A cell spot microarray method for high-throughput biology

High-throughput screening of cellular effects of RNA interference (RNAi) libraries is now being increasingly applied to explore the role of genes in specific cell biological processes and disease states. However, the technology is still limited to specialty laboratories, due to the requirements for robotic infrastructure, access to expensive reagent libraries, expertise in high-throughput screening assay development, standardization, data analysis and applications. In the future, alternative screening platforms will be required to expand functional large-scale experiments to include more RNAi constructs, allow combinatorial loss-of-function analyses (e.g. genegene or gene-drug interaction), gain-of-function screens, multi-parametric phenotypic readouts or comparative analysis of many different cell types. Such comprehensive perturbation of gene networks in cells will require a major increase in the flexibility of the screening platforms, throughput and reduction of costs. As an alternative for the conventional multi-well based high-throughput screening -platforms, here the development of a novel cell spot microarray method for production of high density siRNA reverse transfection arrays is described. The cell spot microarray platform is distinguished from the majority of other transfection cell microarray techniques by the spatially confined array layout that allow highly parallel screening of large-scale RNAi reagent libraries with assays otherwise difficult or not applicable to high-throughput screening. This study depicts the development of the cell spot microarray method along with biological application examples of high-content immunofluorescence and phenotype based cancer cell biological analyses focusing on the regulation of prostate cancer cell growth, maintenance of genomic integrity in breast cancer cells, and functional analysis of integrin protein-protein interactions in situ.

A study of combustion phenomena in circulating fluidized beds by developing and applying experimental and modelling methods for laboratory-scale reactors

The results shown in this thesis are based on selected publications of the 2000s decade. The work was carried out in several national and EC funded public research projects and in close cooperation with industrial partners. The main objective of the thesis was to study and quantify the most important phenomena of circulating fluidized bed combustors by developing and applying proper experimental and modelling methods using laboratory scale equipments. An understanding of the phenomena plays an essential role in the development of combustion and emission performance, and the availability and controls of CFB boilers. Experimental procedures to study fuel combustion behaviour under CFB conditions are presented in the thesis. Steady state and dynamic measurements under well controlled conditions were carried out to produce the data needed for the development of high efficiency, utility scale CFB technology. The importance of combustion control and furnace dynamics is emphasized when CFB boilers are scaled up with a once through steam cycle. Qualitative information on fuel combustion characteristics was obtained directly by comparing flue gas oxygen responses during the impulse change experiments with fuel feed. A one-dimensional, time dependent model was developed to analyse the measurement data Emission formation was studied combined with fuel combustion behaviour. Correlations were developed for NO, N2O, CO and char loading, as a function of temperature and oxygen concentration in the bed area. An online method to characterize char loading under CFB conditions was developed and validated with the pilot scale CFB tests. Finally, a new method to control air and fuel feeds in CFB combustion was introduced. The method is based on models and an analysis of the fluctuation of the flue gas oxygen concentration. The effect of high oxygen concentrations on fuel combustion behaviour was also studied to evaluate the potential of CFB boilers to apply oxygenfiring technology to CCS. In future studies, it will be necessary to go through the whole scale up chain from laboratory phenomena devices through pilot scale test rigs to large scale, commercial boilers in order to validate the applicability and scalability of the, results. This thesis shows the chain between the laboratory scale phenomena test rig (bench scale) and the CFB process test rig (pilot). CFB technology has been scaled up successfully from an industrial scale to a utility scale during the last decade. The work shown in the thesis, for its part, has supported the development by producing new detailed information on combustion under CFB conditions.

The Dynamics of Force Fluctuations in Shear Granular Flows

Tämän työn tavoitteena oli tutkia rakeisen materiaalin kinematiikkaa ja rakentaa koelaitteisto rakeisen materiaalin leikkausjännitysvirtauksien tutkimiseen. Kokeellisessa osassa on keskitytty sisäisiin voimaheilahteluihin ja niiden ymmärtämiseen. Teoriaosassa on käyty läpi rakeisen materiaalin yleisiä ominaisuuksia ja lisäksi on esitetty kaksi eri tapaa mallintaa fysikaalisien ominaisuuksien heilahteluja rakeisessa materiaalissa. Nämä kaksi esitettyä mallinnusmenetelmää ovat skalaarinen q-malli ja simulointi. Skalaarinen q-malli määrittelee jokaiseen yksittäiseen rakeeseen kohdistuvan jännityksen, rakeen ollessa osa 2- tai 3-dimensionaalista asetelmaa. Tämän mallin perusidea on kuvata jännityksien epähomogeenisuutta, joka johtuu rakeiden satunnaisasettelusta. Simulointimallinnus perustuu event-driven algoritmiin, missä systeemin dynamiikkaa kuvataan yksittäisillä partikkelien törmäyksillä. Törmäyksien vaiheet ratkaistiin käyttämällä liikemääräyhtälöitä ja restituution määritelmää. Teoriaosuudessa käytiin vielä pieniltä osin läpi syitä jännitysheilahteluihin ja rakeisen materiaalin lukkiintumiseen. Tutkimuslaitteistolla tutkittiin rakeisen materiaalin käyttäytymistä rengasmaisessa leikkausjännitysvirtauksessa. Tutkimusosuuden päätavoitteena oli mitata partikkelien kosketuksista ja törmäyksistä johtuvia hetkellisiä voimaheilahteluja rengastilavuuden pohjalta. Rakeisena materiaalina tutkimuksessa käytettiin teräskuulia. Jännityssignaali ajan funktiona osoittaa suurta heilahtelua, joka voi olla jopa kertalukua keskiarvosta suurempaa. Tällainen suuren amplitudin omaava heilahtelu on merkittävä haittapuoli yleisesti rakeisissa materiaaleissa käytettyjen jatkuvuusmallien kanssa. Tällainen heilahtelu tekee käytetyt jatkuvuusmallit epäpäteviksi. Yleisellä tasolla jännityksien todennäköisyysjakauma on yhtäpitävä skalaarisen q-mallin tuloksien kanssa. Molemmissa tapauksissa todennäköisyysjakaumalla on eksponentiaalinen muoto.

On Variational Ensemble Kalman Filtering

The Extended Kalman Filter (EKF) and four dimensional assimilation variational method (4D-VAR) are both advanced data assimilation methods. The EKF is impractical in large scale problems and 4D-VAR needs much effort in building the adjoint model. In this work we have formulated a data assimilation method that will tackle the above difficulties. The method will be later called the Variational Ensemble Kalman Filter (VEnKF). The method has been tested with the Lorenz95 model. Data has been simulated from the solution of the Lorenz95 equation with normally distributed noise. Two experiments have been conducted, first with full observations and the other one with partial observations. In each experiment we assimilate data with three-hour and six-hour time windows. Different ensemble sizes have been tested to examine the method. There is no strong difference between the results shown by the two time windows in either experiment. Experiment I gave similar results for all ensemble sizes tested while in experiment II, higher ensembles produce better results. In experiment I, a small ensemble size was enough to produce nice results while in experiment II the size had to be larger. Computational speed is not as good as we would want. The use of the Limited memory BFGS method instead of the current BFGS method might improve this. The method has proven succesful. Even if, it is unable to match the quality of analyses of EKF, it attains significant skill in forecasts ensuing from the analysis it has produced. It has two advantages over EKF; VEnKF does not require an adjoint model and it can be easily parallelized.

Molecular modeling of asymmetric induction in heterogeneously catalyzed hydrogenation of the C=O bond

Modifiering av metallytor med starkt adsorberade kirala organiska molekyler är eventuellt den mest relevanta teknik man vet i dag för att skapa kirala ytor. Den kan utnyttjas i katalytisk produktion av enantiomeriskt rena kirala föreningar som behövs t.ex. som läkemedel och aromkemikalier. Trots många fördelar av asymmetrisk heterogen katalys jämfört med andra sätt för att få kirala föreningar, har den ändå inte blivit ett allmänt verktyg för storskaliga tillämpningar. Detta beror t.ex. på brist på djupare kunskaper i katalytiska reaktionsmekanismer och ursprunget för asymmetrisk induktion. I denna studie användes molekylmodelleringstekniker för att studera asymmetriska, heterogena katalytiska system, speciellt hydrering av prokirala karbonylföreningar till motsvarande kirala alkoholer på cinchona-alkaloidmodifierade Pt-katalysatorer. 1-Fenyl-1,2-propandion (PPD) och några andra föreningar, som innehåller en prokiral C=O-grupp, användes som reaktanter. Konformationer av reaktanter och cinchona-alkaloider (som kallas modifierare) samt vätebundna 1:1-komplex mellan dem studerades i gas- och lösningsfas med metoder som baserar sig på vågfunktionsteori och täthetsfunktionalteori (DFT). För beräkningen av protonaffiniteter användes också högst noggranna kombinationsmetoder såsom G2(MP2). Den relativa populationen av modifierarnas konformationer varierade som funktion av modifieraren, dess protonering och lösningsmedlet. Flera reaktant–modifierareinteraktionsgeometrier beaktades. Slutsatserna på riktning av stereoselektivitet baserade sig på den relativa termodynamiska stabiliteten av de diastereomeriska reaktant–modifierare-komplexen samt energierna hos π- och π*-orbitalerna i den reaktiva karbonylgruppen. Adsorption och reaktioner på Pt(111)-ytan betraktades med DFT. Regioselektivitet i hydreringen av PPD och 2,3-hexandion kunde förklaras med molekyl–yta-interaktioner. Storleken och formen av klustret använt för att beskriva Pt-ytan inverkade inte bara på adsorptionsenergierna utan också på de relativa stabiliteterna av olika adsorptionsstrukturer av en molekyl. Populationerna av modifierarnas konformationer i gas- och lösningsfas korrelerade inte med populationerna på Pt-ytan eller med enantioselektiviteten i hydreringen av PPD på Pt–cinchona-katalysatorer. Vissa modifierares konformationer och reaktant–modifierare-interaktionsgeometrier var stabila bara på metallytan. Teoretiskt beräknade potentialenergiprofiler för hydrering av kirala α-hydroxiketoner på Pt implicerade preferens för parvis additionsmekanism för väte och selektiviteter i harmoni med experimenten. De uppnådda resultaten ökar uppfattningen om kirala heterogena katalytiska system och kunde därför utnyttjas i utvecklingen av nya, mera aktiva och selektiva kirala katalysatorer.

Thermal Stress in a Roll-to-Roll Printed Electronics Substrate

The Roll-to-Roll process makes it possible to print electronic products continuously onto a uniform substrate. Printing components on flexible surfaces can bring down the costs of simple electronic devices such as RFID tags, antennas and transistors. The possibility of quickly printing flexible electronic components opens up a wide array of novel products previously too expensive to produce on a large scale. Several different printing methods can be used in Roll-to-Roll printing, such as gravure, spray, offset, flexographic and others. Most of the methods can also be mixed in one production line. Most of them still require years of research to reach a significant commercial level. The research for this thesis was carried out at the Konkuk University Flexible Display Research Center (KU-FDRC) in Seoul, Korea. A system using Roll-to-Roll printing requires that the motion of the web can be controlled in every direction in order to align different layers of ink properly. Between printers the ink is dried with hot air. The effects of thermal expansion on the tension of the web are studied in this work, and a mathematical model was constructed on Matlab and Simulink. Simulations and experiments lead to the conclusion that the thermal expansion of the web has a great influence on the tension of the web. Also, experimental evidence was gained that the particular printing machine used for these experiments at KU-FDRC may have a problem in controlling the speeds of the cylinders which pull the web.

Modeling of Liquid-Solid Flow in Industrial Scale

In the present work, liquid-solid flow in industrial scale is modeled using the commercial software of Computational Fluid Dynamics (CFD) ANSYS Fluent 14.5. In literature, there are few studies on liquid-solid flow in industrial scale, but any information about the particular case with modified geometry cannot be found. The aim of this thesis is to describe the strengths and weaknesses of the multiphase models, when a large-scale application is studied within liquid-solid flow, including the boundary-layer characteristics. The results indicate that the selection of the most appropriate multiphase model depends on the flow regime. Thus, careful estimations of the flow regime are recommended to be done before modeling. The computational tool is developed for this purpose during this thesis. The homogeneous multiphase model is valid only for homogeneous suspension, the discrete phase model (DPM) is recommended for homogeneous and heterogeneous suspension where pipe Froude number is greater than 1.0, while the mixture and Eulerian models are able to predict also flow regimes, where pipe Froude number is smaller than 1.0 and particles tend to settle. With increasing material density ratio and decreasing pipe Froude number, the Eulerian model gives the most accurate results, because it does not include simplifications in Navier-Stokes equations like the other models. In addition, the results indicate that the potential location of erosion in the pipe depends on material density ratio. Possible sedimentation of particles can cause erosion and increase pressure drop as well. In the pipe bend, especially secondary flows, perpendicular to the main flow, affect the location of erosion.

Large-eddy simulation of wind flows over complex terrains for wind energy applications

Wind energy has obtained outstanding expectations due to risks of global warming and nuclear energy production plant accidents. Nowadays, wind farms are often constructed in areas of complex terrain. A potential wind farm location must have the site thoroughly surveyed and the wind climatology analyzed before installing any hardware. Therefore, modeling of Atmospheric Boundary Layer (ABL) flows over complex terrains containing, e.g. hills, forest, and lakes is of great interest in wind energy applications, as it can help in locating and optimizing the wind farms. Numerical modeling of wind flows using Computational Fluid Dynamics (CFD) has become a popular technique during the last few decades. Due to the inherent flow variability and large-scale unsteadiness typical in ABL flows in general and especially over complex terrains, the flow can be difficult to be predicted accurately enough by using the Reynolds-Averaged Navier-Stokes equations (RANS). Large- Eddy Simulation (LES) resolves the largest and thus most important turbulent eddies and models only the small-scale motions which are more universal than the large eddies and thus easier to model. Therefore, LES is expected to be more suitable for this kind of simulations although it is computationally more expensive than the RANS approach. With the fast development of computers and open-source CFD software during the recent years, the application of LES toward atmospheric flow is becoming increasingly common nowadays. The aim of the work is to simulate atmospheric flows over realistic and complex terrains by means of LES. Evaluation of potential in-land wind park locations will be the main application for these simulations. Development of the LES methodology to simulate the atmospheric flows over realistic terrains is reported in the thesis. The work also aims at validating the LES methodology at a real scale. In the thesis, LES are carried out for flow problems ranging from basic channel flows to real atmospheric flows over one of the most recent real-life complex terrain problems, the Bolund hill. All the simulations reported in the thesis are carried out using a new OpenFOAM® -based LES solver. The solver uses the 4th order time-accurate Runge-Kutta scheme and a fractional step method. Moreover, development of the LES methodology includes special attention to two boundary conditions: the upstream (inflow) and wall boundary conditions. The upstream boundary condition is generated by using the so-called recycling technique, in which the instantaneous flow properties are sampled on aplane downstream of the inlet and mapped back to the inlet at each time step. This technique develops the upstream boundary-layer flow together with the inflow turbulence without using any precursor simulation and thus within a single computational domain. The roughness of the terrain surface is modeled by implementing a new wall function into OpenFOAM® during the thesis work. Both, the recycling method and the newly implemented wall function, are validated for the channel flows at relatively high Reynolds number before applying them to the atmospheric flow applications. After validating the LES model over simple flows, the simulations are carried out for atmospheric boundary-layer flows over two types of hills: first, two-dimensional wind-tunnel hill profiles and second, the Bolund hill located in Roskilde Fjord, Denmark. For the twodimensional wind-tunnel hills, the study focuses on the overall flow behavior as a function of the hill slope. Moreover, the simulations are repeated using another wall function suitable for smooth surfaces, which already existed in OpenFOAM® , in order to study the sensitivity of the flow to the surface roughness in ABL flows. The simulated results obtained using the two wall functions are compared against the wind-tunnel measurements. It is shown that LES using the implemented wall function produces overall satisfactory results on the turbulent flow over the two-dimensional hills. The prediction of the flow separation and reattachment-length for the steeper hill is closer to the measurements than the other numerical studies reported in the past for the same hill geometry. The field measurement campaign performed over the Bolund hill provides the most recent field-experiment dataset for the mean flow and the turbulence properties. A number of research groups have simulated the wind flows over the Bolund hill. Due to the challenging features of the hill such as the almost vertical hill slope, it is considered as an ideal experimental test case for validating micro-scale CFD models for wind energy applications. In this work, the simulated results obtained for two wind directions are compared against the field measurements. It is shown that the present LES can reproduce the complex turbulent wind flow structures over a complicated terrain such as the Bolund hill. Especially, the present LES results show the best prediction of the turbulent kinetic energy with an average error of 24.1%, which is a 43% smaller than any other model results reported in the past for the Bolund case. Finally, the validated LES methodology is demonstrated to simulate the wind flow over the existing Muukko wind farm located in South-Eastern Finland. The simulation is carried out only for one wind direction and the results on the instantaneous and time-averaged wind speeds are briefly reported. The demonstration case is followed by discussions on the practical aspects of LES for the wind resource assessment over a realistic inland wind farm.

The role of metal ions in selective and sustainable processes

Sustainability and recycling are core values in today’s industrial operations. New materials, products and processes need to be designed in such a way as to consume fewer of the diminishing resources we have available and to put as little strain on the environment as possible. An integral part of this is cleaning and recycling. New processes are to be designed to improve the efficiency in this aspect. Wastewater, including municipal wastewaters, is treated in several steps including chemical and mechanical cleaning of waters. Well-cleaned water can be recycled and reused. Clean water for everyone is one of the greatest challenges we are facing today. Ferric sulphate, made by oxidation from ferrous sulphate, is used in water purification. The oxidation of ferrous sulphate, FeSO4, to ferric sulphate in acidic aqueous solutions of H2SO4 over finely dispersed active carbon particles was studied in a vigorously stirred batch reactor. Molecular oxygen was used as the oxidation agent and several catalysts were screened: active carbon, active carbon impregnated with Pt, Rh, Pd and Ru. Both active carbon and noble metal-active carbon catalysts enhanced the oxidation rate considerably. The order of the noble metals according to the effect was: Pt >> Rh > Pd, Ru. By the use of catalysts, the production capacities of existing oxidation units can be considerably increased. Good coagulants have a high charge on a long polymer chain effectively capturing dirty particles of the opposite charge. Analysis of the reaction product indicated that it is possible to obtain polymeric iron-based products with good coagulation properties. Systematic kinetic experiments were carried out at the temperature and pressure ranges of 60B100°C and 4B10 bar, respectively. The results revealed that both non-catalytic and catalytic oxidation of Fe2+ to Fe3+ take place simultaneously. The experimental data were fitted to rate equations, which were based on a plausible reaction mechanism: adsorption of dissolved oxygen on active carbon, electron transfer from Fe2+ ions to adsorbed oxygen and formation of surface hydroxyls. A comparison of the Fe2+ concentrations predicted by the kinetic model with the experimentally observed concentrations indicated that the mechanistic rate equations were able to describe the intrinsic oxidation kinetics of Fe2+ over active carbon and active carbon-noble metal catalysts. Engineering aspects were closely considered and effort was directed to utilizing existing equipment in the production of the new coagulant. Ferrous sulphate can be catalytically oxidized to produce a novel long-chained polymeric iron-based flocculent in an easy and affordable way in existing facilities. The results can be used for modelling the reactors and for scale-up. Ferric iron (Fe3+) was successfully applied for the dissolution of sphalerite. Sphalerite contains indium, gallium and germanium, among others, and the application can promote their recovery. The understanding of the reduction process of ferric to ferrous iron can be used to develop further the understanding of the dissolution mechanisms and oxidation of ferrous sulphate. Indium, gallium and germanium face an ever-increasing demand in the electronics industry, among others. The supply is, however, very limited. The fact that most part of the material is obtained through secondary production means that real production quota depends on the primary material production. This also sets the pricing. The primary production material is in most cases zinc and aluminium. Recycling of scrap material and the utilization of industrial waste, containing indium, gallium and geranium, is a necessity without real options. As a part of this study plausible methods for the recovery of indium, gallium and germanium have been studied. The results were encouraging and provided information about the precipitation of these valuables from highly acidic solutions. Indium and gallium were separated from acidic sulphuric acid solutions by precipitation with basic sulphates such as alunite or they were precipitated as basic sulphates of their own as galliunite and indiunite. Germanium may precipitate as a basic sulphate of a mixed composition. The precipitation is rapid and the selectivity is good. When the solutions contain both indium and gallium then the results show that gallium should be separated before indium to achieve a better selectivity. Germanium was separated from highly acidic sulphuric acid solutions containing other metals as well by precipitating with tannic acid. This is a highly selective method. According to the study other commonly found metals in the solution do not affect germanium precipitation. The reduction of ferric iron to ferrous, the precipitation of indium, gallium and germanium, and the dissolution of the raw materials are strongly depending on temperature and pH. The temperature and pH effect were studied and which contributed to the understanding and design of the different process steps. Increased temperature and reduced pH improve the reduction rate. Finally, the gained understanding in the studied areas can be employed to develop better industrial processes not only on a large scale but also increasingly on a smaller scale. The small amounts of indium, gallium and germanium may favour smaller and more locally bound recovery.

Liquid-phase alcohol promoted methanol synthesis from CO2 and H2

Methanol is an important and versatile compound with various uses as a fuel and a feedstock chemical. Methanol is also a potential chemical energy carrier. Due to the fluctuating nature of renewable energy sources such as wind or solar, storage of energy is required to balance the varying supply and demand. Excess electrical energy generated at peak periods can be stored by using the energy in the production of chemical compounds. The conventional industrial production of methanol is based on the gas-phase synthesis from synthesis gas generated from fossil sources, primarily natural gas. Methanol can also be produced by hydrogenation of CO2. The production of methanol from CO2 captured from emission sources or even directly from the atmosphere would allow sustainable production based on a nearly limitless carbon source, while helping to reduce the increasing CO2 concentration in the atmosphere. Hydrogen for synthesis can be produced by electrolysis of water utilizing renewable electricity. A new liquid-phase methanol synthesis process has been proposed. In this process, a conventional methanol synthesis catalyst is mixed in suspension with a liquid alcohol solvent. The alcohol acts as a catalytic solvent by enabling a new reaction route, potentially allowing the synthesis of methanol at lower temperatures and pressures compared to conventional processes. For this thesis, the alcohol promoted liquid phase methanol synthesis process was tested at laboratory scale. Batch and semibatch reaction experiments were performed in an autoclave reactor, using a conventional Cu/ZnO catalyst and ethanol and 2-butanol as the alcoholic solvents. Experiments were performed at the pressure range of 30-60 bar and at temperatures of 160-200 °C. The productivity of methanol was found to increase with increasing pressure and temperature. In the studied process conditions a maximum volumetric productivity of 1.9 g of methanol per liter of solvent per hour was obtained, while the maximum catalyst specific productivity was found to be 40.2 g of methanol per kg of catalyst per hour. The productivity values are low compared to both industrial synthesis and to gas-phase synthesis from CO2. However, the reaction temperatures and pressures employed were lower compared to gas-phase processes. While the productivity is not high enough for large-scale industrial operation, the milder reaction conditions and simple operation could prove useful for small-scale operations. Finally, a preliminary design for an alcohol promoted, liquid-phase methanol synthesis process was created using the data obtained from the experiments. The demonstration scale process was scaled to an electrolyzer unit producing 1 Nm3 of hydrogen per hour. This Master’s thesis is closely connected to LUT REFLEX-platform.