Enabling a High Throughput Real Time Data Pipeline for a Large Radio Telescope Array with GPUs

The Murchison Widefield Array (MWA) is a next-generation radio telescope currently under construction in the remote Western Australia Outback. Raw data will be generated continuously at 5GiB/s, grouped into 8s cadences. This high throughput motivates the development of on-site, real time processing and reduction in preference to archiving, transport and off-line processing. Each batch of 8s data must be completely reduced before the next batch arrives. Maintaining real time operation will require a sustained performance of around 2.5TFLOP/s (including convolutions, FFTs, interpolations and matrix multiplications). We describe a scalable heterogeneous computing pipeline implementation, exploiting both the high computing density and FLOP-per-Watt ratio of modern GPUs. The architecture is highly parallel within and across nodes, with all major processing elements performed by GPUs. Necessary scatter-gather operations along the pipeline are loosely synchronized between the nodes hosting the GPUs. The MWA will be a frontier scientific instrument and a pathfinder for planned peta- and exascale facilities.Comment: Version accepted by Comp. Phys. Com

Allosteric activation unveils protein-mass modulation of ATP phosphoribosyltransferase product release

Funding: This work was supported by the Biotechnology and Biological Sciences Research Council (BBSRC) [Grant BB/M010996/1] via an EASTBIO Doctoral Training Partnership studentship to B.J.R.Heavy-isotope substitution into enzymes slows down bond vibrations and may alter transition-state barrier crossing probability if this is coupled to fast protein motions. ATP phosphoribosyltransferase from Acinetobacter baumannii is a multi-protein complex where the regulatory protein HisZ allosterically enhances catalysis by the catalytic protein HisGS. This is accompanied by a shift in rate-limiting step from chemistry to product release. Here we report that isotope-labelling of HisGS has no effect on the nonactivated reaction, which involves negative activation heat capacity, while HisZ-activated HisGS catalytic rate decreases in a strictly mass-dependent fashion across five different HisGS masses, at low temperatures. Surprisingly, the effect is not linked to the chemical step, but to fast motions governing product release in the activated enzyme. Disruption of a specific enzyme-product interaction abolishes the isotope effects. Results highlight how altered protein mass perturbs allosterically modulated thermal motions relevant to the catalytic cycle beyond the chemical step.Peer reviewe

Crystal structure, steady-state and pre-steady-state kinetics of Acinetobacter baumannii ATP phosphoribosyltransferase

Funding: This work was supported by the Biotechnology and Biological Sciences Research Council (BBSRC) (grant BB/M010996/1) via an EASTBIO Doctoral Training Partnership studentship to B.J.R.The first step of histidine biosynthesis in Acinetobacter baumannii, the condensation of ATP and 5-phospho-α-d-ribosyl-1-pyrophosphate to produce N1-(5-phospho-β-d-ribosyl)-ATP (PRATP) and pyrophosphate, is catalyzed by the hetero-octameric enzyme ATP phosphoribosyltransferase, a promising target for antibiotic design. The catalytic subunit, HisGS, is allosterically activated upon binding of the regulatory subunit, HisZ, to form the hetero-octameric holoenzyme (ATPPRT), leading to a large increase in kcat. Here, we present the crystal structure of ATPPRT, along with kinetic investigations of the rate-limiting steps governing catalysis in the nonactivated (HisGS) and activated (ATPPRT) forms of the enzyme. A pH-rate profile showed that maximum catalysis is achieved above pH 8.0. Surprisingly, at 25 °C, kcat is higher when ADP replaces ATP as substrate for ATPPRT but not for HisGS. The HisGS-catalyzed reaction is limited by the chemical step, as suggested by the enhancement of kcat when Mg2+ was replaced by Mn2+, and by the lack of a pre-steady-state burst of product formation. Conversely, the ATPPRT-catalyzed reaction rate is determined by PRATP diffusion from the active site, as gleaned from a substantial solvent viscosity effect. A burst of product formation could be inferred from pre-steady-state kinetics, but the first turnover was too fast to be directly observed. Lowering the temperature to 5 °C allowed observation of the PRATP formation burst by ATPPRT. At this temperature, the single-turnover rate constant was significantly higher than kcat, providing additional evidence for a step after chemistry limiting catalysis by ATPPRT. This demonstrates allosteric activation by HisZ accelerates the chemical step.Publisher PDFPeer reviewe

Love Letters for Liberatory Futures

This collection of letters serves to explore the narratives of a collective of women of color in academia by examining individual, collective, spiritual, and institutional strategies for surviving and transforming our institutional spaces and the ways that White Supremacy has shaped our journeys. Multiple perspectives are viewed, and we have written to our children, our future social work students, our future selves, our BIPOC faculty siblings, and our feared enemies to envision and embody more liberatory futures. Keywords: liberation, academia, BIPOC faculty, institutional racism, White Supremac

Extracting Br(omega->pi^+ pi^-) from the Time-like Pion Form-factor

We extract the G-parity-violating branching ratio Br(omega->pi^+ pi^-) from the effective rho-omega mixing matrix element Pi_{rho omega}(s), determined from e^+e^- -> pi^+ pi^- data. The omega->pi^+ pi^- partial width can be determined either from the time-like pion form factor or through the constraint that the mixed physical propagator D_{rho omega}^{mu nu}(s) possesses no poles. The two procedures are inequivalent in practice, and we show why the first is preferred, to find finally Br(omega->pi^+ pi^-) = 1.9 +/- 0.3%.Comment: 12 pages (published version

Geometric Phase, Curvature, and Extrapotentials in Constrained Quantum Systems

We derive an effective Hamiltonian for a quantum system constrained to a submanifold (the constraint manifold) of configuration space (the ambient space) by an infinite restoring force. We pay special attention to how this Hamiltonian depends on quantities which are external to the constraint manifold, such as the external curvature of the constraint manifold, the (Riemannian) curvature of the ambient space, and the constraining potential. In particular, we find the remarkable fact that the twisting of the constraining potential appears as a gauge potential in the constrained Hamiltonian. This gauge potential is an example of geometric phase, closely related to that originally discussed by Berry. The constrained Hamiltonian also contains an effective potential depending on the external curvature of the constraint manifold, the curvature of the ambient space, and the twisting of the constraining potential. The general nature of our analysis allows applications to a wide variety of problems, such as rigid molecules, the evolution of molecular systems along reaction paths, and quantum strip waveguides.Comment: 27 pages with 1 figure, submitted to Phys. Rev.

A strap-on monitoring system for rail car applications

A joint Sandia National Laboratories, University of New Mexico, and New Mexico Engineering Research Institute project to investigate an architecture implementing real-time monitoring and tracking technologies in the railroad industry is presented. The work examines a strap-on sensor package, designed as a value-added component, integrated into existing industry systems and standards. As applied to freight trains, the sensors` primary purpose is to minimize operating costs by decreasing losses due to theft, and by reducing the number, severity, and a consequence of hazardous materials incidents. Product requirements are based on a cost-benefit analysis of operating losses. Results of a concept validation experiment conducted on a revenue generating train are reported

Electromagnetic form factors of light vector mesons

The electromagnetic form factors G_E(q^2), G_M(q^2), and G_Q(q^2), charge radii, magnetic and quadrupole moments, and decay widths of the light vector mesons rho^+, K^{*+} and K^{*0} are calculated in a Lorentz-covariant, Dyson-Schwinger equation based model using algebraic quark propagators that incorporate confinement, asymptotic freedom, and dynamical chiral symmetry breaking, and vector meson Bethe-Salpeter amplitudes closely related to the pseudoscalar amplitudes obtained from phenomenological studies of pi and K mesons. Calculated static properties of vector mesons include the charge radii and magnetic moments: r_{rho+} = 0.61 fm, r_{K*+} = 0.54 fm, and r^2_{K*0} = -0.048 fm^2; mu_{rho+} = 2.69, mu_{K*+} = 2.37, and mu_{K*0} = -0.40. The calculated static limits of the rho-meson form factors are similar to those obtained from light-front quantum mechanical calculations, but begin to differ above q^2 = 1 GeV^2 due to the dynamical evolution of the quark propagators in our approach.Comment: 8 pages of RevTeX, 5 eps figure

Pitch canker fungus, Fusarium circinatum : implications for South African forestry

Fusarium circinatum, the causal agent of pitch canker of mature pines and root/collar rot of pine seedlings/cuttings, has resulted in large-scale losses to pine forestry in various parts of the world. The disease caused by this fungus is now regarded as one of the most important threats to pine plantations by a pathogen. Fusarium circinatum was first discovered in South Africa in 1990 where it infected Pinus patula seedlings in a nursery. Subsequently, the pathogen spread to pine nurseries in all other parts of the country, where it affects several Pinus species. Fusarium circinatum then appeared in the field where it has resulted in large-scale mortality of mostly young P. patula seedlings after planting. Pitch canker first appeared on mature P. radiata in 2006 and sporadic outbreaks of the disease have occurred subsequently on this species and on P. greggii in the western, southern and north-eastern Cape. Pinus patula is the most important softwood species grown in South Africa, comprising 50% of all softwoods planted, and is highly susceptible to F. circinatum. The pathogen, therefore, poses a potentially devastating threat to the future sustainability of the South African softwood industry. Strategic measures to minimise further spread are urgently needed. This review presents an overview of the impact that F. circinatum has had on South African forestry, and it considers the long-term prospects for pine forestry in the country as this relates to the presence of the pitch canker fungus.http://www.tandfonline.com/loi/tsfs2

Scaling algebras and pointlike fields: A nonperturbative approach to renormalization

We present a method of short-distance analysis in quantum field theory that does not require choosing a renormalization prescription a priori. We set out from a local net of algebras with associated pointlike quantum fields. The net has a naturally defined scaling limit in the sense of Buchholz and Verch; we investigate the effect of this limit on the pointlike fields. Both for the fields and their operator product expansions, a well-defined limit procedure can be established. This can always be interpreted in the usual sense of multiplicative renormalization, where the renormalization factors are determined by our analysis. We also consider the limits of symmetry actions. In particular, for suitable limit states, the group of scaling transformations induces a dilation symmetry in the limit theory.Comment: minor changes and clarifications; as to appear in Commun. Math. Phys.; 37 page