Petascale computations for Large-scale Atomic and Molecular collisions

Petaflop architectures are currently being utilized efficiently to perform large scale computations in Atomic, Molecular and Optical Collisions. We solve the Schroedinger or Dirac equation for the appropriate collision problem using the R-matrix or R-matrix with pseudo-states approach. We briefly outline the parallel methodology used and implemented for the current suite of Breit-Pauli and DARC codes. Various examples are shown of our theoretical results compared with those obtained from Synchrotron Radiation facilities and from Satellite observations. We also indicate future directions and implementation of the R-matrix codes on emerging GPU architectures.Comment: 14 pages, 5 figures, 3 tables, Chapter in: Workshop on Sustained Simulated Performance 2013, Published by Springer, 2014, edited by Michael Resch, Yevgeniya Kovalenko, Eric Focht, Wolfgang Bez and Hiroaki Kobaysah

Relativistic photoionization cross sections for C II

High resolution measurements of photoionization cross sections for atomic ions are now being made on synchrotron radiation sources. The recent measurements by Kjeldsen etal. (1999) showed good agreement between the observed resonance features and the the theoretical calculations in the close coupling approximation (Nahar 1995). However, there were several observed resonances that were missing in the theoretical predictions. The earlier theoretical calculation was carried out in LS coupling where the relativistic effects were not included. Present work reports photoionization cross sections including the relativistic effects in Breit-Pauli R-matrix (BPRM) approximation. The configuration interaction eigenfunction expansion for the core ion C III consists of 20 fine structure levels dominated by the configurations from 1s^22s^2 to 1s^22s3d. Detailed features in the calculated cross sections exhibit the missing resonances due to fine structure. The results benchmark the accuracy of BPRM photoionization cross sections as needed for recent and ongoing experiments.Comment: 13 pages, 3 figure

Mechanisms of Spontaneous Current Generation in an Inhomogeneous d-Wave Superconductor

A boundary between two d-wave superconductors or an s-wave and a d-wave superconductor generally breaks time-reversal symmetry and can generate spontaneous currents due to proximity effect. On the other hand, surfaces and interfaces in d-wave superconductors can produce localized current-carrying states by supporting the T-breaking combination of dominant and subdominant order parameters. We investigate spontaneous currents in the presence of both mechanisms and show that at low temperature, counter-intuitively, the subdominant coupling decreases the amplitude of the spontaneous current due to proximity effect. Superscreening of spontaneous currents is demonstrated to be present in any d-d (but not s-d) junction and surface with d+id' order parameter symmetry. We show that this supercreening is the result of contributions from the local magnetic moment of the condensate to the spontaneous current.Comment: 4 pages, 5 figures, RevTe

Quasiclassical Theory of Spontaneous Currents at Surfaces and Interfaces of d-Wave Superconductors

We investigate the properties of spontaneous currents generated at surfaces and interfaces of d-wave superconductors using the self-consistent quasiclassical Eilenberger equations. The influence of the roughness and reflectivity of the boundaries on the spontaneous current are studied. We show that these have very different effects at the surfaces compared to the interfaces, which reflects the different nature of the time reversal symmetry breaking states in these two systems. We find a signature of the ``anomalous proximity effect'' at rough d-wave interfaces. We also show that the existence of a subdominant order parameter, which is necessary for time reversal symmetry breaking at the surface, suppresses the spontaneous current generation due to proximity effect at the interface between two superconductors. We associate orbital moments to the spontaneous currents to explain the ``superscreening'' effect, which seems to be present at all ideal d-wave surfaces and interfaces, where d_{xy} is the favorite subdominant symmetry.Comment: 13 pages, 17 postscript figure

Tilt Grain-Boundary Effects in S- and D-Wave Superconductors

We calculate the s- and d-wave superconductor order parameter in the vicinity of a tilt grain boundary. We do this self-consistently within the Bogoliubov de Gennes equations, using a realistic microscopic model of the grain boundary. We present the first self-consistent calculations of supercurrent flows in such boundaries, obtaining the current-phase characteristics of grain boundaries in both s-wave and d-wave superconductors

Older Adults with Cancer: A Randomized Controlled Trial of Occupational and Physical Therapy

OBJECTIVES: The impact of occupational therapy (OT) and physical therapy (PT) on functional outcomes in older adults with cancer is unknown. DESIGN: Two-arm single-institution randomized controlled trial of outpatient OT/PT. SETTING: Comprehensive cancer center with two off-site OT/PT clinics. PARTICIPANTS: We recruited adults 65 years and older with a recent diagnosis or recurrence of cancer within 5 years, with at least one functional limitation as identified by a geriatric assessment. Participants were randomized to OT/PT or usual care. INTERVENTION: Rehabilitation consisted of individualized OT and PT that addressed functional activities and strength/endurance needs. MEASUREMENTS: Primary outcome was functional status as measured by the Nottingham Extended Activities of Daily Living scale. Secondary outcomes were Patient-Reported Outcomes Measurement Information System-Global Mental Health (GMH) and Global Physical Health (GPH), ability to participate in Social Roles (SR), physical function, and activity expectations and self-efficacy (Possibilities for Activity Scale [PActS]). RESULTS: Among those recruited (N = 63), only 45 patients (71%) were evaluable due to loss of follow-up and/or nonreceipt of intervention. The median age was 74 years; 53% were female, and 91% were white. Overall, 30% patients had hematologic malignancies, 30% breast cancer, and 16% colorectal cancers. A total of 65% were in active treatment; 49% had stage 3 or 4 disease. At follow-up, both OT/PT (P =.02) and usual care (P =.03) groups experienced a decline in functional status. PActS scores between groups (P =.04) was significantly improved in the intervention group. GMH and SR met criteria for minimally important clinical difference favoring the intervention, but not statistical significance. Several barriers were noted in the implementation of the intervention program: recruitment, concerns about cost, distance, scheduling, and limited treatment provided. CONCLUSION: OT/PT may positively influence activity expectations and self-efficacy. Future research needs to address significant barriers to implementation to increase use of OT/PT services and access to quality care

Spin-Polarized Transport Across an La0.7_{0.7}Sr0.3_{0.3}MnO3_{3}/YBa2_{2}Cu3_{3}O7_{7} Interface: Role of Andreev Bound States

Transport across an La$_{0.7}$Sr$_{0.3}MnO$_{3}/YBa$_{2}Cu$_{3}$O$_{7}$(LSMO/YBCO), interface is studied as a function of temperature and surface morphology. For comparison, control measurements are performed in non-magnetic heterostructures of LaNiO$_{3}$/YBCO and Ag/YBCO. In all cases, YBCO is used as bottom layer to eliminate the channel resistance and to minimize thermal effects. The observed differential conductance re ects the role of Andreev bound states in a-b planes, and brings out for the first time the suppression of such states by the spin-polarized transport across the interface. The theoretical analysis of the measured data reveals decay of the spin polarization near the LSMO surface with temperature, consistent with the reported photoemission data.Comment: 5 pages LaTeX, 3 eps figures included, accepted by Physical Review

Dissipation and noise in adiabatic quantum pumps

We investigate the distribution function, the heat flow and the noise properties of an adiabatic quantum pump for an arbitrary relation of pump frequency $\omega$ and temperature. To achieve this we start with the scattering matrix approach for ac-transport. This approach leads to expressions for the quantities of interest in terms of the side bands of particles exiting the pump. The side bands correspond to particles which have gained or lost a modulation quantum $\hbar \omega$. We find that our results for the pump current, the heat flow and the noise can all be expressed in terms of a parametric emissivity matrix. In particular we find that the current cross-correlations of a multiterminal pump are directly related a to a non-diagonal element of the parametric emissivity matrix. The approach allows a description of the quantum statistical correlation properties (noise) of an adiabatic quantum pump

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

The chemical compound 'Heatin' stimulates hypocotyl elongation and interferes with the Arabidopsis NIT1-subfamily of nitrilases

Temperature passively affects biological processes involved in plant growth. Therefore, it is challenging to study the dedicated temperature signalling pathways that orchestrate thermomorphogenesis, a suite of elongation growth-based adaptations that enhance leaf-cooling capacity. We screened a chemical library for compounds that restored hypocotyl elongation in the pif4-2-deficient mutant background at warm temperature conditions in Arabidopsis thaliana to identify modulators of thermomorphogenesis. The small aromatic compound 'Heatin', containing 1-iminomethyl-2-naphthol as a pharmacophore, was selected as an enhancer of elongation growth. We show that ARABIDOPSIS ALDEHYDE OXIDASES redundantly contribute to Heatin-mediated hypocotyl elongation. Following a chemical proteomics approach, the members of the NITRILASE1-subfamily of auxin biosynthesis enzymes were identified among the molecular targets of Heatin. Our data reveal that nitrilases are involved in promotion of hypocotyl elongation in response to high temperature and Heatin-mediated hypocotyl elongation requires the NITRILASE1-subfamily members, NIT1 and NIT2. Heatin inhibits NIT1-subfamily enzymatic activity in vitro and the application of Heatin accordingly results in the accumulation of NIT1-subfamily substrate indole-3-acetonitrile in vivo. However, levels of the NIT1-subfamily product, bioactive auxin (indole-3-acetic acid), were also significantly increased. It is likely that the stimulation of hypocotyl elongation by Heatin might be independent of its observed interaction with NITRILASE1-subfamily members. However, nitrilases may contribute to the Heatin response by stimulating indole-3-acetic acid biosynthesis in an indirect way. Heatin and its functional analogues present novel chemical entities for studying auxin biology