Thermodynamics of electron flow in the bacterial deca-heme cytochrome MtrF

Electron-transporting multi-heme cytochromes are essential to the metabolism of microbes that inhabit soils and carry out important biogeochemical processes. Recently the first crystal structure of a prototype bacterial deca-heme cytochrome (MtrF) has been resolved and its electrochemistry characterized. However, the molecular details of electron transport along heme chains in the cytochrome are difficult to access via experiment due to the nearly identical chemical nature of the heme cofactors. Here we employ large-scale molecular dynamics simulations to compute the redox potentials of the 10 hemes of MtrF in aqueous solution. We find that as a whole they fall within a range of ~0.3 V, in agreement with experiment. Individual redox potentials give rise to a free energy profile for electron transport that is approximately symmetric with respect to the center of the protein. Our calculations indicate that there is no significant potential bias along the orthogonal octa- and tetra-heme chains, suggesting that under aqueous conditions MtrF is a nearly reversible two-dimensional conductor.     

Challenging the curse of dimensionality in multivariate local linear regression

Local polynomial fitting for univariate data has been widely studied and discussed, but up until now the multivariate equivalent has often been deemed impractical, due to the so-called curse of dimensionality. Here, rather than discounting it completely, we use density as a threshold to determine where over a data range reliable multivariate smoothing is possible, whilst accepting that in large areas it is not. The merits of a density threshold derived from the asymptotic influence function are shown using both real and simulated data sets. Further, the challenging issue of multivariate bandwidth selection, which is known to be affected detrimentally by sparse data which inevitably arise in higher dimensions, is considered. In an effort to alleviate this problem, two adaptations to generalized cross-validation are implemented, and a simulation study is presented to support the proposed method. It is also discussed how the density threshold and the adapted generalized cross-validation technique introduced herein work neatly together.     

Numerical and experimental investigation of the turbulent flow through a low-pressure turbine cascade in the endwall region

In the present work, direct numerical simulations (DNS) of the flow through a low-pressure linear turbine cascade T106 with parallel endwalls were conducted to investigate the effects of unsteady passing wakes of the upstream blade row on the secondary flow in the endwall region of the passage. The impact of the wakes on the secondary flow is discussed by means of the time-averaged values. Furthermore, the results of DNS are compared with experimental data. (© 2013 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Characterisation of bubble clusters in simulations of upward turbulent channel flow

The paper reports on Direct Numerical Simulations of bubble-laden flows performed to investigate the interaction of bubbles with turbulence in an upward flow between two parallel vertical plates. Two simulations are presented with uniform bubble diameter and a third one with bi-disperse bubbles. Three different approaches are used to characterize bubble clustering in the investigated configuration. Horizontal pairing and tendency to form cluster has been found for all reported cases, slightly less pronounced in the bi-disperse swarm. Among other results, a 60°-alignment has been found by means of the angular pair correlation function for the mixed pairs in the bi-disperse swarm. (© 2013 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Solid State Behaviour of Vinyl Quinones

Abstract

2,5-Bisvinyl-1,4-benzoquinones 1 and 2-vinyl-1,4-bsnzoquinones 2 substituted with aryl or ester end groups have been synthesized. The 2,5-bisstyryl-1,4-benzoquinones 1 (R=phenyl, p-tolyl, o-tolyl) crystallize with a 7 Å-stacking axis. But only for the o-tolyl derivative the contacts between the vinyl groups are close enough to allow a four-center type photopolymerization. The ester derivative 1 (R=COOEt) has a layer structure and can be photooligomerized in the crystal. The generated cyclobutane subgroups have twofold symmetry. The vinylquinones 2 (R=aryl) may be dimerized photochemically in the crystal at the vinyl groups to centrosymmetric cyclobutanes. Crystals with 4 Å stacking axis are also photoreactive.     

Preservation of the Morphology of a Self‐Encapsulated Thin Titania Film in a Functional Multilayer Stack: An X‐Ray Scattering Study

Looks matter: Generally, the morphology of titania thin films is crucial for their performance, hence much effort is spent to tailor the desired morphology. X‐ray scattering enables the monitoring of the crystalline titania layer morphology during build‐up of the functional multilayer stack (see Figure). Herein evidence is provided that the morphology is preserved throughout the fabrication process.

     

Total Internal Reflection Ellipsometry under SPR Conditions: In-Situ Monitoring of the Growth of Poly(N-isopropylacrylamide) (PNIPAAm) Brushes

Total internal reflection ellipsometry (TIRE) under surface plasmon resonance (SPR) conditions represents a powerful characterization technique combining the conveniences of spectroscopic ellipsometry with SPR. Besides the very high sensitivity to small changes in the optical constants (up to 10 times more sensitive than conventional ellipsometry), the possibility to investigate media of different optical densities or even opaque media makes this analytical method very convenient for different sensing applications. This article presents an example of application of TIRE under SPR conditions for the continuously in-situ monitoring of the growth of covalently tethered poly(N-isopropylacrylamide) (PNIPAAm) chains on a gold surface.     

Domination in bipartite graphs

We prove that the domination number of a graph of order n and minimum degree at least 2 that does not contain cycles of length 4, 5, 7, 10 or 13 is at most . Furthermore, we derive upper bounds on the domination number of bipartite graphs of given minimum degree.     

Low-dimensional compounds containing cyano groups. XVII. Crystal structure, spectroscopic, thermal and magnetic properties of [Cu(bmen)2][Pt(CN)4] (bmen=N,N′-dimethylethylenediamine)

The synthesis, structural analysis, spectroscopic studies, susceptibility and specific-heat measurements of {[Cu(bmen)₂][Pt(CN)₄]}_n (bmen=N,N′-dimethylethylenediamine) are presented. X-ray crystal-structure analysis revealed that the [Pt(CN)₄]²⁻ building blocks are combined with [Cu(bmen)₂]²⁺ units to form a chain-like structure along the a axis. The Cu(II) atoms are hexacoordinated by four nitrogen atoms in the equatorial plane belonging to two molecules of bidentate bmen ligands with average Cu-N distance of 2.043(18) Å. The axial positions are occupied by two nitrogen atoms from bridging [Pt(CN)₄]²⁻ anions at a longer axial Cu-N distance of 2.490(4) Å. The compound is characterized by the presence of a weak antiferromagnetic exchange coupling J/k_B=0.6 K. Despite the one-dimensional (1D) character of the structure, the analysis of the magnetic properties and specific heat at very low temperatures shows that [Cu(bmen)₂][Pt(CN)₄] behaves as a two-dimensional (2D) square-lattice Heisenberg magnet with weak interlayer coupling.