Crystallization of Arthrobacter sp. strain 1C N-(1-D-carboxyethyl)-L-norvaline dehydrogenase and its complex with NAD+

The novel NAD+-linked opine dehydrogenase from a soil isolate Arthrobacter sp. strain 1C belongs to an enzyme superfamily whose members exhibit quite diverse substrate specificites. Crystals of this opine dehydrogenase, obtained in the presence or absence of co-factor and substrates, have been shown to diffract to beyond 1.8 ? resolution. X-ray precession photographs have established that the crystals belong to space group P21212, with cell parameters a = 104.9, b = 80.0, c = 45.5 ? and a single subunit in the asymmetric unit. The elucidation of the three-dimensional structure of this enzyme will provide a structural framework for this novel class of dehydrogenases to enable a comparison to be made with other enzyme families and also as the basis for mutagenesis experiments directed towards the production of natural and synthetic opine-type compounds containing two chiral centres.     

Short separating geodesics for multiply connected domains

We consider the following questions: given a hyperbolic plane domain and a separation of its complement into two disjoint closed sets each of which contains at least two points, what is the shortest closed hyperbolic geodesic which separates these sets and is it a simple closed curve? We show that a shortest geodesic always exists although in general it may not be simple. However, one can also always find a shortest simple curve and we call such a geodesic a meridian of the domain. We prove that, although they are not in general uniquely defined, if one of the sets of the separation of the complement is connected, then they are unique and are also the shortest possible geodesics which separate the complement in this fashion.     

Experimental and modeling studies of B atom number density distributions in hot filament activated B2H6/H2 and B2H6/CH4/H2 gas mixtures

Experimental and modeling studies of the gas-phase chemistry occurring in dilute, hot filament (HF) activated B2H6/H2 and B2H6/CH4/H2 gas mixtures are reported. Spatially resolved relative number densities of B (and H) atoms have been measured by resonance enhanced multiphoton ionization methods, as a function of process conditions (e.g. the HF material and its temperature, the B2H6/H2 mixing ratio, and the presence (or not) of added CH4). Three-dimensional modeling of the H/B chemistry prevailing in such HF activated gas mixtures using a simplified representation of the gas phase chemistry succeeds in reproducing all of the experimentally observed trends, and in illustrating the key role of the "H-shifting" reactions BHx + H <= => BHx-1 + H2 (x = 1-3) in enabling rapid interconversion between the various BHx (x = 0-3) species. CH4 addition, at partial pressures appropriate for growth of boron-doped diamond by chemical vapor deposition methods, leads to approximately 30% reduction in the measured B atom signal near the HF. The modeling suggests that this is mainly due to concomitant H atom depletion near the HF, but it also allows us a first assessment of the possible contributions from B/C coupling reactions upon CH4 addition to HF activated B2H6/H2 gas mixtures.     

The Carathéodory topology for multiply connected domains II

We continue our exposition concerning the Carathéodory topology for multiply connected domains which we began in [Comerford M., The Carathéodory topology for multiply connected domains I, Cent. Eur. J. Math., 2013, 11(2), 322–340] by introducing the notion of boundedness for a family of pointed domains of the same connectivity. The limit of a convergent sequence of n-connected domains which is bounded in this sense is again n-connected and will satisfy the same bounds. We prove a result which establishes several equivalent conditions for boundedness. This allows us to extend the notions of convergence and equicontinuity to families of functions defined on varying domains.     

Computable error bounds for pointwise derivatives of a Neumann problem

In this paper we discuss the recovery of derivatives and thecomputation of rigorous and useful upper bounds for the pointwiseerror in the recovered derivatives, for finite element approximationsof the Laplace equation with Neumann boundary conditions, especiallyat points close to or on a smooth, curved boundary. We analyzethe dipole image technique for the case of curved boundaries,and show how to compute reliable recovered derivatives and errorbounds even in the limiting case of points lying on the curvedboundary. Numerical experiments show reasonably tight errorbounds for points both close to and away from a curved boundary.     

An algebraic variational multiscale–multigrid method for large‐eddy simulation of turbulent pulsatile flows in complex geometries with detailed insight into pulmonary airway flow

The algebraic variational multiscale–multigrid method, an advanced computational approach recently proposed for large‐eddy simulation of turbulent flow, is further developed in this study for turbulent flow simulations in complex geometries. In particular, it is applied to the complex case of pulsatile turbulent flow dynamics of the upper and lower pulmonary airways up to generation 7 and carefully investigated for this important application. Among other things, the results obtained with the proposed method are compared with the results obtained with a rather traditional stabilized finite element method. As opposed to previous large‐eddy simulations of pulmonary airways, we consider a pulsatile inflow condition, allowing the development of turbulence over a pulse cycle to be investigated, which obviously makes these results more physiologically realistic. Our results suggest that turbulent effects in the bronchial airways are rather weak and can completely decay as early as the third generation, depending on geometry and flow distribution. Both methods utilized in this study are able to adequately capture all flow stages from laminar via transitional to turbulent regimes without any modifications. However, the algebraic variational multiscale–multigrid method provides superior results as soon as the flow enters the most challenging, turbulent flow regime. Furthermore, the robustness of the scale‐separation approach based on plain aggregation algebraic multigrid inherent to the algebraic variational multiscale–multigrid method is demonstrated for the present complex geometry. Copyright © 2012 John Wiley & Sons, Ltd.     

Non-autonomous Julia sets with escaping critical points

We consider non-autonomous iteration which is a generalization of standard polynomial iteration where we deal with Julia sets arising from composition sequences for arbitrarily chosen polynomials with uniformly bounded degrees and coefficients. In this paper, we look at examples where all the critical points escape to infinity. In the classical case, any example of this type must be hyperbolic and there can be only one Fatou component, namely the basin at infinity. This result remains true in the non-autonomous case if we also require that the dynamics on the Julia set be hyperbolic or semi-hyperbolic. However, in general it fails and we exhibit three counterexamples of sequences of quadratic polynomials all of whose critical points escape but which have bounded Fatou components.     

Preservation of external rays in non-autonomous iteration

We consider the dynamics arising from the iteration of an arbitrary sequence of polynomials with uniformly bounded degrees and coefficients and show that, as parameters vary within a single hyperbolic component in parameter space, certain properties of the corresponding Julia sets are preserved. In particular, we show that if the sequence is hyperbolic and all the Julia sets are connected, then the whole basin at infinity moves holomorphically. This extends also to the landing points of external rays and the resultant holomorphic motion of the Julia sets coincides with that obtained earlier in [9] using grand orbits. In addition, we have combinatorial rigidity in the sense that if a finite set of external rays separates the Julia set for a particular parameter value, then the rays with the same external angles separate the Julia set for every parameter in the same hyperbolic component.