Random packing of spheres in Menger sponge

Random packing of spheres inside fractal collectors of dimension 2 < d < 3 is studied numerically using Random Sequential Adsorption (RSA) algorithm. The paper focuses mainly on the measurement of random packing saturation limit. Additionally, scaling properties of density autocorrelations in the obtained packing are analyzed. The RSA kinetics coefficients are also measured. Obtained results allow to test phenomenological relation between random packing saturation density and collector dimension. Additionally, performed simulations together with previously obtained results confirm that, in general, the known dimensional relations are obeyed by systems having non-integer dimension, at least for d < 3.Comment: 13 pages, 6 figure

Using cascading Bloom filters to improve the memory usage for de Brujin graphs

De Brujin graphs are widely used in bioinformatics for processing next-generation sequencing data. Due to a very large size of NGS datasets, it is essential to represent de Bruijn graphs compactly, and several approaches to this problem have been proposed recently. In this work, we show how to reduce the memory required by the algorithm of [3] that represents de Brujin graphs using Bloom filters. Our method requires 30% to 40% less memory with respect to the method of [3], with insignificant impact to construction time. At the same time, our experiments showed a better query time compared to [3]. This is, to our knowledge, the best practical representation for de Bruijn graphs.Comment: 12 pages, submitte

Nonlinear Dynamics of Capacitive Charging and Desalination by Porous Electrodes

The rapid and efficient exchange of ions between porous electrodes and aqueous solutions is important in many applications, such as electrical energy storage by super-capacitors, water desalination and purification by capacitive deionization (or desalination), and capacitive extraction of renewable energy from a salinity difference. Here, we present a unified mean-field theory for capacitive charging and desalination by ideally polarizable porous electrodes (without Faradaic reactions or specific adsorption of ions) in the limit of thin double layers (compared to typical pore dimensions). We illustrate the theory in the case of a dilute, symmetric, binary electrolyte using the Gouy-Chapman-Stern (GCS) model of the double layer, for which simple formulae are available for salt adsorption and capacitive charging of the diffuse part of the double layer. We solve the full GCS mean-field theory numerically for realistic parameters in capacitive deionization, and we derive reduced models for two limiting regimes with different time scales: (i) In the "super-capacitor regime" of small voltages and/or early times where the porous electrode acts like a transmission line, governed by a linear diffusion equation for the electrostatic potential, scaled to the RC time of a single pore. (ii) In the "desalination regime" of large voltages and long times, the porous electrode slowly adsorbs neutral salt, governed by coupled, nonlinear diffusion equations for the pore-averaged potential and salt concentration

On the Response of an OST to a Point-like Heat Source

A new technique of superconducting cavity diagnostics has been introduced by D. Hartrill at Cornell University, Ithaca, USA. Oscillating Superleak Transducers (OST) detect the heat transferred from a cavity's quench point via "Second Sound" through the superfluid He bath, needed to cool the superconducting cavity. The observed response of an OST is a complex, but reproducible pattern of oscillations. A small helium evaporation cryostat was built which allows the investigation of the response of an OST in greater detail. The distance between a point-like electrical heater and the OST can be varied. The OST can be mounted either parallel or perpendicular to the plate, housing the heat source. If the artificial quench-point releases an amount of energy compatible to a real quench spot on a cavity's surface, the OST signal starts with a negative pulse, which is usually strong enough to allow automatic detection. Furthermore, the reflection of the Second Sound on the wall is observed. A reflection coefficient R = 0.39 +- 0.05 of the glass wall is measured. This excludes a strong influence of multiple reflections in the complex OST response. Fourier analyses show three main frequencies, found in all OST spectra. They can be interpreted as modes of an oscillating circular membrane.Comment: 10 pages, 16 figure

Discovery of circularly polarised radio emission from SS 433

We report the discovery of circularly polarised radio emission from the radio-jet X-ray binary SS 433 with the Australia Telescope Compact Array. The flux density spectrum of the circular polarization, clearly detected at four frequencies between 1 - 9 GHz, has a spectral index of (-0.9 +/- 0.1). Multiple components in the source and a lack of very high spatial resolution do not allow a unique determination of the origin of the circular polarization, nor of the spectrum of fractional polarization. However, we argue that the emission is likely to arise in the inner regions of the binary, possibly via propagation-induced conversion of linear to circular polarization, and the fractional circular polarization of these regions may be as high as 10%. Observations such as these have the potential to investigate the composition, whether pairs or baryonic, of the ejecta from X-ray binaries.Comment: Accepted for publication in ApJ Letter

Residue codes of extremal Type II Z_4-codes and the moonshine vertex operator algebra

In this paper, we study the residue codes of extremal Type II Z_4-codes of length 24 and their relations to the famous moonshine vertex operator algebra. The main result is a complete classification of all residue codes of extremal Type II Z_4-codes of length 24. Some corresponding results associated to the moonshine vertex operator algebra are also discussed.Comment: 21 pages, shortened from v

Concurrent Learning of Adjacent and Nonadjacent Dependencies in Visuo-Spatial and Visuo-Verbal Sequences

Both adjacent and non-adjacent dependencies (AD and NAD) are present in natural language and other domains, yet the learning of non-adjacent sequential dependencies generally only occurs under favorable circumstances. It is currently unknown to what extent adults can learn AD and NAD, presented concurrently in spatial and verbal sequences during a single session, and whether a second session improves performance. In addition, the relationship between AD and NAD learning and other theoretically related cognitive and language processes has not yet been fully established. In this study, participants reproduced two types of sequences generated from an artificial grammar: visuo-spatial sequences with stimuli presented in four spatial locations, and visuo-verbal sequences with printed syllables. Participants were tested for incidental learning by reproducing novel sequences, half consistent with the grammar and half containing violations of either AD or NAD. The procedure was repeated on a second day. Results showed that both AD and NAD were learned in both visuo-spatial and visuo-verbal tasks, although AD learning was better than NAD and learning of NAD decreased over time. Furthermore, NAD learning for both spatial and verbal tasks was positively correlated with a language measure, whereas AD learning for both spatial and verbal tasks was negatively associated with working memory measures in the opposite domain. These results demonstrate that adults can learn both AD and NAD within a single session, but NAD learning is more easily disrupted than AD and both types of learning are sub-served by partially distinct cognitive processes. These findings increase our understanding of the processes governing the learning of AD and NAD in verbal and spatial domains

Anaerobic Respiration of \u3cem\u3eEscherichia coli\u3c/em\u3e in the Mouse Intestine

The intestine is inhabited by a large microbial community consisting primarily of anaerobes and, to a lesser extent, facultative anaerobes, such as Escherichia coli, which we have shown requires aerobic respiration to compete successfully in the mouse intestine (S. A. Jones et al., Infect. Immun. 75:4891-4899, 2007). If facultative anaerobes efficiently lower oxygen availability in the intestine, then their sustained growth must also depend on anaerobic metabolism. In support of this idea, mutants lacking nitrate reductase or fumarate reductase have extreme colonization defects. Here, we further explore the role of anaerobic respiration in colonization using the streptomycin-treated mouse model. We found that respiratory electron flow is primarily via the naphthoquinones, which pass electrons to cytochrome bd oxidase and the anaerobic terminal reductases. We found that E. coli uses nitrate and fumarate in the intestine, but not nitrite, dimethyl sulfoxide, or trimethylamine N-oxide. Competitive colonizations revealed that cytochrome bd oxidase is more advantageous than nitrate reductase or fumarate reductase. Strains lacking nitrate reductase outcompeted fumarate reductase mutants once the nitrate concentration in cecal mucus reached submillimolar levels, indicating that fumarate is the more important anaerobic electron acceptor in the intestine because nitrate is limiting. Since nitrate is highest in the absence of E. coli, we conclude that E. coli is the only bacterium in the streptomycin-treated mouse large intestine that respires nitrate. Lastly, we demonstrated that a mutant lacking the NarXL regulator (activator of the NarG system), but not a mutant lacking the NarP-NarQ regulator, has a colonization defect, consistent with the advantage provided by NarG. The emerging picture is one in which gene regulation is tuned to balance expression of the terminal reductases that E. coli uses to maximize its competitiveness and achieve the highest possible population in the intestine