Study of the kinetics and mechanism of rapid self-assembly in block copolymer thin films during solvo-microwave annealing

Microwave annealing is an emerging technique for achieving ordered patterns of block copolymer films on substrates. Little is understood about the mechanisms of microphase separation during the microwave annealing process and how it promotes the microphase separation of the blocks. Here, we use controlled power microwave irradiation in the presence of tetrahydrofuran (THF) solvent, to achieve lateral microphase separation in high- lamellar-forming poly(styrene-b-lactic acid) PS-b-PLA. A highly ordered line pattern was formed within seconds on silicon, germanium and silicon on insulator (SOI) substrates. In-situ temperature measurement of the silicon substrate coupled to condition changes during "solvo-microwave" annealing allowed understanding of the processes to be attained. Our results suggest that the substrate has little effect on the ordering process and is essentially microwave transparent but rather, it is direct heating of the polar THF molecules that causes microphase separation. It is postulated that the rapid interaction of THF with microwaves and the resultant temperature increase to 55 degrees C within seconds causes an increase of the vapor pressure of the solvent from 19.8 to 70 kPa. This enriched vapor environment increases the plasticity of both PS and PLA chains and leads to the fast self-assembly kinetics. Comparing the patterns formed on silicon, germanium and silicon on insulator (SOI) and also an in situ temperature measurement of silicon in the oven confirms the significance of the solvent over the role of substrate heating during "solvo-microwave" annealing. Besides the short annealing time which has technological importance, the coherence length is on a micron scale and dewetting is not observed after annealing. The etched pattern (PLA was removed by an Ar/O-2 reactive ion etch) was transferred to the underlying silicon substrate fabricating sub-20 nm silicon nanowires over large areas demonstrating that the morphology is consistent both across and through the film.

Tourism in Albarracín and Region. Local Public Action and dynamics in recent key sustainable tourism development

Spanish tourist destinations in rural areas have been established over more than two decades of implementation of various public policy instruments (mainly tourism and rural development policies). These convey complementary objectives in theory but provoke distant results in practice. The intervention of these instruments produces in the region of Sierra de Albarracín (Teruel) two types of destination whose sustainability is committed: the historical urban site of Albarracín as a consolidated cultural tourism destination based on heritage and the Sierra as a generic and incipient destination of rural tourism. It is discussed how the deployment of the local public action causes a fragmented territory in two models of management and tourism development. Cooperation is presented as a key element for the necessary rethinking of tourism development in the region.

Shapes and Dynamics of Blood Cells in Poiseuille and Shear Flows

The dynamics, shape, deformation, and orientation of red blood cells in microcirculation affect the rheology, flow resistance and transport properties of whole blood. This leads to important correlations of cellular and continuum scales. Furthermore, the dynamics of RBCs subject to different flow conditions and vessel geometries is relevant for both fundamental research and biomedical applications (e.g drug delivery). In this thesis, the behaviour of RBCs is investigated for different flow conditions via computer simulations. We use a combination of two mesoscopic particle-based simulation techniques, dissipative particle dynamics and smoothed dissipative particle dynamics. We focus on the microcapillary scale of several μm. At this scale, blood cannot be considered at the continuum but has to be studied at the cellular level. The connection between cellular motion and overall blood rheology will be investigated. Red blood cells are modelled as viscoelastic objects interacting hydrodynamically with a viscous fluid environment. The properties of the membrane, such as resistance against bending or shearing, are set to correspond to experimental values. Furthermore, thermal fluctuations are considered via random forces. Analyses corresponding to light scattering measurements are performed in order to compare to experiments and suggest for which situations this method is suitable. Static light scattering by red blood cells characterises their shape and allows comparison to objects such as spheres or cylinders, whose scattering signals have analytical solutions, in contrast to those of red blood cells. Dynamic light scattering by red blood cells is studied concerning its suitability to detect and analyse motion, deformation and membrane fluctuations. Dynamic light scattering analysis is performed for both diffusing and flowing cells. We find that scattering signals depend on various cell properties, thus allowing to distinguish different cells. The scattering of diffusing cells allows to draw conclusions on their bending rigidity via the effective diffusion coefficient. The scattering of flowing cells allows to draw conclusions on the shear rate via the scattering amplitude correlation. In flow, a RBC shows different shapes and dynamic states, depending on conditions such as confinement, physiological/pathological state and cell age. Here, two essential flow conditions are studied: simple shear flow and tube flow. Simple shear flow as a basic flow condition is part of any more complex flow. The velocity profile is linear and shear stress is homogeneous. In simple shear flow, we find a sequence of different cell shapes by increasing the shear rate. With increasing shear rate, we find rolling cells with cup shapes, trilobe shapes and quadrulobe shapes. This agrees with recent experiments. Furthermore, the impact of the initial orientation on the dynamics is studied. To study crowding and collective effects, systems with higher haematocrit are set up. Tube flow is an idealised model for the flow through cylindric microvessels. Without cell, a parabolic flow profile prevails. A single red blood cell is placed into the tube and subject to a Poiseuille profile. In tube flow, we find different cell shapes and dynamics depending on confinement, shear rate and cell properties. For strong confinements and high shear rates, we find parachute-like shapes. Although not perfectly symmetric, they are adjusted to the flow profile and maintain a stationary shape and orientation. For weak confinements and low shear rates, we find tumbling slippers that rotate and moderately change their shape. For weak confinements and high shear rates, we find tank-treading slippers that oscillate in a limited range of inclination angles and strongly change their shape. For the lowest shear rates, we find cells performing a snaking motion. Due to cell properties and resultant deformations, all shapes differ from hitherto descriptions, such as steady tank-treading or symmetric parachutes. We introduce phase diagrams to identify flow regimes for the different shapes and dynamics. Changing cell properties, the regime borders in the phase diagrams change. In both flow types, both the viscosity contrast and the choice of stress-free shape are important. For in vitro experiments, the solvent viscosity has often been higher than the cytosol viscosity, leading to a different pattern of dynamics, such as steady tank-treading. The stress-free state of a RBC, which is the state at zero shear stress, is still controversial, and computer simulations enable direct comparisons of possible candidates in equivalent flow conditions.

Social relations and dynamics shaping the implementation of the voluntary guidelines on small-scale fisheries (SSF guidelines) in South Africa

Integral to achieving the SSF Guidelines goal of targeting the most vulnerable and marginalized persons and eliminating discrimination is the need to have adequate understanding of the power relations and intersectionalities that shape access to and control over marine and other resources according to gender, age, race, ethnicity, labour and migratory status, disability, geographic location and other characteristics relevant in each national contexts. This monograph identifies and explores the key social relations and dynamics in the SSF fisheries sector in South Africa impacting the implementation of the SSF Guidelines. The monograph will be useful for researchers, scientists, fishworker organizations, environmentalists and anyone interested in the protection of marine biodiversity and the promotion of sustainable fisheries management.

Kinetics and Adsorption Isotherms of Bisphenol A, Estrone, 17 beta-Estradiol, and 17 alpha-Ethinylestradiol in Tropical Sediment Samples

The sorption of four endocrine disruptors, bisphenol A (BPA), estrone (E1), 17 beta-estradiol (E2), and 17 alpha-ethinylestradiol (EE2) in tropical sediment samples was studied in batch mode under different conditions of pH, time, and sediment amount. Data obtained from sorption experiments using the endocrine disruptors (EDs) and sediments containing different amounts of organic matter showed that there was a greater interaction between the EDs and organic matter (OM) present in the sediment, particularly at lower pH values. The pseudosecond order kinetics model successfully explained the interaction between the EDs and the sediment samples. The theoretical and experimentally obtained q (e) values were similar, and k values were smaller for higher SOM contents. The k (F) values, obtained from the Freundlich isotherms, varied in the ranges 4.2-7.4 x 10(-2) (higher OM sediment sample, S(2)) and 1.7 x 10(-3)-3.1 x 10(-2) (lower OM sediment sample, S(1)), the latter case indicating an interaction with the sediment that increased in the order: EE2 > > E2 > E1 > BPA. These results demonstrate that the availability of endocrine disruptors may be directly related to the presence of organic material in sediment samples. Studies of this kind provide an important means of understanding the mobility, transport, and/or reactivity of this type of emergent contaminant in aquatic systems.

Species-specific kinetics and zonation of hepatic DNA synthesis induced by ligands of PPARα

PPARα ligands evoke a profound mitogenic response in rodent liver, and the aim of this study was to characterise the kinetics of induction of DNA synthesis. The CAR ligand, 1,4-bis[2-(3,5- dichoropyridyloxy)]benzene, caused induction of hepatocyte DNA synthesis within 48 hours in 129S4/SvJae mice, but the potent PPARα ligand, ciprofibrate, induced hepatocyte DNA synthesis only after 3 or 4 days dosing; higher or lower doses did not hasten the DNA synthesis response. This contrasted with the rapid induction (24 hours) reported by Styles et al. (Carcinogenesis 9:1647-1655). C57BL/6 and DBA/2J mice showed significant induction of DNA synthesis after 4, but not 2, days ciprofibrate treatment. Alderley Park and 129S4/SvJae mice dosed with methylclofenapate induced hepatocyte DNA synthesis at 4, but not 2, days after dosing, and proved that inconsistency with prior work was not due to a difference in mouse strain or PPARα ligand. Ciprofibrate-induced liver DNA synthesis and growth was absent in PPARα- null mice, and are PPARα-dependent. In the Fisher344 rat, hepatocyte DNA synthesis was induced at 24 hours after dosing, with a second peak at 48 hours. Lobular localisation of hepatocyte DNA synthesis showed preferential periportal induction of DNA synthesis in rat, but panlobular zonation of hepatocyte DNA synthesis in mouse. These results characterise a markedly later hepatic induction of panlobular DNA synthesis by PPARα ligands in mouse, compared to rapid induction of periportal DNA synthesis in rat.

An in-house real-time polymerase chain reaction: standardisation and comparison with the Cobas Amplicor HBV monitor and Cobas AmpliPrep/Cobas TaqMan HBV tests for the quantification of hepatitis B virus DNA

This study aimed to standardise an in-house real-time polymerase chain reaction (rtPCR) to allow quantification of hepatitis B virus (HBV) DNA in serum or plasma samples, and to compare this method with two commercial assays, the Cobas Amplicor HBV monitor and the Cobas AmpliPrep/Cobas TaqMan HBV test. Samples from 397 patients from the state of São Paulo were analysed by all three methods. Fifty-two samples were from patients who were human immunodeficiency virus and hepatitis C virus positive, but HBV negative. Genotypes were characterised, and the viral load was measure in each sample. The in-house rtPCR showed an excellent success rate compared with commercial tests; inter-assay and intra-assay coefficients correlated with commercial tests (r = 0.96 and r = 0.913, p < 0.001) and the in-house test showed no genotype-dependent differences in detection and quantification rates. The in-house assay tested in this study could be used for screening and quantifying HBV DNA in order to monitor patients during therapy.

Metastability and dynamics of stem cells: from direct observations to inference at the single cell level

Organismal development, homeostasis, and pathology are rooted in inherently probabilistic events. From gene expression to cellular differentiation, rates and likelihoods shape the form and function of biology. Processes ranging from growth to cancer homeostasis to reprogramming of stem cells all require transitions between distinct phenotypic states, and these occur at defined rates. Therefore, measuring the fidelity and dynamics with which such transitions occur is central to understanding natural biological phenomena and is critical for therapeutic interventions.

While these processes may produce robust population-level behaviors, decisions are made by individual cells. In certain circumstances, these minuscule computing units effectively roll dice to determine their fate. And while the 'omics' era has provided vast amounts of data on what these populations are doing en masse, the behaviors of the underlying units of these processes get washed out in averages.

Therefore, in order to understand the behavior of a sample of cells, it is critical to reveal how its underlying components, or mixture of cells in distinct states, each contribute to the overall phenotype. As such, we must first define what states exist in the population, determine what controls the stability of these states, and measure in high dimensionality the dynamics with which these cells transition between states.

To address a specific example of this general problem, we investigate the heterogeneity and dynamics of mouse embryonic stem cells (mESCs). While a number of reports have identified particular genes in ES cells that switch between 'high' and 'low' metastable expression states in culture, it remains unclear how levels of many of these regulators combine to form states in transcriptional space. Using a method called single molecule mRNA fluorescent in situ hybridization (smFISH), we quantitatively measure and fit distributions of core pluripotency regulators in single cells, identifying a wide range of variabilities between genes, but each explained by a simple model of bursty transcription. From this data, we also observed that strongly bimodal genes appear to be co-expressed, effectively limiting the occupancy of transcriptional space to two primary states across genes studied here. However, these states also appear punctuated by the conditional expression of the most highly variable genes, potentially defining smaller substates of pluripotency.

Having defined the transcriptional states, we next asked what might control their stability or persistence. Surprisingly, we found that DNA methylation, a mark normally associated with irreversible developmental progression, was itself differentially regulated between these two primary states. Furthermore, both acute or chronic inhibition of DNA methyltransferase activity led to reduced heterogeneity among the population, suggesting that metastability can be modulated by this strong epigenetic mark.

Finally, because understanding the dynamics of state transitions is fundamental to a variety of biological problems, we sought to develop a high-throughput method for the identification of cellular trajectories without the need for cell-line engineering. We achieved this by combining cell-lineage information gathered from time-lapse microscopy with endpoint smFISH for measurements of final expression states. Applying a simple mathematical framework to these lineage-tree associated expression states enables the inference of dynamic transitions. We apply our novel approach in order to infer temporal sequences of events, quantitative switching rates, and network topology among a set of ESC states.

Taken together, we identify distinct expression states in ES cells, gain fundamental insight into how a strong epigenetic modifier enforces the stability of these states, and develop and apply a new method for the identification of cellular trajectories using scalable in situ readouts of cellular state.

Factors affecting current and future treeline locations and dynamics in the Peruvian Andes

The elevational distributions of tropical treelines are thought to be determined by temperature, and are predicted to shift upslope in response to global warming. In contrast to this hypothesis, global-scale studies have shown that only half of all studied treelines are shifting upslope. Understanding how treelines will respond to climate change has important implications for global biodiversity, especially in the tropics, because tropical treelines generally represent the upper-elevation distribution limit of the hyper-diverse cloudforest ecosystem. In Chapter 1, I introduce the idea that grasslands found above tropical treelines may represent a potential grass ceiling which forest species cannot cross or invade. I use an extensive literature review to outline potential mechanisms which may be acting to stabilize treeline and prevent forest expansion into high-elevation grasslands. In Chapters 2-4, I begin to explore these potential mechanisms through the use of observational and experimental methods. In Chapter 2, I show that there are significant numbers of seedlings occurring just outside of the treeline in the open grasslands and that seed rain is unlikely to limit seedling recruitment above treeline. I also show that microclimates outside of the closed-canopy cloudforest are highly variable and that mean temperatures are likely a poor explanation of tropical treeline elevations. In Chapter 3, I show that juvenile trees maintain freezing resistances similar to adults, but nighttime radiative cooling near the ground in the open grassland results in lower cold temperatures relative to the free atmosphere, exposing seedlings of some species growing above treeline to lethal frost events. In Chapter 4, I use a large-scale seedling transplant experiment to test the effects of mean temperature, absolute low temperature and shade on transplanted seedling survival. I find that increasing mean temperature negatively affects seedling survival of two treeline species while benefiting another. In addition, low temperature extremes and the presence of shade also appear to be important factors affecting seedling survival above tropical treelines. This work demonstrates that mean temperature is a poor predictor of tropical treelines and that temperature extremes, especially low temperatures, and non-climatic variables should be included in predictions of current and future tropical treeline dynamics.^

Multi-functional electrocatalysts for CO2 reduction reaction: towards the modulation of selectivity

The electrocatalytic reduction of CO2 (CO2RR) is a captivating strategy for the conversion of CO2 into fuels, to realize a carbon neutral circular economy. In the recent years, research has focused on the development of new materials and technology capable of capturing and converting CO2 into useful products. The main problem of CO2RR is given by its poor selectivity, which can lead to the formation of numerous reaction products, to the detriment of efficiencies. For this reason, the design of new electrocatalysts that selectively and efficiently reduce CO2 is a fundamental step for the future exploitation of this technology. Here we present a new class of electrocatalysts, designed with a modular approach, namely, deriving from the combination of different building blocks in a single nanostructure. With this approach it is possible to obtain materials with an innovative design and new functionalities, where the interconnections between the various components are essential to obtain a highly selective and efficient reduction of CO2, thus opening up new possibilities in the design of optimized electrocatalytic materials. By combining the unique physic-chemical properties of carbon nanostructures (CNS) with nanocrystalline metal oxides (MO), we were able to modulate the selectivity of CO2RR, with the production of formic acid and syngas at low overpotentials. The CNS have not only the task of stabilizing the MO nanoparticles, but the creation of an optimal interface between two nanostructures is able to improve the catalytic activity of the active phase of the material. While the presence of oxygen atoms in the MO creates defects that accelerate the reaction kinetics and stabilize certain reaction intermediates, selecting the reaction pathway. Finally, a part was dedicated to the study of the experimental parameters influencing the CO2RR, with the aim of improving the experimental setup in order to obtain commercial catalytic performances.

Factors Affecting Photopolymerization Stress in Dental Composites

Polymerization stress development results from the complex interplay of volumetric shrinkage, reaction kinetics, and viscoelastic properties. The objective of this study was to examine the relationships among volumetric shrinkage, degree of conversion, rate of polymerization (RPmax), and stress development for 2 model bis-GMA-based composites. Three irradiances were used 220, 400, or 600 mW/cm(2) - with exposure times adjusted to deliver the same radiant energy. Volumetric shrinkage was determined with a mercury dilatometer, degree of conversion and RPmax by differential scanning calorimetry (DSC), and polymerization stress with a low-compliance device (Sakaguchi et al., 2004b). Results indicated that polymerization reaction rate and shrinkage were not correlated. Irradiance was directly related to polymerization reaction rate and to stress development. The group with the highest stress/degree of conversion exhibited the lowest RPmax, so it can be assumed, within the limitations of this study, that the conversion was most closely related to stress development.

Kuplivan leijukerroksen poltto- ja lämpötekninen tarkastelu

Työn tavoitteena oli luoda menetelmä leijukerroskattilan petin lämpötilojen ja toiminta-alueen arvioimiseksi annetuilla lähtötiedoilla. Toimintatapana oli tutkia polttoaineen ominaisuuksien ja kattilan geometrian vaikutuksia petin energiataseeseen ja tätä kautta petin lämpötilaan kattilan ajotapa huomioiden. Työn teoriaosassa esitellään aluksi biopolttoaineiden ominaisuuksia ja leijukerroskattilan toimintaa petin toimintaympäristön selvittämiseksi. Teoriaosan lopussa käsitellään perusteellisesti petin hydrodynamiikkaa ja reaktiokinettikkaa sekä petin alueen mekaanista mitoitusta. Lisäksi polttoaineen syöttötapa ja palaminen petissä tuodaan esille. Tutkimusosassa selvitetään petin energiatasemallin määrittämistä teoriaan ja diplomityön aikana eri kattiloilla suoritettuihin mittauksiin perustuen. Mittauksista on erillinen selvitys seitsemännessä kappaleessa. Lopuksi kuvaillaan petin energiatasetta mallintavan menetelmän toimintaa sekä siihen syötettäviä lähtötietoja. Tuloksena on saatu suppealla alueella toimiva laajennettavissa oleva petin energiataseen malli. Menetelmän testaamiseen käytetään mittaustietoa kahdelta kattilalta, joita ei olla käytetty petin energiatasemallin virityksessä.

Fischer-Tropsch Slurry Bubble Column Reactor Modeling

The literature part of the work reviews overall Fischer-Tropsch process, Fischer-Tropsch reactors and catalysts. Fundamentals of Fischer-Tropsch modeling are also presented. The emphasis is on the reactor unit. Comparison of the reactors and the catalysts is carried out to choose the suitable reactor setup for the modeling work. The effects of the operation conditions are also investigated. Slurry bubble column reactor model operating with cobalt catalyst is developed by taking into account the mass transfer of the reacting components (CO and H2) and the consumption of the reactants in the liquid phase. The effect of hydrostatic pressure and the change in total mole flow rate in gas phase are taken into account in calculation of the solubilities. The hydrodynamics, reaction kinetics and product composition are determined according to literature. The cooling system and furthermore the required heat transfer area and number of cooling tubes are also determined. The model is implemented in Matlab software. Commercial scale reactor setup is modeled and the behavior of the model is investigated. The possible inaccuraries are evaluated and the suggestions for the future work are presented. The model is also integrated to Aspen Plus process simulation software, which enables the usage of the model in more extensive Fischer-Tropsch process simulations. Commercial scale reactor of diameter of 7 m and height of 30 m was modeled. The capacity of the reactor was calculated to be about 9 800 barrels/day with CO conversion of 75 %. The behavior of the model was realistic and results were in the right range. The highest uncertainty to model was estimated to be caused by the determination of the kinetic rate.

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.

Catalysis by gold for biomass transformations

The development of new technologies to supplement fossil resources has led to a growing interest in the utilization of alternative routes. Biomass is a rich renewable feedstock for producing fine chemicals, polymers, and a variety of commodities replacing petroleumderived chemicals. Transformation of biomass into diverse valuable chemicals is the key concept of a biorefinery. Catalytic conversion of biomass, which reduces the use of toxic chemicals is one of the important approaches to improve the profitability of biorefineries. Utilization of gold catalysts allows conducting reactions under environmentally-friendly conditions, with a high catalytic activity and selectivity. Gold-catalyzed valorization of several biomass-derived compounds as an alternative approach to the existing technologies was studied in this work. Isomerization of linoleic acid via double bond migration towards biologically active conjugated linoleic acid isomers (CLA) was investigated. The activity and selectivity of various gold catalysts towards cis-9,trans-11-CLA and trans-10,cis-12-CLA were investigated in a semi-batch reactor, showing that the yield of the desired products varied, depending on the catalyst support. The structure sensitivity in the selective oxidation of arabinose was demonstrated using a series of gold catalysts with different Au cluster sizes in a shaker reactor operating in a semibatch mode. The gas-phase selective oxidation of ethanol was studied and the influence of the catalyst support on the catalytic performance was investigated. The selective oxidation of the lignan hydroxymatairesinol (HMR), extracted from the Norway spruce (Picea abies) knots, to the lignan oxomatairesinol (oxoMAT) was extensively investigated. The influence of the reaction conditions and catalyst properties on the yield of oxoMAT was evaluated. In particular, the structure sensitivity of the reaction was demonstrated. The catalyst deactivation and regeneration procedures were studied. The reaction kinetics and mechanism were advanced.