Distributed-memory parallelization of an explicit time-domain volume integral equation solver on Blue Gene/P

Two distributed-memory schemes for efficiently parallelizing the explicit marching-on in-time based solution of the time domain volume integral equation on the IBM Blue Gene/P platform are presented. In the first scheme, each processor stores the time history of all source fields and only the computationally dominant step of the tested field computations is distributed among processors. This scheme requires all-to-all global communications to update the time history of the source fields from the tested fields. In the second scheme, the source fields as well as all steps of the tested field computations are distributed among processors. This scheme requires sequential global communications to update the time history of the distributed source fields from the tested fields. Numerical results demonstrate that both schemes scale well on the IBM Blue Gene/P platform and the memory efficient second scheme allows for the characterization of transient wave interactions on composite structures discretized using three million spatial elements without an acceleration algorithm

Interface Ferromagnetism in a SrMnO3/LaMnO3 Superlattice

Resonant soft x-ray absorption measurements at the O K edge on a SrMnO3/LaMnO3 superlattice show a shoulder at the energy of doped holes, which corresponds to the main peak of resonant scattering from the modulation in the doped hole density. Scattering line shape at the Mn L3,2 edges has a strong variation below the ferromagnetic transition temperature. This variation has a period equal to half the superlattice superperiod and follows the development of the ferromagnetic moment, pointing to a ferromagnetic phase developing at the interfaces. It occurs at the resonant energies for Mn3+ and Mn4+ valences. A model for these observations is presented, which includes a double-exchange two-site orbital and the variation with temperature of the hopping frequency tij between the two sites.Comment: 8.1 pages, 6 figure

Isolation of 39 polymorphic microsatellite loci and the development of a fluorescently labelled marker set for the Eurasian badger

We have isolated 78 microsatellite loci from the Eurasian badger (Meles meles). Of the 52 loci characterized, 39 were found to be polymorphic. A fluorescently labelled primer set was developed to enable individual-specific 17-locus genotypes to be obtained efficiently

Sensing centromere tension: Aurora B and the regulation of kinetochore function

Maintaining genome integrity during cell division requires regulated interactions between chromosomes and spindle microtubules. To ensure that daughter cells inherit the correct chromosomes, the sister kinetochores must attach to opposite spindle poles. Tension across the centromere stabilizes correct attachments, whereas phosphorylation of kinetochore substrates by the conserved Ipl1/Aurora B kinase selectively eliminates incorrect attachments. Here, we review our current understanding of how mechanical forces acting on the kinetochore are linked to biochemical changes to control chromosome segregation. We discuss models for tension sensing and regulation of kinetochore function downstream of Aurora B, and mechanisms that specify Aurora B localization to the inner centromere and determine its interactions with substrates at distinct locations.National Institutes of Health (U.S.) (Grant GM088313)Kinship Foundation. Searle Scholars Progra

Cation-ordering effects in the single layered manganite La(2/3)Sr(4/3)MnO4

We have synthesized epitaxial La(1-x)Sr(1+x)MnO4 (x=1/3) films as random alloys and cation-ordered analogues to probe how cation order affects the properties of a 2D manganite. The films show weak ferromagnetic ordering up to 130 K, although there is a dramatic difference in magnetic anisotropy depending on the cation order. While all films exhibit similar gapped insulator behavior above 130 K, there is a significant difference in the low temperature transport mechanism depending on the cation order. Differences in magnetic anisotropy and low temperature transport are consistent with differences in Mn 3d orbital occupancies. Together this work suggests that cation ordering can significantly alter the Mn 3d orbital ground state in these correlated electron systems.Comment: 4 figure

Aurora B phosphorylates spatially distinct targets to differentially regulate the kinetochore-microtubule interface

Accurate chromosome segregation requires carefully regulated interactions between kinetochores and microtubules, but how plasticity is achieved to correct diverse attachment defects remains unclear. Here we demonstrate that Aurora B kinase phosphorylates three spatially distinct targets within the conserved outer kinetochore KNL1/Mis12 complex/Ndc80 complex (KMN) network, the key player in kinetochore-microtubule attachments. The combinatorial phosphorylation of the KMN network generates graded levels of microtubule-binding activity, with full phosphorylation severely compromising microtubule binding. Altering the phosphorylation state of each protein causes corresponding chromosome segregation defects. Importantly, the spatial distribution of these targets along the kinetochore axis leads to their differential phosphorylation in response to changes in tension and attachment state. In total, rather than generating exclusively binary changes in microtubule binding, our results suggest a mechanism for the tension-dependent fine-tuning of kinetochore-microtubule interactions.Smith Family FoundationMassachusetts Life Sciences CenterKinship Foundation. Searle Scholars ProgramNational Institute of General Medical Sciences (U.S.) (Grant number GM088313

Exhaustive enumeration unveils clustering and freezing in random 3-SAT

We study geometrical properties of the complete set of solutions of the random 3-satisfiability problem. We show that even for moderate system sizes the number of clusters corresponds surprisingly well with the theoretic asymptotic prediction. We locate the freezing transition in the space of solutions which has been conjectured to be relevant in explaining the onset of computational hardness in random constraint satisfaction problems.Comment: 4 pages, 3 figure

The Peculiar Phase Structure of Random Graph Bisection

The mincut graph bisection problem involves partitioning the n vertices of a graph into disjoint subsets, each containing exactly n/2 vertices, while minimizing the number of "cut" edges with an endpoint in each subset. When considered over sparse random graphs, the phase structure of the graph bisection problem displays certain familiar properties, but also some surprises. It is known that when the mean degree is below the critical value of 2 log 2, the cutsize is zero with high probability. We study how the minimum cutsize increases with mean degree above this critical threshold, finding a new analytical upper bound that improves considerably upon previous bounds. Combined with recent results on expander graphs, our bound suggests the unusual scenario that random graph bisection is replica symmetric up to and beyond the critical threshold, with a replica symmetry breaking transition possibly taking place above the threshold. An intriguing algorithmic consequence is that although the problem is NP-hard, we can find near-optimal cutsizes (whose ratio to the optimal value approaches 1 asymptotically) in polynomial time for typical instances near the phase transition.Comment: substantially revised section 2, changed figures 3, 4 and 6, made minor stylistic changes and added reference