiners: Professor Erkki Lähderanta D.Sc. Ivan Zakharchuk Keywords: polystyrene, multi-walled carbon nanotubes, MWCNT, composite, magnetization, SQUID. In this thesis magnetic properties of polystyrene/multiwall carbon nanotube (MWCNT) composites are investigated with Quantum Design SQUID magnetometer (MPMS XL). The surface of the composite films is studied via BRUKER Multimode 8 Atomic Force Microscope, as well. The polystyrene/MWCNT composites have been prepared by the group of professor Okotrub (Physics Chemistry of Nanomaterials laboratory, Nikolaev Institute of Inorganic Chemistry, Russia). The composite films have been prepared by solution processing and stretching method. The approximate length and inner diameter of the MWCNTs used in fabrication are 260 μm and 10 nm, respectively. The content of MWCNTs is 1 and 2.5 contents percent (wt%) for studied samples. The stretching of the samples is 30% for samples with 1 and 2.5 wt% content, and one sample with 1 wt% loading of MWCNTs is 100% stretched. MWCNTs aligned perpendicular to a silicon substrate are used as a reference sample. The magnetization field dependencies of the samples exhibit hysteresis behavior. The values of saturation magnetization of composite films are much less compared to that of the reference sample. The saturation magnetization coercitivity field value drops with decrease of MWCNT content. At high magnetic fields strong presence of diamagnetism is observed. Measurements in magnetic field parallel and perpendicular to the composite plate display anisotropy with respect to the direction of stretching. Temperature dependences of magnetization for all samples display difference between zero-field cooled and field-cooled curves of magnetization. This divergence confirms the presence of magnetic interactions in the material. The atomic force microscopy study of the composites’ surfaces revealed that they are relatively smooth and the nanotubes are aligned with the axis of stretching to some extent. 

Structural and functional Studies of angucycline tailoring enzymes

Polyketides are a diverse group of natural products produced in many bacteria, fungi and plants. These metabolites have diverse biological activities and several members of this group are in clinical use as antibiotics, anticancer agents, antifungals and immunosuppressants. The different polyketides are produced by polyketide synthases, which catalyze the condensation of extender units into various polyketide scaffolds. After the biosynthesis of the polyketide backbone, more versatility is created to the molecule by tailoring enzymes catalyzing for instance hydroxylations, methylations and glycosylations. Flavoprotein monooxygenases (FPMO) and short-chain alcohol dehydrogenases/reductases (SDR) are two enzyme families that catalyze unusual tailoring reactions in the biosynthesis of natural products. In the experimental section, functions of homologous FPMO and SDR tailoring enzymes from five different angucycline pathways were studied in vitro. The results revealed how different angucyclinones are produced from a common intermediate and that FPMO JadH and SDR LanV are responsible for the divergence of jadomycins and landomycins, respectively, from other angucyclines. Structural studies of these tailoring enzymes revealed differences between homologous enzymes and enabled the use of structure-based protein engineering. Mutagenesis experiments gave important information about the enzymes behind the evolution of distinct angucycline metabolites. These experiments revealed a correlation between the substrate inhibition and bi-functionality in JadH homologue PgaE. In the case of LanV, analysis of mutagenesis results revealed that the difference between the stereospecificities of LanV and its homologues CabV and UrdMred is unexpectedly related to the conformation of the substrate rather than to the structure of the enzyme. Altogether, the results presented here have improved our knowledge about different steps of angucycline biosynthesis and the reaction mechanisms used by the tailoring enzymes behind these steps. This information can hopefully be used to modify these enzymes to produce novel metabolites, which have new biological targets or possess novel modes-of-action. The understanding of these unusual enzyme mechanisms is also interesting to enzymologists outside the field of natural product research.

Scalable Feature Selection Applications for Genome-Wide Association Studies of Complex Diseases

Personalized medicine will revolutionize our capabilities to combat disease. Working toward this goal, a fundamental task is the deciphering of geneticvariants that are predictive of complex diseases. Modern studies, in the formof genome-wide association studies (GWAS) have afforded researchers with the opportunity to reveal new genotype-phenotype relationships through the extensive scanning of genetic variants. These studies typically contain over half a million genetic features for thousands of individuals. Examining this with methods other than univariate statistics is a challenging task requiring advanced algorithms that are scalable to the genome-wide level. In the future, next-generation sequencing studies (NGS) will contain an even larger number of common and rare variants. Machine learning-based feature selection algorithms have been shown to have the ability to effectively create predictive models for various genotype-phenotype relationships. This work explores the problem of selecting genetic variant subsets that are the most predictive of complex disease phenotypes through various feature selection methodologies, including filter, wrapper and embedded algorithms. The examined machine learning algorithms were demonstrated to not only be effective at predicting the disease phenotypes, but also doing so efficiently through the use of computational shortcuts. While much of the work was able to be run on high-end desktops, some work was further extended so that it could be implemented on parallel computers helping to assure that they will also scale to the NGS data sets. Further, these studies analyzed the relationships between various feature selection methods and demonstrated the need for careful testing when selecting an algorithm. It was shown that there is no universally optimal algorithm for variant selection in GWAS, but rather methodologies need to be selected based on the desired outcome, such as the number of features to be included in the prediction model. It was also demonstrated that without proper model validation, for example using nested cross-validation, the models can result in overly-optimistic prediction accuracies and decreased generalization ability. It is through the implementation and application of machine learning methods that one can extract predictive genotype–phenotype relationships and biological insights from genetic data sets.

Fiber-reinforced composite fixed dental prostheses: Studies of the materials used as pontics

Fiber-reinforced composite fixed dental prostheses – Studies of the materials used as pontics University of Turku, Faculty of Medicine, Institute of Dentistry, Department of Biomaterials Science, Finnish Doctoral Program in Oral Sciences – FINDOS, Annales Universitatis Turkuensis, Turku, Finland 2015 Fiber-reinforced composites (FRC), a non-metallic biomaterial, represent a suitable alternative in prosthetic dentistry when used as a component of fixed dental prostheses (FDPs). Some drawbacks have been identified in the clinical performance of FRC restorations, such as delamination of the veneering material and fracture of the pontic. Therefore, the current series of studies were performed to investigate the possibilities of enhancing the mechanical and physical properties of FRC FDPs by improving the materials used as pontics, to then heighten their longevity. Four experiments showed the importance of the pontic design and surface treatment in the performance of FRC FDPs. In the first, the load-bearing capacities of inlay-retained FRC FDPs with pontics of various materials and thicknesses were evaluated. Three different pontic materials were assessed with different FRC framework vertical positioning. Thicker pontics showed increased load-bearing capacities, especially ceramic pontics. A second study was completed investigating the influence of the chemical conditioning of the ridge-lap surface of acrylic resin denture teeth on their bonding to a composite resin. Increased shear bond strength demonstrated the positive influence of the pretreatment of the acrylic surfaces, indicating dissolution of the denture surfaces, and suggesting potential penetration of the monomer systems into the surface of denture teeth. A third study analyzed the penetration depth of different monomer systems on the acrylic resin denture teeth surfaces. The possibility of establishing a durable bond between acrylic pontics and FRC frameworks was demonstrated by the ability of monomers to penetrate the surface of acrylic resin denture teeth, measured by a confocal scanning type microscope. A fourth study was designed to evaluate the load-bearing capacities of FRC FDPs using the findings of the previous three studies. In this case, the performance of pre-shaped acrylic resin denture teeth used as pontics with different composite resins as filling materials was evaluated. The filling material influenced the load-bearing capacities, providing more durable FRC FDPs. It can be concluded that the mechanical and physical properties of FRC FDPs can be improved as has been shown in the development of this thesis. The improvements reported then might provide long lasting prosthetic solutions of this kind, positioning them as potentially permanent rehabilitation treatments. Key words: fiber-reinforced composite, fixed dental prostheses, inlay-retained bridges, adhesion, acrylic resin denture teeth, dental material.