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Extreme-scale Mathematically-based Computational Chemistry

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Publications

Tinker-HP: Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields Using GPUs and Multi-GPU Systems

Author(s): Olivier Adjoua, Louis Lagardère, Luc-Henri Jolly, Arnaud Durocher, Thibaut Very, Isabelle Dupays, Zhi Wang, Théo Jaffrelot Inizan, Frédéric Célerse, Pengyu Ren, Jay W. Ponder, Jean-Philip Piquemal
Published in: Journal of Chemical Theory and Computation, Issue 17/4, 2021, Page(s) 2034-2053, ISSN 1549-9618
DOI: 10.1021/acs.jctc.0c01164

Post-processing of the planewave approximation of Schrödinger equations. Part I: linear operators.

Author(s): E. Cancès, G. Dusson, Y. Maday, B. Stamm, M. Vohralík.
Published in: IMA Journal of Numerical Analysis, 2020, ISSN 0000-0000
DOI: 10.1093/imanum/draa044

Raising the Performance of the Tinker-HP Molecular Modeling Package [Article v1.0]

Author(s): L.-H. Jolly, A. Duran, L. Lagardère, J. W. Ponder, P. Ren, J.-P. Piquemal.
Published in: Living Journal of Computational Molecular Science, University of Colorado Boulder, 2019, ISSN 0000-0000
DOI: 10.33011/livecoms.1.2.10409

Convergence analysis of direct minimization and self-consistent iterations

Author(s): Eric Cancès, Gaspard Kemlin, Antoine Levitt
Published in: SIAM Journal on Matrix Analysis and Applications, Issue Volume 42, Issue 1, 2020, Page(s) 243–274. (32 pages), ISSN 0895-4798
DOI: 10.1137/20m1332864

Molecular Dynamics using Non-variational Polarizable Force Fields: Theory, Periodic Boundary Conditions Implementation and Application to the Bond Capacity Model. 

Author(s): Poier Pier Paolo, L. Lagardère, J.-P. Piquemal, F. Jensen.
Published in: Journal of Chemical Theory and Computation, American Chemical Society, 2019, ISSN 0000-0000
DOI: 10.1021/acs.jctc.9b00721

Accurate biomolecular simulations account for electronic polarization. 

Author(s): J. Melcr, J.-P. Piquemal
Published in: Frontiers in Molecular Biosciences, Frontiers Media, 2019, 6, pp.143., 2019, ISSN 0000-0000
DOI: 10.3389/fmolb.2019.00143

NCIPLOT4: fast, robust and quantitative analysis of noncovalent interactions.

Author(s): R. Boto, F. Peccati, R. Laplaza, C. Quan, A. Carbone, J.-P. Piquemal, Y. Maday, J. Contreras-Garcia. 
Published in: Journal of Chemical Theory and Computation, American Chemical Society, Issue J. Chem. Theory Comput. 2020, 16, 7, 4150–4158, 2020, ISSN 0000-0000
DOI: 10.1021/acs.jctc.0c00063

Numerical algorithms for high-performance computational science

Author(s): Dongarra, Laura Grigori, Nicholas J. Higham
Published in: Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Issue Volume 378 Issue 2166 pp.20190066. ⟨10.1098/rsta.2019.0), 2020, ISSN 0000-0000
DOI: 10.1098/rsta.2019.0066

Guaranteed a posteriori bounds for eigenvalues and eigenvectors: multiplicities and clusters

Author(s): E. Cancès, G. Dusson, Y. Maday, B. Stamm, M. Vohralík
Published in: Mathematics of Computation, 2020, ISSN 0025-5718
DOI: 10.1090/mcom/3549

A posteriori error estimation for the non-self consistent Kohn-Sham equations. 

Author(s): M. F. Herbst, A. Levitt, E. Cancès.
Published in: Faraday Discussions, 2020, ISSN 0000-0000
DOI: 10.1039/d0fd00048e

Numerical quadrature in the Brillouin zone for periodic Schrödinger operators

Author(s): Eric Cancès, Virginie Ehrlacher, David Gontier, Antoine Levitt, Damiano Lombardi 
Published in: Springer Link, Issue Numerische Mathematik volume 144, pages479–526(2020), 2020, ISSN 0000-0000
DOI: 10.1007/s00211-019-01096-w

Solvation Effects Drive the Selectivity in Diels-Alder Reaction Under Hyperbaric Conditions.

Author(s): Tony Lelièvre, Gabriel Stoltz, Wei Zhang.
Published in: Chemical Communications. Issue 49, 2020, ISSN 0000-0000
DOI: 10.1039/d0cc01938k

Implementation of Geometry Dependent Charge Flux into Polarizable AMOEBA+ Potential

Author(s): C. Liu, J.-P. Piquemal, P. Ren.
Published in: Journal of Physical Chemistry Letters, American Chemical Society, 2019, ISSN 0000-0000
DOI: 10.1021/acs.jpclett.9b03489

Scaling limits for the generalized Langevin equation

Author(s): G. Pavliotis, G. Stoltz, U. Vaes.
Published in: Springer Link, 2020, ISSN 0000-0000
DOI: 10.1007/s00332-020-09671-4

Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field

Author(s): Rae A. Corrigan, Guowei Qi, Andrew C. Thiel, Jack R. Lynn, Brandon D. Walker, Thomas L. Casavant, Louis Lagardere, Jean-Philip Piquemal, Jay W. Ponder, Pengyu Ren, Michael J. Schnieders
Published in: Journal of Chemical Theory and Computation, Issue 17/4, 2021, Page(s) 2323-2341, ISSN 1549-9618
DOI: 10.1021/acs.jctc.0c01286

Adaptive Hierarchical Subtensor Partitioning for Tensor Compression

Author(s): Virginie Ehrlacher, Laura Grigori, Damiano Lombardi, Hao Song
Published in: SIAM Journal on Scientific Computing, Issue 43/1, 2021, Page(s) A139-A163, ISSN 1064-8275
DOI: 10.1137/19m128689x

Assessment of SAPT and Supermolecular EDA Approaches for the Development of Separable and Polarizable Force Fields

Author(s): Sehr Naseem-Khan, Nohad Gresh, Alston J. Misquitta, Jean-Philip Piquemal
Published in: Journal of Chemical Theory and Computation, 2020, ISSN 1549-9618
DOI: 10.1021/acs.jctc.0c01337

Velocity jump processes: an alternative to multi-time-step methods for faster and accurate molecular dynamics simulations.

Author(s): P. Monmarché, J. Weisman, L. Lagardère, J.-P. Piquemal.
Published in: AIP The Journal of Chemical Physics, 2020, ISSN 0000-0000
DOI: 10.1063/5.0005060

Analysis of an Adaptive Biasing Force method based on self-interacting dynamics

Author(s): Michel Benaïm, Charles-Edouard Bréhier, Pierre Monmarché
Published in: Electronic Journal of Probability, Issue Vol.25 • 2020, 2020, ISSN 0000-0000
DOI: 10.1214/20-ejp490

Quantum-Chemistry based design of halobenzene derivatives with augmented affinities for the HIV-1 viral G4/C16 base-pair.

Author(s): P. El Darazi, L. El Khoury, K. El Hage, R. Maroun, Z. Hobaika, J.-P. Piquemal, N. Gresh.
Published in: Theoretical and Computational Chemistry, 2019, ISSN 0000-0000
DOI: 10.3389/fchem.2020.00440

Quantifying the error of the core-valence separation approximation.

Author(s): M. F. Herbst, T. Fransson.
Published in: The Journal of Chemical Physics, Issue Volume 153, Issue 5 > 10.1063/5.0013538, 2020, ISSN 0000-0000
DOI: 10.1063/5.0013538

Reconciling NMR Structures of the HIV-1 Nucleocapsid Protein (NCp7) using Extensive Polarizable Force Field Free-Energy Simulations.

Author(s): L. El Khoury, F. Célerse, Louis Lagardère, L.-.H Jolly, E. Derat, Z. Hobaika, R. Maroun, P. Ren, S. Bouaziz, N. Gresh, J.-P. Piquemal.
Published in: Journal of Chemical Theory and Computation, 2020, ISSN 0000-0000
DOI: 10.1021/acs.jctc.9b01204

Geometric ergodicity of the Bouncy Particle Sampler

Author(s): Alain Durmus, Arnaud Guillin, Pierre Monmarché
Published in: The Annals of Applied Probability, Issue 30/5, 2020, ISSN 1050-5164
DOI: 10.1214/19-aap1552

Insights into the ππ - ππ interaction driven non-covalent functionalization of carbon nanotubes of various diameters by conjugated fluorene and carbazole copolymers

Author(s): Robert Benda, Gaël Zucchi, Eric Cancès, Bérengère Lebental
Published in: AIP The Journal of Chemical Physics, Issue Volume 152, Issue 6 > 10.1063/1.5133634, 2020, ISSN 0000-0000
DOI: 10.1063/1.5133634

Spectrometric and computational studies of the binding of HIV-1 integrase inhibitors to viral DNA extremities

Author(s): L. El-Khoury, K. El Hage, J.-P. Piquemal, S. Fermandjian, R. Maroun, N. Gresh, Z. Hobaika.
Published in: PeerJ Physical Chemistry, PeerJ, 2019, 1, pp.e6., 2019, ISSN 0000-0000
DOI: 10.7717/peerj-pchem.6

NCIPLOT and the analysis of noncovalent interactions using the reduced density gradient

Author(s): R. Laplaza, F. Peccati, R. Boto, C. Quan, A. Carbone, J.-P. Piquemal, Y. Maday, J. Contreras-Garcia. 
Published in: WIREs Computational Molecular Science, Issue Volume11, Issue2 March/April 2021 e1497, 2020, ISSN 0000-0000
DOI: 10.1002/wcms.1497

High-resolution mining of the SARS-CoV-2 main protease conformational space: supercomputer-driven unsupervised adaptive sampling

Author(s): Théo Jaffrelot Inizan, Frédéric Célerse, Olivier Adjoua, Dina El Ahdab, Luc-Henri Jolly, Chengwen Liu, Pengyu Ren, Matthieu Montes, Nathalie Lagarde, Louis Lagardère, Pierre Monmarché, Jean-Philip Piquemal
Published in: Chemical Science, Issue 12/13, 2021, Page(s) 4889-4907, ISSN 2041-6520
DOI: 10.1039/d1sc00145k

Convergence of the likelihood ratio method for linear response of non-equilibrium stationary states

Author(s): Ting Wang, Gabriel Stoltz, Petr Plechac
Published in: ESAIM: Mathematical Modelling and Numerical Analysis (ESAIM: M2AN), Issue Volume 55, 2021, 2021, Page(s) S593 - S623, ISSN 0000-0000
DOI: 10.1051/m2an/2020050

A New Way for Probing Bond Strength

Author(s): J. Klein, H. Khartabil, J.C. Boisson, J. Contreras-Garcia, J.-P. Piquemal, E. Henon.
Published in: Journal of Physical Chemistry A, American Chemical Society, Issue 124 (9), pp.1850-1860, 2020, ISSN 0000-0000
DOI: 10.1021/acs.jpca.9b09845