Conrad Steenberg

UNLABELLED: The Nucleic Acid Package (NUPACK) is a growing software suite for the analysis and design of nucleic acid systems. The NUPACK web server (http://www.nupack.org) currently enables: ANALYSIS: thermodynamic analysis of dilute solutions of interacting nucleic acid strands. DESIGN: sequence design for complexes of nucleic acid strands intended to adopt a target secondary structure at equilibrium.Utilities: evaluation, display, and annotation of equilibrium properties of a complex of nucleic acid strands. NUPACK algorithms are formulated in terms of nucleic acid secondary structure. In most cases, pseudoknots are excluded from the structural ensemble.

Interstellar pickup ions accelerated by the termination shock of the solar wind dominate the anomalous cosmic-ray (ACR) intensities observed by the Voyager spacecraft in the outer heliosphere. Using a two-dimensional acceleration and propagation model, we derive the relative abundances of these interstellar ACRs and determine the mass dependence of the injection/acceleration efficiency for the diffusive acceleration of H^+, He^+, N^+, O^+, and Ne^+. The energy spectra of C, Na, Mg, Si, S, and Ar also exhibit ACR increases at low energies. To interpret these observations, we have developed a new set of ionization rates for 11 neutral atoms, H, He, C, N, O, Ne, Na, Mg, Si, S, and Ar at 1 AU, and a new set of filtration factors relating neutral densities in the local interstellar medium to those at the location of the solar wind termination shock. Using the injection/acceleration efficiencies and the Ar filtration factor, we estimate the density of neutral Ar to be (3.5 ± 1.6) × 10^(-7) cm^(-3) in the local interstellar medium. ACR C may have a significant contribution from interstellar neutral C, but the observed intensities of ACR Na, Mg, Si, and S significantly exceed that expected from interstellar neutrals, providing evidence of another source of pickup ions. One possibility discussed is the recently discovered "inner source" of singly charged ions that is thought to be solar wind atoms desorbed from interplanetary dust grains.

The Grid2003 Project has deployed a multivirtual organization, application-driven grid laboratory (Grid3) that has sustained for several months the production-level services required by physics experiments of the Large Hadron Collider at CERN (ATLAS and CMS), the Sloan Digital Sky Survey project, the gravitational wave search experiment LIGO, the BTeV experiment at Fermilab, as well as applications in molecular structure analysis and genome analysis, and computer science research projects in such areas as job and data scheduling. The deployed infrastructure has been operating since November 2003 with 27 sites, a peak of 2800 processors, work loads from 10 different applications exceeding 1300 simultaneous jobs, and data transfers among sites of greater than 2 TB/day. We describe the principles that have guided the development of this unique infrastructure and the practical experiences that have resulted from its creation and use. We discuss application requirements for grid services deployment and configuration, monitoring infrastructure, application performance, metrics, and operational experiences. We also summarize lessons learned.

The Grid2003 Project has deployed a multivirtual organization, application-driven grid laboratory ("Grid3") that has sustained for several months the production-level services required by physics experiments of the Large Hadron Collider at CERN (ATLAS and CMS), the Sloan Digital Sky Survey project, the gravitational wave search experiment LIGO, the BTeV experiment at Fermilab, as well as applications in molecular structure analysis and genome analysis, and computer science research projects in such areas as job and data scheduling. The deployed infrastructure has been operating since November 2003 with 27 sites, a peak of 2800 processors, work loads from 10 different applications exceeding 1300 simultaneous jobs, and data transfers among sites of greater than 2 TB/day. We describe the principles that have guided the development of this unique infrastructure and the practical experiences that have resulted from its creation and use. We discuss application requirements for grid services deployment and configuration, monitoring infrastructure, application performance, metrics, and operational experiences. We also summarize lessons learned.

A modulation model that includes shock acceleration of cosmic rays at the solar wind termination shock is used to study the characteristics of anomalous cosmic ray hydrogen, guided by the 1987 solar minimum spectra as observed by IMP 8, Voyager 2, and Pioneer 10. This first attempt at a comprehensive data fit excludes the effects of drifts and must therefore be considered as preliminary. It is found that an anomalous component dominates hydrogen spectra in the outer heliosphere but, due to large radial gradients, the anomalous contribution in the inner heliosphere is negligible. Similar model fits are shown for anomalous cosmic ray He and O to demonstrate the degree of internal consistency of the model.