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

The role of magnetic anisotropy in spin filter junctions

We have fabricated oxide based spin filter junctions in which we demonstrate that magnetic anisotropy can be used to tune the transport behavior of spin filter junctions. Until recently, spin filters have been largely comprised of polycrystalline materials where the spin filter barrier layer and one of the electrodes are ferromagnetic. These spin filter junctions have relied on the weak magnetic coupling between one ferromagnetic electrode and a barrier layer or the insertion of a nonmagnetic insulating layer in between the spin filter barrier and electrode. We have demonstrated spin filtering behavior in La0.7Sr0.3MnO3/chromite/Fe3O4 junctions without nonmagnetic spacer layers where the interface anisotropy plays a significant role in determining transport behavior. Detailed studies of chemical and magnetic structure at the interfaces indicate that abrupt changes in magnetic anisotropy across the non-isostructural interface is the cause of the significant suppression of junction magnetoresistance in junctions with MnCr2O4 barrier layers.Comment: 7 pages, 7 figure

Potential acoustic benefits of circulation control rotors

The fundamental aeroacoustic mechanisms responsible for noise generation on a rotating blade are theoretically examined. Their contribution to the overall rotor sound pressure level is predicted. Results from a theory for airfoil trailing edge noise are presented. Modifications and extensions to other source theories are described where it is necessary to account for unique aspects of circulation control (CC) aerodynamics. The circulation control rotor (CCR), as embodied on an X-wing vertical takeoff and landing (VTOL) aircraft, is used as an example for computational purposes, although many of the theoretical results presented are generally applicable to other CC applications (such as low speed rotors, propellers, compressors, and fixed wing aircraft). Using the analytical models, it is shown that the utilization CC aerodynamics theoretically makes possible unprecedented advances in rotor noise reduction. For the X-wing VTOL these reductions appear to be feasible without incurring significant attendant performance and weight penalties

Induced dicentric chromosome formation promotes genomic rearrangements and tumorigenesis

Chromosomal rearrangements can radically alter gene products and their function, driving tumor formation or progression. However, the molecular origins and evolution of such rearrangements are varied and poorly understood, with cancer cells often containing multiple, complex rearrangements. One mechanism that can lead to genomic rearrangements is the formation of a “dicentric” chromosome containing two functional centromeres. Indeed, such dicentric chromosomes have been observed in cancer cells. Here, we tested the ability of a single dicentric chromosome to contribute to genomic instability and neoplastic conversion in vertebrate cells. We developed a system to transiently and reversibly induce dicentric chromosome formation on a single chromosome with high temporal control. We find that induced dicentric chromosomes are frequently damaged and mis-segregated during mitosis, and that this leads to extensive chromosomal rearrangements including translocations with other chromosomes. Populations of pre-neoplastic cells in which a single dicentric chromosome is induced acquire extensive genomic instability and display hallmarks of cellular transformation including anchorage-independent growth in soft agar. Our results suggest that a single dicentric chromosome could contribute to tumor initiation.Leukemia & Lymphoma Society of America (Scholar Award)National Institute of General Medical Sciences (U.S.) (Grant GM088313)American Cancer Society (Research Scholar Grant 121776

Dynamic regulation of dynein localization revealed by small molecule inhibitors of ubiquitination enzymes

Cytoplasmic dynein is a minus-end-directed microtubule-based motor that acts at diverse subcellular sites. During mitosis, dynein localizes simultaneously to the mitotic spindle, spindle poles, kinetochores and the cell cortex. However, it is unclear what controls the relative targeting of dynein to these locations. As dynein is heavily post-translationally modified, we sought to test a role for these modifications in regulating dynein localization. We find that dynein rapidly and strongly accumulates at mitotic spindle poles following treatment with NSC697923, a small molecule that inhibits the ubiquitin E2 enzyme, Ubc13, or treatment with PYR-41, a ubiquitin E1 inhibitor. Subsets of dynein regulators such as Lis1, ZW10 and Spindly accumulate at the spindle poles, whereas others do not, suggesting that NSC697923 differentially affects specific dynein populations. We additionally find that dynein relocalization induced by NSC697923 or PYR-41 can be suppressed by simultaneous treatment with the non-selective deubiquitinase inhibitor, PR-619. However, we did not observe altered dynein localization following treatment with the selective E1 inhibitor, TAK-243. Although it is possible that off-target effects of NSC697923 and PYR-41 are responsible for the observed changes in dynein localization, the rapid relocalization upon drug treatment highlights the highly dynamic nature of dynein regulation during mitosis. Keywords:dynein, ubiquitin, NSC697923, PYR-41, mitosis, microtubule

Probing the Role of the Barrier Layer in Magnetic Tunnel Junction Transport

Magnetic tunnel junctions with a ferrimagnetic barrier layer have been studied to understand the role of the barrier layer in the tunneling process - a factor that has been largely overlooked until recently. Epitaxial oxide junctions of highly spin polarized La0.7Sr0.3MnO3 and Fe3O4 electrodes with magnetic NiMn2O4 (NMO) insulating barrier layers provide a magnetic tunnel junction system in which we can probe the effect of the barrier by comparing junction behavior above and below the Curie temperature of the barrier layer. When the barrier is paramagnetic, the spin polarized transport is dominated by interface scattering and surface spin waves; however, when the barrier is ferrimagnetic, spin flip scattering due to spin waves within the NMO barrier dominates the transport.Comment: 10 pages, 3 figure

CDK-dependent phosphorylation and nuclear exclusion coordinately control kinetochore assembly state

Accurate chromosome segregation requires assembly of the multiprotein kinetochore complex. Prior work has identified more than 100 different kinetochore components in human cells. However, little is known about the regulatory processes that specify their assembly upon mitotic entry and disassembly at mitotic exit. In this paper, we used a live-cell imaging–based assay to quantify kinetochore disassembly kinetics and systematically analyze the role of potential regulatory mechanisms in controlling kinetochore assembly state. We find that kinetochore assembly and disassembly was driven primarily by mitotic phosphorylation downstream of cyclin-dependent kinase (CDK). In addition, we demonstrate that nuclear exclusion of the Ndc80 complex helped restrict kinetochore formation to mitosis. Combining constitutive CDK-dependent phosphorylation of CENP-T and forced nuclear localization of the Ndc80 complex partially prevented kinetochore disassembly at mitotic exit and led to chromosome segregation defects in subsequent divisions. In total, we find that the coordinated temporal regulation of outer kinetochore assembly is essential for accurate cell division.Kinship Foundation. Searle Scholars ProgramLeukemia & Lymphoma Society of AmericaNational Institutes of Health (U.S.) (National Institute of General Medical Sciences (U.S.) Grant GM088313)Leukemia & Lymphoma Society of America (Special Fellows Award

Single-Step Quantum Search Using Problem Structure

The structure of satisfiability problems is used to improve search algorithms for quantum computers and reduce their required coherence times by using only a single coherent evaluation of problem properties. The structure of random k-SAT allows determining the asymptotic average behavior of these algorithms, showing they improve on quantum algorithms, such as amplitude amplification, that ignore detailed problem structure but remain exponential for hard problem instances. Compared to good classical methods, the algorithm performs better, on average, for weakly and highly constrained problems but worse for hard cases. The analytic techniques introduced here also apply to other quantum algorithms, supplementing the limited evaluation possible with classical simulations and showing how quantum computing can use ensemble properties of NP search problems.Comment: 39 pages, 12 figures. Revision describes further improvement with multiple steps (section 7). See also http://www.parc.xerox.com/dynamics/www/quantum.htm