ArrayBridge: Interweaving declarative array processing with high-performance computing

Scientists are increasingly turning to datacenter-scale computers to produce and analyze massive arrays. Despite decades of database research that extols the virtues of declarative query processing, scientists still write, debug and parallelize imperative HPC kernels even for the most mundane queries. This impedance mismatch has been partly attributed to the cumbersome data loading process; in response, the database community has proposed in situ mechanisms to access data in scientific file formats. Scientists, however, desire more than a passive access method that reads arrays from files. This paper describes ArrayBridge, a bi-directional array view mechanism for scientific file formats, that aims to make declarative array manipulations interoperable with imperative file-centric analyses. Our prototype implementation of ArrayBridge uses HDF5 as the underlying array storage library and seamlessly integrates into the SciDB open-source array database system. In addition to fast querying over external array objects, ArrayBridge produces arrays in the HDF5 file format just as easily as it can read from it. ArrayBridge also supports time travel queries from imperative kernels through the unmodified HDF5 API, and automatically deduplicates between array versions for space efficiency. Our extensive performance evaluation in NERSC, a large-scale scientific computing facility, shows that ArrayBridge exhibits statistically indistinguishable performance and I/O scalability to the native SciDB storage engine.Comment: 12 pages, 13 figure

Statistical physics of isotropic-genesis nematic elastomers: I. Structure and correlations at high temperatures

Isotropic-genesis nematic elastomers (IGNEs) are liquid crystalline polymers (LCPs) that have been randomly, permanently cross-linked in the high-temperature state so as to form an equilibrium random solid. Thus, instead of being free to diffuse throughout the entire volume, as they would be in the liquid state, the constituent LCPs in an IGNE are mobile only over a finite length-scale controlled by the density of cross-links. We address the effects that such network-induced localization have on the liquid-crystalline characteristics of an IGNE, as probed via measurements made at high temperatures. In contrast with the case of uncross-linked LCPs, for IGNEs these characteristics are determined not only by thermal fluctuations but also by the quenched disorder associated with the cross-link constraints. To study IGNEs, we consider a microscopic model of dimer nematogens in which the dimers interact via orientation-dependent excluded volume forces. The dimers are, furthermore, randomly, permanently cross-linked via short Hookean springs, the statistics of which we model by means of a Deam-Edwards type of distribution. We show that at length-scales larger than the size of the nematogens this approach leads to a recently proposed phenomenological Landau theory of IGNEs [Lu et al., Phys. Rev. Lett. 108, 257803 (2012)], and hence predicts a regime of short-ranged oscillatory spatial correlations in the nematic alignment, of both thermal and glassy types. In addition, we consider two alternative microscopic models of IGNEs: (i) a wormlike chain model of IGNEs that are formed via the cross-linking of side-chain LCPs; and (ii) a jointed chain model of IGNEs that are formed via the cross-linking of main-chain LCPs. At large length-scales, both of these models give rise to liquid-crystalline characteristics that are qualitatively in line with those predicted by the dimer-and-springs model.Comment: 33 pages, 6 figures, 6 appendice

Elastic heterogeneity of soft random solids

Spatial heterogeneity in the elastic properties of soft random solids is investigated via a two-pronged approach. First, a nonlocal phenomenological model for the elastic free energy is examined. This features a quenched random kernel, which induces randomness in the residual stress and Lame coefficients. Second, a semi-microscopic model network is explored using replica statistical mechanics. The Goldstone fluctuations of the semi-microscopic model are shown to reproduce the phenomenological model, and via this correspondence the statistical properties of the residual stress and Lame coefficients are inferred. Correlations involving the residual stress are found to be long-ranged and governed by a universal parameter that also gives the mean shear modulus.Comment: 5 page

Thermal Fluctuations and Rubber Elasticity

The effects of thermal elastic fluctuations in rubber materials are examined. It is shown that, due to an interplay with the incompressibility constraint, these fluctuations qualitatively modify the large-deformation stress-strain relation, compared to that of classical rubber elasticity. To leading order, this mechanism provides a simple and generic explanation for the peak structure of Mooney-Rivlin stress-strain relation, and shows a good agreement with experiments. It also leads to the prediction of a phonon correlation function that depends on the external deformation.Comment: 4 RevTeX pages, 1 figure, submitted to PR

Phenomenological Theory of Isotropic-Genesis Nematic Elastomers

We consider the impact of the elastomer network on the structure and fluctuations in the isotropic-genesis nematic elastomer, via a phenomenological model that underscores the role of network compliance. The model contains a network-mediated nonlocal interaction as well as a new kind of random field, which reflects the memory of the nematic order present at cross-linking, and also encodes local anisotropy due to localized polymers. Thus, we predict a regime of short-ranged oscillatory spatial correlations (both thermal and glassy) in the nematic alignment trapped into the network

Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication

Horseshoe crabs are marine arthropods with a fossil record extending back approximately 450 million years. They exhibit remarkable morphological stability over their long evolutionary history, retaining a number of ancestral arthropod traits, and are often cited as examples of "living fossils." As arthropods, they belong to the Ecdysozoa}, an ancient super-phylum whose sequenced genomes (including insects and nematodes) have thus far shown more divergence from the ancestral pattern of eumetazoan genome organization than cnidarians, deuterostomes, and lophotrochozoans. However, much of ecdysozoan diversity remains unrepresented in comparative genomic analyses. Here we use a new strategy of combined de novo assembly and genetic mapping to examine the chromosome-scale genome organization of the Atlantic horseshoe crab Limulus polyphemus. We constructed a genetic linkage map of this 2.7 Gbp genome by sequencing the nuclear DNA of 34 wild-collected, full-sibling embryos and their parents at a mean redundancy of 1.1x per sample. The map includes 84,307 sequence markers and 5,775 candidate conserved protein coding genes. Comparison to other metazoan genomes shows that the L. polyphemus genome preserves ancestral bilaterian linkage groups, and that a common ancestor of modern horseshoe crabs underwent one or more ancient whole genome duplications (WGDs) ~ 300 MYA, followed by extensive chromosome fusion