How random are intrinsically disordered proteins? A small angle scattering perspective

While the crucial role of intrinsically disordered proteins (IDPs) in the cell cycle is now recognized, deciphering their molecular mode of action at the structural level still remains highly challenging and requires a combination of many biophysical approaches. Among them, small angle X-ray scattering (SAXS) has been extremely successful in the last decade and has become an indispensable technique for addressing many of the fundamental questions regarding the activities of IDPs. After introducing some experimental issues specific to IDPs and in relation to the latest technical developments, this article presents the interest of the theory of polymer physics to evaluate the flexibility of fully disordered proteins. The different strategies to obtain 3-dimensional models of IDPs, free in solution and associated in a complex, are then reviewed. Indeed, recent computational advances have made it possible to readily extract maximum information from the scattering curve with a special emphasis on highly flexible systems, such as multidomain proteins and IDPs. Furthermore, integrated computational approaches now enable the generation of ensembles of conformers to translate the unique flexible characteristics of IDPs by taking into consideration the constraints of more and more various complementary experiment. In particular, a combination of SAXS with high-resolution techniques, such as x-ray crystallography and NMR, allows us to provide reliable models and to gain unique structural insights about the protein over multiple structural scales. The latest neutron scattering experiments also promise new advances in the study of the conformational changes of macromolecules involving more complex systems.     

CO adsorption on amorphous silica-alumina: electrostatic or Brønsted acidity probe?

The adsorption of CO on amorphous silica-alumina (ASA) was calculated by DFT. CO appears as a probe of the electrostatic field induced by the whole surface, at the origin of a so-called vibrational Stark effect responsible for the CO frequency shifts. Br?nsted acidity of the ASA sites does not directly correlate CO frequency shifts.     

Enzymatic Reaction in Droplets Manipulated with Liquid Dielectrophoresis

Droplet generation and transportation for biological reactions are conducted with liquid dielectrophoresis (LDEP), forming two hundred picoliter droplets and aligning them in an open environment above the micro‐machined electrodes. The generation of the dielectrophoresis signals was critically examined to actuate droplets in biological solutions without excessive Joule heating. Enzymatic reactions between β‐galactosidase and fluorescein di‐β‐D ‐galactopyranoside were succeeded in manipulated droplets, which was confirmed by fluorescence imaging. These results allow us to propose the integration of LDEP actuation in high throughput biomolecular assays.     

Experimental test of universality of the Anderson transition

We experimentally test the universality of the Anderson three dimensional metal-insulator transition, using a quasiperiodic atomic kicked rotor. Nine sets of parameters controlling the microscopic details have been tested. Our observation indicates that the transition is of second order, with a critical exponent independent of the microscopic details; the average value 1.63±0.05 agrees very well with the numerically predicted value ν=1.58.     

Signed words and permutations, V; a sextuple distribution

We calculate the distribution of the sextuple statistic over the hyperoctahedral group B _n that involves the flag-excedance and flag-descent numbers “fexc” and “fdes,” the flag-major index “fmaj,” the positive and negative fixed point numbers “ ” and “ ” and the negative letter number “neg.” Several specializations are considered. In particular, the joint distribution for the pair is explicitly derived.      

Chemical functionalization of electrodes for detection of gaseous nerve agents with carbon nanotube field-effect transistors

An innovative sensor for the detection of nerve agents in the gas phase based on a carbon nanotube field-effect transistor was developed. A high sensitivity to organophosphorus gases was obtained by modifying gold electrodes with specific tailor-made self-assembled monolayers.     

High efficiency of cavity-based triaryl-phosphines in nickel-catalysed Kumada-Tamao-Corriu cross-coupling

Combining diaryl-calixarenyl phosphines with [Ni(cod)(2)] resulted in highly active Kumada-Tamao-Corriu cross-coupling catalysts. With one of the ligands, TOFs up to 439,000 mol(ArBr) mol(Ni)(-1) h(-1) were observed in the reaction of 1-bromonaphthalene with PhMgBr. The systems were also found to be active at room temperature with aryl chlorides.     

Iron(III) chloride-tandem catalysis for a one-pot regioselective protection of glycopyranosides

Tandem catalysis by using iron(III) chloride hexahydrate leads to carbohydrate building blocks displaying an orthogonal protecting group pattern as illustrated by the regioselective protection of trehalose and maltose disaccharides.     

Turbulence Modelling of Unsteady Turbulent Flows Using the Stress Strain Lag Model

This paper reports the application of a recently developed turbulence modelling scheme known as the C _as model. This model was specifically developed to capture the effects of stress-strain misalignment observed in turbulent flows with mean unsteadiness. Earlier work has reported the approach applied within a linear k-ε modelling framework, and some initial testing of it within the k-ω SST model of Menter (AIAA J 32:1598–1605, 1994). The resulting k-ε-C _as and SST-C _as models have been shown to result in some of the advantages of a full Reynolds Stress transport Model (RSM), whilst retaining the computational efficiency and stability benefits of a eddy viscosity model (EVM). Here, the development of the the high-Reynolds-number version of the C _as model is outlined, with some example applications to steady and unsteady homogeneous shear flows. The SST-C _as form of the model is then applied to further, more challenging cases of 2-D flow around a NACA0012 aerofoil beyond stall and the 3-D flow around a circular cylinder in a square duct, both being flows which exhibit large, unsteady, separated flow regions. The predictions returned by a range of other common turbulence modelling schemes are included for comparison and the SST-C _as scheme is shown to return generally good results, comparable in some respects to those obtainable from far more complex schemes, for only moderate computing resource requirements.     

Numerical Simulation of Coherent Structures over Plant Canopy

This paper reports large eddy simulations of the interaction between an atmospheric boundary layer and a canopy (representing a forest cover). The problem is studied for a homogeneous configuration representing the situation encountered above a continuous forest cover, as well as for a heterogeneous configuration representing the situation similar to an edge or a clearing in a forest. The numerical results reproduces correctly all the main characteristics of this flow as reported in the literature: the formation of a first generation of coherent structures aligned transversally with the wind flow direction, the reorganization and the deformation of these vortex tubes into horse-shoe structures. The results obtained when introducing a discontinuity in the canopy (reproducing a clearing or a fuel break in a forest), are compared with the experimental data collected in a wind tunnel; here, the results confirm the existence of a strong turbulence activity inside the canopy at a distance equal to 8 times the height of the canopy, referenced in the literature as the Enhance Gust Zone (EGZ) characterized by a local peak of the skewness factor.