Radiotherapy Monte Carlo simulation using cloud computing technology

Cloud computing allows for vast computational resources to be leveraged quickly and easily in bursts as and when required. Here we describe a technique that allows for Monte Carlo radiotherapy dose calculations to be performed using GEANT4 and executed in the cloud, with relative simulation cost and completion time evaluated as a function of machine count. As expected, simulation completion time decreases as 1=n for n parallel machines, and relative simulation cost is found to be optimal where n is a factor of the total simulation time in hours. Using the technique, we demonstrate the potential usefulness of cloud computing as a solution for rapid Monte Carlo simulation for radiotherapy dose calculation without the need for dedicated local computer hardware as a proof of principal. Funding source Cancer Australia (Department of Health and Ageing) Research Grant 614217

CCI-CCI Creative City Index 2012

The CCI-Creative City Index was commissioned in 2010 by the Beijing Academy of Science & Technology's Beijing Research Center for the Science of Science. John Hartley was asked to develop a new creative global city index. The brief was to improve on the existing indexes with a specific focus on creative industries and the sources of creative development. This report, by John Hartley, Jason Potts, Trent MacDonald, with Chris Erkunt and Carl Kufleitner, sets out the new model we have developed, which we call the CCI Creative City Index (CCI-CCI). It presents the results of a pilot application of the index to six cities: London, Cardiff, Berlin, Bremen, Melbourne and Brisbane. The index incorporates many elements from other global and creative city indexes, but also adds several new dimensions relating to creative industries scope, micro-productivity, and the economy of attention. The report and Excel spreadsheets of index calculations can be found on this site.

Subliquidus glass-glass immiscibility along the albite-diopside join

A calorimetric study has shown that glasses along the albite-diopside join in the system albiteanorthite-diopside have positive enthalpies of mixing. Thermodynamic calculations based on these data describe a nearly symmetric, metastable, subliquidus irascibility gap along the join with a critical temperature at 910 K. The existence of the miscibility gap was tested experimentally by annealing an Ab50Di50 glass at 748 K and 823 K. Annealed glasses were examined by optical microscopy and by scanning and transmission electron microscopy. The glasses showed morphological and chemical features consistent with unmixing of two glass phases. The apparent mechanism of phase separation involves initial spinodal decomposition followed by coarsening to produce 0.1 μm–0.3 μm spherical glass phases.

Swept source OCT with air puff chamber for corneal dynamics measurements

None of currently used tonometers produce estimated IOP values that are free of errors. Measurement incredibility arises from indirect measurement of corneal deformation and the fact that pressure calculations are based on population averaged parameters of anterior segment. Reliable IOP values are crucial for understanding and monitoring of number of eye pathologies e.g. glaucoma. We have combined high speed swept source OCT with air-puff chamber. System provides direct measurement of deformation of cornea and anterior surface of the lens. This paper describes in details the performance of air-puff ssOCT instrument. We present different approaches of data presentation and analysis. Changes in deformation amplitude appears to be good indicator of IOP changes. However, it seems that in order to provide accurate intraocular pressure values an additional information on corneal biomechanics is necessary. We believe that such information could be extracted from data provided by air-puff ssOCT.

Ruthenium(II) dichloro or dithiocyanato complexes with 4,4′:2′,2″:4″,4‴-quaterpyridinium ligands : towards photosensitisers with enhanced low-energy absorption properties

Fourteen new complexes of the form cis-\[RuIIX2(R2qpy2+)2]4+ (R2qpy2+ = a 4,4′:2′,2″:4″,4‴-quaterpyridinium ligand, X = Cl− or NCS−) have been prepared and isolated as their PF6− salts. Characterisation involved various techniques including 1H NMR spectroscopy and +electrospray or MALDI mass spectrometry. The UV–Vis spectra display intense intraligand π → π∗ absorptions, and also metal-to-ligand charge-transfer (MLCT) bands with two resolved maxima in the visible region. Red-shifts in the MLCT bands occur as the electron-withdrawing strength of the pyridinium groups increases, while replacing Cl− with NCS− causes blue-shifts. Cyclic voltammograms show quasi-reversible or reversible RuIII/II oxidation waves, and several ligand-based reductions that are irreversible. The variations in the redox potentials correlate with changes in the MLCT energies. A single-crystal X-ray structure has been obtained for a protonated form of a proligand salt, \[(4-(CO2H)Ph)2qpyH3+]\[HSO4]3·3H2O. Time-dependent density functional theory calculations give adequate correlations with the experimental UV–Vis spectra for the two carboxylic acid-functionalised complexes in DMSO. Despite their attractive electronic absorption spectra, these dyes are relatively inefficient photosensitisers on electrodes coated with TiO2 or ZnO. These observations are attributed primarily to weak electronic coupling with the surfaces, since the DFT-derived LUMOs include no electron density near the carboxylic acid anchors.

Power of QTL detection using association tests with family controls

The power of testing for a population-wide association between a biallelic quantitative trait locus and a linked biallelic marker locus is predicted both empirically and deterministically for several tests. The tests were based on the analysis of variance (ANOVA) and on a number of transmission disequilibrium tests (TDT). Deterministic power predictions made use of family information, and were functions of population parameters including linkage disequilibrium, allele frequencies, and recombination rate. Deterministic power predictions were very close to the empirical power from simulations in all scenarios considered in this study. The different TDTs had very similar power, intermediate between one-way and nested ANOVAs. One-way ANOVA was the only test that was not robust against spurious disequilibrium. Our general framework for predicting power deterministically can be used to predict power in other association tests. Deterministic power calculations are a powerful tool for researchers to plan and evaluate experiments and obviate the need for elaborate simulation studies.

Hybrid graphene and graphitic carbon nitride nanocomposite : gap opening, electron–hole puddle, interfacial charge transfer, and enhanced visible light response

Opening up a band gap and finding a suitable substrate material are two big challenges for building graphene-based nanodevices. Using state-of-the-art hybrid density functional theory incorporating long range dispersion corrections, we investigate the interface between optically active graphitic carbon nitride (g-C3N4) and electronically active graphene. We find an inhomogeneous planar substrate (g-C3N4) promotes electronrich and hole-rich regions, i.e., forming a well-defined electron−hole puddle, on the supported graphene layer. The composite displays significant charge transfer from graphene to the g-C3N4 substrate, which alters the electronic properties of both components. In particular, the strong electronic coupling at the graphene/g-C3N4 interface opens a 70 meV gap in g-C3N4-supported graphene, a feature that can potentially allow overcoming the graphene’s band gap hurdle in constructing field effect transistors. Additionally, the 2-D planar structure of g-C3N4 is free of dangling bonds, providing an ideal substrate for graphene to sit on. Furthermore, when compared to a pure g-C3N4 monolayer, the hybrid graphene/g-C3N4 complex displays an enhanced optical absorption in the visible region, a promising feature for novel photovoltaic and photocatalytic applications.

Dots versus antidots : computational exploration of structure, magnetism, and half-metallicity in boron−nitride nanostructures

Triangle-shaped nanohole, nanodot, and lattice antidot structures in hexagonal boron-nitride (h-BN) monolayer sheets are characterized with density functional theory calculations utilizing the local spin density approximation. We find that such structures may exhibit very large magnetic moments and associated spin splitting. N-terminated nanodots and antidots show strong spin anisotropy around the Fermi level, that is, half-metallicity. While B-terminated nanodots are shown to lack magnetism due to edge reconstruction, B-terminated nanoholes can retain magnetic character due to the enhanced structural stability of the surrounding two-dimensional matrix. In spite of significant lattice contraction due to the presence of multiple holes, antidot super lattices are predicted to be stable, exhibiting amplified magnetism as well as greatly enhanced half-metallicity. Collectively, the results indicate new opportunities for designing h-BNbased nanoscale devices with potential applications in the areas of spintronics, light emission, and photocatalysis.

Hybrid graphene/titania nanocomposite : interface charge transfer, hole doping, and sensitization for visible light response

We demonstrated for the first time by large-scale ab initio calculations that a graphene/titania interface in the ground electronic state forms a charge-transfer complex due to the large difference of work functions between graphene and titania, leading to substantial hole doping in graphene. Interestingly, electrons in the upper valence band can be directly excited from graphene to the conduction band, that is, the 3d orbitals of titania, under visible light irradiation. This should yield well-separated electron−hole pairs, with potentially high photocatalytic or photovoltaic performance in hybrid graphene and titania nanocomposites. Experimental wavelength-dependent photocurrent generation of the graphene/titania photoanode demonstrated noticeable visible light response and evidently verified our ab initio prediction.

Hydrogen spillover mechanism on a pd-doped mg surface as revealed by ab initio density functional calculation

The hydrogenation kinetics of Mg is slow, impeding its application for mobile hydrogen storage. We demonstrate by ab initio density functional theory (DFT) calculations that the reaction path can be greatly modified by adding transition metal catalysts. Contrasting with Ti doping, a Pd dopant will result in a very small activation barrier for both dissociation of molecular hydrogen and diffusion of atomic H on the Mg surface. This new computational finding supports for the first time by ab initio simulationthe proposed hydrogen spillover mechanism for rationalizing experimentally observed fast hydrogenation kinetics for Pd-capped Mg materials.

The molecular structure of the phosphate mineral chalcosiderite – a vibrational spectroscopic study

The mineral chalcosiderite with formula CuFe6(PO4)4(OH)8⋅4H2O has been studied by Raman spectroscopy and by infrared spectroscopy. A comparison of the chalcosiderite spectra is made with the spectra of turquoise. The spectra of the mineral samples are very similar in the 1200–900 cm−1 region but strong differences are observed in the 900–100 cm−1 region. The effect of substitution of Fe for Al in chalcosiderite shifts the bands to lower wave numbers. Factor group analysis (FGA) implies four OH stretching vibrations for both the water and hydroxyl units. Two bands ascribed to water are observed at 3276 and 3072 cm−1. Three hydroxyl stretching vibrations are observed. Calculations using a Libowitzky type formula show that the hydrogen bond distances of the water molecules are 2.745 and 2.812 Å which are considerably shorter than the values for the hydroxyl units 2.896, 2.917 and 2.978 Å. Two phosphate stretching vibrations at 1042 and 1062 cm−1 in line with the two independent phosphate units in the structure of chalcosiderite. Three bands are observed at 1102, 1159 and 1194 cm−1 assigned to the phosphate antisymmetric stretching vibrations. FGA predicts six bands but only three are observed due to accidental degeneracy. Both the ν2 and ν4 bending regions are complex. Four Raman bands observed at 536, 580, 598 and 636 cm−1 are assigned to the ν4 bending modes. Raman bands at 415, 420, 475 and 484 cm−1are assigned to the phosphate ν2 bending modes. Vibrational spectroscopy enables aspects of the molecular structure of chalcosiderite to be assessed.

Assessing the damage caused by deepwater horizon : not just another Exxon Valdez

In light of the high stakes of the deepwater horizon civil trial and the important precedent-setting role that the case will have on the assessment of future marine disasters, the methodologies underpinning the calculations of damage on both sides will be subjected to considerable scrutiny. Despite the importance of the case, however, there seems to be a pronounced lack of convergence about it in the academic literature. Contributions from scientific journals frequently make comparisons to the Ixtoc I oil spill off the coast of Mexico in 1979; the legal literature, by stark contrast, seems to be much more focused on the Exxon Valdez spill that occurred off the shores of Alaska in 1989. This paper accordingly calls for a more thorough consideration of other analogs beyond the Exxon Valdez spill—most notably, the Ixtoc I incident—in arriving at an assessment of the damage caused by the Deepwater Horizon disaster.

Nitrogen removal from natural gas using solid boron : A first-principles computational study

Selective separation of nitrogen (N2) from methane (CH4) is highly significant in natural gas purification, and it is very challenging to achieve this because of their nearly identical size (the molecular diameters of N2 and CH4 are 3.64 Å and 3.80 Å, respectively). Here we theoretically study the adsorption of N2 and CH4 on B12 cluster and solid boron surfaces a-B12 and c-B28. Our results show that these electron-deficiency boron materials have higher selectivity in adsorbing and capturing N2 than CH4, which provides very useful information for experimentally exploiting boron materials for natural gas purification.

Surface sulfur measurements on stratospheric particles

The surface chemistries of three particulate samples collected from the lower stratosphere have been determined using a Scanning Auger Microprobe (SAM). These samples are typical of the most abundant natural and anthropogenic particles observed within the stratosphere in the >2µm diameter size fraction. Successive sputtering and analysis below the first few adsorbed monolayers of all particles shows the presence of a thin <150A) sulphur layer. These sulphur regions probably formed by surface reaction of sulphur-rich aerosols with each particle within the stratosphere. Settling rate calculations show that a typical sphere (10µm diameter) may reside within the aerosol layer for ~20 days and thus, provide a qualitative guide to surface sulphur reaction rates.

Condensation kinetics in a turbulent nebular cloud

Model calculations, which include the effects of turbulence during subsequent solar nebula evolution after the collapse of a cool interstellar cloud, can reconcile some of the apparent differences between physical parameters obtained from theory and the cosmochemical record. Two important aspects of turbulence in a protoplanetary cloud include the growth and transport of solid grains. While the physical effects of the process can be calculated and compared with the probable remains of the nebula formulation period, the more subtle effects on primitive grains and their survival in the cosmochemical record cannot be readily evaluated. The environment offered by the Space Station (or Space Shuttle) experimental facility can provide the vacuum and low gravity conditions for sufficiently long time periods required for experimental verification of these cosmochemical models.