Search

In the recent years, digital games have solidified their role as important parts of life for a considerable portion of the population. Game development has become an extremely important industrial branch with a great deal of competition between developers and publishers. There is only a limited amount of resources to put in the development of a game, but the modern customers expect high quality.Taking these constraints into account, this dissertation focuses on developing implementations of a structure that is used widely in different games: technology trees (TTs). This term covers here also so-called skill trees, talent trees, perk trees, and other such structures used to limit and guide in-game development and define development possibilities. The aim is to propose methods and usage of tools helping to achieve high TT quality, simultaneously facilitating the actual development process and reducing human workload.The main contributions of this dissertation consist of ideas, models, methods, and software tool prototypes constructed during the research work. The significance of the thesis is amplified by the fact that there are only very few previous academic studies focusing on TTs.The thesis proposes a generic approach to implement TTs. The design and implementation work are facilitated by tool support and automated code generation. The central prototype tool, Tech Tree Tool (TTT) is introduced, first in its core form and then as improved by TT measuring (and limited automatic adjusting) capabilities. The challenge of modifying TTs during runtime is addressed, also taking advantage of related improvements on TTT. Because TTs are often operated by artificially intelligent entities, discussion on a generic artificial intelligence approach and related tools is included. Moreover, contemporary real-life TTs are analyzed and generic TTs characterized.

Global energy demand continues to increase, which raises the question regarding how to solve the energy crisis caused by diminishing fossil fuels. There is no single alternative energy source that could substitute the fossil fuels, but microbial single cell oils (SCO) could be part of the solution. SCOs can be produced by cultivating microorganisms in wastewater in which nutrients and carbon from the wastewater are used for biomass production. In optimized conditions, microorganisms begin to accumulate lipids, and these lipids can be further refined for the production of biodiesel or renewable diesel. The lipid accumulation of the microorganisms may be enhanced by culturing the microorganisms under stressful conditions. The most commonly used strategy for enhancing lipid accumulation is nitrogen starvation, but it is even more effective when combined with another stress factor, such as moderately increased salinity. In microbial lipid production, the major cost factor is often the substrate needed for the microorganisms. Therefore, utilizing inexpensive substrates and waste materials for the cultivation of oleaginous microorganisms is very desirable. Various wastewaters from municipalities, agriculture, and industrial sources have been studied, and many of these wastewaters have shown the potential for lipid-rich biomass production. Unfortunately, most of the studies have been conducted using sterilized wastewater. In large-scale applications, the sterilization of the wastewater is not cost-effective; therefore, lipid-accumulating microorganisms able to compete with the indigenous microorganisms of the wastewater need to be further studied. The aim of this work was to sustainably produce oleaginous biomass by reusing the carbon and nutrients from wastewaters. This work included an evaluation of the suitability of various wastewaters for lipid-lipid rich biomass production (Paper I), the isolation of yeasts and fungi, which could possibly accumulate lipids by utilizing wastewater as substrate (Paper II), and the determination of the ability of the isolated microorganisms to accumulate lipids by comparing them with known lipid accumulating yeasts (Paper II). Unlike yeasts and fungi, microalgae are able to use an inorganic carbon source for their growth. This feature enables the combination of wastewater and flue gas treatment. Therefore, the growth and lipid accumulation of three microalgal species were compared (Paper III), and the suitability of the most potential microalgal species for accumulating lipids in sterilized and non-sterilized wastewater was studied (Paper III & IV). Based on the results of this study, palm oil mill effluent (POME) has more potential for lipid production than chemithermomechanical pulp mill effluent (CTMP) or municipal wastewate r (MWW) (Paper I). The residual lipids and solids of POME obstructed the analyses of the microbial SCOs. Eukaryotes isolated from POME with agar plates were genetically identified as Candida silvae NRRL Y-6725 (with 100% similarity), Galactomyces geotrichum LMA-20 (with 99.8% similarity), Lecythophora hoffmannii CBS245.38T (with 96.7% similarity), and Graphium penicillioides JCM9300 (with 99.3% similarity) (Paper II). The fungus Graphium penicillioides had a great potential for lipid accumulation based on the comparison study with well-known oleaginous yeast strains (Yarrowia lipolytica DSMZ8212, Cryptococcus curvatus DSMZ70022, & Cryptococcus albidus DSMZ701097) in a synthetic medium (Paper II). The lipid content per dry weight was higher with G. penicillioides compared to C. curvatus after 15 days of incubation (29.1±3.0 wt% vs 20.2±2.9 wt%, Paper II). Unfortunately, the overall lipid concentration was lower due to a lower biomass concentration. G. penicillioides contained more than 20% lipids, so it can be called oleaginous. From the three microalgae isolated from a Taiwanese freshwater area (Chlorella sorokiniana CY1, Chlorella vulgaris CY5, & Chlamydomonas sp. JSC-04), C. vulgaris accumulated more lipids when various media, nitrogen sources, and nitrogen concentrations were studied (Paper III). The C. vulgaris in the BG-11 medium, initially containing 0.38 g NaNO3/L, produced 3.8 g/L biomass and 57.5 wt% lipids after 12 days of incubation. The most suitable wastewater dilution for the lipid accumulation of C. vulgaris on sterilized anaerobically treated piggery wastewater was 5x dilution, which resulted in initial chemical oxygen demand and total Kjeldahl nitrogen of 75.4 mg/L and 57.4 mg/L, respectively. C. vulgaris was suitable for accumulating lipids on both sterilized and non-sterilized anaerobically treated piggery wastewater (PW) (Paper IV). The highest lipid content and productivity with the non-sterilized wastewater were rather promising (32.5±3.2 wt%, 71.2±2.2 g/L/d). However, under the conditions of these experiments, C. vulgaris excreted dissolved organic carbon (Paper III & IV), and the aim in wastewater treatment is the removal of organic carbon. In summary, this work demonstrates the potential of indigenous eukaryotic microorganisms for lipid-rich biomass production. G. penicillioides isolated from POME has the potential for lipid-rich biomass production in a synthetic medium, which has not been previously reported. Similarly, C. vulgaris has the potential for lipid-rich biomass production in non-sterilized piggery wastewater, while most of the studies in the literature on C. vulgaris and wastewater have been conducted using sterilized wastewater. To enable simultaneous accumulation of lipids and efficient treatment of wastewater, special attention should be focused on the growth conditions.

Recent advances in the fabrication of nanoscale structures have enabled the production of almost arbitrarily shaped nanoparticles and so-called optical metamaterials. Such materials can be designed to have optical properties not found in nature, such as negative index of refraction. Noble metal nanostructures can enhance the local electric field, which is beneficial for nonlinear optical effects. The study of nonlinear optical properties of nanostructures and metamaterials is becoming increasingly important due to their possible uses in nanoscale optical switches, frequency converters and many other devices.The responses of nanostructures depend heavily on their geometry, which calls for versatile modeling methods. In this work, we develop a boundary element method for the modeling of surface second-harmonic generation from isolated nanoparticles of very general shape. The method is also capable of modeling spatially periodic structures by the use of appropriate Green’s function. We further show how to utilize geometrical symmetries to lower the computational time and memory requirements in the boundary element method even in cases where the incident field is not symmetrical.We validate the boundary element approach by the calculation of second-harmonic scattering from gold spheres of different radii. Comparison to analytical solution reveals that under one percent relative error is easily achieved. The method is then applied to model second-harmonic microscopy of single gold nanodots and second-harmonic generation from arrays of L- and T-shaped gold particles. The agreement between the calculations and measurements is shown to be excellent.To provide a more intuitive understanding of the optical response of nanostructures, we develop a full-wave spectral approach, which is based on boundary integral operators. We present a theory which proves that the resonances of a smooth scatterer are isolated poles that occur at complex frequencies. Other types of singularities, such as branch-cuts, may occur only via the fundamental Green function or material dispersion. We propose a definition of an eigenvalue problem at fixed real frequencies which gives rise to modes defined over the surface of the scatterer. We illustrate that these modes accurately describe the optical responses that are usually seen for certain particle shapes when using plane-wave excitations. With the spectral approach, the resonance frequencies and the modal responses of a scatterer can be found as intrinsic properties independent of any incident field. We show that the spectral theory is compatible with the Mie theory for pherical particles and with a previously studied quasi-static theory in the limit of zero frequency.

Nanotechnology, the manipulation of matter at the scale of 1–100 nm, is present in everyday life and continues extending into new areas of application. Aerosol synthesis routes, the production of nanoparticles in the gas phase, are known to be continuous, highly controllable, and even suitable for fabricating different types of nanostructured metamaterials—materials with properties not found in nature. In this thesis, single and multicomponent engineered aerosol nanoparticles with different morphologies were synthesized for applications involving interactions between light and matter. The synthesized nanoparticles included spherical silver particles, titania-encapsulated iron oxide particles, silver-decorated silica particles, and silver–titania composite doublet particles. Furthermore, the studied applications for the nanoparticles were magnetically separable photocatalyst nanopowders and nanostructured metal–dielectric metamaterials with linear and nonlinear optical properties, more specifically, localized surface plasmon resonance and second-harmonic generation, respectively.The aerosol synthesis techniques utilized for the nanoparticle production in this thesis included particle size selection, sintering, encapsulation, and coating. The sintering of the size-selected silver agglomerates to spheres continued the trends found from the literature. In the simple encapsulation process, liquid precursor containing solid particles was sprayed into a tubular furnace where the precursor thermally decomposed on the surface of the solid particles, forming multicomponent particles. This approach was demonstrated by synthesizing titania-encapsulated iron oxide particles. As titania and iron oxide are known to be photocatalytic and magnetic, respectively, the produced nanopowder could find use as a magnetically separable photocatalyst. The silver coatings on the silica and titania carrier particles, accomplished by physical vapor condensation, were found to form different types of morphologies due to the migration of the silver on the carrier particles.The wavelength of the localized surface plasmon resonance of spherical silver particles deposited on glass substrates was tuned between 400–450 nm with the particle size. Due to the random deposition process, particle–particle contacts on the substrate caused broadening of the extinction spectrum with higher area fractions. On the other hand, the silver-decorated silica nanoparticles maintained the narrow plasmon resonance band even with high particle number densities. This enabled the fabrication of thicker bulk-type optical materials. The nonlinear optical properties of bulk-type multilayer nanostructures consisting of alternating layers of silver-decorated silica nanoparticles and pure silica were investigated. It was proposed that the porous particle layers were in a key role in the formation of the required non-centrosymmetric structure. Furthermore, both the silver particles and the multilayer structure were important for the second-harmonic generation, whose intensity increased with the number of layers. The fabricated structures could be further optimized in order to increase the conversion efficiency of the second-order nonlinear optical process.

The bioleaching of metal sulphide ore has developed into an important industrial process to recover valuable base metals from low-grade ores, because high grade ore resources are depleting. The Talvivaara deposits in Finland have been known for decades, but have not been utilized until now, because of the low nickel concentration. The aim of this work was to study the bioleaching process of a Finnish complex multimetal black schist ore in boreal conditions. The effects of pH and leaching temperature on the dissolution of valuable metals and gangue minerals were studied. The effect of low temperature on iron oxidation and mineral bioleaching was investigated. Microbial community development at different pH values and temperatures was tested in laboratory-scale bioleaching columns and finally the community dynamics were studied in a demonstration-scale bioheap over a period of three years in Talvivaara Finland.The experiments were carried out using laboratory-scale columns containing about 9 kg of agglomerated ore. The columns were loaded with the ore, irrigated with pregnant leaching solution (PLS) by recycling and aerated from the bottom. The tested pH range was from 1.5 to 3.0 at 21 ºC and temperature range was from 7 to 50 ºC at pH 2.5. The particle size (d80) of the ore was 7.6 mm. Surface water taken from lake near the Sotkamo deposit (slightly affected by acid mine drainage) supplemented with nutrients was used for irrigation. Aeration was provided through a diffuser inserted at the base of the column. The iron- and sulphur-oxidizing bacterial culture used in inoculation of the columns, was enriched from surface water samples (pH 4.5-6.9) obtained from the ore deposit. The pH of irrigation solution was maintained with continuous titration with H2SO4. The ore was acid consuming in all tested conditions. The actual pH of the irrigation solutions after 140 days were 0.1-0.5 units over the target values in all columns. Leaching at low pH resulted in increased acid consumption of 160 and 38 H2SO4 g kg-1 ore at pH 1.5 and 2.0 after 140 days. Temperature, at pH 2.5, had also effect on acid consumption. At 50 ºC acid consumption was highest and lowest at 21 ºC, being 29 and 8 H2SO4 g kg-1 ore, respectively.The pH of the irrigation solution clearly affected to the dissolution of nickel and zinc. Nickel solubilization rate was 3.3 times higher at pH 1.5 than at pH 3.0, being 0.42 and 0.13 % (Ni) d-1, respectively. At pH 1.5 valuable metals yields were 59 % for Ni, 52 % for Zn, 13 % for Cu and 16 % for Co, whereas at pH 3.0 yields were 15 % for Ni, 10 % for Zn, 0.5 % for Cu and 6 % for Co after 140 days of bioleaching. No significant bioleaching happened after that at pH 1.5, 2.5 or 3.0. At pH 2.0 the maximum yields were achieved after 230 days of bioleaching. Nickel and zinc leaching rates and yields decreased nearly linearly as pH increased. Copper did not bioleach at high pH (2.5-3.0). After the beginning, no further cobolt dissolution happened at pH 3.0. Decrease in leaching rates may be due to a lack of dissolved ferric iron, serving as a leaching agent, or metal dissolution barriers created by precipitates on the ore surfaces. The ferric iron concentration in PLS increased all the time at pH 1.5, being 36 g l-1 after 140 days. At pH 2.0 the ferric iron concentrations varied, being highest 3.8 g l-1 after 97 days. At 2.5 and 3.0 no ferric iron was present in PLS and iron concentration remained low, being 15 mg l-1.After 60 days of bioleaching the leach liquor at pH 1.5 became jelly-like due to solubilization of Si from the ore, which contained 42 % (w w-1) of SiO2. Quartz, phlogopite, and feldspars (anorthite and microcline) were the main Si-containing phases. After 110 days the Si concentration reached 2.96 g L-1 at pH 1.5. Soluble Si increases the solution viscosity and thus hinders leach liquor percolation trough the heap, lowers the oxygen transfer rate, and complicates subsequent metal extraction. Although, dissolved Si did not affect the solubilization of valuable metals, the pH value of the PLS must be kept at over 1.5 to slow down Si-containing mineral dissolution. At pH 2.5 less than 200 mg L-1 Si was solubilized and different temperatures had no effect on Si dissolution at that pH.Based on an optimisation between the maximum valuable metal yields, leaching rates, the acid consumption, and the low dissolution of cations (Si, Al, Ca, Mg and Mn), the leaching solution pH of 2.0 was recommended for a bioheap application. At pH 2.0, the maximum leaching yields were achieved after 230 days, being 54 % for Ni, 37 % for Zn, 13 % for Cu and 12 % for Co.Temperature strongly affected the valuable metal yields at pH 2.5. Leaching at low temperature (7 ºC) resulted in yields of 24 % for Ni, 17 % for Zn, 2 % for Cu and 6 % for Co after 496 days. The Cu leaching increased all the time during the experiment at 7 ºC, while at other temperatures it slowed down after 100 days. The highest yields were obtained at 21 ºC (26 % for Ni, 18 % for Zn, 0.5 % for Cu and 6 % for Co) after 153 days. After re-inoculation (day 65) with a thermophilic Sulfolobus culture, leaching at 50 ºC accelerated but slowed down soon and resulted in 18 % for Ni, 11 for Zn, 0.3% for Cu and 2% for Co (after 140 days). In the column leaching study, after the maximum yields, longer leaching time did not result more metals in solutions.The redox increased during the first two months at 7 ºC and reflected the start of ferrous iron oxidation and microbial activity. The concentration of ferric iron was around 400 mg L-1 after two months. After that ferric iron was present all the time at 7 ºC and this demonstrated that more ferric iron was available for the oxidation of the mineral sulphide than at other temperatures. The leach liquor redox potential stabilized to 500-600 mV (Ag0/AgCl reference) at 7 ºC after 40 days and at 21 ºC right after beginning, whereas at 35 ºC and at 50 ºC it varied between 300-500 mV. At 50 ºC, all dissolved iron was in ferrous form inspite the variation of redox. After 50 days Fe2+ and Fetot were both 350 mg L-1 indicating that iron oxidation and precipitation occurred at the same time. Brown precipitates accumulated to the surfaces of the agglomerated ore in columns from 7 ºC to 50 ºC. Additionally, bright yellow precipitates were formed indicating elemental sulphur or Na-jarosite accumulation at 7 ºC and 21 ºC.After 50 days of bioleaching, at 7 ºC leach liquor total cell counts (108-109 cells mL-1) were significantly higher than at other temperatures (106-107 cells mL-1). Cell counts remained that high troughout the column study. At the end of the experiment, total cell counts in the leach residues were studied. At 7, 21, 35 and 50 ºC cell counts of the leach residues were 3.4· 108, 2.3· 108, 1.1· 107 and 8.7· 106 cells ore g-1, respectively. The pH did not affect at 21 ºC the numbers of microorganisms in the PLS and cell counts remained at 106-108 cell mL-1 throughout the study and the leach residues contained about 108 cells g ore-1.The microbial community composition and dynamics was by investigated by DNA extraction PCR-DGGE-sequencing approach. The microbial community were not affected by pH. In contrast, temperature affected the microbial populations. After the first months, Acidithiobacillus ferrooxidans AP 310 (96-99% sequence similarity, accession DQ35518) was the only species detected at 7 ºC and was also present at other temperatures. After the data of this study was published (2007), two new Acidithiobacillus species were described, A. ferrivorans and A. ferridurans. Genetically these species are very near each other. The 16S rRNA gene sequences of the bands that corresponded 99% of A. ferrooxidans AP310 (DQ35518) were identified again in 2015 using the basic local alignment search tool (BLAST). The 16S rRNA gene sequences of A. ferrooxidans at temperatures of 7 and 21 ºC corresponded 99% as A. ferrivorans SS3 (CP002985). One of the 16S rRNA gene sequences of A. ferroxidans strains at 35 ºC corresponded 99% as A. ferridurans ATCC 3302 (NR_117036). At 50 ºC, no proper A. ferroxidans 16S rRNA gene sequences were gained with the used methods. The presence of A. ferroxidans at 50 ºC was concluded based on the fact that the DGGE band was in the same place as the other A. ferrooxidans bands. The 16S rRNA gene sequences of Acidithiobacillus ferrooxidans strains in pH between 1.5 and 3.0, at 21 ºC, corresponded also 99% as A. ferrivorans SS3 (CP002985). In the light of increased knowledge, these species cannot be separated with the denaturing gradient from 40 to 70% that were used in the DGGE. A. ferrooxidans, A. ferrivorans and A. ferridurans are able to oxidize both iron and sulphur compounds.Leptospirillum ferrooxidans DSM 2705 (98-100%, X86776) and Sulfobacillus thermotolerans KR-1 (99%, DQ124681) were mainly detected at 21 ºC and 35 ºC. Sb. thermotolerans was present at 50 ºC. L. ferriphilum D1 (99 %, DQ665909) appeared after 300 days of bioleaching and was present in every leach residue, except at 7 ºC and pH 3.0. L. ferrooxidans and L. ferriphilum are able to oxidize only iron. Sb. thermotolerans is able to oxidize both iron and sulphur compounds.Archaeal species were analyzed two times from leach liquors and three species were detected. A species related to an uncultured archaeon clone ant b7 (99%, DQ303249), nearest known species Thermoplasma acidiphilum DSM1728 (91%, AL445067) was present in all of the leach liquors except at pH 1.5. Archaea related to Sulfolobus metallicus DSM 6482 (98%, SM16SRRN1) were present at pH values 2.5 and 3.0 and in all other temperatures, except at 7 ºC. Sulfolobus metallicus is able to oxidize both iron and sulphur compounds. Ferroplasma acidiphilum DR1 (98%, AY222042) that can oxidize only iron, was present at pH 2.5 and 2.0, and in all temperatures, expect at 35 ºC.The mixed iron- and sulphur-oxidizing culture in the recirculation solution at 7 ºC was used in the experiments where Fe2+-oxidation rate and optimum temperature were determined over a temperature range of 2-40 ºC. Two temperature optima of 22.4 ºC and 32.4 ºC were observed. This indicated the presence of both psychrotolerant and/ or mesophilic microorganisms in the culture. This supports the suggestion that A. ferrooxidans was actually A. ferrivorans, or both species were present. The specific oxidation rates for the culture were similar, with 13.5·10-8 and 12.8·10-8 mg Fe2+ cell-1 h-1 for 22.4 ºC and 32.4 ºC, respectively.The two demonstration-scale bioheaps (17 000 t) at the Talvivaara mine site were operated and monitored by Talvivaara Mining Company for 30 months. After the start-up of heap irrigation, oxidation of pyrrhotite and pyrite increased the heap temperature in central locations up to 90 ºC. In the second winter temperatures inside the heaps decreased being still 80 ºC at the hottest spots. Leach liquor temperatures varied between 60 ºC and 15 ºC over the whole operation period. The target pH of the PLS was 2.0. Inspite of continuous titration pH varied during the 10 months between 3.5 and 3.0 and after that between 3.0 and 2.5.The bacterial community composition on the heaps was monitored over time from manholes and the leach liquor collection ponds. At the end of the primary bioleach phase (18 months) cell counts were around 106 cells mL-1. Large temperature gradients resulted in the simultaneous presence of mesophilic and thermophilic iron- and sulphur-oxidisers in the heap. In the beginning diversity was broad, but decreased with time. A. ferrooxidans/ ferrivorans SS3 (99%, CP002985) was the dominant bacterium and an unknown bacterium related to clone H70 (91%, DQ328625) was present. After six months of bioheap operation L. ferrooxidans DSM 2705 (98%, X86776) was observed for the first time and it was present thereafter in nearly all samples. Archaea were analysed during the primary leaching phase from leach liquors. Two novel archaea and one archaea related to Thermoplasma acidophilum strain 122-1B2 (91-93%, NR_028235) were detected.Several ore samples were drilled from the primary bioheaps after one year of bioheap operation. A. ferrooxidans/ A. ferrivorans SS3 (99%, CP002985) was present in nearly all samples. The novel bacterium related to clone H70 (91%, DQ328625) and A. caldus related bacteria (95%, AY427958) was detected from the areas of wide temperature variation. Sb. thermosulfidooxidans strain YN22 (99%, DQ650351) was found from the high temperature zones of the heap. Ferrimicrobium acidiphilum T23 (99%, AF251436) was present in the areas where temperature varied between 20 and 35 ºC. After 18 months of demonstration-scale heap operation, the heaps were reclaimed and restacked to the secondary bioheap. At the secondary leaching phase the community remained steady. A. ferrooxidans/ ferrivorans SS3 (99%, CP002985) dominated and the novel bacterium related to a clone H70 (91%, DQ328625) and L. ferrooxidans DSM 2705 (98-100%, X86776) were present in the leach liquors of secondary phase bioheaps.

Excessive usage of traditional energy reserves leading to increased environmental pollution and global warming have strongly urged for alternative sustainable energy sources. Due to non-polluting nature and high energy yields, hydrogen (H₂) gas is considered as an ideal candidate for alternative fuel. Biohydrogen (bioH₂) production from organic wastes is a sustainable approach, addressing energy production through organic waste disposal. Organic wastes such as lignocellulosic biomass and industrial glycerol, a by-product of biodiesel manufacturing process, have been recently investigated for their bioconversion potential. However, bioconversion of such organic wastes is a challenge due to the presence of impurities, toxic degradation products and complex nature. In comparison to pure bacterial strains, natural microflora could be an ideal inoculum choice offering better adaptability, substrate utilization efficiency and bioconversion rates. Another challenge to ensure efficient fermentation is to optimize various physico-chemical factors such as pH, temperature, substrate selection and concentration, medium compounds, and H₂ removal and collection due to individual and interactive effects on microbial growth, metabolism and hydrogenase enzyme. Hydrogenases are metalloenzymes that reversibly catalyzes proton reduction to H₂, and are divided into three classes based on the metal cofactor at the active site, [Fe-Fe], [Ni-Fe] and [Fe] hydrogenase. Among the hydrogenase classes, [Fe-Fe] hydrogenases exhibit highest catalytic activity involving mostly in H₂ production. Apart from their pivotal role in fermentative H₂ production, [Fe-Fe] hydrogenases promise an alternative catalyst choice in fuel cells. However, in spite of their preference towards H₂ production, [Fe-Fe] hydrogenases are extremely prone to catalytic inactivation upon oxygen exposure. This is the major challenge, at the protein level, that hinders a cost-effective approach for biotechnological applications and suggests the requirement of targeted tools to investigate the inactivation process at the molecular level. The purpose of the present study was to investigate bioH₂ production in protein to community level perspective. More specifically the aims were to (1) establish an anaerobic biopanning procedure to enrich antibody binders specific against clostridial [Fe-Fe] hydrogenase protein, (2) develop and standardize a novel enrichment system, (3) implement the enrichment technique to enrich functional inoculum capable of degrading complex substrates, (4) enrich crude glycerol fermenting microbial community and finally, (5) optimize the physico-chemical factors influencing fermentative H₂ production for efficient bioprocess. In the present study, biopanning with synthetic ‘mixed’ single chain variable fragment (scFv) libraries against active and inactive clostridial [Fe-Fe] hydrogenases aided the enrichment of anti-hydrogenase antibodies. Out of ninety four (from inactive hydrogenase) and ninety two (from active hydrogenase) random clones screened, nine potential antibody clones with recognition specificity towards Clostridium acetobutylicum [Fe-Fe] hydrogenase were selected. The enriched binders also recognized [Fe-Fe] hydrogenase from C. butyricum. Based on the results from this study, it could be reasoned that the binders with generic specificity against closely related clostridial [Fe-Fe] hydrogenases can be used as novel molecular tools for quantitative monitoring [Fe-Fe] hydrogenases at the protein level. Another of-note observation was the specificity of the antibody binders towards active and inactive hydrogenases. Preliminary experiments indicated 7Ac binder (enriched against active hydrogenase) specificity towards the catalytically active [Fe-Fe] hydrogenase rather to the inactive state and 48In (enriched against inactive hydrogenase) recognized both catalytic states. These findings indicate the possibility to apply the isolated antibody clones for functional detection of clostridial [Fe-Fe] hydrogenases. The study progresses in investigating bioH₂ production in perspective of microbial community. The novel microbial enrichment system was developed and the proof-of-principle experiments conducted using artificial mixed microbial community and varied selection criteria allowed the enrichment of the best H₂ producer. The system was implemented in enriching cellobiose degrading H₂ producer from an environmental sample. The bacterial strain isolated by spread plate technique on agar plates containing CMC was affiliated with Citrobacter sp. and named as Citrobacter sp. CMC-1. Citrobacter sp. CMC-1 utilized glucose, cellobiose and CMC and followed mixed-acid fermentation profile producing H₂ and carbon dioxide (CO₂) as gaseous metabolites and acetate, formate, lactate and ethanol as liquid metabolites. At optimized values of cultivation conditions (pH 6.0 and 34 ˚C) the H₂ yield was 1.82 mol-H₂/mol-glucose. The isolate efficiently fermented monomeric hemi-cellulose sugars to H₂ (mol-H₂/mol-substrate): Galactose, 1.18; Mannose, 1.23; Xylose, 1.22; Arabinose, 0.94 and Rhamnose, 1.01). Except for arabinose, an increase in cultivation period improved the biomass and H₂ yield (mol-H₂/mol-substrate): Galactose, 1.68; Mannose, 1.93 and Xylose, 1.63) followed with observations of reduced formate accumulation in the medium, indicating that Citrobacter sp. CMC-1 produced H₂ from formate breakdown via the FHL complex. Microbial community pre-dominated with Clostridium spp. enriched from activated sludge fermented crude glycerol mainly to H₂, CO₂, acetate, butyrate and ethanol. Optimal bioprocess conditions for the enriched inoculum were experimentally observed to be pH 6.5, 40˚C and 1g/L crude glycerol. The H₂ yield from raw glycerol at optimal cultivation conditions was 1.1 mol-H₂/mol-glycerol consumed . At elevated crude glycerol concentrations, substrate utilization and H₂ production were limited due to the presence of impurities in the crude glycerol fraction. The bioconversion of crude glycerol to H₂ was further improved by statistical optimization of the growth medium composition. Initial screening with Plackett – Burman design identified NH₄Cl, K₂HPO and KH₂PO₄ with individual and interactive effects on H₂ yield. Among the three identified media components, NH₄Cl and KH₂PO₄ imparted the maximal significance and were optimized in scrutiny. A series of statistical models identified the optimal media composition for improved H₂ production from crude glycerol fermentations and were successful in improving the H₂ yield by 29% (1.42 mol-H₂/mol-glycerol consumed ) in comparison to previously reported value (1.1 mol-H₂/mol-glycerol consumed ).

Aerosol particles produced in the atmosphere have major effects on the life on Earth: cloud formation starts on seed particles, often formed by photochemical oxidation of biogenic volatile organic compounds; visibility, corrosion, and health problems are caused by anthropogenic hydrocarbon and sulfur emission processed into particles by the atmosphere and the sun.Naturally occurring secondary organic aerosol (SOA) particles can produce up to a half of the non-refractory mass of aerosol particles of less than micrometer in size. This makes SOA a large contributing factor to the climate system of the Earth. The actual effect that these particles have is, however, not well known, compared to the other effects affecting the climate. The research effort to increase the understanding and reduce the uncertainties around the climate effects of SOA encompasses an interdisciplinary research community.The recent advance made by the observation of a solid phase of SOA by Virtanen et al. (2010) was the starting point for this thesis. The solid phase of SOA particles means that a long-held assumption of a partition equilibrium between the condensed phase and the gas phase of the semivolatile species may be wrong and produce too low a timescale for the particle chemical reaction rates and uptake coefficients.This work consists of new developments in the instrumentation of particle properties as well as new observations of laboratory-generated secondary organic aerosol. The method development has two branches, one concentrates on finding more information from the measurement signal of an electrical low pressure impactor (ELPI) used in a somewhat unconventional way, whereas the other consists of a new detection method for particle bounce and response to different humidity and phase hysteresis induced by a carefully controlled humidity history.The methods and observations made during this work are by no means the final word on the subject, but they are being used and further developed by the scientific community. Study of the particle phase and bounce as well as SOA mechanical properties and kinetics is well underway, and its results will be used to further refine the understanding of both aerosol fundamentals as well as the climate system.

Solar cells generate green energy directly from sunlight. The energy conversion efficiency of solar cells depends strongly on materials used as absorbers and the cell architecture. Currently, the best solar cells convert sunlight energy to electricity with an efficiency of up to 46%. This thesis focuses on the development of dilute-nitride materials and related solar cells, which are one of the most promising approaches for achieving even higher efficiencies. Applications for these cells include concentrated photovoltaic and space power systems. In particular, the thesis focuses on developing solar cell materials based on GaInNAsSb, which can provide efficient light absorption and energy conversion for a photon energy range of 0.8 eV- 1eV, typically challenging for conventional III-V semiconductors. The GaInNAsSb semiconductor materials were synthesized by molecular beam epitaxy.The experimental work of this thesis explored the dependence of the fabrication parameters on the GaInNAsSb material and solar cell properties. It was observed that for many of the growth parameters even a slight change of the value can have a significant effect on the solar cell performance. A N incorporation model was developed to help the iteration process for growth parameter tuning. For optimized growth conditions, nearly ideal current generation for GaInNAsSb based material was achieved. Based on external quantum efficiency measurements it was possible to collect up to ~90% of the photons in the spectral range of the GaInNAsSb junction. In addition, an excellent fill factor of 0.7 and voltages in the range of 0.5 V for a 1 eV GaInNAsSb junction were measured.Simulation based on a state-of-the-art GaInP/GaAs double junction cell, a commercial GaInP/GaAs/Ge triple junction cell and GaInNAsSb single junction cells studied in this thesis, revealed that a GaInP/GaAs/GaInNAsSb/Ge cell at the one sun concentration can have 1.7 percentage points higher efficiency than GaInP/GaAs/GaInNAsSb cell. In addition, the estimated efficiency of a four junction cell at 300 suns would be 3.6 percentage points higher than for a GaInP/GaAs/GaInNAsSb cell. The optimized single junction GaInNAsSb cell was experimentally tested into a GaInP/GaAs/GaInNAsSb cell in this work. The one sun efficiency of the cell under AM1.5G spectral conditions was 31% and the efficiency of the cell at 70 suns concentration was 37-39%. The one sun result is 91% of the projected efficiency. The results under concentrated conditions are expected to be improved by optimizing of the cell top grid design, layer structure and interfaces. As future concepts are concerned, a nanopatterned moth eye antireflection coating was fabricated on top of the GaInP/GaAs/GaInNAs cell, which was then compared to a cell that had a traditional two layer TiO2/SiO2 coating. The moth eye nanostructure had a low average reflection of 2% in the spectral range of 400-1700 nm, being less than half of the reflectance of the TiO2/SiO2 coating. For future work, the absorption loss for the nanostructure coating at wavelengths below 500 nm needs to be reduced.

One of the aims of synthetic biology is the sustainable production of high-value compounds and bioenergy molecules. Synthetic biologists exploit fundamental engineering principles, such as DNA component standardization, modular genetic circuits, and de novo design, to create novel production pathways and products. A well-characterized host cell serves as the chassis for the system construction; generally, the model bacterium Escherichia coli is applied. However, the metabolism and characteristics of E. coli are not ideal for all applications. Furthermore, many E. coli based systems are patent protected which restricts the use in forthcoming application. Acinetobacter baylyi ADP1 is a potential alternative host for synthetic biology. The metabolism and genetics of the strain are well-understood, and the engineering of its genome is technically straight-forward. The versatile and unusual metabolic pathways, including those producing long chain hydrocarbons, can be rerouted, modified, and integrated into novel ones. I exploited A. baylyi ADP1 as a model host for the production of high-value hydrocarbons, triacylglycerols and wax esters. I employed metabolic engineering, novel molecular monitoring tools, and synthetic pathway design to improve the production, and to demonstrate the utility of ADP1 as a synthetic biology host. In particular, the production of triacylglycerols was improved over 5-folds by targeted gene deletions which resulted in redirected carbon flux towards the product and elimination of competitive pathways. The long-chain hydrocarbon metabolism, including alcohol and wax ester biosynthesis, is not yet fully understood. These pathways are regulated through several mechanisms sensitive to specific environmental conditions and the cellular states. However, the lack of robust and straight-forward analysis tools has restricted the studies of lipid metabolism and production kinetics. I developed a simple in vivo tool for the investigation of the long chain hydrocarbon metabolism in real-time. The tool is based on a light-producing reporter enzyme, bacterial luciferase. The enzyme utilizes a specific intermediate of the hydrocarbon synthesis pathway as a substrate for bioluminescence production. Initially, the tool was applied for monitoring the wax ester metabolism of A. baylyi ADP1. Subsequently, I modified the monitoring tool for studying the degradation of alkanes. The studies suggest that the tool can be applied for production optimization in different hosts and for a variety of products. I also reconstructed the wax ester synthesis pathway of A. baylyi ADP1 by replacing a natural key enzyme with an alternative well-characterized component, enabling a regulated production of unnatural wax esters. Bioprocess control and scale-up of production systems are challenging. Multispecies cultures are suggested to improve the robustness and performance of bacterial production processes. I exploited the metabolic versatility of A. baylyi ADP1 to construct a rationally engineered synthetic coculture with E. coli. The designed coculture exhibited improved biomass and recombinant protein production compared to the pure culture of E. coli. To conclude, I have shown that the strain ADP1 is a suitable host for synthetic biology applications, especially for long-chain hydrocarbon production, the development of novel tools for metabolic studies, and for exploiting the existing unusual metabolic networks of the cell. Thus, further studies of the remaining challenges related to ADP1 bioprocess and as-of-yet uncharacterized cell mechanisms, are warranted.

The mechanism of polyethylenimine−DNA, poly(L-lysine)−DNA, peptide–DNA, and PBAE–DNA complex formation was studied by a time-resolved spectroscopic method. The data were analysed by a cooperative model for multivalent ligand binding to multisubunit substrate. The formation of polyplexes with polyethylenimines, poly(L-lysine) and peptide (KK)₂KGGC is observed to be positively cooperative and negatively cooperative with PBAEs. Polymers with positive cooperativity reach about 100% saturation in binding DNA, whereas for polymers with negative cooperativity, the saturation level remains at about 80–90%. The type of amine groups (primary, secondary and tertiary) of the polymers has an effect on the binding constants and the degree of cooperativity. The effects of pH, type of amine groups and polymer structure on the mechanism of the polyplex formation were studied with polyethylenimines (PEI) and poly(L-lysine) (PLL). At pH 5.2 and 7.4 for PEIs and PLL, the formation of the polyplex core was observed to be complete at N/P = 2, at which point nearly all DNA phosphate groups were bound by polymer amine groups. At higher N/P ratios, excess polymer binds to the core polyplex, forming a shell over the core. At pH 9.2, the core is formed at higher N/P ratios than at lower pH levels except for PLL, which behaves similarly at all pH levels. The overall cooperative binding constants are higher at pH 5.2 than at 9.2 due to the higher degree of amine group protonation at lower pH levels. The ionic strength and pH affect the binding mechanism with peptide (KK)₂KGGC polyplexes, but changing the buffer does not. Molecular weight shows a clear effect on the mechanism and efficiency of the polyplex formation: for the high-molecular weight polymers (BPEI and PLL), the saturation level is reached at lower N/P ratios than for low-molecular weight polymers (SPEI and peptide). In the absence of excess PEI, the transgene expression levels are lower than in the presence of it. However, the fluorescence properties of the polyplexes in the absence and the presence of excess PEI are similar. Hence, the original structure of the polyplex core is retained during the shell formation. The molecular structures of the poly(β-amino ester)s (PBAEs) can be modified in a controlled way with the accuracy of single carbon unit. The effect of very small changes in the polymer structure on the formation of the polyplexes was studied by changing the length of the backbone and the side chain, by adding end caps to the polymers and by changing the molecular weight of the polymers. For PBAEs without end caps, the highest saturation levels and overall binding constants were observed for the linear backbones and side chains when the number of carbons was four or five, respectively. The end-capping of PBAEs increases the amine density and the efficiency of polyplex formation, which is observed as higher saturation levels for the end-capped PBAEs. The presence of an OH-group in the end cap induces a change in the binding mechanism. The length of the backbone and the side chain of PBAEs were observed to be important via amine density, hydrophobicity and steric hindrance to the complex formation. High-molecular weight PBAEs formed polyplexes more effectively than smaller ones.

Real-world driving consist mostly of transients, where the engine parameters are constantly changing. In emission regulation this has been partially considered by including transient driving cycles in emission standards. However, specific particle emissions data for detailed driving conditions have remained limited. This thesis covers results of transient exhaust particle emissions, including both diesel and gasoline engines. The experiments were performed in laboratories and on the road. The focus was always on the real-world particle emissions. During transient cycles both heavy-duty (HD) diesel engines and light-duty (LD) gasoline vehicles produced elevated soot particle concentrations during accelerations. For instance, in on-road experiment of a LD gasoline vehicle, the exhaust plume particle concentrations at steady speeds were at clean ambient levels, but during accelerations concentrations were 10-50 times the background level. For gasoline vehicles the soot particle size distributions were bi-modal in nature. Currently neither LD gasoline nor nonroad HD diesel engines necessarily need to employ particle filtration in the exhaust system in order to meet the demands of the relevant legislation. Sulfur originating in the fuel or lubricant oil can be stored inside catalysts, and later be released, forming semivolatile nucleation mode (NM) particles when temperature rises. This behavior was detected for LD and HD engines in the engine laboratory, for a HD vehicle on the road and in a simplified measurement setup in an aerosol laboratory. The aerosol laboratory test indicated that the NM formation does not necessarily require hydrocarbons or sulfated hydrocarbons; particles are electrically neutral and evaporate when they undergo thermal treatment. While sulfur is released from the catalysts, the HD road engine study indicated that the increased NM particle emission is not explained by the concentration of gaseous sulfuric acid. The sulfur storage and release depends greatly on the driving history, also due to this NM particle emissions seem plausible, even with low sulfur fuels. With catalytic particle filters, the amount of soot is reduced, promoting semivolatile NM particle emissions. An unexpected observation was made that some engines produce nanoparticles containing lubricant oil derived metals during driving while not fueled. Exhaust particles were observed during engine braking events for a HD truck and LD gasoline vehicles. For the truck and gasoline vehicles, the engine braking related particles contributed up to 20-30% and 3-30% of the total number emissions, respectively. These particle emissions can be a reality for all vehicle types not using particle filtration, including the latest technology vehicles. In particle filters, engine braking related particles can affect the ash accumulation and transport mechanisms.

This work focuses on exploring the properties and functions of charged monolayer-protected gold nanoparticles (AuNPs) in biologically relevant environments by use of atomic-scale molecular dynamics (MD) simulations.The use of nanoparticles (NPs) in modern technology has been increasing rapidly during the last few years. NPs of different kinds have already been employed, e.g., in nanomedicine as cancer treatments, cleaning agents, cosmetics and new materials for industrial purposes. AuNPs are one type of nanoagents that are being employed for such purposes, and according to recent experimental findings they may have cytotoxic properties. In particular, AuNPs of 2-nm diameter or less are known to permeate through plasma membranes and induce cell death. Hence, studying potential harmful effects of AuNPs is of importance. Understanding the interaction between NPs and cell membranes is relevant also because all trafficking between the cell interior and extracellular space takes place through the cell membrane.The first study concentrated on the properties of AuNPs in aqueous solution at physiological temperature (310 K). The results showed that electrostatic properties modulate the formation of a complex comprised of the AuNP together with surrounding ions and water, and suggested that electrostatics is one of the central factors in the complexation of AuNPs with other nanomaterials and biological systems. The results highlighted the importance of long-range electrostatic interactions in determining NP properties in aqueous solutions. This observation was concluded to indicate an important a role in the interplay between NPs and lipid membranes, which surround cells.The second part of the research comprises of studying AuNPs in the presence of model cell membranes. The binding of AuNP and membrane reorganization processes were discovered to be governed by co-operative effects where AuNP, counter ions, water and membrane all contribute. The results suggest that a permeation of a cationic AuNP takes place through pore-formation with partial NP neutralization, leading to membrane disruption at higher NP concentrations. The results also suggested a potential mechanism for cytotoxity as cationic AuNP binding to the extracellular leaflet may trigger apoptosis through translocation of phophatidylserine.Summa summarum, the work presented here provides novel aspects on the interactions of functional AuNPs on cellular level by means of atomistic MD simulation. Tutkimuksessa mallinnettiin kultananohiukkasia laskennallisen molekyylidynamiikan keinoin biologisesti relevantissa ympäristössä. Kultananohiukkasia ja solukalvoja kuvaamaan luotiin teoreettiset mallit, joille suoritettiin atomitason simulaatioita. Tutkimuksella saavutettiin uutta informaatiota kultananohiukkasten vuorovaikutuksista solutasolla.Nanohiukkasia käytetään nykypäivänä teknologiassa yhä enenevissä määrin ja mitä moninaisimpiin tarkoituksiin. Käyttökohteita ovat muun muassa nanolääketieteen syöpähoidot, puhdistusaineet, kosmetiikka sekä uudet teollisuusmateriaalit. Kultananohiukkaset muodostavat yhden lukuisista nanohiukkastyypeistä. Viimeaikaiset tutkimuslöydökset ovat antaneet viitteitä siitä, että nanohiukkasilla olisi sytotoksisia ominaisuuksia. Erityisesti pienten, 2-nm kokoisten ja sitä pienempien, nanohiukkasten on todettu kulkeutuvan solukalvojen läpi ja aiheuttavan solukuolemia. Mahdollisten terveyshaittojen vuoksi kultananohiukkasten solutason vaikutusten kartoittaminen on tärkeää. Lisäksi nanohiukkasten ja solukalvojen vuorovaikutusprosessien ymmärtäminen on merkityksellistä, sillä kaikki liikenne solujen sisä- ja ulkopuolen välillä on solukalvovälitteistä.Tutkimuksen ensimmäisessä osassa tarkasteltiin kultananohiukkasten ominaisuuksia nestemäisessä vesiliuoksessa fysiologisessa lämpötilassa (310 K). Tulokset osoittivat, että sähköstaattiset vuorovaikutukset karakterisoivat kultananohiukkasten käyttäytymistä vesiliuoksessa. Tutkimuksessa selvisi, että kultananohiukkaset muodostavat yhdessä ionien ja veden kanssa komplekseja eikä niitä tule näin ollen käsitellä irrallisina kappaleina. Kompleksoitumisen keskeiseksi aiheuttajaksi osoittautui sähköstatiikka. Tuloksista tehtiin johtopäätös, että pitkän kantaman sähköiset vuorovaikutukset ovat tärkeässä osassa myös kultananohiukkasten ja solukalvojen välisessä dynamiikassa.Tutkittaessa kultananohiukkasen sitoutumista solukalvon pinnalle sekä solukalvon uudelleenjärjestäytymistä, havaittiin, että ilmöiden taustalla on yhteisvaikutteinen prosessi, johon osallistuvat kultananohiukkaset, vastaionit, vesi ja solukalvo. Tulokset puhuvat sen puolesta, että kultananohiukkasen kulkeutuminen solukalvoon voisi tapahtua kalvorakkulan muodostumisen kautta, johtaen solukalvon toiminnan häiriintymiseen. Yksi mahdollinen mekanismi sytotoksisuudelle olisi tulosten perusteella positiivisesti varatun nanopartikkelin solukalvon ulkopintaan sitoutumisesta aiheutuva fosfadityyliseriinin translokaatio, joka käynnistää apoptoosin.

Self-assembled InAs/GaAs quantum dots (QD) are artificial atoms which exhibit extremely high optical and structural quality and enable tailoring of the quantum confinement by adjusting their size, shape, and chemical composition. However, a disadvantage of the self-assembled formation process is that the QDs are randomly located on the GaAs surface. The ability to determine the positions of the QDs at the moment of nucleation, i.e. site-controlled growth, is essential for the new generation of photonic applications including single- and entangled-photon sources and nanophotonic integrated circuits. The purpose of this thesis is to introduce a new nanomaterial system composed of site-controlled InAs quantum dot chains (QDC) grown by molecular beam epitaxy in nanoimprint lithography prepared grooves. A thorough investigation of the structural and optical properties of QDCs is also presented. The thesis demonstrates that, regardless of the inherent anisotropy of the GaAs(100) surface, QDCs having similar density, size, and emission energy can be grown simultaneously on nanopatterns with different orientations by carefully selecting the growth parameters. However, the in-plane optical polarization of the spontaneous emission from the QDCs depends on their orientation. In more general perspective, this thesis reveals that the nanopattern on which the site-controlled QDs are grown has a strong influence on their morphological properties, including shape, size, strain profile, and composition profile. These properties are strongly cross-correlated and they all influence the electronic and optical characteristics of the QDs. For example, the growth of QDs in the grooves increases their oscillator strength for the vertically polarized spontaneous emission, which is the polarization component that can be coupled to surface plasmons in a metal film. This polarization property accompanied by the possibility of deterministic lateral positioning makes the site-controlled QDCs potential building blocks for plasmonic and nanophotonic waveguides.

In this work, new photoactive materials were tested in the active and anode buffer layers of the inverted ITO|ZnO|donor:PC60/70BM|Buffer|Au/Ag organic bulk heterojunction (BHJ) solar cell. The molecular properties of the materials synthesized for this work were designed in order to improve the efficiency of the inverted solar cell structure. In addition to testing the materials in the cells, their effect on the cell function was investigated. The work aimed to understand the effects of the studied buffer and active layer materials in the cell function and photovoltaic performance. Organometallic n-type tris-(8-hydroxyquinoline)aluminum (Alq3) derivatives, p-type aryl end-capped quaterthiophenes, and a combined p- and n-type Alq3 end-capped hexathiophene were tested as hole transporting anode buffer layer materials. As the various different materials provided a diverse buffer material selection, the properties of the materials for improved cell function were investigated by spectroscopic, electrochemical, computational and thermoanalytical methods. The studied Alq3 derivatives have electron donating amino substituents, either piperidine, pyrrolidine or morpholine rings, on the 5-position of the 8-hydroxyquinoline ligands, which ease the oxidation of the complexes and elevate the highest occupied molecular orbital (HOMO) energy levels. The higher HOMO levels of the derivatives, compared to that of Alq3, reduce the hole extraction barrier in the cell. Therefore, the cells with the derivatives as buffer layers had a higher short circuit current (Isc) compared to that with Alq3. Simultaneously, due to higher hole injection barrier, the cells with the derivatives as buffer layers had lower open circuit voltage (Voc) than the cell with Alq3. The derivative with the morpholine ring has ideal energy levels with respect to the created energy barriers. Thus, the cell with the morpholine derivative as buffer layer performed better than the cell with Alq3. The quaterthiophenes studied in this work have cyanophenyl or methoxyphenyl end-groups and methyl or hexyl side chains attached to the thiophene backbone. These structural differences affect their electronic distribution, absorption profile, energy levels and molecular packing, especially in the solid state. The use of p-cyano end-capped quaterthiophene with hexyl side chains as an anode buffer layer resulted in a better cell power conversion efficiency compared to that with Alq3. The use of the Alq3 end-capped hexathiophene as an anode buffer layer decreased the cell serial resistance (Rs) and increased Isc. Photoinduced reactions, such as energy or electron transfer, between the Alq3 or aryl end-capped oligothiophene buffer materials and photoactive layer partly explain the improved Isc. A synthesized benzodithiophene-benzotriazole donor-acceptor (D-A) copolymer was compared as donor material with three previously studied fluorine-benzotriazole D-A copolymers. The relation between donor polymer structural properties and photovoltaic performance was studied by combining computational and experimental methods. The cell with the benzodithiophene-benzotriazole copolymer as donor material had better efficiency than the cells with the fluorine- benzotriazole copolymers. Calculations on the molecular geometry, energy levels, molecular orbitals, and lowest energy excitations provided an additional perspective to understand the polymer’s function as donor material. Based on the calculations, the benzodithiophene-benzotriazole copolymer had a more planar backbone, continuous LUMO electron density, longer conjugation and better exciton and charge transport properties compared to those of the fluorine-benzotriazole copolymers. Bulky side groups in the fluorine-benzotriazole copolymers caused steric hindrance and twisting or bending of the backbone. As a result, the electron density concentrates in parts of the polymer structure and π-conjugation weakens or is broken. As the delocalization does not cover the whole polymer structure, excitons or charges are trapped in the gaps of the discontinuous molecular orbitals. Alq3, aryl and 8-phenoxyquinoline end-capped oligothiophenes were used as dopant materials in the P3HT:PC60BM BHJ photoactive layer. In the ternary blend of the dopant, P3HT and PC60BM molecules, intermolecular interactions are likely as the molecules are in close proximity in the solid photoactive layer. The effect of dopant molecules on the cell function was studied by solar cell experiments. To investigate the intermolecular interaction of the dopant molecules with the active layer components, P3HT donor and PC60BM acceptor, steady state and time resolved spectroscopic measurements were carried out in chloroform solutions. Based on the measurements, Alq3 end-capped hexathiophene donates an electron to PC60BM. Photoinduced energy transfer was observed between the cyanophenyl end-capped quaterthiophene and PC60BM. The cell absorption increases with doping. Thus, dopant molecules function as additional light absorbers in the photoactive layer. After excitation, the dopant molecules transfer electrons or energy to PC60BM, which increases the cell Isc and power conversion efficiency. When a cyanophenyl end-capped oligothiophene with diketopyrrolopyrrole (DPP) core was used as dopant, the cell emission decreased. DPP-group inclusion broadens the dopant absorption to the near IR-region. Therefore, the absorption of the dopant overlaps with P3HT emission and the dopant molecules can reabsorb the light emitted by P3HT. In this case, the cell Isc and power conversion efficiency increased further.

Supramolecular donor-acceptor assemblies were prepared and studied with spectro-scopic methods. The two main objectives of this work were: (i) fundamental study of photoinduced energy and electron transfer processes in self-assembled supramolecular donor-acceptor complexes in solutions and (ii) self-assembly and photophysical characterization of donor-acceptor films on titanium dioxide (TiO2) surface. The study of these systems aims to develop more complex architectures for artificial photosynthesis and understand factors that affect efficiency of the photoinduced energy and electron transfer processes in natural and artificial photosynthesis. This knowledge can be used for building photoactive molecular devices such as organic solar cells. The singlet excited state energy transfer in dyads formed via axial metal–ligand coordination of free-base porphyrin to metal (Mg, Ru) complexes of pthalocyanine was observed. The position of imidazole linker group on one of the meso-aryl groups of the free-base porphyrin was used to tune the rates of energy transfer. The two-point binding provides better control over complex geometry and it was implemented utilizing metal-ligand and crown-ether coordination in zinc chlorin–fullerene supramolecular dyads. This approach allowed to increase the binding efficiency and achieve a well-defined mutual orientation between the moieties. The electron transfer rate was found to depend on the donor-acceptor distance as well as the mutual orientation of the entities and could be manipulated by changing positions of binding groups. The donor-acceptor layers were assembled on TiO2 using two methods. First, a layer of covalently linked porphyrin-pthalocyanine dyads was formed on TiO2 via supramolecular approach. Then, a new method was developed to construct donor-acceptor two-layer films using separate porphyrin and fullerene molecules. In both cases, photo-excitation of donor molecules resulted in charge-separation (CS) inside the organic layer and sequential electron transfer towards the TiO2. Furthermore, the charge recombination (CR) process was found to be slower than for systems sensitized with single chromophores.

Due to scientific and technological advancements, investigations in modern medicine are producing more measurement data than ever before. Since a large amount of information exists, and it is also being produced at ever-increasing rates, no single person can digest all current knowledge of diseases. Data collected from large patient cohorts may contain valuable knowledge of diseases, which could be useful to clinicians when making diagnoses or choosing treatments. Making use of the large volumes of data in clinical decision-making requires ancillary help from information technologies, but such systems have not yet become widely available. This thesis addresses the challenge by proposing a computer-based decision support method that is suited to clinical use.This thesis presents the Disease State Index (DSI), a supervised machine learning method intended for the analysis of patient data. The DSI comprehensively compares patient data with previously diagnosed cases with or without a disease. Based on this comparison, the method provides an estimate of the state of disease progression in the patient. Interpreting the DSI is made possible by its visual counterpart, the Disease State Fingerprint (DSF), which allows domain experts to gain a comprehensive view of patient data and the state of the disease at a quick glance. In the design and development of these methods, both performance and applicability in clinical use were taken into account equally.Alzheimer’s disease (AD) is a slowly progressing neurodegenerative disease and one of the largest social and economic burdens in the world today, and it will continue to be so in the future. Studies with large patient cohorts have significantly improved our knowledge of AD during the last decade. This information should be made extensively available at memory clinics to maximize the benefits for diagnostics and treatment of the disease. The DSI and DSF methods proposed in this thesis were studied in the early diagnosis of AD and as a measure of disease progression in six original publications. The methods themselves and their implementation within a clinical decision support system, the PredictAD tool, were quantitatively evaluated with regard to their performance and potential benefits in clinical use. The results show that the methods and clinical decision support tool based on these methods can be used to follow disease progression objectively and provide earlier diagnoses of AD. These, in turn, could improve treatment efficacy due to earlier interventions and make drug trials more efficient by allowing better patient selection.

Dark fermentation is a potential carbon neutral process that exploits fermentative microorganisms to convert renewable organic substrates (e.g. lignocellulosic biomass and wastes) to H2, a non-fuel commodity and an ideal and clean energy carrier for replacing fossil fuels in the future. In the quest for developing a robust and efficient dark fermentative process for H2 production at industrial scale, the organism(s) selected to carry out the bioconversion is crucial. Thermophilic anaerobic bacteria have been drawing attention because they come close to meet the features that an ideal H2-producing organism should possess, including efficient breakdown and conversion of complex organic substrates to H2. In this study, a novel microorganism, Caloramator celer (former Thermobrachium celere), was evaluated for its potential to produce H2 from organic substrates. C. celer is a strict anaerobic, alkalitolerant, thermophilic bacterium capable of converting glucose to H2, CO2, acetate, ethanol and formate by mixed acid fermentation. In addition, C. celer shows remarkable features such as an extremely elevated growth rates (doubling time of 10 minutes) and the ability to grow in extreme conditions (Topt= 67 °C; pH67°Copt= 8.2). For these reasons C. celer may be of industrial interest for the conversion of organic waste material to H2 in an open (non-sterile) bioprocess system. However, for a biotechnological exploitation of this bacterium for H2 production it is crucial to understand the factors that regulate carbon and electron flux and therefore the final distribution of metabolites to channel the metabolic flux towards the desired product. The general goal of this study is to investigate the fermentative and energy metabolism of C. celer in order to understand how factors pertaining to the fermentation process can alter the metabolic fluxes. This is achieved by determining the relationship between fermentation conditions, physiological state, genome content, gene expression, metabolic fluxes and end-product yields through the combination of multiple methodologies such as conventional one-factor-at-a-time optimization, batch fermentations, comparative and functional genomics, transcription analysis and metabolic flux analysis. The final goal is to identify the optimal process conditions and metabolic state that maximize the H2 production from C. celer. In this study, glucose fermentation of C. celer was characterized in controlled and non-controlled cultivations and the effect of several parameters on growth and fermentation of C. celer was investigated to identify the optimal conditions for H2 production. In addition, the inhibitory effect of high concentrations of substrate and soluble end-products on growth and H2 production was studied to assess the robustness of C. celer. The whole-genome sequence provided valuable information for interpretation of experimental results and for directing experimental design. Genomic data were employed to design transcriptional analysis, construct a stoichiometric model employed in metabolic flux analysis (MFA), and infer the metabolic network and possible regulatory mechanisms that dictate metabolic fluxes. End-product synthesis profiles, and consequently H2 production, changed in response to several modifications of the culture conditions namely growth rate, growth phase, iron content in the medium, substrate availability and nutrient content, presence of soluble metabolites, pH and H2 concentration. The distribution of the fluxes at key metabolic nodes was found to be a function of thermodynamics as well as several physiological factors including genome content, growth and glycolytic rate, need for maintaining intracellular redox and pH homeostasis and only to some extent control of gene expression. The synthesis of formate and ethanol, two products of the branched metabolism of C. celer, was found to compete with H2-evolving reactions for the disposal of reducing equivalents. Ethanol and formate production served as an alternative to H2 production for regulating the redox state when hydrogenases were inhibited. Moreover, formate synthesis was strictly linked to the growth rate suggesting its possible role in anabolic metabolism. Low growth rates, low substrate availability and nutrient content, high iron availability, presence of subinhibitory concentration of acetate and ethanol, slightly acidic pH and low H2 concentrations minimized the redirection of carbon and electron flow to ethanol and formate synthesis and thus favored efficient H2 production. Kinetics of growth and H2 production were inhibited, albeit to different degrees, by high concentration of substrate and soluble end-products, whereas H2 yields remained marginally affected even in presence of considerable concentration of inhibitors. Acetate, the main soluble metabolite of the fermentation, inhibited H2 productivity due to the increasing ionic strength in the medium, rather than the uncoupling effect of the undissociated form. The critical substrate and salt concentration estimated for C. celer suggests that this organism is not particularly osmotolerant. In conclusion, this study provides valuable information on the capabilities of C. celer to efficiently produce H2 as well as on its limitations through a comprehensive investigation of its fermentative and energy metabolism. C. celer showed a great metabolic flexibility that allows redistribution of fluxes at key metabolic nodes to simultaneously control redox state and efficiently harvest energy from substrate even under unfavorable conditions. Understanding how fermentation conditions control the metabolic fluxes contributes to expand the knowledge of the thermophilic dark fermentative H2 production process.

The nanofabrication of organic layers on metal and metal alloy surfaces was studied in this thesis by employing photoelectron spectroscopy (PES) as the main analysis method. The motivation for this research is to introduce new properties to metal and metal alloy surfaces via self-assembly driven adsorption processes of organic molecules. Trimesic acid (TMA) and glycine adsorption on single crystal Cu(100) surface was investigated with PES and scanning tunnelling microscopy (STM). TMA on Cu(100) exhibits coverage dependent surface phases with drastic changes in the molecular orientation. The mobile TMA molecules at low coverage transform into Cu atom coordinated TMA networks and finally into carboxyl (COOH) functionalized, densely packed TMA monolayers. This is enabled due to three equivalent COOH groups symmetrically around a rigid benzene ring. Homo- and heterochiral surface phases of achiral glycine on Cu(100) were observed, and a new structural model for glycine bonding on Cu(100) based on STM and density functional theory calculations is presented. The coadsorption of aminopropyl trimethoxysilane (APS) and mercaptopropyl trimethoxysilane (MPS) on stainless steel was studied with an aim to incorporate MPS in APS matrix with tuneable distribution. In addition to the determination of elemental and chemical states at the surface, PES data was also used to determine the surface morphology by employing inelastic electron energy-loss background analysis. Synchrotron radiation mediated PES enabled the study of the in-depth distribution of the chemical states in non-destructive manner. The functionality of the APS/MPS overlayers on stainless steel was studied with chemical derivatization. The studies of TMA and glycine on Cu(100) provide important knowledge of the adsorption behaviour of small molecules on surfaces, which is crucial for understanding the adsorption phenomena of larger molecules, such as proteins on more complex substrates. The fabricated surface structures may also be applicable to molecular electronics or catalytic surfaces. The bifunctional silanization of stainless steel, on the other hand, is directly transferrable to industrial scale processes. The bifunctional APS/MPS nanomolecular layer on stainless steel works as a template, to which biomolecules can be covalently coupled with tuneable distribution. Hence, the stainless steel surface can be biofunctionalized for a range of applications, depending on the properties of the biomolecules.

Proceedings of the Inverse Days 2014 conference organized in Tampere 9th - 11th December 2014. This document contains the schedule of the conference, the list of participants and the abstracts of the talks given at the conference.

This thesis consists of three original articles that deal with lipid-protein interactions investigated using atomistic molecular dynamics simulations method, which in some cases were complemented with experimental data. Since very few molecular details of these important interactions are known, the data shown in this thesis can help to understand and develop a broader view on the role of lipids in protein's function. In the first part of this thesis, the membrane-binding part of the COMT protein was studied using the atomistic molecular dynamics simulations. The results indicate that the role of the transmembrane helix and the linker part of this protein is to enclose the enzymatic part of the protein in the close vicinity of the membrane, and therefore to keep it in the specific membrane-water interface environment. Moreover, the particular kind of protein fold, which includes a specific salt bridge in the linker part of the protein, was found in almost all of the simulations, and this information was evaluated further to reveal that this can be the general folding motif for all similar proteins that possess one transmembrane helix and a short linker part that joins it with the rest of the protein. By continuation of the urge to explain the role of the membrane in enzymatic function of COMT, another idea was also investigated: namely, the suggestion that ligands for that enzyme might have different characteristics in regard to their affinity to how the membrane was evaluated, to check whether the membrane binding part of COMT role is indeed meant to make it more accessible to those ligands which stay close to the membrane. This idea was studied with the atomistic molecular dynamics simulations where two COMT ligands—dopamine and L-dopa—were simulated with the membranes of various compositions, and furthermore the results were validated by experiments. The data from that study was consistent with the suggested idea of preferential binding of some ligands to lipids, but also this finding has been shown to have more possible implications for the neurotransmission process and other highly important physiological processes. The second part of this work focuses on the role of cholesterol in hydrophobic matching of peptides and the resulting sorting of transmembrane peptides according to their hydrophobic length. Experimental data from collaborating team suggested that under negative mismatch and the presence of cholesterol in membranes, peptides could laterally sort. Nevertheless, molecular mechanisms of that were unclear. Atomistic molecular dynamics simulations performed for this part of the thesis revealed that cholesterol increases the significance of the negative hydrophobic mismatch, and thus it shifts preference of proteins in such conditions to cluster into domains to minimize the mismatch. In the second part of this study, extended atomistic molecular dynamics simulations showed that cholesterol has a preference to stay in the vicinity of the peptide under negative mismatch when compared to a positive mismatch case. Even more strikingly, cholesterol orientates around the negatively mismatched peptide in a special geometrical configuration with its rough side exposed in the direction of peptide. In summation, studies for this work demonstrated a view on some aspects of the lipid-protein interactions at the molecular level retrieved through the atomistic molecular dynamics simulations. Importantly, many of the aspects presented here were validated with experiments or suggested explanation for the phenomena observed beforehand by experimental methods. Certainly, lipids are important for the function of proteins, and as it is shown in this thesis, joining experimental and computational approach is a very good way to understand this complicated interplay better and to provide atomistic details of these dynamic processes.

In this work, we study the second-order nonlinear optical properties of two kinds of nanoplasmonic structures. The first part of the study concerns regular arrays of L-shaped gold nanoparticles. The samples are investigated by linear characterization, i.e., extinction spectroscopy, and by second-harmonic generation. By incorporating the e ffective medium theory into the earlier developed nonlinear response tensor formalism, we determine the effects connected to higher-multipolar interactions in the second-order nonlinear response of the samples. We verify the effect of the sample quality on the presence of such multipolar contributions, as well as the effect of the local field enhancement, which is driven by the plasmon resonance. In the second part of the thesis, we investigate bulk-like materials with symmetry breaking along the direction of the normal to the sample surface. These samples are fabricated with aerosol techniques, which are relatively cheap and time efficient. The symmetry breaking is induced by the structure, i.e. by separating consecutive layers of silver-glass nanocomposite with silica glass. It is shown that after optimization such a structure might be interesting as a second-order nonlinear material. We also develop an analytical model that allows us to estimate the surface nonlinear tensor of such structures. Preliminary estimates show that decreasing the effective thickness of such structures could improve their nonlinear properties.

Ferritic stainless steels (FeCr-based alloys with low Ni content) have gained recent interest due to their excellent corrosion resistance, mechanical strength, and competitive price, which make them an attractive choice for many energy applications, for example, energy conversion and exhaust systems. The corrosion resistance results from the Cr-rich protective oxide layer that forms spontaneously under oxidizing conditions. At elevated temperatures, oxidation resistance can be enhanced by controlled surface treatments or by microalloying with elements that affect the oxide layer formation through segregation and interfacial oxidation. Today, further alloy development is required concerning the high-temperature oxidation resistance due to the increased operation temperatures. Furthermore, new alloy materials that form an electrically conductive non-volatile oxide layer under high-temperature conditions are required for the solid-oxide fuel cell interconnect applications. In this thesis, the segregation and oxidation phenomena on non-stabilized and Ti–Nb stabilized ferritic stainless steel alloys were investigated at 50–800 °C by photoemission spectroscopy, inelastic electron energy-loss background analysis, and electrochemical impedance spectroscopy. Firstly, the influence of controlled surface treatments on the initial stages of oxidation was investigated. The surface enrichment of Cr was induced by H2O preadsorption at low temperatures and by thermally induced cosegregation with N at high temperatures. The Cr-enriched surface was found beneficial against further oxidation by O2, but the effect was the most pronounced at low temperatures where the thermal diffusion of ions is not fast enough to support the oxidation. Secondly, microalloying with Nb was shown to improve the electrical properties of ferritic stainless steel alloys at 650 °C. The role of excess Nb was attributed to its high segregation rate and formation of conductive oxides at the oxide–metal interface. Furthermore, the Nb alloying induced the formation of (FeNbSi)-type Laves intermetallic phase in the alloy, which resulted in the non-uniform distribution of electrically resistive SiO2 at the interface. Therefore, the results presented in this thesis can be applied to design ferritic stainless steel alloys and surface treatments that facilitate the formation of the protective oxide layer with the optimum composition under various demanding application conditions, particularly, in the solid-oxide fuel cells.

This thesis explores a new type of gain medium for fiber lasers and amplifiers, active tapered double-clad fibers (TDCF), and describes their distinct properties, design, and applications. The TDCF technology is based on fabrication of axially non-uniform active optical fibers, with the aim to provide highly practical and cost-effective alternatives to the widely used fiber devices of today. While retaining all the flexibility associated to present-day double-clad fiber (DCF) instruments, these fibers offer the added benefits of low-brightness end pumping combined with high output brightness, a robust method for mode area scaling, and mitigation of certain deleterious optical effects. The TDCF technology was first established as a proof of concept during this dissertation work, followed by gradual power scaling to near-kW range in the continuous-wave (CW) regime, and to multi-mJ energies in pulsed operation. Given the preceding, practically nonexistent, high-power fiber laser (HPFL) research at the home university, this progress required substantial developments in thermal management, pumping techniques, and fiber design. The characteristics of the asymmetric and non-reciprocal active fiber waveguides were found to be very distinct from regular, cylindrical fibers. Their special features have been thoroughly studied within this work. The ytterbium-doped flared active DCFs studied in this dissertation work were applied as gain fibers in several types of laser cavities, as amplifiers in master oscillator – power amplifier (MOPA) configurations, and as pump sources for nonlinear processes. The appended publications demonstrate all these applications, and the related TDCF characteristics are discussed in the thesis. Given the directly-applicable wavelength versatility provided by manifold rare-earth dopants, the established technological platform appears particularly feasible for realization of compact MOPA systems for mid-power materials processing at 1 µm, as well as light detection and ranging (LIDAR) and medical applications at 1.5 µm.

Two advanced optical techniques for the detection of alkali vapors in high-temperature gases are introduced in this Thesis. Alkali vapors are released in solid fuel combustion and increase the maintenance costs of the power plant boilers. Especially, biomass and waste are challenging fuels for contemporary technology. Alkali related problems are controlled with proper fuel mixture ratios and additives that are mixed to fuels or sprayed into the boiler. However, the controlling increases the cost of the produced energy and the additives increase SO2 concentration. In order to study the alkali formation mechanisms and to control alkali concentrations in power plant boilers, fast, accurate and highly sensitive detection techniques are needed. This Thesis presents the fundamental absorption properties of the K, KCl and KOH vapors, reviews previously applied techniques for the detection of alkalis, and introduces two novel detection methods. The first method is based on the Photoacoustic Spectroscopy (PAS), that utilizes two branches of physics, namely optics and acoustics. A high-temperature PAS cell is introduced and applied to detect KCl and NaCl. Moreover, the possibility to apply the PAS cell to high-temperature salt-induced metal oxidation is discussed. The second method, which was fully developed during this work, is called Collinear Photofragmentation and Atomic Absorption Spectroscopy (CPFAAS). CPFAAS provides the limit of detection below parts per billion and the dynamic range of eight orders of magnitude in the detection of alkali chlorides. Moreover, the detection time of the CPFAAS measurement is in the order of micro second, which enables the diagnostics of the fast changing processes, such as combustion. The technique is calibration free and is integrable to "see-through" applications. In this Thesis, CPFAAS is applied to determine potassium vapor concentrations from a laboratory cell, flue gases emanated from 10 mg fuel samples, and flue gases in intermediate and large scale combustion boilers. The presented applications, modeling and comparison with previously applied detection methods show that CPFAAS enables new detection and monitoring capabilities from corrosive high temperature gases.

Nanoimprint lithography (NIL) is a novel but already a mature lithography technique. In this thesis it is applied to the fabrication of nanophotonic devices using its main advantage: the fast production of sub-micron features in high volume in a cost-effective way. In this thesis, fabrication methods for conical metal structures for plasmonic applications and sub-wavelength grating based broad-band mirrors are presented. Conical metal structures, nanocones, with plasmonic properties are interesting because they enable concentrating the energy of light in very tight spots resulting in very high local intensities of electromagnetic energy. The nanocone formation process is studied with several metals. Enhanced second harmonic generation using gold nanocones is presented. Bridged-nanocones are used to enhance Raman scattering from a dye solution. The sub-wavelength grating mirror is an interesting structure for photonics because it is very simple to fabricate and its reflectivity can be extended to the far infrared wavelength range. It also has polarization dependent properties which are used in this thesis to stabilize the output beam of infrared semiconductor disk laser. NIL is shown to be useful a technique in the fabrication of nanophotonic devices in the novel and rapidly growing field of plasmonics and also in more traditional, but still developing, semiconductor laser applications.

The demand for renewable energy is increasing due to increasing energy demand and global warming associated with increasing use of fossil fuels. Renewable energy can be derived from biological production of energy carriers from cellulosic biomass. These biochemical processes include biomass fermentation to hydrogen, methane and alcohols, and bioelectricity production in microbial fuel cells (MFCs). The objective of this study was to investigate the production of different energy carriers (hydrogen, methane, ethanol, butanol, bioelectricity) through biochemical processes. Hydrogen production potential of a hot spring enrichment culture from different sugars was determined, and hydrogen was produced continuously from xylose. Cellulolytic and hydrogenic cultures were enriched on cellulose, cellulosic pulp materials, and on silage at different process conditions. The enrichment cultures were further characterized. The effect of acid pretreatment on hydrogen production from pulp materials was studied and compared to direct pulp fermentation to hydrogen. Electricity and alcohol(s) were simultaneously produced from xylose in MFCs and the exoelectrogenic and alcohologenic enrichment cultures were characterized. In the end, the energy yields obtained from different biochemical processes were determined and compared. Hydrogen production potential from various hexose and pentose sugars was investigated with a hot spring enrichment culture. Lignocellulosic and cellulosic materials contain hexose and pentose sugars and thus, their efficient utilization for hydrogen production is important. The culture favored pentoses over hexoses for hydrogen fermentation with the highest yield of 0.71 mol H₂/mol xylose. Hydrogen was further produced continuously from xylose in a completely stirred tank reactor at 37°C and 45°C. Highest hydrogen yield and production rate at 45°C were 1.97 mol H₂/mol xylose and 7.3 mmol H₂/L/h, respectively, and were considerably higher than at 37°C. Clostridium acetobutylicum and Citrobacter freundii were the only bacteria detected at 45°C. Cellulolytic and hydrogenic cultures were enriched on cellulose from compost and rumen fluid materials at elevated temperatures. Elevated temperatures are associated with increased chemical and enzymatic reaction rates and hydrogen yields. Furthermore, elevated temperatures may inhibit hydrogen consuming bacteria and enhance biomass hydrolysis. The need and effects of heat treatments on hydrogen production potentials were determined. Hydrogen consumers remained absent even in cultures that were not heat-treated, while heat treatment enhanced hydrogen production at certain conditions. The highest hydrogen and ethanol yields of 0.4 mol H₂/mol hexose (1.9 mol H₂/mol hexosedegraded) and 0.2 mol EtOH/mol hexose (1.0 mol EtOH/mol hexosedegraded), respectively, were obtained with rumen fluid culture without heat treatment at 60°C and associated with 21 % cellulose hydrolysis. The rumen fluid enrichment culture contained mainly Clostridial species, from which a cellulolytic hydrogen-producer Clostridium stercorarium dominated. With compost enrichment culture, the highest hydrogen yields were obtained after heat treatment at 80°C for 20 min, although hydrogen was also produced without heat treating the culture. At 52°C, 1.4 mol H₂/mol hexose (2.4 mol H₂/mol hexosedegraded) and 0.4 mol EtOH/mol hexose (0.8 mol EtOH/mol hexosedegraded) were produced with 57 % cellulose degradation, while hydrogen production was negligible at temperatures above 52°C. Compost enrichment culture consisted of bacteria belonging to genera Thermoanaerobacterium and Clostridium, from which Clostridium cellulosi and C. stercorarium dominated. With both enrichment cultures, hydrogen yields were controlled by cellulose degradation efficiencies. Hydrogen and methane were produced from dry and wet pulp materials at different pH values. Compost enrichment culture did not produce methane at pH 9, whilst at pH 6 methane was produced from all tested substrates but dry conifer pulp. These pH values could be successfully used to enrich cellulolytic hydrogen-producing cultures. Fermentation of dry pulps at pH 6 resulted in 160 mL H₂/g TS. The highest hydrogen and methane yields were 560 mL H₂/g TS from wet birch pulp at pH 6 and 4800 mL CH₄/g TS from wet conifer pulp at pH 7, respectively. Inhibition of methanogens with BESA (2-Bromoethanesulfonic acid) resulted in decreased hydrogen yields, which may have resulted from the inhibitory effects of BESA on some Clostridial species. Cellulolytic and hydrogenic cultures enriched on pulp materials belonged mainly to phyla Bacteroidetes, Firmicutes and Proteobacteria. Direct pulp fermentation to hydrogen was compared to hydrogen fermentation from acid hydrolyzed pulps. Wet and dry pulps were hydrolyzed with concentrated sulfuric acid at 37°C. The optimal times for hydrolysis and the following sugars yields were 33-37 % after 90 min with wet pulps and 70-84 % after 180 min with dry pulps, respectively. Fermentation of dry conifer pulp hydrolysate resulted in 63 mL H₂/g TS. In conclusion, higher hydrogen yields were obtained from direct pulp fermentation to hydrogen (120 mL H₂/g TS). However, hydrogen production from acid hydrolyzed pulp took 10 days, while direct fermentation was completed in 28 days. Indigenous grass silage bacteria were enriched for hydrogen production at different silage concentrations. Lowest silage concentration of 25 g/L resulted in the highest hydrogen yield of 163 mL H₂/g TS, while increasing silage concentrations up to 200 g/L decreased the hydrogen yields but increased the cumulative hydrogen production. Silage fermentation to hydrogen was associated with bacteria related to Ruminobacillus xylanolyticum, Acetanaerobacterium elongatum and Clostridium populeti. Compost and anaerobic digester samples were enriched on xylose in MFCs resulting in simultaneous production of electricity and ethanol/butanol. Alcohol production was dependent on xylose concentration. Low xylose concentration of 1.0 g/L resulted in electron recoveries of 13-24 % and 40-65 % as electricity and ethanol, respectively. With higher xylose concentration of 4.0 g/L, electrons were directed mainly to butanol (33 %) and 4 % of the electrons were recovered as electricity. Ruminobacillus xylanolyticum was mainly responsible for xylose degradation in MFCs, while denitrifying bacteria, Comamonas denitrificans and Paracoccus pantotrophus, produced electricity from soluble metabolites. In this study, hydrogen, methane, alcohols and electricity were produced at laboratory scale in batch systems. The highest overall energy yields of 167 kJ/g TS and 113-130 kJ/g TS were obtained from direct pulp fermentation to both hydrogen and methane and from simultaneous production of electricity and butanol in MFCs, respectively. Cellulose fermentation resulted in the simultaneous production of hydrogen and ethanol with the highest overall energy yield of 4.9 kJ/g TS with compost enrichment culture. The highest energy yield as hydrogen, 5.3-6.0 kJ/g TS, was obtained from wet pulps. In summary, bacterial cultures producing different energy carrier(s) can be enriched from the same environmental sample by controlling the enrichment conditions. For example, compost sample was enriched for the production of (i) hydrogen and ethanol from cellulose at elevated temperatures by heat-treating the sample, (ii) hydrogen and/or methane from pulp materials at 37°C by changing the pH values, and (iii) electricity and alcohol(s) at 37°C in MFCs by changing xylose concentrations. It was shown that different operational conditions enrich for different microbial communities that are responsible for changes in fermentation patterns. In this study, cultures carrying out simultaneous cellulose hydrolysis and hydrogen fermentation were enriched from different sources at different operational conditions. These cultures were successfully utilized for cellulose to hydrogen fermentation in batch systems. Based on these results further research should be conducted on continuous hydrogen production from cellulosic materials.

In many application fields, like in biosensors, the sensing biomolecules are immobilized on solid surfaces to enable measuring of very small concentrations of molecules to be analysed. Such application fields are, for example, diagnostics, detection of abused drugs, environmental monitoring of toxins and tissue engineering.This thesis studies the immobilization of biomolecules (antibodies and Fab’-fragments, avidins and oligonucleotide sequences) on gold surfaces in biosensors. In order to achieve high nanomolar sensitivity even in difficult sample matrices, the effect of the sensing molecule immobilization type and concentration within these biomolecular surfaces were studied in detail. The suitability of these surfaces for neuronal stem cell attachment was also one of the topics. Real-time label-free detection was performed with surface plasmon resonance (SPR). The molecular surfaces in this study were constructed of biomolecules and repellent molecules, which formed self-assembled monolayers on gold. The molecules were immobilized on surfaces via reactive thiol- or disulphide groups. On surfaces assembled of proteins, the non-specific binding was minimized by hydrophilic polymer molecules and on surfaces assembled of oligonucleotides by means of lipoate molecules embedded on the surface in between the biomolecules, respectively.With these highly sensitive biomolecular surfaces, a nanomolar detection of small sized molecules such as the 3,4-methylenedioxymethamphetamine (MDMA) drug was achieved. MDMA was analysed from a difficult sample matrix of diluted saliva. Improved orientation of surface immobilized Fab’-fragments leading to a higher sensitivity was shown with surfaces constructed of cys-tagged avidins: Fab’-fragments immobilized via thiol-biotinylation to a surface constructed of cystagged avidins bound almost ten times the amount of antigen when compared to a conventional surface constructed of non-oriented wild-type avidins. Polymer molecules embedded in between the biomolecules efficiently reduced non-specific binding. Selective neuronal cell attachment was also shown with polymer and neuronal-specific antibody molecules physisorbed on cell culture plates. Only the differentiated neuronal cells attached to surfaces physisorbed with neuronalspecific antibodies, while the non-differentiated neurospheres did not.Selective surfaces were also developed for oligonucleotide sequences. Lipoatebased molecules efficiently reduced the non-specific binding of proteins and noncomplementary DNA. A nanomolar detection range was achieved for singlestranded, breast cancer-specific polymerase chain reaction (PCR) products. First, the shorter single-stranded PCR-products were analysed and a nanomolar detection range was achieved in buffer. In the following study, the DNA-surfaces were analysed in the presence of diluted serum. Even in diluted serum matrix, nanomolar concentrations of longer single- stranded sequences could be analysed due to the efficient blocking of non-specific binding of serum proteins.It was found that sensitive detection surfaces for biomolecular recognition can be achieved, when optimal function of the biomolecules is ensured by immobilizing the molecules on surfaces in an oriented manner towards the analyte. Efficient reduction of non-specific binding is also important in reaching highly sensitive label-free detection. The surfaces were also found to be effective in selective neuronal stem cell attachment. Monilla sovellusalueilla, kuten bioantureissa, tietylle analyytille herkät biomolekyylit kiinnitetään kiinteälle pinnalle, mikä mahdollistaa hyvin pienten analyyttipitoisuuksien määrittämisen. Tällaisia sovellusalueita ovat esimerkiksi sairauksien merkkiaineiden määritys, huumausaineiden tai ympäristömyrkkyjen määritys ja kudosteknologia.Tämä väitöskirja käsittelee biomolekyylien (vasta-aineiden ja Fab´-fragmenttien, avidiinien ja deoksiribonukleiinihappo (DNA) -koettimien) kiinnittämistä kultapinnoille bioantureissa. Tunnistavien molekyylien kiinnittämistapaa ja pitoisuutta biomolekulaarisilla pinnoilla tutkittiin yksityiskohtaisesti nanomolaarisen herkkyyden saavuttamiseksi myös vaikeista lähtömateriaaleista. Lisäksi tutkittiin, miten nämä pinnat soveltuvat kantasoluista erilaistettujen hermosolujen tartuttamiseen. Reaaliaikainen määritys ilman leima-aineita tehtiin pintaplasmoniresonanssin (SPR) avulla. Tutkimuksessa käytetyt itseasettuvat kalvot muodostettiin biomolekyyleistä ja hylkivistä molekyyleistä kultapinnoille. Molekyylit kiinnitettiin pinnoille tioli- tai disulfidiryhmien kautta. Proteiinipinnoilla epäspesifistä sitoutumista vähennettiin hydrofiilisten polymeerien avulla ja DNA-koetinpinnoilla vastaavasti lipoaattipohjaisten molekyylien avulla, jotka oli asetettu pinnoilla biomolekyylien väliin.Biomolekulaaristen pintarakenteiden avulla pystyttiin mittaamaan myös pienikokoinen 3,4-dimetyleenidioksimetyyliamfetamiini (MDMA) -huumausaine nanomolaarisessa pitoisuudessa. MDMA pystyttiin määrittämään myös laimennetusta sylkinäytteestä. Kysteiinimuokattujen avidiinipintojen avulla pystyttiin parantamaan Fab´-fragmenttien orientaatiota pinnoilla, mikä johti tavoiteltuihin, korkeampiin antigeenivasteisiin. Tioli-ryhmiin biotinyloituja Fab´-fragmentteja pystyttiin kiinnittämään kysteiinimuokattuihin avidiinipintoihin kymmenkertainen määrä verrattuna villityypin ei-orientoituihin avidiinipintoihin. Biomolekyylien väliin pinnoille kiinnitetyt polymeerimolekyylit ehkäisivät tehokkaasti epäspesifistä sitoutumista. Kun hermosolujen kasvatuslevyille kiinnitettiin polymeeriä ja hermosoluille spesifisiä vastaainemolekyylejä, levyille saatiin tarttumaan valikoidusti vain kantasoluista erilaistuneita hermosoluja. Kantasoluista erilaistumattomat solut eivät kiinnittyneet vastaainepolymeeripinnoille.Valikoivia pintoja kehitettiin myös DNA-koettimille. Proteiinien ja ei-pariutuvan DNA:n epäspesifinen sitoutuminen DNA-koetinpinnoille pystyttiin ehkäisemään tehokkaasti lipoaattipohjaisten molekyylien avulla. Yksijuosteiset rintasyöpäspesifiset DNA-juosteet pystyttiin tunnistamaan nanomolaarisella herkkyydellä. Ensin tutkittiin lyhyiden yksijuosteisten DNA-näytteiden tunnistusta puskuriliuoksessa saavuttaen nanomolaarinen herkkyys. Seuraavaksi DNA-pintojen toiminnallisuutta tutkittiin seerumiin laimennetuilla näytteillä. Myös pidempiä yksijuosteisia DNA-näytteitä pystyttiin määrittämään nanomolaarisina pitoisuuksina seerumilaimennoksesta, koska lipoaattipohjaiset molekyylit estivät tehokkaasti seerumin proteiinien epäspesifisen sitoutumisen pinnoille.Biomolekyylien määritykseen pystytään tekemään herkästi tunnistavia pintoja, kunhan biomolekyylien optimaalinen toiminta varmistetaan kiinnittämällä biomolekyylit pinnoille siten, että analyytin tunnistavat osat ovat orientoituneet analyyttiä kohden. Myös epäspesifisen sitoutumisen estäminen pinnoille on tärkeää korkean herkkyyden saavuttamiseksi leimavapaissa mittauksissa. Vasta-aine-polymeeripinnat todettiin hyvin toiminnallisiksi myös haluttaessa tartuttaa pinnoille valikoiden vain hermosoluja.

In this thesis, the robust output regulation problem is studied both in the time domain and in the frequency domain. The problem to be addressed is to find a stabilizing controller for a given plant so that every signal generated by an exogenous system, or shortly exosystem, is asymptotically tracked despite perturbations in the plant or some external disturbances. The exosystem generating the reference and disturbance signals is assumed to be infinite-dimensional. The main contribution of this thesis is to develop the robust regulation theory for an infinite-dimensional exosystem in the frequency domain framework. In order to do that, the time domain theory is studied in some detail and new results that emphasize the smoothness requirement on the reference and disturbance signals due to infinite-dimensionality of the exosystem are presented. Two types of controllers are studied, the feedforward controllers and the error feedback controllers, the latter of which facilitate robust regulation. These results exploit the structure at infinity of tha plant transfer function. In this thesis, a new definition of the structure at infinity suitable for infinite-dimensional systems is developed and its properties are studied. The frequency domain theory developed is based on the insights into the corresponding time domain theory. By following some recent time domain ideas the type of robustness and stability types are chosen so that they facilitate the use of an infinite-dimensional exosystem. The robustness is understood in the sense that stability should imply regulation. The chosen stability types resemble the time domain polynomial and strong stabilities and allow robust regulation of signals that have an infinite number of unstable dynamics along with transfer functions vanishing at infinity. The main contribution of this thesis is the formulation of the celebrated internal model principle in the frequency domain terms in a rather abstract algebraic setting. Unlike in the existing literature, no topological aspect of the problem is needed because of the adopted definition of robustness. The plant transfer function is only assumed to have a right or a left coprime factorization but not necessarily both. The internal model principle leads to a necessary and sufficient condition for the solvability of the robust regulation problem. The second main contribution of the thesis is to design frequency domain controllers for infinite-dimensional systems and exosystems. In this thesis, the Davison’s simple controller design for stable plants is extended to infinite-dimensional systems and exosystems. Then a controller design procedure for unstable plants containing two phases is proposed. In the first phase, a stabilizing controller is constructed for a given plant. The second phase is to design a robustly regulating controller for a stable part of the plant. This design procedure nicely combines with the Davison’s type controllers and is especially suitable for infinite-dimensional plants with transfer functions in the Callier-Desoer class of transfer functions.

Photoinduced electron transfer (ET) in dyads consisting of zinc porphyrins or zinc phthalocyanines as the electron donors and fullerene C60 as the electron acceptor was studied in different environments. Time-resolved absorption and emission spectroscopy studies were performed to monitor the populations of the transient states involved in the ET reaction. In porphyrin-fullerene dyads the reaction proceeds via an intramolecular exiplex intermediate. The precursor of this state can be observed as a broad absorption band, also known as charge transfer (CT) band, in the far red part of the spectrum. The molar absorption of the CT band was strong enough to populate the intramolecular exciplex directly from the ground state by exciting the dyad at its CT band. By using this strategy the number of intermediate states in the excitation relaxation process was reduced to two, and the quantitative analysis of the ET reactions involving the exciplex and the complete charge-separated (CS) state was carried out by constructing a kinetic model based on the Marcus theory of ET and Boltzmann distribution law. The model was successfully applied to a zinc porphyrin-fullerene dyad and it allowed to evaluate the ET parameters, e.g. the free and reorganization energies, the electronic couplings for the exciplex and the complete CS state, and the charge separation degree in the exciplex. The developed model can be applied for such dyads at any value of the dielectric constant of the solvent. Chloride binding to the central zinc of a zinc porphyrin-fullerene dyad results in drastic changes in the energies and lifetimes of the locally excited singlet state of porphyrin, the exciplex, and the complete CS state. The effects of the chloride coordination on the energies and lifetimes of the ET intermediates were examined and explained by the electric field effect on the donor chromophore induced by the negative charge of the chloride ion ligated to the central metal of porphyrin. The ligation results also in an increase of the oscillator strength of the CT absorption band. Compared to porphyrin-fullerene dyads the chloride binding effect was found to be much weaker in zinc phthalocyanine-fullerene dyads. The forward ET reaction in the zinc phthalocyaninefullerene dyads was found to occur in the Marcus inverted region. The latter conclusion was made because the chloride ligation to the zinc phthalocyanine moiety of the dyad was found to result in (i) an increase in the driving force of the ET reaction and (ii) a decrease in the ET rate constant.

This work focuses on the properties of model membranes rich in two lipids: cholesterol and cardiolipin. Despite being structurally very different, the biological significance of both of these lipids is partly related to their ability to promote order in lipid membranes. The studies presented here explore the function of these two lipids in membrane environments by use of atomic-scale molecular dynamics simulations. The first study concentrates on the properties of cholesterol and related sterols. The question as to whether the structure of cholesterol could be optimized by removing certain methyl groups is tackled by examining the effect of several modified sterols on general lipid bilayer properties. The results indicate an important role for the methyl groups and speak against calling them molecular fossils. The studies involving cardiolipin comprise three parts. At first, the influence of salt on general properties of cardiolipin-rich membranes is described. The field of research is subsequently broadened to include the interplay of cardiolipin with membrane-associated proteins: a membrane-embedded protein complex and\ a membrane-attacking antimicrobial peptide. The results show that cardiolipin amplifies some of the effects that salt has on membranes, particularly through restricting the dynamics of the other lipids' head groups. More generally, the presence of salt seems to mainly affect the dynamic properties of the bilayer, whereas changes in the structural properties are rather small. In the case of the protein embedded in a cardiolipin-rich membrane, three cardiolipin molecules are observed to freely diffuse to locations near the active sites of the protein. Notably, the locations are similar to those seen in crystal structures. When located in these spots, cardiolipin may participate in the proton uptake of the complex. The evidence supports the integral role of cardiolipin in the structure and function of this membrane protein. Finally, in the study involving antimicrobial peptides, the cardiolipin-rich membrane is observed to respond to the peptide attack by increasing membrane curvature. Notably, the bilayer structure is never broken, i.e. no lysis is observed. This may indicate a possible mechanism with which cardiolipin would be able to protect microbial membranes against the attacks of antimicrobial peptides. In summary, this work provides novel views on the functions of two vital lipids, cholesterol and cardiolipin, with use of atomic-scale molecular dynamics simulations.

The GaSb material system enables reaching the 2–3.5 µm wavelength range, which is important for many applications. Optically-pumped semiconductor disk lasers are attractive for producing high-power, high-brightness laser radiation with the wavelength controlled by the selection of materials. Such lasers can be quite compact, offer good beam quality, and produce ultra-short pulses by mode-locking with a semiconductor saturable absorber mirror. This thesis is concerned with the development of GaSb-based heterostructures for novel laser sources (i.e. semiconductor disk lasers) operating at 2–2.5 µm wavelengths, with both continuous wave and pulsed operation. In particular, the thesis includes new results concerning the development of GaSb/(AlGaIn)(AsSb) semiconductor disk lasers emitting high-power with broad wavelength tunability of about 50–150 nm. The broad tunability has been achieved by employing quantum wells with different operation wavelengths with asymmetric positioning in the microcavity. GaSb-based nonlinear saturable absorber mirrors were also studied and novel techniques related to their fabrication are presented. A semiconductor saturable absorber mirror was successfully used to mode-lock a high-power disk laser at 2 µm wavelength. Naturally fast absorption recovery of the absorber mirror was discovered and several techniques to control it were studied. Unlike for more conventional absorber materials, low-temperature growth revealed no relation to absorption recovery time. Instead the absorption recovery time could be changed by tailoring the strain and energy band structure in quantum wells and by using an optical cavity design with surface proximity quantum wells.

In this work, nonlinear light-matter interactions occurring at the focal volume of a tightly focused laser beam are studied and two new techniques for microscopy are developed. The techniques are based on the nonlinear phenomenon of second-harmonic generation, where two photons at the fundamental frequency combine into a single photon with doubled frequency. A mathematical treatment based on vector diffraction theory is applied for modelling the optical phenomena occurring at the focus. The vector treatment also predicts the occurrence of a new kind of multipolar light-matter interaction, which can lead to considerably large deviations from traditional scalar diffraction approaches. In order to demonstrate the predicted deviations and the capabilities of the developed imaging techniques, a nonlinear microscope is built and utilized. The first actual microscopy technique is developed to study chiral materials on a microscopic scale. Chirality, or handedness, is a symmetry property which has importance in several branches of science as well as in nature itself. Chiral objects lack mirror symmetry, and can occur in two different configurations, known as enantiomers, which are mirror images of each other. The optical and chemical behaviour of the enantiomers can vary drastically from each other. We show that the developed imaging technique is capable of recognizing chiral objects, such as molecules or nanostructures, from their enantiomers. The second imaging technique is developed to characterize the optical responses of three-dimensional nanostructures. These tiny man-made structures are utilized in the emerging fields of plasmonics and metamaterials. Recent advances in nanofabrication have made it possible to realize these nanostructures, which may in the future enable the control of light in unprecedented ways at the nanoscale. But these fabricated nanostructures often possess small defects, which may hinder their functionality. We show that by combining polarization-engineered focused vector beams with second- harmonic generation microscopy, we can provide an extremely sensitive tool to study the effects of nanoscale deformations on optical responses. The technique is used to characterize the optical responses of metallic nanocones, where nanoscale defects and deformations are seen to sometimes play a substantial role.

Glycerol is produced in large amounts as a by-product in biodiesel industry (10 kg per 100 kg biodiesel). By-products and waste materials are typically economical substrates for bioprocesses. Furthermore, microorganisms are able to combine the degradation of organic material with production of a wide range of metabolites and other cellular products. The current biotechnological interest of industrial glycerol lies on bioprocesses yielding environmentally friendly energy carrier molecules (hydrogen, methane, ethanol, butanol) and reduced chemicals (1,3-propanediol, dihydroxyacetone). Industrial glycerol also called as raw or crude glycerol, however, is a challenging substrate for microorganisms due to its impurities including alcohol, soaps, salts and metals. Halophiles (the salt-loving microorganisms) require salt for growth and heavy metal resistances have been characterized for numerous halophiles. Therefore, halophiles are potentially useful for the utilization of raw glycerol from biodiesel waste streams without pre-processing. Another challenge for large-scale microbial bioprocesses is a potential contamination with unfavorable microorganisms. For example, H2-producing systems tend to get contaminated with H2-consuming microorganisms. Extremophiles are organisms that have been adapted for life under extreme conditions, such as high salinity, high or low temperature, asidic or basic pH, dryness or high pressure. For extremophilic pure cultures contamination and thus the need to ensure a sterile environment might not be a problem due to the extreme process conditions that efficiently prevent the growth of most other bacteria. In addition, hypersaline environments (above 12 % NaCl) do not support the growth of H2 utilizing methanogens due to bioenergetic reasons. Halophilic fermentative H2 producers, on the other hand, have been shown to be active up to near salt saturation. The aims of the present study can be divided into two categories: 1) to develop an open raw glycerol degrading bioprocess primarily for H2 (clean and renewable energy carrier molecule) and secondarily for 1,3-PD (component of biopolymers) production employing halophilic pure cultures and 2) to obtain information on the genome of salt-tolerant organisms, halophilic survival strategies, and fermentation pathways via whole-genome sequencing. In the present study, glycerol fermentation of halophilic Halanaerobium saccharolyticum subsp. saccharolyticum and Halanaerobium saccharolyticum subsp. senegalense were characterized and H2 as well as 1,3-PD formation were initially optimized using commercial pure glycerol as a substrate. Growth, as well as the H2 and 1,3-PD production of H. saccharolyticum subsp. saccharolyticum were further optimized as small-scale batch experiments for vitamin B12 content, process conditions and medium composition. In addition, inhibitory effect of unpurified raw glycerol and the fermentation end-products (H2, acetate and 1,3-PD) along with contamination risk of an halophilic bioprocess were assessed. The glycerol fermentation and raw glycerol inhibition were compared to non-halophilic microorganisms Escherichia coli and/or Clostridium butyricum. Eventually, the halophilic H2 and 1,3-PD production from unpurified raw glycerol were combined in an open (non-sterile) two-stage fermentation process. The halophilic bacterial subspecies fermented glycerol mainly to H2, CO2 and acetate. H. saccharolyticum subsp. saccharolyticum yielded also 1,3-PD via a vitamin B12 dependent pathway. The subsp. senegalense grew poorly and after vitamin B12 optimization produced H2 less efficiently, and thus the subsp. saccharolyticum was chosen for the further studies. The H2 and 1,3-PD yielding pathways of H. saccharolyticum subsp. saccharolyticum were observed to compete, and the H2 production was remarkably enhanced when the 1,3-PD production was blocked by the unavailability of vitamin B12. The growth limiting factor of the particular raw glycerol fraction used in these studies was observed being methanol or other impurities rather than salt. Hypersaline environment (at and above 12.5 % NaCl) decreased efficiently the risk for contaminations and non-sterile conditions along with communal tap water were successfully applied in a bioprocess employing H. saccharolyticum subsp. saccharolyticum for production of H2 and 1,3-PD from unpurified raw glycerol. The genome of H. saccharolyticum subsp. saccharolyticum was sequenced and analysed on genetic level for phylogenetic and physiological characteristics, fermentation pathways as well as for resistances for metals, antibiotics and other toxic compounds. The genome sequence analysis revealed four putative hydrogen producing enzymes and a range of putative genes causing resistance for variety of antibiotics, heavy metals and other toxins. In conclusion, an open anaerobic bioprocess is applicable for halophilic pure cultures with no adverse contaminations. Additionally, H. saccharolyticum subsp. saccharolyticum is capable for direct utilization of the by-product from biodiesel production process and high-yield production of H2 and/or 1,3-PD. The genome sequence data provides insight into the relatively little-studied group of halophilic fermentative bacteria on genetic level.

Personal positioning is a dynamic estimation problem where the ability to assess the quality of the positioning service is as important as obtaining accurate position estimates. When estimating the position of a person, as opposed to e.g. an airplane, the type of motion can change at any time as a pedestrian can board a bus, or a cyclist can board a train. Also the changing surroundings in urban navigation influence the observation noise as tall buildings blocking the line of sight to satellites are full of reflecting surfaces. First we investigate classic robust estimation methods applied to the positioning problem, but then we focus on the Bayesian framework, as its generality allows us to take into account the abrupt changes in the state-space system. Gaussian mixture distributions and Markov chain indicator processes are used to model the changing systems. We evaluate the resulting systems mainly with sequential Monte Carlo methods, as this approach gives us an approximative joint posterior distribution of the errors and the state. We propose a general framework for the Bayesian receiver autonomous integrity monitoring in urban navigation based on the posterior probabilities. We also use the Bayesian framework to solve the explicit effect of the sensor errors in a nominal system that estimates the state with the assumption of no changes in the models. We use the estimated cumulated effect of the errors in the time series to determine whether error is present in the system at any time. Finally, a variational Bayes algorithm is developed for detecting changes in the system noise covariances.

Complex systems theory is a mathematical framework for studying interconnected dynamical objects. Usually these objects themselves are by construction simple, and their temporal behavior in isolation is easily predictable, but the way they are interconnected into a network allows emergence of complex, non-obvious phenomena. The emergent phenomena and their stability are dependent on both the intrinsic dynamics of the objects, the types of interactions between the objects, and the connectivity patterns between the objects. This work focuses on the third aspect, i.e., the structure of the network, although the other two aspects are inherently present in the study as well. Tools from graph theory are applied to generate and analyze the network structure, and the effect of the structure on the network dynamics is analyzed by various methods. The objects of interest are biological and physical systems, and special attention is given to spiking neuronal networks, i.e., networks of nerve cells that communicate by transmitting and receiving action potentials. In this thesis, methods for modelling spiking neuronal networks are introduced. Different point neuron models, including the integrate-and-fire model, are presented and applied to study the collective behaviour of the neurons. Special focus is placed on the emergence of network bursts, i.e., short periods of network-wide high-frequency firing. The occurrence of this behaviour is stable in certain regimes of connection strengths. This work shows that the network bursting is found to be more frequent in locally connected networks than in non-local networks, such as randomly connected networks. To gain a deeper insight, the aspects of structure that promote the bursting behaviour are analyzed by graph-theoretic means. The clustering coefficient and the maximal eigenvalue of the connectivity matrix are found the most important measures of structure in this matter, both expressing their relevance under different structural conditions. A range of different network structures are applied to confirm this result. A special class of connectivity is studied in more detail, namely, the connectivity patterns produced by simulations of growing and interconnecting neurons placed on a 2-dimensional array. Two simulators of growth are applied for this purpose. In addition, a more abstract class of dynamical systems, the Boolean networks, are considered. These systems were originally introduced as a model for genetic regulatory networks, but have thereafter been extensively used for more general studies of complex systems. In this work, measures of information diversity and complexity are applied to several types of systems that obey Boolean dynamics. The random Boolean networks are shown to possess high temporal complexity prior to reaching an attractor. Similarly, high values of complexity are found at a transition stage of another dynamical system, the lattice gas automaton, which can be formulated using the Boolean network framework as well. The temporal maximization of the complexity near the transitions between different dynamical regimes could therefore be a more general phenomenon in complex networks. The applicability of the information-theoretic framework is also confirmed in a study of bursting neuronal networks, where different types of networks are shown to be separable by the intrinsic information distance distributions they produce. The connectivities of the networks studied in this thesis are analyzed using graph-theoretic tools. The graph theory provides a mathematical framework for studying the structure of complex systems and how it affects the system dynamics. In the studies of the nervous system, detailed maps on the connections between neurons have been collected, although such data are yet scarce and laborious to obtain experimentally. This work shows which aspects of the structure are relevant for the dynamics of spontaneously bursting neuronal networks. Such information could be useful in directing the experiments to measure only the relevant aspects of the structure instead of assessing the whole connectome. In addition, the framework of generating the network structure by animating the growth of the neurons, as presented in this thesis, could serve in simulations of the nervous system as a reliable alternative to importing the experimentally obtained connectome.

Tässä diplomityössä esitetään tilastollisia lähestymistapoja GPS-satelliitin kellopoikkeaman estimoimiseksi ja ennustamiseksi satelliitin lähettämien broadcast-viestien pohjalta. Työ keskittyy esittämään bayesiläisen tilastotieteen perusteet riittäviltä osin ja kuvaamaan, miten teoria kytkeytyy GPS-satelliitin kellopoikkeaman estimoimiseen ja ennustamiseen. Satelliitin kellopoikkeamaprosessille esitetään löyhästi atomikellojen fysiikkaan perustuva malli ja sekä estimointi- että ennustustehtävä puetaan bayesiläisen tilastotieteen ongelmaksi. Erityistä huomiota kiinnitetään kellopoikkeamaprosessin mittaus- ja liikemallien valitsemiseen, sekä näiden muodostamien estimointitehtävien ratkaisumenetelmien esittämiseen. Diplomityössä esitettyjä algoritmeja testataan todellisilla GPS-satelliittien broadcast-viesteillä käyttäen National Geospatial-Intelligence Agencyn (NGA) tarkkoja efemeridejä vertailukohtana algoritmien esittämille ennusteille. Kokeellisista tuloksista voidaan havaita esitettyjen menetelmien parantavan hieman ennustuksen laatua, mutta suurempana hyötynä voidaan pitää prosessissa tapahtuvien häiriöiden tarkkailun, jolloin kellopoikkeaman ennustaminen on robustimpaa kuin pelkästään yksittäisiin broadcast-viesteihin pohjaavat ratkaisut.

Transbilayer phospholipid transfer (flip–flop) is a vital process for all cellular life. This intrinsically slow process is facilitated by integral membrane proteins called flippases and scramblases, which lower the free energy barrier to such a level that phospholipid flip–flop can rapidly occur either with help of external energy sources such as ATP or by thermal fluctuations alone. The existence of flippases has been known for some time, but the identities of the phospholipid translocators are still unknown. The existence of scramblases is less clear, since only related gene sequences have been identified so far. Also, the mechanisms by which phospholipids carry out flip–flops are yet to be identified. Further knowledge on scramblase activities could be helpful in understanding and preventing many diseases. For instance, programmed cell death begins when phosphatidylserine flips in an uncontrollable manner from the cytosolic leaflet to the extracellular side and this process is assumed to take place due to certain membrane proteins. This event in turn creates a signal for extracellular phagocytes by marking the cell for apoptosis. Apoptotic cells are often linked to tumor progression in which it is suggested that mutations in the scramblase genes can facilitate cancer growth. Proper scramblase activation during cancer progression could be used to remove harmful cells. Recent experimental studies have suggested that opsin, one of the G protein- coupled receptors found in photoreceptor cells of the retina, is a phospholipid flip- pase and its counterpart rhodopsin could be a possible scramblase. The purpose of this thesis is to use atomistic molecular dynamics simulations to examine the phos- pholipid scrambling properties of rhodopsin. The results can be used as a basis for further research regarding the subject. The possible flipping routes are investigated using steered MD simulations, and the free energy differences along the translocation paths are calculated by the umbrella sampling method. The results show that rhodopsin significantly lowers the free energy barrier of the membrane, thus functioning as a flippase. The observed flip–flop route taken by the phospholipids is located near the surface of rhodopsin.

Tämän diplomityön tarkoituksena oli tutkia huokoisen komposiitin biohajoavuuden alkuvaiheita materiaalin pinnalla. Materiaalista kehitetään huokoisia, biohajoavia kudostukirakenteita lääketieteellisiin sovelluksiin. Materiaalien pinta-analyyttisellä tutkimuksella pyritään selvittämään biomateriaalin pinnan rakennetta ja rakenteen muutoksia biohajoavuuden alussa. Tässä työssä tutkittu materiaali on poly(L-laktidi-co-kaprolaktoni):n β-trikalsiumfosfaattikomposiittia ja tutkimuksen kohteena on sekä ylikriittisellä hiilidioksidilla (scCO 2 ) huokoistettuja että huokoistamattomia näytteitä. Pinta-analyyttisenä tutkimusmenetelmänä on käytetty röntgenviritteistä fotoelektronispektroskopiaa (XPS) ja näytteiden biohajoaminen on toteutettu upottamalla tutkittavat näytteet suunnitelluiksi ajoiksi hydrolyysiliuokseen, joka jäljittelee biomateriaalin ympäristöä ihmiskehossa. Varsinaisten biohajoamisen alkuvaiheiden tutkimusten lisäksi on määritetty materiaalin sopivuutta elektronispektrokooppiseen tutkimukseen sekä röntgenviritteisen fotoelektronispektroskopian vaikutuksia tutkittavan materiaalin pinnalle. Röntgensäteilyn on todettu muokkaavan materiaalin pintaa ja se on huomioitava mittauksissa, vaikka se ei merkittävästi rajoitakaan mittauksia. Työn tulosten analysoinnissa on kehitetty sovitusparametrit erottamaan kopolymeerin eri monomeereista tulevat signaalit. Tämän työn tutkimuksissa on havaittu, että materiaalin biohajoaminen hydrolyysiliuoksessa käynnistyy 2 ja 12 viikon välisenä aikana. Biohajoamisen käynnistyminen voidaan havaita hydroksyyliryhmien suhteellisen pintakonsentraation kasvuna ja komonomeerien suhteiden muutoksena. Tulos on biomateriaalin ja biologisen ympäristön vuorovaikutuksen kannalta hyvä, koska tavoitteena on biomateriaalin biohajoamisen eteneminen kudoksen kasvun kanssa samassa tahdissa. Lisäksi pinta-analyyttisissä tutkimuksissa on havaittu, että β-trikalsiumfosfaatti on materiaalissa kopolymeerikalvon peittämänä. Tässä työssä saavutettujen tulosten avulla voidaan ymmärtää materiaalin pinnan koostumus ja biohajoaminen, ja tulosten avulla materiaalin ominaisuuksia voidaan parantaa entistä biofunktionaalisemmiksi.

Interferon gamma (IFNγ) is an immunomodulatory cytokine hormone, which participates in producing a host defense response to viral and bacterial infections. It has an important role in coordinating expression of immunologically relevant genes overall the human body. Malfunction of IFNγ signaling has been associated with many diseases, for instance deficiencies in resistance to infections such as tuberculosis, and autoimmune diseases including diabetes mellitus and multiple sclerosis. IFNγ acts via binding to the extracellular domains of its two specific transmembrane receptors, IFNγR1 and IFNγR2, which consequently bind signaling proteins on their intracellular domains, causing a signaling cascade into the nucleus. In this study, IFNγ and its two full length receptors were expressed and purified using protocols modified from previous studies of another transmembrane receptor rhodopsin. The structure of expressed IFNγ and binding of putative antibodies against IFNγ was analyzed using nuclear magnetic resonance (NMR) spectroscopy. IFNγ and IFNγR1 were successfully expressed transiently in COS-1 cell line, while IFNγR2 was stably expressed in HEK-293 cell line. Full length IFNγR1 and IFNγR2 were found to be expressed as covalently bound dimers with high resistance to reducing conditions. Expressed IFNγ was observed to undergo partial cleavage of glycosylation products and dimerization during storage. Overall, the experimented protocols produced the desired target proteins as heavily glycosylated forms with a high tendency for covalent oligomerization. The comparison of measured 2D NMR spectrum with an assigned reference spectrum confirmed the identity of the expressed full length IFNγ. One of the examined putative antibodies against IFNγ was observed to bind to the dimer interface and shift the NMR spectrum towards closer correspondence with monomeric IFNγ. Antibody binding is thus expected to change the conformation of IFNγ towards its native state from the observed higher oligomerization states and disturb its signaling function by disrupting the active dimer. In these experiments, enough protein was expressed for confirming the identity and functionality of IFNγ signaling complex proteins, and for a preliminary study of antibody binding. In order to produce sufficiently protein for studying the interactions of the IFNγ signaling complex in more detail, an inducible stably expressing cell line needs to be established for both receptors and IFNγ. The results of conducted NMR experiments show feasibility of detailed NMR studies of the mechanisms of protein-protein interactions both within the IFNγ signaling complex and with antibodies, in view of drug development. Interferon gamma (IFNγ) on immuunijärjestelmän sytokiinihormoni, joka osallistuu kehon puolustusreaktion aikaansaamiseen virus- ja bakteeri-infektioissa. Sillä on myös tärkeä rooli immuunijärjestelmän kannalta olennaisten geenien ilmentymisen säätelyssä kehon eri osissa. Monien sairauksien ilmenemiseen liittyy häiriöitä IFNγ-signaalinvälityksessä. IFNγ:n toimintahäiriö on yhdistetty muun muassa altistumisherkkyyteen tuberkuloosille ja useille muille infektiosairauksille sekä autoimmuunisairauksiin, kuten diabetekseen ja multippeliskleroosiin. IFNγ vaikuttaa sitoutumalla kahden kalvoreseptorinsa, IFNγR1:n ja IFNγR2:n, solunulkoisiin osiin. Tämän seurauksena reseptorien solunsisäisiin osiin liittyy spesifisiä viestinviejäproteiineja aikaansaaden tumaan johtavan viestinvälitysketjun. Tässä tutkimuksessa IFNγ ja sen molemmat reseptorit ilmennettiin ja puhdistettiin soveltamalla aiemmin tutkitun kalvoreseptorin, rhodopsinin, tuottamiseen käytettyjä menetelmiä. NMR-spektroskopialla suoritettiin tuotetun IFNγ:n rakenneanalyysi sekä tutkittiin sen sitoutumista kehitteillä oleviin IFNγ-vasta-aineisiin. IFNγ ja IFNγR ilmennettiin tilapäisesti tuottavassa COS-1 solulinjassa, kun taas IFNγR2:lle rakennettiin jatkuvasti tuottava HEK-293 solulinja. Täysmittaiset IFNγR1 ja IFNγR2 ilmenivät kovalenttisesti sitoutuneina dimeereinä, jotka pysyivät sitoutuneina tavallisesti neutraloivissa olosuhteissa. Tuotetussa IFNγ:ssa havaittiin osittaista glykosylaatiotuotteiden pilkkoutumista ja dimerisaatiota säilytettäessä sekä 4 °C että -20 °C lämpötilassa. Sovelletut proteiinien ilmentämis- ja puhdistusmenetelmät tuottivat siis kohdeproteiineja vahvasti glykosyloituneina muotoina, joilla oli taipumus oligomerisoitua kovalenttisesti. Ilmennetyn IFNγ:n identiteetti vahvistettiin vertaamalla sen mitattua 2D NMR-spektriä tunnettuun referenssispektriin. Yhden tutkituista vasta-aineista havaittiin sitoutuvan dimeerin rajapinnalla sijaitseviin aminohappoihin ja siirtävän NMR-spektriä kohti monomeerisen IFNγ:n spektriä. Vasta-aineen sitoutuminen todennäköisesti muuttaa IFNγ:n konformaatiota ja ehkäisee sen viestinvälitystoimintoa murtamalla aktiivisen dimeerin monomeereiksi. Tässä tutkimuksessa onnistuttiin tuottamaan riittävästi proteiinia ilmennetyn IFNγ:n identiteetin ja toiminnallisuuden todentamiseksi sekä vasta-aineiden sitoutumisen alustavaan analyysiin. Jotta IFNγ:n signaalinvälitysmekanismien yksityiskohtaiseen tutkimukseen saadaan riittävästi proteiinia, on sekä IFNγ:lle että sen molemmille reseptoreille vakiinnutettava indusoituva jatkuvatuottoinen solulinja. Suoritettujen NMR-kokeiden tulokset osoittavat, että NMR-analyysi on käyttökelpoinen menetelmä sekä INFγ-signaalinvälitysketjun että sitä vastaan kehitettävien vasta-aineiden proteiini–proteiini-vuorovaikutusten tutkimukseen.

If a molecule contains a proton donor and a proton acceptor group in close proximity, an intramolecular hydrogen bond may be formed between the groups. Upon electronic excitation, a proton transfer from the donor to the acceptor is possible. This process is called an excited-state intramolecular proton transfer (ESIPT). The ESIPT processes can be studied with spectroscopic techniques, because the different tautomers of an ESIPT compound have different spectroscopic properties. The energy difference between the ground state and first excited state is smaller for the proton transfer tautomer than for the normal tautomer, and thus the fluorescence bands of these two species are located at quite different wavelengths. One of the most promising compounds for ESIPT applications is 10-hydroxybenzo[h]quinoline (HBQ). Due to its restricted geometry and the specific alignment of oxygen and nitrogen atoms, this compound possesses an exceptionally strong intramolecular hydrogen bond. Thus, the ESIPT reaction is fast and does not suffer from solvent perturbation, not even in protic solvents. In this Thesis, a systematic study on the substituent effect on the ESIPT kinetics of HBQ derivatives is presented. The used measurement techniques include steady-state absorption and emission spectroscopy as well as time-resolved methods for determining fluorescence lifetimes. Several different HBQ derivatives are studied, and the performance of compounds with different substituents at the same position is compared. Furthermore, the effect of solvent polarity on the ESIPT rate is investigated by repeating the measurements in solvents with different polarities. ESIPT is reported to occur in most of the studied compounds. An electron-donating substituent at the methylenepyridine part of the molecule shifts the fluorescence emission of the proton transfer tautomer to shorter wavelengths compared to the non-substituted HBQ. An electron-withdrawing substituent has the opposite effect, respectively. Furthermore, the electron-withdrawing substituents induce an increase in the relaxation rate of the proton transfer tautomer, caused by the lowered basicity and proton-binding ability of the proton acceptor moiety. A remarkable solvent effect in the proton transfer relaxation rate is observed only for two compounds with a nitro substituent. Perhaps the position and the electron-withdrawing character of the substituent weaken the intramolecular hydrogen bond in these compounds, making it more vulnerable to perturbation by polar solvents. /Kir12

Testiaerosolien luotettava generointi on oleellinen osa aerosolifysiikan mittalaitteiden kalibrointia. Ilman onnistunutta kalibrointia laitteen käyttäytyminen nojaisi yksinään teoriaan, eikä teorian paikkansapitävyyttä pystyttäisi käytännössä todentamaan. Ali-paineimpaktorien kalibrointia varten tuotettavien testiaerosolien generoinnissa joudutaan turvautumaan useampaan menetelmään, sillä impaktorien toimintaskaala on hyvin laaja. Testiaerosoleiksi kelpaavia hiukkasia on kohtalaisen helppoa ja yksinkertaista valmistaa, mutta generointimenetelmien haasteet liittyvätkin siihen, miten hiukkasista saadaan monodispersiivisiä eli halkaisijaltaan mahdollisimman yhdenkokoisia. Mono-dispersiivisten hiukkasten avulla saadaan mitattua hiukkasten luokitteluun perustuvien mittalaitteiden vaste hiukkaskoon funktiona ja täten toimintaparametrit kalibroitua. Työssä on pyritty kuvaamaan käytetyimmät testiaerosolien generointimenetelmät, kuvaamaan generointiin liittyvät ongelmat sekä antamaan kehitysehdotuksia luotetta-vamman hiukkasgeneroinnin toteuttamiseksi. Tulokset on kuvattu uuden sähköisen ali-paineimpaktorin (ELPI+) kalibroinnin yhteydessä, mitä varten testiaerosoleja tuli tuottaa laajalla hiukkaskokoalueella 10 nm … 10 μm. Työn tuloksena osoittautui, että aikaisemmissa impaktorien kalibrointiraporteissa käytettyä haihdutus-tiivistysgeneraattoria (ECG) ei tulisi jatkossa käyttää ultrapieniä hiukkaskokoja suuremmille hiukkasille. Hiukkasten neutraloinnin yhteydessä muodos-tuvan bipolaarisen varausjakauman seurauksena hiukkasilla on liian suuri todennäköisyys varautua useammin kuin yhden alkeisvarauksen verran, mikä huonontaa sähköisen luokittelun avulla saatujen hiukkasten monodispersiivisyyttä. Vaikka impaktorien kalib-roinnin tuloksia voidaan jälkikäteen korjata niin kutsutun monivarauskorjauksen avulla, ei korjausta voida pitää luotettavana, ellei hiukkasiin muodostuvaa varausjakaumaa tun-neta täsmällisesti. Toistaiseksi bipolaariselle varausjakaumalle ei ole olemassa tarpeeksi yleispätevää mallia. Vaihtoehtona perinteisille sähköiseen luokitteluun perustuville menetelmille suosi-tellaan uutta kerran varattujen hiukkasten tuottamiseen perustuvaa hiukkaspitoisuus referenssiä (SCAR) mahdollisimman laajalle hiukkaskokoalueelle, minkä johdosta säh-köinen luokittelu voidaan toteuttaa huomattavasti luotettavammin ja täten generoida monodispersiivisempiä hiukkasia. Alipaineimpaktorien mittaamien suurimpien hiukkas-ten generointiin suositellaan edelleen perinteistä värähtelevään aukkoon perustuvaa ae-rosoligeneraattoria (VOAG). /Kir12

In this work designing and pricing of the recovery boiler were studied. The main goal was to find out how furnace screen heat transfer surface affects the recovery boiler price and performance. Two different boiler sizes were studied. Four different boilers were designed in both boiler sizes. One boiler was designed without furnace screen and three others with different size of furnace screens. The boilers were desinged so that they reached the same performances and were comparable. The furnace screen is an effective heat transfer surface and by adding the furnace screen the furnace can be designed lower. Furnace height has a significant effect on the total price of the boiler. On the other hand, the reduced furnace height yields shorter flue gas residence time, which can lead to incomplete combustion resulting e.g. increased emissions. Combustion air ratio and mixing of reactants with the air jets have a great effect on the combustion efficiency. In this study, the reduced residence time was compensated by the higher combustion air ratio by feeding more combustion air into the furnace. This way the effective mixing and the complete combustion were ensured. In order to find out the required amount of combustion air for the complete combustion CFD simulations and field data analysis were made. The target was to find out the effect of the combustion air ratio and the residence time on the CO emissions. According to these results boilers with the different heights could be designed so that they achieve also the same CO emissions. The designed boilers were priced and compared. Only the changing boiler structures were taken into account in pricing, which was sorted out to heat transfer surfaces, high pressure pipes, steel structures, auxiliary equipment and civil/structural costs. The material, manufacturing and erection costs were studied. The heat transfer surfaces and boiler building had the most significant portions in the share of costs.

Van der Waals -vuorovaikutus on suhteellisen heikko elektronien monen kappaleen dynamiikasta aiheutuva atomien, molekyylien ja pintojen välinen attraktio. Vuorovaikutus on merkittävä erityisesti silloin, kun vuorovaikuttavien kappaleiden välillä ei ole kemiallista sidosta. Diplomityön tarkoituksena on selvittää, kuinka hyvin Langreth–Lundqvist-funktionaali mallintaa van der Waals -vuorovaikutuksen. Tutkimuksessa käytetään GPAW-ohjelmistoon toteutettua Langreth–Lundqvist-funktionaalia (vdW-DFT). Funktionaalin toimivuutta verrataan Gaussian-ohjelmiston konfiguraatiovuorovaikutuslaskuihin ja tutkimusryhmän polkuintegraali–Monte Carlo -ohjelmiston tuloksiin. Menetelmien vertailu tehdään sovittamalla laskettuihin vetymolekyylin dissosiaatiopotentiaalikäyriin potenssifunktioita ja vertaamalla sovitettujen parametrien arvoja. Sovitettujen potenssifunktioiden eksponentti vastaa van der Waals -eksponenttia. Saaduista Langreth–Lundqvist-funktionaalin eksponentin arvoista nähdään, että lasketusta potentiaalikäyrästä löytyy van der Waals -vuorovaikutukselle ominainen 1/R^6 -termi. Menetelmiä vertailemalla voidaan kuitenkin todeta, että funktionaali ei mallinna vetymolekyylin kaikkia vuorovaikutuksia samalla tavalla, kuin konfiguraatiovuorovaikutus tai polkuintegraali–Monte Carlo. Lisäksi sovitusfunktioista saadaan C_6 van der Waals -kerroin, jonka Langreth–Lundqvist-funktionaalille saadut arvot poikkeavat kirjallisuudessa julkaistuista arvoista. Tämän voidaan todeta olevan puute funktionaalissa, koska konfiguraatiovuorovaikutuslaskun tuloksista saadut parametrin arvot ovat lähellä kirjallisuusarvoja.