A biomimetic algorithm for the improved detection of microarray features,

One the major difficulties of microarray technology relate to the processing of large and - importantly - error-loaded images of the dots on the chip surface. Whatever the source of these errors, those obtained in the first stage of data acquisition - segmentation - are passed down to the subsequent processes, with deleterious results. As it has been demonstrated recently that biological systems have evolved algorithms that are mathematically efficient, this contribution attempts to test an algorithm that mimics a bacterial-"patented" algorithm for the search of available space and nutrients to find, "zero-in" and eventually delimitate the features existent on the microarray surface

'Extremotaxis': Computing with a bacterial-inspired algorithm

We present a general-purpose optimization algorithm inspired by “run-and-tumble”, the biased random walk chemotactic swimming strategy used by the bacterium Escherichia coli to locate regions of high nutrient concentration The method uses particles (corresponding to bacteria) that swim through the variable space (corresponding to the attractant concentration profile). By constantly performing temporal comparisons, the particles drift towards the minimum or maximum of the function of interest. We illustrate the use of our method with four examples. We also present a discrete version of the algorithm. The new algorithm is expected to be useful in combinatorial optimization problems involving many variables, where the functional landscape is apparently stochastic and has local minima, but preserves some derivative structure at intermediate scales

Pomitaxis: Computing with a bacterial-inspired algorithm

We present a general-purpose optimisation algorithm inspired by "run-and-tumble2, the biased random chemotactic swimming strategy used by the bacterium E coli to locate regions of high nutrient concentration. The method uses particles (corresponding to bacteria) that swim through the variable space (corresponding to the attractant concentration profile). By constantly performing temporal comparisons, the particles drift towards the minimum or maximum of the function of interest. We illustrate the use of our method with three simple examples. We also present a discrete version of the algorithm. The new algorithm is expected to be useful in combinatorial optimisation problems involving many variables, where the functional landscape is apparently stochastic and has local minima, but preserves some derivative structure at the mesoscale

HI Narrow Line Absorption in Dark Clouds

We have used the Arecibo telescope to carry out an survey of 31 dark clouds in the Taurus/Perseus region for narrow absorption features in HI ($\lambda$ 21cm) and OH (1667 and 1665 MHz) emission. We detected HI narrow self--absorption (HINSA) in 77% of the clouds that we observed. HINSA and OH emission, observed simultaneously are remarkably well correlated. Spectrally, they have the same nonthermal line width and the same line centroid velocity. Spatially, they both peak at the optically--selected central position of each cloud, and both fall off toward the cloud edges. Sources with clear HINSA feature have also been observed in transitions of CO, \13co, \c18o, and CI. HINSA exhibits better correlation with molecular tracers than with CI. The line width of the absorption feature, together with analyses of the relevant radiative transfer provide upper limits to the kinetic temperature of the gas producing the HINSA. Some sources must have a temperature close to or lower than 10 K. The correlation of column densities and line widths of HINSA with those characteristics of molecular tracers suggest that a significant fraction of the atomic hydrogen is located in the cold, well--shielded portions of molecular clouds, and is mixed with the molecular gas. The average number density ratio [HI]/[\h2] is $1.5\times10^{-3}$. The inferred HI density appears consistent with but is slightly higher than the value expected in steady state equilibrium between formation of HI via cosmic ray destruction of H$_2$ and destruction via formation of H$_2$ on grain surfaces. The distribution and abundance of atomic hydrogen in molecular clouds is a critical test of dark cloud chemistry and structure, including the issues of grain surface reaction rates, PDRs, circulation, and turbulent diffusion.Comment: 40 pages, 10 figures, accepted by Ap

NaNet: a Low-Latency, Real-Time, Multi-Standard Network Interface Card with GPUDirect Features

While the GPGPU paradigm is widely recognized as an effective approach to high performance computing, its adoption in low-latency, real-time systems is still in its early stages. Although GPUs typically show deterministic behaviour in terms of latency in executing computational kernels as soon as data is available in their internal memories, assessment of real-time features of a standard GPGPU system needs careful characterization of all subsystems along data stream path. The networking subsystem results in being the most critical one in terms of absolute value and fluctuations of its response latency. Our envisioned solution to this issue is NaNet, a FPGA-based PCIe Network Interface Card (NIC) design featuring a configurable and extensible set of network channels with direct access through GPUDirect to NVIDIA Fermi/Kepler GPU memories. NaNet design currently supports both standard - GbE (1000BASE-T) and 10GbE (10Base-R) - and custom - 34~Gbps APElink and 2.5~Gbps deterministic latency KM3link - channels, but its modularity allows for a straightforward inclusion of other link technologies. To avoid host OS intervention on data stream and remove a possible source of jitter, the design includes a network/transport layer offload module with cycle-accurate, upper-bound latency, supporting UDP, KM3link Time Division Multiplexing and APElink protocols. After NaNet architecture description and its latency/bandwidth characterization for all supported links, two real world use cases will be presented: the GPU-based low level trigger for the RICH detector in the NA62 experiment at CERN and the on-/off-shore data link for KM3 underwater neutrino telescope

Embedded software developments in KM3NeT phase I

TheKM3NeT collaboration has already produced more than one thousand acquisition boards, used for building two deep-sea neutrino detectors at the bottom of the Mediterranean Sea, with the aim of instrumenting a volume of several cubic kilometers with light sensors to detect the Cherenkov radiation produced in neutrino interactions. The so-called digital optical modules, house the PMTs and the acquisition and control electronics of the module, the central logic board, which includes a Xilinx FPGA and embedded soft processor. The present work presents the architecture and functionalities of the software embedded in the soft processor of the central logic board

Conformational spread as a mechanism for cooperativity in the bacterial flagellar switch

The bacterial flagellar switch that controls the direction of flagellar rotation during chemotaxis has a highly cooperative response. This has previously been understood in terms of the classic two-state, concerted model of allosteric regulation. Here, we used high-resolution optical microscopy to observe switching of single motors and uncover the stochastic multistate nature of the switch. Our observations are in detailed quantitative agreement with a recent general model of allosteric cooperativity that exhibits conformational spread—the stochastic growth and shrinkage of domains of adjacent subunits sharing a particular conformational state. We expect that conformational spread will be important in explaining cooperativity in other large signaling complexes

Saturation of fishbone instability by self-generated zonal flows in tokamak plasmas

Gyrokinetic simulations of the fishbone instability in DIII-D tokamak plasmas find that self-generated zonal flows can dominate the nonlinear saturation by preventing coherent structures from persisting or drifting in the energetic particle phase space with mode down-chirping. Results from the simulation with zonal flows agree quantitatively, for the first time, with experimental measurements of the fishbone saturation amplitude and energetic particle transport. Moreover, the suppression of the microturbulence by fishbone-induced zonal flows is likely responsible for the formation of an internal transport barrier that was observed after fishbone bursts in this DIII-D experiment. Finally, gyrokinetic simulations of a related ITER baseline scenario show that the fishbone induces insignificant energetic particle redistribution and may enable high performance scenarios in ITER burning plasma experiments