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

Communicating Josephson Qubits

We propose a scheme to implement a quantum information transfer protocol with a superconducting circuit and Josephson charge qubits. The information exchange is mediated by an L-C resonator used as a data bus. The main decoherence sources are analyzed in detail.Comment: 4 pages, 2 figure

Measurement of pH. Definition, standards, and procedures (IUPAC Recommendations 2002)

The definition of a "primary method of measurement" [1] has permitted a full consideration of the definition of primary standards for pH, determined by a primary method (cell without transference, Harned cell), of the definition of secondary standards by secondary methods, and of the question whether pH, as a conventional quantity, can be incorporated within the internationally accepted system of measurement, the International System of Units (SI, Syst\ue8me International d'Unit\ue9s). This approach has enabled resolution of the previous compromise IUPAC 1985 Recommendations [2]. Furthermore, incorporation of the uncertainties for the primary method, and for all subsequent measurements, permits the uncertainties for all procedures to be linked to the primary standards by an unbroken chain of comparisons. Thus, a rational choice can be made by the analyst of the appropriate procedure to achieve the target uncertainty of sample pH. Accordingly, this document explains IUPAC recommended definitions, procedures, and terminology relating to pH measurements in dilute aqueous solutions in the temperature range 5-50 \ub0C. Details are given of the primary and secondary methods for measuring pH and the rationale for the assignment of pH values with appropriate uncertainties to selected primary and secondary substances

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

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

PAMOP: Petascale atomic, molecular and optical collision calculations

Petaflop architectures are currently being utilized efficiently to perform large scale computations in Atomic, Molecular and Optical Collisions. We solve the Schr\"odinger 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. In this report, various examples are shown from our theoretical results compared with experimental results obtained from Synchrotron Radiation facilities where the Cray architecture at HLRS is playing an integral part in our computational projects.Comment: 16 pages, 6 figures, Chapter 4, in High Performance Computing in Science and Engineering 2014, edited by W. E. Nagel, D. B. Kroner, and M. Reich (Springer, New York and Berlin, 2014). http://www.springer.com/mathematics/computational+science+%26+engineering/book/978-3-319-10809-

Photoionization of Sc2+ ions by synchrotron radiation: High resolution measurements and absolute cross sections in the photon energy range 23-68 eV

Cross sections for photoionization of doubly-charged scandium ions has been measured using a merged-beams technique. Results are compared with the time-reversed process of photorecombination