Simulations of dimensionally reduced effective theories of high temperature QCD

Quantum chromodynamics (QCD) is the theory describing interaction between quarks and gluons. At low temperatures, quarks are confined forming hadrons, e.g. protons and neutrons. However, at extremely high temperatures the hadrons break apart and the matter transforms into plasma of individual quarks and gluons. In this theses the quark gluon plasma (QGP) phase of QCD is studied using lattice techniques in the framework of dimensionally reduced effective theories EQCD and MQCD. Two quantities are in particular interest: the pressure (or grand potential) and the quark number susceptibility. At high temperatures the pressure admits a generalised coupling constant expansion, where some coefficients are non-perturbative. We determine the first such contribution of order g^6 by performing lattice simulations in MQCD. This requires high precision lattice calculations, which we perform with different number of colors N_c to obtain N_c-dependence on the coefficient. The quark number susceptibility is studied by performing lattice simulations in EQCD. We measure both flavor singlet (diagonal) and non-singlet (off-diagonal) quark number susceptibilities. The finite chemical potential results are optained using analytic continuation. The diagonal susceptibility approaches the perturbative result above 20T_c$, but below that temperature we observe significant deviations. The results agree well with 4d lattice data down to temperatures 2T_c.

Effect of soil preparation of boreal spruce forest on air and soil temperature conditions in forest regeneration areas.

The effect of scarification, ploughing and cross-directional plouhing on temperature conditions in the soil and adjacent air layer have been studied during 11 consecutive growth periods by using an unprepared clear-cut area as a control site. The maximum and minimum temperatures were measured daily in the summer months, and other temperature observations were made at four-hour intervals by means of a Grant measuring instrument. The development of the seedling stand was also followed in order to determine its shading effect on the soil surface. Soil preparation decreased the daily temperature amplitude of the air at the height of 10 cm. The maximum temperatures on sunny days were lower in the tilts of the ploughed and in the humps of the cross-directional ploughed sites compared with the unprepared area. Correspondingly, the night temperatures were higher and so the soil preparation considerably reduced the risk of night frost. In the soil at the depth of 5 cm, soil preparation increased daytime temperatures and reduced night temperatures compared with unprepared area. The maximum increase in monthly mean temperatures was almost 5 °C, and the daily variation in the surface parts of the tilts and humps increased so that excessively high temperatures for the optimal growth of the root system were measured from time to time. The temperature also rose at the depths of 50 and 100 cm. Soil preparation also increased the cumulative temperature sum. The highest sums accumulated during the summer months were recorded at the depth of 5 cm in the humps of cross-directional ploughed area (1127 dd.) and in the tilts of the ploughed area (1106 dd.), while the corresponding figure in the unprepared soil was 718 dd. At the height of 10 cm the highest temperature sum was 1020 dd. in the hump, the corresponding figure in the unprepared area being 925 dd. The incidence of high temperature amplitudes and percentage of high temperatures at the depth of 5 cm decreased most rapidly in the humps of cross-directional ploughed area and in the ploughing tilts towards the end of the measurement period. The decrease was attributed principally to the compressing of tilts, the ground vegetation succession and the growth of seedlings. The mean summer temperature in the unprepared area was lower than in the prepared area and the difference did not diminish during the period studied. The increase in temperature brought about by soil preparation thus lasts at least more than 10 years.

Heated Nebulizer Microchips for Mass Spectrometry

Miniaturized analytical devices, such as heated nebulizer (HN) microchips studied in this work, are of increasing interest owing to benefits like faster operation, better performance, and lower cost relative to conventional systems. HN microchips are microfabricated devices that vaporize liquid and mix it with gas. They are used with low liquid flow rates, typically a few µL/min, and have previously been utilized as ion sources for mass spectrometry (MS). Conventional ion sources are seldom feasible at such low flow rates. In this work HN chips were developed further and new applications were introduced. First, a new method for thermal and fluidic characterization of the HN microchips was developed and used to study the chips. Thermal behavior of the chips was also studied by temperature measurements and infrared imaging. An HN chip was applied to the analysis of crude oil – an extremely complex sample – by microchip atmospheric pressure photoionization (APPI) high resolution mass spectrometry. With the chip, the sample flow rate could be reduced significantly without loss of performance and with greatly reduced contamination of the MS instrument. Thanks to its suitability to high temperature, microchip APPI provided efficient vaporization of nonvolatile compounds in crude oil. The first microchip version of sonic spray ionization (SSI) was presented. Ionization was achieved by applying only high (sonic) speed nebulizer gas to an HN microchip. SSI significantly broadens the range of analytes ionizable with the HN chips, from small stable molecules to labile biomolecules. The analytical performance of the microchip SSI source was confirmed to be acceptable. The HN microchips were also used to connect gas chromatography (GC) and capillary liquid chromatography (LC) to MS, using APPI for ionization. Microchip APPI allows efficient ionization of both polar and nonpolar compounds whereas with the most popular electrospray ionization (ESI) only polar and ionic molecules are ionized efficiently. The combination of GC with MS showed that, with HN microchips, GCs can easily be used with MS instruments designed for LC-MS. The presented analytical methods showed good performance. The first integrated LC–HN microchip was developed and presented. In a single microdevice, there were structures for a packed LC column and a heated nebulizer. Nonpolar and polar analytes were efficiently ionized by APPI. Ionization of nonpolar and polar analytes is not possible with previously presented chips for LC–MS since they rely on ESI. Preliminary quantitative performance of the new chip was evaluated and the chip was also demonstrated with optical detection. A new ambient ionization technique for mass spectrometry, desorption atmospheric pressure photoionization (DAPPI), was presented. The DAPPI technique is based on an HN microchip providing desorption of analytes from a surface. Photons from a photoionization lamp ionize the analytes via gas-phase chemical reactions, and the ions are directed into an MS. Rapid analysis of pharmaceuticals from tablets was successfully demonstrated as an application of DAPPI.

Anthraquinones from the Fungus Dermocybe sanguinea as Textile Dyes

This study is based on the multidiciplinary approach of using natural colorants as textile dyes. The author was interested in both the historical and traditional aspects of natural dyeing as well as the modern industrial applications of the pure natural compounds. In the study, the anthraquinone compounds were isolated as aglycones from the ectomycorrhizal fungus Dermocybe sanguinea. The endogenous beta-glucosidase of the fungus was used to catalyse the hydrolysis of the O-glycosyl linkage in emodin- and dermocybin-1-beta-D-glucopyranosides. The method, in which 10.45 kg of fresh fungi was starting material, yielded two fractions: 56.0 g of Fraction 1 (94% of the total amount of pigment,) consisting almost exclusively of the main pigments emodin and dermocybin, and 3.3 g of Fraction 2 (6%) consisting mainly of the anthraquinone carboxylic acids. The anthraquinone compounds in Fractions 1 and 2 were separated by one- and two-dimensional thin-layer-chromatography (TLC) using silica plates. 1D TLC showed that neither an acidic nor a basic solvent system alone separated completely all the anthraquinones isolated from D. sanguinea, in spite of the variation of the rations of the solvent components in the systems. Thus, a new 2D TLC technique was developed, applying n-pentanol-pyridine-methanol (6:4:3, v/v/v) and toluene-ethyl acetate-ethanol-formic acid (10:8:1:2, v/v/v/v) as eluents. Fifteen different anthraquinone derivatives were completely separated from one another. Emodin, physcion, endocrocin, dermolutein, dermorubin, 5-chlorodermorubin, emodin-1-beta-D-glucopyranoside, dermocybin-1-beta-D-glucopyranoside and dermocybin, and five new compounds, not earlier identified in D. sanguinea, 7-chloroemodin, 5,7-dichloroemodin, 5,7-dichloroendocrocin, 4-hydroxyaustrocorticone and austrocorticone, were separated and identified on the basis of their Rf-values, UV/Vis spectra and mass spectra. One substance remained unidentified, because of its very low concentration. The anthraquinones in Fractions 1 and 2 were preparatively separeted by liquid-liquid partition, with isopropylmethyl ketone and aqueous phosphate buffer as the solvent system. Advantage was taken of the principle of stepwise pH-gradient elution. The multiple liquid-liquid partition (MLLP) offered an excellent method for the preparative separation of compounds, which contain acidic groups such as the phenolic OH and COOH groups. Due to their strong aggregation properties, these compounds are, without derivatization, very difficult to separate on a preparative scale by chromatographic methods. By the MLLP method remarkable separations were achieved for the components in each mixture. Emodin and dermocybin were both obtained from Fraction 1 in a purity of at least 99%. Pure emodin and dermocybin were applied as mordant dyes to wool and polyamide and as disperse dyes to polyester and polyamide, using the high temperature (HT) technique. A mixture of dermorubin and 5-chlorodermorubin was applied as an acid dye to wool. In these experiments, synthetic dyes were used as references. Experiments were also performed using water extract of the air-dried fungi as dye liquor for wool and silk. The main colouring compounds in the crude water extract were emodin and dermocybin, which indicated that the O-glycosyl linkages in emodin- and dermocybin-1-beta-D-glucopyranosides were broken by the beta-glucosidase enzyme. Apparently, the hydrolysis occurred during the drying of the fungi and during the soaking of the dried fruit bodies overnight when preparing the dyebath. The colour of each dyed material was investigated in terms of the CIELAB L*, a* and b* values, and the colour fastness to light, washing and rubbing was tested according to the ISO standards. In the mordant dyeing experiments, emodin dyed wool and polyamide yellow and red, depending on the pH of the dyebath. Dermocybin gave purple and violet colours. The colour fastness of the mordant-dyed fabrics varied from good to moderate. The fastness properties of the natural anthraquinone carboxylic acids on wool were good, indicating the strength of the ionic bonds between the COO- groups of the dyes and the NH3+ groups of the fibres. In the disperse dyeing experiments, emodin dyed polyester bright yellow and dermocybin bright reddish-orange, and the fabrics showed excellent colour fastness. In contrast, emodin and dermocybin successfully dyed polyamide brownish-orange and wine-red, respectively, but with only moderate fastness. In industrial dyeing processes, natural anthraquinone aglycone mixtures dyed wool and silk well even at low concentrations of mordants, i.e. with 10% of the weight of the fibre (owf) of KAl(SO4)2 and 1 or 0.5% owf of other mordants. This study showed that purified natural anthraquinone compounds can produce bright hues with good colour-fastness properties in different textile materials. Natural anthraquinones have a significant potential for new dyeing techniques and will provide useful alternatives to synthetic dyes.

Microfiltration in cheese and whey processing

Milk microfiltration (0.05-0.2 um) is a membrane separation technique which divides milk components into casein-enriched and native whey fractions. Hitherto the effect of intensive microfiltration including a diafiltration step for both cheese and whey processing has not been studied. The microfiltration performance of skimmed milk was studied with polymeric and ceramic MF membranes. The changes caused by decreased concentration of milk lactose, whey protein and ash content for cheese milk quality and ripening were studied. The effects of cheese milk modification on the milk coagulation properties, cheese recovery yield, cheese composition, ripening and sensory quality as well as on the whey recovery yield and composition by microfiltration were studied. The functional properties of whey protein concentrate from native whey were studied and the detailed composition of whey protein concentrate powders made from cheese wheys after cheese milk pretreatments such as high temperature heat treatment (HH), microfiltration (MF) and ultrafiltration (UF) were compared. The studied polymeric spiral wound microfiltration membranes had 38.5% lower energy consumption, 30.1% higher retention of whey proteins to milk retentate and 81.9% lower permeate flux values compared to ceramic membranes. All studied microfiltration membranes were able to separate main whey proteins from skimmed milk. The optimal lactose content of Emmental cheese milk exceeded 3.2% and reduction of whey proteins and ash content of cheese milk with high concentration factor (CF) values increased the rate of cheese ripening. Reduction of whey protein content in cheese milk increased the concentration of caseinomacropeptide (CMP) of total proteins in cheese whey. Reduction of milk whey protein, lactose and ash content reduces milk rennet clotting time and increased the firmness of the coagulum. Cheese yield calculated from raw milk to cheese was lower with microfiltrated milks due to native whey production. Amounts of a-lactalbumin (a-LA) and b-lactoglobulin (b-LG) were significantly higher in the reference whey, indicating that HH, MF and UF milk pretreatments decrease the amounts of these valuable whey proteins in whey. Even low CF values in milk microfiltration (CF 1.4) reduced nutritional value of cheese whey. From the point of view of utilization of milk components it would be beneficial if the amount of native whey and the CMP content of cheese whey could be maximized. Whey protein concentrate powders made of native whey had excellent functional properties and their detailed amino acid composition differed from those of cheese whey protein concentrate powders.

Assessment and control of Bacillus cereus emetic toxin in food

Despite of improving levels of hygiene, the incidence of registered food borne disease has been at the same level for many years: there were 40 to 90 epidemics in which 1000-9000 persons contracted food poisoning through food or drinking water in Finland. Until the year 2004 salmonella and campylobacter were the most common bacterial causes of food borne diseases, but in years 2005-2006 Bacillus cereus was the most common. Similar developement has been published i.e. in Germany already in the 1990´s. One reason for this can be Bacillus cereus and its emetic toxin, cereulide. Bacillus cereus is a common environmental bacterium that contaminates raw materials of food. Otherwise than salmonella and campylobacter, Bacillus cereus is a heat resistant bacterium, capable of surviving most cooking procedures due to the production of highly thermo resistant spores. The food involved has usually been heat treated and surviving spores are the source of the food poisoning. The heat treatment induces germination of the spore and the vegetative cells then produce toxins. This doctoral thesis research focuses on developing methods for assessing and eliminating risks to food safety by cereulide producing Bacillus cereus. The biochemistry and physiology of cereulide production was investigated and the results were targeted to offer tools for minimizing toxin risk in food during the production. I developed methods for the extraction and quantitative analysis of cereulide directly from food. A prerequisite for that is knowledge of the chemical and physical properties of the toxin. Because cereulide is practically insoluble in water, I used organic solvents; methanol, ethanol and pentane for the extraction. For extraction of bakery products I used high temperature (100C) and pressure (103.4 bars). Alternaties for effective extraction is to flood the plain food with ethanol, followed by stationary equilibration at room temperature. I used this protocol for extracting cereulide from potato puree and penne. Using this extraction method it is also possible also extract cereulide from liquid food, like milk. These extraction methods are important improvement steps for studying of Bacillus cereus emetic food poisonings. Prior my work, cereulide extraction was done using water. As the result, the yield was poor and variable. To investigate suspected food poisonings, it is important to show actual toxicity of the incriminated food. Many toxins, but not cereulide, inactivate during food processing like heating. The next step is to identify toxin by chemical methods. I developed with my colleague Maria Andesson a rapid assay for the detection of cereulide toxicity, within 5 to 15 minutes. By applying this test it is possible to rapidly detect which food was causing the food poisoning. The chemical identification of cereulide was achieved using mass spectrometry. I used cereulide specific molecular ions, m/z (+/-0.3) 1153.8 (M+H+), 1171.0 (M+NH4+), 1176.0 (M+Na+) and 1191.7 (M+K+) for reliable identification. I investigated foods to find out their amenability to accumulate cereulide. Cereulide was formed high amounts (0.3 to 5.5 microg/g wet wt) when of cereulide producing B. cereus strains were present in beans, rice, rice-pastry and meat-pastry, if stored at non refrigerated temperatures (21-23C). Rice and meat pastries are frequently consumed under conditions where no cooled storage is available e.g. picnics and outdoor events. Bacillus cereus is a ubiquitous spore former and is therefore difficult to eliminate from foods. It is therefore important to know which conditions will affect the formation of cereulide in foods. My research showed that the cereulide content was strongly (10 to 1000 fold differences in toxin content) affected by the growth environment of the bacterium. Storage of foods under nitrogen atmosphere (> 99.5 %) prevented the production of cereulide. But when also carbon dioxide was present, minimizing the oxygen contant (< 1%) did not protect the food from formation of cereulide in preliminary experiments. Also food supplements affected cereulide production at least in the laboratory. Adding free amino acids, leucine and valine, stimulated cereulide production 10 to 20 fold. In peptide bonded form these amino acids are natural constituents in all proteins. Interestingly, adding peptide bonded leucine and valine had no significant effect on cereulide production. Free amino acids leucine and valine are approved food supplements and widely used as flawour modifiers in food technology. My research showed that these food supplements may increase food poisoning risk even though they are not toxic themselves.

Oxidative stability of phytosterols in food models and foods

An important safety aspect to be considered when foods are enriched with phytosterols and phytostanols is the oxidative stability of these lipid compounds, i.e. their resistance to oxidation and thus to the formation of oxidation products. This study concentrated on producing scientific data to support this safety evaluation process. In the absence of an official method for analyzing of phytosterol/stanol oxidation products, we first developed a new gas chromatographic - mass spectrometric (GC-MS) method. We then investigated factors affecting these compounds' oxidative stability in lipid-based food models in order to identify critical conditions under which significant oxidation reactions may occur. Finally, the oxidative stability of phytosterols and stanols in enriched foods during processing and storage was evaluated. Enriched foods covered a range of commercially available phytosterol/stanol ingredients, different heat treatments during food processing, and different multiphase food structures. The GC-MS method was a powerful tool for measuring the oxidative stability. Data obtained in food model studies revealed that the critical factors for the formation and distribution of the main secondary oxidation products were sterol structure, reaction temperature, reaction time, and lipid matrix composition. Under all conditions studied, phytostanols as saturated compounds were more stable than unsaturated phytosterols. In addition, esterification made phytosterols more reactive than free sterols at low temperatures, while at high temperatures the situation was the reverse. Generally, oxidation reactions were more significant at temperatures above 100°C. At lower temperatures, the significance of these reactions increased with increasing reaction time. The effect of lipid matrix composition was dependent on temperature; at temperatures above 140°C, phytosterols were more stable in an unsaturated lipid matrix, whereas below 140°C they were more stable in a saturated lipid matrix. At 140°C, phytosterols oxidized at the same rate in both matrices. Regardless of temperature, phytostanols oxidized more in an unsaturated lipid matrix. Generally, the distribution of oxidation products seemed to be associated with the phase of overall oxidation. 7-ketophytosterols accumulated when oxidation had not yet reached the dynamic state. Once this state was attained, the major products were 5,6-epoxyphytosterols and 7-hydroxyphytosterols. The changes observed in phytostanol oxidation products were not as informative since all stanol oxides quantified represented hydroxyl compounds. The formation of these secondary oxidation products did not account for all of the phytosterol/stanol losses observed during the heating experiments, indicating the presence of dimeric, oligomeric or other oxidation products, especially when free phytosterols and stanols were heated at high temperatures. Commercially available phytosterol/stanol ingredients were stable during such food processes as spray-drying and ultra high temperature (UHT)-type heating and subsequent long-term storage. Pan-frying, however, induced phytosterol oxidation and was classified as a rather deteriorative process. Overall, the findings indicated that although phytosterols and stanols are stable in normal food processing conditions, attention should be paid to their use in frying. Complex interactions between other food constituents also suggested that when new phytosterol-enriched foods are developed their oxidative stability must first be established. The results presented here will assist in choosing safe conditions for phytosterol/stanol enrichment.

Aspects and Applications of Pulse Sequence Design for Solution-State Nuclear Magnetic Resonance Spectroscopy

NMR spectroscopy enables the study of biomolecules from peptides and carbohydrates to proteins at atomic resolution. The technique uniquely allows for structure determination of molecules in solution-state. It also gives insights into dynamics and intermolecular interactions important for determining biological function. Detailed molecular information is entangled in the nuclear spin states. The information can be extracted by pulse sequences designed to measure the desired molecular parameters. Advancement of pulse sequence methodology therefore plays a key role in the development of biomolecular NMR spectroscopy. A range of novel pulse sequences for solution-state NMR spectroscopy are presented in this thesis. The pulse sequences are described in relation to the molecular information they provide. The pulse sequence experiments represent several advances in NMR spectroscopy with particular emphasis on applications for proteins. Some of the novel methods are focusing on methyl-containing amino acids which are pivotal for structure determination. Methyl-specific assignment schemes are introduced for increasing the size range of 13C,15N labeled proteins amenable to structure determination without resolving to more elaborate labeling schemes. Furthermore, cost-effective means are presented for monitoring amide and methyl correlations simultaneously. Residual dipolar couplings can be applied for structure refinement as well as for studying dynamics. Accurate methods for measuring residual dipolar couplings in small proteins are devised along with special techniques applicable when proteins require high pH or high temperature solvent conditions. Finally, a new technique is demonstrated to diminish strong-coupling induced artifacts in HMBC, a routine experiment for establishing long-range correlations in unlabeled molecules. The presented experiments facilitate structural studies of biomolecules by NMR spectroscopy.

Polymer Protected Gold Nanoparticles

Polymer protected gold nanoparticles have successfully been synthesized by both "grafting-from" and "grafting-to" techniques. The synthesis methods of the gold particles were systematically studied. Two chemically different homopolymers were used to protect gold particles: thermo-responsive poly(N-isopropylacrylamide), PNIPAM, and polystyrene, PS. Both polymers were synthesized by using a controlled/living radical polymerization process, reversible addition-fragmentation chain transfer (RAFT) polymerization, to obtain monodisperse polymers of various molar masses and carrying dithiobenzoate end groups. Hence, particles protected either with PNIPAM, PNIPAM-AuNPs, or with a mixture of two polymers, PNIPAM/PS-AuNPs (i.e., amphiphilic gold nanoparticles), were prepared. The particles contain monodisperse polymer shells, though the cores are somewhat polydisperse. Aqueous PNIPAM-AuNPs prepared using a "grafting-from" technique, show thermo-responsive properties derived from the tethered PNIPAM chains. For PNIPAM-AuNPs prepared using a "grafting-to" technique, two-phase transitions of PNIPAM were observed in the microcalorimetric studies of the aqueous solutions. The first transition with a sharp and narrow endothermic peak occurs at lower temperature, and the second one with a broader peak at higher temperature. In the first transition PNIPAM segments show much higher cooperativity than in the second one. The observations are tentatively rationalized by assuming that the PNIPAM brush can be subdivided into two zones, an inner and an outer one. In the inner zone, the PNIPAM segments are close to the gold surface, densely packed, less hydrated, and undergo the first transition. In the outer zone, on the other hand, the PNIPAM segments are looser and more hydrated, adopt a restricted random coil conformation, and show a phase transition, which is dependent on both particle concentration and the chemical nature of the end groups of the PNIPAM chains. Monolayers of the amphiphilic gold nanoparticles at the air-water interface show several characteristic regions upon compression in a Langmuir trough at room temperature. These can be attributed to the polymer conformational transitions from a pancake to a brush. Also, the compression isotherms show temperature dependence due to the thermo-responsive properties of the tethered PNIPAM chains. The films were successfully deposited on substrates by Langmuir-Blodgett technique. The sessile drop contact angle measurements conducted on both sides of the monolayer deposited at room temperature reveal two slightly different contact angles, that may indicate phase separation between the tethered PNIPAM and PS chains on the gold core. The optical properties of amphiphilic gold nanoparticles were studied both in situ at the air-water interface and on the deposited films. The in situ SPR band of the monolayer shows a blue shift with compression, while a red shift with the deposition cycle occurs in the deposited films. The blue shift is compression-induced and closely related to the conformational change of the tethered PNIPAM chains, which may cause a decrease in the polarity of the local environment of the gold cores. The red shift in the deposited films is due to a weak interparticle coupling between adjacent particles. Temperature effects on the SPR band in both cases were also investigated. In the in situ case, at a constant surface pressure, an increase in temperature leads to a red shift in the SPR, likely due to the shrinking of the tethered PNIPAM chains, as well as to a slight decrease of the distance between the adjacent particles resulting in an increase in the interparticle coupling. However, in the case of the deposited films, the SPR band red-shifts with the deposition cycles more at a high temperature than at a low temperature. This is because the compressibility of the polymer coated gold nanoparticles at a high temperature leads to a smaller interparticle distance, resulting in an increase of the interparticle coupling in the deposited multilayers.