PUBLICATIONS

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

Below is a selection of papers that appeared in 2019 reporting the results of research using the Massachusetts Green High Performance Computing Center (MGHPCC), or acknowledging the use of Harvard’s former Odyssey Cluster and new Cannon Cluster, Northeastern’s Discovery Cluster,the Boston University Shared Computing Cluster and MIT’s Engaging Cluster all of which are housed at the MGHPCC.

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

2020

João Alves, Catherine Zucker, Alyssa A. Goodman, Joshua S. Speagle, Stefan Meingast, Thomas Robitaille, Douglas P. Finkbeiner, Edward F. Schlafly and Gregory M. Green (2020), A Galactic-scale gas wave in the solar neighborhood, Nature, doi: 10.1038/s41586-019-1874-z

Erin Arai, Alexandre Tartakovsky, R. Glynn Holt, Sheryl Grace, Emily Ryan (2020), Comparison of Surface Tension Generation Methods in Smoothed Particle Hydrodynamics for Dynamic Systems, Computers and Fluids, doi: 10.1016/j.compfluid.2020.104540

Brian Arnold, Mashaal Sohail, Crista Wadsworth, Jukka Corander, William P Hanage, Shamil Sunyaev, Yonatan H Grad (2020), Fine-Scale Haplotype Structure Reveals Strong Signatures of Positive Selection in a Recombining Bacterial Pathogen, Molecular Biology and Evolution, doi: 10.1093/molbev/msz225

Mehraj R. Awal, Gregory S. Wirak, Christopher V. Gabel, Christopher W. Connor (2020), Collapse of Global Neuronal States in Caenorhabditis elegans under Isoflurane Anesthesia, Anesthesiology doi: 10.1097/ALN.0000000000003304

Caitlin M. Baker, Sarah L. Boyer, Gonzalo Giribet (2020), A well‐resolved transcriptomic phylogeny of the mite harvestman family Pettalidae (Arachnida, Opiliones, Cyphophthalmi) reveals signatures of Gondwanan vicariance, Journal of Biogeography, doi: 10.1111/jbi.13828

Amir Bitran, William M. Jacobs, Xiadi Zhai, and Eugene Shakhnovich (2020), Cotranslational folding allows misfolding-prone proteins to circumvent deep kinetic traps, PNAS, doi: 10.1073/pnas.1913207117

Wenyu Chen and Rahul Mazumder (2020), Multivariate Convex Regression at Scale, arXiv:2005.11588 [math.OC]

Arielle Cohen, D. Kirk Lewis, Tianlun Huang, Sahar Sharifzadeh (2020), Localized Excitons in Defective Monolayer Germanium Selenide, arXiv:2005.10102 [cond-mat.mtrl-sci]

Ofer Cohen, C. Garraffo, Sofia-Paraskevi Moschou, Jeremy J. Drake, J. D. Alvarado-Gomez, Alex Glocer, and Federico Fraschetti (2020), The Space Environment and Atmospheric Joule Heating of the Habitable Zone Exoplanet TOI700-d, arXiv:2005.11587 [astro-ph.SR]

B.A. Cook, Charlie Conroy, and Pieter van Dokkum (2020), Measuring Star Formation Histories, Distances, and Metallicities with Pixel Color-Magnitude Diagrams II: Applications to nearby elliptical galaxies, arXiv: 2004.10213 [astro-ph.GA]

Jordan M Cox, Bradley Mileson, Ananthan Sadagopan, Steven Lopez (2020), Molecular Recognition and Band Alignment in 3-D Covalent Organic Frameworks for Co-Crystalline Organic Photovoltaics, ChemRxiv, doi: 10.26434/chemrxiv.10792877

Cox, Jordan; Lopez, Steven (2020), Multiconfigurational Dynamics Explain Photochemical Reactivity and Torquoselectivity Towards Fluorinated Polyacetylenes, ChemRxiv. Preprint., doi: 10.26434/chemrxiv.11980827

Earnest, Rebecca; Rönn, Minttu M.; Bellerose, Meghan Gift, Thomas L.; Berruti, Andrés A.; Hsu, Katherine K. ; Testa, Christian; Zhu, Lin ; Malyuta, Yelena; Menzies, Nicolas A.; Salomon, Joshua A. (2020) Population-Level Benefits of Extragenital Gonorrhea Screening among Men Who Have Sex with Men, Sexually Transmitted Diseases, doi: 10.1097/OLQ.0000000000001189

M. Francisquez, T. N. Bernard, B. Zhu, A. Hakim, B. N. Rogers, and G. W. Hammett (2020), Fluid & Gyrokinetic turbulence in open field-line, helical plasmas, arXiv: 2002.11136 [physics.plasm-ph]

Alexander V. Gramolin, Deniz Aybas, Dorian Johnson, Janos Adam, and Alexander O. Sushkov (2020), Search for axion-like dark matter with ferromagnets, arXiv: 2003.03348 [hep-ex]

Sam Hadden and Matthew J. Payne (2020), Modeling Radial Velocity Data of Resonant Planets to Infer Migration Histories, arXiv:2005.03034 [astro-ph.EP]

Yiwen Huang, Carl-Johan Haster, Salvatore Vitale, Vijay Varma, Francois Foucart, and Sylvia Biscoveanu (2020), Statistical and systematic uncertainties in extracting the source properties of neutron star – black hole binaries with gravitational waves, arXiv: 2005:11850 [gr-qc]

Weronika Jasinska, Michael Manhart, Jesse Lerner, Louis Gauthier, Adrian W. R. Serohijos and Shimon Bershtein (2020), Chromosomal barcoding of E. coli populations reveals lineage diversity dynamics at high resolution, Nat Ecol Evol, doi: 10.1038/s41559-020-1103-z

Zhiguang Jia, Jeremy D. Schmit, and Jianhan Chen (2020), Amyloid assembly is dominated by misregistered kinetic traps on an unbiased energy landscape, PNAS, doi: 10.1073/pnas.1911153117

C. Rose Kennedy, Bo Young Choi, Mary‐Grace R. Reeves, Eric N. Jacobsen (2020), Enantioselective Catalysis of an Anionic Oxy‐Cope Rearrangement Enabled by Synergistic Ion Binding, Israel Journal of Chemistry, doi: 10.1002/ijch.201900168

Leonard C. Kogos, Yunzhe Li, Jianing Liu, Yuyu Li, Lei Tian & Roberto Paiella (2020), Plasmonic ommatidia for lensless compound-eye vision, Nature Communications. doi: 10.1038/s41467-020-15460-0

Dibyendu Kumar Das, Uriel Bulow, William E. Diehl, Natasha D. Durham, Fernando Senjobe, Kartik Chandran, Jeremy Luban, James B. Munro (2020), Conformational changes in the Ebola virus membrane fusion machine induced by pH, Ca2+, and receptor binding, PLOS Biology, doi: 10.1371/journal.pbio.3000626

Daniel T. Larson, Wei Chen, Steven B. Torrisi, Jennifer Coulter, Shiang Fang, and Efthimios Kaxiras (2020), Effects of Structural Distortions on the Electronic Structure of T-type Transition Metal Dichalcogenides, arXiv: 2003.10473 [cond-mat.mes-hall]

Joel Leja, Joshua S. Speagle, Benjamin D. Johnson, Charlie Conroy, Pieter van Dokkum, and Marijn Franx (2020), A New Census of the 0.2 < z < 3.0 Universe. I. The Stellar Mass Function, The Astrophysical Journal, doi; 10.3847/1538-4357/ab7e27

Christopher M. Lemon, Andrew G. Maher, Anthony R. Mazzotti, David C. Powers, Miguel I. Gonzaleza and Daniel G. Nocera (2020), Multielectron C–H photoactivation with an Sb(v) oxo corrole, Chemical Communications, doi: 10.1039/C9CC09892E

Yuyu Li, Khwanchai Tantiwanichapan, Anna K. Swan and Roberto Paiella (2020), Graphene plasmonic devices for terahertz optoelectronics, Nanophotonics, doi: 10.1515/nanoph-2020-0211

Jiaqi Lin, Lei Miao, Grace Zhong, Chih-Hsin Lin, Roozbeh Dargazangy & Alfredo Alexander-Katz (2020), Understanding the synergistic effect of physicochemical properties of nanoparticles and their cellular entry pathways, Communications Biology., doi: s42003-020-0917-1

Jaclyn Y. Lock, Taylor L. Carlson, Yueyue Yu, Jing Lu, Erika C. Claud & Rebecca L. Carrier (2020), Impact of Developmental Age, Necrotizing Enterocolitis Associated Stress, and Oral Therapeutic Intervention on Mucus Barrier Properties, Scientific Reports, doi: 10.1038/s41598-020-63593-5

Qiyang Lu , Samuel Huberman , Hantao Zhang, Qichen Song , Jiayue Wang , Gulin Vardar, Adrian Hunt, Iradwikanari Waluyo, Gang Chen  and Bilge Yildiz  (2020), Bi-directional tuning of thermal transport in SrCoOx with electrochemically induced phase transitions, Nature Materials, doi: 10.1038/s41563-020-0612-0

Robert Marsland III, Cui Wenping, Mehta Pankaj (2020), A minimal model for microbial biodiversity can reproduce experimentally observed ecological patterns, Scientific Reports, doi: 10.1038/s41598-020-60130-2

Morovatiyan, Mohammadrasool (2020), Fundamental Investigation of Symmetrically Expanding Premixed Flames of Gaseous Fuels and Noble Gas Working Fluids in a Constant Volume Combustion Chamber, University of Massachusetts Lowell, ProQuest Dissertations Publishing

Jeffrey Z. Pan and Nicholas Zufelt (2020), On Intrinsic Dataset Properties for Adversarial Machine Learning, arXiv: 2005.0917 [cs.LG]

T. Patel and D. Tiwari (2020), CLITE: Efficient and QoS-Aware Co-Location of Multiple Latency-Critical Jobs for Warehouse Scale Computers, 2020 IEEE International Symposium on High Performance Computer Architecture (HPCA), San Diego, CA, USA, 2020, doi: 10.1109/HPCA47549.2020.00025

Monica Pengshung, Patrick Neal, Timothy L. Atallah, Junho Kwon, Justin R. Caram, Steven A. Lopez, Ellen M. Sletten (2020), Silicon incorporation in polymethine dyes, The Royal Society of Chemistry via ChemrXiv

Achilleas Pipertzis, George Papamoko, Markus Mühlinghaus, Markus Mezger, Ullrich Scherf, George Floudas (2020), What Determines the Glass Temperature and dc-Conductivity in Imidazolium-Polymerized Ionic Liquids with a Polythiophene Backbone? Macromolecules, doi: 10.1021/acs.macromol.0c00226

Reza Pourhaghighi et al (2020), BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain, Cell Systems, doi: 10.1016/j.cels.2020.03.003

Dmitry Prokopenko, Julian Hecker, Rory Kirchner, Brad A. Chapman, Oliver Hoffman, Kristina Mullin, Winston Hide, Lars Bertram, Nan Laird, Dawn L. DeMeo, Christoph Lange & Rudolph E. Tanzi (2020), Identification of Novel Alzheimer’s Disease Loci Using Sex-Specific Family-Based Association Analysis of Whole-Genome Sequence Data, Scientific Reports, doi: s41598-020-61883-6

Yangzhong Qin, Christoph Schnedermann, Mariusz Tasior, Daniel T. Gryko, and Daniel G. Nocera (2020), Direct Observation of Different One- and Two-Photon Fluorescent States in a Pyrrolo[3,2‐b]pyrrole Fluorophor, J. Phys. Chem. Lett. , doi: 10.1021/acs.jpclett.0c00669

Loïc M. Roch, Semion K. Saikin, Florian Häse, Pascal Friederich, Randall H. Goldsmith, Salvador León, and Alán Aspuru-Guzik (2020), From Absorption Spectra to Charge Transfer in Nanoaggregates of Oligomers with Machine Learning, ACS Nano, doi: 10.1021/acsnano.0c00384

Andrés N Salcedo, Benjamin D Wibking, David H Weinberg, Hao-Yi Wu, Douglas Ferrer, Daniel Eisenstein, Philip Pinto (2020), Cosmology with stacked cluster weak lensing and cluster–galaxy cross-correlations, Monthly Notices of the Royal Astronomical Society, doi: 10.1093/mnras/stz2963

Anders W. Sandvik and Bowen Zhao (2020), Consistent scaling exponents at the deconfined quantum-critical point, arXiv: 2003.14305 [ cond-mat.str-el]

Mehmet Gokhan Sensoy, Matthew M. Montemore (2020), A Density Functional Theory Investigation of Oxidation Intermediates on Gold and Gold-Silver Surfaces, J. Phys. Chem. C, doi: 10.1021/acs.jpcc.0c01386

Debjani Sihi, Eric A. Davidson, Kathleen E. Savage, Dong Liang (2020), Simultaneous numerical representation of soil microsite production and consumption of carbon dioxide, methane, and nitrous oxide using probability distribution functions, Global Change Biology, doi: 10.1111/gcb.14855

A. Soliman et al (2020), Optical Design and Characterization of 40-GHz Detector and Module for the BICEP Array, arXiv: 2002.05254 [astro-ph.IM]

T. St. Germaine et al (2020), Optical characterization of the Keck Array and BICEP3 CMB Polarimeters from 2016 to 2019, arXiv: 2002.05197 [astro-ph.IM]

Jun Takahashi and Anders W. Sandvik (2020), Valence-bond solids, vestigial order, and emergent SO(5) symmetry in a two-dimensional quantum magnet, arXiv: 2001.10045 [cond-mat.str-el]

Lindsay J. Underhill, W. Stuart Dols, Sharon K. Lee, M. Patricia Fabian and Jonathan I. Levy (2020), Quantifying the impact of housing interventions on indoor air quality and energy consumption using coupled simulation models, J Expo Sci Environ Epidemiol., doi: 10.1038/s41370-019-0197-3

V.V. Volkov, R. Chelli, R. Righini, C.C. Perry (2020), Indigo chromophores and pigments: Structure and dynamics, Dyes and Pigments, doi: 10.1016/j.dyepig.2019.107761

Yichao Wang Prof. Sooran Kim Dr. Jingyu Lu Guangyuan Feng Prof. Xin Li (2020), A Study of Cu Doping Effects in P2‐Na0.75Mn0.6Fe0.2(CuxNi0.2‐x)O2 Layered Cathodes for Sodium‐Ion Batteries, Batteries and Supercaps, doi: 10.1002/batt.201900172

Xiaowei Wang, Yuyu Li, Reyhaneh Toufanian, Leonard C. Kogos, Allison M. Dennis, Roberto Paiella (2020), Geometrically Tunable Beamed Light Emission from a Quantum‐Dot Ensemble Near a Gradient Metasurface, Advanced Optical Materials, doi: 10.1002/adom.201901951

Jack Wisdom (2020), Meteorite transport—Revisited II, Meteoritics and Planetary Science, doi: 10.1111/maps.13463

Xiao Wu, Rachel C. Nethery, M. Benjamin Sabath, Danielle Braun, Francesca Dominici (2020), Exposure to air pollution and COVID-19 mortality in the United States, [pdf]

Xiao Wu Yi Xu Bradley P. Carlin (2020), Optimizing interim analysis timing for Bayesian adaptive commensurate designs, Statistics in Medicine, doi: 10.1002/sim.8414

Sibin Yang, Dao-Xin Yao and Anders W. Sandvik (2020), Deconfined quantum criticality in spin-1/2 chains with long-range interactions, arXiv: 2001.02821 [physics.comp-ph]

Mahdieh Yazdani, Guohui Zhang, Zhiguang Jia, Jingyi Shi, Jianmin Cui, and Jianhan Chen (2020), Nonspecific Membrane Interactions Can Modulate BK Channel Activation, bioRxiv: 2020/02/06/2020.02.05.936161

Jingjie Yeo, Yimin Qiu, Gang Seob Jung, Yong-Wei Zhang, Markus J. Buehler, David L. Kaplan (2020), Adverse effects of Alport syndrome-related Gly missense mutations on collagen type IV: Insights from molecular simulations and experiments, Biomaterials, doi: 10.1016/j.biomaterials.2020.119857

Hailong Wang, Erik T. Nilsen and Moneesh Upmanyu (2020), Mechanical basis for thermonastic movements of cold-hardy Rhododendron leaves, Journal f the Royal Society Interface, doi: 10.1098/rsif.2019.0751

Huize Wang and Robin Wordsworth (2020), Extremely Long Convergence Times in a 3D GCM Simulation of the Sub-Neptune Gliese 1214b, The Astrophysical Journal, doi: 10.3847/1538-4357/ab6dcc

Michael E. Xie, Yoav Adam, Linlin Z. Fan, Urs L. Böhm, Ian Kinsella, Ding Zhou, Liam Paninski, Adam E. Cohen (2020), High fidelity estimates of spikes and subthreshold waveforms from 1-photon voltage imaging in vivo, bioRxiv, doi: 10.1101/2020.01.26.920256

C. Zhang et al (2020), Characterizing the Sensitivity of 40 GHz TES Bolometers for BICEP Array, arXiv:2002.05219 [astro-ph.IM]

Lei Zhang, Justin A. Reyes, Stefanos Kourtis, Claudio Chamon, Eduardo R. Mucciolo, and Andrei E. Ruckenstein (2020), Nonuniversal entanglement level statistics in projection-driven quantum circuits, arXiv: 2001.11428 [cond-mat.stat-mech]

Yong Zhang, He Yang, David Turra, Shiguo Zhou, Dilay Hazal Ayhan, Gregory A. DeIulio, Li Guo, Karen Broz, Nathan Wiederhold, Jeffrey J. Coleman, Kerry O’ Donnell, Ilan Youngster, Alexander J. McAdam, Sergey Savinov, Terrance Shea, Sarah Young, Qiandong Zeng, Martijn Rep, Eric Pearlman, David C. Schwartz, Antonio Di Pietro, H. Corby Kistler & Li-Jun Ma  (2020), The genome of opportunistic fungal pathogen Fusarium oxysporum carries a unique set of lineage-specific chromosomes, Nature Communications Biology, doi: s42003-020-0770-2

Bowen Zhao, Jun Takahashi, and Anders W. Sandvik1 (2020), Multicritical deconfined quantum-criticality and Lifshitz point of a helical valence-bond phase, arXiv:2005:10184 [cond-mat.str.el]

Muni Zhou, Nuno F. Loureiro, Dmitri A. Uzdensky (2020), Multi-scale dynamics of magnetic flux tubes and inverse magnetic energy transfer, arXiv: 2001.07291 [astro-ph.HE]

Catherine Zucker, Joshua S. Speagle, Edward F. Schlafly, Gregory M. Green, Douglas P. Finkbeiner, Alyssa Goodman, João Alves (2020), A compendium of distances to molecular clouds in the Star Formation Handbook, arXiv: 2001.00591 [astro-ph.GA]

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

 


Prior Years

2019 | 2018 | 2017 | 2016 and earlier