Skip to content Skip to navigation

SRCC-enabled publications

Below are selected publications that have utilized and acknowledged Stanford Research Computing Center's computational resources and expertise.

It is important that publications resulting from computations performed on Sherlock, Farmshare or SCG acknowledge this. The following wording is suggested for your Acknowledgements section:

"Some of the computing for this project was performed on the Sherlock (or XStream, Farmshare, SCG, Nero) cluster. We would like to thank Stanford University and the Stanford Research Computing Center for providing computational resources and support that contributed to these research results."

Thank You!

Also, check out the Goolge Scholar search for Stanford Research Computing Center

2019

Pseudogap crossover in the electron-phonon system
I. Esterlis, S. A. Kivelson, and D. J. Scalapino
Phys. Rev. B 99, 174516 – Published 24 May 2019

Global warming has increased global economic inequality
Noah S. Diffenbaugh and Marshall Burke
PNAS May 14, 2019 116 (20) 9808-9813; https://doi.org/10.1073/pnas.1816020116

Uncovering the structure of self-regulation through data-driven ontology discovery
Ian W. Eisenberg, Patrick G. Bissett, A. Zeynep Enkavi, Jamie Li, David P. MacKinnon, Lisa A. Marsch & Russell A. Poldrack
Nature Communications 10, Article number: 2319 (2019)

Global analysis of epigenetic heterogeneity identifies divergent drivers of esophageal squamous cell carcinoma
Wei Cao, Hayan Lee, Wei Wu, Aubhishek Zaman, Sean McCorkle, Ming Yan, Justin Chen, Qinghe Xing, Nasa Sinnott-Armstrong, Hongen Xu, M.Reza Sailani, Wenxue Tang, Yuanbo Cui, Jia liu, Hongyan Guan, Pengju Lv, Xiaoyan Sun, Lei Sun, Pengli Han, Yanan Lou, Jing Chang, Jinwu Wang, Yuchi Gao, Jiancheng Guo, Gundolf Schenk, Alan Hunter Shain, Fred G. Biddle, Eric Collisson, Michael Snyder, Trever G. Bivona
doi: https://doi.org/10.1101/641357 Posted May 18, 2019

Towards a Flexible Deep Learning Method for Automatic Detection of Clinically Relevant Multi-Modal Events in the Polysomnogram
Alexander Neergaard Olesen, Stanislas Chambon, Valentin Thorey, Poul Jennum, Emmanuel Mignot, Helge B. D. Sorensen
arXiv:1905.08059 (Submitted on 16 May 2019)

Transplantation of donor grafts with defined ratio of conventional and regulatory T cells in HLA-matched recipients
Everett H. Meyer, Ginna Laport, Bryan J. Xie, Kate MacDonald, Kartoosh Heydari, Bita Sahaf, Sai-Wen Tang, Jeanette Baker, Randall Armstrong, Keri Tate, Cynthia Tadisco, Sally Arai, Laura Johnston, Robert Lowsky, Lori Muffly, Andrew R. Rezvani, Judith Shizuru, Wen-Kai Weng, Kevin Sheehan, David Miklos, and Robert S. Negrin
Published in Volume 4, Issue 10 on May 16, 2019 JCI Insight. 2019;4(10):e127244. https://doi.org/10.1172/jci.insight.127244

Molecular Origins of Complex Heritability in Natural Genotype-to-Phenotype Relationships
Christopher M.Jakobson, Daniel F.Jarosz
Cell Systems, Published: May 1, 2019 https://doi.org/10.1016/j.cels.2019.04.002

Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts
Surag Nair, Daniel S. Kim, Jacob Perricone, Anshul Kundaje
doi: https://doi.org/10.1101/605717

Blind tests of RNA–protein binding affinity prediction
Kalli Kappel, Inga Jarmoskaite, Pavanapuresan P. Vaidyanathan, William J. Greenleaf, Daniel Herschlag, and Rhiju Das
PNAS April 23, 2019 116 (17) 8336-8341; https://doi.org/10.1073/pnas.1819047116

Robust mouse tracking in complex environments using neural networks
Brian Q. Geuther, Sean P. Deats, Kai J. Fox, Steve A. Murray, Robert E. Braun, Jacqueline K. White, Elissa J. Chesler, Cathleen M. Lutz & Vivek Kumar    
Nature Communications, Biology volume 2, Article number: 124 (2019)

Pervasive function and evidence for selection across standing genetic variation in S. cerevisiae
Christopher M. Jakobson, Richard She & Daniel F. Jarosz   
Nature Communications Volume 10, Article number: 1222 (2019)

Predicting gait adaptations due to ankle plantarflexor muscle weakness and contracture using physics-based musculoskeletal simulations
Carmichael F. Ong, Thomas Geijtenbeek, Jennifer L. Hicks, Scott L. Delp
doi: https://doi.org/10.1101/597294

Efficient construction of generalized master equation memory kernels for multi-state systems from nonadiabatic quantum-classical dynamics
William C. Pfalzgraff, Andrés Montoya Castillo, Aaron Kelly, Thomas E. Markland
(Submitted on 22 Mar 2019)

Pairing and non-Fermi liquid behavior in partially flat-band systems
Sharareh Sayyad, Edwin W. Huang, Motoharu Kitatani, Mohammad-Sadegh Vaezi, Zohar Nussinov, Abolhassan Vaezi, Hideo Aoki
Submitted on 23 Mar 2019, last revised 29 Mar 2019

Uncertainty quantification of simulated biomechanical stimuli in coronary artery bypass grafts
Justin S. Trana, Daniele E. Schiavazzi, Andrew M. Kahn, Alison L. Marsden
Computer Methods in Applied Mechanics and Engineering, Volume 345, 1 March 2019, Pages 402-428
https://doi.org/10.1016/j.cma.2018.10.024

Gut microbiota plasticity is correlated with sustained weight loss on a low-carb or low-fat dietary intervention
Jessica A Grembi, Lan H Nguyen, Thomas D Haggerty, Christopher D Gardner, Susan P Holmes, Julie Parsonnet
doi: https://doi.org/10.1101/580217

A functional subset of CD8+ T cells during chronic exhaustion is defined by SIRPα expression
Lara M. Myers, Michal Caspi Tal, Laughing Bear Torrez Dulgeroff, Aaron B. Carmody, Ronald J. Messer, Gunsagar Gulati, Ying Ying Yiu, Matthew M. Staron, Cesar Lopez Angel, Rahul Sinha, Maxim Markovic, Edward A. Pham, Benjamin Fram, Aijaz Ahmed, Aaron M. Newman, Jeffrey S. Glenn, Mark M. Davis, Susan M. Kaech, Irving L. Weissman & Kim J. Hasenkrug
Nature Communications Volume 10, Article number: 794 (2019)

Non-invasive machine learning estimation of effort differentiates sleep-disordered breathing pathology
Umaer Hanif, Logan D Schneider, Lotte Trap, Eileen B Leary, Hyatt Moore IV, Christian Guilleminault, Poul Jennum, Helge B D Sorensen, and Emmanuel J M Mignot
Published 26 February 2019, Institute of Physics and Engineering in Medicine
Physiological Measurement, Volume 40, Number 2

Thermal transport in MoS2 from molecular dynamics using different empirical potentials
Ke Xu, Alexander J. Gabourie, Arsalan Hashemi, Zheyong Fan, Ning Wei, Amir Barati Farimani, Hannu-Pekka Komsa, Arkady V. Krasheninnikov, Eric Pop, and Tapio Ala-Nissila
Phys. Rev. B 99, 054303 – Published 11 February 2019

Super-geometric electron focusing on the hexagonal Fermi surface of PdCoO2
Maja D. Bachmann, Aaron L. Sharpe, Arthur W. Barnard, Carsten Putzke, Markus König, Seunghyun Khim, David Goldhaber-Gordon, Andrew P. Mackenzie, Philip J. W. Moll
arXiv:1902.03769

Imidazole and 1-Methylimidazole Hydrogen Bonding and Non-Hydrogen Bonding Liquid Dynamics: Ultrafast IR Experiments
Jae Yoon Shin, Yong-Lei Wang, Steven A. Yamada, Samantha Ting Hung, and Michael D. Fayer
J. Phys. Chem. B, DOI: 10.1021/acs.jpcb.8b11299
Publication Date (Web): February 6, 2019

Sub-Femtosecond Stark Control of Molecular Photoexcitation with Near Single-Cycle Pulses
Benoit Mignolet, Basile F. E. Curchod, Francoise Remacle and Todd J. Martínez            
J. Phys. Chem. Lett., 2019, 10, pp 742–747
DOI: 10.1021/acs.jpclett.8b03814 Publication Date (Web): January 29, 2019

Intradomain Interactions in an NMDA Receptor Fragment Mediate N-Glycan Processing and Conformational Sampling
Ganesh P. Subedi, Anton V. Sinitskiy, Jacob T. Roberts, Kashyap R. Patel, Vijay S.Pande, Adam W. Barb
Structure, Volume 27, Issue 1, 2 January 2019, Pages 55-65.e3

Combinatorial processing of bacterial and host-derived innate immune stimuli at the single-cell level
Miriam V. Gutschow, John C. Mason, Keara M. Lane, Inbal Maayan, Jacob J. Hughey, Bryce T. Bajar, Debha N. Amatya, Sean D. Valle, and Markus W. Covert
Molecular Biology of the Cell Vol. 30, No. 2
Published Online:14 Jan 2019 https://doi.org/10.1091/mbc.E18-07-0423

Sampling Native-like Structures of RNA-Protein Complexes through Rosetta Folding and Docking
Kalli Kappel, Rhiju Das
Structure, Volume 27, Issue 1, 2 January 2019, Pages 140-151.e5
https://doi.org/10.1016/j.str.2018.10.001

RNA design movesets and strategies from an Internet-scale videogame
Rohan Koodli, Benjamin Keep, Katherine R Coppess, Fernando Portela, Eterna Players, Rhiju Das
doi: https://doi.org/10.1101/326736 Posted January 15, 2019

Modeling of radiation-induced defect recovery in 3C-SiC under high field bias conditions
Ricardo Peterson, Debbie Senesky
Computational Materials Science, Volume 161, 15 April 2019, Pages 10-15
https://doi.org/10.1016/j.commatsci.2019.01.016

Globally Constructed Adaptive Local Basis Set for Spectral Projectors of Second Order Differential Operators
Yingzhou Li and Lin Lin
Multiscale Model. Simul., 17(1), 92–116. (25 pages)
https://doi.org/10.1137/17M1140236

fMRIPrep: a robust preprocessing pipeline for functional MRI
Oscar Esteban, Christopher J. Markiewicz, Ross W. Blair, Craig A. Moodie, A. Ilkay Isik, Asier Erramuzpe, James D. Kent, Mathias Goncalves, Elizabeth DuPre, Madeleine Snyder, Hiroyuki Oya, Satrajit S. Ghosh, Jessey Wright, Joke Durnez, Russell A. Poldrack & Krzysztof J. Gorgolewski     
Nature Methods volume 16, pages111–116 (2019)

Revealing quantum mechanical effects in enzyme catalysis with large-scale electronic structure simulation
Zhongyue Yang, Rimsha Mehmood, Mengyi Wang, Helena W. Qi, Adam H. Steeves and Heather J. Kulik
React. Chem. Eng., 2019, Advance Article DOI: 10.1039/C8RE00213D (Paper)

The unWISE Catalog: Two Billion Infrared Sources from Five Years of WISE Imaging
Edward F. Schlafly, Aaron M. Meisner, Gregory M. Green
 arXiv:1901.03337 (Submitted on 10 Jan 2019)

An Algebraic Sparsified Nested Dissection Algorithm Using Low-Rank Approximations
Léopold Cambier, Chao Chen, Erik G Boman, Sivasankaran Rajamanickam, Raymond S. Tuminaro, Eric Darve
arXiv:1901.02971 (Submitted on 9 Jan 2019)

Thermal Boundary Conductance of Two-Dimensional MoS2 Interfaces
Saurabh V. Suryavanshi, Alexander J. Gabourie, Amir Barati Farimani, Eric Pop
arXiv:1901.02447 (Submitted on 8 Jan 2019)

The Buzzard Flock: Dark Energy Survey Synthetic Sky Catalogs
Joseph DeRose, Risa H. Wechsler, Matthew R. Becker, Michael T. Busha, Eli S. Rykoff, Niall MacCrann, Brandon Erickson, August E. Evrard, Andrey Kravtsov, Daniel Gruen, Sahar Allam, Santiago Avila, Sarah Bridle, David Brooks, Elizabeth Buckley-Geer, Aurelio Carnero Rosell, Matias Carrasco Kind, Jorge Carretero, Francisco J. Castander, Ross Cawthon, Martin Crocce, Luiz N. da Costa, Christopher Davis, Juan De Vicente, Jörg P. Dietrich, Peter Doel, Alex Drlica-Wagner, Pablo Fosalba, Josh Frieman, Juan Garcia-Bellido, Gaston Gutierrez, Will G. Hartley, Devon L. Hollowood, Ben Hoyle, David J. James, Elisabeth Krause, Kyler Kuehn, Nikolay Kuropatkin, Marcos Lima, Marcio A. G. Maia, Felipe Menanteau, Christopher J. Miller, Ramon Miquel, Ricardo L. C. Ogando, Andrés Plazas Malagón, A. Kathy Romer, Eusebio Sanchez, Rafe Schindler, Santiago Serrano, Ignacio Sevilla-Noarbe, Mathew Smith, Eric Suchyta, Molly E. C. Swanson, Gregory Tarle, Vinu Vikram
arXiv:1901.02401 (Submitted on 8 Jan 2019)

2018

Automated design of collective variables using supervised machine learning featured
Mohammad M. Sultan and Vijay S. Pande
J. Chem. Phys. 149, 094106 (2018); https://doi.org/10.1063/1.5029972

Exploiting graphical processing units to enable quantum chemistry calculation of large solvated molecules with conductor‐like polarizable continuum models
Fang Liu, David M. Sanchez, Heather J. Kulik, Todd J. Martínez
https://doi.org/10.1002/qua.25760 First published: 11 October 2018

Biochat: a database for natural language processing of Gene Expression Omnibus data
Bohdan B Khomtchouk, Vsevolod Dyomkin, Kasra A Vand, Themistocles Assimes, Or Gozani
doi: https://doi.org/10.1101/480020

PathFX provides mechanistic insights into drug efficacy and safety for regulatory review and therapeutic development
Jennifer L. Wilson, Rebecca Racz, Tianyun Liu, Oluseyi Adeniyi, Jielin Sun, Anuradha Ramamoorthy, Michael Pacanowski, Russ Altman
PLOS Published: December 7, 2018
https://doi.org/10.1371/journal.pcbi.1006614

Combinatorial processing of bacterial and host-derived innate immune stimuli at the single-cell level
Miriam V. Gutschow, John C. Mason, Keara M. Lane, Inbal Maayan, Jacob J. Hughey, Bryce T. Bajar, Debha N. Amatya, Sean D., Valle, Markus W. Covert
Molecular Biology of the Cell Published Online: 21 Nov 2018
https://doi.org/10.1091/mbc.E18-07-0423

Enhanced correlations and superconductivity in weakly interacting partially flat band systems: a determinantal quantum Monte Carlo study
Edwin W. Huang, Mohammad-Sadegh Vaezi, Zohar Nussinov, Abolhassan Vaezi
arXiv:1811.08848 (Submitted on 21 Nov 2018)

Convolutional models of RNA energetics
Michelle J Wu
doi: https://doi.org/10.1101/470740

Searching for Subsecond Stellar Variability with Wide-field Star Trails and Deep Learning
David Thomas and Steven M. Kahn
The Astrophysical Journal, Volume 868, Number 1, Published 2018 November 16

A global test of ecoregions
Jeffrey R. Smith, Andrew D. Letten, Po-Ju Ke, Christopher B. Anderson, J. Nicholas Hendershot, Manpreet K. Dhami, Glade A. Dlott, Tess N. Grainger, Meghan E. Howard, Beth M. L. Morrison, Devin Routh, Priscilla A. San Juan, Harold A. Mooney, Erin A. Mordecai, Thomas W. Crowther & Gretchen C. Daily     
Nature Ecology & Evolution,  Published: 05 November 2018
DOI https://doi.org/10.1038/s41559-018-0709-x

An energetic reformulation of kinetic rate laws enables scalable parameter estimation for biochemical networks
John C. Mason, Markus W. Covert
Journal of Theoretical Biology, 24 October 2018
DOI https://doi.org/10.1016/j.jtbi.2018.10.041

Spectroscopic Signature of Oxidized Oxygen States in Peroxides
Zengqing Zhuo, Chaitanya Das Pemmaraju, John Vinson, Chunjing Jia, Brian Moritz, Ilkyu Lee, Shawn Sallis, Qinghao Li, Jinpeng Wu, Kehua Dai, Yi-De Chuang, Zahid Hussain, Feng Pan, Thomas P. Devereaux, and Wanli Yang
J. Phys. Chem. Lett.
DOI 10.1021/acs.jpclett.8b02757 Publication Date (Web): October 16, 2018

Three-dimensional collective charge excitations in electron-doped copper oxide superconductors
M. Hepting, L. Chaix, E. W. Huang, R. Fumagalli, Y. Y. Peng, B. Moritz, K. Kummer, N. B. Brookes, W. C. Lee, M. Hashimoto, T. Sarkar, J.-F. He, C. R. Rotundu, Y. S. Lee, R. L. Greene, L. Braicovich, G. Ghiringhelli, Z. X. Shen, T. P. Devereaux & W. S. Lee     
Nature volume 563, pages374–378 (2018)
Published: 31 October 2018
DOI https://doi.org/10.1038/s41586-018-0648-3

Probing the Electron Accepting Orbitals of Ni-Centered Hydrogen Evolution Catalysts with Noninnocent Ligands by Ni L-Edge and S K-Edge X-ray Absorption
Sergey Koroidov, Kiryong Hong, Kasper S. Kjaer, Lin Li, Kristjan Kunnus, Marco Reinhard, Robert W. Hartsock, Das Amit, Richard Eisenberg, C. Das Pemmaraju, Kelly J. Gaffney, and Amy A. Cordones
Inorg. Chem., Article ASAP DOI: 10.1021/acs.inorgchem.8b01497
Publication Date (Web): October 11, 2018

Data-driven human transcriptomic modules determined by independent component analysis
Weizhuang Zhou and Russ B. Altman
BMC Bioinformatics 201819:327 Published: 17 September 2018
https://doi.org/10.1186/s12859-018-2338-4

Landscape of stimulation-responsive chromatin across diverse human immune cells
Diego Calderon, Michelle L.T. Nguyen, Anja Mezger, Arwa Kathiria, Vinh Nguyen, Ninnia Lescano, Beijing Wu, John Trombetta, Jessica V. Ribado, David A. Knowles, Ziyue Gao, Audrey V. Parent, Trevor D. Burt, Mark S. Anderson, Lindsey A. Criswell, William J. Greenleaf, Alexander Marson, Jonathan K. Pritchard
doi: https://doi.org/10.1101/409722, Posted September 5, 2018.

A parallel direct cut algorithm for high-order overset methods with application to a spinning golf ball
J. Crabill, F.D. Witherden, A. Jameson
Journal of Computational Physics, 2018 - Elsevier
https://doi.org/10.1016/j.jcp.2018.05.036

Deep Neural Network Computes Electron Densities and Energies of a Large Set of Organic Molecules Faster than Density Functional Theory (DFT)
Anton V. Sinitskiy, Vijay S. Pande
arXiv preprint arXiv:1809.02723, 2018 - arxiv.org

Analyzing interferometric observations of strong gravitational lenses with recurrent and convolutional neural networks
Warren R. Morningstar, Yashar D. Hezaveh, Laurence Perreault Levasseur, Roger D. Blandford, Philip J. Marshall, Patrick Putzky, Risa H. Wechsler
arXiv:1808.00011 (Submitted on 31 Jul 2018)

Imaging CF3I conical intersection and photodissociation dynamics with ultrafast electron diffraction
Jie Yang, Xiaolei Zhu, Thomas J. A. Wolf, Zheng Li, J. Pedro F. Nunes, Ryan Coffee, James P. Cryan, Markus Gühr, Kareem Hegazy, Tony F. Heinz, Keith Jobe, Renkai Li,
 Xiaozhe Shen, Theodore Veccione, Stephen Weathersby, Kyle J. Wilkin, Charles Yoneda, Qiang Zheng, Todd J. Martinez, Martin Centurion, Xijie Wang
Science  06 Jul 2018: Vol. 361, Issue 6397, pp. 64-67
DOI: 10.1126/science.aat0049

Unraveling electronic absorption spectra using nuclear quantum effects: Photoactive yellow protein and green fluorescent protein chromophores in water
Tim J. Zuehlsdorff1, Joseph A. Napoli, Joel M. Milanese, Thomas E. Markland, and Christine M. Isborn
The Journal of Chemical Physics 149, 024107 (2018); https://doi.org/10.1063/1.5025517

Simple, direct and efficient multi-way spectral clustering
A Damle, V Minden, L Ying
Information and Inference: A Journal of the IMA, 2018
https://doi.org/10.1093/imaiai/iay008

Bioimpedance and New‐Onset Heart Failure: A Longitudinal Study of >500 000 Individuals From the General Population
Daniel Lindholm, Eri Fukaya, Nicholas J. Leeper, Erik Ingelsson
Journal of the American Heart Association. 2018;7:e008970,
https://doi.org/10.1161/JAHA.118.008970 Originally published June 29, 2018

Investigating the role of non-covalent interactions in conformation and assembly of triazine-based sequence-defined polymers
Surl-Hee Ahn, Jay W. Grate, and Eric F. Darve
The Journal of Chemical Physics 149, 072330 (2018); https://doi.org/10.1063/1.5024552

Direct Methane to Methanol: The Selectivity–Conversion Limit and Design Strategies
Allegra A. Latimer, Arvin Kakekhani, Ambarish R. Kulkarni, and Jens K. Nørskov
ACS Catal., 2018, 8, pp 6894–6907
DOI: 10.1021/acscatal.8b00220 Publication Date (Web): June 29, 2018

AIM: An Abstraction for Improving Machine Learning Prediction
V Stodden, X Wu, V Sochat
2018 IEEE Data Science Workshops, June 2018, DOI: 10.1109/DSW.2018.8439914

Efficient Threshold Selection for Multivariate Total Variation Denoising  
Sylvain Sardy & Hatef Monajemi       
Journal of Computational and Graphical Statistics
10 May 2018 DOI: 10.1080/10618600.2018.1476251

MRI to MGMT: predicting methylation status in glioblastoma patients using convolutional recurrent neural networks
Han L, Kamdar MR.
Pacific Symposium on Biocomputing Pacific Symposium on Biocomputing.
2018;23:331-342.

Nutrient transport suggests an evolutionary basis for charged archaeal surface layer proteins
Po-Nan Li, Jonathan Herrmann, Bradley B. Tolar, Frédéric Poitevin, Rasika Ramdasi, John R. Bargar, David A. Stahl, Grant J. Jensen,
Christopher A. Francis, Soichi Wakatsuki, Henry van den Bedem
The ISME Journal https://doi.org/10.1038/s41396-018-0191-0 Accepted: 14 April 201

Biological Insights Into Muscular Strength: Genetic Findings in the UK Biobank
Emmi Tikkanen, Stefan Gustafsson, David Amar, Anna Shcherbina, Daryl Waggott, Euan A. Ashley & Erik Ingelsson
Nature Scientific Reports volume 8, Article number: 6451 (2018)
doi:10.1038/s41598-018-24735-y

Architecture of an HIV-1 reverse transcriptase initiation complex
Kevin P. Larsen, Yamuna Kalyani Mathiharan, Kalli Kappel, Aaron T. Coey, Dong-Hua Chen, Daniel Barrero, Lauren Madigan, Joseph D. Puglisi, Georgios Skiniotis &
Elisabetta Viani Puglisi
Nature volume 557, pages118–122 (2018)
doi:10.1038/s41586-018-0055-9

The Scientific Filesystem
Vanessa Sochat
GigaScience, Volume 7, Issue 5, 1 May 2018, giy023,
https://doi.org/10.1093/gigascience/giy023

Breakdown of the Migdal-Eliashberg theory: A determinant quantum Monte Carlo study
I. Esterlis, B. Nosarzewski, E. W. Huang, B. Moritz, T. P. Devereaux, D. J. Scalapino, and S. A. Kivelson
Phys. Rev. B 97, 140501(R) – Published 2 April 2018

CRISPR–Cas9 screens in human cells and primary neurons identify modifiers of C9ORF72 dipeptide-repeat-protein toxicity
Nicholas J. Kramer, Michael S. Haney, David W. Morgens, Ana Jovičić, Julien Couthouis, Amy Li, James Ousey, Rosanna Ma, Gregor Bieri, C. Kimberly Tsui, Yingxiao Shi, Nicholas T. Hertz, Marc Tessier-Lavigne, Justin K. Ichida, Michael C. Bassik & Aaron D. Gitler
Nature Genetics (2018)
doi:10.1038/s41588-018-0070-7

Bad metallic transport in a modified Hubbard model
Connie H. Mousatov, Ilya Esterlis, Sean A. Hartnoll
arXiv:1803.08054, 2018 (Submitted on 21 Mar 2018)

Cholesterol enhances influenza binding avidity by controlling nanoscale receptor clustering
I. N. Goronzy, R. J. Rawle, S. G. Boxer and P. M. Kasson
DOI: 10.1039/C7SC03236F Chem. Sci., 2018, 9, 2340-2347

Natural Gradient Deep Q-learning
Ethan Knight, Osher Lerner
arXiv:1803.07482 [cs.LG] (Submitted on 20 Mar 2018)

Machine Learning Harnesses Molecular Dynamics to Discover New μ Opioid Chemotypes
Evan N. Feinberg, Amir Barati Farimani, Rajendra Uprety, Amanda Hunkele, Gavril W. Pasternak, Susruta Majumdar, Vijay S. Pande
arXiv:1803.04479 [q-bio.BM] (Submitted on 12 Mar 2018)

Using Deep Learning for Segmentation and Counting within Microscopy Data
Carlos X. Hernández, Mohammad M. Sultan, Vijay S. Pande
arXiv:1802.10548 [cs.CV] (Submitted on 28 Feb 2018)

Decision functions from supervised machine learning algorithms as collective variables for accelerating molecular simulations
Mohammad M. Sultan, Vijay S. Pande
arXiv:1802.10510 [stat.ML] (Submitted on 28 Feb 2018)

Sterically controlled mechanochemistry under hydrostatic pressure
Hao Yan, Fan Yang, Ding Pan, Yu Lin, J. Nathan Hohman, Diego Solis-Ibarra, Fei Hua Li, Jeremy E. P. Dahl, Robert M. K. Carlson,Boryslav A. Tkachenko, Andrey A. Fokin, Peter R. Schreiner, Giulia Galli, Wendy L. Mao, Zhi-Xun Shen & Nicholas A. Melosh
Nature volume 554, pages 505–510 (22 February 2018)  
DOI:10.1038/nature25765

Comparing fully general relativistic and Newtonian calculations of structure formation
William E. East, Radosław Wojtak, and Tom Abel
Phys. Rev. D 97, 043509 – Published 13 February 2018

Intermolecular correlations are necessary to explain diffuse scattering from protein crystals
A Peck, F Poitevin, TJ Lane
IUCrJ, 2018 - scripts.iucr.org

Unprecedented climate events: Historical changes, aspirational targets, and national commitments
Noah S. Diffenbaugh, Deepti Singh, and Justin S. Mankin
Science Advances  14 Feb 2018:
Vol. 4, no. 2, eaao3354
DOI: 10.1126/sciadv.aao3354

Transferable neural networks for enhanced sampling of protein dynamics  
Mohammad M. Sultan, Hannah K. Wayment-Steele, Vijay S. Pande
eprint arXiv:1801.00636 Publication Date:01/02/2018

Gene-expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ
Joseph W Foley, Chunfang Zhu, Philippe Jolivet, Shirley X Zhu, Peipei Lu, Michael J Meaney, Robert B West
doi: https://doi.org/10.1101/207340, January 11, 2018

Reducing Noise in Cosmological N-body Simulations with Neutrinos
Arka Banerjee, Devon Powell, Tom Abel, Francisco Villaescusa-Navarro
arXiv:1801.03906  Submitted 11 Jan 2018
 

2017

Comprehensive computational design of ordered peptide macrocycles
Parisa Hosseinzadeh, Gaurav Bhardwaj, Vikram Khipple Mulligan, Matthew D. Shortridge, Timothy W. Craven, Fátima Pardo-Avila, Stephen A. Rettie, David E. Kim, Daniel-Adriano Silva, Yehia M. Ibrahim, Ian K. Webb, John R. Cort, Joshua N. Adkins, Gabriele Varani, David Baker
Science  15 Dec 2017:
Vol. 358, Issue 6369, pp. 1461-1466
DOI: 10.1126/science.aap7577

Towards understanding feedback from supermassive black holes using convolutional neural networks
Stanislav Fort
arXiv:1712.00523

Variational Encoding of Complex Dynamics
Carlos X. Hernández, Hannah K. Wayment-Steele, Mohammad M. Sultan, Brooke E. Husic, Vijay S. Pande
arXiv:1711.08576v2

Numerical evidence of fluctuating stripes in the normal state of high-Tc cuprate superconductors
Edwin W. Huang, Christian B. Mendl, Shenxiu Liu, Steve Johnston, Hong-Chen Jiang, Brian Moritz, Thomas P. Devereaux
Science  01 Dec 2017: Vol. 358, Issue 6367, pp. 1161-1164
DOI: 10.1126/science.aak9546

Comparing Fully General Relativistic and Newtonian Calculations of Structure Formation
William E. East, Radosław Wojtak, Tom Abel
(Submitted on 17 Nov 2017) https://arxiv.org/abs/1711.06681

Structural sensitivity in HIV modeling: A case study of vaccination
Cora L. Bernard Margaret L. Brandeau
Infectious Disease Modelling, Volume 2, Issue 4, November 2017, Pages 399-411
https://doi.org/10.1016/j.idm.2017.08.002

Photoactivated Molecular Layer Deposition through Iodo−Ene Coupling Chemistry
Mie Lillethorup , David S. Bergsman , Tania E. Sandoval , and Stacey F. Bent
Chem. Mater., 2017, 29 (23), pp 9897–9906
DOI: 10.1021/acs.chemmater.7b01780 Publication Date (Web): November 12, 2017

Timeslice experiments for understanding regional climate projections: applications to the tropical hydrological cycle and European winter circulation
Chadwick, R., Douville, H. & Skinner, C.B.
Clim Dyn (2017) 49: 3011.
https://doi.org/10.1007/s00382-016-3488-6

Ultrafast Intersystem Crossing in Acetylacetone via Femtosecond X-ray Transient Absorption at the Carbon K-Edge
Aditi Bhattacherjee, Chaitanya Das Pemmaraju, Kirsten Schnorr, Andrew R. Attar, and Stephen R. Leone
J. Am. Chem. Soc., 2017, 139 (46), pp 16576–16583
DOI: 10.1021/jacs.7b07532

Enhancing reproducibility in scientific computing: Metrics and registry for Singularity containers
Vanessa V. Sochat, Cameron J. Prybol, Gregory M. Kurtzer
PLoS One. 2017 Nov 29;12(11):e0188511. doi: 10.1371/journal.pone.0188511. eCollection 2017.

Simulated Dynamics of Glycans on Ligand-Binding Domain of NMDA Receptors Reveals Strong Dynamic Coupling between Glycans and Protein Core
Anton V. Sinitskiy and Vijay S. Pande
J. Chem. Theory Comput.,DOI: 10.1021/acs.jctc.7b00817  October 11, 2017

The DECam Plane Survey: Optical photometry of two billion objects in the southern Galactic plane
E. F. Schlafly, G. M. Green, D. Lang, T. Daylan, D. P. Finkbeiner, A. Lee, A. M. Meisner, D. Schlegel, F. Valdes
(Submitted on 3 Oct 2017) arXiv:1710.01309

MRIQC: Advancing the automatic prediction of image quality in MRI from unseen sites
Oscar Esteban, Daniel Birman, Marie Schaer, Oluwasanmi O. Koyejo, Russell A. Poldrack, Krzysztof J. Gorgolewski
PLOS Published: September 25, 2017 https://doi.org/10.1371/journal.pone.0184661

Proton Network Flexibility Enables Robustness and Large Electric Fields in the Ketosteroid Isomerase Active Site
Lu Wang, Stephen D. Fried, and Thomas E. Markland
J. Phys. Chem. B, 2017, 121 (42), pp 9807–9815
DOI: 10.1021/acs.jpcb.7b06985 Publication Date (Web): September 15, 2017

Stripe order from the perspective of the Hubbard model
Edwin W. Huang, Christian B. Mendl, Hong-Chen Jiang, Brian Moritz, Thomas P. Devereaux
Submitted on 7 Sep 2017, arXiv:1709.02398

Bioimpedance and new onset heart failure: A longitudinal study of ~500,000 individuals from the general population
Daniel Lindholm, Eri Fukaya, Nicholas J. Leeper, Erik Ingelsson
doi: https://doi.org/10.1101/183483

Transfer Learning from Markov Models Leads to Efficient Sampling of Related Systems
Mohammad M. Sultan and Vijay S. Pande
J. Phys. Chem. B, Article ASAP
DOI: 10.1021/acs.jpcb.7b06896

Impact of Hydrogen Bonding on the Dynamics and Structure of Protic Ionic Liquid/Water Binary Mixtures
Heather E. Bailey, Yong-Lei Wang , and Michael D. Fayer
J. Phys. Chem. B, 2017, 121 (36), pp 8564–8576
DOI: 10.1021/acs.jpcb.7b06376

Decoding the spectroscopic features and timescales of aqueous proton defects
Joseph A. Napoli, Ondrej Marsalek, and Thomas E. Markland
arXiv:1709.05740

Kinetic Machine Learning Unravels Ligand-Directed Conformational Change of μ Opioid Receptor
Evan N. Feinberg, Amir Barati Farimani, Carlos Xavier Hernandez, Vijay S. Pande
doi: https://doi.org/10.1101/170886

Fast automated analysis of strong gravitational lenses with convolutional neural networks
Yashar D. Hezaveh, Laurence Perreault Levasseur & Philip J. Marshall
Nature 548, 555–557 (31 August 2017) doi:10.1038/nature23463

Analytical gradients for tensor hyper-contracted MP2 and SOS-MP2 on graphical processing units
Chenchen Song and Todd J. Martínez
The Journal of Chemical Physics 147, 161723 (2017); https://doi.org/10.1063/1.4997997

Mechanochemical unzipping of insulating polyladderene to semiconducting polyacetylene
Zhixing Chen, Jaron A. M. Mercer, Xiaolei Zhu, Joseph A. H. Romaniuk, Raphael Pfattner, Lynette Cegelski, Todd J. Martinez, Noah Z. Burns, Yan Xia,
Science  04 Aug 2017:Vol. 357, Issue 6350, pp. 475-479
DOI: 10.1126/science.aan2797

Ab Initio Simulations of a Supernova-driven Galactic Dynamo in an Isolated Disk Galaxy
Iryna Butsky, Jonathan Zrake, Ji-hoon Kim, Hung-I Yang, and Tom Abel
The Astrophysical Journal, Volume 843, Number 2, Published 2017 July 12

Is Multitask Deep Learning Practical for Pharma?
Bharath Ramsundar, Bowen Liu, Zhenqin Wu, Andreas Verras, Matthew Tudor, Robert P. Sheridan, and Vijay Pande
J. Chem. Inf. Model., 2017, 57 (8), pp 2068–2076
DOI: 10.1021/acs.jcim.7b00146 Publication Date (Web): July 10, 2017

Wen Torng, Russ B. Altman
BMC Bioinformatics. 2017; 18: 302. Published online 2017 Jun 14. doi: 10.1186/s12859-017-1702-0
 
Philippe Joly, Hélène Vignaud, Julie Di Martino, Mathias Ruiz, Roman Garin, Lioara Restier, Abdelouahed Belmalih, Christelle Marchal, Christophe Cullin, Benoit Arveiler, Patricia Fergelot, Aaron D. Gitler, Alain Lachaux, Julien Couthouis, Marion Bouchecareilh
PLoS One. 2017; 12(6): e0179369. Published online 2017 Jun 15. doi: 10.1371/journal.pone.0179369
 
Decrease of d-wave pairing strength in spite of the persistence of magnetic excitations in the overdoped Hubbard model
Edwin W. Huang, Douglas J. Scalapino, Thomas A. Maier, Brian Moritz, Thomas P. Devereaux
(Submitted on 10 May 2017) arXiv:1705.03949
 
α-CASSCF: An Efficient, Empirical Correction for SA-CASSCF To Closely Approximate MS-CASPT2 Potential Energy Surfaces
James W. Snyder Jr., Robert M. Parrish, and Todd J. Martínez
J. Phys. Chem. Lett., 2017, 8 (11), pp 2432–2437
DOI: 10.1021/acs.jpclett.7b00940 Publication Date (Web): May 17, 2017
 
Computing Localized Representations of the Kohn--Sham Subspace Via Randomization and Refinement
Anil Damle, Lin Lin, and Lexing Ying
SIAM J. Sci. Comput., 39(6), B1178–B1198.
https://doi.org/10.1137/16M1098589
 
A geographically-diverse collection of 418 human gut microbiome pathway genome databases
Aria S. Hahn, Tomer Altman,Kishori M. Konwar, Niels W. Hanson, Dongjae Kim, David A. Relman, David L. Dill and Steven J. Hallam
doi:10.1038/sdata.2017.35 Published online: 11 April 2017
 
Unravelling the influence of quantum proton delocalization on electronic charge transfer through the hydrogen bond
Christoph Schran Ondrej Marsalek Thomas E.Markland
Accepted 10 April 2017
https://doi.org/10.1016/j.cplett.2017.04.034
 
Han Altae-Tran, Bharath Ramsundar, Aneesh S. Pappu, Vijay Pande
ACS Cent Sci. 2017 Apr 26; 3(4): 283–293. Published online 2017 Apr 3. doi: 10.1021/acscentsci.6b00367
 
Anton V. Sinitskiy, Nathaniel H. Stanley, David H. Hackos, Jesse E. Hanson, Benjamin D. Sellers, Vijay S. Pande
Sci Rep. 2017; 7: 44578. Published online 2017 Apr 5. doi: 10.1038/srep44578
 
Phase Field Model for Morphological Transition in Nanowire Vapor–Liquid–Solid Growth
Yanming Wang, Paul C. McIntyre, and Wei Cai
Cryst. Growth Des., 2017, 17 (4), pp 2211–2217
DOI: 10.1021/acs.cgd.7b00197
 
Superradiant Instability and Backreaction of Massive Vector Fields around Kerr Black Holes
William E. East and Frans Pretorius
Phys. Rev. Lett. 119, 041101 – Published 24 July 2017
 
Statistical algorithms improve accuracy of gene fusion detection 
Gillian Hsieh Rob Bierman Linda Szabo Alex Gia Lee Donald E. FreemanNathaniel Watson E. Alejandro Sweet-Cordero Julia Salzman
Nucleic Acids Research, Volume 45, Issue 13, 27 July 2017, Pages e126, https://doi.org/10.1093/nar/gkx453

Topology-optimized metasurfaces: impact of initial geometric layout

Jianji Yang and Jonathan A. Fan

Opt. Lett. 42, 3161-3164 (2017)

Previous Models of Diffuse Scattering From Protein Crystals Do Not Explain Experimental Observations
Ariana Peck, Frédéric Poitevin, Thomas J. Lane

Application of the inverse fast multipole method as a preconditioner in a 3D Helmholtz boundary element method
T Takahashi, P Coulier, E Darve
Journal of Computational Physics, 2017 - Elsevier

Intertwined order in a frustrated four-leg t−J cylinder
John F. Dodaro, Hong-Chen Jiang, and Steven A. Kivelson
Phys. Rev. B 95, 155116 – Published 12 April 2017
 
Atomic Convolutional Networks for Predicting Protein-Ligand Binding Affinity
Joseph Gomes, Bharath Ramsundar, Evan N. Feinberg, Vijay S. Pande
(Submitted on 30 Mar 2017) arXiv:1703.10603
 
A direct-compatible formulation of the coupled perturbed complete active space self-consistent field equations on graphical processing units
James W. Snyder Jr. B. Scott Fales, Edward G. Hohenstein, Benjamin G. Levine, and Todd J. Martínez
The Journal of Chemical Physics 146, 174113 (2017); https://doi.org/10.1063/1.4979844
 
Seasonally fluctuating selection can maintain polymorphism at many loci via segregation lift
Meike J. Wittmann, Alan O. Bergland, Marcus W. Feldman, Paul S. Schmidt, and Dmitri A. Petrov
PNAS,  March 8, 2017 doi: 10.1073/pnas.1702994114
 
MoleculeNet: A Benchmark for Molecular Machine Learning
Zhenqin Wu, Bharath Ramsundar, Evan N. Feinberg, Joseph Gomes, Caleb Geniesse, Aneesh S. Pappu, Karl Leswing, Vijay Pande
(Submitted on 2 Mar 2017) arXiv:1703.00564
 
Quantum Dynamics and Spectroscopy of Ab Initio Liquid Water: The Interplay of Nuclear and Electronic Quantum Effects
Ondrej Marsalek and Thomas E. Markland
J. Phys. Chem. Lett., 2017, 8 (7), pp 1545–1551
DOI: 10.1021/acs.jpclett.7b00391 Publication Date (Web): March 15, 2017
 
The Role of Plant CO2 Physiological Forcing in Shaping Future Daily-Scale Precipitation
Christopher B. Skinner and Christopher J. Poulsen, Robin Chadwick, Noah S. Diffenbaugh, Richard P. Fiorella
https://doi.org/10.1175/JCLI-D-16-0603.1 Published 9 March 2017
 
Fast Spatial Gaussian Process Maximum Likelihood Estimation via Skeletonization Factorizations
Victor Minden, Anil Damle, Kenneth L. Ho, and Lexing Ying
Multiscale Model. Simul., 15(4), 1584–1611.
https://doi.org/10.1137/17M1116477
 
Electrostatic Control of Regioselectivity in Au(I)-Catalyzed Hydroarylation
Vivian M. Lau, William C. Pfalzgraff, Thomas E. Markland, and Matthew W. Kanan
J. Am. Chem. Soc., 2017, 139 (11), pp 4035–4041
DOI: 10.1021/jacs.6b11971 Publication Date (Web): February 22, 2017
 

Hatef Monajemi, David L. Donoho
(Submitted on 10 Feb 2017) arXiv:1702.03062

Spacetime dynamics of a Higgs vacuum instability during inflation
WE East, J Kearney, B Shakya, H Yoo, KM Zurek
Physical Review D, 2017 - APS

2016

Au–Ge MEAM potential fitted to the binary phase diagram
Yanming Wang, Adriano Santana and Wei Cai
Published 23 December 2016 Modelling and Simulation in Materials Science and Engineering, Volume 25, Number 2

Reverse time migration for microseismic sources using the geometric mean as an imaging condition
Nori Nakata and Gregory C. Beroza (2016) GEOPHYSICS, 81(2), KS51-KS60.
https://doi.org/10.1190/geo2015-0278.1

Atomic orbital-based SOS-MP2 with tensor hypercontraction. I. GPU-based tensor construction and exploiting sparsity
Chenchen Song and Todd J. Martínez
The Journal of Chemical Physics 144, 174111 (2016); doi: http://dx.doi.org/10.1063/1.4948438

Massively Parallel Computation of Accurate Densities for N-body Dark Matter Simulations using the Phase-Space-Element Method
Ralf Kaehler

Communication: A difference density picture for the self-consistent field ansatz
Robert M. Parrish, Fang Liu and Todd J. Martínez
The Journal of Chemical Physics 144, 131101 (2016); doi: http://dx.doi.org/10.1063/1.4945277

Electronic pair binding and Hund's rule violations in doped C60
Hong-Chen Jiang and Steven Kivelson
Phys. Rev. B 93, 165406 – Published 5 April 2016

Eco-evolutionary buffering: rapid evolution facilitates regional coexistence of species engaged in local priority effects
Meike J. Wittmann, Tadashi Fukami
doi: https://doi.org/10.1101/040659

Freely decaying turbulence in force-free electrodynamics
Jonathan Zrake, William E. East
Published 2016 January 22

2015

Spontaneous Decay of Periodic Magnetostatic Equilibria
William E. East, Jonathan Zrake, Yajie Yuan, and Roger D. Blandford
Phys. Rev. Lett. 115, 095002 – Published 28 August 2015