Defining user perception of distributed multimedia quality

This article presents the results of a study that explored the human side of the multimedia experience. We propose a model that assesses quality variation from three distinct levels: the network, the media and the content levels; and from two views: the technical and the user perspective. By facilitating parameter variation at each of the quality levels and from each of the perspectives, we were able to examine their impact on user quality perception. Results show that a significant reduction in frame rate does not proportionally reduce the user's understanding of the presentation independent of technical parameters, that multimedia content type significantly impacts user information assimilation, user level of enjoyment, and user perception of quality, and that the device display type impacts user information assimilation and user perception of quality. Finally, to ensure the transfer of information, low-level abstraction (network-level) parameters, such as delay and jitter, should be adapted; to maintain the user's level of enjoyment, high-level abstraction quality parameters (content-level), such as the appropriate use of display screens, should be adapted

Elastic energy of proteins and the stages of protein folding

We propose a universal elastic energy for proteins, which depends only on the radius of gyration $R_{g}$ and the residue number $N$. It is constructed using physical arguments based on the hydrophobic effect and hydrogen bonding. Adjustable parameters are fitted to data from the computer simulation of the folding of a set of proteins using the CSAW (conditioned self-avoiding walk) model. The elastic energy gives rise to scaling relations of the form $R_{g}\sim N^{\nu}$ in different regions. It shows three folding stages characterized by the progression with exponents $\nu = 3/5, 3/7, 2/5$, which we identify as the unfolded stage, pre-globule, and molten globule, respectively. The pre-globule goes over to the molten globule via a break in behavior akin to a first-order phase transition, which is initiated by a sudden acceleration of hydrogen bonding

A systematically coarse-grained model for DNA, and its predictions for persistence length, stacking, twist, and chirality

We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with minimal phenomenology. Persistence length, degree of stacking, and twist are studied by molecular dynamics simulation as functions of temperature, salt concentration, sequence, interaction potential strength, and local position along the chain, for both single- and double-stranded DNA where appropriate. The model of DNA shows several phase transitions and crossover regimes in addition to dehybridization, including unstacking, untwisting, and collapse which affect mechanical properties such as rigidity and persistence length. The model also exhibits chirality with a stable right-handed and metastable left-handed helix.Comment: 30 pages, 20 figures, Supplementary Material available at http://www.physics.ubc.ca/~steve/publications.htm

Mean-field methods in evolutionary duplication-innovation-loss models for the genome-level repertoire of protein domains

We present a combined mean-field and simulation approach to different models describing the dynamics of classes formed by elements that can appear, disappear or copy themselves. These models, related to a paradigm duplication-innovation model known as Chinese Restaurant Process, are devised to reproduce the scaling behavior observed in the genome-wide repertoire of protein domains of all known species. In view of these data, we discuss the qualitative and quantitative differences of the alternative model formulations, focusing in particular on the roles of element loss and of the specificity of empirical domain classes.Comment: 10 Figures, 2 Table

Energy Storage in a Hamiltonian System in Partial Contact with a Heat Bath

To understand the mechanism allowing for the long-term storage of excess energy in proteins, we study a Hamiltonian system consisting of several coupled pendula in partial contact with a heat bath. It is found that energy storage is possible when the motion of each pendulum switches between oscillatory (vibrational) and rotational (phase-slip) modes. The storage time increases almost exponentially to the square root of the injected energy. The relevance of our mechanism to protein motors is discussed.Comment: 8 pages, 4 figures, to appear in J.Phys.Soc.Jp

Radiative lifetime measurements of rubidium Rydberg states

We have measured the radiative lifetimes of ns, np and nd Rydberg states of rubidium in the range 28 < n < 45. To enable long-lived states to be measured, our experiment uses slow-moving Rb atoms in a magneto-optical trap (MOT). Two experimental techniques have been adopted to reduce random and systematic errors. First, a narrow-bandwidth pulsed laser is used to excite the target Rydberg state, resulting in minimal shot-to-shot variation in the initial state population. Second, we monitor the target state population as a function of time delay from the laser pulse using a short-duration, millimetre-wave pulse that is resonant with a one- or two-photon transition. We then selectively field ionize the monitor state, and detect the resulting electrons with a micro-channel plate. This signal is an accurate mirror of the target state population, and is uncontaminated by contributions from other states which are populated by black body radiation. Our results are generally consistent with other recent experimental results obtained using a less sensitive method, and are also in excellent agreement with theory.Comment: 27 pages,6 figure

Essential facts of the monitoring of the sand extraction and its impact on the Flemish banks on the Belgian Continental Shelf from 2003 to 2012

The monitoring of sand extraction on the Flemish sandbanks of the Belgian continental shelf is based on multiple types of data: statistics derived from the extraction registers, data from the Electronic Monitoring System (EMS = “black-boxes”) on board the dredging vessels (complete records are available since 2003), and regular bathymetric surveys with the multibeam echosounders MBES) EM1002 and EM3002D (installed on the R/V Belgica) across the sandbanks along parallel lines and on specific areas. The analysis of the various types of data provides a 4D (space and time) view of the evolution of the extraction and admits robust and pragmatic conclusions about the real impact of the sand extraction on the marine environment. From 2003 to 2012, the global bathymetric evolution, based on MBES EM1002 and EM3002D measurements along lines across the control zones, confirms thestraightforward relation between the extraction and the bathymetrical evolution. On a larger scale, virtually all ofthe bathymetric variation can be explained by the extraction itself. In areas without any extraction, no significanttrend of the bathymetry is observed

ProtoEXIST: Advanced Prototype CZT Coded Aperture Telescopes for EXIST

{\it ProtoEXIST1} is a pathfinder for the {\it EXIST-HET}, a coded aperture hard X-ray telescope with a 4.5 m$^2$ CZT detector plane a 90$\times$70 degree field of view to be flown as the primary instrument on the {\it EXIST} mission and is intended to monitor the full sky every 3 h in an effort to locate GRBs and other high energy transients. {\it ProtoEXIST1} consists of a 256 cm$^2$ tiled CZT detector plane containing 4096 pixels composed of an 8$\times$8 array of individual 1.95 cm $\times$ 1.95 cm $\times$ 0.5 cm CZT detector modules each with a 8 $\times$ 8 pixilated anode configured as a coded aperture telescope with a fully coded $10^\circ\times10^\circ$ field of view employing passive side shielding and an active CsI anti-coincidence rear shield, recently completed its maiden flight out of Ft. Sumner, NM on the 9th of October 2009. During the duration of its 6 hour flight on-board calibration of the detector plane was carried out utilizing a single tagged 198.8 nCi Am-241 source along with the simultaneous measurement of the background spectrum and an observation of Cygnus X-1. Here we recount the events of the flight and report on the detector performance in a near space environment. We also briefly discuss {\it ProtoEXIST2}: the next stage of detector development which employs the {\it NuSTAR} ASIC enabling finer (32$\times$32) anode pixilation. When completed {\it ProtoEXIST2} will consist of a 256 cm$^2$ tiled array and be flown simultaneously with the ProtoEXIST1 telescope