Publications

Conference papers, peer-reviewed journal articles, and other scholarly works are the result of your hard work of which Hyak was one helping hand. Please consider citing or acknowleding Hyak in your final work and then let us know so it can be considered to appear in our select publication list.

The Hyak Consortium. "Title TBD." arXiv:4444.55555 (2021)

Select Publications

These are select works that were produced using a Hyak cluster in any given year. While hundreds of papers are produced each year using Hyak, we limit the select list below to 10 for the sake of brevity. If you would like your publication to be considered for inclusion onto this list please e-mail us with the citation.

2022
2021
2020
2019

Computer Science

Liu, Alisa, et al. "WANLI: Worker and AI Collaboration for Natural Language Inference Dataset Creation." arXiv preprint arXiv:2201.05955 (2022).
Shridhar, Mohit, Lucas Manuelli, and Dieter Fox. "Cliport: What and where pathways for robotic manipulation." Conference on Robot Learning. PMLR, 2022. URL: PDF

Aeronautics and Astronautics

TE Benedett and CJ Hansen. "Effect of geometric and magnetic boundary conditions on magnetic islands in 3D force-free ideal MHD equilibria." Nuclear Fusion 61 (3) 036022 (2021) DOI: 10.1088/1741-4326/abd41c

Chemical Engineering

A. Joseph, C. Nyambura1,D. Bondurant, K. Corry, D. Beebout, T. Wood, Jim Pfaendtner, E. Nance, “Formulation and Efficacy of Catalase-Loaded Nanoparticles for the Treatment of Neonatal Hypoxic-Ischemic Encephalopathy”, Pharmaceutics, 2021, 13(8), 1131. DOI: 10.3390/pharmaceutics13081131
J. Prelesnik1, R. Alberstein, S. Zhang, H. Pyles, D. Baker, J. Pfaendtner, J. De Yoreo, A. Tezcan, R.. Remsing, C. J. Mundy, “Ion-dependent protein–surface interactions from intrinsic solvent response”, PNAS, 2021, 118(26), e2025121118. DOI: 10.1073/pnas.2025121118
C. Jia, S. Xie, W. Zhang, N. Intan2, J. Sampath2, J. Pfaendtner, H. Lin, “Deconstruction of high-density polyethylene into liquid hydrocarbon fuels and lubricants by hydrogenolysis over Ru catalyst”, Chem. Cat., 2021, 1(2), 437-455. DOI: 10.1016/j.checat.2021.04.002
J. Ludwig1, J. Smith, J. Pfaendtner, “Analyzing the Long Time-Scale Dynamics of Uremic Toxins Bound to Sudlow Site II in Human Serum Albumin”, J. Phys. Chem. B., 2021, 125(11), 2910-2920. DOI: 10.1021/acs.jpcb.1c00221
S. Roeters, T. Golbek, M. Bregnhøj, T. Drace, S. Alamdari1, W. Roseboom, G. Kramer, T Šantl-Temkiv, K. Finster, J. Pfaendtner, S. Woutersen, T. Boesen, T. Weidner, “Ice-nucleating proteins are activated by low temperatures to control the structure of interfacial water” Nat Commun, 2021, 12, 1183 . DOI: 10.1038/s41467-021-21349-3
N. Intan2, J. Pfaendtner, “Effect of Fluoroethylene Carbonate Additives on the Initial Formation of the Solid Electrolyte Interphase on an Oxygen-Functionalized Graphitic Anode in Lithium-Ion Batteries”, 2021, 13(7), 8169-8180: DOI: 10.1021/acsami.0c18414

Chemistry

Zhang, L., Kang, C., Zhang, G., Pan, Z., Huang, Z., Xu, S., Rao, H., Liu, H., Wu, S., Wu, X. and Li, X., 2021. All‐Inorganic CsPbI3 Quantum Dot Solar Cells with Efficiency over 16% by Defect Control. Advanced Functional Materials, 31(4), p.2005930. DOI: 10.1002/adfm.202005930

Computer Science

Alisa Liu, Maarten Sap, Ximing Lu, Swabha Swayamdipta, Chandra Bhagavatula, Noah A. Smith, Yejin Choi. 2021. DExperts: Decoding-Time Controlled Text Generation with Experts and Anti-Experts. Proceedings of the 59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing. Virtual Event, USA. DOI: 10.18653/v1/2021.acl-long.522
Xin Liu, Ziheng Jiang, Josh Fromm, Xuhai Xu, Shwetak Patel, and Daniel McDuff. 2021. MetaPhys: Few-Shot Adaptation for Non-Contact Physiological Measurement. ACM Conference on Health, Inference, and Learning (ACM CHIL ’21) April 8–10, 2021, Virtual Event, USA. ACM, New York, NY, USA, 10 pages. 10.1145/3450439.3451870

Physics

AA Kaptanoglu, KD Morgan, CJ Hansen, and SL Brunton. "Physics-constrained, low-dimensional models for magnetohydrodynamics: First-principles and data-driven approaches." Physical Review E 104(1), 015206 (2021) DOI: 10.1103/PhysRevE.104.015206
Montague Z, Lv H, Otwinowski J, DeWitt WS, Isacchini G, Yip GK, Ng WW, Tsang OTY, Yuan M, Liu H, and Wilson IA, 2021. Dynamics of B cell repertoires and emergence of cross-reactive responses in patients with different severities of COVID-19. Cell Reports, 35(8), p.109173. DOI: 10.1016/j.celrep.2021.109173

Aeronautics and Astronautics

TE Benedett, CJ Hansenb, KD Morganc, TR Jarboed. "Effects of temperature and density evolution in MHD simulations of HIT-SI." Physics of Plasmas 27, 042508 (2020) DOI: 10.1063/1.5142298

Chemical Engineering

Komp, Evan, and Stéphanie Valleau. "Machine Learning Quantum Reaction Rate Constants." The Journal of Physical Chemistry A 124.41 (2020): 8607-8613. DOI: 10.1021/acs.jpca.0c05992
L.D. Gibson1, J. Pfaendtner, “Solvent Oligomerization Pathways Facilitated by Electrolyte Additives During Solid-Electrolyte Interphase Formation”, PhysChemChemPhys, 2020, 22, 21494-21503. DOI: 10.1039/D0CP03286G
S. Alamdari1, S. Roeters, T. Golbek, L. Schmüser, T. Weidner, J. Pfaendtner, “Orientation and Conformation of Proteins at the Air-Water Interface Determined from Integrative Molecular Dynamics Simulations and Sum Frequency Generation Spectroscopy”, Langmuir, 2020, 36(40), 11855-11685. DOI: 10.1021/acs.langmuir.0c01881
W. Beckner1, C.M. Ashraf2, J. Lee, D.A.C. Beck, J. Pfaendtner, “Continuous Molecular Representations of Ionic Liquids”, J. Phys. Chem. B. 2020, 124(38), 8437-8357. DOI: 10.1021/acs.jpcb.0c05938
M. Xue, J. Sampath2, R. Gebhart, H.J. Haugen, S.P. Lyngstadaas, J. Pfaendtner, G.P. Drobny,” Studies of dynamic binding of amino acids to TiO2 nanoparticle surfaces by Solution NMR and Molecular Dynamics Simulations”, Langmuir, 2020, in press. DOI: 10.1021/acs.langmuir.0c01256
J. Sampath32, S. Alamdari1, J. Pfaendtner, “Closing the Gap Between Modeling and Experiments in the Self-assembly of Biomolecules at Interfaces and in Solution”, Chem. Matl., 2020, 32(19), 8043-8059. DOI: 10.1021/acs.chemmater.0c01891
S. Summers, C. Kraft, S. Alamdari1, J. Pfaendtner, J. Kaar, “Enhanced Activity and Stability of Acidothermus cellulolyticus Endoglucanase 1 in Ionic Liquids via Engineering Active Site Residues and Non-native Disulfide Bridges”, ACS Sus. Chem & Eng, 2020, 8(30), 11299-11307. DOI: 10.1021/acssuschemeng.0c03242
E.L. Buckle, J. Sampath2, N. Michael, S.D. Whedon, C.J.A. Leonen, J. Pfaendtner, G. Drobny, C. Chatterjee, “Trimethylation of the R5 silica‐precipitating peptide increases silica particle size by redirecting orthosilicate binding,” ChemBioChem, 2020, 22, 3208-3211
J. Smith1, J. Pfaendtner, “Elucidating the molecular interactions between uremic toxins and the Sudlow II binding site of human serum albumin,” J. Phys. Chem. B, 2020, 124(19), 3922-3930. DOI: 10.1021/acs.jpcb.0c02015
J. Sampath2, A. Kullman1, R. Gebhart, G. Drobny, J. Pfaendtner, “Molecular recognition and specificity of biomolecules to titanium dioxide from molecular dynamics simulations,” npj Comput. Mater. 2020, 6(34), DOI: 10.1038/s41524-020-0288-7
B. Hellner, S. Alamdari1, H. Pyles, S. Zhang, A. Prakash1, K. G. Sprenger1, J. DeYoreo, D. Baker, J. Pfaendtner, F. Baneyx, “Sequence–Structure–Binding Relationships Reveal Adhesion Behavior of the Car9 Solid-Binding Peptide: An Integrated Experimental and Simulation Study,” J. Am. Chem. Soc. 2020, 142(5), 2355-2363. DOI: 10.1021/jacs.9b11617
S. Alamdari1, J. Pfaendtner, “Impact of glutamate carboxylation in the adsorption of the α-1 domain of osteocalcin to hydroxyapatite and titania,” Mol. Syst. Des. Eng. 2020, 5, 620-631. DOI: 10.1039/C9ME00158A
J. Smith1, P. McMullen, Z. Yuan, J. Pfaendtner, S. Jiang, “Elucidating Molecular Design Principles for Charge-Alternating Peptides,” Biomacromolecules 2020, 21(2), 435-443. DOI: 10.1021/acs.biomac.9b01191

Chemistry

Kasper, J.M. and Li, X., 2020. Natural transition orbitals for complex two‐component excited state calculations. Journal of computational chemistry, 41(16), pp.1557-1563. DOI: 10.1002/jcc.26196

Computer Science

William Agnew, Christopher Xie, Aaron Walsman, Octavian Murad, Caelen Wang, Pedro Domingos, and Siddhartha Srinivasa. "Amodal 3D Reconstruction for Robotic Manipulation via Stability and Connectivity" 4th Conference on Robot Learning (CORL) for a Plenary Talk (20/485). Spotlight at Object-Oriented Learning Workshop @ ICML2020. DOI: arXiv:2009.13146
Xin Liu, Josh Fromm, Shwetak Patel, Daniel McDuff. 2020. Multi-Task Temporal Shift Attention Networks for On-Device Contactless Vitals Measurement. 34th Conference on Neural Information Processing Systems (NeurIPS 2020), Vancouver, Canada. arXiv:2006.03790

Physics

AA Kaptanoglu, KD Morgan, CJ Hansen, SL Brunton. "Characterizing magnetized plasmas with dynamic mode decomposition." Physics of Plasmas 27, 032108 (2020) DOI: 10.1063/1.5138932

Public Health

PE Rummo, N Pho, MA Bragg, CA Roberto, B Elbel. "Trends in Store-Level Sales of Sugary Beverages and Water in the US, 2006–2015." American Journal of Preventive Medicine 59 (4), 522-529 (2020) DOI: 10.1016/j.amepre.2020.04.022

Chemical Engineering

J. Sampath2, J. Pfaendtner, “Amphiphilic peptide binding on crystalline vs. amorphous silica from molecular dynamics simulations,” Mol. Phys. 2019, 117(23-24), 3642-3650. DOI: 10.1080/00268976.2019.1657192
P. Emani, Y. Yimer2, S. Davidowski, R. Gebhart, H. Ferreira, I. Kuprov, J. Pfaendtner, G. Drobny, “Combining Molecular and Spin Dynamics Simulations with Solid-State NMR to Study Amphiphilic Lysine-Leucine Repeat Peptide Aggregates,” J. Phys. Chem. B 2019, 123(51), 10915-10929. DOI: 10.1021/acs.jpcb.9b09245
B. Li, P. Jain, J. Ma, J. Smith1, Z. Yuan, H.C. Hung, Y. He, X. Lin, K. Wu, J. Pfaendtner, S. Jiang, “Trimethylamine N-oxide–derived zwitterionic polymers: A new class of ultralow fouling bioinspired materials,” Sci. Adv. 2019, 5(6), eaaw9562. DOI: 10.1126/sciadv.aaw9562.
W. Beckner1, J. Pfaendtner, “Fantastic Liquids and Where to Find Them: Optimizations of Discrete Chemical Space,” J. Chem. Inf. Model. 2019, 59(6), 2617-2625. DOI: 10.1021/acs.jcim.9b00087
M. Mao1, J. Sampath2, K.G. Sprenger1, G. Drobny, J. Pfaendtner, “Molecular Driving Forces in Peptide Adsorption to Metal Oxide Surfaces,” Langmuir 2019, 35(17), 5911-5920. DOI: 10.1021/acs.langmuir.8b01392
C.D. Fu1, Y. He, J. Pfaendtner, “Diagnosing the Impact of External Electric Fields Chemical Kinetics: Application to Toluene Oxidation and Pyrolysis,” J. Phys. Chem A 2019, 123(14), 3080-3089. DOI: 10.1021/acs.jpca.8b11780
E.L. Buckle*, A. Prakash1*, M. Bonomi, J. Sampath2, J. Pfaendtner, G.P. Drobny, “A Solid-State NMR and MD Study of the Structure of the Statherin Mutant SNa15 on Mineral Surfaces,” J. Am. Chem. Soc. 2019, 141(5), 1998-2011. DOI: 10.1021/jacs.8b10990

Chemistry

Bai, F., Zhang, J., Yuan, Y., Liu, H., Li, X., Chueh, C.C., Yan, H., Zhu, Z. and Jen, A.K.Y., 2019. A 0D/3D Heterostructured All‐Inorganic Halide Perovskite Solar Cell with High Performance and Enhanced Phase Stability. Advanced Materials, 31(48), p.1904735. DOI: 10.1002/adma.201904735
Fu, W., Liu, H., Shi, X., Zuo, L., Li, X. and Jen, A.K.Y., 2019. Tailoring the Functionality of Organic Spacer Cations for Efficient and Stable Quasi‐2D Perovskite Solar Cells. Advanced Functional Materials, 29(25), p.1900221. DOI: 10.1002/adfm.201900221
Stetina, T.F., Clark, A.E. and Li, X., 2019. X‐ray absorption signatures of hydrogen‐bond structure in water–alcohol solutions. International Journal of Quantum Chemistry, 119(1), p.e25802. DOI: 10.1002/qua.25802