Ripples and Shear Bands in Plowed Granular Media

Monodisperse packings of dry, air-fluidized granular media typically exist between volume fractions from $\Phi$= 0.585 to 0.64. We demonstrate that the dynamics of granular drag are sensitive to volume fraction $\Phi$ and their exists a transition in the drag force and material deformation from smooth to oscillatory at a critical volume fraction $\Phi_{c}=0.605$. By dragging a submerged steel plate (3.81 cm width, 6.98 cm depth) through $300 \mu m$ glass beads prepared at volume fractions between 0.585 to 0.635 we find that below $\Phi_{c}$ the media deformation is smooth and non-localized while above $\Phi_{c}$ media fails along distinct shear bands. At high $\Phi$ the generation of these shear bands is periodic resulting in the ripples on the surface. Work funded by The Burroughs Wellcome Fund and the Army Research Lab MAST CT

Entangled granular media

We study the geometrically induced cohesion of ensembles of granular "u-particles" which mechanically entangle through particle interpenetration. We vary the length-to-width ratio $l/w$ of the u-particles and form them into free-standing vertical columns. In laboratory experiment we monitor the response of the columns to sinusoidal vibration (frequency $f$, peak acceleration $\Gamma$). Column collapse occurs in a characteristic time, $\tau$, which follows the relation $\tau = f^{-1} \exp(\Delta / \Gamma)$. $\Delta$ resembles an activation energy and is maximal at intermediate $l/w$. Simulation reveals that optimal strength results from competition between packing and entanglement.Comment: 4 pages, 5 figure

A model of evolution and structure for multiple sequence alignment

We have developed a phylogeny-aware progressive alignment method that recognizes insertions and deletions as distinct evolutionary events and thus avoids systematic errors created by traditional alignment methods. We now extend this method to simultaneously model regional heterogeneity and evolution. This novel method can be flexibly adapted to alignment of nucleotide or amino acid sequences evolving under processes that vary over genomic regions and, being fully probabilistic, provides an estimate of regional heterogeneity of the evolutionary process along the alignment and a measure of local reliability of the solution. Furthermore, the evolutionary modelling of substitution process permits adjusting the sensitivity and specificity of the alignment and, if high specificity is aimed at, leaving sequences unaligned when their divergence is beyond a meaningful detection of homology

Short-range template switching in great ape genomes explored using pair hidden Markov models.

Many complex genomic rearrangements arise through template switch errors, which occur in DNA replication when there is a transient polymerase switch to an alternate template nearby in three-dimensional space. While typically investigated at kilobase-to-megabase scales, the genomic and evolutionary consequences of this mutational process are not well characterised at smaller scales, where they are often interpreted as clusters of independent substitutions, insertions and deletions. Here we present an improved statistical approach using pair hidden Markov models, and use it to detect and describe short-range template switches underlying clusters of mutations in the multi-way alignment of hominid genomes. Using robust statistics derived from evolutionary genomic simulations, we show that template switch events have been widespread in the evolution of the great apes' genomes and provide a parsimonious explanation for the presence of many complex mutation clusters in their phylogenetic context. Larger-scale mechanisms of genome rearrangement are typically associated with structural features around breakpoints, and accordingly we show that atypical patterns of secondary structure formation and DNA bending are present at the initial template switch loci. Our methods improve on previous non-probabilistic approaches for computational detection of template switch mutations, allowing the statistical significance of events to be assessed. By specifying realistic evolutionary parameters based on the genomes and taxa involved, our methods can be readily adapted to other intra- or inter-species comparisons

Genomic DNA k-mer spectra: models and modalities

Tetrapods, unlike other organisms, have multimodal spectra of k-mers in their genome

Integrated planning and scheduling for Earth science data processing

Several current NASA programs such as the EOSDIS Core System (ECS) have data processing and data management requirements that call for an integrated planning and scheduling capability. In this paper, we describe the experience of applying advanced scheduling technology operationally, in terms of what was accomplished, lessons learned, and what remains to be done in order to achieve similar successes in ECS and other programs. We discuss the importance and benefits of advanced scheduling tools, and our progress toward realizing them, through examples and illustrations based on ECS requirements. The first part of the paper focuses on the Data Archive and Distribution (DADS) V0 Scheduler. We then discuss system integration issues ranging from communication with the scheduler to the monitoring of system events and re-scheduling in response to them. The challenge of adapting the scheduler to domain-specific features and scheduling policies is also considered. Extrapolation to the ECS domain raises issues of integrating scheduling with a product-generation planner (such as PlaSTiC), and implementing conditional planning in an operational system. We conclude by briefly noting ongoing technology development and deployment projects being undertaken by HTC and the ISTB