TriCheck: Memory Model Verification at the Trisection of Software, Hardware, and ISA

Memory consistency models (MCMs) which govern inter-module interactions in a shared memory system, are a significant, yet often under-appreciated, aspect of system design. MCMs are defined at the various layers of the hardware-software stack, requiring thoroughly verified specifications, compilers, and implementations at the interfaces between layers. Current verification techniques evaluate segments of the system stack in isolation, such as proving compiler mappings from a high-level language (HLL) to an ISA or proving validity of a microarchitectural implementation of an ISA. This paper makes a case for full-stack MCM verification and provides a toolflow, TriCheck, capable of verifying that the HLL, compiler, ISA, and implementation collectively uphold MCM requirements. The work showcases TriCheck's ability to evaluate a proposed ISA MCM in order to ensure that each layer and each mapping is correct and complete. Specifically, we apply TriCheck to the open source RISC-V ISA, seeking to verify accurate, efficient, and legal compilations from C11. We uncover under-specifications and potential inefficiencies in the current RISC-V ISA documentation and identify possible solutions for each. As an example, we find that a RISC-V-compliant microarchitecture allows 144 outcomes forbidden by C11 to be observed out of 1,701 litmus tests examined. Overall, this paper demonstrates the necessity of full-stack verification for detecting MCM-related bugs in the hardware-software stack.Comment: Proceedings of the Twenty-Second International Conference on Architectural Support for Programming Languages and Operating System

Combining independent de novo assemblies optimizes the coding transcriptome for nonconventional model eukaryotic organisms

Perl script used to perform our assembly pipeline. (PL 43 kb

Measuring the notched compressive strength of composite laminates: Specimen size effects

Large fibre reinforced composite structures can give much lower strengths than small test specimens, so a proper understanding of scaling is vital for their safe and efficient use. Small size (scale) specimens are commonly tested to justify allowable stresses, but could be dangerous if results are extrapolated without accounting for scaling effects. On the other hand large factors are sometimes applied to compensate for uncertainties, resulting in overweight designs. The most important variables of scaling effects on the strength of composites with open holes have been identified from experimental tests as notch size, ply and laminate thickness. In this study, these have been scaled both independently and simultaneously over a large range of combinations. The specimens are fabricated from commercially available (Hexcel Composites Ltd.) carbon/epoxy pre-impregnated tapes 0.125 mm thick (IM7/8552). The material is laid up by hand in unidirectional [04]ns with n = 2, 3, 4, and 8 (i.e., 2, 3, 4 and 8 mm thick) and multidirectional laminates; two generic quasi-isotropic lay-ups, one fabricated with blocked plies [45n/90n/−45n/0n]s and the other with distributed layers [45/90/−45/0]ns with n = 2, 4 and 8 are examined. It is shown that the critical failure mechanism in these laminates is in the form of fibre microbuckling or kinking. The unnotched compressive strength in unidirectional specimens thicker than 2 mm is found to be limited by the stress concentration developed at the end tabs and manufacturing induced defects in the form of ply waviness, fibre misalignment and voids rather than specimen size (scaling). In the open hole specimens, for both lay-ups, the strength reduction observed is due to hole size effect rather than specimen thickness or volume increase. The open hole (notched) compressive strength results obtained compare favourably to predictions by a linear softening cohesive zone fracture model developed in earlier work by the second author

Dynamic expression of ancient and novel molluscan shell genes during ecological transitions

Background: The Mollusca constitute one of the most morphologically and ecologically diverse metazoan phyla, occupying a wide range of marine, terrestrial and freshwater habitats. The evolutionary success of the molluscs can in part be attributed to the evolvability of the external shell. Typically, the shell first forms during embryonic and larval development, changing dramatically in shape, colour and mineralogical composition as development and maturation proceeds. Major developmental transitions in shell morphology often correlate with ecological transitions (e.g. from a planktonic to benthic existence at metamorphosis). While the genes involved in molluscan biomineralisation are beginning to be identified, there is little understanding of how these are developmentally regulated, or if the same genes are operational at different stages of the mollusc's life. Results: Here we relate the developmental expression of nine genes in the tissue responsible for shell production – the mantle – to ecological transitions that occur during the lifetime of the tropical abalone Haliotis asinina (Vetigastropoda). Four of these genes encode evolutionarily ancient proteins, while four others encode secreted proteins with little or no identity to known proteins. Another gene has been previously described from the mantle of another haliotid vetigastropod. All nine genes display dynamic spatial and temporal expression profiles within the larval shell field and juvenile mantle. Conclusion: These expression data reflect the regulatory complexity that underlies molluscan shell construction from larval stages to adulthood, and serves to highlight the different ecological demands placed on each stage. The use of both ancient and novel genes in all stages of shell construction also suggest that a core set of shell-making genes was provided by a shared metazoan ancestor, which has been elaborated upon to produce the range of molluscan shell types we see today

Variation in rates of early development in Haliotis asinina generate competent larvae of different ages

<p>Abstract</p> <p>Introduction</p> <p>Inter-specific comparisons of metazoan developmental mechanisms have provided a wealth of data concerning the evolution of body form and the generation of morphological novelty. Conversely, studies of intra-specific variation in developmental programs are far fewer. Variation in the rate of development may be an advantage to the many marine invertebrates that posses a biphasic life cycle, where fitness commonly requires the recruitment of planktonically dispersing larvae to patchily distributed benthic environments.</p> <p>Results</p> <p>We have characterised differences in the rate of development between individuals originating from a synchronised fertilisation event in the tropical abalone <it>Haliotis asinina</it>, a broadcast spawning lecithotrophic vetigastropod. We observed significant differences in the time taken to complete early developmental events (time taken to complete third cleavage and to hatch from the vitelline envelope), mid-larval events (variation in larval shell development) and late larval events (the acquisition of competence to respond to a metamorphosis inducing cue). We also provide estimates of the variation in maternally provided energy reserves that suggest maternal provisioning is unlikely to explain the majority of the variation in developmental rate we report here.</p> <p>Conclusions</p> <p>Significant differences in the rates of development exist both within and between cohorts of synchronously fertilised <it>H. asinina </it>gametes. These differences can be detected shortly after fertilisation and generate larvae of increasingly divergent development states. We discuss the significance of our results within an ecological context, the adaptive significance of mechanisms that might maintain this variation, and potential sources of this variation.</p

A horizontal gene transfer supported the evolution of an early metazoan biomineralization strategy

Background: The synchronous and widespread adoption of the ability to biomineralize was a defining event for metazoan evolution during the late Precambrian/early Cambrian 545 million years ago. However our understanding on the molecular level of how animals first evolved this capacity is poor. Because sponges are the earliest branching phylum of biomineralizing metazoans, we have been studying how biocalcification occurs in the coralline demosponge Astrosclera willeyana. Results: We have isolated and characterized a novel protein directly from the calcified spherulites of A. willeyana. Using three independent lines of evidence (genomic architecture of the gene in A. willeyana, spatial expression of the gene product in A. willeyana and genomic architecture of the gene in the related demosponge Amphimedon queenslandica), we show that the gene that encodes this protein was horizontally acquired from a bacterium, and is now highly and exclusively expressed in spherulite forming cells. Conclusions: Our findings highlight the ancient and close association that exists between sponges and bacteria, and provide support for the notion that horizontal gene transfer may have been an important mechanism that supported the evolution of this early metazoan biomineralisation strategy

Correlating the Energetics and Atomic Motions of the Metal-Insulator Transition of M1 Vanadium Dioxide

Materials that undergo reversible metal-insulator transitions are obvious candidates for new generations of devices. For such potential to be realised, the underlying microscopic mechanisms of such transitions must be fully determined. In this work we probe the correlation between the energy landscape and electronic structure of the metal-insulator transition of vanadium dioxide and the atomic motions occurring using first principles calculations and high resolution X-ray diffraction. Calculations find an energy barrier between the high and low temperature phases corresponding to contraction followed by expansion of the distances between vanadium atoms on neighbouring sub-lattices. X-ray diffraction reveals anisotropic strain broadening in the low temperature structure's crystal planes, however only for those with spacings affected by this compression/expansion. GW calculations reveal that traversing this barrier destabilises the bonding/anti-bonding splitting of the low temperature phase. This precise atomic description of the origin of the energy barrier separating the two structures will facilitate more precise control over the transition characteristics for new applications and devices.Comment: 11 Pages, 8 Figure

Creation of Entanglement by Interaction with a Common Heat Bath

I show that entanglement between two qubits can be generated if the two qubits interact with a common heat bath in thermal equilibrium, but do not interact directly with each other. In most situations the entanglement is created for a very short time after the interaction with the heat bath is switched on, but depending on system, coupling, and heat bath, the entanglement may persist for arbitrarily long times. This mechanism sheds new light on the creation of entanglement. A particular example of two quantum dots in a closed cavity is discussed, where the heat bath is given by the blackbody radiation.Comment: 4 revtex pages, 1 eps figure; replaced with published version; short discussion on entanglement distillation adde