College of Engineering | Computer Science and Engineering

Journal Publications

1. S. B. Kylasa, H. M. Aktulga, A. Y. Grama, "Reactive Molecular Dynamics on Massively Parallel Heterogeneous Architectures," accepted for publication (2016)
2. T. P. Senftle, S. Hong, M. M. Islam, S. B. Kylasa, Y. Zheng, Y. K. Shin, C. Junkermeier, R. Engel-Herbert, M. J. Janik, T. Verstraelen, H. M. Aktulga, A. Grama, Adri C. T. van Duin, "The ReaxFF Reactive Force-field: Development, Applications, and Future Directions," Nature Computational Materials, 2, 15011 (2016)
3. D. Oryspayev, H. M. Aktulga, M. Sosonkina, P. Maris, J. P. Vary, "A Memory-efficient Scalable Symmetric Sparse Matrix Vector Multiplication Algorithm for Distributed Memory Architectures", Concurrency and Computation: Practice and Experience, 27 (17), 5019-5036 (2015)
4. M. Dittner, J. Muller, H. M. Aktulga, B. Hartke, "Efficient global optimization of ReaxFF parameters," Journal Computational Chemistry, 36 (20), 1550-1561 (2015)
5. M. Jung, E. H.Wilson III, W. Choi, J. Shalf, H. M. Aktulga, C. Yang, E. Saule, U. V. Catalyurek, M. Kandemir, "Exploring the Future of Out-Of-Core Computing with Compute-Local Non-Volatile Memory", Scientific Programming 22(2), pp. 125-139 (2014)
6. S. B. Kylasa, H. M. Aktulga, A. Y. Grama, "PuReMD-GPU: A Reactive Molecular Dynamics Simulation Package for GPUs", Journal of Computational Physics, vol. 272, pp. 343-359 (2014)
7. H. M. Aktulga, L. Lin, C. Haine, E. G. Ng, C. Yang, "Parallel Eigenvalue Calculation based on Multiple Shift-invert Lanczos and Contour Integral based Spectral Projection Method", Parallel Computing 40 (7), pp. 195-212 (2014)
8. H. M. Aktulga, C. Yang, E. G. Ng, P. Maris, J. P. Vary, "Improving the Scalability of a Symmetric Iterative Eigensolver for Multi-core Platforms", Concurrency and Computation: Practice & Experience, 26 (16), 2631-2651 (2013)
9. H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, "Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques", Parallel Computing 38 (4-5), pp. 245-259 (2012) doi:10.1016/j.parco.2011.08.005
10. H. M. Aktulga, S. A. Pandit, A. C. T. van Duin, A. Y. Grama, "Reactive Molecular Dynamics: Numerical Methods and Algorithmic Tehniques", SIAM J. Sci. Comput. 34(1), pp. 1-23 (2012)
11. J. C. Fogarty, H. M. Aktulga, A. van Duin, A. Y. Grama, S. A. Pandit, "A Reactive Simulation of the Silica-Water Interface", J. Chem. Phys. 132, p. 174704 (2010) doi:10.1063/1.3407433
12. Y. Park, H. M. Aktulga, A. Y. Grama, A. Strachan, "Strain relaxation in Si/Ge/Si nanoscale bars from molecular dynamics simulations", J. Appl. Phys. 106, 034304 (2009) doi:10.1063/1.3168424
13. H. M. Aktulga, I. Kontoyiannis, L. Lyznik, L. Szpankowski, W. Szpankowski, A. Y. Grama, "Identifying Statistical Dependence in Genomic Sequences via Mutual Information", EURASIP Journal on Bioinformatics and Systems Biology, 2007:1474 (2007) doi:10.1155/2007/14741

Book Chapters, Thesis

1. E. Saule, H. M. Aktulga, C. Yang, E. G. Ng, U. V. Catalyurek, "An Out-of-core Task-based Middleware for Data Intensive Scientific Computing", Handbook on Data Centers, pp. 647-667, Springer-Verlag New York, Feb 2015, ISBN: 978-1-4939-2091-4
2. A. Y. Grama, J. C. Fogarty, H. M. Aktulga, S. A. Pandit, "N-Body Computational Methods", Encyclopedia of Parallel Computing, pp. 1259-1268, Springer US (2011) doi:10.1007/978-0-387-09766-4_97
3. "Algorithmic and Numerical Techniques for Atomistic Modeling", H. M. Aktulga, PhD, Purdue University, July 29, 2010

Conference Publications (Peer-reviewed)

1. J. P. Vary, P. Maris, H. Potter, M. Caprio, R. Smith, S. Binder, A. Calci, J. Langhammerd, R. Roth, H. M. Aktulga, E. Ng , C. Yang , D. Oryspayev, M. Sosonkina, U. Catalyurek, "Ab initio no core shell model: Recent results and further prospects," in Proceedings of The International Conference on Nuclear Theory in the Supercomputing Era 2014 (NTSE 2014), Khabarovsk, Russia (June 2014)
2. H. M. Aktulga, A. Buluc, S. Williams, C. Yang, "Optimizing Sparse Matrix-Multiple Vector Multiplication for Nuclear Configuration Interaction Calculations", 2014 International Parallel and Distributed Processing Symposium (IPDPS 2014), Phoenix, AZ (May 2014) doi:10.1109/IPDPS.2014.125
3. M. Jung, E. H. Wilson III, W. Choi, J. Shalf, H. M. Aktulga, C. Yang, E. Saule, U. V. Catalyurek, M. Kandemir, "Exploring the Future of Out-Of-Core Computing with Compute-Local Non-Volatile Memory", in Proceedings of Supercomputing 2013 (SC13), Denver, CO. (Nov 2013)
4. C. Yang, H. M. Aktulga, P. Maris, E. Ng, J. Vary, "Recent Advances in MFDn," in Proceedings of The International Conference on Nuclear Theory in the Supercomputing Era 2013 (NTSE 2013), Ames, IA, USA (May 2013)
5. P. Maris, H. M. Aktulga, S. Binder, A. Calci, U. V. Catalyurek, J. Langhammer, E. Ng, E. Saule, R. Roth, J. P. Vary, and C. Yang, "No-core CI calculations for light nuclei with chiral 2- and 3-body forces", Journal of Physics: Conference Series, vol. 454, no. 1, p. 012063 (2013)
6. P. Maris, H. M. Aktulga, M. A. Caprio, U. V. Catalyurek, E. G. Ng, D. Oryspayev, H. Potter, E. Saule, M. Sosonkina, J. P. Vary, C. Yang, Z. Zhou, "Large-scale Ab-initio Configuration Interaction Calculations for Light Nuclei", J. Phys. Conf. Ser., 403:012019, IOP Publishing, December 18, 2012, doi: doi:10.1088/1742-6596/403/1/012019
7. Z. Zhou, E. Saule, H. M. Aktulga, C. Yang, E. G. Ng, P. Maris, J. P. Vary, U. V. Catalyurek, "An Out-of-core Eigensolver on SSD-equipped Clusters", in Proceeding of 2012 IEEE International Conference on Cluster Computing (CLUSTER12), pp. 248 - 256, Beijing, China, September 26, 2012, doi:10.1109/CLUSTER.2012.76
8. Z. Zhou, E. Saule, H. M. Aktulga, C. Yang, E. G. Ng, P. Maris, J. P. Vary, U. V. Catalyurek, "An Out-Of-Core Dataflow Middleware to Reduce the Cost of Large Scale Iterative Solvers", in Proceedings of 41st International Conference on Parallel Processing Workshops (ICPPW 2012), pp. 71 - 80, Pittsburgh, PA, September 10, 2012, doi:10.1109/ICPPW.2012.13
9. H. M. Aktulga, C. Yang, P. Maris, J. P. Vary, E. G. Ng, "Topology-Aware Mappings for Large-Scale Eigenvalue Problems", in Proceedings of 2012 Euro-Par Parallel Processing Conference (Euro-Par 2012), LNCS 748:830-842, Rhode Island, Greece, August 31, 2012, doi:10.1007/978-3-642-32820-6_82
10. H. M. Aktulga, C. Yang, U. V. Catalyurek, P. Maris, J. P. Vary, E. G. Ng, "On Reducing I/O Overheads in Large-Scale Invariant Subspace Projections", in Proceedings of 2011 Euro-Par Parallel Processing Workshops (Euro-Par 2011 Workshops), LNCS 715:305-314, Bordeaux, France, August 29, 2011, doi:10.1007/978-3-642-29737-3_35
11. E. G. Ng, J. Sarich, S. M. Wild, T. Munson, H. M. Aktulga, C. Yang, P. Maris, J. P. Vary, N. Schunck, M. G. Bertolli, M. Kortelainen, W. Nazarewicz, T. Papenbrock, M. V. Stoitsov, "Advancing Nuclear Physics Through TOPS Solvers and Tools", in Proceedings of SciDAC 2011 Conference, Denver, CO, July 10, 2011, arXiv:1110.1708
12. H. M. Aktulga, C. Yang, P. Maris, J. P. Vary, E. G. Ng, "Large-scale Parallel Null Space Calculation for Nuclear Configuration Interaction", in Proceedings of 2011 International Conference on High Performance Computing and Simulation (HPCS 2011), pp. 176-185, Istanbul, Turkey, July 8, 2011, doi:10.1109/HPCSim.2011.5999822
13. H. M. Aktulga, A. Y. Grama, S. Plimpton, and A. Thompson, "A fast ILU preconditioning-based solver for the charge equilibration problem", CSRI Summer Proceedings 2009, pp. 50-59, Albuquerque, NM, Aug 10, 2009
14. H. M. Aktulga, I. Kontoyiannis, L. Lyznik, L. Szpankowski, W. Szpankowski, A. Y. Grama, "Statistical Dependence in Biological Sequences", in Proceedings of 2007 IEEE International Symposium on Information Theory (ISIT 2007), pp. 2676 - 2680, Nice, France, June 25, 2007, doi:10.1109/ISIT.2007.4557183