PUBLICATIONS

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

Below is a selection of papers that appeared in 2020 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

2021

T. Aarrestad et al (2021), The Dark Machines Anomaly Score Challenge: Benchmark Data and Model Independent Event Classification for the Large Hadron Collider, arXiv: 2105:14027 [hep.ph]

Amin Aboubrahim, Pran Nath and Raza M. Syed (2021), Corrections to Yukawa couplings from higher dimensional operators in a natural SUSY SO(10) and HL-LHC implications, Journal of High Energy Physics, doi: 10.1007/JHEP01(2021)047

Meishan Ai et al (2021), The daily activity study of health (DASH): A pilot randomized controlled trial to enhance physical activity in sedentary older adults, Contemporary Clinical Trials, doi: 10.1016/j.cct.2021.106405

P. Ambati, N. Bashir, D. Irwin, and P. Shenoy (2021), Modeling and Analyzing Waiting Policies for Cloud-Enabled Schedulers, IEEE Transactions on Parallel and Distributed Systems, vol. 32, no. 12, pp. 3081-3100, 1 Dec. 2021, doi: 10.1109/TPDS.2021.3086270

Shi Jun Ang, Wujie Wang, Daniel Schwalbe-Koda, Simon Axelrod, Rafael Gómez-Bombarelli (2021),
Active learning accelerates ab initio molecular dynamics on reactive energy surfaces, Chem, doi: 10.1016/j.chempr.2020.12.009

A. Ashtari Esfahani et al. (2021), Bayesian Analysis of a Future Beta Decay Experiment’s Sensitivity to Neutrino Mass Scale and Order, arXiv: 2012.14341 [physics.data-an]

Simon Axelrod, Eugene Shakhnovich, and Rafael Gómez-Bombarelli (2021), Excited state, non-adiabatic dynamics of large photoswitchable molecules using a chemically transferable machine learning potential, arXiv: 2108.04879 [physics.chem-ph]

Deniz Aybas et al. (2021), Search for axion-like dark matter using solid-state nuclear magnetic resonance, arXiv:2101.01241 [hep-ex]

Dimitris Bertsimas, Jack Dunn, Yuchen Wang (2021), Near-optimal Nonlinear Regression Trees, Operations Research Letters, doi: 10.1016/j.orl.2021.01.002

BICEP/Keck Collaboration (2021), BICEP / Keck XIV: Improved constraints on axion-like polarization oscillations in the cosmic microwave background, arXiv:2108.03316 [astro-ph.CO]

Bodhi Biswas, Syun’ichi Shiraiwa, Seung-Gyou Baek, Paul Bonoli, Abhay Ram, and Anne White (2021), A hybrid full-wave Markov chain approach to calculating radio-frequency wave scattering from Scrape-off Layer filaments, arXiv:2108.07077 [physics.plasm-ph]

Sebastian Bohr, Jesús Zavala, Francis-Yan Cyr-Racine and Mark Vogelsberger (2021), The halo mass function and inner structure of ETHOS haloes at high redshift, arXiv: 2101.08790 [astro-ph.CO]

Sebastian Bohr (2021), Dark Acoustic Oscillations in Structure Formation: The High Redshift Universe, Doctoral Dissertation University of Iceland,

Matteo Braglia, Xingang Chen, and Dhiraj Kumar Hazra (2021), Uncovering the History of Cosmic Inflation from Anomalies in Cosmic Microwave Background Spectra, arXiv: 2106.07546 [astro-ph.CO]

Matteo Braglia, Xingang Chen, and Dhiraj Kumar Hazra (2021), Primordial Standard Clock Models and CMB Residual Anomalies, arXiv: 2108.10110 [astro-ph.CO]

Manuel A. Buen-Abad, Rouven Essig, David McKeen, Yi-Ming Zhong (2021), Cosmological Constraints on Dark Matter Interactions with Ordinary Matter, arXiv:2107.12377 [astro-ph.CO]

Jonathan Chamberlain, Eran Simhon, David Starobinski (2021), Preemptible queues with advance reservations: Strategic behavior and revenue management, European Journal of Operational Research, doi: 10.1016/j.ejor.2020.12.044

Mengxi Chen, Asanka Weerasinghe, Andre R. Muniz, Ashwin Ramasubramaniam, and Dimitrios Maroudas (2021), Molecular-Dynamics Simulations on Nanoindentation of Graphene-Diamond Composite Superstructures in Interlayer-Bonded Twisted Bilayer Graphene: Implications for Mechanical Metamaterials, Applied Nano Materials, doi: 10.1021/acsanm.1c02236

Qiuming Chen, Yanchang Wu, Zhaolin Huang, Wenli Zhang, and Wanmeng Mu (2021), Molecular Characterization of a Mesophilic Cellobiose 2-Epimerase That Maintains a High Catalytic Efficiency at Low Temperatures, Journal of Agricultural and Food Chemistry Article ASAP, doi: 10.1021/acs.jafc.1c02025

Xi Chen, Hao Tang, Yichao Wang, and Xin Li (2021), Balancing orbital effects and on-site Coulomb repulsion through Na modulations in NaxVO2, Physical Review Materials, doi: 10.1103/PhysRevMaterials.5.084402

Alberto Concellón, Ru-Qiang Lu, Kosuke Yoshinaga, Hsiu-Fu Hsu, and Timothy M. Swager (2021), Electric-Field-Induced Chirality in Columnar Liquid Crystals, J. Am. Chem. Soc. , doi: 10.1021/jacs.1c05268

Qiang Cui, Tanmoy Pal, and Luke Xie (2021), Biomolecular QM/MM Simulations: What Are Some of the “Burning Issues”?, J. Phys. Chem. B, doi: 10.1021/acs.jpcb.0c09898

Olivia Curtis, Tereasa G. Brainerd, Anthony Hernandez (2021), Cosmic Voids in Generated N-body Simulations, arXiv: 2106.04014 [astro-ph.CO]

Jiahua Deng and Qiang Cui (2021), Reverse Protonation of Buried Ion-Pairs in Staphylococcal Nuclease Mutants, J. Chem. Theory Comput., doi: 10.1021/acs.jctc.1c00355

Esteban Dodero-Rojas, Jose N. Onuchic, Paul C. Whitford (2021), Sterically-Confined Rearrangements of SARS-CoV-2 Spike Protein Control Cell Invasion, bioRxiv, doi: 10.1101/2021.01.18.427189

Donmez, Bilgehan (2020), Topology Error Detection in Power System State Estimation, Northeastern University Doctoral Dissertation, Proquest 28261370

Rebecca Earnest et al (2021), Modeling the Cost-Effectiveness of Express Multi-Site Gonorrhea Screening among Men Who Have Sex with Men in the United States, Sexually Transmitted Diseases, doi: 10.1097/OLQ.0000000000001467

William Fitzhugh, Xi Chen, Yichao Wang, Luhan Ye and Xin Li (2021), Solid–electrolyte-interphase design in constrained ensemble for solid-state batteries, Energy Environ. Sci., doi: 10.1039/D1EE00754H

Anyuan Gao et al (2021), Layer Hall effect in a 2D topological Axion antiferromagnet, arXiv:2107.10233 [cond.mat.mtrl-sci]

Benjamin E. Goulet-Scott, Austin G. Garner, Robin Hopkins (2021), Genomic analyses overturn two long-standing homoploid hybrid speciation hypotheses, Evolution, doi: 10.1111/evo.14279

Mark T. Gregory, Yang Gao, Qiang Cui, and Wei Yang (2021), Multiple deprotonation paths of the nucleophile 3′-OH in the DNA synthesis reaction, PNAS, doi: 10.1073/pnas.2103990118

Harms, Nathan D. (2020), Improving Detailed Kinetic Models through Automated Transition State Theory Calculations, Northeastern University Doctoral Dissertation, Proquest 28260517

Daniel Hartman, Dávid Lehotzky, Iulian Ilieş, Mariana Levi & Günther K. H. Zupanc (2021), Modeling of sustained spontaneous network oscillations of a sexually dimorphic brainstem nucleus: the role of potassium equilibrium potential, Journal of Computational Neuroscience, doi: 10.1007/s10827-021-00789-2

Florian Häse, Matteo Aldeghi, Riley J. Hickman, Loïc M. Roch, and Alán Aspuru-Guzik (2021), Gryffin: An algorithm for Bayesian optimization of categorical variables informed by expert knowledge, Applied Physics Reviews, doi: 10.1063/5.0048164

Nathan T. Howard et al (2021), The role of ion and electron-scale turbulence in setting heat and particle transport in the DIII-D ITER Baseline Scenario, Nuclear Fusion, doi: 10.1088/1741-4326/ac1bc2

Zeyuan Hu, Fayçal Lamraoui, and Zhiming Kuang (2021), Influence of Upper-Troposphere Stratification and Cloud-Radiation Interaction on Convective Overshoots in the Tropical Tropopause Layer, Journal of Atmospheric Sciences, doi: 10.1175/JAS-D-20-0241.1

Huanping Huang et al (2021), Rise in Northeast US extreme precipitation caused by Atlantic variability and climate change, Weather and Climate Extremes, doi: 10.1016/j.wace.2021.100351

Theodore Huang, Matthew Ploenzke, Danielle Braun (2021), SNIP: An Adaptation of Sorted Neighborhood Methods for Deduplicating Pedigree Data, arXiv:2108.08773 [stat.AP]

ITALSGEN Consortium (2021), Genome-wide Analyses Identify KIF5A as a Novel ALS Gene, Neuron, doi: 10.1016/j.neuron.2018.02.027

Weiwen Ji, Alexander Robel, Eli Tziperman, Jun Yang (2021), Laurentide Ice Saddle Mergers Drive Rapid Sea Level Drops During Glaciations, Geophysical Research Letters, doi: 10.1029/2021GL094263

Shao-Kai Jian, Zhi-Cheng Yang, Zhen Bi, and Xiao Chen (2021), Yang-Lee edge singularity triggered entanglement transition, arXiv:2101.04115 [cond-mat.str-el]

Cheng-Wei Ju et al (2021), Stacked Ensemble Machine Learning for Range-Separation Parameters, ChemRxiv. Cambridge: Cambridge Open Engage

Harshil Kamdar, Charlie Conroy, Yuan-Sen Ting (2021), Stellar Streams in the Galactic Disk: Predicted Lifetimes and Their Utility in Measuring the Galactic Potential, arXiv: 2106.02050 [astro-ph.GA]

Franklyn Kanyako and Erin Baker (2021), Uncertainty analysis of the future cost of wind energy on climate change mitigation, Climatic Change, doi: 10.1007/s10584-021-03105-0

Ned Kleiner, Pak Wah Chan, Lei Wang, Ding Ma, Zhiming Kuang (2021), Effects of Climate Model Mean-State Bias on Blocking Underestimation, Geophysical Research Letters, doi: 10.1029/2021GL094129

Justine Kozubal, Tristan Heck, and Ricardo B. Metz (2021), Structures of M+(CH4)n (M = Ti, V) Based on Vibrational Spectroscopy and Density Functional Theory, J. Phys. Chem. A, doi: 10.1021/acs.jpca.1c02217

Aaron Kucy, Michael Esterman, James Capella, Allison Green, Mai Uchida, Joseph Biederman, John D.E. Gabrieli, Eve M. Valera, Susan Whitfield-Gabrieli (2021), Generalizable prediction of stimulus-independent, task-unrelated thought from functional brain networks, biorXiv, doi: 10.1101/2021.01.25.428126

Benjamin Levy, Kristen Windoloski, John Ludlam (2021), Matrix and agent-based modeling of threats to a diamond-backed terrapin population, Mathematical Biosciences, doi: 10.1016/j.mbs.2021.108672

Daniel Li, Sheila M. Gaynor, Corbin Quick, Jarvis T. Chen, Briana J.K. Stephenson, Brent A. Coull, Xihong Lin (2021), Identifying US Counties with High Cumulative COVID-19 Burden and Their Characteristics, medRxiv, doi: 10.1101/2020.12.02.20234989

Li J, Stein R, Adrion D, Lopez S. (2021), Machine-learning photodynamics simulations uncover the role of substituent effects on the photochemical formation of cubanes, ChemRxiv. Cambridge: Cambridge Open Engage

June Li et al (2021), Silica-copper catalyst interfaces enable carbon-carbon coupling towards ethylene electrosynthesis, Nature Communications, doi: 10.1038/s41467-021-23023-0

Longxiang Li et al (2021), Predicting Monthly Community-Level Domestic Radon Concentrations in the Greater Boston Area with an Ensemble Learning Model, Environmental Science & Technology Article ASAP, doi: 10.1021/acs.est.0c08792

Longxiang Li et al (2021), A spatiotemporal ensemble model to predict gross beta particulate radioactivity across the contiguous United States, Environmental International, doi: 10.1016/j.envint.2021.106643

Qiaohao Liang et al (2021), Benchmarking the Performance of Bayesian Optimization Across Multiple Experimental Materials Science Domains, arXiv: 2106.01309 [cond-mat.mtr-sci]

David M. Long, Philip J. D. Crowley, and Anushya Chandran (2021), Many-Body Localization with Quasiperiodic Driving, arXiv: 2108.04834 [cond-mat.dis-nn]

Longchamps RJ et al (2021), Genome-wide analysis of mitochondrial DNA copy number reveals multiple loci implicated in nucleotide metabolism, platelet activation, and megakaryocyte proliferation, biorXiv, doi: 10.1101/2021.01.25.428086

Song Luo, Tongkun Wang, Jason Gulbinski, Long Qi, Geoffrey A. Tompsett, Michael T. Timko, Scott M. Auerbach, and Wei Fan (2021), Identifying Order and Disorder in Double Four-Membered Rings via Raman Spectroscopy during Crystallization of LTA Zeolite, Chemistry of Materials, doi: 10.1021/acs.chemmater.1c01420

Shao-Xiong Lennon Luo, Richard Y. Liu, Sungsik Lee, and Timothy M. Swager (2021), Electrocatalytic Isoxazoline–Nanocarbon Metal Complexes, Journal of the American Chemical Society, doi: 10.1021/jacs.1c05439

Anindita Maiti, Keegan Stoner, and James Halverson (2021), Symmetry-via-Duality: Invariant Neural Network Densities from Parameter-Space Correlators, arXiv: 2106.00694 [cs.LG]

Smarak Maity et al. (2021), Coherent coupling of mechanics to a single nuclear spin, arXiv: 2107.10961 [quant.ph]

Taraknath Mandal, Saverio E. Spagnolie, Anjon Audhya, QiangCui (2021), Protein Induced Membrane Curvature in Coarse-Grained Simulations: Binding Interface, Insertion Depth and Lipid Spontaneous Curvature, Biophysical Journal, doi: 10.1016/j.bpj.2021.05.029

Rahul Mazumder and Haoyue Wang (2021), Linear regression with partially mismatched data: local search with theoretical guarantees, arXiv: 2106.02175 [math.OC]

Mazzoni, Fernando (2021), Time Scales in Nucleation of Active Matter, University of Massachusetts, Lowell, Masters Thesis

Brendan F. Miller, Dhananjay Bambah-Mukku, Catherine Dulac, Xiaowei Zhuang, Jean Fan (2021), Characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities. Genome Research, doi: 10.1101/gr.271288.120

Juan Moles, Tauana Junqueira Cunha, Sarah Lemer, David J Combosch, Gonzalo Giribet (2021), Tightening the girdle: phylotranscriptomics of Polyplacophora, Journal of Molluscan Studies, doi: 10.1093/mollus/eyab019

Fatemah Mukadum et al (2021), Efficient discovery of visible light-activated azoarene photoswitches with long half-lives using active search, Theoretical and Computational Chemistry, doi: 10.33774/chemrxiv-2021-w32rs

Raviv Murciano-Goroff, Ran Zhuo, Shane Greenstein (2021), Hidden Software and Veiled Value Creation: IlIustrations from server software usage, NBER Working Paper Series, https://www.nber.org/system/files/working_papers/w28738/w28738.pdf

Jack G. Nedell et al (2021), Deep learning of deformation-dependent conductance in thin films: nanobubbles in graphene, arXiv: 2108.01057 [cond-mat.mes-hall]

Seyed Ardalan Nejat et al (2021), Topology optimization of lightweight periodic lattices under stiffness and stability constraints, International Journal of Mechanical Sciences, doi: 10.1016/j.ijmecsci.2021.106727

Erica L. Nelson, Saira A. Khan, Swapna Thorve, P. Gregg Greenough (2021), Modeling pastoralist movement in response to environmental variables and conflict in Somaliland: Combining agent-based modeling and geospatial data, PLOS ONE, doi: 10.1371/journal.pone.0244185

Oner, Ahmet (2021), Improving the Resilience of the Power Grid, Northeastern University Doctoral dissertation

Michael T. Payne, Constanze N. Neumann, Eli Stavitski, and Mircea Dincǎ (2021), Complexes of Platinum Group Metals with a Conformationally Locked Scorpionate in a Metal–Organic Framework: An Unusually Close Apical Interaction of Palladium(II), Inorganic Chemistry Article ASAP, doi: 10.1021/acs.inorgchem.1c00941

George V. Papamokos, George Tziatzos, Dimitrios G. Papageorgiou, Spyros Georgatos, Efthimios Kaxiras, and Anastasia S. Politou (2021), Progressive Phosphorylation Modulates the Self-Association of a Variably Modified Histone H3 Peptide, Front. Mol. Biosci., doi: 10.3389/fmolb.2021.698182

F. Sciortino et al (2021), Experimental Inference of Neutral and Impurity Transport in Alcator C-Mod Using High-Resolution X-Ray and Ultra-Violet Spectra, arXiv: 21.07.1371 [physics.plasm-ph]

Sha Sha et al (2021), Characterization of dynamic regulation in Chinese hamster ovary (CHO) cell cultures in the late exponential phase, Science Direct, doi: 10.1016/j.bej.2020.107897

Junjie Shi et al (2021), Formation of a Ti–Cu(111) single atom alloy: Structure and CO binding, The Journal of Chemical Physics, doi: 10.1063/5.0050800

Strauss, David Edwin. (2021), Comparative Phylogeography of the Northern Australian Monsoon Tropics by Whole Genome Resequencing of two Species of the Avian Genus Climacteris, Master’s thesis, Harvard University Division of Continuing Education.

A. Molavi Tabrizi et al, (2021), Spatiotemporal Organization of Electromechanical Phase Singularities during High-Frequency Cardiac Arrhythmias, arXiv: 2107.09223 [cond-mat.soft]

Waleed Tahir and Lei Tian (2021), Adaptive 3D descattering with a dynamic synthesis network, arXiv: 2107.00484 [eess.IV]

Georgios A. Tritsaris, Stephen Carr, Gabriel R. Schleder (2021), Computational Design of Moiré Assemblies Aided by Artificial Intelligence, arXiv: 2011.04795 [cond-mat.mes-hall]

Jonathan Vandermause et al (2021), Active learning of reactive Bayesian force fields: Application to heterogeneous hydrogen-platinum catalysis dynamics, ArXiv: 2106.01949 [cond-mat.mtrl-sci]

Victor V. Volkov, Hendrik Heinz and Carole C. Perry (2021), Anchoring of a hydrophobic heptapeptide (AFILPTG) on silica facilitates peptide unfolding at the abiotic–biotic interface, Physical Chemistry Chemical Physics, doi: 10.1039/d1cp02072b

Haoyue Wang, Haihao Lu, Rahul Mazumder (2021), Frank-Wolfe Methods with an Unbounded Feasible Region and Applications to Structured Learning, arXiv:2012.15361 [math.OC]

Haoyue Wang, Shibal Ibrahim, Rahul Mazumder (2021), Nonparametric Finite Mixture Models with Possible Shape Constraints: A Cubic Newton Approach, arXiv: 2107.08535 [stats.CO]

Isabelle R. Weir, Jennifer R. Rider, Ludovic Trinquart (2021), Counterfactual mediation analysis in the multistate model framework for surrogate and clinical time-to-event outcomes in randomized controlled trials, Pharmaceutical Statistics, doi: 10.1002/pst.2159

Wolfe, Pierre-François W. (2021), Enabling Secure Multi-Party Computation with FPGAS in the Datacenter, Boston University Doctoral Dissertation,

Yujing Yan, Charles C Davis, Dimitar Dimitrov, Zhiheng Wang, Carsten Rahbek, Michael Krabbe Borregaard (2021), Phytogeographic history of the Tea family inferred through high-resolution phylogeny and fossils, Systematic Biology, doi: 10.1093/sysbio/syab042

Zhi-Cheng Yang, Yaodong Li, Matthew P. A. Fisher, and Xiao Chen (2021), Entanglement phase transitions in random stabilizer tensor networks, arXiv: 2107.12376 [cond.mat.stat-mech]

Linda Ye et al (2021), A flat band-induced correlated kagome metal, arXiv: 2106.10824 [cond-mat.mtrl-sci]

Zihao Yuan, Prachi Shukla, Sofiane Chetoui, Sean Nemtzow, Sherief Reda, Ayse K. Coskun (2021), PACT: An Extensible Parallel Thermal Simulator for Emerging Integration and Cooling Technologies, IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems, doi: 10.1109/TCAD.2021.3079166

Biwei Xiao et al. (2021), Vacancy‐Enabled O3 Phase Stabilization for Manganese‐rich Layered Sodium Cathodes, Angewandte Chemie, doi: 10.1002/anie.20201633

Ioana A. Zelko and Douglas P. Finkbeiner (2021), Impact of Dust on Spectral Distortion Measurements of the Cosmic Microwave Background, The Astrophysical Journal, doi: 10.3847/1538-4357/abfa12

Kunyan Zhang et al (2021), Spectroscopic Signatures of Interlayer Coupling in Janus MoSSe/MoS2 Heterostructures, arXiv: 2108.10995

Xi Zhang et al (2021), Gate-tunable Veselago Interference in a Bipolar Graphene Microcavity, arXiv: 2106.09651

Yancong Zhang, Kelsey N Thompson, Curtis Huttenhower, Eric A Franzosa (2021), Statistical approaches for differential expression analysis in metatranscriptomics, Bioinformatics, doi: 10.1093/bioinformatics/btab327

Bo Zhi et al. (2020), Multicolor polymeric carbon dots: synthesis, separation and polyamide-supported molecular fluorescence, Chemical Science, doi: 10.1039/d0sc05743f

Muni Zhou, David H. Wu, Nuno F. Loureiro and Dmitri A. Uzdensky (2021), Statistical description of coalescing magnetic islands via magnetic reconnection, arXiv: 2104.13757 [physics.plasma-ph]

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

2020 | 2019 | 2018 | 2017 | 2016 and earlier