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

Below is a selection of papers that appeared in May 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


Anders Andreassen, Ilya Feige, Christopher Frye, and Matthew D. Schwartz (2019), Binary JUNIPR: an interpretable probabilistic model for discrimination, arXiv: 1906.10137 [hep-ph]

Asanga Bandara, Afra Panahi, George A. Pantelopulos, Tetsuro Nagai, and John E. Straub (2019), Exploring the impact of proteins on the line tension of a phase-separating ternary lipid mixture, The Journal of Chemical Physics, doi: 10.1063/1.5091450

Ronen Bar-Ziv, Priyadarshi Ranjan, Anna Lavie, Akash Jain, Somenath Garai, Avraham Bar Hen, Ronit Popovitz-Biro, Reshef Tenne, Raul Arenal, Ashwin Ramasubramaniam, Luc Lajaunie, Maya Bar-Sadan (2019), Au-MoS2 Hybrids as Hydrogen Evolution Electrocatalysts, ACS Appl. Energy Mater, doi: 10.1021/acsaem.9b01147

Ligia R. Benavides, Julia G. Cosgrove, Mark S. Harvey, Gonzalo Giribet (2019),Phylogenomic interrogation resolves the backbone of the Pseudoscorpiones Tree of Life, Molecular Phylogenetics and Evolution, doi: 10.1016/j.ympev.2019.05.023

T.T.G. Beucler (2019), Interaction between water vapor, radiation and convection in the tropics, MIT Doctoral Dissertation

Blakesley Burkhart and Philip Mocz (2019), The Self-gravitating Gas Fraction and the Critical Density for Star Formation, The Astrophysical Journal, doi: 10.3847/1538-4357/ab25ed

Sylvain Capponi et al (2019), NMR relaxation in the spin-1 Heisenberg chain, arXiv: 1905.12697 [cond-mat.str-el]

Phillip A. Cargile, Charlie Conroy, Benjamin D. Johnson, Yuan-sen Ting, Ana Bonaca, Aaron Dotter (2019), MINESweeper: Spectrophotometric Modeling of Stars in the Gaia Era, arXiv: 1907:07690 [astro-ph.SR]

Stephen Carr, Chenyuan Li, Ziyan Zhu, Efthimios Kaxiras, Subir Sachdev, and Alex Kruchkov (2019), Coexistence of ultraheavy and ultrarelativistic Dirac quasiparticles in sandwiched trilayer graphene, arXiv:1907.00952 [cond-mat.str-el]

Pak‐Wah Chan, Pedram Hassanzadeh, Zhiming Kuang (2019), Evaluating Indices of Blocking Anticyclones in Terms of Their Linear Relations With Surface Hot Extremes, Geophysical Research Letters, doi: 10.1029/2019GL083307

Cheng-Chieh Chuang, Hsun-Chen Chu, Sheng-Bor Huang, Wei-Shun Chang, Hsing-Yu Tuan (2019), Laser-induced plasmonic heating in copper nanowire fabric as a photothermal catalytic reactor, Chemical Engineering Journal, doi: 10.1016/j.cej.2019.122285

Sarah C. Conner, Sara Lodi, Kathryn L. Lunetta, Juan P. Casas, Steven A. Lubitz, Patrick T. Ellinor, Christopher D. Anderson, Qiuxi Huang, Justin Coleman, Wendy B. White, Emelia J. Benjamin, and Ludovic Trinquart (2019), Refining the Association Between Body Mass Index and Atrial Fibrillation: G‐Formula and Restricted Mean Survival Times, Journal of the American Heart Association, doi: 10.1161/JAHA.119.013011

Charlie Conroy, Ana Bonaca, Phillip Cargile, Benjamin D. Johnson, Nelson Caldwell, Rohan P. Naidu, Dennis Zaritsky, Daniel Fabricant, Sean Moran, Jaehyon Rhee, Andrew Szentgyorgyi (2019), Mapping the Stellar Halo with the H3 Spectroscopic Survey, arXiv: 1907.07684 [astro-ph.GA]

Sarah C. Conner, Lisa M. Sullivan, Emelia J. Benjamin, Michael P. LaValley, Sandro Galea, Ludovic Trinquart (2019), Adjusted restricted mean survival times in observational studies, Statistics in Medicine, doi: 10.1002/sim.8206

B. A. Cook, Charlie Conroy, Pieter van Dokkum, and Joshua S. Speagle (2019), Measuring Star-formation Histories, Distances, and Metallicities with Pixel Color-Magnitude Diagrams I: Model Definition and Mock Tests, arXiv:1904.00011 [astro-Ph.GA]

A. Devarakonda, H. Inoue, S. Fang,  C. Ozsoy-Keskinbora, T. Suzuki, M. Kriener, L. Fu, E. Kaxiras, D. C. Bell, and J. G. Checkelsky (2019), Evidence for clean 2D superconductivity and field-induced finite-momentum pairing in a bulk vdW superlattice, arXiv:19809.02065 [cond-mat.supr-con]

Qian Di, Heresh Amini, Liuhua Shi, Itai Kloog, Rachel Silvern, James Kelly, M. Benjamin Sabath, Christine Choirat, Petros Koutrakis, Alexei Lyapustin, Yujie Wang, Loretta J. Mickley, Joel Schwartz (2019), An ensemble-based model of PM2.5 concentration across the contiguous United States with high spatiotemporal resolution, Environmental International, doi: 10.1016/j.envint.2019.104909

Feng Ding and Robin D. Wordsworth (2019), A New Line-by-line General Circulation Model for Simulations of Diverse Planetary Atmospheres: Initial Validation and Application to Exoplanet GJ 1132B, arXiv: 1905.04635 [astro-ph.EP]

Shiang Fang, Stephen Carr, Ziyan Zhu, Daniel Massatt, Efthimios Kaxiras (2019), Angle-Dependent Ab initio Low-Energy Hamiltonians for a Relaxed Twisted Bilayer
Graphene Heterostructure, arXiv: 1908.00058 [cond-mat.mes-hall]

Richard M. Feder, Stephen K. N. Portillo, Tansu Daylan, and Douglas Finkbeiner (2019), Multiband Probabilistic Cataloging: A Joint Fitting Approach to Point Source Detection and Deblending, arXiv: 1907.04929 [astro-ph.IM]

William Fitzhugh, Fan Wu, Luhan Ye, Haoqing Su, Xin Li (2019), Strain‐Stabilized Ceramic‐Sulfide Electrolytes, Small, doi: 10.1002/smll.201901470

William Fitzhugh, Fan Wu, Luhan Ye, Wenye Deng, Pengfei Qi, Xin Li (2019), A High‐Throughput Search for Functionally Stable Interfaces in Sulfide Solid‐State Lithium Ion Conductors, Advanced Energy Materials, doi: 10.1002/aenm.201900807

Barak Gabai, Xi Yin (2019), On The S-Matrix of Ising Field Theory in Two Dimensions, arXiv: 1905.00710 [hep-th]

Brandt A.L. Gaches, Stella S.R. Offner, Thomas G. Bisbas (2019), The Astrochemical Impact of Cosmic Rays in Protoclusters I: Molecular Cloud Chemistry, arXiv: 1905.02232 [astro-ph.GA]

Brandt A. L. Gaches. Stellar S. R. Offner, and Thomas G. Bisbas (2019), The Astrochemical Impact of Cosmic Rays in Protoclusters II: CI-to-H2 and CO-to-H2 Conversion Factors, arXiv:1908.06999 [astro-ph.GA]

Gregory M. Green, Edward Schlafly, Catherine Zucker, Joshua S Speagle, Douglas Finkbeiner (2019), A 3D Dust Map Based on Gaia, Pan-STARRS 1 and 2MASS, arXiv: 1905.02734 [astro-ph.GA]

Jing Guo, Guangyu Sun, Bowen Zhao, Ling Wang, Wenshan Hong, Vladimir A. Sidorov, Nvsen Ma, Qi Wu, Shiliang Li, Zi Yang Meng, Anders W. Sandvik, and Liling Sun(2019), Quantum phases of SrCu2(BO3)2 from high-pressure thermodynamics, arXiv:1904.09927 [cond-mat.str-el]

Kyle S. Honegger, Matthew A.-Y. Smith, Matthew A. Churgin, Glenn C. Turner, and Benjamin L. de Bivorta (2019), Idiosyncratic neural coding and neuromodulation of olfactory individuality in Drosophila, PNAS, doi: 10.1073/pnas.1901623116

Mingu Kang et al. (2019), Dirac fermions and flat bands in the ideal kagome metal FeSn, arXiv:1906.02167

Paul Michael Kielstra and Marius Lemm (2019), On the Finite-size Lyapunov Exponent for the Schrodinger Operator with Skew-shift Potential, arXiv: 1904:08871 [math-ph]

Jonathan I. Leckenby, Miranda A. Chacon, Adriaan O. Grobbelaar, Jeff W. Lichtman (2019), Imaging Peripheral Nerve Regeneration: A New Technique for 3D Visualization of Axonal Behavior, Journal of Surgical Research, doi: 10.1016/j.jss.2019.04.046

Joel Leja, Sandro Tacchella, and Charlie Conroy (2019), Beyond UVJ: More efficient selection of quiescent galaxies with UV / mid-IR fluxes, arXiv: 1907.02970 [astro-ph.GA]

Marius Lemm, Anders Sandvik, and Sibin Yang (2019), The AKLT model on a hexagonal chain is gapped, arXiv:1904.01043 [quant-ph]

Mariana Levi, Jeffrey K. Noel, Paul C. Whitford (2019), Studying ribosome dynamics with simplified models, Methods, doi: 10.1016/j.ymeth.2019.03.023

Xinzhi Li, Amit Das, Dapeng Bi (2019), Mechanical heterogeneity in tissues promotes rigidity and controls cellular invasion, arXiv: 1905.02697 []

Jilei Liu et al (2019), Integrated Catalysis-Surface Science-Theory Approach to Understand Selectivity in the Hydrogenation of 1-Hexyne to 1-Hexene on PdAu Single-Atom Alloy Catalysts, ACS Catal, doi: 10.1021/acscatal.9b00491

Xiaorong Liu, Jianhan Chen (2019), Residual Structures and Transient Long-Range Interactions of p53 Transactivation Domain: Assessment of Explicit Solvent Protein Force Fields, Journal of Chemical Theory and Computing, doi: 10.1021/acs.jctc.9b00397

Xiya Lu, Juan Duchimaza-Heredia, Qiang Cui (2019), Analysis of Density Functional Tight Binding with Natural Bonding Orbitals,J. Phys. Chem. A, doi: 10.1021/acs.jpca.9b05072

Ziqiang Lü, Haiying Gao, Jianshe Lei, Xiaotao Yang, Sampath Rathnayaka, Cong Li (2019), Crustal and upper mantle structure of the Tien Shan orogenic belt from full‐wave ambient noise tomography, Journal of Geophysical Research – Solid Earth, doi: 10.1029/2019JB017387

Dimitrios Maroudas and Brian D Wirth (2019), Atomic-scale modeling toward enabling models of surface nanostructure formation in plasma-facing materials, Current Opinion in Chemical Engineering, doi: 10.1016/j.coche.2019.03.001

A. Mesgarnejad, A. Karma (2019), Phase Field Modeling of Chemomechanical Fracture of Intercalation Electrodes: Role of Charging Rate and Dimensionality, arXiv:1906.07655 [cond-mat.mtrl-sci]

Atoallah Mesgarnejad and Alain Karma (2019), Vulnerable Window of Yield Strength for Swelling-Driven Fracture of Phase-Transforming Battery Materials, arXiv: 1908.02175 []

Julian B. Mu˜noz (2019), A Standard Ruler at Cosmic Dawn, arXiv:1904:07868 [astro-ph.CO]

Julian B. Mu˜noz (2019), Velocity-induced Acoustic Oscillations at Cosmic Dawn, arXiv:1904:07881 [astro-ph.CO]

Pavitra Muralidhar (2019), Mating preferences of selfish sex chromosomes, Nature, doi: 10.1038/s41586-019-1271-7

Shilo Ohayon, Arik Girsault, Maisa Nasser, Shai Shen-Orr, Amit Meller (2019), Simulation of single-protein nanopore sensing shows feasibility for whole-proteome identification, PLOS Computational Biology, doi: 10.1371/journal.pcbi.1007067

César Omar Ramírez Quiroz et al (2019), Interface Molecular Engineering for Laminated Monolithic Perovskite/Silicon Tandem Solar Cells with 80.4% Fill Factor, Advanced Functional Materials, doi: 10.1002/adfm.201901476

Andreea Panaitescu, Meng Xin, Benny Davidovitch, Julien Chopin, and Arshad Kudrolli (2019), Birth and decay of tensional wrinkles in hyperelastic sheets, arXiv: 1906.10054 [cond-mat.soft]

George Papamokos, Theodoros Dimitriadi, Dimitrios N. Bikiaris, George Z. Papageorgiou, George Floudas (2019), Chain Conformation, Molecular Dynamics, and Thermal Properties of Poly(n-methylene 2,5-furanoates) as a Function of Methylene Unit Sequence Length, The Macromolecules, doi: 10.1021/acs.macromol.9b01320

Joonha Park, Yves Atchad (2019), Markov chain Monte Carlo algorithms with sequential proposals, arXiv: 1907.06544 [stat.CO]

Sun, Qinfang (2019), Simulating Hydrogen Bonded Clusters and Zeolite Clusters for Renewable Energy Applications, University of Massachusetts, Amherst, Doctoral Dissertation.

Deena A. Rennerfeldt, Joana S. Raminhos, Samantha M. Leff, Pristinavae Manning, Krystyn J. Van Vliet (2019), Emergent heterogeneity in putative mesenchymal stem cell colonies: Single-cell time-lapsed analysis, PLOS One, doi: 10.1371/journal.pone.0213452

Timothy B. Sackton, Phil Grayson, Alison Cloutier, Zhirui Hu, Jun S. Liu, Nicole E. Wheeler, Paul P. Gardner, Julia A. Clarke, Allan J. Baker, Michele Clamp, Scott V. Edwards (2019), Convergent regulatory evolution and loss of flight in paleognathous birds, Science, doi: 10.1126/science.aat7244

Andres N. Salcedo, Benjamin D. Wibking, David H. Weinberg, Hao-Yi Wu, Douglas Ferrer, Daniel Eisenstein, and Philip Pinto (2019), Cosmology with Stacked Cluster Weak Lensing and Cluster-Galaxy Cross-Correlations, arXiv:1906.06499 [astro-ph.CO]

Hui Shao, Wenan Guo and Anders W. Sandvik (2019), Monte Carlo Renormalization Flows in the Space of Relevant and Irrelevant Operators: Application to Three-Dimensional Clock Models, arXiv: 1905.13640 [cond-mat.str-el]

Sherer, Zachary (2019), A Comparison of Two Architectures for Breadth-First Search on FPGA SoC Platforms, University of Massachusetts, Lowell, Masters Dissertation

Joshua Stern, Qingqing Xiong, Anthony Skjellum, and Martin C. Herbordt (2019), A Novel Approach to Supporting Communicators for In-Switch Processing of MPI Collectives

Su, Jiaying (2019), A Numerical Study of Heat Transfer in a Square Channel With and Without Bleed Holes Roughened With Staggered Square Ribs, Masters Thesis, Northeastern University

Mirac Suzgun, Sebastian Gehrmann, Yonatan Belinkov, Stuart M. Shieber (2019), LSTM Networks Can Perform Dynamic Counting, arXiv:1906.03648 [cs.CL]

Waleed Tahir, Jiabei Zhu, Sreekanth Kura, Xiaojun Cheng, David Boas, and Lei Tian (2019), A Deep Learning Approach to 3D Segmentation of Brain Vasculature, in Biophotonics Congress: Optics in the Life Sciences Congress 2019 (BODA,BRAIN,NTM,OMA,OMP), The Optical Society (Optical Society of America, 2019), paper BT2A.6.

Waleed Tahir, Ulugbek S. Kamilov, and Lei Tian (2019), Holographic particle localization under multiple scattering, Advanced Photonics, doi: 10.1117/1.AP.1.3.036003

Austin Thai and Sheryl M. Grace (2019), Prediction of small quadrotor blade induced noise, 25th AIAA/CEAS Aeroacoustics Conference, 20-23 May, 2019, Delft, The Netherlands, doi: 10.2514/6.2019-2684

Tirado, Luis Eladio (2019), On-the-move Detection of Security Threats Using 3D MM-Wave Radar Imaging, Northeastern University Doctoral Dissertation

V.V. Volkov, R. Chelli, R. Righini, C.C. Perry (2019), Indigo chromophores and pigments: Structure and dynamics, Dyes and Pigments, doi: 10.1016/j.dyepig.2019.107761

Isabelle R Weir, Lu Tian, Ludovic Trinquart (2019), Multivariate meta-analysis model for the difference in restricted mean survival times, Biostatistics, doi: 10.1093/biostatistics/kxz018

Yi Wen, Colin Ophus, Christopher S. Allen, Shiang Fang, Jun Chen, Efthimios Kaxiras, Angus I. Kirkland, Jamie H. Warner (2019), Simultaneous Identification of Low and High Atomic Number Atoms in Monolayer 2D Materials Using 4D Scanning Transmission Electron Microscopy, Nano Lett., doi: 10.1021/acs.nanolett.9b02717

Thomas L. Williams, Steven A. Lopez, Leila F. Deravi (2019), A Sustainable Route To Synthesize the Xanthommatin Biochrome via an Electro-catalyzed Oxidation of Tryptophan Metabolites, ACS Sustainable Chem. Eng., doi: 10.1021/acssuschemeng.9b01144

Xiao Wu, Yi Xu, Bradley P. Carlin (2019), Optimizing Interim Analysis Timing for Bayesian Adaptive Commensurate Designs, arXiv: 1905.07456 [stat.AP]

Yaqin Xia, Qiuming Chen, Eugene I. Shakhnovich, Wenli Zhang, Wanmeng Mu (2019), Simulation-guided enzyme discovery: A new microbial source of cellobiose 2-epimerase,International Journal of Biological Macromolecules, doi: 10.1016/j.ijbiomac.2019.08.075

Qingqing Xiong, Rushi Patel, Chen Yang, Tong Geng, Anthony Skjellum, Martin C. Herbordt (2019), GhostSZ: A Transparent FPGA-Accelerated Lossy Compression Framework

Huan Yang, Prasad Bandarkar, Ransom Horne, Vitor B. P. Leite, Jorge Chahine, and Paul C. Whitford (2019), Diffusion of tRNA inside the ribosome is position-dependent, The Journal of Chemical Physics, doi: 10.1063/1.5113814

Phelan Yu, Lawrence W. Cheuk, Ivan Kozyryev, and John M. Doyle (2019), A Scalable Quantum Computing Platform Using Symmetric-Top Molecules, arXiv: 1905.06439 [physics.atom-ph]

Krissia Zawadzki and Adrian E. Feiguin (2019), Time and momentum-resolved tunneling spectroscopy of pump-driven non-thermal excitations in Mott insulators, arXiv: 1905.08166 [cond-mat.str-el]

Yifan Zhang, Lorenzo Trippa, Giovanni Parmigiani (2019), Frequentist operating characteristics of Bayesian optimal designs via simulation, Statistics in Medicine, doi: 10.1002/sim.8279

Bowen Zhao, Phillip Weinberg and Anders W. Sandvik (2019), Symmetry-enhanced discontinuous phase transition in a two-dimensional quantum magnet, Nature Physics, doi: s41567-019-0484-x

Jiawei Zhuang, Daniel J. Jacob, Judit Flo Gaya, Robert M. Yantosca, Elizabeth W. Lundgren, Melissa P. Sulprizio, Sebastian D. Eastham (2019), Enabling immediate access to Earth science models through cloud computing: application to the GEOS-Chem model, Bulletin of the American Meteorological Society, doi: 10.1175/BAMS-D-18-0243.1

Prior Years

2018 | 2017 | 2016 and earlier