2017 Publications

A selection of research using the Massachusetts Green High Performance Computing Center

Do you have news about research using computing resources at the MGHPCC? If you have an interesting project that you want to tell people about or a paper you would like listed, contact hlh@mit.edu

Ross Altman (2017), Systematic Phenomenology on the Landscape of Calabi-Yau Hypersurfaces in Toric Varieties, Northeastern University, ProQuest Dissertations Publishing, 10272560

Edmon Begoli, J. Blair ChristianVijay, GadepallyStavros Papadopoulos (2017), An Emerging Role for Polystores in Precision Medicine, Data Management and Analytics for Medicine and Healthcare, DMAH 2017. Lecture Notes in Computer Science, vol 10494. Springer, Cham, doi: 10.1007/978-3-319-67186-4_5

Sophie Blondel, Karl D. Hammond, Lin Hu, Dimitrios Maroudas, Brian D. Wirth (2017), Modeling Helium Segregation to the Surfaces of Plasma-Exposed Tungsten as a Function of Temperature and Surface Orientation, American Nuclear Society, Fusion Science and Technology, Volume 71, Number 1, pp 22-35, doi: 10.13182/FST16-112

Laura Brattain, Mihnea Bulugioiu, Adam Brewster, Mark Hernandez, Heejin Choi, Taeyun Ku, Kwanghun Chung, Vijay Gadepally (2017), A cloud-based brain connectivity analysis tool, High Performance Extreme Computing Conference (HPEC), 2017 IEEE, doi: 10.1109/HPEC.2017.8091080

Isaac R. Bruss, Gregory M. Grason (2017), Defect-driven shape instabilities of filament bundles, arXiv: 1712.00671 [cond-mat.soft]

Alexander Chen, Alan Edelman, Jeremy Kepner, Vijay Gadepally, Dylan Hutchison (2017), Julia implementation of the Dynamic Distributed Dimensional Data Model, High Performance Extreme Computing Conference (HPEC), 2016 IEEE, doi: 10.1109/HPEC.2016.7761626

Coudron., Matthew Ryan (2017), Entangled protocols and non-local games for testing quantum systems, Thesis: Ph. D., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, http://hdl.handle.net/1721.1/111879

Vijay Gadepally, Kyle O’Brien, Adam Dziedzic, Aaron Elmore, Jeremy Kepner, Samuel Madden, Tim Mattson, Jennie Rogers, Zuohao She, Michael Stonebraker (2017), BigDAWG version 0.1,  High Performance Extreme Computing Conference (HPEC), 2017 IEEE, doi: 10.1109/HPEC.2017.8091077

Lin Hu, Karl D. Hammond, Brian D. Wirth, Dimitrios Maroudas (2017), Dynamics of Small Mobile Helium Clusters Near a Symmetric Tilt Grain Boundary of Plasma-Exposed Tungsten, American Nuclear Society, Fusion Science and Technology, Volume 71, Number 1 , pp 36-51, doi: 10.13182/FST16-105

Hayden Jananthan, Karia Dibert, Jeremy Kepner (2017), Constructing Adjacency Arrays from Incidence Arrays, Parallel and Distributed Processing Symposium Workshops (IPDPSW), 2017 IEEE International, doi: 10.1109/IPDPSW.2017.71

Michael Jones, Jeremy Kepner, William Arcand, David Bestor, Bill Bergeron, Vijay Gadepally, Michael Houle, Matthew Hubbell, Peter Michaleas, Andrew Prout, Albert Reuther, Siddharth Samsi, Paul Monticiollo (2017), Performance Measurements of Supercomputing and Cloud Storage Solutions, High Performance Extreme Computing Conference (HPEC), 2017 IEEE, doi: 10.1109/HPEC.2017.8091073

Edward Kao, Vijay Gadepally, Michael Hurley, Michael Jones, Jeremy Kepner, Sanjeev Mohindra, Paul Monticciolo, Albert Reuther, Siddharth Samsi, William Song, Diane Staheli, Steven Smith (2017), Streaming graph challenge: Stochastic block partition, High Performance Extreme Computing Conference (HPEC), 2017 IEEE, doi: 10.1109/HPEC.2017.8091040

Jeremy Kepner, Manoj Kumar, José Moreira, Pratap Pattnaik, Mauricio Serrano, Henry Tufo (2017), Enabling massive deep neural networks with the GraphBLAS, High Performance Extreme Computing Conference (HPEC), 2017 IEEE, doi: 10.1109/HPEC.2017.8091098

Olga Kononova, Rustem I. Litvinov, Dmitry S. Blokhin, Vladimir V. Klochkov, John W. Weisel, Joel S. Bennett, and Valeri Barsegov (2017), Mechanistic Basis for the Binding of RGD- and AGDV-Peptides to the Platelet Integrin αIIbβ3, Biochemistry, 56 (13), pp 1932–1942, doi: 10.1021/acs.biochem.6b01113

Dima Kozakov, David R Hall, Bing Xia, Kathryn A Porter, Dzmitry Padhorny, Christine Yueh, Dmitri Beglov, Sandor Vajda (2017), The ClusPro web server for protein–protein docking, Nature Protocols, 12, pp 255–278, doi: 10.1038/nprot.2016.169

D. K. Lewis, M. Matsubara, E. Bellotti, and S. Sharifzadeh (2017), Quasiparticle and hybrid density functional methods in defect studies: An application to the nitrogen vacancy in GaN,
Phys. Rev. B 96, 235203, doi: 10.1103/PhysRevB.96.23520

Xiaorong Liu and Jianhan Chen (2017), HyRes: a coarse-grained model for multi-scale enhanced sampling of disordered protein conformations, Physical Chemistry Chemical Physics, doi: cp/c7cp06736d

Lauren Milechin, Vijay Gadepally, Siddharth Samsi, Jeremy Kepner,
Alexander Chen, Dylan Hutchison (2017), D4M 3.0: Extended database and language capabilities,  High Performance Extreme Computing Conference (HPEC), 2017 IEEE, doi: 10.1109/HPEC.2017.8091083

Oscar Moll, Aaron Zalewski, Sudeep Pillai, Sam Madden, Michael Stonebraker, Vijay Gadepally (2017), Exploring big volume sensor data with vroom, Proceedings of the VLDB, Volume 10 Issue 12, August 2017, Pages 1973-1976, doi: 10.14778/3137765.3137822

Julia Mullen, Chansup Byun, Vijay Gadepally, Siddharth Samsi, Albert Reuther, Jeremy Kepner (2017), Learning by doing, High Performance Computing education in the MOOC era, Journal of Parallel and Distributed Computing, Volume 105, July 2017, Pages 105-115, doi: 10.1016/j.jpdc.2017.01.015

Kien Nguyen , Huan Yang, and Paul C. Whitford (2017),  How the Ribosomal A-Site Finger Can Lead to tRNA Species-Dependent Dynamics, J. Phys. Chem. B, 2017, 121 (13), pp 2767–2775,
doi: 10.1021/acs.jpcb.7b01072

Jeremy M. Plante and Vinod M. Vokkarane (2017), Spatially and Spectrally Flexible Scheduling With Time-Slotted Lightpath-Switching, Journal of Optical Communications and Networking Vol. 9, Issue 11, pp. 945-959 (2017), doi: 10.1364/JOCN.9.000945

Ishan Prasad, Christian Santangelo, and Gregory Grason (2017), Sub-Jamming Transition in Binary Sphere Mixtures, arXiv: 1707.06751

Andrew Prout, William Arcand, David Bestor, Bill Bergeron, Chansup Byun, Vijay Gadepally, Matthew Hubbell, Michael Houle, Michael Jones, Peter Michaleas, Lauren, Milechin, Julie Mullen, Antonio Rosa, Siddharth Samsi, Albert Reuther, Jeremy Kepner (2017), MIT SuperCloud portal workspace: Enabling HPC web application deployment, High Performance Extreme Computing Conference (HPEC), 2017 IEEE, doi: 10.1109/HPEC.2017.8091097

Jing Qian, Sara Nunez, Soohyun Kim, Muredach P. Reilly, Andrea S. Foulkes (2017), A score test for genetic class-level association with nonlinear biomarker trajectories, Statistics in Medicine, doi: 10.1002/sim.7314

Patrick A. Ray, Laura Bonzanigo, Sungwook Wi, Yi-Chen E. Yang, Pravin Karki, Luis E. Garcia, Diego J. Rodriguez, Casey M. Brown (2017), Multidimensional stress test for hydropower investments facing climate, geophysical and financial uncertainty, Global Environmental Change, doi:10.1016/j.gloenvcha.2017.11.013

Michael J. Rynkiewicz, Thavanareth Prum, Stephen Hollenberg, Farooq A. Kiani, Patricia M. Fagnant, Steven B. Marston, Kathleen M. Trybus, Stefan Fischer, Jeffrey R. Moore, William Lehman (2017), Tropomyosin Must Interact Weakly with Actin to Effectively Regulate Thin Filament Function, Biophysical Journal
Volume 113, Issue 11, 5 December 2017, Pages 2444–2451, doi: 10.1016/j.bpj.2017.10.004

Siddharth Samsi, Vijay Gadepally, Michael Hurley, Michael Jones, Edward Kao, Sanjeev Mohindra, Paul Monticciolo, Albert Reuther, Steven Smith, William Song, Diane Staheli, Jeremy Kepner (2017), Static graph challenge: Subgraph isomorphism, High Performance Extreme Computing Conference (HPEC), 2017 IEEE, 10.1109/HPEC.2017.8091039

Prateek Sharma, Patrick Pegus, David Irwin, Prashant Shenoy, John Goodhue, James Culbert (2017), Design and Operational Analysis of a Green Data Center, IEEE Internet Computing ( Volume: 21, Issue: 4, 2017 ), doi: 10.1109/MIC.2017.2911421

Slakman, Belinda Leigh (2017), New Domains in Automatic Mechanism Generation, Northeastern University, ProQuest Dissertations Publishing, 2017, 10623195.

Austin E. Soplata , Michelle M. McCarthy, Jason Sherfey, Shane Lee, Patrick L. Purdon, Emery N. Brown, Nancy Kopell (2017), Thalamocortical control of propofol phase-amplitude coupling, PLOS, Computational Biology, doi: 10.1371/journal.pcbi.1005879

Matthew Staib, Stefanie Jegelka (2017), Robust Budget Allocation via Continuous Submodular Functions, Proceedings of the 34th International Conference on Machine Learning, PMLR 70:3230-3240, 2017.

M. Staib, S. Claici, J. Solomon, S. Jegelka (2017), Parallel Streaming Wasserstein Barycenters, Neural Information Processing Systems (NIPS), arXiv:1705.07443 [cs.LG]

Zi Wang, Stefanie Jegelka (2017), Robust Budget Allocation via Continuous Submodular Functions, Proceedings of the 34th International Conference on Machine Learning, PMLR 70:3627-3635, 2017.

Zi Wang, Stefanie Jegelka (2017), Max-value Entropy Search for Efficient Bayesian Optimization,  Proceedings of the 34th International Conference on Machine Learning, PMLR 70:3627-3635, 2017.

Zi Wang, Chengtao Li, Stefanie Jegelka, Pushmeet Kohli (2017), Max-value Entropy Search for Efficient Bayesian Optimization, Proceedings of the 34th International Conference on Machine Learning, PMLR 70:3627-3635, 2017.

Asanka Weerasinghe, Chang-Tsan Lu, Dimitrios Maroudas, and Ashwin Ramasubramaniam (2017), A Multiscale Shear-Lag Analysis of Stiffness Enhancement in Polymer-Graphene Nanocomposites, Applied Materials & Interfaces, doi: 10.1021/acsami.7b03159