Christopher J. Fluke

The influence of nano-scale surface roughness on bacterial adhesion to ultrafine-grained titanium.

We discuss the effect of extreme grain refinement in the bulk of commercial purity titanium (CP, Grade-2) on bacterial attachment to the mechano-chemically polished surfaces of the material. The ultrafine crystallinity of the bulk was achieved by severe plastic deformation by means of equal channel angular pressing (ECAP). The chemical composition, wettability, surface topography and roughness of titanium surfaces were characterized using X-ray photoelectron spectroscopy (XPS) and water contact angle (WCA) measurements, as well as atomic force microscopy (AFM) with 3D interactive visualization of the titanium surface morphology. It was found that physico-chemical surface characteristics of the as-received and the ECAP-modified CP titanium did not differ in any significant way, while the surface roughness at the nano-scale did. Optical profilometry performed on large scanning areas of approximately 225 mum x 300 mum showed that there was no significant difference between the roughness parameters R(a) and R(q) for surfaces in the two conditions, the overall level of roughness being lower for the ECAP-processed one. By contrast, topographic profile analysis at the nano-scale by AFM did reveal a difference in these parameters. This difference was sensitive to the size of the scanned surface area. A further two surface roughness parameters, skewness (R(skw)) and kurtosis (R(kur)), were also used to describe the morphology of titanium surfaces. It was found that the bacterial strains used in this study as adsorbates, viz. Staphylococcus aureus CIP 65.8 and Pseudomonas aeruginosa ATCC 9025, showed preference for surfaces of ECAP-processed titanium. S. aureus cells were found to have a greater propensity for attachment to surfaces of ECAP-modified titanium, while the attachment of P. aeruginosa, while also showing some preference for the ECAP-processed material, was less sensitive to the ECAP processing.

Biophysical model of bacterial cell interactions with nanopatterned cicada wing surfaces

The nanopattern on the surface of Clanger cicada (Psaltoda claripennis) wings represents the first example of a new class of biomaterials that can kill bacteria on contact based solely on their physical surface structure. The wings provide a model for the development of novel functional surfaces that possess an increased resistance to bacterial contamination and infection. We propose a biophysical model of the interactions between bacterial cells and cicada wing surface structures, and show that mechanical properties, in particular cell rigidity, are key factors in determining bacterial resistance/sensitivity to the bactericidal nature of the wing surface. We confirmed this experimentally by decreasing the rigidity of surface-resistant strains through microwave irradiation of the cells, which renders them susceptible to the wing effects. Our findings demonstrate the potential benefits of incorporating cicada wing nanopatterns into the design of antibacterial nanomaterials.

Impact of nanoscale roughness of titanium thin film surfaces on bacterial retention

Two human pathogenic bacteria, Staphylococcus aureus CIP 68.5 and Pseudomonas aeruginosa ATCC 9025, were adsorbed onto surfaces containing Ti thin films of varying thickness to determine the extent to which nanoscale surface roughness influences the extent of bacterial attachment. A magnetron sputter thin film system was used to deposit titanium films with thicknesses of 3, 12, and 150 nm on glass substrata with corresponding surface roughness parameters of R(q) 1.6, 1.2, and 0.7 nm (on a 4 microm x 4 microm scanning area). The chemical composition, wettability, and surface architecture of titanium thin films were characterized using X-ray photoelectron spectroscopy, contact angle measurements, atomic force microscopy, three-dimensional interactive visualization, and statistical approximation of the topographic profiles. Investigation of the dynamic evolution of the Ti thin film topographic parameters indicated that three commonly used parameters, R(a), R(q), and R(max), were insufficient to effectively characterize the nanoscale rough/smooth surfaces. Two additional parameters, R(skw) and R(kur), which describe the statistical distributions of roughness character, were found to be useful for evaluating the surface architecture. Analysis of bacterial retention profiles indicated that bacteria responded differently to the surfaces on a scale of less than 1 nm change in the R(a) and R(q) Ti thin film surface roughness parameters by (i) an increased number of retained cells by a factor of 2-3, and (ii) an elevated level of secretion of extracellular polymeric substances.

Incorporating interactive three-dimensional graphics in astronomy research papers

Most research data collections created or used by astronomers are intrinsically multi-dimensional. In contrast, all visual representations of data presented within research papers are exclusively two-dimensional (2D). We present a resolution of this dichotomy that uses a novel technique for embedding three-dimensional (3D) visualisations of astronomy data sets in electronic-format research papers. Our technique uses the latest Adobe Portable Document Format extensions together with a new version of the S2PLOT programming library. The 3D models can be easily rotated and explored by the reader and, in some cases, modified. We demonstrate example applications of this technique including: 3D figures exhibiting subtle structure in redshift catalogues, colour-magnitude diagrams and halo merger trees; 3D isosurface and volume renderings of cosmological simulations; and 3D models of instructional diagrams and instrument designs.

The 6dF Galaxy Survey: peculiar velocity field and cosmography

We derive peculiar velocities for the 6dF Galaxy Survey (6dFGS) and describe the velocity field of the nearby ( z< 0.055) Southern hemisphere. The survey comprises 8885 galaxies for which we have previously reported Fundamental Plane data. We obtain peculiar velocity probability distributions for the redshift-space positions of each of these galaxies using a Bayesian approach. Accounting for selection bias, we find that the logarithmic distance uncertainty is 0.11 dex, corresponding to 26 per cent in linear distance. We use adaptive kernel smoothing to map the observed 6dFGS velocity field out to cz ∼ 16000 km s −1 , and compare this to the predicted velocity fields from the PSCz Survey and the 2MASS Redshift Survey. We find a better fit to the PSCz prediction, although the reduced χ 2 for the whole sample is approximately unity for both comparisons. This means that, within the observational uncertainties due to redshift-independent distance errors, observed galaxy velocities and those predicted by the linear approximation from the density field agree. However, we find peculiar velocities that are systematically more positive than model predictions in the direction of the Shapley and Vela superclusters, and systematically more negative than model predictions in the direction of the Pisces-Cetus Supercluster, suggesting contributions from volumes not covered by the models.

An Advanced, Three-Dimensional Plotting Library for Astronomy

We present a new, three-dimensional (3D) plotting library with advanced features, and support for standard and enhanced display devices. The library — s2plot — is written in c and can be used by c, c++, and fortran programs on GNU/Linux and Apple/OSX systems. s2plot draws objects in a 3D (x,y,z) Cartesian space and the user interactively controls how this space is rendered at run time. With a pgplot-inspired interface, s2plot provides astronomers with elegant techniques for displaying and exploring 3D data sets directly from their program code, and the potential to use stereoscopic and dome display devices. The s2plot architecture supports dynamic geometry and can be used to plot time-evolving data sets, such as might be produced by simulation codes. In this paper, we introduce s2plot to the astronomical community, describe its potential applications, and present some example uses of the library.

Differential attraction and repulsion of Staphylococcus aureus and Pseudomonas aeruginosa on molecularly smooth titanium films

Magnetron sputtering techniques were used to prepare molecularly smooth titanium thin films possessing an average roughness between 0.18 nm and 0.52 nm over 5 μm × 5 μm AFM scanning areas. Films with an average roughness of 0.52 nm or lower were found to restrict the extent of P. aeruginosa cell attachment, with less than 0.5% of all available cells being retained on the surface. The attachment of S. aureus cells was also limited on films with an average surface roughness of 0.52 nm, however they exhibited a remarkable propensity for attachment on the nano-smoother 0.18 nm average surface roughness films, with the attachment density being almost twice as great as that observed on the nano-rougher film. The difference in attachment behaviour can be attributed to the difference in morphology of the rod-shaped P. aeruginosa compared to the spherical S. aureus cells.

Scientific Visualization in Astronomy: Towards the Petascale Astronomy Era

Astronomy is entering a new era of discovery, coincident with the establishment of new facilities for observation and simulation that will routinely generate petabytes of data. While an increasing reliance on automated data analysis is anticipated, a critical role will remain for visualization-based knowledge discovery. We have investigated scientific visualization applications in astronomy through an examination of the literature published during the last two decades. We identify the two most active fields for progress — visualization of large-N particle data and spectral data cubes — discuss open areas of research, and introduce a mapping between astronomical sources of data and data representations used in general-purpose visualization tools. We discuss contributions using high-performance computing architectures (e.g. distributed processing and GPUs), collaborative astronomy visualization, the use of workflow systems to store metadata about visualization parameters, and the use of advanced interaction devices. We examine a number of issues that may be limiting the spread of scientific visualization research in astronomy and identify six grand challenges for scientific visualization research in the Petascale Astronomy Era.

Teraflop per second gravitational lensing ray-shooting using graphics processing units

Abstract Gravitational lensing calculation using a direct inverse ray-shooting approach is a computationally expensive way to determine magnification maps, caustic patterns, and light-curves (e.g. as a function of source profile and size). However, as an easily parallelisable calculation, gravitational ray-shooting can be accelerated using programmable graphics processing units (GPUs). We present our implementation of inverse ray-shooting for the NVIDIA G80 generation of graphics processors using the NVIDIA Compute Unified Device Architecture (CUDA) software development kit. We also extend our code to multiple GPU systems, including a 4-GPU NVIDIA S1070 Tesla unit. We achieve sustained processing performance of 182 Gflop/s on a single GPU, and 1.28 Tflop/s using the Tesla unit. We demonstrate that billion-lens microlensing simulations can be run on a single computer with a Tesla unit in timescales of order a day without the use of a hierarchical tree-code.

Embedding and Publishing Interactive, 3-Dimensional, Scientific Figures in Portable Document Format (PDF) Files

With the latest release of the S2PLOT graphics library, embedding interactive, 3-dimensional (3-d) scientific figures in Adobe Portable Document Format (PDF) files is simple, and can be accomplished without commercial software. In this paper, we motivate the need for embedding 3-d figures in scholarly articles. We explain how 3-d figures can be created using the S2PLOT graphics library, exported to Product Representation Compact (PRC) format, and included as fully interactive, 3-d figures in PDF files using the movie15 LaTeX package. We present new examples of 3-d PDF figures, explain how they have been made, validate them, and comment on their advantages over traditional, static 2-dimensional (2-d) figures. With the judicious use of 3-d rather than 2-d figures, scientists can now publish, share and archive more useful, flexible and faithful representations of their study outcomes. The article you are reading does not have embedded 3-d figures. The full paper, with embedded 3-d figures, is recommended and is available as a supplementary download from PLoS ONE (File S2).