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SRCC selected 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 acknowledge this. The following wording is suggested for your Acknowledgements section:

"Some of the computing for this project was performed on the Sherlock 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!

2018

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

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

Breakdown of Migdal-Eliashberg theory; a determinant quantum Monte Carlo study
Ilya Esterlis, Benjamin Nosarzewski, Edwin W. Huang, Brian Moritz, Thomas P. Devereaux, Douglas J. Scalapino, Steven A. Kivelson
(Submitted on 4 Nov 2017) arXiv:1711.01493

Biological Insights Into Muscular Strength: Genetic Findings in the UK Biobank
Emmi Tikkanen, Stefan Gustafsson, David Amar, Anna Shcherbina, Daryl Waggott, Euan Ashley, Erik Ingelsson
doi: https://doi.org/10.1101/201020

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

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

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

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