Table of Contents

• A learning outcome driven cyber infrastructure for thermodynamics educationSubrata Bhattacharjee, Christopher Paolini, Mahesh Kumar. [doi]
• The data supercellPaul Nowoczynski, Jason Sommerfield, Jared Yanovich, J. Ray Scott, Zhihui Zhang, Michael Levine. [doi]
• What is campus bridging and what is XSEDE doing about it?Craig A. Stewart, Richard Knepper, James Ferguson, Felix Bachmann, Ian T. Foster, Andrew S. Grimshaw, Victor Hazlewood, David Lifka. [doi]
• Roadmaps, not blueprints: paving the way to science gateway successKatherine A. Lawrence, Nancy Wilkins-Diehr. [doi]
• Achieve better performance with PEAK on XSEDE resourcesBilel Hadri, Haihang You, Shirley Moore. [doi]
• The initial role of evaluation in a large-scale multi-site projectLizanne DeStefano, Lorna Rivera. [doi]
• Membrane protein simulations under asymmetric ionic concentrationsFatemeh Khalili-Araghi, Brigitte Ziervogel, Benoît Roux, James C. Gumbart. [doi]
• Optimization of density functional tight-binding and classical reactive molecular dynamics for high-throughput simulations of carbon materialsJacek Jakowski, Bilel Hadri, Steven J. Stuart, Predrag Krstic, Stephan Irle, Dulma Nugawela, Sophya Garashchuk. [doi]
• A distributed memory out-of-core method on HPC clusters and its application to quantum chemistry applicationsChristopher S. Simmons, Karl W. Schulz. [doi]
• Benchmark calculations for multi-photon ionization of the hydrogen molecule and the hydrogen molecular ion by short-pulse intense laser radiationXiaoxu Guan, Klaus Bartschat, Barry I. Schneider. [doi]
• Computational science certificates for the current workforce: lessons learnedSteven I. Gordon, Judith D. Gardiner, Brian Guilfoos. [doi]
• Offline parallel debugging: a case study reportDoug James, Carlos Rosales, Dan Stanzione. [doi]
• High accuracy gravitational waveforms from black hole binary inspirals using OpenCLJustin McKennon, Gary Forrester, Gaurav Khanna 0001. [doi]
• A high throughput workflow environment for cosmological simulationsBrandon M. S. Erickson, Raminderjeet Singh, August E. Evrard, Matthew R. Becker, Michael T. Busha, Andrey V. Kravtsov, Suresh Marru, Marlon E. Pierce, Risa H. Wechsler. [doi]
• Cloud-enabling biological simulations for scalable and sustainable access: an experience reportBina Ramamurthy, Jessica Poulin, Katharina Dittmar. [doi]
• Enhancing chemistry teaching and learning through cyberinfrastructureDavid R. Mattson, R. Jay Mashl, Edee Norman Wiziecki. [doi]
• Massively parallel direct numerical simulations of forced compressible turbulence: a hybrid MPI/OpenMP approachShriram Jagannathan, Diego A. Donzis. [doi]
• Three-dimensional simulations of geometrically complex subduction with large viscosity variationsMargarete A. Jadamec, Magali I. Billen, Oliver Kreylos. [doi]
• Using the XSEDE supercomputing and visualization resources to improve tornado prediction using data miningBradley Pirtle, Ross Kimes, Amy McGovern, Rodger A. Brown. [doi]
• A systematic process for efficient execution on Intel's heterogeneous computation nodesAshay Rane, James C. Browne, Lars Koesterke. [doi]
• Mojave: a development environment for the Cactus computational frameworkHari Krishnan, Dennis G. Castleberry, Steven R. Brandt. [doi]
• A framework for federated two-factor authentication enabling cost-effective secure access to distributed cyberinfrastructureMatthew A. Ezell, Gary L. Rogers, Gregory D. Peterson. [doi]
• Computing MATTERS: building pathways to cyberinfrastructurePatricia Jacobs. [doi]
• Electrostatic screening effects on a model system for molecular electronicsHanning Chen, Xiao Zhu. [doi]
• Exploring similarities among many species distributionsScott Simmerman, Jingyuan Wang, James Osborne 0003, Kimberly Shook, Jian Huang 0007, William Godsoe, Theodore Simons. [doi]
• Analyzing throughput and utilization on trestlesRichard L. Moore, Adam Jundt, Leonard K. Carson, Kenneth Yoshimoto, Amin Ghadersohi, William S. Young. [doi]
• Evaluation of parallel and distributed file system technologies for XSEDEChris Jordan. [doi]
• The CIPRES science gateway: enabling high-impact science for phylogenetics researchers with limited resourcesMark A. Miller, Wayne Pfeiffer, Terri Schwartz. [doi]
• Minority student involvement in computational science research at Texas Southern UniversityM. Farrukh Khan, Daniel Vrinceanu, Kiran Chilakamarri, Christopher John Tymczak. [doi]
• Managing the long tail of science: data and communitiesBeth Plale. [doi]
• High performance mining of social media dataJudith Gelernter, Gang Wu. [doi]
• Quantum algorithms for predicting the properties of complex materialsGrady Schofield, Yousef Saad, James R. Chelikowsky. [doi]
• Radiation modeling using the Uintah heterogeneous CPU/GPU runtime systemAlan Humphrey, Qingyu Meng, Martin Berzins, Todd Harman. [doi]
• The Eclipse parallel tools platform: toward an integrated development environment for XSEDE resourcesJay Alameda, Wyatt Spear, Jeffrey L. Overbey, Kevin A. Huck, Gregory R. Watson, Beth Tibbitts. [doi]
• Exploiting HPC resources for the 3D-time series analysis of caries lesion activityHui Zhang 0006, Huian Li, Michael J. Boyles, Robert Henschel, Eduardo Kazuo Kohara, Masatoshi Ando. [doi]
• The Prickly Pear Archive: a portable hypermedia for scholarly publicationDennis G. Castleberry, Steven R. Brandt, Frank Löffler 0001, Hari Krishnan. [doi]
• Ensemble modeling of storm interaction with XSEDEBrian F. Jewett, Jay C. Alameda, Robert Wilhelmson, Ann M. Syrowski. [doi]
• Computational challenges in nanoparticle partition function calculationEric Jankowski. [doi]
• Trinity RNA-Seq assembler performance optimizationRobert Henschel, Matthias Lieber, Le-Shin Wu, Phillip M. Nista, Brian J. Haas, Richard D. LeDuc. [doi]
• WaterHUB: a resource for students and educators for learning hydrologyVenkatesh Merwade, Wei Feng, Lan Zhao, Carol X. Song. [doi]
• Multiscale simulations of Langmuir cells and submesoscale eddies using XSEDE resourcesLuke P. Van Roekel, Peter E. Hamlington, Baylor Fox-Kemper. [doi]
• Extending parallel scalability of LAMMPS and multiscale reactive molecular simulationsYuxing Peng, Chris Knight 0001, Philip Blood, Lonnie Crosby, Gregory A. Voth. [doi]
• Transforming molecular biology research through extreme acceleration of AMBER molecular dynamics simulations: sampling for the 99%Ross C. Walker, Levi C. T. Pierce, Romelia Salomón-Ferrer. [doi]
• Multiple concurrent queries on demand: large scale video analysis in a flash memory environment as a case for humanities supercomputingVirginia Kuhn, Alan B. Craig, Ritu Arora. [doi]
• A tale of two systems: flexibility of usage of Kraken and Nautilus at the National Institute for Computational SciencesAmy F. Szczepanski, Jian Huang 0007, Sean Ahern, Mark R. Fahey. [doi]
• Longitudinal user and usage patterns in the XSEDE user communityDavid L. Hart. [doi]
• Ultrascan solution modeler: integrated hydrodynamic parameter and small angle scattering computation and fitting toolsEmre H. Brookes, Raminderjeet Singh, Marlon E. Pierce, Suresh Marru, Borries Demeler, Mattia Rocco. [doi]
• Multiscale simulations of blood-flow: from a platelet to an arteryLeopold Grinberg, Mingge Deng, Huan Lei, Joseph A. Insley, George Em Karniadakis. [doi]
• An analysis of GPU utilization trends on the Keeneland initial delivery systemTabitha K. Samuel, Stephen Taylor McNally, John Wynkoop. [doi]
• Building a partnership for computer science educationDiane A. Baxter, Beth Simon. [doi]
• The anatomy of successful ECSS projects: lessons of supporting high-throughput high-performance ensembles on XSEDEMelissa Romanus, Pradeep Kumar Mantha, Matt McKenzie, Thomas C. Bishop, Emilio Gallicchio, André Merzky, Yaakoub El Khamra, Shantenu Jha. [doi]
• Campus bridging pilot project reports: XSEDE12 panelRichard Knepper, Guy Almes, Thorbjörn Axelsson, Paul Muzio, Joel Zysman. [doi]
• Excited states in lattice QCD using the stochastic LapH methodC. Morningstar, J. Bulava, J. Foley, K. J. Juge, C. H. Wong. [doi]
• Using stereoscopic 3D videos to inform the public about the benefits of computational scienceMichael J. Boyles, Albert M. William, Chauncey Frend, Chris Eller. [doi]
• SaaS for science: the path to reality for research in the cloudIan T. Foster, Vas Vasiliadis. [doi]
• A blended, multimodal access eTextBook in computational physicsRubin H. Landau, Manuel J. Paez, Cristian C. Bordeianu. [doi]
• Security for science gateways and campus bridging: XSEDE12 panelJim Basney, Randy Butler, Dan Fraser, Suresh Marru, Craig Stewart. [doi]
• Conducting K-12 outreach to evoke early interest in IT, science, and advanced technologyKristy A. Kallback-Rose, Kurt Seiffert, Danko Antolovic, Therese Miller, Robert Ping, Craig Stewart. [doi]
• Campus bridging made easy via Globus servicesIan T. Foster, Rajkumar Kettimuthu, Stuart Martin, Steven Tuecke, Daniel Milroy, Brock Palen, Thomas Hauser, Jazcek Braden. [doi]
• FutureGrid education: using case studies to develop a curriculum for communicating parallel and distributed computing conceptsJerome E. Mitchell, Judy Qiu, Massimo Canonio, Shantenu Jha, Linda Hayden, Barbara Ann O'Leary, Renato Figueiredo, Geoffrey C. Fox. [doi]
• Comparing the performance of group detection algorithm in serial and parallel processing environmentsChanning Brown, Iftekhar Ahmed 0002, Y. Dora Cai, Marshall Scott Poole, Andrew Pilny, Yannick Atouba Ada. [doi]
• Multiscale modeling of high explosives for transportation accidentsJoseph R. Peterson, Jacqueline C. Beckvermit, Todd Harman, Martin Berzins, Charles A. Wight. [doi]
• Enabling large-scale scientific workflows on petascale resources using MPI master/workerMats Rynge, Scott Callaghan, Ewa Deelman, Gideon Juve, Gaurang Mehta, Karan Vahi, Philip J. Maechling. [doi]
• Monte Carlo strategies for first-principles simulations of elemental systemsLev D. Gelb. [doi]
• Gordon: design, performance, and experiences deploying and supporting a data intensive supercomputerShawn M. Strande, Pietro Cicotti, Robert S. Sinkovits, William S. Young, Rick Wagner, Mahidhar Tatineni, Eva Hocks, Allan Snavely, Mike Norman. [doi]
• Running many molecular dynamics simulations on many supercomputersRajib Mukherjee, Abhinav Thota, Hideki Fujioka, Thomas C. Bishop, Shantenu Jha. [doi]
• Using kerberized lustre over the WAN for high energy physics dataJosephine Palencia, Robert Budden, Kathy Benninger, Jorge Rodríguez 0002, John Dilascio, Dimitri Bourilkov, Paul Avery, Mengxing Cheng, Yu Fu, Bockjoo Kim, Drew Oliver, Daniel Majchrzak, Dave Dykstra, Nirmal Seenu, Donald Shrum, Jim Wilgenbusch. [doi]
• A toolkit for the analysis and visualization of free volume in materialsFrank T. Willmore. [doi]