## Selected Publications

E. Chow and J. Skolnick,
Effects of Confinement on Models of Intracellular Macromolecular Dynamics,
*Proceedings of the National Academy of Sciences USA*, 2015.
DOI: 10.1073/pnas.1514757112

E. Chow, X. Liu, S. Misra, M. Dukhan, M. Smelyanskiy, J. R. Hammond,
Y. Du, X.-K. Liao, and P. Dubey,
Scaling Up Hartree–Fock Calculations on Tianhe-2, *International Journal of High Performance Computing Applications*,
2015. DOI: 10.1177/1094342015592960

E. Chow, X. Liu, M. Smelyanskiy, and J. R. Hammond,
Parallel Scalability of Hartree-Fock Calculations,
*The Journal of Chemical Physics*, **142**, 104103 (2015).
DOI: 10.1063/1.4913961

E. Chow and A. Patel,
Fine-grained Parallel Incomplete LU Factorization,
*SIAM Journal on Scientific Computing*, **37**, pp. C169-C193 (2015).

H. Anzt, E. Chow, and J. Dongarra,
Iterative Sparse Triangular Solves for Preconditioning,
21st International European Conference on Parallel and
Distributed Computing (Euro-Par 2015), Vienna, Austria, Aug. 24-28, 2015,
*Lecture Notes in Computer Science*, **9233**, pp. 650-661 (2015).

G. Kamath, L. Shi, E. Chow, and W. Song,
__Distributed Multigrid Technique for Seismic Tomography in Sensor Networks__,
1st International Conference on Big Data Computing and Communications,
Taiyuan, Shanxi, China, Aug. 1-3, 2015,
*Lecture Notes in Computer Science*, **9196**, pp. 297-310 (2015).

E. Chow, H. Anzt, and J. Dongarra,
Asynchronous Iterative Algorithm for Computing Incomplete Factorizations on GPUs,
ISC High Performance, Frankfurt, Germany, July 12-16, 2015,
*Lecture Notes in Computer Science*, **9137**, pp. 1-16 (2015).

K. Pamnany, S. Misra, V. Md., X. Liu, E. Chow and S. Aluru,
Dtree: Dynamic Task Scheduling at Petascale,
ISC High Performance, Frankfurt, Germany, July 12-16, 2015,
*Lecture Notes in Computer Science*, **9137**, pp. 122-138 (2015).

X. Guo, X. Liu, P. Xu, Z. Du, and E. Chow,
Efficient Particle-Mesh Spreading on GPUs,
ICCS 2015 International Conference on Computational Science,
Reykjavik, Iceland, June 1-3, 2015,
*Procedia Computer Science*, **51**, pp. 120-129 (2015).

G. Kamath, L. Shi, E. Chow, and W. Song,
__Distributed Tomography with Adaptive Mesh Refinement in Sensor Networks__,
*International Journal of Sensor Networks*, to appear, 2015.

M. G. Lopez, M. D. Horton, and E. Chow,
__Large-scale Hydrodynamic Brownian Simulations on Multicore and GPU Architectures__,
XSEDE'14 Proceedings of the 2014 Annual Conference on Extreme Science
and Engineering Discovery Environment, Atlanta, GA, July 13-18, 2014.

E. Chow,
__Massive Asynchronous Parallelization of Sparse Matrix Factorizations__,
SIAM Workshop on Exascale Applied Mathematics Challenges and Opportunities
(EX14), Chicago, IL, July 6, 2014.

X. Liu, A. Patel, and E. Chow,
A New Scalable Parallel Algorithm for Fock Matrix Construction,
28th IEEE International Parallel and Distributed Processing Symposium (IPDPS),
Phoenix, AZ, May 19-23, 2014, pp. 902-914.
**(Best Paper Award in Applications Track)**

X. Liu and E. Chow, Large-scale Hydrodynamic Brownian Simulations on Multicore and Manycore Architectures, 28th IEEE International Parallel and Distributed Processing Symposium (IPDPS), Phoenix, AZ, May 19-23, 2014, pp. 563-572.

E. Chow and Y. Saad,
Preconditioned Krylov Subspace Methods for Sampling Multivariate
Gaussian Distributions,
*SIAM Journal on Scientific Computing*, **36**, pp. A588-A608 (2014).

T. Ando, E. Chow, and J. Skolnick,
Dynamic Simulation of Concentrated Macromolecular Solutions with Screened Long-range Hydrodynamic Interactions: Algorithm and Limitations,
*The Journal of Chemical Physics*, **139**, 121922 (2013).
DOI: 10.1063/1.4817660

X. Liu, M. Smelyanskiy, E. Chow, and P. Dubey, Efficient Sparse Matrix-Vector Multiplication on x86-based Many-core Processors, 27th International Conference on Supercomputing (ICS), Eugene, OR, June 10-14, 2013.

D. P. Scarpazza, D. J. Ierardi, A. K. Lerer, K. M. Mackenzie,
A. C. Pan, J. A. Bank, E. Chow, R. O. Dror, J. P. Grossman, D. Killebrew,
M. A. Moraes, C. Predescu, J. K. Salmon, and D. E. Shaw,
Extending the Generality of Molecular Dynamics Simulations on a
Special-Purpose Machine,
27th IEEE International Parallel and Distributed Processing Symposium (IPDPS),
Boston, MA, May 20-24, 2013.
**(Best Paper Award in Applications Track)**

Z. Xia, C. Ding, and E. Chow,
__Robust Kernel Nonnegative Matrix Factorization__,
ICDM 2012 Workshop on
Optimization Based Techniques for Emerging Data Mining (OEDM 2012),
Brussels, Belgium, Dec. 10, 2012.

T. Ando, E. Chow, Y. Saad, and J. Skolnick,
Krylov Subspace Methods for Computing Hydrodynamic Interactions in Brownian Dynamics Simulations,
*The Journal of Chemical Physics*, **137**, 064106 (2012).
DOI: 10.1063/1.4742347

W. B. March, K. Czechowski, M. Dukhan, T. Benson, D. Lee, A. J. Connolly,
R. Vuduc, E. Chow, and A. G. Gray,
__Optimizing the Computation of N-Point Correlations on Large-Scale Astronomical Data__,
Proceedings of the 2012 ACM/IEEE International Conference for High Performance
Computing, Networking, Storage and Analysis (SC12),
Salt Lake City, UT, Nov. 10-16, 2012.

X. Liu, E. Chow, K. Vaidyanathan, and M. Smelyanskiy, Improving the Performance of Dynamical Simulations via Multiple Right-Hand Sides, 26th IEEE International Parallel and Distributed Processing Symposium (IPDPS), Shanghai, China, May 21-25, 2012.

E. Chow, J. L. Klepeis, C. A. Rendleman, R. O. Dror, and D. E. Shaw,
__New Technologies for Molecular Dynamics Simulations__,
*Comprehensive Biophysics*, Ed. E. Egelman. Vol. 9.
Academic Press, Waltham, MA, 2012.

M. Ferronato, E. Chow, and K.-K. Phoon,
__Preconditioning Techniques for Sparse Linear Systems__ (editorial),
*Journal of Applied Mathematics*,
Volume 2012 (2012), Article ID 518165.

R. Dror, J. P. Grossman, K. Mackenzie, B. Towles, E. Chow,
J. Salmon, C. Young, J. Bank, B. Batson, and D. E. Shaw,
Overcoming Communication Latency Barriers in Massively Parallel
Scientific Computation,
*IEEE Micro*, 31, (2011), pp. 8-19.

R. Gunasekaran, D. Dillow, G. Shipman, R. Vuduc, and E. Chow,
__Characterizing Application Runtime Behavior from System
Logs and Metrics__, CACHES 2011: The First International Workshop on Characterizing
Applications for Heterogeneous Exascale Systems,
Tucson, AZ, June 4, 2011.

R. O. Dror, J. P. Grossman, K. M. Mackenzie, B. Towles,
E. Chow, J. K. Salmon, C. Young, J. A. Bank, B. Batson,
M. M. Deneroff, J. S. Kuskin, R. H. Larson, M. A. Moraes, and D. E. Shaw,
Exploiting 162-Nanosecond End-to-End Communication Latency on Anton,
Proceedings of the 2010 ACM/IEEE International Conference on High Performance
Computing, Networking, Storage and Analysis (SC10), New Orleans, LA,
November 13-19, 2010.
**(Best Paper Award Finalist)**

D. E. Shaw, R. O. Dror, J. K. Salmon, J. P. Grossman, K.
M. Mackenzie, J. A. Bank, C. Young, M. M. Deneroff, B.
Batson, K. J. Bowers, E. Chow, M. P. Eastwood, D.
J. Ierardi, J. L. Klepeis, J. S. Kuskin, R. H. Larson,
K. Lindorff-Larsen, P. Maragakis, M. A. Moraes, S. Piana,
Y. Shan, and B. Towles,
Millisecond-Scale Molecular Dynamics Simulations on Anton,
Proceedings of the 2009 ACM/IEEE International Conference on High Performance
Computing, Networking, Storage and Analysis (SC09), Portland, Oregon,
November 14-20, 2009.
**(Best Paper Award)**

I. T. Arkin, H. Xu, M. Ø. Jensen, E. Arbely, E. R. Bennett, K. J. Bowers, E. Chow, R. O. Dror, M. P. Eastwood, R. Flitman-Tene, B. A. Gregersen, J. L. Klepeis, I. Kolossváry, Y. Shan, and D. E. Shaw, Mechanism of Na+/H+ Antiporting, *Science*, 317, No. 5839 (2007), pp. 799-803.

K. J. Bowers, E. Chow, H. Xu, R. O. Dror, M. P. Eastwood, B. A. Gregersen, J. L. Klepeis, I. Kolossvary, M. A. Moraes, F. D. Sacerdoti, J. K. Salmon, Y. Shan, and D. E. Shaw, Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters, Proceedings of the ACM/IEEE SC2006 Conference, Tampa, Florida, November 11-17, 2006.
**(Best Paper Award)**

Edmond Chow, An Aggregation Multilevel Method Using Smooth Error Vectors, *SIAM Journal on Scientific Computing*, 27 (2006), pp. 1727-1741.

Ali Pinar, Edmond Chow, and Alex Pothen, Combinatorial Algorithms for Computing Column Space Bases That Have Sparse Inverses, *Electronic Transactions on Numerical Analysis*, 22 (2006), pp. 122-145.

Andy Yoo, Edmond Chow, Keith Henderson, William McLendon, Bruce Hendrickson, and Umit Catalyurek, A Scalable Distributed Parallel Breadth-First Search Algorithm on BlueGene/L, Proceedings of the ACM/IEEE SC2005 Conference, Seattle, Washington, November 12-18, 2005. **(Gordon Bell Prize Finalist)**

Marc Barthélemy, Edmond Chow, and Tina Eliassi-Rad, Knowledge Representation Issues in Semantic Graphs for Relationship Detection, AI Technologies for Homeland Security: Papers from the 2005 AAAI Spring Symposium, AAAI Press, 2005, pp. 91-98.

Edmond Chow, Keith Henderson, and Andy Yoo, Distributed Breadth-First Search with 2-D Partitioning, LLNL Technical Report UCRL-CONF-210829.

Edmond Chow, A Graph Search Heuristic for Shortest Distance Paths, LLNL Technical Report UCRL-CONF-210878.

Tina Eliassi-Rad and Edmond Chow, __"Using Ontological Information to Accelerate Search in Large Semantic Graphs: A Probabilistic Approach__, LLNL Technical Report UCRL-CONF-202002.

Edmond Chow, Robert D. Falgout, Jonathan J. Hu, Raymond S. Tuminaro, and Ulrike Meier Yang, A Survey of Parallelization Techniques for Multigrid Solvers, *Frontiers of Parallel Processing for Scientific Computing*, SIAM Publications, Philadelphia, PA, 2005.

Na Li, Yousef Saad, and Edmond Chow, Crout Versions of ILU for General Sparse Matrices, *SIAM J. Sci. Comput.* **25**, (2004), pp. 716-728.

Edmond Chow and Panayot Vassilevski, Multilevel Block Factorizations in Generalized Hierarchical Bases, *Numer. Linear Algebra Apps.* **10**, (2003), pp. 105-127.

Edmond Chow, An Unstructured Multigrid Method Based on Geometric Smoothness, *Numer. Linear Algebra Apps.* **10**, (2003), pp. 401-421.

Edmond Chow, Thomas A. Manteuffel, Charles Tong, and Bradley K. Wallin, Algebraic Elimination of Slide Surface Constraints in Implicit Structural Analysis, *Intern. J. Num. Meth. Engrg.* **57**, (2003), pp. 1129-1144.

Edmond Chow and David Hysom, Assessing Performance of Hybrid MPI/OpenMP Programs on SMP Clusters, Lawrence Livermore National Laboratory Technical Report UCRL-JC-143957, May 2001.

Edmond Chow, Parallel Implementation and Practical Use of Sparse Approximate Inverse Preconditioners With A Priori Sparsity Patterns, *Int. J. High Perf. Comput. Apps.,* **15**, (2001), pp. 56-74.

Edmond Chow, A Priori Sparsity Patterns for Parallel Sparse Approximate Inverse Preconditioners, *SIAM J. Sci. Comput.,* **21**, (2000), pp. 1804-1822.

Tony F. Chan, Edmond Chow, Yousef Saad, and M. C. Yeung, Preserving Symmetry in Preconditioned Krylov Subspace Methods, *SIAM J. Sci. Comput.,* **20**, (1999), pp. 568-581.

Edmond Chow and Michael A. Heroux, An Object-Oriented Framework for Block Preconditioning, *ACM Trans. Math. Softw.,* **24**, (1998), pp. 159-183.

Edmond Chow and Yousef Saad, Approximate Inverse Preconditioners Via Sparse-Sparse Iterations, *SIAM J. Sci. Comput.,* **19**, (1998), pp. 995-1023.

Edmond Chow and Yousef Saad, Experimental Study of ILU Preconditioners for Indefinite Matrices, *J. Comput. Appl. Math,* **86**, (1997), pp. 387-414.

Edmond Chow and Yousef Saad, ILUS: an Incomplete LU Factorization for Matrices in Sparse Skyline Format, *Int. J. Numer. Meth. Fluids,* **25**, (1997), pp. 739-748.

Edmond Chow and Yousef Saad, Approximate Inverse Techniques for Block-Partitioned Matrices, *SIAM J. Sci. Comput.,* **18**, (1997), pp. 1657-1675.

## Selected Invited Presentations

Minisymposium on Combinatorial Scientific Computing, SIAM Conference on Parallel Processing for Scientific Computing, Paris, France, April 12-15, 2016.

SPPEXA Annual Plenary Meeting (Software for Exascale Computing), Garching, Germany, Jan. 26-27, 2016.

Laboratory for Biomolecular Function Simulation, RIKEN, Kobe, Japan, Dec. 8, 2015.

International Workshop on Software for Peta-Scale Numerical Simulation, Tokyo, Japan, Dec. 3-4, 2015 (1 of 3 international invitees).

Numerical Analysis Group, Applied Mathematics Department, Delft University of Technology, Delft, The Netherlands, Nov. 9, 2015.

“Sparse approximate inverse preconditioners, revisited,” SIAM Conference on Applied Linear Algebra, Atlanta, GA, Oct. 26-30, 2015.

Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN, Oct. 13, 2015.

Innovative Computing Laboratory, University of Tennessee, Knoxville, TN, Oct. 12, 2015.

EMSL Seminar, Pacific Northwest National Laboratory, Richland, WA, Aug. 27, 2015.

Eighth International Congress on Industrial and Applied Mathematics, Beijing, China, Aug. 10-14, 2015 (2 minisymposium talks).

ISC Workshop: The Road to Application Performance on Intel Xeon Phi, Frankfurt, Germany, July 12-16, 2015. (Panelist)

International Conference on Preconditioning Techniques for Scientific and
Industrial Applications,
Eindhoven, The Netherlands, June 17-19, 2015.
**(Plenary Talk)**

“Quantum Chemistry on Large-scale Heterogeneous Clusters,”
Sparse Solvers for Exascale: From Building Blocks to Applications,
Greifswald, Germany, Mar. 22-26, 2015.
**(Plenary Talk)**

“Asynchronous Preconditioning on Accelerators” and “Scaling comparison of dense eigensolvers and purification techniques to large node counts”, SIAM Conference on Computational Science and Engineering, Salt Lake City, UT, March 14-18, 2015.

“Fine-grained Parallel Computation of Approximate Sparse Matrix Factorizations,” Applied Math and Scientific Computing Seminar, Department of Mathematics, Temple University, Philadelphia, PA, Feb. 25, 2015.

“Partitioning and Load Balancing in Parallel Quantum Chemistry,” Recent Advances in Parallel and High Performance Computing Techniques and Applications, Institute for Mathematical Sciences, National University of Singapore, Jan. 12-16, 2015.

“Partitioning, Load Balancing, and Other Problems in Computational Chemistry,” IBM T. J. Watson Research Center Seminar, Yorktown Heights, NY, Dec. 8, 2014.

“Scaling Up Hartree-Fock Calculations,” New and Future Directions in Atomistic Simulation and Modeling Workshop, Seattle, WA, Oct 27-29, 2014.

“Computational Methods for Large-Scale Macromolecular Simulations,” Department of Biochemistry Seminar, University of Iowa, Iowa City, IA, Oct. 23, 2014.

“A Parallel Iterative Approach for Computing and Updating an Approximate Sparse Matrix Factorization,” Department of Mathematics Colloquium, Virginia Tech, Blacksburg, VA, Oct. 10, 2014.

“Massive Asynchronous Parallelization of Sparse Matrix Factorizations,” Parallel Computing Lab Seminar, Intel Corporation, Santa Clara, CA, Aug. 14, 2014.

“Large-scale Hartree-Fock Calculations on Heterogeneous Clusters,” Computing Sciences Seminar, Lawrence Berkeley National Laboratory, Berkeley, CA, Aug. 12, 2014.

“Toward Quantum Chemistry on Millions of Cores,” Future of Computational Chemistry Symposium, 248th American Chemical Society National Meeting, San Francisco, CA, Aug. 10-14, 2014.

“Preconditioned Methods for Sampling Multivariate Gaussian Distributions,” Householder Symposium XIX, Spa, Belgium, June 8-13, 2014.

“A Paradigm for Very Fine-Grained Parallel Matrix Computations,”
and
“Tuning and Optimization of Particle Simulations with Long-Range Interactions,”
2014 Conference
on Advanced Topics and Auto Tuning in High Performance and Scientific
Computing, National Taiwan University, March 14-15, 2014.
**(Invited plenary talk and tutorial)**

“Large-Scale Brownian Dynamics Simulations,”
Georgia Scientific Computing Symposium,
Kennesaw State University, Feb. 22, 2014.
**(Plenary Talk)**

“High-Performance Computing and Algorithms for Biomolecular Simulations,” 2012 Frontiers of Information Science and Technology (FIST) Workshop, Shanghai, China, Dec. 9-13, 2012.

“Computational Methods for Studying In Vivo Macromolecular Motion,” Second EITA-Bio Conference, Princeton, NJ, Oct. 27-28, 2012.

“Algorithms for Large-Scale Macromolecular Simulations of the Cell,” Computer Science Department Colloquium, College of William and Mary, Williamsburg, VA, Oct. 12, 2012.

“Orderings and Solvers for Non-Uniform Sparse Matrices,” SIAM Conference on Applied Linear Algebra, Valencia, Spain, June 18-22, 2012.

“New Numerical Linear Algebra Techniques for Brownian Simulation of Macromolecules,” Applied and Computational Mathematics Seminar, School of Mathematics, Georgia Tech, Atlanta, GA, March 26, 2012.

“Solution Methods for Stokesian Dynamics Simulation of Macromolecular Motion”, Computational Mathematics Seminar, Department of Mathematical Sciences, Clemson University, Clemson, SC, Oct. 28, 2011.

Chalk Talk, Scientific Computing Seminar, Department of Mathematics and Computer Science, Emory University, Atlanta, GA, April 15, 2011.

“Iterative Solution Methods for Stokesian Dynamics,” SIAM Conference on Mathematical and Computational Issues in the Geosciences, Long Beach, CA, March 21-24, 2011.

“Load-Balanced Bonded Force Calculations on Anton,” International Supercomputing Conference (ISC’10), Special Session on High Performance Computational Life Sciences—The Challenge for HPC Systems, Hamburg, Germany, May 30-June 3, 2010.

“Load-Balanced Bonded Force Calculations on Anton,” Virginia Polytechnic Institute and State University Department of Mathematics Colloquium, Blacksburg, VA, April 30, 2010.

“Non-MPI Applications,” Sandia CSRI Workshop on Next-Generation Scalable Applications, Santa Fe, NM, June 3-5, 2008.

“Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters,” Southern Methodist University Department of Mathematics Research Colloquium, April 18, 2007.

“Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters,” Columbia University Applied Mathematics Colloquium, November 28, 2006.

“Applications and Algorithms for Semantic Graphs,” IBM Almaden Research Center, San Jose, CA, April 13, 2005.

“Knowledge Representation Issues in Semantic Graphs for Relationship Detection,” 2005 AAAI Spring Symposium on AI Technologies for Homeland Security, Stanford University, Palo Alto, CA, March 21-23, 2005.

“Distributed Computation for Complex Networks,” SIAM Conference on Computational Science and Engineering, Orlando, FL, Feb. 12-15, 2005.

“A Social Influence Heuristic for Searching Complex Networks,” Hewlett Packard Laboratories, Palo Alto, CA, June 14, 2004.

“Complex Networks and Six Degrees of Separation,” Stanford SCCM Department Colloquium, Stanford University, Palo Alto, CA, Feb. 2, 2004.

“A Survey of Incomplete Factorization Preconditioners,” Pacific Institute for Mathematical Sciences Workshop on Numerical Linear Algebra and Applications, Vancouver, Canada, August 4-8, 2003.

“Multilevel Methods Based on Aggregation,” ICIAM 2003, Fifth International Congress on Industrial and Applied Mathematics, Sydney, Australia, July 7-11, 2003.

“MATLAB in Numerical Linear Algebra Research” and “Spectral-Type Multilevel Preconditioners,” SIAM Annual Meeting 2003, Montreal, Canada, June 16-20, 2003.

“How to use Hybrid MPI-OpenMP on IBM SP Systems,” SIAM Conference on Computational Science and Engineering, San Diego, CA, Feb. 10-13, 2003.

“Multilevel Preconditioners for Finite Element Computations,” SIAM Annual Meeting 2001, San Diego, CA, July 9-13, 2001.

“Hybrid multithreaded/message-passing on SMP clusters,” College of William and Mary Computer Science Department Colloquium, Williamsburg, VA, Oct. 27, 2000.

“Practical Use and Implementation of Sparse Approximate Inverse Preconditioners,” Seventh SIAM Conference on Applied Linear Algebra, Raleigh, NC, Oct. 23-26, 2000.

“Preconditioners for Multiphysics Applications with Slide Surfaces,” First SIAM Conference on Computational Science and Engineering, Washington, DC, Sept. 21-24, 2000.

“Sparse Approximate Inverse Preconditioners,” Parallel Algorithms Seminar, CERFACS, Toulouse, France, Sept. 1, 2000.

“Improving the Scalability of One-Level Preconditioning Methods for Solving Large-Scale Linear Systems,” IMACS World Congress on Scientific Computation, Applied Mathematics and Simulation, Lausanne, Switzerland, Aug. 21-25, 2000.