Pattern matching and pattern discovery algorithms for protein topologies

We describe algorithms for pattern matching and pattern learning in TOPS diagrams (formal descriptions of protein topologies). These problems can be reduced to checking for subgraph isomorphism and finding maximal common subgraphs in a restricted class of ordered graphs. We have developed a subgraph isomorphism algorithm for ordered graphs, which performs well on the given set of data. The maximal common subgraph problem then is solved by repeated subgraph extension and checking for isomorphisms. Despite the apparent inefficiency such approach gives an algorithm with time complexity proportional to the number of graphs in the input set and is still practical on the given set of data. As a result we obtain fast methods which can be used for building a database of protein topological motifs, and for the comparison of a given protein of known secondary structure against a motif database

A wireless ECG plaster for real-time cardiac health monitoring in body sensor networks

10.1109/BioCAS.2011.61077632011 IEEE Biomedical Circuits and Systems Conference, BioCAS 2011205-20

Tunnel shotcrete lining for hydroelectric projects in British Columbia

In British Columbia (BC), Canada, the primary source of power supply is hydroelectricity. The BC government, through its crown corporation, BC Hydro, has been working with private companies to provide sustainable and renewable energy. Private companies are building hydroelectric projects throughout the province of BC. Innergex has been constructing three hydroelectric projects; two are in the Upper Lilllooet area, which is about 250 km north of Vancouver and 80km north of Whistler and the third is in the Big Silver area, which is about 250 km east of Vancouver and 50 km north of Harrison Lake. All of these tunnels are hard rock and have been constructed by the drill and blast method. At the beginning of the projects, dry-mix shotcrete was applied based on the contractor’s previous underground project experience. Wet-mix shotcrete was subsequently introduced as a trial method. The contractor was impressed with its productivity and performance and consequently adopted it as the primary shotcrete placement method. Dry-mix steel fiber reinforced shotcrete continued to be used for special ground conditions. The construction schedule was reduced significantly by using wet-mix shotcrete, with resultant substantial cost savings. The wet-mix shotcrete was initially reinforced with wire mesh and hand-applied. Shortly after, the tunnel lining method was changed to the use of robotic sprayed macrosynthetic fiber reinforced wet-mix shotcrete. A silica fume modified shotcrete mixture was designed and trial shot. Tests results met the project specification requirements for tunnel construction. The wet-mix macrosynthetic fiber reinforced shotcrete was placed, since July 2013, using pre-bagged materials supplied from Vancouver and mixed on site. Later, the contractor set up a dry-batch concrete batch plant on site and started batching shotcrete using local aggregates. The shotcrete mixture was qualified for use on the project by testing for compressive strength, boiled absorption and volume of permeable voids, and flexural toughness based on use of the round determinate panel to ASTM C1550. The effect on shotcrete performance of different addition rates of alkali-free accelerator was tested in trials. An addition rate of 6% alkali-free accelerator by mass of cement was selected and used. Shotcrete nozzlemen were trained with a specially designed shotcrete training program. All shotcrete nozzlemen were qualified to shoot a basic Level I, and a more challenging Level II, for shotcrete with reinforcing steel or lattice girders. The construction quality control tests results for the project from August 2013 to December 2016 demonstrated that the shotcrete quality consistently met the project specification requirements. The projects were completed ahead of schedule because of productivity gains achieved from using wet-mix macrosynthetic fiber reinforced shotcrete. The contractors developed proper skills and techniques for application of wet-mix macrosynthetic fiber reinforced shotcrete applied by robotic sprayers with zero safety incidents or accident

Physics of Psychophysics: Stevens and Weber-Fechner laws are transfer functions of excitable media

Sensory arrays made of coupled excitable elements can improve both their input sensitivity and dynamic range due to collective non-linear wave properties. This mechanism is studied in a neural network of electrically coupled (e.g. via gap junctions) elements subject to a Poisson signal process. The network response interpolates between a Weber-Fechner logarithmic law and a Stevens power law depending on the relative refractory period of the cell. Therefore, these non-linear transformations of the input level could be performed in the sensory periphery simply due to a basic property: the transfer function of excitable media.Comment: 4 pages, 5 figure

Issues and Observations on Applications of the Constrained-Path Monte Carlo Method to Many-Fermion Systems

We report several important observations that underscore the distinctions between the constrained-path Monte Carlo method and the continuum and lattice versions of the fixed-node method. The main distinctions stem from the differences in the state space in which the random walk occurs and in the manner in which the random walkers are constrained. One consequence is that in the constrained-path method the so-called mixed estimator for the energy is not an upper bound to the exact energy, as previously claimed. Several ways of producing an energy upper bound are given, and relevant methodological aspects are illustrated with simple examples.Comment: 28 pages, REVTEX, 5 ps figure

Very long optical path-length from a compact multi-pass cell

The multiple-pass optical cell is an important tool for laser absorption spectroscopy and its many applications. For most practical applications, such as trace-gas detection, a compact and robust design is essential. Here we report an investigation into a multi-pass cell design based on a pair of cylindrical mirrors, with a particular focus on achieving very long optical paths. We demonstrate a path-length of 50.31 m in a cell with 40 mm diameter mirrors spaced 88.9 mm apart - a 3-fold increase over the previously reported longest path-length obtained with this type of cell configuration. We characterize the mechanical stability of the cell and describe the practical conditions necessary to achieve very long path-lengths

A polarized beam splitter using an anisotropic medium slab

The propagation of electromagnetic waves in the anisotropic medium with a single-sheeted hyperboloid dispersion relation is investigated. It is found that in such an anisotropic medium E- and H-polarized waves have the same dispersion relation, while E- and H-polarized waves exhibit opposite amphoteric refraction characteristics. E- (or H-) polarized waves are positively refracted whereas H- (or E-) polarized waves are negatively refracted at the interface associated with the anisotropic medium. By suitably using the properties of anomalous refraction in the anisotropic medium it is possible to realize a very simple and very efficient beam splitter to route the light. It is shown that the splitting angle and the splitting distance between E- and H- polarized beam is the function of anisotropic parameters, incident angle and slab thickness.Comment: 14 pages, 6 figure

Comparison of Structural Development and Biochemical Accumulation of Waxy and Non-waxy Wheat Caryopses

This study was conducted to compare structural development and biochemical accumulation of waxy and non-waxy wheat (NW) caryopses. The caryopses’ microstructure of the waxy wheat (WW) and NW cultivars at different developmental stages were observed under light, fluorescence, and scanning electron microscope. The results were as follows: Compared with NW,WWhad a shorter maturation duration, which was reflected in several following characteristics. Programmed cell death of the pericarp began earlier, and the chlorophyll-containing layer in the pericarp was smaller. Vacuoles in chalazal cells accumulated more tannins at different developmental stages. Starch granules and protein bodies in the endosperm showed a higher accumulation level in developing caryopses, and aleurone cells were larger in size with larger numbers of aleurone grains. An analysis of the element content indicated that the mineral elements Mg, P, K, and Ca exhibited a higher content, while the heavy elements Cr, Cd, and Pb exhibited a lower content in the aleurone layer

Source population synthesis and the Galactic diffuse gamma-ray emission

Population synthesis is used to study the contribution from undetected sources to the Galactic ridge emission measured by EGRET. Synthesized source counts are compared with the 3rd EGRET catalogue at low and high latitudes. For pulsar-like populations, 5-10% of the emission >100 MeV comes from sources below the EGRET threshold. A steeper luminosity function can increase this to 20% without violating EGRET source statistics. Less luminous populations can produce much higher values without being detected. Since the unresolved source spectrum is different from the interstellar spectrum, it could provide an explanation of the observed MeV and GeV excesses above the predictions, and we give an explicit example of how this could work.Comment: Astrophysics and Space Science, in press. (Proceedings of Conference 'The multi-messenger approach to high-energy gamma-ray sources', Barcelona, 2006). Minor changes for accepted version, updated reference

Hydrodynamics of Spatially Ordered Superfluids

We derive the hydrodynamic equations for the supersolid and superhexatic phases of a neutral two-dimensional Bose fluid. We find, assuming that the normal part of the fluid is clamped to an underlying substrate, that both phases can sustain third-sound modes and that in the supersolid phase there are additional modes due to the superfluid motion of point defects (vacancies and interstitials).Comment: 24 pages of ReVTeX and 7 uuencoded figures. Submitted for publication in Phys. Rev.