Scaling up in isolation of medium-size uraemic toxins

Plasmatic accumulation of uraemic toxins in the middle molecular mass range has been reported to be associated with several pathologies observed in uraemic patients. The very low concentration of these toxins in uraemic body fluids makes classical chromatography techniques inadequate in isolating sufficient amounts of these endogenous substances, thus precluding their identification. A scaling up of gel permeation and ion-exchange chromatographies was therefore developed. This considerably increased the amount of uraemic toxins isolated, thus allowing the study of their chemical nature and facilitating understanding of their biological activities.     

A general solution to the Schrödinger–Poisson equation for a charged hard wall: Application to potential profile of an AlN/GaN barrier structure

A general, system-independent, formulation of the parabolic Schrödinger–Poisson equation is presented for a charged hard wall in the limit of complete screening by the ground state. It is solved numerically using iteration and asymptotic boundary conditions. The solution gives a simple relation between the band bending and sheet charge density at an interface. Approximative analytical expressions for the potential profile and wave function are developed based on properties of the exact solution. Specific tests of the validity of the assumptions leading to the general solution are made. The assumption of complete screening by the ground state is found be a limitation; however, the general solution provides a fair approximate account of the potential profile when the bulk is doped. The general solution is further used in a simple model for the potential profile of an AlN/GaN barrier structure. The result compares well with the solution of the full Schrödinger–Poisson equation.     

Wall modeling for implicit large-eddy simulation and immersed-interface methods

We propose and analyze a wall model based on the turbulent boundary layer equations (TBLE) for implicit large-eddy simulation (LES) of high Reynolds number wall-bounded flows in conjunction with a conservative immersed-interface method for mapping complex boundaries onto Cartesian meshes. Both implicit subgrid-scale model and immersed-interface treatment of boundaries offer high computational efficiency for complex flow configurations. The wall model operates directly on the Cartesian computational mesh without the need for a dual boundary-conforming mesh. The combination of wall model and implicit LES is investigated in detail for turbulent channel flow at friction Reynolds numbers from Re _τ  = 395 up to Re _τ =100,000 on very coarse meshes. The TBLE wall model with implicit LES gives results of better quality than current explicit LES based on eddy viscosity subgrid-scale models with similar wall models. A straightforward formulation of the wall model performs well at moderately large Reynolds numbers. A logarithmic-layer mismatch, observed only at very large Reynolds numbers, is removed by introducing a new structure-based damping function. The performance of the overall approach is assessed for two generic configurations with flow separation: the backward-facing step at Re _h = 5,000 and the periodic hill at Re _H = 10,595 and Re _H = 37,000 on very coarse meshes. The results confirm the observations made for the channel flow with respect to the good prediction quality and indicate that the combination of implicit LES, immersed-interface method, and TBLE-based wall modeling is a viable approach for simulating complex aerodynamic flows at high Reynolds numbers. They also reflect the limitations of TBLE-based wall models.     

Calorimetric and rheological properties of wheat flour suspensions and doughs: Effects of wheat types and milling procedure

Three types of wheat were submitted to two different milling procedures, giving rise to six flours which differed by some physico-chemical characteristics such as particle size, level of damaged starch and protein content. Differential scanning calorimetry was used for monitoring heat-induced structural changes in flour aqueous dispersions 80% water and in doughs 45% water. Differences between the thermal behaviour of the flour dispersions and doughs were explained mainly by differences in protein content. This result was confirmed after partial substitution of flour by gluten. Dynamic mechanical analysis performed at 20°C on the flour doughs indicated, as expected, a linear increase in the elastic modulus with increasing protein content. The results did not bring any evidence that, under these experimental conditions, starch damage might affect gluten hydration.This revised version was published online in November 2005 with corrections to the Cover Date.     

Shear softening and thixotropic properties of wheat flour doughs in dynamic testing at high shear strain

Shear softening and thixotropic properties of wheat flour doughs are demonstrated in dynamic testing with a constant stress rheometer. This behaviour appears beyond the strictly linear domain (strain amplitude ₀ 0.2%),G,G and |^*| decreasing with ₀, the strain response to a sine stress wave yet retaining a sinusoidal shape. It is also shown thatG recovers progressively in function of rest time. In this domain, as well as in the strictly linear domain, the Cox-Merz rule did not apply but() and | ^*())| may be superimposed by using a shift factor, its value decreasing in the former domain when ₀ increases. Beyond a strain amplitude of about 10–20%, the strain response is progressively distorted and the shear softening effects become irreversible following rest.     

Phase networks of cross-β peptide assemblies

Recent evidence suggests that simple peptides can access diverse amphiphilic phases, and that these structures underlie the robust and widely distributed assemblies implicated in nearly 40 protein misfolding diseases. Here we exploit a minimal nucleating core of the Aβ peptide of Alzheimer's disease to map its morphologically accessible phases that include stable intermolecular molten particles, fibers, twisted and helical ribbons, and nanotubes. Analyses with both fluorescence lifetime imaging microscopy (FLIM) and transmission electron microscopy provide evidence for liquid-liquid phase separations, similar to the coexisting dilute and dense protein-rich liquid phases so critical for the liquid-solid transition in protein crystallization. We show that the observed particles are critical for transitions to the more ordered cross-β peptide phases, which are prevalent in all amyloid assemblies, and identify specific conditions that arrest assembly at the phase boundaries. We have identified a size dependence of the particles in order to transition to the para-crystalline phase and a width of the cross-β assemblies that defines the transition between twisted fibers and helically coiled ribbons. These experimental results reveal an interconnected network of increasing molecularly ordered cross-β transitions, greatly extending the initial computational models for cross-β assemblies.     

Mixing stochastic dynamic programming and scenario aggregation

This paper describes a serial and parallel implementation of a hybrid stochastic dynamic programming and progressive hedging algorithm. Numerical experiments show good speedups in the parallel implementation. In spite of this, our hybrid algorithm has difficulties competing with a pure stochastic dynamic programming approach on a given test case from macroeconomic control theory.This research has been conducted with financial support from the Norwegian Research Council. As most of this work was conducted under the TRACS program at the University of Edinburgh, we want to thank Ken McKinnon and all other helpful people at the Department of Mathematics and Statistics of Edinburgh University and at the Edinburgh Parallel Computing Centre. We are also very grateful to our colleague Stein W. Wallace for his continuing support of our work. Without him, this research would probably never have taken place. We would also like to thank an anonymous referee for helpful corrections and comments.     

Intersubband energies in Al1−yInyN/Ga1−xInxN heterostructures with lattice constant close to aGaN

We have studied the conduction band profile and the intersubband transition energy, E₁₂, of Al_1−yIn_yN/Ga_1−xIn_xN quantum well structures. We have considered how material parameters such as non-parabolicity and the uncertainty in the bowing parameter affect E₁₂ and the corresponding wavelength, λ₁₂. The calculations include strain and cover the transition range from telecommunication wavelengths (1.55 μm) to the mid-infrared (∼ 10 μm).     

Mechanisms Involved in Microbially Enhanced Oil Recovery

Microbial enhanced oil recovery (MEOR) represents a possible cost-effective tertiary oil recovery method. Although the idea of MEOR has been around for more than 75 years, even now little is known of the mechanisms involved. In this study, Draugen and Ekofisk enrichment cultures, along with Pseudomonas spp. were utilized to study the selected MEOR mechanisms. Substrates which could potentially stimulate the microorganisms were examined, and l-fructose, d-galacturonic acid, turnose, pyruvic acid and pyruvic acid methyl ester were found to be the best utilized by the Ekofisk fermentative enrichment culture. Modelling results indicated that a mechanism likely to be important for enhanced oil recovery is biofilm formation, as it required a lower in situ cell concentration compared with some of the other MEOR mechanisms. The bacterial cells themselves were found to play an important role in the formation of emulsions. Bulk coreflood and flow cell experiments were performed to examine MEOR mechanisms, and microbial growth was found to lead to possible alterations in wettability. This was observed as a change in wettability from oil wet (contact angle 154°) to water wet (0°) due to the formation of biofilms on the polycarbonate coupons.