Travel grants for US students announced

We received 68 eligible applications for travel grants from students and postdocs from the US and Canada. This made the exercise of selecting the awardees for these travel grants epecially difficult, and unfortunately means that many highly qualified applicants will not receive a grant. We would like to extend to all the interested students who cannot be offered support at this time our sincerest expression of regret. Hopefully, some of you may be able to find support from another source to attend. If this were the case, we will be able to offer a waiver of the registration fees for these students/postdocs.

The selected applicants for a travel grant are listed below. The travel grant consists of US$1000 towards air fare, and a per-diem allowance of $120 capped at $1200 (in other words, the value of the grant is $2200).

Name and position	Supervisor and institution	Background
Arya, Anshu PhD student(2009–) BE ChemE BS Comp Sc UDelaware	Laxmikant Kale Dept. Computer Science University of Illinois at Urbana-Champaign	Improving the massively parallel quantum chemistry package, OpenAtom, to operate efficiently on petaFLOP machines, in collaboration with IBM Watson. Research goals: improving the efficiency and utilization of heterogeneous (accelerated) clusters, e.g., using an an adaptive run-time system capable of load- balancing during program execution, although currently has limited first-hand experience with GPUs.
Bhagatwala, Ankit PhD student (2005–) BSc / MSc Ocean Engrg. IIT Madras	Sanjiva, Lele Dept. Aeronautics & Astronautics, Stanford University	Working on shock-turbulence and shock-interface interactions in spherical geometry for inertial confinement fusion. Did internship at Max-Planck on helioseismology. Author of a 3D massively parallel Navier-Stokes solver scaling up to 32k cores on the Blue Gene/P supercomputer at the Argonne National Laboratories. Attended GPU course at Stanford Spring 2010.
Corona, Eduardo PhD student 3rd yr BSc Applied Math Mexico 2007	Denis Zorin Courant Institute of Mathematical Sciences, NYU	In his undergraduate, worked with Finite Element Methods. Has been working on kernel-independent FMM since summer 2008, now developing fast direct solver for boundary-integral equations on surfaces (application is vesicles in Stokes flow). Currently attending HPC course by Berger and Klockner; knows C/C++ but no parallel experience on CV. Research very much in line with topics of PASI courses.
Espinosa, Allan PhD student (2008–) BSc ECEng (Philippines)	Ian Foster Dept. Computer Science University of Chicago	Has designed scientific workflows to support bioinformatics, earthquake/geoinformatics and molecular dynamics simulations as loosely-coupled and tightly-coupled applications in petascale systems (Argonne IBM BlueGene/P and TACC Ranger SUN Constellation). Current work consists in running several 30,000 CPU-hour earthquake simulations on distributed resources like the Open Science Grid.
Fierst, Janna Postdoctoral researcher PhD 2010 FSU MSc 2004 CalState Biology	Patrick Phillips Center for Ecology and Evolutionary Biology, University of Oregon	NSF-funded postoctoral fellow in biology, working on bioinformatics and evolutionary genetics. Using computational modeling and data on genetic interactions in yeast to integrate current evolutionary theory with a modern, mechanistic understanding of biological networks. Four publications: Evolution, Phycologia. Would like to attend PASI to learn about modern approaches to large-scale computing and how these can be implemented in biological research. Learned to program in a “Programming for Biologists” class, C/C++, Java, Python,and Unix shell but no parallel experience.
Ho, Kenneth PhD student (2007–) BSc 2007 Applied Comp. Math. Caltech	Leslie Greengard Courant Institute of Mathematical Sciences New York University	As an undergraduate, did research on synthetic DNA switches. Caltech Bioengineering Bootcamp 2008. Two journal publications: PLoS Comp. Biol. and Theor. Biol. Med. Model. Now working on fast direct methods for molecular electrostatics, using boundary integral formulation and wishes to learn about parallelization of these methods. Additional interests in systems biology and neuroscience.
Karpenko, Oleksiy PhD student (2008–) MSc Comp. Sci. 2001 (Ukraine)	Yang Dai Bioinformatics, University of Illinois at Chicago	His interest is massively parallel approaches to processing epigenomic data. Worked as software engineer before starting PhD; extensive programming experience in C++ and OOP and many languages and environments. Publications in Bioinformatics, Immunogentics, Methods in Molecular Biology.
Layton, Simon PhD student (2008–) BSc Math/CS Bristol	Lorena Barba Mechanical Engr. Dept., Boston University	Ample programming experience in Python, C/C++ and other languages. Has experience with CUDA and is working on the shallow water equation model for storm surges with high-order (WENO) methods; has knowledge of vortex methods and FMM.
Li, Ying-Wai PhD student (2007–) BSc / MSc Physics Univ. Hong Kong	David P. Landau, Dept. Physics & Astronomy, University of Georgia	Research focuses on Monte Carlo simulations of simplified lattice protein models, with focus on interaction of proteins with attractive substrates. Three journal papers: Phys Rev E, Comp Phys Comp. Has attended two summer schools on GPU, so some experience with CUDA. Python programmer, also C++
McKenzie, Amber PhD student MSc linguistics	Manton Matthews Computer Science, University of South Carolina	Her research is in parallel natural language processing (NLP), including efforts to improve performance by shortcuts in data processing; identifying areas for parallelization within different NLP applications. Some limited experience with CUDA
Payne, Benjamin PhD student (2009–) MSc Physics MST BSc UWi	Alexey Yamilov Dept. Physics, Missouri University of Science and Technology	Worked as system administrator (100 users) at UWi-Madison. Air Force National Guard. Teragrid experience up to 1000 procs. Four journal publications: Phys. Rev. B, Physica B, J. Mod. Opt. PhD research focused on light propagation through media with randomly-placed scatterers. Has parallel prog. experience with MPI
Perilla, Juan PhD student (2005–) BSc Physics (Colombia)	Thomas Woolf Dept. of Biophysics and Physical Chemistry, Johns Hopkins University	Has developed and published new methods that tackle the problem of transition states for large biological systems reducing the computational cost compared to other alternatives. Has mainly focused on large parallel architectures (Kraken, Steele). Researcher at the Epilepsy Center, doing volumetric reconstructions from MRI and CT scans for accurately locating electrodes in patients with epilepsy that have to undergo brain surgery.
Peters, Amanda PhD student (2008–) BA Physics/CS 2005 Duke U	Efthimios Kaxiras Applied Physics, Harvard University	She has extensive programming experience, mainly MPI. Was software engineer for Blue Gene, 4 years working for IBM before starting PhD, in various roles. Multiple conference (CS) publications. Now working on large-scale simulation of cardiovascular hemodynamics. Has worked scaling CFD application to 294k procs. and is a finalist for Gordon Bell prize 2010. Starting to get involved with CUDA.
Stuart, Jeffery PhD student BB/MS Univ NV both in CS	John Owens Computer Science, University of California, Davis	Internships in Nvidia and Google; multiple computing conference presentations. Focusing almost exclusively on GPUs in his PhD research. Part of the SciDAC UltraViz institute. MapReduce implementation on a GPU cluster.

Name and position

Supervisor and institution

Background

Arya, Anshu
PhD student(2009–)

BE ChemE BS Comp Sc UDelaware

Laxmikant Kale

Dept. Computer Science
University of Illinois at Urbana-Champaign

Improving the massively parallel quantum chemistry package, OpenAtom, to operate efficiently on petaFLOP machines, in collaboration with IBM Watson. Research goals: improving the efficiency and utilization of heterogeneous (accelerated) clusters, e.g., using an an adaptive run-time system capable of load- balancing during program execution, although currently has limited first-hand experience with GPUs.

Bhagatwala, Ankit
PhD student (2005–)

BSc / MSc Ocean Engrg. IIT Madras

Sanjiva, Lele

Dept. Aeronautics & Astronautics, Stanford University

Working on shock-turbulence and shock-interface interactions in spherical geometry for inertial confinement fusion. Did internship at Max-Planck on helioseismology. Author of a 3D massively parallel Navier-Stokes solver scaling up to 32k cores on the Blue Gene/P supercomputer at the Argonne National Laboratories. Attended GPU course at Stanford Spring 2010.

Corona, Eduardo
PhD student 3rd yr

BSc Applied Math Mexico 2007

Denis Zorin

Courant Institute of Mathematical Sciences, NYU

In his undergraduate, worked with Finite Element Methods. Has been working on kernel-independent FMM since summer 2008, now developing fast direct solver for boundary-integral equations on surfaces (application is vesicles in Stokes flow). Currently attending HPC course by Berger and Klockner; knows C/C++ but no parallel experience on CV. Research very much in line with topics of PASI courses.

Espinosa, Allan
PhD student (2008–)

BSc ECEng (Philippines)

Ian Foster

Dept. Computer Science
University of Chicago

Has designed scientific workflows to support bioinformatics, earthquake/geoinformatics and molecular dynamics simulations as loosely-coupled and tightly-coupled applications in petascale systems (Argonne IBM BlueGene/P and TACC Ranger SUN Constellation). Current work consists in running several 30,000 CPU-hour earthquake simulations on distributed resources like the Open Science Grid.

Fierst, Janna
Postdoctoral researcher

PhD 2010 FSU
MSc 2004 CalState Biology

Patrick Phillips

Center for Ecology and Evolutionary Biology, University of Oregon

NSF-funded postoctoral fellow in biology, working on bioinformatics and evolutionary genetics. Using computational modeling and data on genetic interactions in yeast to integrate current evolutionary theory with a modern, mechanistic understanding of biological networks. Four publications: Evolution, Phycologia. Would like to attend PASI to learn about modern approaches to large-scale computing and how these can be implemented in biological research. Learned to program in a “Programming for Biologists” class, C/C++, Java, Python,and Unix shell but no parallel experience.

Ho, Kenneth
PhD student (2007–)

BSc 2007 Applied Comp. Math. Caltech

Leslie Greengard

Courant Institute of Mathematical Sciences
New York University

As an undergraduate, did research on synthetic DNA switches. Caltech Bioengineering Bootcamp 2008. Two journal publications: PLoS Comp. Biol. and Theor. Biol. Med. Model. Now working on fast direct methods for molecular electrostatics, using boundary integral formulation and wishes to learn about parallelization of these methods. Additional interests in systems biology and neuroscience.

Karpenko, Oleksiy
PhD student (2008–)

MSc Comp. Sci. 2001 (Ukraine)

Yang Dai

Bioinformatics, University of Illinois at Chicago

His interest is massively parallel approaches to processing epigenomic data. Worked as software engineer before starting PhD; extensive programming experience in C++ and OOP and many languages and environments. Publications in Bioinformatics, Immunogentics, Methods in Molecular Biology.

Layton, Simon
PhD student (2008–)

BSc Math/CS Bristol

Lorena Barba

Mechanical Engr. Dept., Boston University

Ample programming experience in Python, C/C++ and other languages. Has experience with CUDA and is working on the shallow water equation model for storm surges with high-order (WENO) methods; has knowledge of vortex methods and FMM.

Li, Ying-Wai
PhD student (2007–)

BSc / MSc Physics Univ. Hong Kong

David P. Landau,

Dept. Physics & Astronomy, University of Georgia

Research focuses on Monte Carlo simulations of simplified lattice protein models, with focus on interaction of proteins with attractive substrates. Three journal papers: Phys Rev E, Comp Phys Comp. Has attended two summer schools on GPU, so some experience with CUDA. Python programmer, also C++

McKenzie, Amber
PhD student

MSc linguistics

Manton Matthews

Computer Science, University of South Carolina

Her research is in parallel natural language processing (NLP), including efforts to improve performance by shortcuts in data processing; identifying areas for parallelization within different NLP applications. Some limited experience with CUDA

Payne, Benjamin
PhD student (2009–)

MSc Physics MST
BSc UWi

Alexey Yamilov

Dept. Physics, Missouri University of Science and Technology

Worked as system administrator (100 users) at UWi-Madison. Air Force National Guard. Teragrid experience up to 1000 procs. Four journal publications: Phys. Rev. B, Physica B, J. Mod. Opt. PhD research focused on light propagation through media with randomly-placed scatterers. Has parallel prog. experience with MPI

Perilla, Juan
PhD student (2005–)

BSc Physics (Colombia)

Thomas Woolf

Dept. of Biophysics and Physical Chemistry, Johns Hopkins University

Has developed and published new methods that tackle the problem of transition states for large biological systems reducing the computational cost compared to other alternatives. Has mainly focused on large parallel architectures (Kraken, Steele). Researcher at the Epilepsy Center, doing volumetric reconstructions from MRI and CT scans for accurately locating electrodes in patients with epilepsy that have to undergo brain surgery.

Peters, Amanda
PhD student (2008–)

BA Physics/CS 2005 Duke U

Efthimios Kaxiras

Applied Physics, Harvard University

She has extensive programming experience, mainly MPI. Was software engineer for Blue Gene, 4 years working for IBM before starting PhD, in various roles. Multiple conference (CS) publications. Now working on large-scale simulation of cardiovascular hemodynamics. Has worked scaling CFD application to 294k procs. and is a finalist for Gordon Bell prize 2010. Starting to get involved with CUDA.

Stuart, Jeffery
PhD student

BB/MS Univ NV both in CS

John Owens

Computer Science, University of California, Davis

Internships in Nvidia and Google; multiple computing conference presentations. Focusing almost exclusively on GPUs in his PhD research. Part of the SciDAC UltraViz institute. MapReduce implementation on a GPU cluster.

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