The use of NMR for determination of new structures in irradiated TFE/PMVE fluoropolymers

The radiation chemistry of two TFE/PMVE copolymers with TFE mole fractions of 0.66 and 0.81 has been studied under vacuum using Co-60 gamma -radiation over absorbed dose ranges up to 4.2 MGy. The radiolysis temperature was 313 K for both TFE/PMVE copolymers. New structure formation in the copolymers was identified by solid-state F-19 NMR and the G-values for new chain ends of 2.1 and 0.5 and for branching sites of 0.9 and 0.2 have been obtained for the TFE/PMVE with TFE mole fractions of 0.66 and 0.81, respectively. The relative yields of-O-CF3 and -CF2-CF3 chain ends were found to be proportional to the copolymer composition, but the yields of the -CF2-CF3 chain ends and -CF- branch points mere not linearly related ia the composition. rather they wets correlated with the radical yields measured at 77 K. (C) 2001 Elsevier Science Ltd. All rights reserved.

Porous solids from layered clays by combined pillaring and templating approaches

The pore structure formation in bentonite, pillared with a mixed sol of silicon and titanium hydroxides and treated subsequently with quaternary ammonium surfactants, is investigated. The surfactant micelles act as a template, similar to their role in MCM41 synthesis. Because both the surfactant micelles and the sol particles are positively charged, it is greatly favorable for them to form meso-phase assembles in the galleries between the clay layers that bear negative charges. Besides, the sol particles do not bond the clay layers strongly as other kinds of pillar precursors do, so that the treatment with surfactants can result in radical structure changes in sol-pillared clays. This allows us to tailor the pore structure of these porous clays by choice of surfactant. The surfactant treatment also results in profound increases in porosity and improvement in thermal stability. Therefore, the product porous clays have great potential to be Used to deal with large molecules or at high operating temperatures. We also found that titanium in these samples is highly dispersed in the silica matrix rather than existing in the form of small particles of pure titania. Such highly dispersed Ti active centers may offer excellent activities for catalytic oxidation reactions such as alkanes into alcohols and ketones.

Gold nanoparticle-DNA conjugates for oligonucleotide vectorization towards gene silencing

Dissertação para obtenção do Grau de Mestre em Genética Molecular e Biomedicina

Design of bio-based supramolecular structures through self-assembly of α-lactalbumin and lysozyme

Bovine α-lactalbumin (α-La) and lysozyme (Lys), two globular proteins with highly homologous tertiary structures and opposite isoelectric points, were used to produce bio-based supramolecular structures under various pH values (3, 7 and 11), temperatures (25, 50 and 75 °C) and times (15, 25 and 35 min) of heating. Isothermal titration calorimetry experiments showed protein interactions and demonstrated that structures were obtained from the mixture of α-La/Lys in molar ratio of 0.546. Structures were characterized in terms of morphology by transmission electron microscopy (TEM) and dynamic light scattering (DLS), conformational structure by circular dichroism and intrinsic fluorescence spectroscopy and stability by DLS. Results have shown that protein conformational structure and intermolecular interactions are controlled by the physicochemical conditions applied. The increase of heating temperature led to a significant decrease in size and polydispersity (PDI) of α-La–Lys supramolecular structures, while the increase of heating time, particularly at temperatures above 50 °C, promoted a significant increase in size and PDI. At pH 7 supramolecular structures were obtained at microscale – confirmed by optical microscopy – displaying also a high PDI (i.e. > 0.4). The minimum size and PDI (61 ± 2.3 nm and 0.14 ± 0.03, respectively) were produced at pH 11 for a heating treatment of 75 °C for 15 min, thus suggesting that these conditions could be considered as critical for supramolecular structure formation. Its size and morphology were confirmed by TEM showing a well-defined spherical form. Structures at these conditions showed to be stable at least for 30 or 90 days, when stored at 25 or 4 °C, respectively. Hence, α-La–Lys supramolecular structures showed properties that indicate that they are a promising delivery system for food and pharmaceutical applications.

Cosmological perturbations from stochastic gravity

In inflationary cosmological models driven by an inflaton field the origin of the primordial inhomogeneities which are responsible for large-scale structure formation are the quantum fluctuations of the inflaton field. These are usually calculated using the standard theory of cosmological perturbations, where both the gravitational and the inflaton fields are linearly perturbed and quantized. The correlation functions for the primordial metric fluctuations and their power spectrum are then computed. Here we introduce an alternative procedure for calculating the metric correlations based on the Einstein-Langevin equation which emerges in the framework of stochastic semiclassical gravity. We show that the correlation functions for the metric perturbations that follow from the Einstein-Langevin formalism coincide with those obtained with the usual quantization procedures when the scalar field perturbations are linearized. This method is explicitly applied to a simple model of chaotic inflation consisting of a Robertson-Walker background, which undergoes a quasi-de Sitter expansion, minimally coupled to a free massive quantum scalar field. The technique based on the Einstein-Langevin equation can, however, deal naturally with the perturbations of the scalar field even beyond the linear approximation, as is actually required in inflationary models which are not driven by an inflaton field, such as Starobinsky¿s trace-anomaly driven inflation or when calculating corrections due to nonlinear quantum effects in the usual inflaton driven models.

Dislocation jamming and Andrade creep

We simulate the glide motion of an assembly of interacting dislocations under the action of an external shear stress and show that the associated plastic creep relaxation follows Andrades law. Our results indicate that Andrade creep in plastically deforming crystals involves the correlated motion of dislocation structures near a dynamic transition separating a flowing from a jammed phase. Simulations in the presence of dislocation multiplication and noise confirm the robustness of this finding and highlight the importance of metastable structure formation for the relaxation process.

Targeting vascular NADPH oxidase 1 blocks tumor angiogenesis through a PPARα mediated mechanism.

Reactive oxygen species, ROS, are regulators of endothelial cell migration, proliferation and survival, events critically involved in angiogenesis. Different isoforms of ROS-generating NOX enzymes are expressed in the vasculature and provide distinct signaling cues through differential localization and activation. We show that mice deficient in NOX1, but not NOX2 or NOX4, have impaired angiogenesis. NOX1 expression and activity is increased in primary mouse and human endothelial cells upon angiogenic stimulation. NOX1 silencing decreases endothelial cell migration and tube-like structure formation, through the inhibition of PPARα, a regulator of NF-κB. Administration of a novel NOX-specific inhibitor reduced angiogenesis and tumor growth in vivo in a PPARα dependent manner. In conclusion, vascular NOX1 is a critical mediator of angiogenesis and an attractive target for anti-angiogenic therapies.

Experimental insights into deformation dynamics and intermittency in rapid granular shear flows

This work concerns the experimental study of rapid granular shear flows in annular Couette geometry. The flow is induced by continuous driving of the horizontal plate at the top of the granular bed in an annulus. The compressive pressure, driving torque, instantaneous bed height and rotational speed of the shearing plate are measured. Moreover, local stress fluctuations are measured in a medium made of steel spheres 2 and 3 mm in diameter. Both monodisperse packing and bidisperse packing are investigated to reveal the influence of size diversity in intermittent features of granular materials. Experiments are conducted in an annulus that can contain up to 15 kg of spherical steel balls. The shearing granular medium takes place via the rotation of the upper plate which compresses the material loaded inside the annulus. Fluctuations of compressive force are locally measured at the bottom of the annulus using a piezoelectric sensor. Rapid shear flow experiments are pursued at different compressive forces and shear rates and the sensitivity of fluctuations are then investigated by different means through monodisperse and bidisperse packings. Another important feature of rapid granular shear flows is the formation of ordered structures upon shearing. It requires a certain range for the amount of granular material (uniform size distribution) loaded in the system in order to obtain stable flows. This is studied more deeply in this thesis. The results of the current work bring some new insights into deformation dynamics and intermittency in rapid granular shear flows. The experimental apparatus is modified in comparison to earlier investigations. The measurements produce data for various quantities continuously sampled from the start of shearing to the end. Static failure and dynamic shearing ofa granular medium is investigated. The results of this work revealed some important features of failure dynamics and structure formation in the system. Furthermore, some computer simulations are performed in a 2D annulus to examine the nature of kinetic energy dissipation. It is found that turbulent flow models can statistically represent rapid granular flows with high accuracy. In addition to academic outcomes and scientific publications our results have a number of technological applications associated with grinding, mining and massive grain storages.

Microscopic simulation of pigment coating consolidation

The control of coating layer properties is becoming increasingly important as a result of an emerging demand for novel coated paper-based products and an increasing popularity of new coating application methods. The governing mechanisms of microstructure formation dynamics during consolidation and drying are nevertheless, still poorly understood. Some of the difficulties encountered by experimental methods can be overcome by the utilisation of numerical modelling and simulation-based studies of the consolidation process. The objective of this study was to improve the fundamental understanding of pigment coating consolidation and structure formation mechanisms taking place on the microscopic level. Furthermore, it is aimed to relate the impact of process and suspension properties to the microstructure of the coating layer. A mathematical model based on a modified Stokesian dynamics particle simulation technique was developed and applied in several studies of consolidation-related phenomena. The model includes particle-particle and particle-boundary hydrodynamics, colloidal interactions, Born repulsion, and a steric repulsion model. The Brownian motion and a free surface model were incorporated to enable the specific investigation of consolidation and drying. Filter cake stability was simulated in various particle systems, and subjected to a range of base substrate absorption rates and system temperatures. The stability of the filter cake was primarily affected by the absorption rate and size of particles. Temperature was also shown to have an influence. The consolidation of polydisperse systems, with varying wet coating thicknesses, was studied using imposed pilot trial and model-based drying conditions. The results show that drying methods have a clear influence on the microstructure development, on small particle distributions in the coating layer and also on the mobility of particles during consolidation. It is concluded that colloidal properties can significantly impact coating layer shrinkage as well as the internal solids concentration profile. Visualisations of particle system development in time and comparison of systems at different conditions are useful in illustrating coating layer structure formation mechanisms. The results aid in understanding the underlying mechanisms of pigment coating layer consolidation. Guidance is given regarding the relationship between coating process conditions and internal coating slurry properties and their effects on the microstructure of the coating.

RNA recurrent motifs : identification and characterization

La détermination de la structure tertiaire du ribosome fut une étape importante dans la compréhension du mécanisme de la synthèse des protéines. Par contre, l’élucidation de la structure du ribosome comme tel ne permet pas une compréhension de sa fonction. Pour mieux comprendre la nature des relations entre la structure et la fonction du ribosome, sa structure doit être étudiée de manière systématique. Au cours des dernières années, nous avons entrepris une démarche systématique afin d’identifier et de caractériser de nouveaux motifs structuraux qui existent dans la structure du ribosome et d’autres molécules contenant de l’ARN. L’analyse de plusieurs exemples d’empaquetage de deux hélices d’ARN dans la structure du ribosome nous a permis d’identifier un nouveau motif structural, nommé « G-ribo ». Dans ce motif, l’interaction d’une guanosine dans une hélice avec le ribose d’un nucléotide d’une autre hélice donne naissance à un réseau d’interactions complexes entre les nucléotides voisins. Le motif G-ribo est retrouvé à 8 endroits dans la structure du ribosome. La structure du G-ribo possède certaines particularités qui lui permettent de favoriser la formation d’un certain type de pseudo-nœuds dans le ribosome. L’analyse systématique de la structure du ribosome et de la ARNase P a permis d’identifier un autre motif structural, nommé « DTJ » ou « Double-Twist Joint motif ». Ce motif est formé de trois courtes hélices qui s’empilent l’une sur l’autre. Dans la zone de contact entre chaque paire d’hélices, deux paires de bases consécutives sont surenroulées par rapport à deux paires de bases consécutives retrouvées dans l’ARN de forme A. Un nucléotide d’une paire de bases est toujours connecté directement à un nucléotide de la paire de bases surenroulée, tandis que les nucléotides opposés sont connectés par un ou plusieurs nucléotides non appariés. L’introduction d’un surenroulement entre deux paires de bases consécutives brise l’empilement entre les nucléotides et déstabilise l’hélice d’ARN. Dans le motif DTJ, les nucléotides non appariés qui lient les deux paires de bases surenroulées interagissent avec une des trois hélices qui forment le motif, offrant ainsi une stratégie élégante de stabilisation de l’arrangement. Pour déterminer les contraintes de séquences imposées sur la structure tertiaire d’un motif récurrent dans le ribosome, nous avons développé une nouvelle approche expérimentale. Nous avons introduit des librairies combinatoires de certains nucléotides retrouvés dans des motifs particuliers du ribosome. Suite à l’analyse des séquences alternatives sélectionnées in vivo pour différents représentants d’un motif, nous avons été en mesure d’identifier les contraintes responsables de l’intégrité d’un motif et celles responsables d’interactions avec les éléments qui forment le contexte structural du motif. Les résultats présentés dans cette thèse élargissent considérablement notre compréhension des principes de formation de la structure d’ARN et apportent une nouvelle façon d’identifier et de caractériser de nouveaux motifs structuraux d’ARN.

Effect of ambient gas on the expansion dynamics of plasma plume formed by laser blow off of thin film

A study has been carried out to understand the influence of ambient gases on the dynamics of laser-blow-off plumes of multi-layered LiF–C thin film. Plume images at various time intervals ranging from 100 to 3000 ns have been recorded using an intensified CCD camera. Enhancement in the plume intensity and change in size and shape occurs on introducing ambient gases and these changes are highly dependent on the nature and composition of the ambient gas used. Velocity of the plume was found to be higher in helium ambient whereas intensity enhancement is greater in argon environment. The plume shapes have maximum size at 10−2 and 10−1 Torr of Ar and He pressures, respectively. As the background pressure increases further (>10−2 Torr: depending on the nature of gas), the plume gets compressed/focused in the lateral direction. Internal structure formation and turbulences are observed at higher pressures (>10−1 Torr) in both ambient gases.

Effects of different tillage treatments on labile soil organic matter pools and stabilization processes

An improved understanding of soil organic carbon (Corg) dynamics in interaction with the mechanisms of soil structure formation is important in terms of sustainable agriculture and reduction of environmental costs of agricultural ecosystems. However, information on physical and chemical processes influencing formation and stabilization of water stable aggregates in association with Corg sequestration is scarce. Long term soil experiments are important in evaluating open questions about management induced effects on soil Corg dynamics in interaction with soil structure formation. The objectives of the present thesis were: (i) to determine the long term impacts of different tillage treatments on the interaction between macro aggregation (>250 µm) and light fraction (LF) distribution and on C sequestration in plots differing in soil texture and climatic conditions. (ii) to determine the impact of different tillage treatments on temporal changes in the size distribution of water stable aggregates and on macro aggregate turnover. (iii) to evaluate the macro aggregate rebuilding in soils with varying initial Corg contents, organic matter (OM) amendments and clay contents in a short term incubation experiment. Soil samples were taken in 0-5 cm, 5-25 cm and 25-40 cm depth from up to four commercially used fields located in arable loess regions of eastern and southern Germany after 18-25 years of different tillage treatments with almost identical experimental setups per site. At each site, one large field with spatially homogenous soil properties was divided into three plots. One of the following three tillage treatments was carried in each plot: (i) Conventional tillage (CT) with annual mouldboard ploughing to 25-30 cm (ii) mulch tillage (MT) with a cultivator or disc harrow 10-15 cm deep, and (iii) no tillage (NT) with direct drilling. The crop rotation at each site consisted of sugar beet (Beta vulgaris L.) - winter wheat (Triticum aestivum L.) - winter wheat. Crop residues were left on the field and crop management was carried out following the regional standards of agricultural practice. To investigate the above mentioned research objectives, three experiments were conducted: Experiment (i) was performed with soils sampled from four sites in April 2010 (wheat stand). Experiment (ii) was conducted with soils sampled from three sites in April 2010, September 2011 (after harvest or sugar beet stand), November 2011 (after tillage) and April 2012 (bare soil or wheat stand). An incubation study (experiment (iii)) was performed with soil sampled from one site in April 2010. Based on the aforementioned research objectives and experiments the main findings were: (i) Consistent results were found between the four long term tillage fields, varying in texture and climatic conditions. Correlation analysis of the yields of macro aggregate against the yields of free LF ( ≤1.8 g cm-3) and occluded LF, respectively, suggested that the effective litter translocation in higher soil depths and higher litter input under CT and MT compensated in the long term the higher physical impact by tillage equipment than under NT. The Corg stocks (kg Corg m−2) in 522 kg soil, based on the equivalent soil mass approach (CT: 0–40 cm, MT: 0–38 cm, NT: 0–36 cm) increased in the order CT (5.2) = NT (5.2) < MT (5.7). Significantly (p ≤ 0.05) highest Corg stocks under MT were probably a result of high crop yields in combination with reduced physical tillage impact and effective litter incorporation, resulting in a Corg sequestration rate of 31 g C-2 m-2 yr-1. (ii) Significantly higher yields of macro aggregates (g kg-2 soil) under NT (732-777) and MT (680-726) than under CT (542-631) were generally restricted to the 0-5 cm sampling depth for all sampling dates. Temporal changes on aggregate size distribution were only small and no tillage induced net effect was detectable. Thus, we assume that the physical impact by tillage equipment was only small or the impact was compensated by a higher soil mixing and effective litter translocation into higher soil depths under CT, which probably resulted in a high re aggregation. (iii) The short term incubation study showed that macro aggregate yields (g kg-2 soil) were higher after 28 days in soils receiving OM (121.4-363.0) than in the control soils (22.0-52.0), accompanied by higher contents of microbial biomass carbon and ergosterol. Highest soil respiration rates after OM amendments within the first three days of incubation indicated that macro aggregate formation is a fast process. Most of the rebuilt macro aggregates were formed within the first seven days of incubation (42-75%). Nevertheless, it was ongoing throughout the entire 28 days of incubation, which was indicated by higher soil respiration rates at the end of the incubation period in OM amended soils than in the control soils. At the same time, decreasing carbon contents within macro aggregates over time indicated that newly occluded OM within the rebuilt macro aggregates served as Corg source for microbial biomass. The different clay contents played only minor role in macro aggregate formation under the particular conditions of the incubation study. Overall, no net changes on macro aggregation were identified in the short term. Furthermore, no indications for an effective Corg sequestration on the long term under NT in comparison to CT were found. The interaction of soil disturbance, litter distribution and the fast re aggregation suggested that a distinct steady state per tillage treatment in terms of soil aggregation was established. However, continuous application of MT with a combination of reduced physical tillage impact and effective litter incorporation may offer some potential in improving the soil structure and may therefore prevent incorporated LF from rapid decomposition and result in a higher C sequestration on the long term.

Effect of PEG crystallization on the self-assembly of PEG/peptide copolymers containing amyloid peptide fragments

The effect of poly(ethylene glycol) PEG crystallization on P-sheet fibril formation is studied for a series of three peptide/PEG conjugates containing fragments modified from the amyloid P peptide, specifically KLVFF, FFKLVFF, and AAKLVFF. These are conjugated to PEG with M-n = 3300 g mol(-1). It is found, via small-angle X-ray scattering,X-ray diffraction, atomic force microscopy, and polarized optical microscopy, that PEG crystallinity in dried samples can disturb fibrillization, in particular cross-P amyloid structure formation, for the conjugate containing the weak fibrillizer KLVFF, whereas this is retained for the conjugates containing the stronger fibrillizers AAKLVFF and FFKLVFF. For these two samples, the alignment of peptide fibrils also drives the orientation of the attached PEG chains. Our results highlight the importance of the antagonistic effects of PEG crystallization and peptide fibril formation in PEG/peptide conjugates.

Self-nucleation and crystallization kinetics of double crystalline poly(p-dioxanone)-b-poly(epsilon-caprolactone) diblock copolymers

The crystallization kinetics of each constituent of poly(p-dioxanone)-b-poly(epsilon-caprolactone) diblock copolymers (PPDX-b-PCL) has been determined in a wide composition range by differential scanning calorimetry and compared to that of the equivalent homopolymers. Spherulitic growth rates were also measured by polarized optical microscopy while atomic force microscopy was employed to reveal the morphology of one selected diblock copolymer. It was found that crystallization drives structure formation and both components form lamellae within mixed spherulitic superstructures. The overall isothermal crystallization kinetics of the PPDX block at high temperatures, where the PCL is molten, was determined by accelerating the kinetics through a previous self-nucleation procedure. The application of the Lauritzen and Ho. man theory to overall growth rate data yielded successful results for PPDX and the diblock copolymers. The theory was applied to isothermal overall crystallization of previously self-nucleated PPDX ( where growth should be the dominant factor if self-nucleation was effective) and the energetic parameters obtained were perfectly matched with those obtained from spherulitic growth rate data of neat PPDX. A quantitative estimate of the increase in the energy barrier for crystallization of the PPDX block, caused by the covalently bonded molten PCL as compared to homo-PPDX, was thus determined. This energy increase can dramatically reduce the crystallization rate of the PPDX block as compared to homo-PPDX. In the case of the PCL block, both the crystallization kinetics and the self-nucleation results indicate that the PPDX is able to nucleate the PCL within the copolymers and heterogeneous nucleation is always present regardless of composition. Finally, preliminary results on hydrolytic degradation showed that the presence of relatively small amounts of PCL within PPDX-bPCL copolymers substantially retards hydrolytic degradation of the material in comparison to homo-PPDX. This increased resistance to hydrolysis is a complex function of composition and its knowledge may allow future prediction of the lifetime of the material for biomedical applications.

MPJ express meets gadget: towards a java code for cosmological simulations

Gadget-2 is a massively parallel structure formation code for cosmological simulations. In this paper, we present a Java version of Gadget-2. We evaluated the performance of the Java version by running colliding galaxies simulation and found that it can achieve around 70% of C Gadget-2's performance.