Discrimination of complex synthetic echoes by an echolocating bottlenose dolphin

Bottlenose dolphins (Tursiops truncatus) detect and discriminate underwater objects by interrogating the environment with their native echolocation capabilities. Study of dolphins' ability to detect complex (multihighlight) signals in noise suggest echolocation object detection using an approximate 265-micros energy integration time window sensitive to the echo region of highest energy or containing the highlight with highest energy. Backscatter from many real objects contains multiple highlights, distributed over multiple integration windows and with varying amplitude relationships. This study used synthetic echoes with complex highlight structures to test whether high-amplitude initial highlights would interfere with discrimination of low-amplitude trailing highlights. A dolphin was trained to discriminate two-highlight synthetic echoes using differences in the center frequencies of the second highlights. The energy ratio (delta dB) and the timing relationship (delta T) between the first and second highlights were manipulated. An iso-sensitivity function was derived using a factorial design testing delta dB at -10, -15, -20, and -25 dB and delta T at 10, 20, 40, and 80 micros. The results suggest that the animal processed multiple echo highlights as separable analyzable features in the discrimination task, perhaps perceived through differences in spectral rippling across the duration of the echoes.     

Adaptive numerical components for PDE-based simulations

Numerical simulations based on nonlinear partial differential equations (PDEs) using Newton-based methods require the solution of large, sparse linear systems of equations at each nonlinear iteration. Typically in large-scale parallel simulations such linear systems are solved by using preconditioned Krylov methods. In many cases, especially in time-dependent problems, the attributes of the linear systems can change throughout the stimulation, potentially leading to varying times for solving the linear systems during different nonlinear iterations. We present an approach to characterizing the nonlinear and linear system solution and using the resulting application performance information to dynamically select linear solver methods, with the goal of reducing the total time to solution. We discuss the effect of these adaptive heuristics on fluid dynamics and radiation transport codes. We also introduce general component infrastructure to support dynamic algorithm selection and adaptation in applications involving the solution of nonlinear PDEs. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Jamming in attractive granular media

The jamming transition is studied numerically in systems of particles with attraction. Unlike the purely repulsive case where a single transition separates the jammed from unjammed phase, the presence of even an infinitesimal amount of attraction yields two distinct transitions: connectivity and rigidity percolation. We measure critical exponents of these two percolation transitions and find that they are different than the corresponding lattice values. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Direct Visualization of Vesicle Maturation and Plasma Membrane Protein Trafficking

Internalization and intracellular trafficking of membrane proteins are now recognized as essential mechanisms that contribute to a number of cellular processes. Current methods lack the ability to specifically label the plasma membrane of a live cell, follow internalization of labeled membrane molecules, and conclusively differentiate newly formed membrane-derived vesicles from pre-existing endocytic or secretory structures in the cytoplasm. Here, we detail a visualization method for surface biotinylation of plasma membrane-derived vesicles that allows us to follow their progress from membrane to cytosol at specific time points. Using the transmembrane receptor RET as a model, we demonstrate how this method can be applied to identify plasma membrane-derived vesicle maturation, determine RET’s presence within these structures, and monitor RET’s recycling to the cell surface. This method improves on static and less discriminatory methods, providing a tool for analysis of real-time vesicle trafficking that is applicable to many systems.     

Controlling bandgap energy and multivibronic modes of a poly(2,5-thiophene-1,4-dialkoxyphenylene) derivative by gamma photons

In this work, the influence of γ radiation on electronic, structural, and vibrational properties of a poly(2,5-thiophene-1,4-dialkoxyphenylene) derivative is studied by optical absorption and photoluminescence. A Gaussian fit of emission spectra within Franck-Condon vertical transitions formalism was carried out in order to understand how vibronic coupling is affected by the dose, because an unexpected luminescence behavior was observed. Aiming to understand the ionizing radiation-matter interaction processes, we employed a molecular modeling procedure, through the use of a semiempirical method (AM1) applied to conjugated oligomers' conformational structure and equilibrium geometries, to clarify the defects induction for the used doses. From AM1 optimized structures, electronic transitions were calculated by ZINDO/S-CI semiempirical method to measure the chain scission degree. Moreover, with the results presented in this work, it is possible to come up with a new physical-chemical route to treat and increase conjugated polymers' efficiency. Finally, we believe that the present paper contributes to the literature about defects on conjugated polymers.     

Inter-DNA attraction mediated by divalent counterions

Can nonspecifically bound divalent counterions induce attraction between DNA strands? Here, we present experimental evidence demonstrating attraction between short DNA strands mediated by Mg2+ ions. Solution small angle x-ray scattering data collected as a function of DNA concentration enable model independent extraction of the second virial coefficient. As the [Mg2+] increases, this coefficient turns from positive to negative reflecting the transition from repulsive to attractive inter-DNA interaction. This surprising observation is corroborated by independent light scattering experiments. The dependence of the observed attraction on experimental parameters including DNA length provides valuable clues to its origin.