Modelling Protein Plasticity: The Example of Frataxin and Its Variants

Frataxin (FXN) is a protein involved in storage and delivery of iron in the mitochondria. Single-point mutations in the FXN gene lead to reduced production of functional frataxin, with the consequent dyshomeostasis of iron. FXN variants are at the basis of neurological impairment (the Friedreich’s ataxia) and several types of cancer. By using altruistic metadynamics in conjunction with the maximal constrained entropy principle, we estimate the change of free energy in the protein unfolding of frataxin and of some of its pathological mutants. The sampled configurations highlight differences between the wild-type and mutated sequences in the stability of the folded state. In partial agreement with thermodynamic experiments, where most of the analyzed variants are characterized by lower thermal stability compared to wild type, the D104G variant is found with a stability comparable to the wild-type sequence and a lower water-accessible surface area. These observations, obtained with the new approach we propose in our work, point to a functional switch, affected by single-point mutations, of frataxin from iron storage to iron release. The method is suitable to investigate wide structural changes in proteins in general, after a proper tuning of the chosen collective variable used to perform the transition.     

Optimisation of a photochemical sensor for total organic carbon measurement

A new tool for the measurement of TOC based on the heterogeneous photocatalysis activated by two different light sources has been planned. The instrument is constituted by a cell where the degradation occurs thanks to both the UV irradiation and the presence of a powered catalyst and by a measurement cell lodging CO2 gas permeable membrane electrode (detector), thermometer, inlet and outlet ways for the samples. One of the sources has a maximum emission at 254nm, while the other simulates the solar spectrum. A suspension (1 g/L) of titanium dioxide (Degussa P25) has been used to catalyse the process. A magnetic stirrer and a circulating pump avoid the deposition of the catalyst on the bottom of the reactor. The online measurement of produced CO2 was performed on 11 molecules (commercial names: Parachlorophenol, D-Glucose, Acid Blue 29, Atraton, Aspirin, Dimethoate, Aldicarb sulfone, Hydroquinone, (R)-Propranolol, Citric acid, Atrazine) to test the system efficiency. The experimental CO2 value was compared with the theoretical TOC value calculated by means of the structure's formula.     

Cracks and topological defects in lyotropic nematic gels

We report on the effects of the coupling of nematic order and elasticity in anisotropic lyotropic gels consisting of large nematic domains of surfactant coated single wall carbon nanotubes embedded in a cross-linked N-isopropyl acrylamide polymer matrix. We observe the following striking features: (i) undulations and then cusping of the gel sidewalls, (ii) a nematic director field that evolves as the gel sidewalls deform, (iii) networks of surface cracks that are orthogonal to the nematic director field, and (iv) fissures at the sidewall cusps and associated topological defects that would not form in liquid nematics.     

Ion implanted induced giant gettering of gold in silicon

Abstract

Ion implanted induced giant gettering of Gold in Silicon has been investigated by using ?111? Si wafer implanted with 10¹⁶ Ar⁺ ions/cm² at 280 keV. Some conditions of the appearance of giant gettering of Au in Si have been establi shed at different temperatures i.e. 500°C and 900°C: (i) annealing in vacuum, (ii) an “infinite” source of Au from a preannealed Au-Si film deposited by sputtering. On the basis of the experimental results a simple thermodinamic model explaining the giant gettering involving the mechanism of a liquid Au-Si phase has been developed.     

Ultrafiltration of Humic Substances in the Presence of Protein and Metal Ions

In this paper factors affecting the ultrafiltration of mixtures of HA and BSA including concentration, pH, ionic strength, ionic charge and size of hydrated ion were elucidated. In the presence of BSA, higher HA rejection and lower flux were obtained during ultrafiltration. This is due to interactions between HA and BSA. A bond may be established between humic acid and protein molecules. Flux was decreased and HA rejection was increased with increasing the humic acid concentration in constant concentration of BSA. At low concentration, the humic macromolecules pass more easily through the membrane pores due to their structure. The HA rejection depends on the molecular weight cut off (MWCO) of the membrane. Higher rejection is anticipated for membranes with lower MWCO. However cake deposition is the dominant mechanism during ultrafiltration of solutions containing mixtures of HA and BSA using XM50, YM100 and XM300 ultrafiltration membranes. By increasing the pH of solutions containing mixture of HA and BSA, higher flux and lower HA rejection were achieved. At the protein isoelectric point, flux showed a minimum and increased for higher pH values. A higher flux was obtained for solutions with lower ionic strength. At the beginning of the filtration, HA rejection was low for solution with higher ionic strength. However during filtration the trend was conversely changed. In the presence of Ba²⁺ cation the HA rejection for solutions containing HA and BSA was higher compare to the solutions containing Na⁺ cation.     

Minimum power multicasting in wireless networks under probabilistic node failures

In this paper we deal with a probabilistic extension of the minimum power multicast (MPM) problem for wireless networks. The deterministic MPM problem consists in assigning transmission powers to the nodes, so that a multihop connection can be established between a source and a given set of destination nodes and the total power required is minimized. We present an extension to the basic problem, where node failure probabilities for the transmission are explicitly considered. This model reflects the necessity of taking uncertainty into account in the availability of the hosts. The novelty of the probabilistic minimum power multicast (PMPM) problem treated in this paper consists in the minimization of the assigned transmission powers, imposing at the same time a global reliability level to the solution network. An integer linear programming formulation for the PMPM problem is presented. Furthermore, an exact algorithm based on an iterative row and column generation procedure, as well as a heuristic method are proposed. Computational experiments are finally presented.     

Formation and dynamics of easy orientation axis in magnetic field on PVCN-F surface

We describe the experiments on a magnetically-induced drift of the easy axis on a soft surface of photoaligning material fluoro-polyvinyl-cinnamate. We found unexpected partial relaxation of the drift of the easy axis after switching the magnetic field off. This relaxation cannot be explained in a framework of the existing models and requires additional assumptions about the drift process. We propose a model that explains the experimental data suggesting elastic-like behaviour of the polymer fragments during the drift of the easy axis.     

Anomalous relaxation of a twisted cell under an external magnetic field: The nearly homogeneous relaxation

We report experimental and theoretical investigations of the dynamic behaviour of a π/2 twisted NLC layer in a magnetic field. When a magnetic field H is applied in the layer plane at a suitable angle β with respect to the easy axis on the first surface, the relaxation towards the equilibrium texture occurs through a slow decay of unstable textures. Depending on the values of H and β, the relaxation of the system can be nearly homogeneous or strongly inhomogeneous. In this paper we restrict our attention to the case where the relaxation occurs in a nearly homogeneous way. The theoretical relaxation time τw of the unstable textures is found to depend strongly on the angle β and on the amplitude of the magnetic field. The experimental dependence of τw on H and β is found to be in good agreement with the theoretical predictions. The relaxation process is extremely sensitive to small dishomogeneities of the director easy alignment on the surfaces. From the measured relaxation we are able to estimate a spread of 0.3° on the surface easy axes at a planar anchored SiO surface.     

High-temperature thermal evolution of SiAs precipitates in silicon

The thermal evolution of monoclinic SiAs precipitates at 1050° C in silicon samples implanted with 1 and 1.5×10¹⁷ As/cm² was followed by transmission electron microscopy (TEM) and secondary neutral mass spectrometry (SNMS). These experiments show, for the first time, the coexistence of two different states of As in silicon, i.e., the electrically active and the inactive mobile dopant, in equilibrium with monoclinic SiAs precipitates. Moreover, they provide, for the saturation concentration of As in silicon, which includes both these states, a value of 3×10²¹ cm^–3 at 1050° C.     

Testing Newtonian gravity in space

We propose to measure the universal constant of gravity G in space by means of a small scale planetary system in geosynchronous orbit; test particle satellites of different nuclear composition and with different distances from the central mass would allow one to check possible variations with material and distance. With current technology G can be measured with a relative accuracy of 10⁻⁵ or better depending on the capability of controlling some perturbations which act at the level of 10⁻⁶ (i.e. ≈ 10⁻¹¹ cm s⁻²; however, particular dynamical configurations mutuated from celestial mechanics should allow detection of differential effects with composition and distance (if any) to at least 10⁻⁶. Distance variations will be detected only if acting on a distance scale of 10 m.