Results of 2013 Survey of Parallel Computing Needs Focusing on NSF-funded Researchers

The field of supercomputing is experiencing a rapid change in system structure, programming models, and software environments in response to advances in application requirements and in underlying enabling technologies. Traditional parallel programming approaches have relied on static resource allocation and task scheduling through programming interfaces such as MPI and OpenMP. These methods are reaching their efficiency and scalability limits on the new emerging classes of systems, spurring the creation of innovative dynamic strategies and software tools, including advanced runtime system software and programming interfaces that use them. To accelerate adoption of these next-generation methods, Indiana University is investigating the creation of a single supported Reconfigurable Execution Framework Testbed (REFT) to be used by parallel application algorithm developers as well as researchers in advanced tools for parallel computing. These investigations are funded by the National Science Foundation Award Number 1205518 to Indiana University with Thomas Sterling as Principal Investigator, and Maciej Brodowicz, Matthew R. Link, Andrew Lumsdaine, and Craig Stewart as Co-Principal Investigators. As a starting point in this research we proposed to assess needs in parallel computing in general and needs for software tools and testbeds in particular within the NSF-funded research community. As one set of data toward understanding these needs, we conducted a survey of researchers funded by the National Science Foundation. Because of the strong possibility of distinct needs of researchers funded by what is now the Division of Advanced Cyberinfrastructure, researchers funded by the other divisions of the Computer and Information Sciences and Engineering Directorate, and researchers funded by the remainder of the NSF, we surveyed these populations separately. The report states the methods and summarize survey results. The data sets and copies of SPSS descriptive statistics describing the data are available online at http://hdl.handle.net/2022/19924.National Science Foundation Award Number 120551

Ice-lens formation and geometrical supercooling in soils and other colloidal materials

We present a new, physically-intuitive model of ice-lens formation and growth during the freezing of soils and other dense, particulate suspensions. Motivated by experimental evidence, we consider the growth of an ice-filled crack in a freezing soil. At low temperatures, ice in the crack exerts large pressures on the crack walls that will eventually cause the crack to split open. We show that the crack will then propagate across the soil to form a new lens. The process is controlled by two factors: the cohesion of the soil, and the geometrical supercooling of the water in the soil; a new concept introduced to measure the energy available to form a new ice lens. When the supercooling exceeds a critical amount (proportional to the cohesive strength of the soil) a new ice lens forms. This condition for ice-lens formation and growth does not appeal to any ad hoc, empirical assumptions, and explains how periodic ice lenses can form with or without the presence of a frozen fringe. The proposed mechanism is in good agreement with experiments, in particular explaining ice-lens pattern formation, and surges in heave rate associated with the growth of new lenses. Importantly for systems with no frozen fringe, ice-lens formation and frost heave can be predicted given only the unfrozen properties of the soil. We use our theory to estimate ice-lens growth temperatures obtaining quantitative agreement with the limited experimental data that is currently available. Finally we suggest experiments that might be performed in order to verify this theory in more detail. The theory is generalizable to complex natural-soil scenarios, and should therefore be useful in the prediction of macroscopic frost heave rates.Comment: Submitted to PR

Calibration and Control of a Redundant Robotic Workcell for Milling Tasks

This article deals with the tuning of a complex robotic workcell of eight joints devoted to milling tasks. It consists of a KUKA (TM) manipulator mounted on a linear track and synchronised with a rotary table. Prior to any machining, the additional joints require an in situ calibration in an industrial environment. For this purpose, a novel planar calibration method is developed to estimate the external joint configuration parameters by means of a laser displacement sensor and avoiding direct contact with the pattern. Moreover, a redundancy resolution scheme on the joint rate level is integrated within a computer aided manufacturing system for the complete control of the workcell during the path tracking of a milling task. Finally, the whole system is tested in the prototyping of an orographic model.Andres De La Esperanza, FJ.; Gracia Calandin, LI.; Tornero Montserrat, J. (2011). Calibration and Control of a Redundant Robotic Workcell for Milling Tasks. International Journal of Computer Integrated Manufacturing. 24(6):561-573. doi:10.1080/0951192X.2011.566284S56157324

Why we need signed poetry in bilingual education

A truly bilingual and bicultural education for deaf children requires them to learn about the deaf art-form of sign language poetry. In this article I outline the advantages and challenges of doing this. Reviewing the scarce literature on teaching deaf children signed poetry, whether translated or original, I relate it to the use of literature in L2-learning settings. Reflections of deaf teacher-poets from the UK show that deaf children readily relate to signed poetry, and with informed language focus from teachers it helps them to develop a range of language skills, and express their emotions. Barriers to this, however, include lack of training and awareness for both deaf and hearing teachers - even when the teachers are poets

Developing Single-Molecule TPM Experiments for Direct Observation of Successful RecA-Mediated Strand Exchange Reaction

RecA recombinases play a central role in homologous recombination. Once assembled on single-stranded (ss) DNA, RecA nucleoprotein filaments mediate the pairing of homologous DNA sequences and strand exchange processes. We have designed two experiments based on tethered particle motion (TPM) to investigate the fates of the invading and the outgoing strands during E. coli RecA-mediated pairing and strand exchange at the single-molecule level in the absence of force. TPM experiments measure the tethered bead Brownian motion indicative of the DNA tether length change resulting from RecA binding and dissociation. Experiments with beads labeled on either the invading strand or the outgoing strand showed that DNA pairing and strand exchange occurs successfully in the presence of either ATP or its non-hydrolyzable analog, ATPγS. The strand exchange rates and efficiencies are similar under both ATP and ATPγS conditions. In addition, the Brownian motion time-courses suggest that the strand exchange process progresses uni-directionally in the 5′-to-3′ fashion, using a synapse segment with a wide and continuous size distribution

Structural basis for inhibition of homologous recombination by the RecX protein

The RecA/RAD51 nucleoprotein filament is central to the reaction of homologous recombination (HR). Filament activity must be tightly regulated in vivo as unrestrained HR can cause genomic instability. Our mechanistic understanding of HR is restricted by lack of structural information about the regulatory proteins that control filament activity. Here, we describe a structural and functional analysis of the HR inhibitor protein RecX and its mode of interaction with the RecA filament. RecX is a modular protein assembled of repeated three-helix motifs. The relative arrangement of the repeats generates an elongated and curved shape that is well suited for binding within the helical groove of the RecA filament. Structure-based mutagenesis confirms that conserved basic residues on the concave side of RecX are important for repression of RecA activity. Analysis of RecA filament dynamics in the presence of RecX shows that RecX actively promotes filament disassembly. Collectively, our data support a model in which RecX binding to the helical groove of the filament causes local dissociation of RecA protomers, leading to filament destabilisation and HR inhibition

Por que precisamos de poesia sinalizada em educação bilíngue

Uma verdadeira educação bilíngue e bicultural para crianças surdas requer que elas aprendam a forma de arte surda de poesia em língua de sinais. Neste artigo apresento as vantagens e desvantagens de se fazer isto. Revisando a escassa literatura sobre o ensino de poesia sinalizada para crianças surdas, seja traduzida ou original, eu a relaciono ao uso de literatura em cenários de aprendizagem de L2. Reflexões de professores-poetas surdos do Reino Unido mostram que a criança surda prontamente se simpatiza com a poesia sinalizada, e com o foco linguístico adequado dos professores, isto as ajuda a desenvolver uma gama de habilidades linguísticas e a expressar suas emoções. Barreiras para isto, contudo, incluem a falta de treinamento e apreensão de professores surdos e ouvintes - mesmo quando os professores são poetas