G-Quadruplex Recognition by DARPIns through Epitope/Paratope Analogy**

We investigated the mechanisms leading to the specific recognition of Guanine Guadruplex (G4) by DARPins peptides, which can lead to the design of G4 s specific sensors. To this end we carried out all-atom molecular dynamic simulations to unravel the interactions between specific nucleic acids, including human-telomeric (h-telo), Bcl-2, and c-Myc, with different peptides, forming a DARPin/G4 complex. By comparing the sequences of DARPin with that of a peptide known for its high affinity for c-Myc, we show that the recognition cannot be ascribed to sequence similarity but, instead, depends on the complementarity between the three-dimensional arrangement of the molecular fragments involved: the α-helix/loops domain of DARPin and the G4 backbone. Our results reveal that DARPins tertiary structure presents a charged hollow region in which G4 can be hosted, thus the more complementary the structural shapes, the more stable the interaction.     

Direct Synthesis of 3-Aryl Substituted Isocoumarins and Phthalides through Palladium Acetate Catalyzed C(sp2)−H Activation in Ionic Liquids

A novel Pd-catalysed oxidative coupling between benzoic acids and vinylarenes or acrylates to furnish isocoumarins and phthalides is reported. The reaction proceeds smoothly in molten tetrabutylammonium acetate via a selective C−H bond activation, with very low percentage of ligand-free palladium acetate as the catalyst, under atmospheric pressure of oxygen. Sub-stoichiometric amount of copper acetate is also required as a reoxidant for the palladium.     

On the pressure dependence of the viscosity of aqueous sugar solutions

New experimental data for the pressure dependence of the viscosity of aqueous solutions of different sugars are presented. Measurements were carried out with a gravity driven high pressure viscometer with a maximum pressure of 700 MPa. The influence of both concentration and temperature on the pressure dependence of the viscosity is considered. Next to the data, a viscosity model based on a suspension model is introduced and it is shown that it is able to predict the viscosity for sugar solutions in a broad parameter range, including pressure. It is demonstrated that the relative viscosity for varying sugar mass fraction at constant pressure coincides with the pressure-dependent relative viscosity for a fixed sugar mass fraction, suggesting that there are no structural changes occurring under pressure. A brief interpretation of the viscosity model is given.     

Bias in modal parameters using the direct and iterative RFP identification procedures

In the rational fraction polynomial method [1] the identification of modal parameters is obtained through a direct linear least-square optimization technique but a particular form of fitting error is minimized. An iterative algorithm has been recently developed which uses the true fitting error [2]. In this paper a statistical analysis is developed to estimate the bias effects on the identified parameters when the data are polluted with noise. Both the direct and iterative procedures are considered. Numerical simulations are used to validate the results predicted by the theoretical analysis, which shows that the iterative approach is by far more efficient than the direct method.A first version of this paper was presented at 17th Int. Seminar on Modal Analysis, Leuven (Belgium), 23–25 September 1992, and preprinted in the Proceedings.     

On Fractional PI λ Controllers: Some Tuning Rules for Robustness to Plant Uncertainties

The objective of this work is to find out optimum settings for a fractional PI ^λ controller in order to fulfill three different robustness specifications of design for the compensated system, taking advantage of the fractional order, λ. Since this fractional controller has one parameter more than the conventional PI controller, one more specification can be fulfilled, improving the performance of the system and making it more robust to plant uncertainties, such as gain and time constant changes. For the tuning of the controller an iterative optimization method has been used, based on a nonlinear function minimization. Two real examples of application are presented and simulation results are shown to illustrate the effectiveness of this kind of unconventional controllers.     

Energy Scaling of Compressed Elastic Films –Three-Dimensional Elasticity¶and Reduced Theories

We derive an optimal scaling law for the energy of thin elastic films under isotropic compression, starting from three-dimensional nonlinear elasticity. As a consequence we show that any deformation with optimal energy scaling must exhibit fine-scale oscillations along the boundary, which coarsen in the interior. This agrees with experimental observations of folds which refine as they approach the boundary. We show that both for three-dimensional elasticity and for the geometrically nonlinear Föppl-von Kármán plate theory the energy of a compressed film scales quadratically in the film thickness. This is intermediate between the linear scaling of membrane theories which describe film stretching, and the cubic scaling of bending theories which describe unstretched plates, and indicates that the regime we are probing is characterized by the interplay of stretching and bending energies. Blistering of compressed thin films has previously been analyzed using the Föppl-von Kármán theory of plates linearized in the in-plane displacements, or with the scalar eikonal functional where in-plane displacements are completely neglected. The predictions of the linearized plate theory agree with our result, but the scalar approximation yields a different scaling.     

An efficient method for solving free-boundary diffusion problems

Summary A new method is introduced for solving free-boundary problems for the heat equation. The method is shown to be uniformly convergent both for first type and nonlinear second type boundary conditions. Approximate solutions are obtained by discretization of the time variable and recursive solution at each time step of classical heat conduction linear problems in slabs of known thickness. An error estimate is given. Numerical tests are presented in a few cases in which exact solutions are known.

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Sommario Si introduce un nuovo metodo per la soluzione di problemi a contorno libero per l'equazione del calore. Si dimostra la convergenza uniforme del metodo sia per condizioni al contorno del primo tipo che per condizioni al contorno del secondo tipo non lineari. Le soluzioni approssimate sono ottenute discretizzando la variabile temporale e risolvendo ricorsivamente ad ogni passo un classico problema lineare di conduzione in uno strato di spessore noto. E' data una stima dell'errore. Per alcuni casi nei quali è nota la soluzione esatta sono presentate prove numeriche.

     

Analysis of hydrodynamic and thermal dispersion in porous media by means of a local approach

A pore scale analysis is implemented in this numerical study to investigate the behavior of microscopic inertia and thermal dispersion in a porous medium with a periodic structure. The macroscopic characteristics of the transport phenomena are evaluated with an averaging technique of the controlling variables at a pore scale level in an elementary cell of the porous structure. The Darcy–Forchheimer model describes the fluid motion through the porous medium while the continuity and Navier–Stokes equations are applied within the unit cell. An average energy equation is employed for the thermal part of the porous medium. The macroscopic pressure loss is computed in order to evaluate the dominant microscopic inertial effects. Local fluctuations of velocity and temperature at the pore scale are instrumental in the quantification of the thermal dispersion through the total effective thermal diffusivity. The numerical results demonstrate that microscopic inertia contributes significantly to the magnitude of the macroscopic pressure loss, in some instances with as much as 70%. Depending on the nature of the porous medium, the thermal dispersion may have a marked bearing on the heat transfer, particularly in the streamwise direction for a highly conducting fluid and certain values of the Peclet number.     

Rheology and microstructure of gluten and soya-based o/w emulsions

Highly concentrated oil-in-water (o/w) emulsion stabilised by means of gluten and soya protein isolate (SPI) at low pH have been characterized by means of linear dynamic viscoelasticity and droplet size distribution analysis (DSD). The microstructure of these emulsions has been characterized at a colloidal level by using confocal laser scanning microscopy (CLSM) and light microscopy (LM). These emulsions always exhibited a behaviour characteristic of highly flocculated emulsions with a mechanical spectrum showing a well-developed plateau region. DSD results generally showed log normal bimodal profiles. Microstructure images revealed occurrence of a close packing of droplets with a broad distribution of sizes participating in the formation of a three dimensional flocculated network. The Mason model of elasticity of compressed emulsions has been used to correlate viscoelastic and microstructural parameters giving adequate fitting but underestimating the elastic properties obtained for the highest concentration of gluten. These deviations may be explained in terms of an enhancement of the elastic network formed in the aqueous phase in which the glutenin fraction must play an important role. Paper presented at the Annual European Rheology Conference (AERC) 2005, April 21-23, Grenoble, France.