Pressure-induced protein-folding/unfolding kinetics

We use an off-lattice minimalist model to describe the effects of pressure in slowing down the folding/unfolding kinetics of proteins when subjected to increasingly larger pressures. The potential energy function used to describe the interactions between beads in the model includes the effects of pressure on the pairwise interaction of hydrophobic groups in water. We show that pressure affects the participation of contacts in the transition state. More significantly, pressure exponentially decreases the chain reconfigurational diffusion coefficient. These results are consistent with experimental results on the kinetics of pressure-denaturation of staphylococcal nuclease.

Equilibration rates in lipid monolayers

A theoretical analysis is given for the rate of change of domain sizes in lipid monolayers at the air–water interface. The calculation is applicable to liquid domains formed from binary mixtures of lipids that form two coexisting liquid phases. Under conditions where the two lipid molecules have approximately equal areas, the equilibration rate does not involve macroscopic hydrodynamic flow in the subphase but rather depends on the diffusion coefficient of the lipid molecules. The calculation shows that the equilibration rate in binary mixtures of cholesterol and phosphatidylcholine is remarkably slow, the radius of a typical 20-μm diameter domain changing by as little as a part in a million per second. Under these circumstances, equilibration times of the order of days or weeks are expected. Even with such long times, the final state reached by the monolayer will in general be a state of metastable equilibrium, rather than true equilibrium.

Non-Arrhenius kinetics for the loop closure of a DNA hairpin

Intramolecular chain diffusion is an elementary process in the conformational fluctuations of the DNA hairpin-loop. We have studied the temperature and viscosity dependence of a model DNA hairpin-loop by FRET (fluorescence resonance energy transfer) fluctuation spectroscopy (FRETfs). Apparent thermodynamic parameters were obtained by analyzing the correlation amplitude through a two-state model and are consistent with steady-state fluorescence measurements. The kinetics of closing the loop show non-Arrhenius behavior, in agreement with theoretical prediction and other experimental measurements on peptide folding. The fluctuation rates show a fractional power dependence (β = 0.83) on the solution viscosity. A much slower intrachain diffusion coefficient in comparison to that of polypeptides was derived based on the first passage time theory of SSS [Szabo, A., Schulten, K. & Schulten, Z. (1980) J. Chem. Phys. 72, 4350–4357], suggesting that intrachain interactions, especially stacking interaction in the loop, might increase the roughness of the free energy surface of the DNA hairpin-loop.

Removal of antibiotic compounds by adsorption using glycerol-based carbon materials

This study is focused on the synthesis and application of glycerol-based carbon materials (GBCM200, GBCM300 and GBCM350) as adsorbents for the removal of the antibiotic compounds flumequine and tetracycline from aqueous solution. The synthesis enrolled the partial carbonization of a glycerol-sulfuric acid mixture, followed by thermal treatments under inert conditions and further thermal activation under oxidative atmosphere. The textural properties were investigated through N2 adsorption–desorption isotherms, and the presence of oxygenated groups was discussed based on zeta potential and Fourier transform infrared (FTIR) data. The kinetic data revealed that the equilibrium time for flumequine adsorption was achieved within 96 h, while for tetracycline, it was reached after 120 h. Several kinetic models, i.e., pseudo-first order, pseudo-second order, fractional power, Elovich and Weber–Morris models, were applied, finding that the pseudo-second order model was the most suitable for the fitting of the experimental kinetic data. The estimated surface diffusion coefficient values, Ds, of 3.88 and 5.06 10 14 m2 s 1, suggests that the pore diffusion is the rate limiting step of the adsorption process. Finally, as it is based on SSE values, Sips model well-fitted the experimental FLQ and TCN adsorption isotherm data, followed by Freundlich equation. The maximum adsorption capacities for flumequine and tetracycline was of 41.5 and 58.2 mg g 1 by GBCM350 activated carbon.

Potencial da ressonância magnética multiparamétrica na deteção de carcinoma da próstata localizado e valor do coeficiente de difusão aparente como possível preditor da agressividade tumoral : revisão de uma técnica em expansão

Trabalho Final do Curso de Mestrado Integrado em Medicina, Faculdade de Medicina, Universidade de Lisboa, 2014

Dissolved iron measured along surface transects of the CARUSO-EISENEX experiment

Measurements of Fe(II) and H2O2 were carried out in the Atlantic sector of the Southern Ocean during EisenEx, an iron enrichment experiment. Iron was added on three separate occasions, approximately every 8 days, as a ferrous sulfate (FeSO4) solution. Vertical profiles of Fe(II) showed maxima consistent with the plume of the iron infusion. While H2O2 profiles revealed a corresponding minima showing the effect of oxidation of Fe(II) by H2O2, observations showed detectable Fe(II) concentrations existed for up to 8 days after an iron infusion. H2O2 concentrations increased at the depth of the chlorophyll maximum when iron concentrations returned to pre-infusion concentrations (<80 pM) possibly due to biological production related to iron reductase activity. In this work, Fe(II) and dissolved iron were used as tracers themselves for subsequent iron infusions when no further SF6 was added. EisenEx was subject to periods of weak and strong mixing. Slow mixing after the second infusion allowed significant concentrations of Fe(II) and Fe to exist for several days. During this time, dissolved and total iron in the infusion plume behaved almost conservatively as it was trapped between a relict mixed layer and a new rain-induced mixed layer. Using dissolved iron, a value for the vertical diffusion coefficient Kz=6.7±0.7 cm**2/s was obtained for this 2-day period. During a subsequent surface survey of the iron-enriched patch, elevated levels of Fe(II) were found in surface waters presumably from Fe(II) dissolved in the rainwater that was falling at this time. Model results suggest that the reaction between uncomplexed Fe(III) and O2? was a significant source of Fe(II) during EisenEx and helped to maintain high levels of Fe(II) in the water column. This phenomenon may occur in iron enrichment experiments when two conditions are met: (i) When Fe is added to a system already saturated with regard to organic complexation and (ii) when mixing processes are slow, thereby reducing the dispersion of iron into under-saturated waters.

Analyzation of marine snow and fecal pellets collected in sediment trap CBi-2 off Cape Blanc, Mauritania

We analyzed size-specific dry mass, sinking velocity, and apparent diffusivity in field-sampled marine snow, laboratory-made aggregates formed by diatoms or coccolithophorids, and small and large zooplankton fecal pellets with naturally varying content of ballast materials. Apparent diffusivity was measured directly inside aggregates and large (millimeter-long) fecal pellets using microsensors. Large fecal pellets, collected in the coastal upwelling off Cape Blanc, Mauritania, showed the highest volume-specific dry mass and sinking velocities because of a high content of opal, carbonate, and lithogenic material (mostly Saharan dust), which together comprised ~80% of the dry mass. The average solid matter density within these large fecal pellets was 1.7 g cm**-3, whereas their excess density was 0.25 ± 0.07 g cm**-3. Volume-specific dry mass of all sources of aggregates and fecal pellets ranged from 3.8 to 960 µg mm**-3, and average sinking velocities varied between 51 and 732 m d**-1. Porosity was >0.43 and >0.96 within fecal pellets and phytoplankton-derived aggregates, respectively. Averaged values of apparent diffusivity of gases within large fecal pellets and aggregates were 0.74 and 0.95 times that of the free diffusion coefficient in sea water, respectively. Ballast increases sinking velocity and, thus, also potential O2 fluxes to sedimenting aggregates and fecal pellets. Hence, ballast minerals limit the residence time of aggregates in the water column by increasing sinking velocity, but apparent diffusivity and potential oxygen supply within aggregates are high, whereby a large fraction of labile organic carbon can be respired during sedimentation.

Modeling molecular transport in slit pores

We examine the transport of methane in microporous carbon by performing equilibrium and nonequilibrium molecular dynamics simulations over a range of pore sizes, densities, and temperatures. We interpret these simulation results using two models of the transport process. At low densities, we consider a molecular flow model, in which intermolecular interactions are neglected, and find excellent agreement between transport diffusion coefficients determined from simulation, and those predicted by the model. Simulation results indicate that the model can be applied up to fluid densities of the order to 0.1-1 nm(-3). Above these densities, we consider a slip flow model, combining hydrodynamic theory with a slip condition at the solid-fluid interface. As the diffusion coefficient at low densities can be accurately determined by the molecular flow model, we also consider a model where the slip condition is supplied by the molecular flow model. We find that both density-dependent models provide a useful means of estimating the transport coefficient that compares well with simulation. (C) 2004 American Institute of Physics.

Using different structure types of microemulsions for the preparation of poly(alkylcyanoacrylate) nanoparticles by interfacial polymerization

A phase diagram of the pseudoternary system ethyloleate, polyoxyethylene 20 sorbitan mono-oleate/sorbitan monolaurate and water with butanol as a cosurfactant was prepared. Areas containing optically isotropic, low viscosity one-phase systems were identified and systems therein designated as w/o droplet-, bicontinuous- or solution-type microemulsions using conductivity, viscosity, cryo-field emission scanning electron microscopy and self-diffusion NMR. Nanoparticles were prepared by interfacial polymerization of selected w/o droplet, bicontinuous- or solution-type microemulsions with ethyl-2-cyanoacrylate. Morphology of the particles and entrapment of the water-soluble model protein ovalbumin were investigated. Addition of monomer to the different types of microemulsions (w/o droplet, bicontinuous, solution) led to the formation of nanoparticles, which were similar in size (similar to 250 nm), polydispersity index (similar to 0.13), zeta-potential (similar to-17 mV) and morphology. The entrapment of the protein within these particles was up to 95%, depending on the amount of monomer used for polymerization and the type of microemulsion used as a polymerization template. The formation of particles with similar characteristics from templates having different microstructure is surprising, particularly considering that polymerization is expected to occur at the water-oil interface by base-catalysed polymerization. Dynamics within the template (stirring, viscosity) or indeed interfacial phenomena relating to the solid-liquid interface appear to be more important for the determination of nanoparticle morphology and characteristics than the microstructure of the template system. (c) 2005 Elsevier B.V. All rights reserved.

Study of the calcification of PHEMA hydrogels using a two compartment permeation cell

To simulate the process of calcification in hydrogel implants, particularly calcification inside hydrogels, in vitro experiments using two compartment permeation cells have been performed. PHEMA hydrogel membranes were synthesized by free radical polymerization in bulk. The permeability and diffusion coefficient for Ca2+ ions at 37 &DEG; C were determined using Fick's laws of diffusion. It was evident that Ca2+ ions either from CaCl2 or SBF solutions may diffuse through PHEMA hydrogel membranes. The fort-nation of calcium phosphate deposits inside the hydrogel was observed and attributed to a heterogeneous nucleation from diffusing calcium and phosphate ions. The morphology of the deposits both on the surface and inside the hydrogels was found to be similar, i.e. spherical aggregates with a diameter of less than one micron. © 2005 Elsevier B.V. All rights reserved.

Preparation of poly (alkylcyanoacrylate) nanoparticles by polymerization of water-free microemulsions

Phase diagrams of the pseudoternary systems ethyloleate, polyoxyethylene 20 sorbitan mono-oleate/sorbitan monolaurate and propylene glycol with and without butanol as a co-surfactant were prepared. Areas containing optically isotropic, one-phase systems were identified and samples therein designated as droplet, bicontinuous or solution type microemulsions using conductivity, viscosity and self-diffusion NMR. Nanoparticles were prepared by polymerization of selected microemulsions with ethyl-2-cyanoacrylate and the morphology of the particles was investigated. Addition of monomer to all types of microemulsions led to the formation of nanoparticles, which had an average size of 244 +/- 25 nm, an average polydispersity index of 0.15 +/- 0.04 and a zeta-potential of -17 +/- 3 mV. The formation of particles from water-free microemulsions of different types is surprising, particularly considering that polymerization is expected to occur at a water-oil interface by base-catalysed polymerization. It would appear that propylene glycol is sufficiently nucleophilic to initiate the polymerization. The use of water-free microemulsions as templates for the preparation of poly (alkylcyanoacrylate) nanoparticles opens up interesting opportunities for the encapsulation of bioactives which do not have suitable properties for encapsulation on the basis of water-containing microemulsions.

The hydration of paper studied with solid-state magnetisation-exchange H-1 NMR spectroscopy

The wide-line H-1 nuclear magnetic resonance (NMR) spectrum of paper in equilibrium with ambient humidity consists of super-imposed relatively broad and narrow lines. The narrower line is of the order of 2 kHz wide at half the maximum height, while the broader line is of the order of 40 kHz in width at half height. On the basis of these line widths, the narrow line is assigned to water sorbed to the paper, and the broad line to the polymeric constituents of the paper. It was not possible to distinguish between the various polymeric components of paper contributing to the H-1 NMR spectra. A modified Goldman-Shen pulse sequence was used to generate a spatial magnetisation gradient between the polymer and water phases. The exchange of magnetisation between protons associated with water and those associated with the macromolecules in paper was observed. The exchange of magnetisation is discussed within a heat transfer model for homonuclear dipolar coupling, with exchange being characterised by a spin-diffusion coefficient. Consideration of the magnitude of the initial rate of the exchange process and estimates of the spin-spin relaxation times based on H-1 line widths indicate that some water must exist in a sufficiently immobile state as to allow homonuclear dipolar interactions between adjacent polymer and water protons. Thus, water sorbed onto paper must exist in at least two states in mass exchange with each other. This observation allows certain conclusions to be drawn about the ratio of free/bound water as a function of moisture content and the dispersal of water within the polymer matrix.

Investigation of spontaneous microemulsion formation in supercritical carbon dioxide using high-pressure NMR

NMR spectroscopy and relaxometry were used to investigate microemulsion formation in supercritical CO2. The droplets were stabilised by the salt of a perfluorinated polyether. Spontaneous microemulsion formation was observed over a period of 5 h in the absence of applied sheer. Time-resolved relaxation times of the surfactant tail showed a stepwise increase in mobility of the tail over this period. Conversely, the translational mobility of water confined within the droplet decreased over the same interval. This data is consistent with the gradual decrease in droplet size as time progressed. Indeed, NMR self-diffusion coefficients were used to show that droplets with a radius of approximately 5 nm were formed at equilibrium.

Osmotic dehydration in plant tissues

The primary aim of the thesis is to provide a comprehensive investigation of the osmotic dehydration processes in plant tissue. Effort has been concentrated on the modelling for simulating the processes. Two mathematical models for simulating the mass transfer during osmotic dehydration processes in plant tissues are developed and verified using existing experimental data. Both models are based on the mechanism of diffusion and convection of any mobile material that can transport in plant tissues. The mass balance equation for the transport of each constituent is established separately for intracellular and extra-cellular volumes with taking into account the mass transfer across the cell membrane the intracellular and extra-cellular volumes and the shrinkage of the whole tissue. The contribution from turgor pressure is considered in both models. Model two uses Darcy’s law to build the relation between shrinkage velocity and hydrostatic pressure in each volume because the plant tissue can be considered as the porous medium. Moreover, it has been extended to solve the multi-dimensional problems. A lot of efforts have been made to the parameter study and the sensitivity analyses. The parameters investigated including the concentration of the osmotic solution, diffusion coefficient, permeability of the cell membrane, elastic modulus of the cell wall, critical cell volume etc. The models allow us to quantitatively simulate the time evolution of intracellular and extra-cellular volumes as well as the time evolution of concentrations in each cross-section.

SO2 sequestration in large volcanic eruptions:high-temperature scavenging by tephra

It is well accepted that the climate impact of large explosive volcanic eruptions results from reduction of solar radiation following atmospheric conversion of magmatic SO emissions into HSO aerosols. Thus, understanding the fate of SO in the eruption plume is crucial for better assessing volcanic forcing of climate. Here we focus on the potential of tephra to interact with and remove SO gas from the eruptive plume. Scavenging of SO by tephra is generally assumed to be driven by in-plume, low-temperature reactions between HSO condensates and tephra particles. However, the importance of SO gas-tephra interaction above the dew point temperature of HSO (190-200°C) has never been constrained. Here we report the results of an experimental study where silicate glasses with representative volcanic compositions were exposed to SO in the temperature range 25-800°C. We show that above 600°C, the uptake of SO on glass exhibits optimal efficiency and emplaces surficial CaSO deposits. This reaction is sustained via Ca diffusion from the bulk to the surface of the glass particles. At 800°C, the diffusion coefficient for Ca in the glasses was in the range 10-10cms. We suggest that high temperature SO scavenging by glass-rich tephra proceeds by the same Ca diffusion-driven mechanism. Using a simple mathematical model, we estimated SO scavenging efficiencies at 800°C varying from