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Publications 1 - 10 of 93- Mengxing Cheng, Matthew T. Glossop, and Kevin Ingersent , Quantum phase transitions in a charge-coupled Bose-Fermi Anderson model
Phys. Rev. B 80, 165113 (2009), 2009-10-09
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- Clay Hughes, James Poe, Amer Qouneh, and Tao L, On the (Dis)similarity of Transactional Memory Workloads
International Symposium on Workload Characterization (IISWC), 2009-10-03
Abstract [+]: Abstract— Programming to exploit the resources in a multicore system remains a major obstacle for both computer and software engineers. Transactional memory offers an attractive alternative to traditional concurrent programming but implementations emerged before the programming model, leaving a gap in the design process. In previous research, transactional microbenchmarks have been used to evaluate designs or lock-based multithreaded workloads have been manually converted into their transactional equivalents; others have even created dedicated transactional benchmarks. Yet, throughout all of the investigations, transactional memory researchers have not settled on a way to describe the runtime characteristics that these programs exhibit; nor has there been any attempt to unify the way transactional memory implementations are evaluated. In addition, the similarity (or redundancy) of these workloads is largely unknown. Evaluating transactional memory designs using workloads that exhibit similar characteristics will unnecessarily increase the number of simulations without contributing new insight. On the other hand, arbitrarily choosing a subset of transactional memory workloads for evaluation can miss important features and lead to biased or incorrect conclusions.
In this work, we propose a set of architecture-independent transaction-oriented workload characteristics that can accurately capture the behavior of transactional code. We apply principle
component analysis and clustering algorithms to analyze the proposed workload characteristics collected from a set of SPLASH-2, STAMP, and PARSEC transactional memory programs. Our results show that using transactional characteristics to cluster the chosen benchmarks can reduce the number of required simulations by almost half. We also show that the methods presented in this paper can be used to identify specific feature subsets. With the increasing number of TM workloads in the future, we believe that the proposed transactional memory workload characterization techniques will help TM architects select a small, diverse, set of TM workloads for their design evaluation.
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- James Poe, Clay Hughes, and Tao Li, TransPlant: A Parameterized Methodology For Generating Transactional Memory Workloads
International Symposium on Modeling, Analysis, and Simulation of Computer and Telecommunication Systems (MASCOTS), 2009-09-21
Abstract [+]: Transactional memory provides a means to bridge the discrepancy between programmer productivity and the difficulty in exploiting thread-level parallelism gains offered by emerging chip multiprocessors. Because the hardware has outpaced the software, there are very few modern multithreaded benchmarks available and even fewer for transactional memory researchers. This hurdle must be overcome for transactional memory research to mature and to gain widespread acceptance. Currently, for performance evaluations, most researchers rely on manually converted lock-based multithreaded workloads or the small group of programs written explicitly for transactional memory. Using converted benchmarks is problematic because they have been tuned so well that they may not be representative of how a programmer will actually use transactional memory. Hand coding stressor benchmarks is unattractive because it is tedious and time consuming. A new parameterized methodology that can automatically generate a program based on the desired high-level program characteristics benefits the transactional memory community.
In this work, we propose techniques to generate parameterized transactional memory benchmarks based on a feature set, decoupled from the underlying transactional model. Using principle component analysis, clustering, and raw transactional performance metrics, we show that TransPlant can generate benchmarks with features that lie outside the boundary occupied by these traditional benchmarks. We also show how TransPlant can mimic the behavior of SPLASH-2 and STAMP transactional memory workloads. The program generation methods proposed here will help transactional memory architects select a robust set of programs for quick design evaluations.
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- Mishra, V.; Vorontsov, A.; Hirschfeld, P. J.; Vekhter, I., Theory of thermal conductivity in extended-state superconductors: application to ferropnictides
eprint arXiv:0907.4657, 2009-07-01
- Tao Liang, Simon R. Phillpot, and Susan B. Sinnott, Parametrization of a reactive many-body potential for Mo–S systems
Phys. Rev. B 79, 245110, 2009-06-08
Abstract [+]: We present an interatomic potential for the Mo-S system based on the second-generation reactive empirical bond-order formalism. An analytic function is introduced to the bond-order term to capture the effect of the coordination number on the binding energy. The fitting scheme used for this potential is optimized by appropriate selection of the functions, training databases, initial guesses, and weights on each residual—the four factors that are involved in a weighted nonlinear least-squares fitting. The resulting potential is able to yield good agreement with the structure and energetics of Mo molecules, two-dimensional Mo structures, three-dimensional Mo crystals, small S molecules, and binary Mo-S crystal structures. We illustrate the capabilities of the new potential by presenting results of the simulation of friction between MoS2 layers. The results are consistent with our previous static potential surface calculations using density-functional theory.
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- A. F. Kemper, H-P. Cheng, N. Kébaïli, S. Benrezzak, M. Schmidt, A. Masson, and C. Bréchignac , Curvature effect on the interaction between folded graphitic surface and silver clusters
Phys. Rev. B 79, 193403 (2009), 2009-05-08
Abstract [+]: Evidence of curvature effects on the interaction and binding of silver clusters on folded graphitic surfaces has been shown from both experiment and theory. Density functional theory (DFT) calculations within the local density and generalized gradient approximations have been performed for the structural relaxation of both Ag and Ag2 on curved surfaces, showing a crossover from chemical to physical behavior. Using Lennard-Jones potential to model the interaction between a single cluster and the graphite surface, evidence is found for the curvature effect on the binding of silver nanoparticles to folding graphitic surfaces. The theoretical results are compared to scanning electron microscopy and atomic force microscopy images of samples obtained from preformed silver cluster deposition on carboneous substrates exhibiting anisotropic pleat structures.
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- Yijun Sun, Yunpeng Cai, Li Liu, Fahong Yu, Michael L. Farrell, William McKendree and William Farmerie, ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences
Nucleic Acids Research, 2009-05-05
Abstract [+]: Recent metagenomics studies of environmental samples suggested that microbial communities are much more diverse than previously reported, and deep sequencing will significantly increase the estimate of total species diversity. Massively parallel pyrosequencing technology enables ultra-deep sequencing of complex microbial populations rapidly and inexpensively. However, computational methods for analyzing large collections of 16S ribosomal sequences are limited. We proposed a new algorithm, referred to as ESPRIT, which addresses several computational issues with prior methods. We developed two versions of ESPRIT, one for personal computers (PCs) and one for computer clusters (CCs). The PC version is used for small- and medium-scale data sets and can process several tens of thousands of sequences within a few minutes, while the CC version is for large-scale problems and is able to analyze several hundreds of thousands of reads within one day. Large-scale experiments are presented that clearly demonstrate the effectiveness of the newly proposed algorithm. The source code and user guide are freely available at http://www.biotech.ufl.edu/people/sun/esprit.html.
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- Chen, W.; Andersen, Brian M.; Hirschfeld, P. J., Theory of Resistivity Upturns in Metallic Cuprates
eprint arXiv:0905.1449, 2009-05-01
- Kitchen A, Ehret D, Assefa S, Mulligan CJ, Bayesian phylogenetic analysis of Semitic languages identifies an Early Bronze Age origin of Semitic in the Near East
Proc R Soc B, 2009-04-29
Abstract [+]: The evolution of languages provides a unique opportunity to study human population history. The origin of Semitic and the nature of dispersals by Semitic-speaking populations are of great importance to our understanding of the ancient history of the Middle East and Horn of Africa. Semitic populations are associated with the oldest written languages and urban civilizations in the region, which gave rise to some of the world's first major religious and literary traditions. In this study, we employ Bayesian computational phylogenetic techniques recently developed in evolutionary biology to analyse Semitic lexical data by modelling language evolution and explicitly testing alternative hypotheses of Semitic history. We implement a relaxed linguistic clock to date language divergences and use epigraphic evidence for the sampling dates of extinct Semitic languages to calibrate the rate of language evolution. Our statistical tests of alternative Semitic histories support an initial divergence of Akkadian from ancestral Semitic over competing hypotheses (e.g. an African origin of Semitic). We estimate an Early Bronze Age origin for Semitic approximately 5750 years ago in the Levant, and further propose that contemporary Ethiosemitic languages of Africa reflect a single introduction of early Ethiosemitic from southern Arabia approximately 2800 years ago.
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- Brian M. Andersen and P. J. Hirschfeld, Extinction of quasiparticle interference in underdoped cuprates with coexisting order
Phys. Rev. B 79, 144515, 2009-04-20
Abstract [+]: Scanning tunneling spectroscopy (STS) measurements [Y. Kohsaka et al., Nature (London) 454, 1072 (2008)] have shown that dispersing quasiparticle interference (QPI) peaks in Fourier-transformed conductance maps disappear as the bias voltage exceeds a certain threshold corresponding to the coincidence of the contour of constant quasiparticle energy with the period-doubled (e.g., antiferromagnetic) zone boundary. Here we show that this may be caused by coexisting order present in the d-wave superconducting phase. We show explicitly how QPI peaks are extinguished in the situation with coexisting long-range spin-density wave order and discuss the connection with the more realistic case where short-range order is created by quenched disorder. Since it is the localized QPI peaks rather than the underlying antinodal states themselves which are destroyed at a critical bias, our proposal resolves a conflict between STS and photoemission spectroscopy regarding the nature of these states. We also study the momentum-summed density of states in the coexisting phase and show how the competing order produces a kink inside the “V”-shaped d-wave superconducting gap in agreement with recent STS measurements [J. W. Alldredge et al., Nat. Phys. 4, 319 (2008)].
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