The local electronic structure of alpha-Li3N

New theoretical and experimental investigations of the occupied and unoccupied local electronic densities of states (DOS) are reported for alpha-Li(3)N. Band-structure and density-functional theory calculations confirm the absence of covalent bonding character. However, real-space full-multiple-scattering (RSFMS) calculations of the occupied local DOS find less extreme nominal valences than have previously been proposed. Nonresonant inelastic x-ray scattering, RSFMS calculations, and calculations based on the Bethe-Salpeter equation are used to characterize the unoccupied electronic final states local to both the Li and N sites. There is a good agreement between experiment and theory. Throughout the Li 1s near-edge region, both experiment and theory find strong similarities in the s-and p-type components of the unoccupied local final DOS projected onto an orbital angular momentum basis (l-DOS). An unexpected, significant correspondence exists between the near-edge spectra for the Li 1s and N 1s initial states. We argue that both spectra are sampling essentially the same final DOS due to the combination of long core-hole lifetimes, long photoelectron lifetimes, and the fact that orbital angular momentum is the same for all relevant initial states. Such considerations may be generally applicable for low atomic number compounds.     

A secondary gate as a mechanism for inhibition of the M2 proton channel by amantadine

The mechanism of inhibition of the influenza A virus M2 proton channel by the antiviral drug amantadine has been under intense investigation. The importance of a mechanistic understanding is heightened by the prevalence of amantadine-resistant mutations. To gain mechanistic insight at the molecular level, we carried out extensive molecular dynamics simulations of the tetrameric M2 proton channel in both apo and amantadine-bound forms in a lipid bilayer. The simulation of the apo form revealed that Val27 from the four M2 subunits can form a secondary gate near the channel entrance and break the water wire in the channel pore. This gate arises from physical occlusion and the elimination of hydrogen-bonding partners for water molecules. In the presence of amantadine, the secondary gate formed by Val27 and the drug molecule lying just below form an extended blockage, which breaks the water wire throughout the simulation. The location and orientation of amantadine inside of the channel pore as found in our simulation are supported by a host of experimental observations. Our study suggests a novel role for Val27 in the inhibition of the M2 proton channel by amantadine.     

Optimizing Omega

This paper considers the Omega function, proposed by Cascon, Keating & Shadwick as a performance measure for comparing financial assets. We discuss the use of Omega as a basis for portfolio selection. We show that the problem of choosing portfolio weights in order to maximize Omega typically has many local solutions and we describe some preliminary computational experience of finding the global optimum using a NAG library implementation of the Huyer & Neumaier MCS method.     

Understanding the optical spectroscopy of amphiphilic molecular rectifiers: a density functional approach

We present results of first principles density functional theory calculations of the electronic and atomic structural properties of model Z-type Langmuir-Blodgett (LB) layers comprising amphiphilic quinolinium tricyanoquinodimethanide (Q3CNQ) chromophores. We find that the chromophore electronic ground state is not as clearly "zwitterionic" as required by models to explain electrical rectification purportedly seen in such systems. The computed visible region transitions are not what have been assumed to be the intervalence charge transfer bands seen in the visible region of molecules in Z-type LB films. Our own LB deposition and spectroscopic studies suggest that almost all visible region features previously seen may be ascribed to aggregates. The calculated lowest energy electronic excitation between HOMO and LUMO levels, which is located in the near infrared region, has a transition moment aligned approximately 9° off the molecular long axis, and has a normalized oscillator strength of 1 order of magnitude higher than those of the visible region transitions. This most dominant feature has been neglected from discussions of Langmuir-Blodgett layer rectification but our own deposition studies show no sign of this feature, indicating that the structure of the modeled system differs from that of typical experimental structures. The model indicates that such idealized LB layer structures cannot confidently be invoked to explain their experimental optical or electrical properties.     

Unifying ontological similarity measures: A theoretical and empirical investigation

This paper theoretically and empirically investigates ontological similarity. Tversky’s parameterized ratio model of similarity [3] is shown as a unifying basis for many of the well-known ontological similarity measures. A new family of ontological similarity measures is proposed that allows parameterizing the characteristic set used to represent an ontological concept. The three subontologies of the prominent Gene Ontology (GO) are used in an empirical investigation of several ontological similarity measures. Another study using well known semantic similarity within two different anatomy ontologies, the NCIT anatomy and the mouse anatomy, is also presented for comparison to several of the GO results. A discussion of the correlation among the measures is presented as well as a comparison of the effects of two different methods of determining a concept’s information content, corpus-based and ontology-based.     

Modelling and validation: Casting of Al and TiAl alloys in gravity and centrifugal casting processes

Components which best utilise the properties of high temperature titanium alloys are characterised by thin sections of a few millimetres thickness and hundreds of millimetres length. These alloys however are difficult to work with, being highly reactive in a molten state, necessitating a low superheat during processing. Centrifugal casting is therefore utilised as a candidate production method, as under the centrifugal force, metal can rapidly fill thicknesses substantially less than a millimetre before it solidifies. However, due to the high liquid metal velocity developed there is a high risk of turbulent flow and of the trapping of any gas present within the liquid metal.This challenging application involves a combination of complex rotating geometries, significant centrifugal forces and high velocity transient free surface flows, coupled with simultaneous heat transfer and solidification. Capturing these interacting physical phenomena, free surface flows, trapped air and associated defects is a complex modelling task.Building upon earlier work on computational modelling the authors have previously described to capture and validate the fluid dynamics behaviour of rotating systems, this contribution considers the modelling and validation of such systems to capture the coupled flow and thermal solidification behaviour and associated defect development.A bench-mark test case is employed to validate the effect of solidification on the fluidity of an aluminium alloy. Validation is also performed against a series of casting experiments to establish the models ability to capture the filling process and predict defects due to air entrapment within the solidified metal.     

Kinetic energy release of C70(+) and its endohedral cation N@C70(+): activation energy for N extrusion

Unimolecular decomposition of C70(+) and its endohedral cation N@C70(+) were studied by high-resolution mass-analyzed ion kinetic energy (MIKE) spectrometry. Information on the energetics and dynamics of these reactions was extracted. C70(+) dissociates unimolecularly by loss of a C2 unit, whereas N@C70(+) expels the endohedral N atom. Kinetic energy release distributions (KERDs) in these reactions were measured. By use of finite heat bath theory (FHBT), the binding energy for C2 emission from C70(+) and the activation energy for N elimination from N@C70(+) were deduced from KERDs in the light of a recent finding that fragmentation of fullerene cations proceeds via a very loose transition state. The activation energy measured for N extrusion from N@C70(+) was found to be lower than that for C2 evaporation, higher than the value from its neutral molecule N@C70 obtained on the basis of thermal stability measurements, and coincident with the theoretical value. The results provide confirmation that the proposed extrusion mechanism in which the N atom escapes from the cage via formation of an aza-bridged intermediate is correct.     

Species identification of Crassostrea and Ostrea oysters by polymerase chain reaction amplification of the 5S rRNA gene

A specific multiplex polymerase chain reaction (PCR) was developed for the identification of Crassostrea angulata, C. gigas, Ostrea edulis, and O. stentina oyster species. Universal primers were used for the amplification of complete repetition units of 5S rDNA in each of the 4 species. The alignment of the obtained sequences was the basis for the specific design of species-specific primers (ED1, ED2, ST1, ST2, CR1, and CR2) located in the nontranscribed spacer regions. The different sizes of the species-specific amplicons, separated by agarose gel electrophoresis, allowed identification of Crassostrea and Ostrea species. A multiplex PCR with a set of the 6 designed primers showed that they did not interfere with each other and bound specifically to the DNA target. This genetic marker can be very useful for traceability of the species, application in the management of oyster cultures, and conservation of the genetic resources of the species.     

Magic angle spinning and oriented sample solid-state NMR structural restraints combine for influenza a M2 protein functional insights

As a small tetrameric helical membrane protein, the M2 proton channel structure is highly sensitive to its environment. As a result, structural data from a lipid bilayer environment have proven to be essential for describing the conductance mechanism. While oriented sample solid-state NMR has provided a high-resolution backbone structure in lipid bilayers, quaternary packing of the helices and many of the side-chain conformations have been poorly restrained. Furthermore, the quaternary structural stability has remained a mystery. Here, the isotropic chemical shift data and interhelical cross peaks from magic angle spinning solid-state NMR of a liposomal preparation strongly support the quaternary structure of the transmembrane helical bundle as a dimer-of-dimers structure. The data also explain how the tetrameric stability is enhanced once two charges are absorbed by the His37 tetrad prior to activation of this proton channel. The combination of these two solid-state NMR techniques appears to be a powerful approach for characterizing helical membrane protein structure.