Grand Challenge Publications and Presentations

2021

  • P.King, K.Miller, N.Lemos et al, PRAB 24, 011302 (2021) 
  • J Lee, FD Malone, MA Morales and DR Reichman (in preparation JCTC, 2021)
  • RAS Project Simulation Team, (2021) Machine Learning-driven Multiscale Modeling Reveals Lipid-Dependent Dynamics of RAS Signaling Proteins. Nature Communication (under review)
  • Bhatia H., T.S. Carpenter, H.I. Ingólfsson, G. Dharuman, P. Karande, S. Liu, T. Oppelstrup, C. Neale, F.C. Lightstone, B.V. Essen, J.N. Glosli and P.T. Bremer. (2021). Machine Learning Based Dynamic-Importance Sampling for Adaptive Multiscale Simulations. Nature Machine Intelligence (under review).

2020

  • FD Malone, S Zhang, MA Morales, J. Chem. Theory Comput. 16, 4286 (2020)
  • J Lee, FD Malone, MA Morales, J. Chem Theory Comput. 16, 3019 (2020)
  • J Lee, FD Malone, DR Reichman, J. Chem. Phys. 153, 126101 (2020)
  • FD Malone, A Benali, MA Morales, M Caffarel, PRC Kent, L Shulenburger, Phys. Rev. B. (rapid) 102, 161104 (2020)
  • MA Morales and FD Malone, J. Chem. Phys. 153, 194111 (2020)
  • J Lee, MA Morales, FD Malone, J. Chem Phys (accepted, 2020)
  • Sun D., T.A. Peyear, S. He, W.F.D. Benne3, S. Iwanami, J.E. Allen, F.C. Lightstone, O.S. Andersen and H.I. Ingólfsson. 2020. Screening for Lipid Bilayer- Modifying Compounds using a Gramicidin Based SimulaMon Assays and Machine Learning. In prepara(on. ¶co-first authors. LLNL-JRNL-TBD
  • Sun D., S. He, W.F.D. Benne3, C. Bilodeau, O.S. Andersen, F.C. Lightstone and H.I. Ingólfsson. 2020. AtomisMc CharacterizaMon of Gramicidin Channel FormaMon. Journal of Chemical Theory and Computa5on, 17:7-12. doi: 10.1021/acs.jctc.0c00989. LLNL-JRNL-813847
  • Benne3 W.F.D., S. He, C. Bilodeau, D. Jones, D. Sun, H. Kim, J.E. Allen, F.C. Lightstone and H.I. Ingólfsson. 2020. PredicMng Small Molecule Transfer Free Energies by Combining Molecular Dynamics SimulaMons and Deep Learning. Journal of Chemical Informa5on and Modeling, 60:5375-5381, doi: 10.1021/acs.jcim.0c00318. LLNL-JRNL-774697
  • Sun D., T.A. Peyear, W.F.D. Benne3, M. Holcomb, S. He, F. Zhu, F.C. Lightstone, O.S. Andersen and H.I. Ingólfsson. 2020. Assessing the Perturbing Effects of Drugs on Lipid Bilayers using Gramicidin Channel-Based in Silico and in Vitro Assays. Journal of Medicinal Chemistry, 63:11809-11818, doi: 10.1021/acs.jmedchem.0c00958. LLNL-JRNL-807837
  • Blumer M., S. Harris, M. Li, L. MarMnez, M. Untereiner, P.N. Saeta, T.S. Carpenter, H.I. Ingólfsson and W.F.D Benne3. 2020. SimulaMons of asymmetric membranes illustrate cooperaMve leaflet coupling and lipid adaptability. Fron5ers Cell Developmental Biology, 8:575, doi: 10.3389/fcell.2020.00575. LLNL-JRNL-801959
  • Sun S., T.A. Peyear, W.F.D. Benne3, O.S. Andersen, F.C. Lightstone and H.I. Ingólfsson. 2019. Molecular mechanism for gramicidin dimerizaMon and dissociaMon in bilayers of different thickness. Biophysical Journal, 117:1831-1844, doi: 10.1016/j.bpj.2019.09.044. LLNL-JRNL-768282
  • Zhang M., T. Peyear, I. Patmanidis, D.V. Greathouse, S.J. Marrink, O.S. Andersen and H.I. Ingólfsson. 2018. Fluorinated alcohols’ effects on lipid bilayer properMes. Biophysical Journal, 115:679-689, doi: 10.1016/j.bpj.2018.07.010. LLNL-JRNL-744560
  • Kemp, Wilks, Physics of Plasmas 27 103106 (2020) and APS-DPP invited talk.
  • P. Marevic et al., Phys. Rev. Lett. 125, 102504 (2020)
  • N. Schunck et al, J. Phys. G: Nucl. Part. Phys. 47 (2020) 074001
  • FK/Fπ from Mobius Domain-Wall fermions solved on gradient-flowed HISQ ensembles”, Phys. Rev. D 102, 034507 (2020), arXiv:2005.04795 [hep-lat].
  • Quantifying uncertainties in neutron-α scattering with chiral nucleon-nucleon and three-nucleon forces – Phys. Rev. C 102, 024616
  • Optimal Control for the Quantum Simulation of Nuclear Dynamics – Phys. Rev. A 101, 062307
  • Recent developments and future prospects in low-energy nuclear theory – APS DNP Plenary
  • Quantum Computing: A Cold Bright Future for Computational Low Energy Nuclear Theory – FRIB LECM
  • Uncertainty quantification for neutrinoless double-beta decay calculations – ISNET 2020
  • Predictive theory for nuclear data – American Nuclear Society Annual Meeting
  • Unifying theories for the structure and dynamics of light nuclei – APS April Meeting
  • Alpha clustering and Alpha-induced reactions – 5th Topical Workshop on Modern Aspects in Nuclear Structure
  • H.I. Ingólfsson, H. Bhatia, T. Zeppelin, W.F.D. Bennett, K.A. Carpenter, P. Hsu, G. Dharuman, P.T. Bremer, B. Schiott, F.C. Lightstone, T.S. Carpenter (2020) Capturing biologically complex tissue-specific membranes at different levels of compositional complexity. Journal of Phyiscal Chemistry B. 124, 36, 7819-7829
  • X. Zhang, S. Sundram, T. Oppelstrup, S.I.L. Kokkila-Schumacher, T.S. Carpenter, H.I. Ingólfsson, F.H. Streitz, F.C. Lightstone, J.N. Glosli (2020) ddcMD: A fully GPU-accelerated molecular dynamics program for the Martini force field. Journal of Chemical Physics, doi: 10.1063/5.0014500
  • D. Goswami, D. Chen, Y. Yang, P. R. Gudla, J. Columbus, K. Worthy, M. Rigby, M. Wheeler, S. Mukhopadhyay, K. Powell, W. Burgan, V. Wall, D. Esposito, D. Simanshu, F. C. Lightstone, D. V. Nissley, F. McCormick, T. Turbyville (2020) Membrane Interactions of the G-domain and the HVR of KRAS4b Defines Its Unique Diffusion Behavior. eLife, 9: e47654
  • F. Fiuza, G. Swadling, A. Grassi et al., Nature Physics (2020) 
  • https://www.nature.com/articles/s41567-020-0919-4
  • G. F. Swadling, C. Bruulsema, F. Fiuza et al. Phys. Rev. Lett. 124, 215001 – Published 27 May 2020
  • https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.124.215001

2019

  • Z. Matheson, S. Giuliani, W. Nazarewicz, J. Sadhukhan and N. Schunck, Phys. Rev. C 99, 041304 (2019)
  • D. Regnier, N. Dubray, and N. Schunck, Phys. Rev. C 99, 024611 (2019)
  • S. Giuliani et al., Rev. Mod. Phys. 91, 011001 (2019)
  • RAS Project Simulation Team, (2019) A Massively Parallel Infrastructure for Adaptive Multiscale Simulations: Modeling RAS Initiation Pathway for Cancer. Proceedings of the 2019 ACM/IEEE Conference on Supercomputing (SC’19). (Best Paper Award of SC’ 19).
  • H. Bhatia, H.I. Ingólfsson, T.S. Carpenter, F.C. Lightstone, and P.T. Bremer (2019) MemSurfer: A Tool for Robust Computation and Characterization of Curved Membranes. Journal of Chemical Theory and Computation 15, 6411-6421
  • Sun, D., T.A. Peyear, W.F.D. Bennett, O.S. Andersen, F.C. Lightstone, and H.I. Ingólfsson. 2019. "Molecular Mechanism for Gramicidin Dimerization and Dissociation in Bilayers of Different Thickness". Biophysical Journal. J. 117:1831–1844."
  • W.F.D. Bennett, S. He, C. Bilodeau, H. Kim, D. Sun, J.E. Allen, F.C. Lightstone and H.I. Ingólfsson. Predicting Small Molecule Transfer Free Energies by Combining Molecular Dynamics Simulations and Deep Learning, Under review.
  • Kemp et al, submitted to POP(2019) 
  • Kemp, invited talk at APS-DPP2019
  • Kemp et al, Nature Comm. (2019)10:4156 
  • Accurate predictions of spin-polarized DT and DHe fusion – Nature Communications 10, 351 
  • Resolved discrepancy between experimental and theoretical 훽-decay rates – Nature Physics 15, 428 
  • Updated fit of 3-nucleon force from chiral effective field theory – Physical Review Letters 122, 029901 
  • Application of an ab-initio S-matrix to data analysis of transfer to the continuum reactions populating Be – Physical Review C 100, 024617
  • Be and Li nuclei within the no-core shell model with continuum – Physical Review C 100, 024304
  • “Ab initio calculations of few-body reactions”, APS April Meeting 2019
  • “Uncertainty Quantification for Three Nucleon force with light ion reactions”, ISNET-6, Germany
  • “Toy model for germanium 76 neutrinoless double-beta decay”, Bayesian Inference in Subatomic Physics,  Sweden, 2019
  • 3 high resolution (0-10 Hz) Hayward Fault simulations (Science Advances)
  •     -Highest resolution, regional-scale simulation for an earthquake in California
  •     -Each run on 2048 nodes (47%) of Sierra, 8192 GPUs for 21 hours
  • 52 Hayward Fault ruptures resolved 0-5 Hz (Journal of Geophysics Research)
  •     -Investigate path and site effects 
  •     -98,509 node-hours
  • Moderate earthquakes in the San Francisco Bay Area (Bulletin of the Seismological Society of America)
  • Z. Matheson, S. Giuliani, W. Nazarewicz, J. Sadhukhan and N. Schunck, Phys. Rev. C 99, 041304 (2019)
  • D. Regnier, N. Dubray, and N. Schunck, Phys. Rev. C 99, 024611 (2019)
  • S. Giuliani et al., Rev. Mod. Phys. 91, 011001 (2019)
  • “Towards grounding nuclear physics in QCD.”, C. Drischler et. al., The European Physical Journal A – Hadrons and Nuclei, to appear. 
  • RAS Project Simulation Team, (2019) A Massively Parallel Infrastructure for Adaptive Multiscale Simulations: Modeling RAS Initiation Pathway for Cancer. Proceedings of the 2019 ACM/IEEE Conference on Supercomputing (SC’19). (Accepted and nominated for the best paper award).
  • H. Bhatia, H. I. Ingólfsson, T. S. Carpenter, F. C. Lightstone, and P.-T. Bremer (2019) MemSurfer: A Tool for Robust Computation and Characterization of Curved Membranes. Journal of Chemical Theory and Computation (submitted)

2018

  • R. Navarro Perez, N. Schunck, A. Dydhalo, D. Furnstahl, S. Bogner, Phys. Rev. C 97, 054304 (2018)
  • A. Bulgac, M.M. Forbes, S. Jin, R. Navarro Perez, and N. Schunck, Phys. Rev. C 97, 044313 (2018)
  • D. Regnier, N. Dubray, M. Verrière, and N. Schunck, Comput. Phys. Commun. 225, 180 (2018)
  • R. Navarro Perez, N. Schunck, A. Dydhalo, D. Furnstahl, S. Bogner, Phys. Rev. C 97, 054304 (2018)
  • A. Bulgac, M.M. Forbes, S. Jin, R. Navarro Perez, and N. Schunck, Phys. Rev. C 97, 044313 (2018)
  • D. Regnier, N. Dubray, M. Verrière, and N. Schunck, Comput. Phys. Commun. 225, 180 (2018)
  • "A per-cent-level determination of the nucleon axial coupling from quantum chromodynamics"
  • Nature 558 (2018) no.7708, 91-94,
  •  “Simulating the weak death of the neutron in a femtoscale universe with near-Exascale computing”, CalLat collaboration, Supercomputing 2018 paper. 
  • T. S. Carpenter, C. A. López, C. Neale, C. Montour, H. I. Ingólfsson, F. Di Natale, F. C. Lightstone and S. Gnanakaran (2018) Capturing Phase Behavior of Ternary Lipid Mixtures with a Refined Martini Coarse-Grained Force Field. Journal of Chemical Theory and Computation, 14, 6050–6062.
  • T. Travers, C. A. López, Q. N. Van, C. Neale, M. Tonelli, A. G. Stephen, and S. Gnanakaran (2018) Molecular recognition of RAS/RAF complex at the membrane: Role of RAF cysteine-rich domain. Scientific Reports, 8, 8461.
  • C. Neale, A. E. Garcia (2018) Methionine 170 is an Environmentally Sensitive Membrane Anchor in the Disordered HVR of K-Ras4B. Journal of Physical Chemistry B, 122 (44), 10086-10096

 

2017

  • The cover of October 26 (2017) issue of Nature featuring one of the configurations of dislocation networks encountered in our direct MD simulations of plasticity and strength of tantalum.  (Bulatov, GC 13)
  •  H. I. Ingólfsson, T. S. Carpenter, H. Bhatia, P.-T. Bremer, S. J. Marrink, and F. C. Lightstone (2017) Computational lipidomics of the neuronal plasma membrane. Biophysics Journal, 113 (10), 2271-2280

 

UNKNOWN

Higginson, Drew GC13

  • "A Corrected Method for Coulomb Scattering in Arbitrarily Weighted Particle-in-Cell Plasma Simulations" - Journal of Computational Physics
  • ”Hybrid Particle-in-Cell Simulations of Laser-Driven Plasma Interpenetration, Heating and Entrainment” - Physics of Plasmas
  • "A Pairwise Nuclear Fusion Algorithm for Weighted Particle-in-Cell Plasma Simulations" - Journal of Computational Physics
  • "Kinetic effects on neutron generation in moderately collisional interpenetrating plasma flows" - Physics of Plasmas
  • "Researchers Improve Model for Laser-Driven Plasma Flows" - general interest article. Web link: https://lasers.llnl.gov/news/researchers-improve-model-for-laser-driven…
  • "Hybrid Modeling Capabilities for Basic Physics Experiments" - Invited talk at National Ignition Facility and Jupiter Laser Facility User Group Meeting, Livermore, Ca.
  • "Kinetic-Ion Quasineutral Hybrid Particle-in-Cell Modeling of Interpenetrating Flows Relevant to ICF" - Invited talk at International Conference on Inertial Fusion Sciences and Applications, Osaka, Japan