On the basis for ELF - An Extensible Language Facility

Computer language for data processing and information retrieva

Using Pilot Systems to Execute Many Task Workloads on Supercomputers

High performance computing systems have historically been designed to support applications comprised of mostly monolithic, single-job workloads. Pilot systems decouple workload specification, resource selection, and task execution via job placeholders and late-binding. Pilot systems help to satisfy the resource requirements of workloads comprised of multiple tasks. RADICAL-Pilot (RP) is a modular and extensible Python-based pilot system. In this paper we describe RP's design, architecture and implementation, and characterize its performance. RP is capable of spawning more than 100 tasks/second and supports the steady-state execution of up to 16K concurrent tasks. RP can be used stand-alone, as well as integrated with other application-level tools as a runtime system

Cyclotron resonant scattering feature simulations. I. Thermally averaged cyclotron scattering cross sections, mean free photon-path tables, and electron momentum sampling

Electron cyclotron resonant scattering features (CRSFs) are observed as absorption-like lines in the spectra of X-ray pulsars. A significant fraction of the computing time for Monte Carlo simulations of these quantum mechanical features is spent on the calculation of the mean free path for each individual photon before scattering, since it involves a complex numerical integration over the scattering cross section and the (thermal) velocity distribution of the scattering electrons. We aim to numerically calculate interpolation tables which can be used in CRSF simulations to sample the mean free path of the scattering photon and the momentum of the scattering electron. The tables also contain all the information required for sampling the scattering electron's final spin. The tables were calculated using an adaptive Simpson integration scheme. The energy and angle grids were refined until a prescribed accuracy is reached. The tables are used by our simulation code to produce artificial CRSF spectra. The electron momenta sampled during these simulations were analyzed and justified using theoretically determined boundaries. We present a complete set of tables suited for mean free path calculations of Monte Carlo simulations of the cyclotron scattering process for conditions expected in typical X-ray pulsar accretion columns (0.01<B/B_{crit}<=0.12, where B_{crit}=4.413x10^{13} G and 3keV<=kT<15keV). The sampling of the tables is chosen such that the results have an estimated relative error of at most 1/15 for all points in the grid. The tables are available online at http://www.sternwarte.uni-erlangen.de/research/cyclo.Comment: A&A, in pres

Kinesiology Tape: A Descriptive Survey of Healthcare Professionals in the United States

# Background The existing body of kinesiology tape (KT) research reveals inconsistent results which challenges the efficacy of the intervention. Understanding professional beliefs and KT clinical application might provide insight for future research and development of evidence-based guidelines. # Purpose The purpose of this study was to survey and document the beliefs and clinical application methods of KT among healthcare professionals in the United States. # Design Cross-sectional survey study. # Methods A 30-question online survey was emailed to members of the National Athletic Trainers Association, Academy of Orthopedic Physical Therapy, and American Academy of Sports Physical Therapy. Professionals were also informed through a recruitment post in different private healthcare Facebook groups. # Results One thousand and eighty-three respondents completed the survey. Most respondents used KT for post-injury treatment (74%), pain modulation (67%), and neuro-sensory feedback (60%). Most believed that KT stimulates skin mechanoreceptors (77%), improve local circulation (69%), and modulates pain (60%). Some respondents believed KT only created a placebo effect (40%) and use it for such therapeutic purposes (58%). Most used a standard uncut roll (67%) in black (71%) or beige (66%). Most respondents did not use any specialty pre-cut tape (83%), infused tape (99.54%), or a topical analgesic with tape (65%). The most common tape tension lengths used by respondents were 50% tension (47%) and 25% (25%) tension. Patient reported outcomes (80%) were the most common clinical measures. Most respondents provided skin prep (64%) and tape removal (77%) instructions. Some did not provide any skin prep (36%) or tape removal (23%) instruction. The average recommended times to wear KT were two to three days (60%). The maximum times ranged from two to five days (81%). # Conclusion This survey provides insight into how professionals use KT and highlights the gap between research and practice. Future research should address these gaps to better determine evidence-based guidelines. # Level of Evidence

Molecular dynamics simulation of multivalent ion mediated DNA attraction

All atom molecular dynamics simulations with explicit water were done to study the interaction between two parallel double-stranded DNA molecules in the presence of the multivalent counterions putrescine (2+), spermidine (3+), spermine (4+) and cobalt hexamine (3+). The inter-DNA interaction potential is obtained with the umbrella sampling technique. The attractive force is rationalized in terms of the formation of ion bridges, i.e. multivalent ions which are simultaneously bound to the two opposing DNA molecules. The lifetime of the ion bridges is short on the order of a few nanoseconds.Comment: 4 pages, 5 figures, to be published in Physical Review Letter

Wringing out DNA

The chiral nature of DNA plays a crucial role in cellular processes. Here we use magnetic tweezers to explore one of the signatures of this chirality, the coupling between stretch and twist deformations. We show that the extension of a stretched DNA molecule increases linearly by 0.42 nm per excess turn applied to the double helix. This result contradicts the intuition that DNA should lengthen as it is unwound and get shorter with overwinding. We then present numerical results of energy minimizations of torsionally restrained DNA that display a behaviour similar to the experimental data and shed light on the molecular details of this surprising effect.Comment: 4 pages revtex4, 4 figure

Online Content : Physical and Structural Techniques Applied to Nucleic Acids

This chapter looks at the physical and structural techniques that can be applied to nucleic acids. The first few sections focus on spectroscopic techniques, nuclear magnetic resonance, mass spectrometry and diffraction techniques. The following sections explore cryogenic electron microscopy, optical microscopy, atomic force microscopy and electrophoresis. Chromatographic methods, centrifugation and light scattering techniques are also discussed. Finally, the chapter concludes with sections on thermodynamic analysis, molecular mechanics and dynamics, and QM/MM methods for modelling nucleic acids reactions

The effect of S-substitution at the O6-guanine site on the structure and dynamics of a DNA oligomer containing a G:T mismatch

The effect of S-substitution on the O6 guanine site of a 13-mer DNA duplex containing a G:T mismatch is studied using molecular dynamics. The structure, dynamic evolution and hydration of the S-substituted duplex are compared with those of a normal duplex, a duplex with Ssubstitution on guanine, but no mismatch and a duplex with just a G:T mismatch. The S-substituted mismatch leads to cell death rather than repair. One suggestion is that the G:T mismatch recognition protein recognises the S-substituted mismatch (GS:T) as G:T. This leads to a cycle of futile repair ending in DNA breakage and cell death. We find that some structural features of the helix are similar for the duplex with the G:T mismatch and that with the S-substituted mismatch, but differ from the normal duplex, notably the helical twist. These differences arise from the change in the hydrogen-bonding pattern of the base pair. However a marked feature of the S-substituted G:T mismatch duplex is a very large opening. This showed considerable variability. It is suggested that this enlarged opening would lend support to an alternative model of cell death in which the mismatch protein attaches to thioguanine and activates downstream damage-response pathways. Attack on the sulphur by reactive oxygen species, also leading to cell death, would also be aided by the large, variable opening