Structure optimization combining soft-core interaction functions, the diffusion equation method, and molecular dynamics

Smoothing the potential energy surface for structure optimization is a general and commonly applied strategy. We propose a combination of soft-core potential energy functions and a variation of the diffusion equation method to smooth potential energy surfaces, which is applicable to complex systems such as protein structures; The performance of the method was demonstrated by comparison with simulated annealing using the refinement of the undecapeptide Cyclosporin A as a test case. Simulations were repeated many times using different initial conditions and structures since the methods are heuristic and results are only meaningful in a statistical sense.

Diffusion modeling of percutaneous absorption kinetics: 2. Finite vehicle volume and solvent deposited solids

The diffusion model for percutaneous absorption is developed for the specific case of delivery to the skin being limited by the application of a finite amount of solute. Two cases are considered; in the first, there is an application of a finite donor (vehicle) volume, and in the second, there are solvent-deposited solids and a thin vehicle with a high partition coefficient. In both cases, the potential effect of an interfacial resistance at the stratum corneum surface is also considered. As in the previous paper, which was concerned with the application of a constant donor concentration, clearance limitations due to the viable eqidermis, the in vitro sampling rate, or perfusion rate in vivo are included. Numerical inversion of the Laplace domain solutions was used for simulations of solute flux and cumulative amount absorbed and to model specific examples of percutaneous absorption of solvent-deposited solids. It was concluded that numerical inversions of the Laplace domain solutions for a diffusion model of the percutaneous absorption, using standard scientific software (such as SCIENTIST, MicroMath Scientific software) on modern personal computers, is a practical alternative to computation of infinite series solutions. Limits of the Laplace domain solutions were used to define the moments of the flux-time profiles for finite donor volumes and the slope of the terminal log flux-time profile. The mean transit time could be related to the diffusion time through stratum corneum, viable epidermal, and donor diffusion layer resistances and clearance from the receptor phase. Approximate expressions for the time to reach maximum flux (peak time) and maximum flux were also derived. The model was then validated using reported amount-time and flux-time profiles for finite doses applied to the skin. It was concluded that for very small donor phase volume or for very large stratum corneum-vehicle partitioning coefficients (e.g., for solvent deposited solids), the flux and amount of solute absorbed are affected by receptor conditions to a lesser extent than is obvious for a constant donor constant donor concentrations. (C) 2001 Wiley-Liss, Inc. and the American Pharmaceutical Association J Pharm Sci 90:504-520, 2001.

Hepatocyte [H-3]-palmitate uptake: effect of albumin surface charge modification

The role of plasma proteins on the cellular uptake of lipophilic substrates has perplexed investigators for many years. We tested the hypothesis that an ionic interaction between the protein-ligand complex and hepatocyte surface may be responsible for supplying more ligand to the cell for uptake. The surface-charged groups on albumin were modified to yield proteins having a range of isoelectric points (ALB, ALBs, ALBm, ALBe had values of 4.8-5.0, 4.5-4.7, 3.0-3.5, 8.4-8.6, respectively). [H-3]-Palmitate uptake studies were performed with adult rat hepatocyte suspensions using similar unbound ligand fractions in the presence of the different binding proteins. Mass spectrometry, isoelectric focusing (pI), and heptane : water partitioning were used to determine protein molecular weight, pI, and protein-palmitate equilibrium binding constant, respectively. Hepatocyte [H-3]-palmitate clearance in the presence of ALBs and ALBm were significantly lower (p < 0.05) than ALB, whereas [H-3]-palmitate clearance in the presence of ALBe was significantly higher (p < 0.05) than ALB. The data were consistent with the notion that ionic interactions between extracellular protein-ligand complexes and the hepatocyte surface facilitate the uptake of long-chain fatty acids.

Static and hydrodynamic monitoring of citalopram based on its electro-oxidation behavior at a glassy-carbon surface

The electrooxidative behavior of citalopram (CTL) in aqueous media was studied by cyclic voltammetry (CV) and square-wave voltammetry (SWV) at a glassy-carbon electrode. The electrochemical behaviour of CTL involves two electrons and two protons in the irreversible and diffusion controlled oxidation of the tertiary amine group. The maximum analytical signal was obtained in a phosphate buffer (pH ¼ 8.2). For analytical purposes, an SWV method and a flow-injection analysis (FIA) system with amperometric detection were developed. The optimised SWV method showed a linear range between 1.10 10 5–1.20 10 4 molL 1, with a limit of detection (LOD) of 9.5 10 6 molL 1. Using the FIA method, a linear range between 2.00 10 6–9.00 10 5 molL 1 and an LODof 1.9 10 6 molL 1 were obtained. The validation of both methods revealed good performance characteristics confirming applicability for the quantification of CTL in several pharmaceutical products.

Laser-induced diffusion decomposition in Fe-V thin-film alloys

We investigate the origin of ferromagnetism induced in thin-film (similar to 20 nm) Fe-V alloys by their irradiation with subpicosecond laser pulses. We find with Rutherford backscattering that the magnetic modifications follow a thermally stimulated process of diffusion decomposition, with formation of a-few-nm-thick Fe enriched layer inside the film. Surprisingly, similar transformations in the samples were also found after their long-time (similar to 10(3) s) thermal annealing. However, the laser action provides much higher diffusion coefficients (similar to 4 orders of magnitude) than those obtained under standard heat treatments. We get a hint that this ultrafast diffusion decomposition occurs in the metallic glassy state achievable in laser-quenched samples. This vitrification is thought to be a prerequisite for the laser-induced onset of ferromagnetism that we observe. 2014 Elsevier B.V. All rights reserved.

Carbon key-properties for microcystin adsorption in drinking water treatment: structure or surface chemistry?

Dissertação para Obtenção de Grau de Mestre em Engenharia Química e Bioquímica

Evaporation from a shallow water table: Diurnal dynamics of measured and simulated water and heat regime at the vicinity of a drying sand surface

Accurate estimates of water losses by evaporation from shallow water tables are important for hydrological, agricultural, and climatic purposes. An experiment was conducted in a weighing lysimeter to characterize the diurnal dynamics of evaporation under natural conditions. Sampling revealed a completely dry surface sand layer after 5 days of evaporation. Its thickness was <1 cm early in the morning, increasing to reach 4?5 cm in the evening. This evidence points out fundamental limitations of the approaches that assume hydraulic connectivity from the water table up to the surface, as well as those that suppose monotonic drying when unsteady conditions prevail. The computed vapor phase diffusion rates from the apparent drying front based on Fick's law failed to reproduce the measured cumulative evaporation during the sampling day. We propose that two processes rule natural evaporation resulting from daily fluctuations of climatic variables: (i) evaporation of water, stored during nighttime due to redistribution and vapor condensation, directly into the atmosphere from the soil surface during the early morning hours, that could be simulated using a mass transfer approach and (ii) subsurface evaporation limited by Fickian diffusion, afterward. For the conditions prevailing during the sampling day, the amount of water stored at the vicinity of the soil surface was 0.3 mm and was depleted before 11:00. Combining evaporation from the surface before 11:00 and subsurface evaporation limited by Fickian diffusion after that time, the agreement between the estimated and measured cumulative evaporation was significantly improved.

Cationic Diffusion in La2/3Ca1/3MnO3 Thin Films Grown on LaAlO3 (001) Substrates.

Microstructural features of La2/3Ca1/3MnO3 layers of various thicknesses grown on top of 001 LaAlO3 substrates are studied by using transmission electron microscopy and electron energy loss spectroscopy. Films are of high microstructural quality but exhibit some structural relaxation and mosaicity both when increasing thickness or after annealing processes. The existence of a cationic segregation process of La atoms toward free surface has been detected, as well as a Mn oxidation state variation through layer thickness. La diffusion would lead to a Mn valence change and, in turn, to reduced magnetization.

Atomic diffusion induced by stress relaxation in InGaAs/GaAs epitaxial layers

The origin of the microscopic inhomogeneities in InxGa12xAs layers grown on GaAs by molecular beam epitaxy is analyzed through the optical absorption spectra near the band gap. It is seen that, for relaxed thick layers of about 2.8 mm, composition inhomogeneities are responsible for the band edge smoothing into the whole compositional range (0.05,x,0.8). On the other hand, in thin enough layers strain inhomogeneities are dominant. This evolution in line with layer thickness is due to the atomic diffusion at the surface during growth, induced by the strain inhomogeneities that arise from stress relaxation. In consequence, the strain variations present in the layer are converted into composition variations during growth. This process is energetically favorable as it diminishes elastic energy. An additional support to this hypothesis is given by a clear proportionality between the magnitude of the composition variations and the mean strain.

Morphological changes in convection-diffusion-limited deposition

The effect of hydrodynamic flow upon diffusion-limited deposition on a line is investigated using a Monte Carlo model. The growth process is governed by the convection and diffusion field. The convective diffusion field is simulated by the biased-random walker resulting from a superimposed drift that represents the convective flow. The development of distinct morphologies is found with varying direction and strength of drift. By introducing a horizontal drift parallel to the deposition plate, the diffusion-limited deposit changes into a single needle inclined to the plate. The width of the needle decreases with increasing strength of drift. The angle between the needle and the plate is about 45° at high flow rate. In the presence of an inclined drift to the plate, the convection-diffusion-limited deposit leads to the formation of a characteristic columnar morphology. In the limiting case where the convection dominates, the deposition process is equivalent to ballistic deposition onto an inclined surface.

Atomic diffusion induced by stress relaxation in InGaAs/GaAs epitaxial layers

The origin of the microscopic inhomogeneities in InxGa1-xAs layers grown on GaAs by molecular beam epitaxy is analyzed through the optical absorption spectra near the band gap. It is seen that, for relaxed thick layers of about 2.8μm, composition inhomogeneities are responsible for the band edge smoothing into the whole compositional range (0.05diffusion at the surface during growth, induced by the strain inhomogeneities that arise from stress relaxation. In consequence, the strain variations present in the layer are converted into composition variations during growth. This process is energetically favorable as it diminishes elastic energy. An additional support to this hypothesis is given by a clear proportionality between the magnitude of the composition variations and the mean strain

Two-dimensional drift-diffusion simulation of organic solar cells

The aim of this master's thesis is to develop a two-dimensional drift-di usion model, which describes charge transport in organic solar cells. The main bene t of a two-dimensional model compared to a one-dimensional one is the inclusion of the nanoscale morphology of the active layer of a bulk heterojunction solar cell. The developed model was used to study recombination dynamics at the donor-acceptor interface. In some cases, it was possible to determine e ective parameters, which reproduce the results of the two-dimensional model in the one-dimensional case. A summary of the theory of charge transport in semiconductors was presented and discussed in the context of organic materials. Additionally, the normalization and discretization procedures required to nd a numerical solution to the charge transport problem were outlined. The charge transport problem was solved by implementing an iterative scheme called successive over-relaxation. The obtained solution is given as position-dependent electric potential, free charge carrier concentrations and current densities in the active layer. An interfacial layer, separating the pure phases, was introduced in order to describe charge dynamics occurring at the interface between the donor and acceptor. For simplicity, an e ective generation of free charge carriers in the interfacial layer was implemented. The pure phases simply act as transport layers for the photogenerated charges. Langevin recombination was assumed in the two-dimensional model and an analysis of the apparent recombination rate in the one-dimensional case is presented. The recombination rate in a two-dimensional model is seen to e ectively look like reduced Langevin recombination at open circuit. Replicating the J-U curves obtained in the two-dimensional model is, however, not possible by introducing a constant reduction factor in the Langevin recombination rate. The impact of an acceptor domain in the pure donor phase was investigated. Two cases were considered, one where the acceptor domain is isolated and another where it is connected to the bulk of the acceptor. A comparison to the case where no isolated domains exist was done in order to quantify the observed reduction in the photocurrent. The results show that all charges generated at the isolated domain are lost to recombination, but the domain does not have a major impact on charge transport. Trap-assisted recombination at interfacial trap states was investigated, as well as the surface dipole caused by the trapped charges. A theoretical expression for the ideality factor n_id as a function of generation was derived and shown to agree with simulation data. When the theoretical expression was fitted to simulation data, no interface dipole was observed.

Surface display of proteins by Gram-negative bacterial autotransporters

Affiliation: Faculté de Médecine Vétérinaire, Université de Montréal

Nanostructures de surface obtenues par dépôt de films minces à base d'assemblage supramoléculaire de copolymères blocs

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal