Micro-scale surface-patterning influences biofilm formation

The formation of biofilms on indwelling/implanted medical devices is a common problem. One of the approaches used to prevent biofilm formation on medical devices is to inhibit bacterial attachment by modification of the synthetic polymers used to fabricate the device. In this work, we assessed how micro-scale features (patterns) imprinted onto the surface of silicone elastomer similar to that used for medical applications influenced biofilm formation by Staphylococcus aureus, Staphylococcus epidermidis, and Pseudomonas aeruginosa. Patterns were transferred from a multi-patterned oxidized silicon-wafer master-template to silicone elastomer. Features consisted of bars, squares, and circles each extending 0.51 µm above the surface. Feature sizes ranged between 1.78 and 22.25 µm. Distances separating features ranged between 0.26 and 17.35 µm. Bacterial biofilm formation on discs cut from imprinted silicone elastomer was assessed by direct microscopic observation and quantified as the surface area covered by biofilm. Unpatterned silicone elastomer served as a control. Several of the micro-scale patterns imprinted into the silicone elastomer significantly reduced biofilm formation by each bacterium and interrupted biofilm continuity. Although there were differences in detail among strains, bacteria tended to attach in the area between features more than to the surface of the feature itself

Noise effect on Grover algorithm

The decoherence effect on Grover algorithm has been studied numerically through a noise modelled by a depolarizing channel. Two types of error are introduced characterizing the qubit time evolution and gate application, so the noise is directly related to the quantum network construction. The numerical simulation concludes an exponential damping law for the successive probability of the maxima as time increases. We have obtained an allowed-error law for the algorithm: the error threshold for the allowed noise behaves as Eth(N) ~ 1/N1.1 (N being the size of the data set). As the power of N is almost one, we consider the Grover algorithm as robust to a certain extent against decoherence. This law also provides an absolute threshold: if the free evolution error is greater than 0.043, Grover algorithm does not work for any number of qubits affected by the present error model. The improvement in the probability of success, in the case of two qubits has been illustrated by using a fault-tolerant encoding of the initial state by means of the [[7,1,3]] quantum code.Comment: Accepted to be published in Eur. Phys. J. D (2008

Quantum heuristic algorithm for traveling salesman problem

We propose a quantum heuristic algorithm to solve a traveling salesman problem by generalizing Grover search. Sufficient conditions are derived to greatly enhance the probability of finding the tours with extremal costs, reaching almost to unity and they are shown characterized by statistical properties of tour costs. In particular for a Gaussian distribution of the tours along the cost we show that the quantum algorithm exhibits the quadratic speedup of its classical counterpart, similarly to Grover search.Comment: Published versio

QuickSNP: an automated web server for selection of tagSNPs

Although large-scale genetic association studies involving hundreds to thousands of SNPs have become feasible, the associated cost is substantial. Even with the increased efficiency introduced by the use of tagSNPs, researchers are often seeking ways to maximize resource utilization given a set of SNP-based gene-mapping goals. We have developed a web server named QuickSNP in order to provide cost-effective selection of SNPs, and to fill in some of the gaps in existing SNP selection tools. One useful feature of QuickSNP is the option to select only gene-centric SNPs from a chromosomal region in an automated fashion. Other useful features include automated selection of coding non-synonymous SNPs, SNP filtering based on inter-SNP distances and information regarding the availability of genotyping assays for SNPs and whether they are present on whole genome chips. The program produces user-friendly summary tables and results, and a link to a UCSC Genome Browser track illustrating the position of the selected tagSNPs in relation to genes and other genomic features. We hope the unique combination of features of this server will be useful for researchers aiming to select markers for their genotyping studies. The server is freely available and can be accessed at the URL http://bioinformoodics.jhmi.edu/quickSNP.pl

Signatures of many-body localisation in a system without disorder and the relation to a glass transition

We study a quantum spin system—adapted from a facilitated spin model for classical glasses—with local bilinear interactions and without quenched disorder which seems to display characteristic signatures of a many-body localisation (MBL) transition. From direct diagonalisation of small systems, we find a change in certain dynamical and spectral properties at a critical value of a coupling, from those characteristic of a thermalising phase to those characteristic of a MBL phase. The system we consider is known to have a quantum phase transition in its ground-state in the limit of large size, related to a first-order active-to-inactive phase transition in the stochastic trajectories of an associated classical model of glasses. Our results here suggest that this first-order transition in the low-lying spectrum may influence the rest of the spectrum of the system in the large size limit. These findings may help understand the connection between MBL and structural glass transitions

Recording Lifetime Behavior and Movement in an Invertebrate Model

Characterization of lifetime behavioral changes is essential for understanding aging and aging-related diseases. However, such studies are scarce partly due to the lack of efficient tools. Here we describe and provide proof of concept for a stereo vision system that classifies and sequentially records at an extremely fine scale six different behaviors (resting, micro-movement, walking, flying, feeding and drinking) and the within-cage (3D) location of individual tephritid fruit flies by time-of-day throughout their lives. Using flies fed on two different diets, full sugar-yeast and sugar-only diets, we report for the first time their behavioral changes throughout their lives at a high resolution. We have found that the daily activity peaks at the age of 15–20 days and then gradually declines with age for flies on both diets. However, the overall daily activity is higher for flies on sugar-only diet than those on the full diet. Flies on sugar-only diet show a stronger diurnal localization pattern with higher preference to staying on the top of the cage during the period of light-off when compared to flies on the full diet. Clustering analyses of age-specific behavior patterns reveal three distinct young, middle-aged and old clusters for flies on each of the two diets. The middle-aged groups for flies on sugar-only diet consist of much younger age groups when compared to flies on full diet. This technology provides research opportunities for using a behavioral informatics approach for understanding different ways in which behavior, movement, and aging in model organisms are mutually affecting

The Phoenix Mars Landing: An Initial Look

This presentation was part of the session : Ongoing and Proposed EDL Technology DevelopmentSixth International Planetary Probe WorkshopNASA's Phoenix Mars Lander will make a landing on Mars on May 25th, 2008. Following on from the overview of the Phoenix entry, descent and landing (EDL) system given at IPPW5, an initial look at the Phoenix landing will be presented, highlighting the salient, high level events that occurred during EDL. Initial EDL flight reconstruction results will be presented, along with a retelling of the flight operations events that occurred on approach to Mars, and during the landing event itself. Note: Given the short time duration between the Phoenix landing and IPPW6, only a presentation will be prepared for the workshop.NAS

Simulating chemistry efficiently on fault-tolerant quantum computers

Quantum computers can in principle simulate quantum physics exponentially faster than their classical counterparts, but some technical hurdles remain. Here we consider methods to make proposed chemical simulation algorithms computationally fast on fault-tolerant quantum computers in the circuit model. Fault tolerance constrains the choice of available gates, so that arbitrary gates required for a simulation algorithm must be constructed from sequences of fundamental operations. We examine techniques for constructing arbitrary gates which perform substantially faster than circuits based on the conventional Solovay-Kitaev algorithm [C.M. Dawson and M.A. Nielsen, \emph{Quantum Inf. Comput.}, \textbf{6}:81, 2006]. For a given approximation error $\epsilon$, arbitrary single-qubit gates can be produced fault-tolerantly and using a limited set of gates in time which is $O(\log \epsilon)$ or $O(\log \log \epsilon)$; with sufficient parallel preparation of ancillas, constant average depth is possible using a method we call programmable ancilla rotations. Moreover, we construct and analyze efficient implementations of first- and second-quantized simulation algorithms using the fault-tolerant arbitrary gates and other techniques, such as implementing various subroutines in constant time. A specific example we analyze is the ground-state energy calculation for Lithium hydride.Comment: 33 pages, 18 figure