Bioimage informatics in the context of drosophila research

Modern biological research relies heavily on microscopic imaging. The advanced genetic toolkit of drosophila makes it possible to label molecular and cellular components with unprecedented level of specificity necessitating the application of the most sophisticated imaging technologies. Imaging in drosophila spans all scales from single molecules to the entire populations of adult organisms, from electron microscopy to live imaging of developmental processes. As the imaging approaches become more complex and ambitious, there is an increasing need for quantitative, computer-mediated image processing and analysis to make sense of the imagery. Bioimage informatics is an emerging research field that covers all aspects of biological image analysis from data handling, through processing, to quantitative measurements, analysis and data presentation. Some of the most advanced, large scale projects, combining cutting edge imaging with complex bioimage informatics pipelines, are realized in the drosophila research community. In this review, we discuss the current research in biological image analysis specifically relevant to the type of systems level image datasets that are uniquely available for the drosophila model system. We focus on how state-of-the-art computer vision algorithms are impacting the ability of drosophila researchers to analyze biological systems in space and time. We pay particular attention to how these algorithmic advances from computer science are made usable to practicing biologists through open source platforms and how biologists can themselves participate in their further development

Review of the ELI-NP-GBS low level rf and synchronization systems

The Gamma Beam System (GBS) of ELI-NP is a linac based gamma-source in construction at Magurele (RO) by the European consortium EuroGammaS led by INFN. Photons with tunable energy and with intensity and brilliance well beyond the state of the art will be produced by Compton back-scattering between a high quality electron beam (up to 740 MeV) and a 515 nm intense laser pulse. Production of very intense photon flux with narrow bandwidth requires multi-bunch operation at 100 Hz repetition rate. A total of 13 klystrons, 3 S-band (2856 MHz) and 10 C-band (5712 MHz) will power a total of 14 Travelling Wave accelerating sections (2 S-band and 12 C-band) plus 3 S-band Standing Wave cavities (a 1.6 cell RF gun and 2 RF deflectors). Each klystron is individually driven by a temperature stabilized LLRF module, for a maximum flexibility in terms of accelerating gradient, arbitrary pulse shaping (e.g. to compensate beam loading effects in multi-bunch regime) and compensation of long-term thermal drifts. In this paper, the whole LLRF system architecture and bench test results, the RF reference generation and distribution together with an overview of the synchronization system will be described

Microscopic Oscillations in the Quantum Nucleation of Vortices Subject to Periodic Pinning Potential in a Thin Superconductor

We present a theory for the decay of a supercurrent through nucleation of vortex-antivortex pairs in a two-dimensional superconductor in the presence of dissipation and of a periodic pinning potential. Through a powerful quantum electrodynamics formulation of the problem we show that the nucleation rate develops oscillations in its current-density dependence which are connected to the pinning periodicity. A remnant of the dissipation-driven localization transition is present, and an estimate of the nucleation rate suggests that these effects might be observable in real thin superconductors.Comment: REVTeX file, 4 pages in two-column mode, 1 Postscript figure, to appear in Phys.Rev.B (Rapid Communications

Realistic Tunneling States for the Magnetic Effects in Non-Metallic Real Glasses

The discovery of magnetic and compositional effects in the low temperature properties of multi-component glasses has prompted the need to extend the standard two-level systems (2LSs) tunneling model. A possible extension \cite{Jug2004} assumes that a subset of tunneling quasi-particles is moving in a three-welled potential (TWP) associated with the ubiquitous inhomogeneities of the disordered atomic structure of the glass. We show that within an alternative, cellular description of the intermediate-range atomic structure of glasses the tunneling TWP can be fully justified. We then review how the experimentally discovered magnetic effects can be explained within the approach where only localized atomistic tunneling 2LSs and quasi-particles tunneling in TWPs are allowed. We discuss the origin of the magnetic effects in the heat capacity, dielectric constant (real and imaginary parts), polarization echo and SQUID magnetization in several glassy systems. We conclude by commenting on a strategy to reveal the mentioned tunneling states (2LSs and TWPs) by means of atomistic computer simulations and discuss the microscopic nature of the tunneling states in the context of the potential energy landscape of glass-forming systems.Comment: 48 pages, 27 figures; mini-review for the Proceedings of the XIV International Workshop on Complex Systems (Fai della Paganella, Trento, March 2015) (submitted to Phil.Mag.). arXiv admin note: text overlap with arXiv:cond-mat/0210221 by other author

Vortex Quantum Nucleation and Tunneling in Superconducting Thin Films: Role of Dissipation and Periodic Pinning

We investigate the phenomenon of decay of a supercurrent in a superconducting thin film in the absence of an applied magnetic field. The resulting zero-temperature resistance derives from two equally possible mechanisms: 1) quantum tunneling of vortices from the edges of the sample; and 2) homogeneous quantum nucleation of vortex-antivortex pairs in the bulk of the sample, arising from the instability of the Magnus field's ``vacuum''. We study both situations in the case where quantum dissipation dominates over the inertia of the vortices. We find that the vortex tunneling and nucleation rates have a very rapid dependence on the current density driven through the sample. Accordingly, whilst normally the superconductor is essentially resistance-free, for the high current densities that can be reached in high-$T_c$ films a measurable resistance might develop. We show that edge-tunneling appears favoured, but the presence of pinning centres and of thermal fluctuations leads to an enhancement of the nucleation rates. In the case where a periodic pinning potential is artificially introduced in the sample, we show that current-oscillations will develop indicating an effect specific to the nucleation mechanism where the vortex pair-production rate, thus the resistance, becomes sensitive to the corrugation of the pinning substrate. In all situations, we give estimates for the observability of the studied phenomena.Comment: 8 pages (LaTeX), 2 postscript figures. Invited talk to the SATT8 (8th Italian Meeting on High-T_c Superconductivity), Como (Italy), Villa Olmo, 1-4 October 1996, to be published in La Rivista del Nuovo Cimento

Edge Tunneling of Vortices in Superconducting Thin Films

We investigate the phenomenon of the decay of a supercurrent due to the zero-temperature quantum tunneling of vortices from the edge in a thin superconducting film in the absence of an external magnetic field. An explicit formula is derived for the tunneling rate of vortices, which are subject to the Magnus force induced by the supercurrent, through the Coulomb-like potential barrier binding them to the film's edge. Our approach ensues from the non-relativistic version of a Schwinger-type calculation for the decay of the 2D vacuum previously employed for describing vortex-antivortex pair-nucleation in the bulk of the sample. In the dissipation-dominated limit, our explicit edge-tunneling formula yields numerical estimates which are compared with those obtained for bulk-nucleation to show that both mechanisms are possible for the decay of a supercurrent.Comment: REVTeX file, 15 pages, 1 Postscript figure; to appear in Phys.Rev.

Characterization of the Local Density of States Fluctuations near the Integer Quantum Hall Transition in a Quantum Dot Array

We present a calculation for the second moment of the local density of states in a model of a two-dimensional quantum dot array near the quantum Hall transition. The quantum dot array model is a realistic adaptation of the lattice model for the quantum Hall transition in the two-dimensional electron gas in an external magnetic field proposed by Ludwig, Fisher, Shankar and Grinstein. We make use of a Dirac fermion representation for the Green functions in the presence of fluctuations for the quantum dot energy levels. A saddle-point approximation yields non-perturbative results for the first and second moments of the local density of states, showing interesting fluctuation behaviour near the quantum Hall transition. To our knowledge we discuss here one of the first analytic characterizations of chaotic behaviour for a two-dimensional mesoscopic structure. The connection with possible experimental investigations of the local density of states in the quantum dot array structures (by means of NMR Knight-shift or single-electron-tunneling techniques) and our work is also established.Comment: 11 LaTeX pages, 1 postscript figure, to appear in Phys.Rev.

Three-dimensional FIB-SEM reconstruction of microtubule-organelle interaction in whole primary mouse beta cells

Microtubules play a major role in intracellular trafficking of vesicles in endocrine cells. Detailed knowledge of microtubule organization and their relation to other cell constituents is crucial for understanding cell function. However, their role in insulin transport and secretion is currently under debate. Here, we use Fib-Sem to image islet beta cells in their entirety with unprecedented resolution. We reconstruct mitochondria, Golgi apparati, centrioles, insulin secretory granules and micro-tubules of seven beta cells, and generate a comprehensive spatial map of microtubule-organelle interactions. We find that micro-tubules form non-radial networks that are predominantly not connected to either centrioles or endomembranes. Microtubule number and length, but not microtubule polymer density, vary with glucose stimulation. Furthermore, insulin secretory granules are enriched near the plasma membrane where they associate with microtubules. In summary, we provide the first 3D reconstructions of complete microtubule networks in primary mammalian cells together with evidence regarding their importance for insulin secretory granule positioning and thus supportive role in insulin secretion

Disordered Flat Phase and Phase Diagram for Restricted Solid on Solid Models of Fcc(110) Surfaces

We discuss the results of a study of restricted solid-on-solid models for fcc (110) surfaces. These models are simple modifications of the exactly solvable BCSOS model, and are able to describe a $(2\times 1)$ missing-row reconstructed surface as well as an unreconstructed surface. They are studied in two different ways. The first is by mapping the problem onto a quantum spin-1/2 one-dimensional hamiltonian of the Heisenberg type, with competing $S^z_iS^z_j$ couplings. The second is by standard Monte Carlo simulations. We find phase diagrams with the following features, which we believe to be quite generic: (i) two flat, ordered phases (unreconstructed and missing-row reconstructed); a rough, disordered phase; an intermediate disordered flat (DF) phase, characterized by monoatomic steps, whose physics is shown to be akin to that of a dimer spin state. (ii) a transition line from the $(2\times 1)$ reconstructed phase to the DF phase showing exponents which appear to be close, within our numerical accuracy, to the 2D-Ising universality class. (iii) a critical (preroughening) line with variable exponents, separating the unreconstructed phase from the DF phase. Possible signatures and order parameters of the DF phase are investigated.Comment: Revtex (22 pages) + 15 figures (uuencoded file