Automated Verification of Practical Garbage Collectors

Garbage collectors are notoriously hard to verify, due to their low-level interaction with the underlying system and the general difficulty in reasoning about reachability in graphs. Several papers have presented verified collectors, but either the proofs were hand-written or the collectors were too simplistic to use on practical applications. In this work, we present two mechanically verified garbage collectors, both practical enough to use for real-world C# benchmarks. The collectors and their associated allocators consist of x86 assembly language instructions and macro instructions, annotated with preconditions, postconditions, invariants, and assertions. We used the Boogie verification generator and the Z3 automated theorem prover to verify this assembly language code mechanically. We provide measurements comparing the performance of the verified collector with that of the standard Bartok collectors on off-the-shelf C# benchmarks, demonstrating their competitiveness

Measuring the impact of observations on the predictability of the Kuroshio Extension in a shallow-water model

In this paper sequential importance sampling is used to assess the impact of observations on a ensemble prediction for the decadal path transitions of the Kuroshio Extension (KE). This particle filtering approach gives access to the probability density of the state vector, which allows us to determine the predictive power — an entropy based measure — of the ensemble prediction. The proposed set-up makes use of an ensemble that, at each time, samples the climatological probability distribution. Then, in a post-processing step, the impact of different sets of observations is measured by the increase in predictive power of the ensemble over the climatological signal during one-year. The method is applied in an identical-twin experiment for the Kuroshio Extension using a reduced-gravity shallow water model. We investigate the impact of assimilating velocity observations from different locations during the elongated and the contracted meandering state of the KE. Optimal observations location correspond to regions with strong potential vorticity gradients. For the elongated state the optimal location is in the first meander of the KE. During the contracted state of the KE it is located south of Japan, where the Kuroshio separates from the coast

A bifurcation study of the three-dimensional thermohaline ocean circulation: the double-hemispheric case

Within a low-resolution primitive-equation model of the three-dimensional ocean circulation, a bifurcation analysis is performed of double-hemispheric basin flows. Main focus is on the connection between results for steady two-dimensional flows in a non-rotating basin and those for three-dimensional flows in a rotating basin. With the use of continuation methods, branches of steady states are followed in parameter space and their linear stability is monitored. There is a close qualitative similarity between the bifurcation structure of steady-state solutions of the two- and three dimensional flows. In both cases, symmetry-breaking pitchfork bifurcations are central in generating a multiple equilibria structure. The locations of these pitchfork bifurcations in parameter space can be characterized through a zero of the tendency of a particular energy functional. Although balances controlling the steady-state ?ows are quantitatively very di?erent, the zonally averaged patterns of the perturbations associated with symmetry-breaking are remarkably similar for two-dimensional and three-dimensional ?ows, and the energetics of the symmetry-breaking mechanism is in essence the same

Model building of disulfide bonds in proteins with known three-dimensional structure

As an aid in the selection of sites in a protein where a disulfide bond might be engineered, a computer program has been developed. The algorithm starts with the generation of Cβ positions from the N, Cα and C atom coordinates available from a three-dimensional model. A first set of residue pairs that might form a disulfide bond is selected on the basis of Cβ-Cβ distances between residues. Then, for each residue in this set, Sγ positions are generated, which satisfy the requirement that, with ideal values for the Cα-Cβ and Cβ-Sγ bond lengths and for the bond angle at Cβ, the distance between Sγ of residue 1 and Cβ of residue 2 in a pair (determined by the bond angle at Sγ2) is at, or very close to its ideal value. Usually two acceptable Sγ positions are found for each half cystine, resulting in up to four different conformations for the disulfide bond. Finally, these conformations are subjected to an energy minimization procedure to remove large deviations from ideal geometry and their final energies are calculated. User input determines which final conformations are energetically acceptable. These conformations are written to a file to allow further analysis and e.g. inspection on a computer graphics device

Mapping and Characterizing Subtidal Oyster Reefs Using Acoustic Techniques, Underwater Videography and Quadrat Counts

Populations of the eastern oyster Crassostrea virginica have been in long-term decline in most areas. A major hindrance to effective oyster management has been lack of a methodology for accurately and economically obtaining data on their distribution and abundance patterns. Here, we describe early results from studies aimed at development of a mapping and monitoring protocol involving acoustic techniques, underwater videography, and destructive sampling (excavated quadrats). Two subtidal reefs in Great Bay, New Hampshire, were mapped with side-scan sonar and with videography by systematically imaging multiple sampling cells in a grid covering the same areas. A single deployment was made in each cell, and a 5-10-s recording was made of a 0.25-m2 area; the location of each image was determined using a differential global position system. A still image was produced for each of the cells and all (n = 40 or 44) were combined into a single photomontage overlaid onto a geo-referenced base map for each reef using Arc View geographic information system. Quadrat (0.25 m2 ) samples were excavated from 9 or 10 of the imaged areas on each reef, and all live oysters were counted and measured. Intercomparisons of the acoustic, video, and quadrat data suggest: (1) acoustic techniques and systematic videography can readily delimit the boundaries of oyster reefs; (2) systematic videography can yield quantitative data on shell densities and information on reef structure; and (3) some combination of acoustics, systematic videography, and destructive sampling can provide spatially detailed information on oyster reef characteristics

The LyAlpha Line Profiles of Ultraluminous Infrared Galaxies: Fast Winds and Lyman Continuum Leakage

We present new Hubble Space Telescope Cosmic Origins Spectrograph far-ultraviolet (far-UV) spectroscopy and Keck Echellete optical spectroscopy of 11 ultraluminous infrared galaxies (ULIRGs), a rare population of local galaxies experiencing massive gas inflows, extreme starbursts, and prominent outflows. We detect H Lyman alpha emission from 8 ULIRGs and the companion to IRAS09583+4714. In contrast to the P Cygni profiles often seen in galaxy spectra, the H Lyman alpha profiles exhibit prominent, blueshifted emission out to Doppler shifts exceeding -1000 km/s in three HII-dominated and two AGN-dominated ULIRGs. To better understand the role of resonance scattering in shaping the H Lyman alpha line profiles, we directly compare them to non-resonant emission lines in optical spectra. We find that the line wings are already present in the intrinsic nebular spectra, and scattering merely enhances the wings relative to the line core. The H Lyman alpha attenuation (as measured in the COS aperture) ranges from that of the far-UV continuum to over 100 times more. A simple radiative transfer model suggests the H Lyman alpha photons escape through cavities which have low column densities of neutral hydrogen and become optically thin to the Lyman continuum in the most advanced mergers. We show that the properties of the highly blueshifted line wings on the H Lyman alpha and optical emission-line profiles are consistent with emission from clumps of gas condensing out of a fast, hot wind. The luminosity of the H Lyman alpha emission increases non-linearly with the ULIRG bolometric luminosity and represents about 0.1 to 1% of the radiative cooling from the hot winds in the HII-dominated ULIRGs.Comment: Submitted to Ap

Ultrasonic distance detection for a closed-loop spinal cord stimulation system

When stimulating the spinal cord at a constant strength, the current density in the spinal cord and thus the effects on chronic, intractable pain and vascular insufficiency will change with body position, due to the varying separation of the spinal cord and the stimulating electrode. The current density in the spinal cord has to remain between the perception and discomfort threshold (stimulation window) for a good therapeutic effect, i.e. that the patient does not suffer from pain. The stimulation window is very small. In current SCS systems the stimulus applied to the electrode is set at a constant value. A major improvement could be achieved when the distance between stimulation electrode and spinal cord could be measured and used to control the stimulus amplitude in a closed-loop system. An ultrasonic piezoelectric transducer was chosen to measure the distance between the electrode and the spinal cor

Accelerated X-ray Structure Elucidation of a 36 kDa Muramidase/Transglycosylase Using wARP

The X-ray structure of the 36kDa soluble lytic transglycosylase from Escherichia coli has been determined starting with the multiple isomorphous replacement method with inclusion of anomalous scattering at 2.7 Å resolution. Subsequently, before any model building was carried out, phases were extended to 1.7 Å, resolution with the weighted automated refinement procedure wARP, which gave a dramatic improvement in the phases. The electron-density maps from wARP were of outstanding quality for both the main chain and the side chains of the protein, which allowed the time spent on the tracing, interpretation and building of the X-ray structure to be substantially shortened. The structure of the soluble lyric transglycosylase was refined at 1.7 Å, resolution with X-PLOR to a final crystallographic R factor of 18.9%. Analysis of the wARP procedure revealed that the use of the maximum-likelihood refinement in wARP gave much better phases than least-squares refinement, provided that the ratio of reflections to protein atom parameters was approximately 1.8 or higher. Furthermore, setting aside 5% of the data for an Rfree test set had a negative effect on the phase improvement. The mean WwARP, a weight determined at the end of the wARP procedure and based on the variance of structure factors from six individually refined wARP models, proved to be a better indicator than the Rfree factor to judge different phase improvement protocols. The elongated Slt35 structure has three domains named the alpha, beta and core domains. The alpha domain contains mainly α-helices, while the beta domain consists of a five-stranded antiparallel β-sheet flanked by a short α-helix. Sandwiched between the alpha and beta domains is the core domain, which bears some resemblance to the fold of the catalytic domain of the previously elucidated 70 kDa soluble lytic transglycosylase from E. coli. The putative active site is at the bottom of a large deep groove in the core domain.