Role of Conformational Changes of Hexameric Bacterial Uridine Phosphorylases in Substrate Binding

Crystallography Reports - Crystals of mutants of uridine phosphorylase from Shewanella oneidensis MR-1 at the active-site threonine residue were obtained, and the three-dimensional structures of...     

The auction algorithm for the transportation problem

The auction algorithm is a parallel relaxation method for solving the classical assignment problem. It resembles a competitive bidding process whereby unassigned persons bid simultaneously for objects, thereby raising their prices. Once all bids are in, objects are awarded to the highest bidder. This paper generalizes the auction algorithm to solve linear transportation problems. The idea is to convert the transportation problem into an assignment problem, and then to modify the auction algorithm to exploit the special structure of this problem. Computational results show that this modified version of the auction algorithm is very efficient for certain types of transportation problems.     

Magnetization vector field in a uniaxial ferromagnetic film

Technical Physics - Analytical models for the magnetization vector field B m in a uniaxial ferromagnetic film are studied. Some of them are found to closely approximate B m even if the quality...     

Three-dimensional structure of Saccharomyces cerevisiae inorganic pyrophosphatase complexed with cobalt and phosphate ions

Crystals of Saccharomyces cerevisiae inorganic pyrophosphatase suitable for X-ray diffraction study were grown by cocrystallization of the enzyme with cobalt chloride and imidodiphosphate. Saccharomyces cerevisiae is a metal-dependent enzyme which catalyzes hydrolysis of inorganic pyrophosphate to orthophosphate. The three-dimensional structure of this enzyme was solved by the molecular-replacement method and refined at 1.8 Å resolution to an R factor of 19.5%. Cobalt and phosphate ions were revealed in the active centers of both identical subunits (A and B) of the pyrophosphatase molecule. In subunit B, a water molecule was found between two cobalt ions. It is believed that this water molecule acts as an attacking nucleophile in the enzymatic cleavage of the pyrophosphate bond. It was demonstrated that cobalt ions and a phosphate group occupy only part of the potential binding sites (two chemically identical and crystallographically independent subunits have different binding sites). The arrangement of ligands and the structure of the nucleophile-binding site are discussed in relation to the mechanism of action of the enzyme and the nature of the metal activator.     

The action of an electron beam on dust structures in a plasma

The action of an electron beam on ordered dust structures in glow and low-pressure RF discharges was studied experimentally. The electron beam produces destruction and dynamic displacement of the dust structure. In the center of a dust structure, an electron beam with a low electron energy (tens of eV) at currents up to 1 mA caused structural disordering and “melting” in the region of its action but did not excite external crystal regions. Local action of an electron beam with a high electron energy (25 keV) and a beam current above 10 mA caused deformation of the whole dust structure and shifted it in the horizontal direction so that it was carried away from the RF discharge zone. The effect of dust structure displacements can be used to locally remove particles from a plasma.     

Generation of mesoscopic magnetic structures by local laser action

New effects are observed wherein the internal structure of the domain walls in a thin magnetic iron garnet film are modified by the action of focused laser radiation. A single laser pulse with increasing power gives rise to the following: 1) displacement of vertical Bloch lines in a domain wall; 2) generation of a pair of vertical Bloch lines on initially line-free walls; and, 3) an irreversible change in shape of a domain wall and the domain structure as a whole. The mechanism leading to the generation and displacement of Bloch lines is connected with the motion of domain walls which is induced by a local change in the distribution of demagnetizing fields as a result of a heating-induced decrease of the magnetization in the focal spot of the laser radiation. Pis’ma Zh. éksp. Teor. Fiz. 66, No. 6, 398–402 (25 September 1997)     

Formation on field emitters coated with fullerenes of microformations producing ordered emission images

Field emission projector studies of fullerene coatings deposited on tungsten tip field emitters reveal specific ordered patterns in the form of doublets, quadruplets, rings, disks, and other forms in the emitter images. The ways in which these types of ordered emission patterns arise and their relation to C₆₀ microformations have been established. Possible causes of the emergence of the ordered emission images are analyzed on the basis of published data and experimental results obtained. A modification of the model of field emission from the surface of microformations taking into account internal reflection of the electronic waves from the formation boundaries has been proposed.     

Ghost-matter mixing and feigenbaum universality in string theory

Branelike vertex operators, defining backgrounds with ghost-matter mixing in Neveu-Schwarz-Ramond superstring theory, play an important role in a world-sheet formulation of D branes and M theory, being creation operators for extended objects in the second quantized formalism. We show that the dilaton beta function in ghost-matter mixing backgrounds becomes stochastic. The renormalization group (RG) equations in ghost-matter mixing backgrounds lead to non-Markovian Fokker-Planck equations whose solutions describe superstrings in curved spacetimes with branelike metrics. We show that the Feigenbaum universality constant δ=4.669 ..., describing transitions from order to chaos in a huge variety of dynamical systems, appears analytically in these RG equations. We find that the appearance of this constant is related to the scaling of relative spacetime curvatures at fixed points of the RG flow. In this picture, the fixed points correspond to the period doubling of Feigenbaum iterational schemes.

     

Identification of dislocations and their influence on the recombination of charge carriers in gallium nitride

The relation between the density of etch pits revealed in GaN by etching in a KOH/NaOH eutectic and the density of dislocations determined by transmission electron microscopy (TEM) is studied along with the relation between the density of dislocations and the density of dark spot defects observed in GaN by microcathodoluminescence (MCL) and electron-beam-induced current (EBIC). It is demonstrated that selective etching is a reliable rapid method for the determination of the type and density of dislocations in GaN in the range 10⁶–10⁸ cm^?2, while MCL and EBIC can be used for the rapid nondestructive determination of the density of dislocations in the range 10⁶–10⁸ cm^?2. It is also found that some deep electron and hole traps are related to dislocations.     

Universality at the edge of the spectrum for unitary,orthogonal, and symplectic ensembles of random matrices

We prove universality at the edge of the spectrum for unitary (β = 2), orthogonal (β = 1), and symplectic (β = 4) ensembles of random matrices in the scaling limit for a class of weights w(x) = e^?V(x) where V is a polynomial, V(x) = κ_2mx^2m + · · ·, κ_2m > 0. The precise statement of our results is given in Theorem 1.1 and Corollaries 1.2 and 1.4 below. For the same class of weights, a proof of universality in the bulk of the spectrum is given in [12] for the unitary ensembles and in [9] for the orthogonal and symplectic ensembles. Our starting point in the unitary case is [12], and for the orthogonal and symplectic cases we rely on our recent work [9], which in turn depends on the earlier work of Widom [46] and Tracy and Widom [42]. As in [9], the uniform Plancherel‐Rotach‐type asymptotics for the orthogonal polynomials found in [12] plays a central role. The formulae in [46] express the correlation kernels for β = 1, 4 as a sum of a Christoffel‐Darboux (CD) term, as in the case β = 2, together with a correction term. In the bulk scaling limit [9], the correction term is of lower order and does not contribute to the limiting form of the correlation kernel. By contrast, in the edge scaling limit considered here, the CD term and the correction term contribute to the same order: this leads to additional technical difficulties over and above [49]. © 2006 Wiley Periodicals, Inc.