Simulation methods in the modelling of bioaffinity assays

Computational model-based simulation methods were developed for the modelling of bioaffinity assays. Bioaffinity-based methods are widely used to quantify a biological substance in biological research, development and in routine clinical in vitro diagnostics. Bioaffinity assays are based on the high affinity and structural specificity between the binding biomolecules. The simulation methods developed are based on the mechanistic assay model, which relies on the chemical reaction kinetics and describes the forming of a bound component as a function of time from the initial binding interaction. The simulation methods were focused on studying the behaviour and the reliability of bioaffinity assay and the possibilities the modelling methods of binding reaction kinetics provide, such as predicting assay results even before the binding reaction has reached equilibrium. For example, a rapid quantitative result from a clinical bioaffinity assay sample can be very significant, e.g. even the smallest elevation of a heart muscle marker reveals a cardiac injury. The simulation methods were used to identify critical error factors in rapid bioaffinity assays. A new kinetic calibration method was developed to calibrate a measurement system by kinetic measurement data utilizing only one standard concentration. A nodebased method was developed to model multi-component binding reactions, which have been a challenge to traditional numerical methods. The node-method was also used to model protein adsorption as an example of nonspecific binding of biomolecules. These methods have been compared with the experimental data from practice and can be utilized in in vitro diagnostics, drug discovery and in medical imaging.

Porous silicon optical filters in gas sensing applications

In this thesis, the gas sensing properties of porous silicon-based thin-film optical filters are explored. The effects of surface chemistry on the adsorption and desorption of various gases are studied in detail. Special emphasis is placed on investigating thermal carbonization as a stabilization method for optical sensing applications. Moreover, the possibility of utilizing the increased electrical conductivity of thermally carbonized porous silicon for implementing a multiparametric gas sensor, which would enable simultaneous monitoring of electrical and optical parameters, is investigated. In addition, different porous silicon-based optical filter-structures are prepared, and their properties in sensing applications are evaluated and compared. First and foremost, thermal carbonization is established as a viable method to stabilize porous silicon optical filters for chemical sensing applications. Furthermore, a multiparametric sensor, which can be used for increasing selectivity in gas sensing, is also demonstrated. Methods to improve spectral quality in multistopband mesoporous silicon rugate filters are studied, and structural effects to gas sorption kinetics are evaluated. Finally, the stability of thermally carbonized optical filters in basic environments is found to be superior in comparison to other surface chemistries currently available for porous silicon. The results presented in this thesis are of particular interest for developing novel reliable sensing systems based on porous silicon, e.g., label-free optical biosensors.

The role of van der Waals interactions in the case of H2 adsorption on ruthenium (0001) surface

Computational material science with the Density Functional Theory (DFT) has recently gained a method for describing, for the first time the non local bonding i.e., van der Waals (vdW) bonding. The newly proposed van der Waals-Density Functional (vdW-DF) is employed here to address the role of non local interactions in the case of H2 adsorption on Ru(0001) surface. The later vdW-DF2 implementation with the DFT code VASP (Vienna Ab-initio Simulation Package) is used in this study. The motivation for studying H2 adsorption on ruthenium surface arose from the interest to hydrogenation processes. Potential energy surface (PES) plots are created for adsorption sites top, bridge, fcc and hcp, employing the vdW-DF2 functional. The vdW-DF yields 0.1 eV - 0.2 eV higher barriers for the dissociation of the H2 molecule; the vdW-DF seems to bind the H2 molecule more tightly together. Furthermore, at the top site, which is found to be the most reactive, the vdW functional suggests no entrance barrier or in any case smaller than 0.05 eV, whereas the corresponding calculation without the vdW-DF does. Ruthenium and H2 are found to have the opposite behaviors with the vdW-DF; Ru lattice constants are overestimated while H2 bond length is shorter. Also evaluation of the CPU time demand of the vdW-DF2 is done from the PES data. From top to fcc sites the vdW-DF computational time demand is larger by 4.77 % to 20.09 %, while at the hcp site it is slightly smaller. Also the behavior of a few exchange correlation functionals is investigated along addressing the role of vdW-DF. Behavior of the different functionals is not consistent between the Ru lattice constants and H2 bond lengths. It is thus difficult to determine the quality of a particular exchange correlation functional by comparing equilibrium separations of the different elements. By comparing PESs it would be computationally highly consuming.

Adsorption of hydrogen sulfide by modified cellulose nano/microcrystals

Hydrogen sulfide is toxic and hazardous pollutant. It has been under great interest for past few years because of all the time tighten environmental regulations and increased interest of mining. Hydrogen sulfide gas originates from mining and wastewater treatment systems have caused death in two cases. It also causes acid rains and corrosion for wastewater pipelines. The aim of this master thesis was to study if chemically modified cellulose nanocrystals could be used as adsorbents to purify hydrogen sulfide out from water and what are the adsorption capacities of these adsorbents. The effects of pH and backgrounds on adsorption capacities of different adsorbents are tested. In theoretical section hydrogen sulfide, its properties and different purification methods are presented. Also analytical detection methods for hydrogen sulfide are presented. Cellulose nano/microcrystals, properties, application and different modification methods are discussed and finally theory of adsorption and modeling of adsorption is shortly discussed. In experimental section different cellulose nanocrystals based adsorbents are prepared and tested at different hydrogen sulfide concentrations and in different conditions. Result of experimental section was that the highest adsorption capacity at one component adsorption had wet MFC/CaCO3. At different pH the adsorption capacities of adsorbents changed quite dramatically. Also change of hydrogen sulfide solution background did have effect on adsorption capacities. Although, when tested adsorbents’ adsorption capacities are compared to those find in literatures, it seems that more development of MFC based adsorbents is needed.

Kinetics of epsilon antitoxin antibodies in different strategies for active immunization of lambs against enterotoxaemia

Enterotoxaemia, a common disease that affects domestic small ruminants, is mainly caused by the epsilon toxin of Clostridium perfringens type D. The present study tested four distinct immunization protocols to evaluate humoral response in lambs, a progeny of non-vaccinated sheep during gestation. Twenty-four lambs were randomly allocated into four groups according to age (7, 15, 30 and 45 days), receiving the first dose of epsilon toxoid commercial vaccine against clostridiosis with booster after 30 days post vaccination. Indirect ELISA was performed after the first vaccine dose and booster to evaluate the immune response of the lambs. Results showed that for the four protocols tested all lambs presented serum title considered protective (≥0.2UI/ml epsilon antitoxin antibodies) and also showed that the anticipation of primovaccination of lambs against enterotoxaemia conferred serum title considered protective allowing the optimization of mass vaccination of lambs.

Ammoniumin, fosfaatin ja nitraatin poisto adsorption avulla

Kiinnostus ravinneionien ammoniumin, fosfaatin ja nitraatin poistoon liittyy niiden ne-gatiivisiin ympäristövaikutuksiin ja niiden poistoon jätevesistä on olemassa erilaisia tekniikoita. Tässä työssä ionien poistoa tutkittiin adsorptiotekniikan avulla. Siinä perus-ajatuksena on ionin kiinnittyminen adsorbentin pintaan, jolloin sen poistaminen käsitel-tävästä vedestä on mahdollista. Tässä diplomityössä tutkittiin eri adsorbentteja ammoniumin, fosfaatin ja nitraatin poistoon, ja päämääränä oli niiden yhtäaikainen poistaminen. Kokeita tehtiin niin laboratoriossa valmistetuille ravinneliuoksille kuin Yara Suomi Oy:n Siilinjärven (Yara) toimipaikalta toimitetuille vesille. Yaran vesien osalta pääpaino oli ammoniumin poistossa. Tutkimuksen haasteina olivat ionien erilaiset varaukset, jolloin esimerkiksi positiivisesti varautunut ammoniumioni kiinnittyi negatiivisesti varautuneen adsorbentin pintaan hel-poiten. Toisaalta negatiivisesti varautuneet anionit fosfaatti ja nitraatti suosivat positiivi-sesti varautuneita adsorbentteja. Myös muiden ionin läsnäolo joko edisti tai esti adsorboitumista ja joissain tapauksissa pH:lla oli suuri merkitys prosessin onnistumiseen. Saatuja tuloksia tarkasteltiin tutkittujen ionien poistoprosenttien ja isotermimallinnuksien kautta unohtamatta muita esille tulleita seikkoja. Saatujen tulosten mukaan etenkin kalsinoitu hydrotalsiitti poisti fosfaattia ja nitraattia, mutta se ei mainittavasti toiminut ammoniumille. Ammoniumille sen sijaan toimi par-haiten zeoliitit ja bentoniitti, jotka vähensivät myös Yaran vesien ammoniumpitoisuutta. Ionien yhtäaikainen poistaminen oli haastavaa ja sen parempi ymmärtäminen edellyttää jatkotutkimuksia. Yksi jatkotutkimuskohde voisi olla eri adsorbenttien yhdistäminen keskenään, ja tästä saatiin jo alustavia, rohkaisevia tuloksia.

Treatment of Fe-containing Acid Mine Waters in Fixed Bed Adsorption Column with Calcite Side-Stone

The acid mining drainage is considered the most significant environmental pollution problem around the world for the extensive formation acidic leachates containing heavy metals. Adsorption is widely used methods in water treatment due to it easy operation and the availability of a wide variety of commercial adsorbent (low cost). The primary goal of this thesis was to investigate the efficiency of neutralizing agents, CaCO3 and CaSiO3, and metal adsorption materials with unmodified limestone from Company Nordkalk Oy. In addition to this, the side materials of limestone mining were tested for iron adsorption from acidic model solution. This study was executed at Lappeenranta University of Technology, Finland. The work utilised fixed-bed adsorption column as the main equipment and large fluidized column. Atomic absorption spectroscopy (AAS) and x-ray diffraction (XRD) was used to determine ferric removal and the composition of material respectively. The results suggest a high potential for the studied materials to be used a low cost adsorbents in acid mine drainage treatment. From the two studied adsorbents, the FS material was more suitable than the Gotland material. Based on the findings, it is recommended that further studies might include detailed analysis of Gotland materials.

Methyl and ethyl chloride synthesis in microreactors

Methyl chloride is an important chemical intermediate with a variety of applications. It is produced today in large units and shipped to the endusers. Most of the derived products are harmless, as silicones, butyl rubber and methyl cellulose. However, methyl chloride is highly toxic and flammable. On-site production in the required quantities is desirable to reduce the risks involved in transportation and storage. Ethyl chloride is a smaller-scale chemical intermediate that is mainly used in the production of cellulose derivatives. Thus, the combination of onsite production of methyl and ethyl chloride is attractive for the cellulose processing industry, e.g. current and future biorefineries. Both alkyl chlorides can be produced by hydrochlorination of the corresponding alcohol, ethanol or methanol. Microreactors are attractive for the on-site production as the reactions are very fast and involve toxic chemicals. In microreactors, the diffusion limitations can be suppressed and the process safety can be improved. The modular setup of microreactors is flexible to adjust the production capacity as needed. Although methyl and ethyl chloride are important chemical intermediates, the literature available on potential catalysts and reaction kinetics is limited. Thus the thesis includes an extensive catalyst screening and characterization, along with kinetic studies and engineering the hydrochlorination process in microreactors. A range of zeolite and alumina based catalysts, neat and impregnated with ZnCl2, were screened for the methanol hydrochlorination. The influence of zinc loading, support, zinc precursor and pH was investigated. The catalysts were characterized with FTIR, TEM, XPS, nitrogen physisorption, XRD and EDX to identify the relationship between the catalyst characteristics and the activity and selectivity in the methyl chloride synthesis. The acidic properties of the catalyst were strongly influenced upon the ZnCl2 modification. In both cases, alumina and zeolite supports, zinc reacted to a certain amount with specific surface sites, which resulted in a decrease of strong and medium Brønsted and Lewis acid sites and the formation of zinc-based weak Lewis acid sites. The latter are highly active and selective in methanol hydrochlorination. Along with the molecular zinc sites, bulk zinc species are present on the support material. Zinc modified zeolite catalysts exhibited the highest activity also at low temperatures (ca 200 °C), however, showing deactivation with time-onstream. Zn/H-ZSM-5 zeolite catalysts had a higher stability than ZnCl2 modified H-Beta and they could be regenerated by burning the coke in air at 400 °C. Neat alumina and zinc modified alumina catalysts were active and selective at 300 °C and higher temperatures. However, zeolite catalysts can be suitable for methyl chloride synthesis at lower temperatures, i.e. 200 °C. Neat γ-alumina was found to be the most stable catalyst when coated in a microreactor channel and it was thus used as the catalyst for systematic kinetic studies in the microreactor. A binder-free and reproducible catalyst coating technique was developed. The uniformity, thickness and stability of the coatings were extensively characterized by SEM, confocal microscopy and EDX analysis. A stable coating could be obtained by thermally pretreating the microreactor platelets and ball milling the alumina to obtain a small particle size. Slurry aging and slow drying improved the coating uniformity. Methyl chloride synthesis from methanol and hydrochloric acid was performed in an alumina-coated microreactor. Conversions from 4% to 83% were achieved in the investigated temperature range of 280-340 °C. This demonstrated that the reaction is fast enough to be successfully performed in a microreactor system. The performance of the microreactor was compared with a tubular fixed bed reactor. The results obtained with both reactors were comparable, but the microreactor allows a rapid catalytic screening with low consumption of chemicals. As a complete conversion of methanol could not be reached in a single microreactor, a second microreactor was coupled in series. A maximum conversion of 97.6 % and a selectivity of 98.8 % were reached at 340°C, which is close to the calculated values at a thermodynamic equilibrium. A kinetic model based on kinetic experiments and thermodynamic calculations was developed. The model was based on a Langmuir Hinshelwood-type mechanism and a plug flow model for the microreactor. The influence of the reactant adsorption on the catalyst surface was investigated by performing transient experiments and comparing different kinetic models. The obtained activation energy for methyl chloride was ca. two fold higher than the previously published, indicating diffusion limitations in the previous studies. A detailed modeling of the diffusion in the porous catalyst layer revealed that severe diffusion limitations occur starting from catalyst coating thicknesses of 50 μm. At a catalyst coating thickness of ca 15 μm as in the microreactor, the conditions of intrinsic kinetics prevail. Ethanol hydrochlorination was performed successfully in the microreactor system. The reaction temperature was 240-340°C. An almost complete conversion of ethanol was achieved at 340°C. The product distribution was broader than for methanol hydrochlorination. Ethylene, diethyl ether and acetaldehyde were detected as by-products, ethylene being the most dominant by-product. A kinetic model including a thorough thermodynamic analysis was developed and the influence of adsorbed HCl on the reaction rate of ethanol dehydration reactions was demonstrated. The separation of methyl chloride using condensers was investigated. The proposed microreactor-condenser concept enables the production of methyl chloride with a high purity of 99%.

Purification of Hydrocarbon Waste Streams

Purification of hydrocarbon waste streams is needed to recycle valuable hydrocarbon products, reduce hazardous impacts on environment, and save energy. To obtain these goals, research must be focused on the search of effective and feasible purification and re-refining technologies. Hydrocarbon waste streams can contain both deliberately added additives to original product and during operation cycle accumulated undesired contaminants. Compounds may have degenerated or cross-reacted. Thus, the presence of unknown species cause additional challenges for the purification process. Adsorption process is most suitable to reduce impurities to very low concentrations. Main advantages are availability of selective commercial adsorbents and the regeneration option to recycle used separation material. Used hydrocarbon fraction was purified with various separation materials in the experimental part. First screening of suitable materials was done. In the second stage, temperature dependence and adsorption kinetics were studied. Finally, one fixed bed experiment was done with the most suitable material. Additionally, FTIR-measurements of hydrocarbon samples were carried out to develop a model to monitor the concentrations of three target impurities based on spectral data. Adsorption capacities of the tested separation materials were observed to be low to achieve high enough removal efficiencies for target impurities. Based on the obtained data, batch process would be more suitable than a fixed bed process and operation at high temperatures is favorable. Additional pretreatment step is recommended to improve removal efficiency. The FTIR-measurement was proven to be a reliable and fast analysis method for challenging hydrocarbon samples.

Kullan talteenotto takaisinuuttoliuoksista

Työssä tutkittiin kirjallisuuden ja laboratoriomittausten avulla vaihtoehtoja kullan pelkistämiseen ja talteenottoon kultauuton takaisinuuttoliuoksista. Tavoitteena oli löytää menetelmä, jolla saadaan puhdasta kiinteää lopputuotetta ilman kullan häviöitä. Käytettyjä pelkistimiä olivat D-(+)-glukoosi, natriumboorihydridi, L-askorbiinihappo, D-(-)-isoaskorbiinihappo ja aktiivihiili. Laboratoriokokeiden perusteella D-(-)-isoaskorbiinihappo sekä aktiivihiili olivat sopivimmat pelkistimet kokeissa käytetylle kultaliuokselle. Isoaskorbiinihapolla suoritettiin panoskokeita lasireaktorissa eri alku-pH:ssa sekä erilaisilla pelkistimen ja kullan moolisuhteilla. Tulosten perusteella havaittiin pH:n ja pelkistimen ylimäärän vaikuttavan merkittävästi lopputuotteen puhtauteen. Myös redox-potentiaalia säätämällä ja happopesulla pelkistyksen jälkeen voidaan vaikuttaa lopputuotteen puhtauteen. Aktiivihiilellä suoritettiin panoskokeita adsorptiotasapainojen (latausisotermi) ja kinetiikan tutkimiseksi. Hiileen on mahdollista saada kultaa 383 mg/g kuivaa hiiltä. Suurempi lataus voitaisiin saavuttaa käyttämällä hiiltä, jolla on pienempi partikkelikoko. Kolonnikokeita tehtiin eri virtausnopeuksilla. Kolonnikokeissa kullan dynaaminen adsorptiokapasiteetti hiileen odotetusti kasvoi virtausnopeuden laskiessa. Pienin käytetty virtausnopeus oli 2,40 BV/h, jolloin kapasiteetti oli 75,4 mg/g kuivaa hiiltä (c (Au feed) = 129 mg/L). Kullasta voidaan poistaa myös kolonnipelkistyksen jälkeen epäpuhtauksia happopesulla. Isoaskorbiinihapolla pelkistyksen kinetiikka on nopea ja sillä saatiin pelkistettyä puhdasta lopputuotetta. Sekä isoaskorbiinihappo, että aktiivihiili ovat potentiaalisia menetelmiä kullan talteenottoon.

Kinetics of TNF-alpha and IFN-gamma mRNA expression in islets and spleen of NOD mice

Insulin-dependent diabetes mellitus is caused by autoimmune destruction of pancreatic ß cells. Non-obese diabetic (NOD) mice spontaneously develop diabetes similar to the human disease. Cytokines produced by islet-infiltrating mononuclear cells may be directly cytotoxic and can be involved in islet destruction coordinated by CD4+ and CD8+ cells. We utilized a semiquantitative RT-PCR assay to analyze in vitro the mRNA expression of TNF-alpha and IFN-gamma cytokine genes in isolated islets (N = 100) and spleen cells (5 x 10(5) cells) from female NOD mice during the development of diabetes and from female CBA-j mice as a related control strain that does not develop diabetes. Cytokine mRNAs were measured at 2, 4, 8, 14 and 28 weeks of age from the onset of insulitis to the development of overt diabetes. An increase in IFN-gamma expression in islets was observed for females aged 28 weeks (149 ± 29 arbitrary units (AU), P<0.05, Student t-test) with advanced destructive insulitis when compared with CBA-j mice, while TNF-alpha was expressed in both NOD and CBA-j female islets at the same level at all ages studied. In contrast, TNF-alpha in spleen was expressed at higher levels in NOD females at 14 weeks (99 ± 8 AU, P<0.05) and 28 weeks (144 ± 17 AU, P<0.05) of age when compared to CBA-j mice. The data suggest that IFN-gamma and TNF-alpha expression in pancreatic islets of female NOD mice is associated with ß cell destruction and overt diabetes.

Adsorption of arsenic from ammonia containing waste water by ferrous hydroxide waste

Arsenic is a toxic substance. The amount of arsenic in waste water is a raising problem because of increasing mining industry. Arsenic is connected to cancers in areas where arsenic concentration in drinking water is higher than recommendations. The main object in this master’s thesis was to research how ferrous hydroxide waste material is adsorbed arsenic from ammonia containing waste water. In this master’s thesis there is two parts: theoretical and experimental part. In theoretical part harmful effects of arsenic, theory of adsorption, isotherms modeling of adsorption and analysis methods of arsenic are described. In experimental part adsorption capacity of ferrous hydroxide waste material and adsorption time with different concentrations of arsenic were studied. Waste material was modified with two modification methods. Based on experimental results the adsorption capacity of waste material was high. The problem with waste material was that at same time with arsenic adsorption sulfur was dissolving in solution. Waste material was purified from sulfur but purification methods were not efficient enough. Purification methods require more research.

Kinetics of cardiac and vascular remodeling by spontaneously hypertensive rats after discontinuation of long-term captopril treatment

Angiotensin-converting enzyme inhibitors reduce blood pressure and attenuate cardiac and vascular remodeling in hypertension. However, the kinetics of remodeling after discontinuation of the long-term use of these drugs are unknown. Our objective was to investigate the temporal changes occurring in blood pressure and vascular structure of spontaneously hypertensive rats (SHR). Captopril treatment was started in the pre-hypertensive state. Rats (4 weeks) were assigned to three groups: SHR-Cap (N = 51) treated with captopril (1 g/L) in drinking water from the 4th to the 14th week; SHR-C (N = 48) untreated SHR; Wistar (N = 47) control rats. Subgroups of animals were studied at 2, 4, and 8 weeks after discontinuation of captopril. Direct blood pressure was recorded in freely moving animals after femoral artery catheterism. The animals were then killed to determine left ventricular hypertrophy (LVH) and the aorta fixed at the same pressure measured in vivo. Captopril prevented hypertension (105 ± 3 vs 136 ± 5 mmHg), LVH (2.17 ± 0.05 vs 2.97 ± 0.14 mg/g body weight) and the increase in cross-sectional area to luminal area ratio of the aorta (0.21 ± 0.01 vs 0.26 ± 0.02 μm²) (SHR-Cap vs SHR-C). However, these parameters increased progressively after discontinuation of captopril (22nd week: 141 ± 2 mmHg, 2.50 ± 0.06 mg/g, 0.27 ± 0.02 μm²). Prevention of the development of hypertension in SHR by using captopril during the prehypertensive period prevents the development of cardiac and vascular remodeling. Recovery of these processes follows the kinetic of hypertension development after discontinuation of captopril.

Moisture adsorption characteristics of ginger slices

The moisture adsorption characteristics of dried ginger slices was studied to determine the effect of storage conditions on moisture adsorption for the purpose of shelf life prediction, selection of appropriate packaging materials, evaluate the goodness-of-fit of sorption models, and determine the thermodynamics of moisture adsorption for application in drying. There was a highly significant effect (p < 0.05) of water activity (a w), temperature, and pre-treatment on the equilibrium moisture content (EMC) of the dried ginger slices. At constant a w, the EMC decreased as temperature increased. The EMC of all samples increased as the a w increased at constant temperature. The sorbed moisture of the unpeeled ginger slices was higher than the peeled while those of unblanched samples were higher than the blanched. Henderson equation allows more accurate predictions about the isotherms with the lowest %RMS, and therefore, it describes best the adsorption data followed by GAB, Oswin, and Halsey models in that order. The monolayer moisture generally decreased with temperature for all samples. The isosteric heat decreased with moisture content approaching the asymptotic value or the latent heat of vaporization of pure water (∆Hst = 0) while the entropy of sorption was observed to increase with moisture content.