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


Hadas Alon, Chen Stern, Moshe Kirshner, Ofer Sinai, Michal Wasserman, Ryan Selhors, Raymond Gasper, Ashwin Ramasubramaniam, Todd Emrick, and Doron Naveh (2018), Lithographically Patterned Functional Polymer–Graphene Hybrids for Nanoscale Electronics, ACS Nano, 2018, 12 (2), pp 1928–1933, doi: 10.1021/acsnano.7b08844

Ross Altman, Yang-Hui He, Vishnu Jejjala, and Brent D. Nelson (2018), New large volume Calabi-Yau threefolds, Phys. Rev. D 97, 046003, doi: 10.1103/PhysRevD.97.04600

Cecilia Bores, Scott M. Auerbach, and Peter A. Monson (2018), Modeling the Role of Excluded Volume in Zeolite Structure Direction, 9 (13), pp 3703–3707, doi: 10.1021/acs.jpclett.8b01467

Cecilia Bores, Scott M. Auerbach and Peter A. Monson (2018), Enhanced replica exchange reactive Monte Carlo simulations for constructing zeolite frameworks, Journal Molecular Simulation, Volume 44, Issue 6: Engineered Self-assembly, Pages 453-462, doi: 10.1080/08927022.2017.1399375

Mengxi Chen, Andre R. Muniz, and Dimitrios Maroudas (2018), Formation and Mechanical Behavior of Nanocomposite Superstructures from Interlayer Bonding in Twisted Bilayer Graphene, ACS Appl. Mater. Interfaces, 2018, 10 (34), pp 28898–28908, doi : 10.1021/acsami.8b09741

Andrew E. Christie, Matthew C. Cieslak, Vittoria Roncalli, Petra H. Lenz, Kaley M. Major, Helen C. Poynton (2018), Prediction of a peptidome for the ecotoxicological model Hyalella azteca (Crustacea; Amphipoda) using a de novo assembled transcriptome, Marine Genomics, Volume 38, Pages 67-88, doi: 10.1016/j.margen.2017.12.003

Arash Deylamsalehi, Dylan A. P. Davis, Pegah Afsharlar, Mehdi Bahrami, Wei-Peng Chen, and Vinod M. Vokkarane (2018), Using Machine Learning to Balance Energy Cost and Emissions in Optical Networks, Journal of Optical Communications and Networking Vol. 10, Issue 10, pp. D72-D83, doi: 10.1364/JOCN.10.000D72

Dwaipayan Dasgupta, AshishKumar, DimitriosMaroudas (2018), Analysis of current-driven oscillatory dynamics of single-layer homoepitaxial islands on crystalline conducting substrates, Surface Science, Volume 669, Pages 25-33, doi: 10.1016/j.susc.2017.10.027

Dylan A. P. Davis and Vinod M. Vokkarane (2018), Generalized Survivability Models for Many-to-Many Communication, 2018 International Conference on Computing, Networking and Communications (ICNC), doi: 10.1109/ICCNC.2018.8390305

Ethan D. Evans and Bradley L. Pentelute (2018), Studies on a landscape of perfluoroaromatic-reactive peptides, Organic and Biomolecular Chemistry, doi:  10.1039/c8ob01678j

Gerrie P. Farman, Michael J. Rynkiewicz, Marek Orzechowski, William Lehman, Jeffrey R. Moore (2018), HCM and DCM cardiomyopathy-linked α-tropomyosin mutations influence off-state stability and crossbridge interaction on thin filaments, Archives of Biochemistry and Biophysics, Volume 647, Pages 84-92, doi: 10.1016/

Haiying Gao (2018), Three-dimensional variations of the slab geometry correlate with earthquake distributions at the Cascadia subduction system, Nature Communications, volume 9, Article number: 1204 (2018), doi: s41467-018-03655-5

Jacob M. Goldberg, Fang Wang, Chanan D. Sessler, Nathan W. Vogler, Daniel Y. Zhang, William H. Loucks, Thanos Tzounopoulos, and Stephen J. Lippard (2018), Photoactivatable Sensors for Detecting Mobile Zinc, Journal of the American Chemical Society, 140 (6), pp 2020–2023, doi: 10.1021/jacs.7b12766

Bhatia, Hemlata (2018), Understanding the Impact of Zinc on CHO Cell Transcriptome, University of Massachusetts, Lowell, Doctoral Dissertation,

Ishan Prasad, Hiroshi Jinnai, Rong-Ming Ho, Edwin L. Thomas and  Gregory M. Grason (2018), Anatomy of triply-periodic network assemblies: characterizing skeletal and inter-domain surface geometry of block copolymer gyroids, Soft Matter, 2018,14, 3612-3623, doi: 10.1039/C8SM00078F

M. Kumar, W. P. Horn, J. Kepner, J. E. Moreira, P. Pattnaik (2018), IBM POWER9 and cognitive computing, IBM Journal of Research and Development, doi: 10.1147/JRD.2018.2846958

Xinzhi Li, Amit Das, and Dapeng Bi (2018), Biological tissue-inspired tunable photonic fluid, PNAS, doi: 10.1073/pnas.1715810115

David P. Markt, Ashish Pathak, Mehdi Raessi (2018), Advanced Computational Simulations of Surface Impingement of a Train of Ethanol Drops: A Pathway to Developing Spray-Wall Interaction Submodels, Computing in Science & Engineering, doi: 10.1109/MCSE.2018.042781326

Aude Nicolas et al. (2018), Genome-wide Analyses Identify KIF5A as a Novel ALS Gene, Neuron, Volume 97, Issue 6, Pages 1268-1283.e6, doi: 10.1016/j.neuron.2018.02.027

Stella S. R. Offner and Yue Liu (2018), Turbulent Action at a Distance due to Stellar Feedback in
Magnetized Clouds, arXiv: 1809.03513 [astro-ph.SR]

Sampath K. Rachakonda, Yue Wang, David P. Schmidt (2018), Flash-boiling Initialization for Spray Simulations Based on Parametric Studies, Atomization and Sprays, Volume 28, Issue 2, doi: 10.1615/AtomizSpr.2018020769

Patrick A. Ray, Laura Bonzanigo, Sungwook Wi, Yi-Chen E. Yang, Pravin Karki, Luis E. García, Diego J. Rodriguez, Casey M. Brown (2018), Multidimensional stress test for hydropower investments facing climate, geophysical and financial uncertainty, Global Environmental Change, Volume 48, Pages 168-181, doi: 10.1016/j.gloenvcha.2017.11.013

Abhiram Reddy, Michael B. Buckley, Akash Arora, Frank S. Bates, Kevin D. Dorfman, Gregory M. Grason (2018), Stable Frank-Kasper phases of self-assembled, soft matter spheres, arXiv:1806.01726 [cond-mat.soft]

Albert Reuther, Chansup Byun, William Arcand, David Bestor, Bill Bergeron, Matthew Hubbell, Michael Jones, Peter Michaleas, Andrew Prout, Antonio Rosa, Jeremy Kepner (2018), Scalable system scheduling for HPC and big data, Journal of Parallel and Distributed Computing, Volume 111, January 2018, Pages 76-92, doi: 10.1016/j.jpdc.2017.06.009

P. Rodriguez-Fernandez, A. E. White, A. J. Creely, M. J. Greenwald, N. T. Howard, F. Sciortino and J. C. Wright (2018), VITALS: A Surrogate-Based Optimization Framework for the Accelerated Validation of Plasma Transport Codes, Fusion Science and Technology, Volume 74, 2018 – Issue 1-2, doi: 10.1080/15361055.2017.1396166

Nestor A. Sepulveda, Jesse D. Jenkins, Fernando J. de Sisternes, Richard K. Lester (2018), The Role of Firm Low-Carbon Electricity Resources in Deep Decarbonization of Power Generation, Joule, doi: 10.1016/j.joule.2018.08.006

Jayson R Vavrek, Brian S Henderson, Areg Danagoulian (2018), High-accuracy Geant4 simulation and semi-analytical modeling of nuclear resonance fluorescence, arXiv:1807.01701 [physics.ins-det]

Camille Washington-Ottombre and Siiri Bigalke (2018), An aggregated and dynamic analysis of innovations in campus sustainability, International Journal of Sustainability in Higher Education, vol 18, issue 2, doi: 10.1108/IJSHE-05-2017-0071

Joanna M. Wolfe and Gregory P. Fournier (2018), Horizontal gene transfer constrains the timing of methanogen evolution, Nature Ecology & Evolution, volume 2, pages 897–903, doi: 10.1038/s41559-018-0513-7

Xiaotao Yang and Haiying Gao (2018), Full‐Wave Seismic Tomography in the Northeastern United States: New Insights Into the Uplift Mechanism of the Adirondack Mountains, Journal of Geophysical Research Letters, doi: 10.1029/2018GL078438


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,

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

2016 and earlier



Andrey Alekseenko, Olga Kononova, Yaroslav Kholodov, Kenneth A. Marx, Valeri Barsegov (2016), SOP-GPU: influence of solvent-induced hydrodynamic interactions on dynamic structural transitions in protein assemblies, Journal of Computational Chemistry, first published: 26 March 2016,
doi: 10.1002/jcc.24368

Inna Aphasizheva, Liye Zhang, Xiaorong Wang, Robyn M. Kaake, Lan Huang, Stefano Monti and Ruslan Aphasizhev (2014) RNA Binding and Core Complexes Constitute the U-Insertion/Deletion Editosome, Mol. Cell. Biol. December 2014 vol. 34 no. 23 4329-4342, doi: 10.1128/MCB.01075-14

Muhammad Affawn Ashraf, Christopher W. Copeland, Abdulkadir Kocak, Alexandra R. McEnroe and Ricardo B. Metz (2015) Vibrational spectroscopy and theory of Fe2+(CH4)n (n = 1–3), Physical Chemistry Chemical Physics, doi:  10.1039/c5cp01757b

M.R.M. Assis and L.F. Bittencourt (2016), A survey on cloud federation architectures: Identifying functional and non-functional propertiesJournal of Network and Computer Applications
Volume 72, September 2016, Pages 51–71, doi: 10.1016/j.jnca.2016.06.014


Bestavros, A., Krieger, O. (2014) Toward an Open Cloud Marketplace: Vision and First Steps, Internet Computing, IEEE (Volume:18 , Issue: 1 ), IEEE p 72-77, doi: 10.1109/MIC.2014.17

R. Brower, A. Hasenfratz, C. Rebbi, E. Weinberg, O. Witzel (2015) A novel approach to the study of conformality in the SU (3) theory with multiple flavors, Journal of Experimental and Theoretical Physics March 2015, Volume 120, Issue 3, pp 423-427, doi: 10.1134/S1063776115030176

Nilda Roma Burgos, Vijay Singh, Te Ming Tseng, Howard Black, Nelson D. Young, Zhongyun Huang, Katie E. Hyma, David R. Gealy and Ana L. Caicedo (2014) The Impact of Herbicide-Resistant Rice Technology on Phenotypic Diversity and Population Structure of United States Weedy Rice, Plant Physiology November 2014 vol. 166 no. 3 1208-1220, doi: 10. 1104/ pp. 114. 242719


Jiajun Cao, Gregory Karr, Kapil Arya, and Gene Cooperman (2014), Transparent Checkpoint-restart over Infiniband, HPDC ’14 Proceedings of the 23rd international symposium on High-performance parallel and distributed computing, Pages 13-24, ACM New York, NY, USA ©2014, ISBN: 978-1-4503-2749-7 doi: 10.1145/2600212.2600219

Vitor Cardoso and Gaurav Khanna (2015) Black holes in anti–de Sitter spacetime: Quasinormal modes, tails, and flat spacetime, Phys. Rev. D 91, 024031 – Published 22 January 2015, doi: 10.1103/PhysRevD.91.024031

Chih-Hung Chen, Tristan Cambonie, Veronique Lazarus, Matteo Nicoli, Antonio Pons, and Alain Karma (2015), Crack Front Segmentation and Facet Coarsening in Mixed-Mode Fracture, arXiv:1509.05077

Peinan Chen, Vijay Gadepally, Michael Stonebraker (2016), The BigDawg monitoring framework, High Performance Extreme Computing Conference (HPEC), 2016 IEEE, doi: 10.1109/HPEC.2016.7761642

Shao-Yu Chen, Thomas Goldstein, Dhandapani Venkataraman, Ashwin Ramasubramaniam, and Jun Yan (2016), Activation of New Raman Modes by Inversion Symmetry Breaking in Type II Weyl Semimetal Candidate T′-MoTe2, online at Nano Letters August 12, 2016, doi: 10.1021/acs.nanolett.6b02666

Jierong Cheng, Wei Li Wang, Hossein Mosallaei, and Efthimios Kaxiras (2014), Surface Plasmon Engineering in Graphene Functionalized with Organic Molecules: A Multiscale Theoretical Investigation, Nano Lett., 2014, 14 (1), pp 50–56, doi: 10.1021/nl403005s

Szu-Chia Chien, Scott M. Auerbach, and Peter A. Monson (2015) Modeling the Self-Assembly of Silica-Templated Nanoparticles in the Initial Stages of Zeolite Formation, Langmuir, 2015, 31 (17), pp 4940–4949, doi: 10.1021/acs.langmuir.5b00382

Kedar C. Chitale, Bart Lipken, Walter Presz Jr. and Olivier Desjardins (2015) Understanding the fluid dynamics associated with macro scale ultrasonic separators, Proceedings of Meetings on Acoustics 23, 045004 (2015), doi: 10.1121/2.0000070

Ekin D. Cubuk, Wei L. Wang, Kejie Zhao, Joost J. Vlassak, Zhigang Suo, and Efthimios Kaxiras (2013) Morphological Evolution of Si Nanowires upon Lithiation: A First-Principles Multiscale Model, Nano Lett., 2013, 13 (5), pp 2011–2015, doi: 10.1021/nl400132q


Paul A. Dalba, Philip S. Muirhead, Jonathan J. Fortney, Matthew M. Hedman, Philip D. Nicholson, and Mark J. Veyette (2015), The Transit Transmission Spectrum of a Cold Gas Giant PlanetThe Astrophysical Journal, Volume 814, Number 2, doi: 10.1088/0004-637X/814/2/154

Karia Dibert, Hayden Jansen, Jeremy Kepner (2016), Algebraic conditions for generating accurate adjacency arrays, MIT Undergraduate Research Technology Conference (URTC), IEEE, doi: 10.1109/URTC.2015.7563745

Patrick Dreher, Chansup Byun, Chris Hill, Vijay Gadepally, Bradley Kuszmaul, Jeremy Kepner (2016), PageRank Pipeline Benchmark: Proposal for a Holistic System Benchmark for Big-Data Platforms, Parallel and Distributed Processing Symposium Workshops, 2016 IEEE International, doi: 10.1109/IPDPSW.2016.89

Jennie Duggan, Aaron J. Elmore, Michael Stonebraker , Magda Balazinska , Bill Howe , Jeremy Kepner , Sam Madden , David Maier, Tim Mattson , Stan Zdonik (2015), The BigDAWG Polystore System, ACM SIGMOD, Volume 44 Issue 2, June 2015, doi: 10.1145/2814710.2814713


A. Elmore , J. Duggan , M. Stonebraker , M. Balazinska , U. Cetintemel, V. Gadepally , J. Heer , B. Howe , J. Kepner, T. Kraska , S. Madden, D. Maier, T. Mattson , S. Papadopoulos, J. Parkhurst Intel, N. Tatbul, M. Vartak, S. Zdonik (2015), A demonstration of the BigDAWG polystore system, Proceedings of the VLDB Endowment – Proceedings of the 41st International Conference on Very Large Data Bases, Kohala Coast, Hawaii VLDB, Volume 8 Issue 12, August 2015, Pages 1908-1911 , doi: 10.14778/2824032.2824098


Moti Fridman, Vlada Artel, Anna Peled, Shir Shahal, Ashwin Ramasubramaniam, Doron Naveh (2016), Realizing Giant Magneto-Optical Effects in 3D Topological Insulators Without Magnetic Fields, arXiv: 1607.04823


Vijay Gadepally, Peinan Chen, Jennie Duggan, Aaron Elmore, Brandon Haynes, Jeremy Kepner, Samuel Madden, Tim Mattson, Michael Stonebraker (2016), The BigDAWG polystore system and architecture, High Performance Extreme Computing Conference (HPEC), 2016 IEEE, doi: 10.1109/HPEC.2016.7761636

Vijay Gadepally, Jake Bolewski, Dan Hook, Dylan Hutchison, Ben Miller, Jeremy Kepner (2015), Graphulo: Linear Algebra Graph Kernels for NoSQL Databases, Parallel and Distributed Processing Symposium Workshop (IPDPSW), 2015 IEEE International, doi: 10.1109/IPDPSW.2015.19

Louis Gagnon, Sava Sakadžić, Fréderic Lesage, Emiri T. Mandeville, Qianqian Fang, Mohammad A. Yaseen, David A. Boas (2015), Multimodal reconstruction of microvascular-flow distributions using combined two-photon microscopy and Doppler optical coherence tomography, Neurophoton. 2(1), 015008 (Mar 12, 2015), doi: 10.1117/1.NPh.2.1.015008

Kimberly Glass, John Quackenbush, Jeremy Kepner (2015), High performance computing of gene regulatory networks using a message-passing model, High Performance Extreme Computing Conference (HPEC), 2015 IEEE, doi: 10.1109/HPEC.2015.7322475

Li Guo, Andrew Breakspear, Guoyi Zhao, Lixin Gao, H. Corby Kistler, Jin-Rong Xu and Li-Jun Ma (2015), Conservation and divergence of the cAMP-PKA pathway in two plant pathogenic fungi, Fusarium graminearum and F. verticillioides, Molecular Plant Pathology (accepted), doi: 10.1111/mpp.12272

Li Guo, Guoyi Zhao, Jin-Rong Xu, H. Corby Kistler, Lixin Gao, Li-Jun Ma (2016), Compartmentalized gene regulatory network of the pathogenic fungus Fusarium graminearum, New Phytologist – published online 14 March 2016, doi: 10.1111/nph.13912

Ankush M. Gupta, Vijay Gadepally, Michael Stonebraker (2016),  Cross-engine query execution in federated database systems, High Performance Extreme Computing Conference (HPEC), 2016 IEEE, 10.1109/HPEC.2016.7761648

Julian Gutierrez, Fanny Nina-Paravecino, David Kaeli (2016), A fast level-set segmentation algorithm for image processing designed for parallel architectures, IA^3 ’16 Proceedings of the Sixth Workshop on Irregular Applications: Architectures and Algorithms, pages 66-69, doi: 10.1109/IA3.2016.17


Douglas M. Hall, Isaac R. Bruss, Justin R. Barone & Gregory M. Grason (2016), Morphology selection via geometric frustration in chiral filament bundles, Nature Materials, published online March 21, doi: 10.1038/nmat4598

G.M. Hall and G.M. Grason (2016), How geometric frustration shapes twisted fibers, inside and out: Competing morphologies of chiral filament assembly, arXiv: 1612.02422

David E. Hill and Jason P. Holland (2015) Computational studies on hypervalent iodonium(III) compounds as activated precursors for 18F radiofluorination of electron-rich arenes, Computational and Theoretical Chemistry, Volume 1066, 15 August 2015, Pages 34–46, doi: 10.1016/j.comptc.2015.05.012

David E. Hill, Neil Vasdev, Jason P. Holland (2015) Evaluating the accuracy of density functional theory for calculating 1H and 13C NMR chemical shifts in drug molecules, Computational and Theoretical Chemistry 1051 (2015) 161–172, doi: 10.1016/j.comptc.2014.11.007

Lin Hu, Spencer Wyant, Andre R. Muniz, Ashwin Ramasubramaniam, and Dimitrios Maroudas (2015) Mechanical Behavior and Fracture of Graphene Nanomeshes, J. Appl. Phys. 117, 024302 (2015); doi: 10.1063/1.4905583

Lin Hu, Karl D. Hammond, Brian D. Wirth and Dimitrios Maroudas (2015) Molecular-dynamics analysis of mobile helium cluster reactions near surfaces of plasma-exposed tungstenJ. Appl. Phys. 118, 163301, doi: 10.1063/1.4933393

Dylan Hutchison, Jeremy Kepner, Vijay Gadepally, Adam Fuchs (2015), Graphulo implementation of server-side sparse matrix multiply in the Accumulo database, High Performance Extreme Computing Conference (HPEC), 2015 IEEE, doi: 10.1109/HPEC.2015.7322448

Dylan Hutchison, Jeremy Kepner, Vijay Gadepally, Bill Howe (2016), From NoSQL Accumulo to NewSQL Graphulo: Design and utility of graph algorithms inside a BigTable database, High Performance Extreme Computing Conference (HPEC), 2016 IEEE, doi: 10.1109/HPEC.2016.7761577


Isenstein, E., Wi, S., and Ethan Yang, Y. (2015) Calibration of a Distributed Hydrologic Model Using Streamflow and Remote Sensing Snow Data. World Environmental and Water Resources Congress 2015: pp. 973-982, doi: 10.1061/9780784479162.093



Jeremy Kepner, Peter Aaltonen, David Bader, Aydin Buluç, Franz Franchetti, John Gilbert, Dylan Hutchison, Manoj Kumar, Andrew, Lumsdaine, Henning Meyerhenke, Scott McMillan, Carl Yang, John D. Owens, Marcin Zalewski, Timothy Mattson, Jose Moreira (2016),  Mathematical foundations of the GraphBLAS, High Performance Extreme Computing Conference (HPEC), 2016 IEEE, 10.1109/HPEC.2016.7761646

Jeremy Kepner, Vijay Gadepally, Dylan Hutchison, Hayden Jananthan, Timothy Mattson, Siddharth Samsi, Albert Reuther (2016), Associative array model of SQL, NoSQL, and NewSQL databases, High Performance Extreme Computing Conference (HPEC), 2016 IEEE, doi: 10.1109/HPEC.2016.7761647

Jeremy Kepner, William Arcand, David Bestor, Bill Bergeron, Chansup Byun, Lauren Edwards, Vijay Gadepally, Matthew Hubbell, Peter Michaleas, Julie Mullen, Andrew Prout, Antonio Rosa, Charles Yee, Albert Reuther (2015), Lustre, hadoop, accumulo, High Performance Extreme Computing Conference (HPEC), 2015 IEEE, doi: 10.1109/HPEC.2015.7322476

Jeremy Kepner, David Bader, Aydın Buluç, John Gilbert, Timothy Mattson, Henning Meyerhenke (2015), Graphs, Matrices, and the GraphBLAS: Seven Good Reasons, Procedia Computer Science
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William Lehman, Greg Medlock, Xiaochuan (Edward) Li, Worawit Suphamungmee, An-Yue Tu, Anja Schmidtmann, Zoltán Ujfalusi, Stefan Fischer, Jeffrey R. Moorea, Michael A. Geeves, Michael Regnier (2015) Phosphorylation of Ser283 enhances the stiffness of the tropomyosin head-to-tail overlap domainArchives of Biochemistry and Biophysics Volume 571, 1 April 2015, Pages 10–15, doi: 10.1016/

Boduo Li, Edward Mazur, Yanlei Diao, Andrew McGregor and Prashant Shenoy, SCALLA: A Platform for Scalable One-Pass Analytics Using MapReduceACM Transactions on Database Systems (TODS) , Volume 37 Issue 4, December 2012, doi: 10.1145/2389241.2389246

Xiaochuan Edward Li, Marek Orzechowskia, William Lehman, and Stefan Fischer (2014) Structure and flexibility of the tropomyosin overlap junction, Biochemical and Biophysical Research Communications, Volume 446, Issue 1, 28 March 2014, Pages 304–308, doi: 10.1016/j.bbrc.2014.02.097

Jiaqi Lin and Alfredo Alexander-Katz (2013), Cell Membranes Open “Doors” for Cationic Nanoparticles/Biomolecules: Insights into Uptake Kinetics, ACS Nano, 2013, 7 (12), pp 10799–10808, doi: 10.1021/nn4040553

Chang-Tsan Lu, Asanka Weerasinghe, Dimitrios Maroudas, and  Ashwin Ramasubramaniam (2016), A Comparison of the Elastic Properties of Graphene- and Fullerene-Reinforced Polymer Composites: The Role of Filler Morphology and SizeScientific Reports 6, Article number: 31735 (published online August 2, 2016), doi: 10.1038/srep31735


Mahram, A. and Herbordt, M.C. (2012), FMSA: FPGA-Accelerated ClustalW-Based Multiple Sequence Alignment through Pipelined Prefiltering, 2012 IEEE 20th Annual International Symposium on Field-Programmable Custom Computing Machines (FCCM), pp. 177 – 183, doi: 10.1109/FCCM.2012.38

Dimitrios Maroudas, Sophie Blondel, Lin Hu, Karl D Hammond and Brian D Wirth (2016), Helium segregation on surfaces of plasma-exposed tungsten, Journal of Physics: Condensed Matter, Volume 28, Number 6

Alexander Mathis, Dan Rokni, Vikrant Kapoor, Matthias Bethge, Venkatesh N. Murthy (2016) Reading Out Olfactory Receptors: Feedforward Circuits Detect Odors in Mixtures without Demixing. Neuron first published September, 7, 2016, doi: 10.1016/j.neuron.2016.08.007

Moran, Andrew (2016), Improving big data visual analytics with interactive virtual reality, Thesis: M. Eng., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2016,

Muhammad Zain Mustafa (2014) Energy Agile Cluster Communication, University of Massachusetts, Amherst, Masters Thesis


Jeffrey K. Noel and Paul Whitford (2016), How EF-Tu can contribute to efficient proofreading of aa-tRNA by the ribosome, Nature Communications 7, Article number: 13314, doi: 10.1038/ncomms13314

Kien Nguyen and Paul Whitford (2016), Steric interactions lead to collective tilting motion in the ribosome during mRNA–tRNA translocationNature Communications 7, Article number: 10586,  doi: 10.1038/ncomms10586


Stella S. R. Offner, Michael M. Dunham, Katherine I. Lee, Hector G. Arce, and Drummond B. Fielding (2016), The Turbulent Origin of Outflow and Spin Misalignment in Multiple Stare Systems, arXiv: 1606.08445

Marek Orzechowski, Jeffrey R. Moore, Stefan Fischer, William Lehman (2014) Tropomyosin movement on F-actin during muscle activation explained by energy landscapes, Archives of Biochemistry and Biophysics, Volume 545, 1 March 2014, Pages 63–68, doi: 10.1016/

Marek Orzechowski, Stefan Fischer, Jeffrey R. Moore, William Lehman, Gerrie P. Farman (2014) Energy landscapes reveal the myopathic effects of tropomyosin mutations, Archives of Biochemistry and Biophysics, Volume 564, 15 December 2014, Pages 89–99, doi: 10.1016/


Leela S. Panchakarla, Luc Lajaunie, Ashwin Ramasubramaniam, Raul Arenal, and Reshef Tenne (2016), Nanotubes from Oxide-Based Misfit Family: The Case of Calcium Cobalt Oxide, ACS Nano, Article ASAP, doi: 10.1021/acsnano.6b02430, Publication Date (Web): May 24, 2016

Leela S. Panchakarla, Luc Lajaunie, Ashwin Ramasubramaniam , Raul Arenal , and Reshef Tenne (2016), Strontium Cobalt Oxide Misfit Nanotubes, Chem. Mater., 2016, 28 (24), pp 9150–9157,
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Patrick Pegus, Benoy Varghese, Tian Guo, David Irwin, Prashant Shenoy, Anirban Mahanti, James Culbert, John Goodhue, Chris Hill (2016), Analyzing the Efficiency of a Green University Data Center, ICPE’16, March 12–18, 2016, Delft, Netherlands, doi: 10.1145/2851553.2851557

Germań Peŕez-Sańchez, Szu-ChiaChien, JoséR.B.Gomes, M.NataĺiaD.S.Cordeiro, Scott M. Auerbach, Peter A. Monson, and Miguel Jorge (2016), Multiscale Model for the Templated Synthesis of Mesoporous Silica: The Essential Role of Silica OligomersChem. Mater. 2016, 28, 2715−2727, doi: 10.1021/acs.chemmater.6b00348

Ishan Prasad, Youngmi Seo, Lisa M. Hall, Gregory M. Grason (2016), Intradomain Textures in Block Copolymers: Multizone Alignment and Biaxiality, Soft Condensed Matter, arXiv: 1612.07994

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 (2016), Enhancing HPC security with a user-based firewall, High Performance Extreme Computing Conference (HPEC), 2016 IEEE, doi: 10.1109/HPEC.2016.7761641



Rabassa, Albert O. III (2014) Economic performance of modularized hot-aisle contained datacenter PODs utilizing horizontal airflow cooling, Masters Thesis, Sloan school of Management, MIT

Ashwin Ramasubramaniam and Andre R. Muniz (2014) Ab initio studies of thermodynamic and electronic properties of phosphorene nano ribbons, Phys. Rev. B 90, 085424, doi: 10.1103/PhysRevB.90.085424

Lawrence A. Renna, Monojit Bag, Timothy S. Gehan, Xu Han, Paul M. Lahti, Dimitrios Maroudas, and D. Venkataraman (2016), Tunable Percolation in Semiconducting Binary Polymer Nanoparticle Glasses, J. Phys. Chem. B, Article ASAP,
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Albert Reuther, Chansup Byun, William Arcand, David Bestor
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Michael J. Rynkiewicz, Veronika Schott, Marek Orzechowski, William Lehman , Stefan Fischer (2015) Electrostatic interaction map reveals a new binding position for tropomyosin on F-actin,  Journal of Muscle Research and Cell Motility, doi: 10.1007/s10974-015-9419-z

Michael J. Rynkiewicz, Stefan Fischer, William Lehman (2016), The propensity for tropomyosin twisting in the presence and absence of F-actinArchives of Biochemistry and Biophysics, Volume 609, 1 November 2016, Pages 51–58, doi: 10.1016/


Ray M. Sehgal and Dimitrios Maroudas (2015), Equilibrium Shape of Colloidal CrystalsLangmuir, 2015, 31 (42), pp 11428–11437
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Florence R. Sullivan, Kevin Keith, Nocholas C. Wilson (2016), Learning from the Periphery in a Collaborative Robotics Workshop for Girls, Universal Journal of Educational Research 4(12): 2814-2825, 2016, doi: 10.13189/ujer.2016.041215

Styers, John M., Gamache Robert (2014), Explicit Parallelization of Robert-Bonamy Formalism, 13th International HITRAN Conference, held 23-25 June 2014 in Cambridge, Massachusetts, USA, doi: 10.5281/zenodo.11186

Latanya Sweeney, Merce Crosas (2015), An Open Science Platform for the Next Generation of Data,  arXiv:1506.05632


Thomas Goldstein, Shao-Yu Chen, Di Xiao, Ashwin Ramasubramaniam and Jun Yan (2016), Raman scattering and anomalous Stokes–anti-Stokes ratio in MoTe2 atomic layers, arXiv: 1603.03740



Vetro, R., Farhoodi, R., Kotla, R., Haspel, N., Weisman, D., Rosen, J., Simovici, D. (2014) TIDE: Inter-chromosomal translocation and insertion detection using embeddings, 2014 IEEE International Conference on Big Data, pages 64-70, pub. IEEE, doi: 10.1109/BigData.2014.7004395

Mark J. Veyette, Philip S. Muirhead, Andrew W. Mann, and Frances Allard (2016), The Physical Mechanism Behind M Dwarf Metallicity Indicators and the Role of C and O Abundancies, arXiv:1605.04904v2 [astro-ph.SR] 20 May 2016


Wei L. Wang and Efthimios Kaxiras (2013) Efficient calculation of the effective single-particle potential and its application in electron microscopy, Phys. Rev. B 87, 085103 – Published 5 February 2013, doi: 10.1103/PhysRevB.87.085103

Wei Li Wang, Elton J. G. Santos, Bin Jiang, Ekin Dogus Cubuk, Colin Ophus, Alba Centeno, Amaia Pesquera, Amaia Zurutuza, Jim Ciston, Robert Westervelt, and Efthimios Kaxiras (2014) Direct Observation of a Long-Lived Single-Atom Catalyst Chiseling Atomic Structures in Graphene, Nano Lett., 2014, 14 (2), pp 450–455, doi: 10.1021/nl403327u

Wi, S., Yang, Y. C. E., Steinschneider, S., Khalil, A., and Brown, C. M.: Calibration approaches for distributed hydrologic models in poorly gaged basins: implication for streamflow projections under climate change, Hydrol. Earth Syst. Sci., 19, 857-876, doi: 10.5194/hess-19-857-2015, 2015.




Zapater, Marina, Ata Turk, Jose M. Moya, Jose L. Ayala, and Ayse K. Coskun (2015), Dynamic Workload and Cooling Management in High-Efficiency Data Centers, The sixth International Green and Sustainable Computing Conference, IEEE, December 14 – 16, 2015

Liye Zhang, Chih-Sheng Yang, Xaralabos Varelas, Stefano Monti (2016), Altered RNA editing in 3′ UTR perturbs microRNA-mediated regulation of oncogenes and tumor-suppressors, Nature, Scientific Reports 6, Article Number: 23226, doi: 10.1038/srep23226