In conjunction with the International Parallel and Distributed Processing Symposium
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HiCOMB 2013 Keynote Talk
Parallel Multiscale Simulations of Brain Aneurysms
George Karniadakis, Brown University
Abstract: Interfacing atomistic-based with continuum-based
simulation codes is now required in many multiscale physical and
biological systems. We present the computational advances that have
enabled the first multiscale simulation on 300,000 processors by
coupling a high-order (spectral element) Navier-Stokes solver with a
stochastic (coarse-grained) Molecular Dynamics solver based on
Dissipative Particle Dynamics (DPD). The key contributions are proper
interface conditions for overlapped domains, topology-aware
communication, SIMDization, multiscale visualization and a new domain
partitioning for atomistic solvers. We study blood flow in a
patient-specific cerebrovasculature with a brain aneurysm, and analyze
the interaction of blood cells with the arterial walls endowed with a
glycocalyx causing thrombus formation and eventual aneurysm
rupture. The macro-scale dynamics (about 10 billion unknowns) are
resolved by Nektar - a spectral element solver; the micro-scale flow
and cell dynamics within the aneurysm are resolved by an in-house
version of DPD-LAMMPS (for an equivalent of about 100 billions
molecules).
Speaker Biography: George Karniadakis received his S.M. (1984) and Ph.D. (1987) from
Massachusetts Institute of Technology. He was appointed Lecturer in the Department of Mechanical Engineering at MIT
in 1987 and subsequently he joined the Center for Turbulence Research at Stanford/Nasa Ames. He joined Princeton University
as Assistant Professor in the Department of Mechanical and Aerospace Engineering and as Associate Faculty in the
Program of Applied and Computational Mathematics. He was a Visiting Professor at Caltech (1993) in the Aeronautics
Department. He joined Brown University as Associate Professor of Applied Mathematics in the Center for Fluid Mechanics
on January 1, 1994. He became a full professor on July 1, 1996. He has been a Visiting Professor and Senior Lecturer of
Ocean/Mechanical Engineering at MIT since September 1, 2000. He was Visiting Professor at Peking University (Fall 2007).
He is a Fellow of the Society for Industrial and Applied Mathematics (SIAM, 2010-), Fellow of the American Physical Society (APS, 2004-),
Fellow of the American Society of Mechanical Engineers (ASME, 2003-) and Associate Fellow of the American Institute of
Aeronautics and Astronautics (AIAA, 2006-). He received the CFD award (2007) by the US Association in Computational Mechanics.
Karniadakis is the lead PI of an OSD/AFOSR MURI on Uncertainty Quantification and Director of a new DOE Center of Mathematics
for Mesoscale Modeling of Materials (CM4).
HiCOMB 2013 Call For Papers
High-performance computing became an integral part of research and
development in bioinformatics and computational biology. The large size
of biological data sets, inherent complexity of biological problems and
the ability to deal with error-prone data, all result in large run-time
and memory requirements. The goal of this workshop is to provide a
forum for discussion of latest research in developing high-performance
computing solutions to data-intensive and compute-intensive problems
arising from molecular biology and related life sciences areas. We are
especially interested in parallel and distributed algorithms,
memory-efficient algorithms, large scale data mining techniques,
including approaches for big data and cloud computing, algorithms on
multicores and GPUs, and design of high-performance software for
biological applications.
The workshop will feature contributed papers as well as invited talks
from reputed researchers in the field.
Topics of interest include but are not limited to:
- Bioinformatic databases
- Computational genomics and metagenomics
- Computational proteomics and metaproteomics
- DNA assembly, clustering, and mapping
- Gene expression analysis with RNASeq and microarrays
- Gene identification and annotation
- Parallel algorithms for biological sequence analysis
- Parallel architectures for biological applications
- Molecular evolution and phylogenetic reconstruction algorithms
- Protein structure prediction and modeling
- Next Generation sequence data analysis
- Parallel algorithms in chemical genetics and chemical informatics
- High performance algorithms for systems biology
- Cloud-enabled solutions for computational biology
Submission guidelines
Papers reporting on original research (both theoretical and experimental) in all areas of bioinformatics and computational biology are sought. Surveys of important recent results and directions are also welcome. To submit a paper, upload a PDF copy of the paper here. Submitted manuscripts may not exceed ten (10) single-spaced double-column pages using 10-point size font on 8.5x11 inch pages (IEEE conference style), including figures, tables, and references (see IPDPS Call for Papers for more details). All papers will be reviewed. IEEE CS Press will publish the IPDPS symposium and workshop abstracts as a printed volume. The complete symposium and workshop proceedings will also be published by IEEE CS Press on CD-ROM and will also be available in the IEEE Digital Library.
Important Dates
| Workshop papers due: | January 4, 2013 11:59PM PST, |
| Authors notification: | February 15, 2013, |
| Camera-ready papers due: | February 28, 2013, |
Download HiCOMB 2013 Call for Papers
Workshop Co-Chairs
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David A. Bader College of Computing Georgia Institute of Technology Atlanta, GA 30332, USA Phone: +1 404 894-3152 Email: |
Srinivas Aluru Dept. of Electrical & Computer Enginering Iowa State University Ames, IA 50011, USA Phone: +1 515 294-3539 Email: |
Program Chair
Jaroslaw Zola
Rutgers Discovery Informatics Institute
Dept. of Electrical & Computer Enginering
Rutgers University
Piscataway, NJ 08854, USA
Email:
Program Committee
- Pratul K. Agarwal - Oak Ridge National Laboratory
- Mario Cannataro - University Magna Graecia of Catanzaro, Italy
- Umit Catalyurek - Ohio State University
- Mark Clement - Brigham Young University
- Scott Emrich - University of Notre Dame
- Mathieu Giraud - University of Lille, France
- Ananth Kalyanaraman - Washington State University
- Marta Kasprzak - Poznan University of Technology, Poland
- Ben Langmead - Johns Hopkins University
- Alba Cristina M.A. de Melo - University of Brasilia, Brazil
- Folker Meyer - Argonne National Laboratory
- Olga Nikolova - Sage Bionetworks
- Fahad Saeed - National Institutes of Health
- Bertil Schmidt - Johannes Gutenberg University Mainz, Germany
- Carlos P. Sosa - Cray, Inc. and University of Minnesota
- Alexandros Stamatakis - HITS gGmbH, Germany
- Michela Taufer - University of Delaware
- Tiffani L. Williams - Texas A&M University
- Xiao Yang - Broad Institute