Optimized hydrogen positions for aluminium and iron containing hydroxide minerals

The structures of a number of hydroxide and oxyhydroxide minerals have previously been reported without the hydrogen positions explicitly defined. Here we use two atomic scale computer simulation techniques, one based on classical ionic potentials, the other on density functional theory (DFT), to predict these positions. The aim is not only to provide data that can be used as the basis for future experimental structure optimizations but also model parameters that can be used to predict complex hydroxide structures. The efficacy of the approach is demonstrated through the comparison of predicted and experimental data for minerals whose hydrogen positions are known.     

An atomic model of the outer layer of the bluetongue virus core derived from X-ray crystallography and electron cryomicroscopy

BACKGROUND: Bluetongue virus (BTV), which belongs to the Reoviridae family and orbivirus genus, is a non-enveloped, icosahedral, double-stranded RNA virus. Several protein layers enclose its genome; upon cell entry the outer layer is stripped away leaving a core, the surface of which is composed of VP7. The structure of the trimeric VP7 molecule has previously been determined using X-ray crystallography. The articulated VP7 subunit consists of two domains, one which is largely alpha-helical and the other, smaller domain, is a beta barrel with jelly-roll topology. The relative orientations of these two domains vary in different crystal forms. The structure of VP7 and the organizations of 780 subunits of this molecule in the core of virus is central to the assembly and function of BTV. RESULTS: A 23 A resolution map of the core, determined using electron cryomicroscopy (cryoEM) data, reveals that the 260 trimers of VP7 are organized on a rather precise T = 13 laevo icosahedral lattice, in accordance with the theory of quasi-equivalence. The VP7 layer occupies a shell that is between 260 A and 345 A from the centre of the core. Below this radius (230-260 A) lies the T = 1 layer of 120 molecules of VP3. By fitting the X-ray structure of an individual VP7 trimer onto the cryoEM BTV core structure, we have generated an atomic model of the VP7 layer of BTV. This demonstrates that one of the molecular structures seen in crystals of the isolated VP7 corresponds to the in vivo conformation of the molecule in the core. CONCLUSIONS: The beta-barrel domains of VP7 are external to the core and interact with protein in the outer layer of the mature virion. The lower, alpha-helical domains of VP7 interact with VP3 molecules which form the inner layer of the BTV core. Adjacent VP7 trimer-trimer interactions in the T = 13 layer are mediated principally through well-defined regions in the broader lower domains, to form a structure that conforms well with that expected from the theory of quasi-equivalence with no significant conformational changes within the individual trimers. The VP3 layer determines the particle size and forms a rather smooth surface upon which the two-dimensional lattice of VP7 trimers is laid down.     

Interleaving solving and elicitation of constraint satisfaction problems based on expected cost

We consider Constraint Satisfaction Problems in which constraints can be initially incomplete, where it is unknown whether certain tuples satisfy the constraint or not. We assume that we can determine the satisfaction of such an unknown tuple, i.e., find out whether this tuple is in the constraint or not, but doing so incurs a known cost, which may vary between tuples. We also assume that we know the probability of an unknown tuple satisfying a constraint. We define algorithms for this problem, based on backtracking search. Specifically, we consider a simple iterative algorithm based on a cost limit on the unknowns that may be determined, and a more complex algorithm that delays determining an unknown in order to estimate better whether doing so is worthwhile. We show experimentally that the more sophisticated algorithms can greatly reduce the average cost.     

Accommodation of impurities in α-Al2O3, α-Cr2O3 and α-Fe2O3

Atomic scale computer simulation was used to predict the mechanisms and energies associated with the accommodation of aliovalent and isovalent dopants in three host oxides with the corundum structure. Here we consider a much more extensive range of dopant ions than has previously been the case. This enables a rigorous comparison of calculated mechanism energetics. From this we predict that divalent ions are charge compensated by oxygen vacancies and tetravalent ions by cation vacancies over the full range of dopant radii. When defect associations are included in the model these conclusions remain valid. At equilibrium, defects resulting from extrinsic dopant solution dominate intrinsic processes, except for the largest dopant cations. Solution reaction energies increase markedly with increasing dopant radius. The behaviour of cluster binding energies is more complex.     

Quantification of multiple bioagents with wireless, remote-query magnetoelastic microsensors

This paper presents a micromagnetoelastic sensor array for simultaneously monitoring multiple biological agents. Magnetoelastic sensors, made of low-cost amorphous ferromagnetic ribbons, are analogous and complementary to piezoelectric acoustic wave sensors, which track parameters of interest via changes in resonance behavior. Magnetoelastic sensors are excited with magnetic ac fields, and, in turn, they generate magnetic fluxes that can be detected with a sensing coil from a distance. As a result, these sensors are highly attractive, not only due to their small size and low cost, but also because of their passive and wireless nature. Magnetoelastic sensors have been applied for monitoring pressure, temperature, liquid density, and viscosity, fluid How velocity and direction, and with chemical/biological responsive coatings that change mass or elasticity, various biological and chemical agents. In this paper, we report the fabrication and application of a six-sensor array for simultaneous measurement of Escherichia coli O157:H7, staphylococcal enterotoxin B, and ricin. In addition, the sensor array also monitors temperature and pH so the measurements are independent from these two parameters.     

Serotonin-1B receptor activity and expression modulate the aggression-stimulating effects of adolescent anabolic steroid exposure in hamsters.

Repeated high dose (5.0 mg/kg) anabolic-androgenic steroid (AAS) exposure during adolescence stimulates offensive aggression in male Syrian hamsters. These studies examined whether AAS-induced aggression was regulated by the activity of serotonin (5HT) type-1B receptors and correlated with altered 5HT1B expression. AAS-treated hamsters were tested for offensive aggression following the administration of the 5HT1B agonist anpirtoline (0.125-0.5 mg/kg). Anpirtoline dose-dependently reduced select components of the AAS-induced aggressive response, with significant reductions observed at 0.25 mg/kg. Aggressive, AAS-treated hamsters showed significant decreases in the area covered by 5HT1B-containing neuronal puncta and increases in the number of 5HT1B-containing neuronal somata in select brain regions implicated in aggression control. Together, these data support a role for site-specific alterations in 5HT1B signaling and expression in adolescent AAS-induced aggression. (PsycINFO Database Record (c) 2010 APA, all rights reserved)