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, 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 acknowledgements.
2020
Nearest Neighbor distributions: new statistical measures for cosmological clustering
Arka Banerjee, Tom Abel
Monthly Notices of the Royal Astronomical Society, staa3604, https://doi.org/10.1093/mnras/staa3604 Published: 20 November 2020
Function-Oriented Synthesis: Design, Synthesis, and Evaluation of Highly Simplified Bryostatin Analogues
Paul A. Wender, Jack L. Sloane, Quang H. Luu-Nguyen, Yasuyuki Ogawa, Akira J. Shimizu, Steven M. Ryckbosch, Jefferson H. Tyler, and Clayton Hardman
J. Org. Chem. November 17, 2020
Identification of highly selective covalent inhibitors
Shiyu Chen, Scott Lovell, Sumin Lee, Matthias Fellner, Peter D. Mace & Matthew Bogyo
Nature Biotechnology (2020) 16 November 2020
Two-component dynamics and the liquid-like to gas-like crossover in supercritical water
Peihao Sun, J. B. Hastings, Daisuke Ishikawa, Alfred Q. R. Baron, Giulio Monaco
arXiv:2008.06811 13 Nov 2020
Atomistic Insight into Cation Effects on Binding Energies in Cu-Catalyzed Carbon Dioxide Reduction
Thomas Ludwig, Joseph A. Gauthier, Colin F. Dickens, Kristopher S. Brown, Stefan Ringe, Karen Chan, and Jens K. Nørskov
J. Phys. Chem. Publication Date: November 3, 2020
Acetonitrile Transition Metal Interfaces from First Principles
Thomas Ludwig, Aayush R. Singh, and Jens K. Nørskov
J. Phys. Chem. Lett. 2020, 11, XXX, 9802–9811 Publication Date:November 5, 2020
Toward Force Estimation in Robot-Assisted Surgery using Deep Learning with Vision and Robot State
Zonghe Chua, Anthony M. Jarc, Allison M. Okamura
Submitted on 4 Nov 2020, arXiv:2011.02112 [cs.RO]
Postselection-free entanglement dynamics via spacetime duality
M Ippoliti, V Khemani
arXiv:2010.15840, Submitted on 29 Oct 2020
A fast and scalable framework for large-scale and ultrahigh-dimensional sparse regression with application to the UK Biobank
Junyang Qian, Yosuke Tanigawa, Wenfei Du, Matthew Aguirre, Chris Chang, Robert Tibshirani,Manuel A. Rivas, Trevor Hastie
PLOS, Published: October 23, 2020 https://doi.org/10.1371/journal.pgen.1009141
Large-Scale Labeling and Assessment of Sex Bias in Publicly Available Expression Data
Emily Flynn, Annie Chang, Russ B. Altman
doi: https://doi.org/10.1101/2020.10.26.356287
SynCity: Using open data to create a synthetic city of hourly building energy estimates by integrating data-driven and physics-based methods
Jonathan Roth, Amory Martin, Clayton Miller, Rishee K. Jain
Applied Energy Volume 280, 15 December 2020
Motion Correction of 3D Dynamic Contrast-Enhanced Ultrasound Imaging without Anatomical Bmode Images
Jia-Shu Chen, Maged Goubran Ph.D., Gaeun Kim, Jurgen K. Willmann M.D., Michael Zeineh M.D., Ph.D., Dimitre Hristov Ph.D., Ahmed El Kaffas Ph.D
Submitted on 5 Oct 2020 arXiv:2010.01721
Prevalence of neural collapse during the terminal phase of deep learning training
Vardan Papyan, X. Y. Han, and David L. Donoho
PNAS October 6, 2020 117 (40) 24652-24663
Carbonate-promoted C–H carboxylation of electron-rich heteroarenes
Tyler M. Porter and Matthew W. Kanan
Chem. Sci., 2020, 11, 11936-11944 DOI: 10.1039/D0SC04548A Accepted 5th October 2020
Dark Energy Survey Year 1 Results: Cosmological Constraints from Cluster Abundances, Weak Lensing, and Galaxy Correlations
C. To, E. Krause, E. Rozo, H. Wu, D. Gruen, R. H. Wechsler, T. F. Eifler, E. S. Rykoff, M. Costanzi, M. R. Becker, G. M. Bernstein, J. Blazek, S. Bocquet, S. L. Bridle, R. Cawthon, A. Choi, M. Crocce, C. Davis, J. DeRose, A. et al.
Submitted on 2 Oct 2020 arXiv:2010.01138
Skyrmion Superconductivity: DMRG evidence for a topological route to superconductivity
Shubhayu Chatterjee, Matteo Ippoliti, Michael P. Zaletel
arXiv:2010.01144 Submitted on 2 Oct 2020
Critical role of the sign structure in the doped Mott insulator: Luther-Emery versus Fermi-liquid-like state in quasi-one-dimensional ladders
Hong-Chen Jiang, Shuai Chen, and Zheng-Yu Weng
Phys. Rev. B 102, 104512 – Published 25 September 2020
Hubbard ladders at small U revisited
Yuval Gannot, Yi-Fan Jiang, and Steven A. Kivelson
Phys. Rev. B 102, 115136 – Published 16 September 2020
Effect of Hetero-Aromaticity on Adsorption of Pyrazine on the Ge(100)-2×1 Surface
Tania E. Sandoval, Fabian Pieck, Ralf Tonner, and Stacey F. Bent
J. Phys. Chem. C 2020 September 9, 2020
Enhancing associative memory recall and storage capacity using confocal cavity QED
Brendan P. Marsh, Yudan Guo, Ronen M. Kroeze, Sarang Gopalakrishnan, Surya Ganguli, Jonathan Keeling, Benjamin L. Lev
arXiv:2009.01227v1 Submitted on 2 Sep 2020
Multi-task deep learning for cardiac rhythm detection in wearable devices
Jessica Torres-Soto & Euan A. Ashley
Nature Partner Journals, npj Digital Medicine volume 3, Article number: 116 (2020)
Age-related loss of neural stem cell O-GlcNAc promotes a glial fate switch through STAT3 activation
Charles W. White III, Xuelai Fan, Jason C. Maynard, V, Elizabeth G. Wheatley, Gregor Bieri, Julien Couthouis, Alma L. Burlingame, and Saul A. Villeda
PNAS first published August 26, 2020 https://doi.org/10.1073/pnas.2007439117
Quantum Algorithmfor a Convergent Series of Approximations towards the Exact Solution of the Lowest Eigenstates of a Hamiltonian
Zhiyong Zhang
arXiv preprint arXiv:2009.03537, 2020
Returning radiation in strong gravity around black holes: reverberation from the accretion disc
D R Wilkins, J A García, T Dauser, A C Fabian
Monthly Notices of the Royal Astronomical Society, Volume 498, Issue 3, November 2020, Pages 3302–3319, https://doi.org/10.1093/mnras/staa2566 Published: 24 August 2020
Absentee Voting Is Popular During COVID-19 But Does Not Change Turnout or Partisan Rates of Voting
Jesse Yoder, Cassandra Handan-Nader, Andrew Myers,Tobias Nowacki, Daniel M. Thompson, Jennifer A. Wu,Chenoa Yorgason, and Andrew B. Hall
Democracy & Polarization Lab, Stanford University August 22, 2020
Combination of cluster number counts and two-point correlations: Validation on Mock Dark Energy Survey
C. To, E. Krause, E. Rozo, H. Wu, D. Gruen, J. DeRose, E. S. Rykoff, R. H. Wechsler, M. R. Becker, M. Costanzi, T. Eifler, M. E. S. Pereira, N. Kokron (DES Collaboration)
Submitted on 25 Aug 2020 arXiv:2008.10757
Theoretical basis for stabilizing messenger RNA through secondary structure design
Hannah K. Wayment-Steele, Do Soon Kim, Christian A. Choe, John J. Nicol, Roger Wellington-Oguri, R. Andres Parra Sperberg, Po-Ssu Huang, Eterna Participants, Rhiju Das
https://doi.org/10.1101/2020.08.22.262931 August 24, 2020
LPA and APOE are associated with statin selection in the UK Biobank
Adam Lavertu, Gregory McInnes, Yosuke Tanigawa, Russ B Altman, Manuel A. Rivas
August 29, 2020 doi: https://doi.org/10.1101/2020.08.28.272765
Drug Response Pharmacogenetics for 200,000 UK Biobank Participants
Gregory McInnes, Russ B Altman
doi: https://doi.org/10.1101/2020.08.09.243311
Probing galaxy evolution in massive clusters using ACT and DES: splashback as a cosmic clock
Susmita Adhikari, Tae-hyeon Shin, Bhuvnesh Jain, Matt Hilton, Eric Baxter, Chihway Chang, Risa H. Wechsler, Nick Battaglia, Marcelle Soares-Santos, Eric Suchyta et al
arXiv:2008.11663 26 Aug 2020
The SAGA Survey. II. Building a Statistical Sample of Satellite Systems around Milky Way-like Galaxies
Yao-Yuan Mao, Marla Geha, Risa H. Wechsler, Benjamin Weiner, Erik J. Tollerud, Ethan O. Nadler, Nitya Kallivayalil
arXiv:2008.12783 28 Aug 2020
Automatic sleep stage classification with deep residual networks in a mixed-cohort setting
Alexander Neergaard Olesen, Poul Jennum, Emmanuel Mignot, Helge B D Sorensen
arXiv:2008.09416v1 10.1093/sleep/zsaa161 21 Aug 2020
Trove: Ontology-driven weak supervision for medical entity classification
Jason A. Fries, Ethan Steinberg, Saelig Khattar, Scott L. Fleming, Jose Posada, Alison Callahan, Nigam H. Shah
arXiv:2008.01972 [Submitted on 5 Aug 2020]
2D Conductive Ni-HAB as a Catalyst for the Electrochemical Oxygen Reduction Reaction
Jihye Park, Zhihua Chen, Raul A. Flores, Gustaf Wallenestrom, Ambarish Kulkarni, Jens K. Nørskov, Thomas F. Jaramillo, and Zhenan Bao
ACS Appl. Mater. Interfaces 2020
August 4, 2020 https://doi.org/10.1021/acsami.0c09323
Second Order Accurate Hierarchical Approximate Factorization of Sparse SPD Matrices
Bazyli Klockiewicz, Léopold Cambier, Ryan Humble, Hamdi Tchelepi, Eric Darve
arXiv:2007.00789 4 Aug 2020
Knockout of reactive astrocyte activating factors slows disease progression in an ALS mouse model
Kevin A. Guttenplan, Maya K. Weigel, Drew I. Adler, Julien Couthouis, Shane A. Liddelow, Aaron D. Gitler & Ben A. Barres
Nature Communications volume 11, Article number: 3753 (2020)
Milky Way Satellite Census. III. Constraints on Dark Matter Properties fromObservations of Milky Way Satellite Galaxies
E. O. Nadler, A. Drlica-Wagner, K. Bechtol, S. Mau, R. H. Wechsler, V. Gluscevic, K. Boddy, A. B. Pace, et al.
arXiv.org arXiv:2008.00022 Submitted on 31 Jul 2020
Reduced Thermal Conductivity of Supported and Encased Monolayer and Bilayer MoS2
Alexander Joseph Gabourie1, Saurabh Vinayak Suryavanshi, Amir Barati Farimani and Eric Pop
2D Materials IOP Science, Accepted Manuscript online 10 July 2020
Methods for Model Calibration under High Uncertainty: Modeling Cholera in Bangladesh
Theresa Ryckman, Stephen Luby, Douglas K. Owens, Eran Bendavid, Jeremy D. Goldhaber-Fiebert
Medical Decision Making, First Published July 8, 2020
https://doi.org/10.1177/0272989X20938683
GANSim: Conditional Facies Simulation Using an Improved Progressive Growing of Generative Adversarial Networks (GANs)
Suihong Song, Tapan Mukerji, Jiagen Hou
EarthArXiv https://doi.org/10.31223/osf.io/fm24b 2020-07-05
Decoding spoken English phonemes from intracortical electrode arrays in dorsal precentral gyrus
Guy H. Wilson, Sergey D. Stavisky, Francis R. Willett, Donald T. Avansino, Jessica N. Kelemen, Leigh R. Hochberg, Jaimie M. Henderson, Shaul Druckmann, Krishna V. Shenoy
doi: https://doi.org/10.1101/2020.06.30.180935 July 01, 2020
An Empirical Characterization of Fair Machine Learning For Clinical Risk Prediction
Stephen R. Pfohl, Agata Foryciarz, Nigam H. Shah
Submitted on 20 Jul 2020 arXiv:2007.10306
Visualizing Energy Transfer at Buried Interfaces in Layered Materials Using Picosecond X‐Rays
Clara Nyby, Aditya Sood, Peter Zalden, Alexander J. Gabourie, Philipp Muscher, Daniel Rhodes, Ehren Mannebach, Jeff Corbett, Apurva Mehta, Eric Pop, Tony F. Heinz, Aaron M. Lindenberg
First published: 30 June 2020
Advanced Functional Materials https://doi.org/10.1002/adfm.202002282
RedMaPPer: Evolution and Mass Dependence of the Conditional Luminosity Functions of Red Galaxies in Galaxy Clusters
Chun-Hao To1, Rachel M. Reddick1, Eduardo Rozo, Eli Rykoff and Risa H. Wechsler
Published June 29, 2020 The Astrophysical Journal, Volume 897, Number 1
Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures
Kalli Kappel, Kaiming Zhang, Zhaoming Su, Andrew M. Watkins, Wipapat Kladwang, Shanshan Li, Grigore Pintilie, Ved V. Topkar, Ramya Rangan, Ivan N. Zheludev, Joseph D. Yesselman, Wah Chiu & Rhiju Das
Nature Methods volume 17, pages699–707(2020)
Weighing neutrinos with the halo environment
Arka Banerjeea, Emanuele Castorinad, Francisco Villaescusa-Navarrof, Travis Courtg, and Matteo Vieli
Journal of Cosmology and Astroparticle Physics, Volume 2020, June 2020
Pervasive additive and non-additive effects within the HLA region contribute to disease risk in the UK Biobank
Guhan Ram Venkataraman, Julia Eve Olivieri, Christopher DeBoever, Yosuke Tanigawa, Johanne Marie Justesen, Alexander Dilthey, Manuel A. Rivas
doi: https://doi.org/10.1101/2020.05.28.119669 June 12, 2020
Active Learning Accelerated Discovery of Stable Iridium Oxide Polymorphs for the Oxygen Evolution Reaction
Raul A. Flores, Christopher Paolucci, Kirsten T. Winther, Ankit Jain, Jose Antonio Garrido Torres, Muratahan Aykol, Joseph Montoya, Jens K. Nørskov, Michal Bajdich, and Thomas Bligaard
Chem. Mater. 2020, 32, 13, 5854–5863 Publication Date:June 18, 2020
A single-cell atlas of the peripheral immune response in patients with severe COVID-19
Aaron J. Wilk, Arjun Rustagi, Nancy Q. Zhao, Jonasel Roque, Giovanny J. Martínez-Colón, Julia L. McKechnie, Geoffrey T. Ivison, Thanmayi Ranganath, Rosemary Vergara, Taylor Hollis, Laura J. Simpson, Philip Grant, Aruna Subramanian, Angela J. Rogers & Catherine A. Blish
Nature Medicine, Published: 08 June 2020
Geological Facies Modeling Based on Progressive Growing of Generative Adversarial Networks (GANs)
Suihong Song, Tapan Mukerji and Jiagen Hou
EarthArXiv https://doi.org/10.31223/osf.io/ycufs 2020-06-22
A genotype-phenotype-fitness map reveals local modularity and global pleiotropy of adaptation
Grant Kinsler, Kerry Geiler-Samerotte, Dmitri Petrov
doi: https://doi.org/10.1101/2020.06.25.172197
Controlling arsenic mobilization during managed aquifer recharge: The role of sediment heterogeneity
Sarah Fakhreddine, Henning Prommer, Steven M. Gorelick, Jason Dadakis, and Scott Fendorf
Environ. Sci. Technol. Publication Date:June 9, 2020
https://doi.org/10.1021/acs.est.0c00794
Stabilization of extensive fine-scale diversity by ecologically driven spatiotemporal chaos
Michael T. Pearce, Atish Agarwala, and Daniel S. Fisher
PNAS first published June 9, 2020
https://doi.org/10.1073/pnas.1915313117
Pharmacogenetics at scale: An analysis of the UK Biobank
Greg McInnes, Adam Lavertu, Katrin Sangkuhl, Teri E. Klein, Michelle Whirl-Carrillo, Russ B. Altman
doi: https://doi.org/10.1101/2020.05.30.125583
Distinct Conformational States Underlie Pausing during Initiation of HIV-1 Reverse Transcription
Kevin P. Larsen, Junhong Choi, Lynnette N. Jackson, Kalli Kappel, Jingji Zhang, Betty Ha, Dong-Hua Chen, Elisabetta Viani Puglisi
Journal of Molecular Biology
Accepted 1 June 2020, https://doi.org/10.1016/j.jmb.2020.06.003
Efficient cosmological analysis of the SDSS/BOSS data from the Effective Field Theory of Large-Scale Structure
Thomas Colasa, Guido d'Amicoa, Leonardo Senatorea, Pierre Zhange and Florian Beutlerh
Journal of Cosmology and Astroparticle Physics, Volume 2020, June 2020
RNA secondary structure packages ranked and improved by high-throughput experiments
Hannah K. Wayment-Steele, Wipapat Kladwang, Eterna Participants, Rhiju Das
doi: https://doi.org/10.1101/2020.05.29.124511
Posted May 31, 2020
A memory of eS25 loss drives resistance phenotypes
Alex G Johnson, Ryan A Flynn, Christopher P Lapointe, Yaw Shin Ooi, Michael L Zhao, Christopher M Richards, Wenjie Qiao, Shizuka B Yamada, Julien Couthouis, Aaron D Gitler, Jan E Carette, Joseph D Puglisi
Nucleic Acids Research, https://doi.org/10.1093/nar/gkaa444
Published: 28 May 2020
Extracting chemical reactions from text using Snorkel
Emily K. Mallory, Matthieu de Rochemonteix, Alex Ratner, Ambika Acharya, Chris Re, Roselie A. Bright & Russ B. Altman
BMC Bioinformatics volume 21, Article number: 217 (2020)
Published: 27 May 2020
De novo 3D models of SARS-CoV-2 RNA elements and small-molecule-binding RNAs to guide drug discovery
Ramya Rangan, Andrew M. Watkins, Wipapat Kladwang, Rhiju Das
Posted April 15, 2020. doi: https://doi.org/10.1101/2020.04.14.041962
Metagenome-assembled genomes reveal unique metabolic adaptations of a basal marine Thaumarchaeota lineage
Linta Reji & Christopher A. Francis
The ISME Journal (2020) Published: 13 May 2020
Structural topology optimization of tall buildings for dynamic seismic excitation using modal decomposition
Amory Martina, Gregory G. Deierlein
https://doi.org/10.1016/j.engstruct.2020.110717
Engineering Structures Volume 216, 1 August 2020, 110717
A radiomics approach to artificial intelligence in echocardiography: Predicting post-operative right ventricular failure
Rohan Shad, Nicolas Quach, Robyn Fong, Curt P. Langlotz, Sandra Kong, Patpilai Kasinpila, Myriam Amsallem, Francois Haddad, Yasuhiro Shudo, Y. Joseph Woo, Jeffrey Teuteberg, William Hiesinger
doi: https://doi.org/10.1101/2020.05.05.20092494
Short- and long-read metagenomics of South African gut microbiomes reveal a transitional composition and novel taxa
Fiona B. Tamburini, Dylan Maghini, Ovokeraye H. Oduaran, Ryan Brewster, Michaella R. Hulley, Venesa Sahibdeen, Shane A. Norris, Stephen Tollman, Kathleen Kahn, Ryan G. Wagner, Alisha N. Wade, Floidy Wafawanaka, Xavier Gómez-Olivé, Rhian Twine, Zané Lombard, Scott Hazelhurst, Ami S. Bhatt
Posted May 19, 2020. doi: https://doi.org/10.1101/2020.05.18.099820
Use of Patient-Specific Computational Models for Optimization of Aortic Insufficiency after Implantation of Left Ventricular Assist Device
Patpilai Kasinpila MD, Sandra Kong, Robyn Fong BS, Rohan Shad MD, Alexander Kaiser PhD, Alison Marsden PhD, Joseph Woo MD, William Hiesinger MD
The Journal of Thoracic and Cardiovascular Surgery Available online 15 May 2020
https://doi.org/10.1016/j.jtcvs.2020.04.164
Integrative profiling of early host chromatin accessibility responses in human neutrophils with sensitive pathogen detection
Nikhil Ram-Mohan, Simone A. Thair, Ulrike M. Litzenburger, Steven Cogill, Nadya Andini, Xi Yang, Howard Y. Chang, Samuel Yang
doi: https://doi.org/10.1101/2020.04.28.066829
bioRxiv Posted April 30, 2020
The Diversity–Innovation Paradox in Science
Bas Hofstra, Vivek V. Kulkarni, Sebastian Munoz-Najar Galvez, Bryan He, Dan Jurafsky, and Daniel A. McFarland
PNAS April 28, 2020 117 (17) 9284-9291; first published April 14, 2020 https://doi.org/10.1073/pnas.1915378117
Blinding multiprobe cosmological experiments
J Muir, G M Bernstein, D Huterer, F Elsner, E Krause, A Roodman, S Allam, J Annis, S Avila, K Bechtol, E Bertin, D Brooks, E Buckley-Geer, D L Burke, A Carnero Rosell, M Carrasco Kind, J Carretero, R Cawthon, M Costanzi, L N da Costa, J De Vicente, S Desai, J P Dietrich, P Doel, T F Eifler, S Everett, P Fosalba, J Frieman, J García-Bellido, D W Gerdes, D Gruen, R A Gruendl, J Gschwend, W G Hartley, D L Hollowood, D J James, M Jarvis, K Kuehn, N Kuropatkin, O Lahav, M March, J L Marshall, P Melchior, F Menanteau, R Miquel, R L C Ogando, A Palmese, F Paz-Chinchón, A A Plazas, A K Romer, E Sanchez, V Scarpine, M Schubnell, S Serrano, I Sevilla-Noarbe, M Smith, E Suchyta, G Tarle, D Thomas, M A Troxel, A R Walker, J Weller, W Wester, J Zuntz
Monthly Notices of the Royal Astronomical Society, Volume 494, Issue 3, May 2020, Pages 4454–4470, https://doi.org/10.1093/mnras/staa965
Published: 15 April 2020
Milky Way Satellite Census. II. Galaxy–Halo Connection Constraints Including the Impact of the Large Magellanic Cloud
E. O. Nadler1, R. H. Wechsler, K. Bechtol, Y.-Y. Mao, G. Green, A. Drlica-Wagner, M. McNanna, S. Mau A. B. Pace1, J. D. Simon et.al.
Published 2020 April 15
The Astrophysical Journal, Volume 893, Number 1
Hierarchy of energy scales in an O(3) symmetric antiferromagnetic quantum critical metal: A Monte Carlo study
Carsten Bauer, Yoni Schattner, Simon Trebst, and Erez Berg
Phys. Rev. Research 2, 023008 – Published 6 April 2020
Minkowski functionals for phase behavior under confinement
Arnout M P Boelens, Hamdi A Tchelepi
Submitted on 3 Apr 2020 arXiv:2004.01344
Initial Review and Analysis of COVID-19 Host Genetics and Associated Phenotypes
Yosuke Tanigawa and Manuel Rivas
Received: 23 March 2020 / Approved: 24 March 2020 / Online: 24 March 2020 (08:36:20 CET)
Deep Quantum Geometry of Matrices
Xizhi Han and Sean A. Hartnoll
Phys. Rev. X 10, 011069 – Published 23 March 2020
A molecular cell atlas of the human lung from single cell RNA sequencing
Kyle J. Travaglini, Ahmad N. Nabhan, Lolita Penland, Rahul Sinha, Astrid Gillich, Rene V. Sit, Stephen Chang, Stephanie D. Conley, Yasuo Mori, Jun Seita, Gerald J. Berry, Joseph B. Shrager, Ross J. Metzger, Christin S. Kuo, Norma Neff, Irving L. Weissman, Stephen R. Quake, Mark A. Krasnow
doi: https://doi.org/10.1101/742320
The impact of the fiducial cosmology assumption on BAO distance scale measurements
Paul Carter, Florian Beutler, Will J Percival, Joseph DeRose, Risa H Wechsler, Cheng Zhao
Monthly Notices of the Royal Astronomical Society, Volume 494, Issue 2, May 2020, Pages 2076–2089
https://doi.org/10.1093/mnras/staa761 Published:18 March 2020
Beyond the Core: Who Has Larger Social Networks?
Bas Hofstra, Rense Corten, Frank van Tubergen
Social Forces, soaa031, https://doi.org/10.1093/sf/soaa031 Published:22 April 2020
Spatial Characterization of Tumor Perfusion Properties from 3D DCE-US Perfusion Maps are Early Predictors of Cancer Treatment Response
Ahmed El Kaffas, Assaf, Hoogi Zhou, Jianhua Durot, Isabelle Wang, Huaijun, Jarrett Rosenberg, Albert tseng, Hersh Sagreiya, Alireza Akhbardeh, Daniel L. Rubin, Aya Kamaya, Dimitre Hristov & Jürgen K. Willmann
Scientific Reports (Nature Publisher Group); London Vol. 10, Iss. 1, (2020).
DOI:10.1038/s41598-020-63810-1
TeraChem Cloud: A High-Performance Computing Service for Scalable Distributed GPU-Accelerated Electronic Structure Calculations
Stefan Seritan, Keiran Thompson and Todd J. Martínez
J. Chem. Inf. Model. April 8, 2020 https://doi.org/10.1021/acs.jcim.9b01152
Inpainting Galactic Foreground Intensity and Polarization maps using Convolutional Neural Network
Giuseppe Puglisi, Xiran Bai
Submitted on 30 Mar 2020 arXiv:2003.13691
A new paradigm for accelerating clinical data science at Stanford Medicine
Somalee Datta, Jose Posada, Garrick Olson, Wencheng Li, Ciaran O'Reilly, Deepa Balraj, Joseph Mesterhazy, Joseph Pallas, Priyamvada Desai, Nigam Shah
arXiv:2003.10534 (Submitted on 17 Mar 2020)
Early warning signals of malaria resurgence in Kericho, Kenya
Mallory J. Harris, Simon I. Hay and John M. Drake
Biology Letters, The Royal Society
Published:18 March 2020 https://doi.org/10.1098/rsbl.2019.0713
Implications of the fractional charge of hydroxide at the electrochemical interface
Joseph A. Gauthier, Leanne D. Chen, Michal Bajdich and Karen Chan
Phys. Chem. Chem. Phys., 2020, Advance Article
https://doi.org/10.1039/D0CP00115E
Lateral Variations of Shear‐Wave Velocity in the D″ Layer Beneath the Indian‐Eurasian Plate Collision Zone
Guohui Li Ling Bai Jeroen Ritsema
First published: 12 March 2020
https://doi.org/10.1029/2019GL086856
Engineered Fluorescent E. coli Lysogens Allow Live-Cell Imaging of Functional Prophage Induction Triggered inside Macrophages
Katie Bodner, Arin L.Melkonian, Angela I.M. Barth, Takamasa Kudo, Yu Tanouchi, Markus W.Covert
Cell Systems, Published: March 18, 2020
https://doi.org/10.1016/j.cels.2020.02.006
A mathematical model of ctDNA shedding predicts tumor detection size
Stefano Avanzini, David M. Kurtz, Jacob J. Chabon, Sharon Seiko Hori, Sanjiv Sam Gambhir, Ash A. Alizadeh, Maximilian Diehn, Johannes G. Reiter
doi: https://doi.org/10.1101/2020.02.12.946228
Excited state charge distribution and bond expansion of ferrous complexes observed with femtosecond valence-to-core x-ray emission spectroscopy
Kathryn Ledbetter, Marco E. Reinharu, Kristjan Kunnus, Alessandro Gallo, Alexander Britz, Elisa Biasin, James M. Glownia, Silke Nelson, Tim B. Van Driel, Clemens Weninger, Diana B. Zederkof, Kristoffer Haldrup, Amy A. Cordones, Kelly J. Gaffney, Dimosthenis Sokaras and Roberto Alonso-Mori
J. Chem. Phys. 152, 074203 (2020); https://doi.org/10.1063/1.5139441
Possible superconductivity with Bogoliubov Fermi surface in lightly doped Kagome U(1) spin liquid
Yi-Fan Jiang, Hong Yao, Fan Yang
Submitted on 5 Mar 2020 arXiv:2003.0285
Detective quantum efficiency of photon-counting CdTe and Si detectors for computed tomography: a simulation study
Mats Persson, Adam Wang, Norbert J. Pelc
Submitted on 1 Mar 2020 arXiv:2003.00390
Wind Turbine Performance in Very Large Wind Farms: Betz Analysis Revisited
Jacob R. West and Sanjiva K. Lele
Energies 2020, 13(5), 1078; https://doi.org/10.3390/en13051078
Published: 1 March 2020
Enhanced Menshutkin SN2 Reactivity in Mesoporous Silica: The Influence of Surface Catalysis and Confinement
Steven A. Yamada, Samantha T. Hung, Weizhen Sun, Ling Zhao, and Michael D. Fayer
J. Am. Chem. Soc. 2020, 142, 12, 5636–5648 Publication Date:February 20, 2020
https://doi.org/10.1021/jacs.9b12666
Effects of the Dopant Site on the Absorption Properties of CsPb1–xMxI2Br (M = Ge, Sn, Sr, and Cu): A First-Principles Investigation
Yanan Liang, Li Guan, Xiaofang Xu, Shichuang Han, Jianxin Guo, Jianglong Wang, Xiaobo Chen Zhiyong Zhang, Xu Li
J. Phys. Chem. C 2020, 124, 11, 6028-6037
Publication Date:February 24, 2020 https://doi.org/10.1021/acs.jpcc.9b08246
Signatures of self-interacting dark matter on cluster density profile and subhalo distributions
Arka Banerjee, Susmita Adhikari, Neal Dalal, Surhud More and Andrey Kravtsov
Journal of Cosmology and Astroparticle Physics, Volume 2020, February 2020
Topological superconductivity in the doped chiral spin liquid on the triangular lattice
Yi-Fan Jiang, Hong-Chen Jiang
arXiv:2002.04686 Submitted on 11 Feb 2020
Causal Inference in Genetic Trio Studies
Stephen Bates, Matteo Sesia, Chiara Sabatti, Emmanuel Candes
arXiv:2002.09644 (Submitted on 22 Feb 2020)
DC Hall coefficient of the strongly correlated Hubbard model
Wen O. Wang, Jixun K. Ding, Brian Moritz, Edwin W. Huang, Thomas P. Devereaux
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Global warming has increased global economic inequality
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Towards a Flexible Deep Learning Method for Automatic Detection of Clinically Relevant Multi-Modal Events in the Polysomnogram
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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
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Nature Communications Volume 10, Article number: 794 (2019)
Non-invasive machine learning estimation of effort differentiates sleep-disordered breathing pathology
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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
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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
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Sub-Femtosecond Stark Control of Molecular Photoexcitation with Near Single-Cycle Pulses
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Intradomain Interactions in an NMDA Receptor Fragment Mediate N-Glycan Processing and Conformational Sampling
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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
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Kalli Kappel, Rhiju Das
Structure, Volume 27, Issue 1, 2 January 2019, Pages 140-151.e5
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RNA design movesets and strategies from an Internet-scale videogame
Rohan Koodli, Benjamin Keep, Katherine R Coppess, Fernando Portela, Eterna Players, Rhiju Das
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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
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Globally Constructed Adaptive Local Basis Set for Spectral Projectors of Second Order Differential Operators
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Revealing quantum mechanical effects in enzyme catalysis with large-scale electronic structure simulation
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The unWISE Catalog: Two Billion Infrared Sources from Five Years of WISE Imaging
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arXiv:1901.03337 (Submitted on 10 Jan 2019)
An Algebraic Sparsified Nested Dissection Algorithm Using Low-Rank Approximations
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Thermal Boundary Conductance of Two-Dimensional MoS2 Interfaces
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arXiv:1901.02447 (Submitted on 8 Jan 2019)
The Buzzard Flock: Dark Energy Survey Synthetic Sky Catalogs
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Exploiting graphical processing units to enable quantum chemistry calculation of large solvated molecules with conductor‐like polarizable continuum models
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Biochat: a database for natural language processing of Gene Expression Omnibus data
Bohdan B Khomtchouk, Vsevolod Dyomkin, Kasra A Vand, Themistocles Assimes, Or Gozani
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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
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Challenges in Modeling Electrochemical Reaction Energetics with Polarizable Continuum Models
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Combinatorial processing of bacterial and host-derived innate immune stimuli at the single-cell level
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Searching for Subsecond Stellar Variability with Wide-field Star Trails and Deep Learning
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A global test of ecoregions
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Journal of Theoretical Biology, 24 October 2018
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Spectroscopic Signature of Oxidized Oxygen States in Peroxides
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A Predictive Model for Postembolization Syndrome after Transarterial Hepatic Chemoembolization of Hepatocellular Carcinoma
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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
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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,
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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
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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)
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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
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
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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
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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
Edwin W. Huang, Douglas J. Scalapino, Thomas A. Maier, Brian Moritz, Thomas P. Devereaux
(Submitted on 10 May 2017) arXiv:1705.03949
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
Anil Damle, Lin Lin, and Lexing Ying
SIAM J. Sci. Comput., 39(6), B1178–B1198.
https://doi.org/10.1137/16M1098589
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
Christoph Schran Ondrej Marsalek Thomas E.Markland
Accepted 10 April 2017
https://doi.org/10.1016/j.cplett.2017.04.034
Yanming Wang, Paul C. McIntyre, and Wei Cai
Cryst. Growth Des., 2017, 17 (4), pp 2211–2217
DOI: 10.1021/acs.cgd.7b00197
William E. East and Frans Pretorius
Phys. Rev. Lett. 119, 041101 – Published 24 July 2017
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
Joseph Gomes, Bharath Ramsundar, Evan N. Feinberg, Vijay S. Pande
(Submitted on 30 Mar 2017) arXiv:1703.10603
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
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
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
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
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
Victor Minden, Anil Damle, Kenneth L. Ho, and Lexing Ying
Multiscale Model. Simul., 15(4), 1584–1611.
https://doi.org/10.1137/17M1116477
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
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
