Extreme-scale Mathematically-based Computational Chemistry

Publications

A parareal algorithm for ahighly oscillating Vlasov-Poisson system with reduced models for the coarse solving

Author(s): Laura Grigori, Sever Hirstoaga, Julien Salomon
Published in: Computers and Mathematics with Applications, Issue Volume 130, 2023, Page(s) Pages 137-148, ISSN 1873-7668
Publisher: Science Direct
DOI: 10.1016/j.camwa.2022.12.004

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
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.0c01164

Computing surface reaction rates by Adaptive Multilevel Splitting combined with Machine Learning and Ab Initio Molecular Dynamics

Author(s): A. Anciaux-Sekadrian, M. Corral-Valero,T. Lelièvre, M. Moreaud, T. Pigeon, P. Raybaud, G. Stoltz
Published in: Journal of Chemical Theory and Computation, Issue 19(12), 2023, Page(s) 3538–3550, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.3c00280

On basis set optimisation in quantum chemistry

Author(s): E Cancès, G Dusson, G Kemlin, L Vidal
Published in: ESAIM: Proceedings and Surveys 73, Issue irregular, 2023, Page(s) 07-129, ISSN 2267-3059
Publisher: EDP Sciences
DOI: 10.1051/proc/202373107

Multiple projection MCMC algorithms on submanifolds

Author(s): Lelièvre, Tony; Stoltz, Gabriel; Zhang, Wei
Published in: IMA Journal of Numerical Analysis, drac006, 2022
Publisher: IMA Journal of Numerical Analysis, drac006
DOI: 10.48550/arxiv.2003.09402

A robust and efficient line search for self-consistent field iterations

Author(s): Michael F. Herbst; Antoine Levitt
Published in: Journal of Computational Physics, Issue 00219991, 2022, Page(s) Volume 459, ISSN 0021-9991
Publisher: Academic Press
DOI: 10.48550/arxiv.2109.14018

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
Publisher: IMA Journal of Numerical Analysis
DOI: 10.1093/imanum/draa044

Nuclear Quantum Effects in Liquid Water at Near Classical Computational Cost Using the Adaptive Quantum Thermal Bath.

Author(s): Nastasia Mauger; Thomas Plé; Louis Lagardère; Sara Bonella; Etienne Mangaud; Jean-Philip Piquemal; Jean-Philip Piquemal; Jean-Philip Piquemal; Simon Huppert
Published in: "Journal of Physical Chemistry Letters, American Chemical Society, 2021, ⟨10.1021/acs.jpclett.1c01722⟩", 2021
Publisher: ACS Publications
DOI: 10.48550/arxiv.2102.00289

Generalized Many-Body Dispersion Correction through Random-phase Approximation for Chemically Accurate Density Functional Theory

Author(s): P. P. Poier, L. Lagardère, J.-P. Piquemal
Published in: Phys. Chem. Lett, Issue 14, 6, 2023, Page(s) 1609–1617, ISSN 1948-7185
Publisher: American Chemical Society
DOI: 10.1021/acs.jpclett.2c03722

A probabilistic study of the kinetic Fokker–Planck equation in cylindrical domains

Author(s): Tony Lelièvre; Mouad Ramil; Julien Reygner
Published in: Journal of Evolution Equations, 2022, Page(s) volume 22, Article number: 38
Publisher: Journal of Evolution Equations
DOI: 10.1007/s00028-022-00796-5

Autoencoders for dimensionality reduction in molecular dynamics: collective variable dimension, biasing and transition states

Author(s): Z. Belkacemi, M. Bianciotto, P. Gkeka, T. Lelièvre, H. Minoux, G. Stoltz,
Published in: The Journal of Chemical Physics, Issue 159, 2023, Page(s) 024122, ISSN 1089-7690
Publisher: AIP Publishing
DOI: 10.48550/arxiv.2306.02935

Extending the regime of linear response with synthetic forcings

Author(s): R. Spacek, G. Stoltz
Published in: Multiscale Modeling and Simulation 21 (4), 1602-1643 1 2023, Issue Quarterly, 2023, Page(s) 602-1643, ISSN 1540-3459
Publisher: Society for Industrial and Applied Mathematics
DOI: 10.1137/23m1557611

Computationally driven discovery of SARS-CoV-2 Mpro inhibitors: from design to experimental validation

Author(s): L. El Khoury, Z. Jing, A. Cuzzolin, A. Deplano, D. Loco, B. Sattarov, F. Hédin, S. Wendeborn, C. Ho, D. El Ahdab, T. Jaffrelot Inizan, M. Sturlese, A. Sosic, M. Volpiana, A. Lugato, M. Barone, B. Gatto, M. Ludovica Macchia, M. Bellanda, R. Battistutta, C. Salata, I. Kondratov, R. Iminov, A. Khairulin, Y. Mykhalonok, A. Pochepko, V. Chashka-Ratushnyi , I. Kos, S. Moro, M. Montes, P. Ren, J. W. Pon
Published in: Chem. Sc., Issue 13, 2022, Page(s) 3674-3687, ISSN 2041-6539
Publisher: The Royal Society of Chemistry’s
DOI: 10.1039/d1sc05892d

Numerical stability and efficiency of response property calculations in density functional theory

Author(s): E. Cancès, M. Herbst, G. Kemlin, A. Levitt, B. Stamm
Published in: Letters in Mathematical Physics, Issue 113, article number 21, 2023, Page(s) 1–32., ISSN 1573-0530
Publisher: Springer
DOI: 10.1007/s11005-023-01645-3

DFTK: A Julian approach for simulating electrons in solids. JuliaCon Proceedings

Author(s): Michael F. Herbst, Antoine Levitt, Eric Cancès
Published in: JuliaCon Proceedings, Issue 3, 69, 2021, ISSN 2642-4029
Publisher: Cambridge MA: JuliaCon
DOI: 10.21105/jcon.00069

The adaptive biasing force algorithm with non-conservative forces and related topics

Author(s): Tony Lelièvre, Lise Maurin, Pierre Monmarché
Published in: ESAIM: M2AN 56 (, 2022, Page(s) 529–564
Publisher: ESAIM: M2AN
DOI: 10.48550/arxiv.2102.09957

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
Publisher: Living Journal of Computational Molecular Science, University of Colorado Boulder
DOI: 10.33011/livecoms.1.2.10409

Generative methods for sampling transition paths in molecular dynamics

Author(s): T. Lelièvre, G. Robin, I. Sekkat, G. Stoltz, G. Victorino Cardoso
Published in: ESAIM: PROCEEDINGS AND SURVEYS, Issue Vol. 73, p. 238-256, 2023, Page(s) p. 238-256, ISSN 2267-3059
Publisher: EDP Sciences
DOI: 10.48550/arxiv.2205.02818

Weighted L2-contractivity of Langevin dynamics with singular potentials

Author(s): E. Camrud, D. P. Herzog, G. Stoltz, M. Gordina,
Published in: Nonlinearity, 2022, Page(s) 35, 998
Publisher: IOP Publishing
DOI: 10.48550/arxiv.2104.10574

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
Publisher: Society for Industrial and Applied Mathematics
DOI: 10.1137/20m1332864

Smooth Particle Mesh Ewald-integrated stochastic Lanczos Many-body Dispersion algorithm

Author(s): P. P. Poier, L. Lagardère, J.-P. Piquemal
Published in: J. Chem. Phys., Issue 159, 154109, 2023, ISSN 1089-7690
Publisher: AIP Publishing
DOI: 10.1063/5.0166476

Gator: A Python-driven program for spectroscopy simulations using correlated wave functions

Author(s): Dirk R. Rehn; Zilvinas Rinkevicius; Zilvinas Rinkevicius; Michael F. Herbst; Xin Li; Maximilian Scheurer; Manuel Brand; Adrian L. Dempwolff; Iulia Emilia Brumboiu; Thomas Fransson; Thomas Fransson; Andreas Dreuw; Patrick Norman
Published in: WIREs Computational Molecular Science, 2021, Page(s) Volume11, Issue6
Publisher: WIREs Computational Molecular Science
DOI: 10.1002/wcms.1528

Overdamped limit at stationarity for non-equilibrium Langevin diffusions

Author(s): Pierre Monmarché, Mouad Ramil
Published in: Electron. Commun, 2022
Publisher: Project Euclid
DOI: 10.1214/22-ecp447

Building Kohn-Sham potentials for ground and excited states

Author(s): Louis Garrigue
Published in: Archive for Rational Mechanics and Analysis volume 245, pages949–1003 (2022), 2022, Page(s) volume 245, pages949–1003 (2022)
Publisher: Springer
DOI: 10.48550/arxiv.2101.01127

ANKH: A Generalized O(N) Interpolated Ewald Strategy for Molecular Dynamics Simulations

Author(s): I. Chollet, L. Lagardère, J.-P. Piquemal
Published in: J. Chem. Theory. Comput., Issue 19, 10, 2023, Page(s) 2887–2905, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.3c00015

Coherent Electronic Transport in Periodic Crystals

Author(s): Eric Cancès; Clotilde Fermanian Kammerer; Antoine Levitt; Sami Siraj-Dine
Published in: Annales Henri Poincaré volume 22, 2021, Page(s) pages 2643–2690
Publisher: Springer
DOI: 10.1007/s00023-021-01026-3

Nonlinear compressive reduced basis approximation for PDE's A

Author(s): A Cohen, C Farhat, A Somacal, Y Maday
Published in: Comptes Rendus Mécanique, 2023, Page(s) pp. 1-18, ISSN 1873-7234
Publisher: Académie des sciences_ Institut de France

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
Publisher: Journal of Chemical Theory and Computation, American Chemical Society
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
Publisher: Frontiers in Molecular Biosciences
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 00000000, 2020, ISSN 0000-0000
Publisher: Journal of Chemical Theory and Computation, American Chemical Society
DOI: 10.1021/acs.jctc.0c00063

Practical error bounds for properties in plane-wave electronic structure calculations

Author(s): Eric Cancès, Geneviève Dusson, Gaspard Kemlin , Antoine Levitt
Published in: SIAM Journal on Scientific Computing, Issue Vol. 44, Iss. 5, 2022, ISSN 1064-8275
Publisher: Society for Industrial and Applied Mathematics
DOI: 10.1137/21m1456224

Hypocoercivity with Schur complements

Author(s): Bernard, Etienne; Fathi, Max; Levitt, Antoine; Stoltz, Gabriel
Published in: Annales Henri Lebesgue, 2022, Page(s) Annales Henri Lebesgue, Volume 5 (2022), pp. 523-557
Publisher: Annales Henri Lebesgue
DOI: 10.48550/arxiv.2003.00726

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
Publisher: The Royal Society Publishing
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
Publisher: American Mathematical Society
DOI: 10.1090/mcom/3549

Analysis of the Single Reference Coupled Cluster Method for Electronic Structure Calculations: The Full Coupled Cluster Equations

Author(s): M Hassan, Y Maday, Y Wang
Published in: ESAIM: M2AN, Issue 57, 2023, Page(s) 545–583, ISSN 2804-7214
Publisher: Springer link
DOI: 10.1051/m2an/2022099

Simple derivation of moiré-scale continuous models for twisted bilayer graphene

Author(s): Éric Cancès; Louis Garrigue; David Gontier
Published in: PHYSICAL REVIEW B, Issue 11, Phys. Rev. B 107, Issue 15,, 2023, Page(s) 155403, ISSN 2469-9969
Publisher: American Physical Society (APS)
DOI: 10.1103/physrevb.107.155403

CP-TT: using TT-SVD to greedily construct a Canonical Polyadic tensor approximation

Author(s): Ehrlacher, Virginie; Fuente-Ruiz, Maria; Lombardi, Damiano
Published in: Molecules, 2022
Publisher: Molecules
DOI: 10.48550/arxiv.2011.09725

SoTT: greedy approximation of a tensor as a sum of Tensor Trains

Author(s): Virginie Ehrlacher; Maria Fuente Ruiz; Damiano Lombardi
Published in: SIAM Journal on Scientific Computing, Society for Industrial and Applied Mathematics, In press, 2021, Page(s) Vol. 44, Iss. 210.1137/20M1381472
Publisher: SIAM
DOI: 10.1137/20m1381472

On basis set optimization in quantum chemistry

Author(s): E. Cancès, G. Dusson, G. Kemlin, L. Vidal
Published in: ESAIM: Proceedings and Surveys, Issue Vol. 73, 2023, Page(s) 107-129, ISSN 2267-3059
Publisher: EDP Sciences
DOI: 10.48550/arxiv.2207.12190

Development of the Quantum Inspired SIBFA Many-Body Polarizable Force Field: I. Enabling Condensed Phase Molecular Dynamics Simulations

Author(s): S. Naseem Kahn, L. Lagardère, C. Narth, G. A. Cisneros, P. Ren, N. Gresh, J.-P. Piquemal,
Published in: J. Chem. Theory Comput, Issue 18, 6, 2022, Page(s) 3607–3621, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.2c00029

Convergence of the kinetic annealing for general potentials

Author(s): L. Journel, P. Monmarché
Published in: Electron. J. Probab, Issue vol. 27article no. 159, 2022, Page(s) pp. 1–37, ISSN 1083-6489
Publisher: Institute of Mathematical Statistics
DOI: 10.1214/22-ejp891

Extension of the trotterized unitary coupled cluster to triple excitations

Author(s): M Haidar, MJ Rancic, Y Maday, JP Piquemal
Published in: The Journal of Physical Chemistry, Issue A 127 (15), 2023, Page(s) 3543-3550, ISSN 1089-7690
Publisher: AIP Publishing
DOI: 10.1021/acs.jpca.3c01753

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
Publisher: Faraday Discussions
DOI: 10.1039/d0fd00048e

Atomistic Polarizable Embeddings: Energy, Dynamics, Spectroscopy, and Reactivity.

Author(s): Daniele Loco; Louis Lagardère; Olivier Adjoua; Jean-Philip Piquemal; Jean-Philip Piquemal; Jean-Philip Piquemal
Published in: "Accounts of Chemical Research, American Chemical Society, 2021, ⟨10.1021/acs.accounts.0c00662⟩", 2021
Publisher: ACS
DOI: 10.1021/acs.accounts.0c00662

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
Publisher: Springer Link
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
Publisher: Chemical Communications
DOI: 10.1039/d0cc01938k

Quantifying the mini-batching error in Bayesian inference for Adaptive Langevin dynamics

Author(s): Inass Sekkat, Gabriel Stoltz
Published in: Journal of Machine Learning Research 24, Issue 8 times annually, 2023, Page(s) 1-58, ISSN 2642-4029
Publisher: Microtome Publishing
DOI: 10.48550/arxiv.2105.10347

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
Publisher: ACS Publications
DOI: 10.1021/acs.jpclett.9b03489

Black-box inhomogeneous preconditioning for self-consistent field iterations in density functional theory

Author(s): Michael F. Herbst; Antoine Levitt
Published in: Journal of Physics: Condensed Matter, Issue 1361648X, 2020, ISSN 1361-648X
Publisher: IOP SCIENCE
DOI: 10.1088/1361-648x/abcbdb

Scaling limits for the generalized Langevin equation

Author(s): G. Pavliotis, G. Stoltz, U. Vaes
Published in: Springer Link, Issue 00000000, 2020, ISSN 0000-0000
Publisher: Springer Link
DOI: 10.1007/s00332-020-09671-4

Accurate Deep Learning-aided Density-free Strategy for Many-Body Dispersion-corrected Density Functional Theory

Author(s): Pier Paolo Poier; Théo Jaffrelot Inizan; Olivier Adjoua; Louis Lagardère; Jean-Philip Piquemal
Published in: Journal of Physical Chemistry Letters, American Chemical Society,, 2022, Page(s) pp.4381-4388
Publisher: ACS Publishing
DOI: 10.48550/arxiv.2203.15739

Improvement of the Gaussian Electrostatic Model by Separate Fitting of Coulomb and Exchange-Repulsion Densities and Implementation of a new Dispersion term

Author(s): S. Naseem-Khan,J.-P. Piquemal, G. A. Cisneros
Published in: J. Chem. Phys., Issue 155, 194103, 2021, ISSN 1089-7690
Publisher: AIP Publishing
DOI: 10.1063/5.0072380

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
Publisher: American Chemical Society
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
Publisher: Society for Industrial and Applied Mathematics
DOI: 10.1137/19m128689x

Ab initio canonical sampling based on variational inference

Author(s): A. Castellano, F. Bottin, J. Bouchet, A. Levitt, G. Stoltz
Published in: Physical Review B, Issue 106, 2022, Page(s) L161110, ISSN 2469-9969
Publisher: American Physical Society
DOI: 10.1103/physrevb.106.l161110

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
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.0c01337

Mathematical foundations for the Parallel Replica algorithm applied to the underdamped Langevin dynamics

Author(s): T. Lelièvre, M. Ramil and J. Reygner
Published in: MRS Communications, 2022, Page(s) Vol. 12, pp. 454–459
Publisher: Springer
DOI: 10.1557/s43579-022-00207-3

Second-Order Homogenization of Periodic Schrödinger Operators with Highly Oscillating Potentials

Author(s): E. Cancès, L. Garrigue, D. Gontier
Published in: SIAM Journal on Mathematicla Analysis, Issue Vol. 55, Iss. 3, 2023, ISSN 1095-7154
Publisher: Society for Industrial and Applied Mathematics Publications
DOI: 10.1137/22m1478446

Tensor approximation of the self-diffusion matrix of tagged particle processes

Author(s): Jad Dabaghi, Virginie Ehrlacher, Christoph Strössner
Published in: Journal of Computational Physics, Issue Volume 480, 2023, Page(s) 112017, ISSN 0021-9991
Publisher: Academic Press
DOI: 10.1016/j.jcp.2023.112017

Van der Waals interactions between two hydrogen atoms: The next orders

Author(s): E. Cancès, R. Coyaud, L.R. Scott
Published in: Communications Mathematical Sciences, Issue 21, 2023, Page(s) 915–948, ISSN 1945-0796
Publisher: International Press
DOI: 10.48550/arxiv.2007.04227

Adaptive force biasing algorithms: new convergence results and tensor approximations of the bias

Author(s): Virginie Ehrlacher, Tony Lelièvre, Pierre Monmarché
Published in: The Annals of Applied Probability, Issue 32(5), 2022, Page(s) 3850-3888, ISSN 2168-8737
Publisher: Institute of Mathematical Statistics
DOI: 10.48550/arxiv.2007.09941

Photoionization and core resonances from range-separated time-dependent density-functional theory for open-shell states: Example of the lithium atom

Author(s): J. Toulouse, K. Schwinn, F. Zapata, A. Levitt, E. Cancès and E. Luppi
Published in: J. Chem. Phys., Issue Volume 157, Issue 24 (244104), 2022, ISSN 1089-7690
Publisher: AIP Publising
DOI: 10.1063/5.0134645

Variational projector-augmented wave method: a full-potential approach for electronic structure calculations in solid-state physics

Author(s): M. S. Dupuy
Published in: Journal of Computational Physics, Issue 00000000, 2021, ISSN 0000-0000
Publisher: ScienceDirect
DOI: 10.1016/j.jcp.2021.110510

A parareal Monte Carlo algorithm for parabolic problems hybrid

Author(s): J Dabaghi, Y Maday, A Zoia
Published in: Journal of Computational and Applied Mathematics 420, 114800, Issue 420, 2023, Page(s) 114800, ISSN 0377-0427
Publisher: Elsevier BV
DOI: 10.1016/j.cam.2022.114800

Efficient and Accurate Description of Diels-Alder Reactions using Density Functional Theory

Author(s): D. Loco, I. Chataignier, J.-P. Piquemal, R. Spezia
Published in: Chem. Phys. Chem., Issue Volume23, Issue18, e202200349, 2022, ISSN 1439-7641
Publisher: Chemistry Europe
DOI: 10.1002/cphc.202200349

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: J. Chem. Science Chem. Sci., 2021,12,, Issue 20416539, 2021, Page(s) 4889-4907, ISSN 2041-6539
Publisher: Publishing
DOI: 10.26434/chemrxiv.13003166.v2

DFT Exchange: Sharing Perspectives on the Workhorse of Quantum Chemistry and Materials Science

Author(s): Andrew M. Teale, Trygve Helgaker, Andreas Savin, Carlo Adamo, Ba´lint Aradi, Alexei V. Arbuznikov, Paul W. Ayers, Evert Jan Baerends, Vincenzo Barone, Patrizia Calaminici, Eric Cance`s, Emily A. Carter, Pratim Kumar Chattaraj, Henry Chermette, Ilaria Ciofini, T. Daniel Crawford, Frank De Proft, John F. Dobson, Claudia Draxl, Thomas Frauenheim, Emmanuel Fromager, Patricio Fuentealba, Laura Gagl
Published in: Physical Chemistry Chemical Physics, Issue Issue 47 Phys. Chem. Chem. Phys., 2022, 24 (47), 2022, Page(s) 28700-28781, ISSN 1463-9076
Publisher: Royal Society of Chemistry
DOI: 10.1039/d2cp02827a

Frequency and field-dependent response of confined electrolytes from Brownian dynamics simulations

Author(s): T. Hoang Ngoc Minh, G. Stoltz, B. Rotenberg
Published in: The Journal of Chemical Physics, Issue Vol. 158, Issue 10, 2023, Page(s) 4103, ISSN 1089-7690
Publisher: AIP Publishing
DOI: 10.1063/5.0139258

The NCIWEB Server: A Novel Implementation of the Noncovalent Interactions Index for Biomolecular Systems

Author(s): Trinidad Novoa; Rubén Laplaza; Francesca Peccati; Franck Fuster; Julia Contreras-García
Published in: Journal of Chemical Information and Modeling, Issue 4, 2023, ISSN 1549-9596
Publisher: American Chemical Society
DOI: 10.1021/acs.jcim.3c00271

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
Publisher: AIP The Journal of Chemical Physics
DOI: 10.1063/5.0005060

Directed message passing based on attention for prediction of molecular properties

Author(s): G Chen, Y Maday
Published in: Computational Materials Science, Issue Volume 229, 2023, Page(s) 112443, ISSN 0927-0256
Publisher: Elsevier BV
DOI: 10.1016/j.commatsci.2023.112443

Interfacial Water Many-body Effects Drive Structural Dynamics and Allosteric interactions in SARS-CoV-2 Main Protease Dimerization Interface

Author(s): D. El Ahdab, L. Lagardère, T. Jaffrelot Inizan, F. Célerse, C. Liu, O. Adjoua, L.H. Jolly, N. Gresh, Z. Hobaika, P. Ren, R. G. Maroun,J.-P. Piquemal
Published in: The Journal of Physical Chemistry Letters, 2021, Page(s) 12, 26, 6218–6226, ISSN 1948-7185
Publisher: American Chemical Society
DOI: 10.1021/acs.jpclett.1c01460

Mobility Estimation for Langevin Dynamics Using Control Variates

Author(s): G. A. Pavliotis, G. Stoltz, U. Vaes,
Published in: Mutiscale Modeling & Simulation, Issue Vol. 21 Issue 2, 2023, Page(s) 680-715, ISSN 1540-3467
Publisher: Society for Industrial and Applied Mathematics
DOI: 10.1137/22m1504378

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
Publisher: Electronic Journal of Probability
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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.
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Combining machine-learned and empirical force fields with the parareal algorithm: application to the diffusion of atomistic defects, à paraître dans Comptes Rendus Mécanique

Author(s): O. Gorynina, F. Legoll, T. Lelièvre, D. Perez
Published in: Comptes Rendus Mécanique, 2023, Page(s) pp. 1-25, ISSN 1873-7234
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Quantifying the error of the core-valence separation approximation.

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Published in: The Journal of Chemical Physics, Issue Volume 153, Issue 5 > 10.1063/5.0013538, 2020, ISSN 0000-0000
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Chasing Collective Variables Using Autoencoders and Biased Trajectories

Author(s): Zineb Belkacemi; Paraskevi Gkeka; Tony Lelièvre; Gabriel Stoltz
Published in: "Journal of Chemical Theory and Computation, American Chemical Society, 2022, 18 (1), pp.59-78. ⟨10.1021/acs.jctc.1c00415⟩", 2022
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Constrained overdamped Langevin dynamics for symmetric multimarginal optimal transportation

Author(s): Alfonsi, Aur��lien; Coyaud, Rafa��l; Ehrlacher, Virginie
Published in: MAS Mathematical Models and Methods in Applied Sciences, Issue 02182025, 2022, Page(s) Vol. 32, No. 03, pp. 403-455, ISSN 0218-2025
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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
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Some Formal Tools for Computer Arithmetic: Flocq and Gappa

Author(s): S. Boldo, G. Melquiond
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Improving Condensed Phase Water Dynamics with Explicit Nuclear Quantum Effects: the Polarizable Q-AMOEBA Force Field

Author(s): N. Mauger, T. Plé, L. Lagardère, S. Huppert, J.-P. Piquemal, J.
Published in: J. Phys. Chem. B, 126, 43, Issue 126, 43, 2022, Page(s) 8813–8826, ISSN 1439-7641
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Scalable Hybrid Deep Neural Networks/Polarizable Potentials Biomolecular Simulations including long-range effects

Author(s): T. Jaffrelot Inizan, T. Plé, O. Adjoua, P. Ren, H. Gökcan, O. Isayev, L. Lagardère, J.-P. Piquemal
Published in: Chem. Sci., Issue 14, 2023, Page(s) 5438-5452, ISSN 2041-6539
Publisher: The Royal Society of Chemistry’s
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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
Publisher: Institute of Mathematical Statistics
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Factorized structure of the long-range two-electron integrals tensor and its application in quantum chemistry

Author(s): S. Badreddine, I. Chollet, L. Grigori
Published in: Journal of Computational Physics, Issue Vol. 493, 112460, 2023, ISSN 0021-9991
Publisher: Academic Press
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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
Publisher: AIP The Journal of Chemical Physics
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Bounding the Round-Off Error of the Upwind Scheme for Advection

Author(s): L. B. Salem-Knapp, S. Boldo, W. Weens
Published in: IEEE Transactions on Emerging Topics in Computing, 2022, Page(s) vol. 10, no. 3, pp. 1253-1262
Publisher: IEEE Transactions on Emerging Topics in Computing
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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
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Multi-center decomposition of molecular densities: a mathematical perspective

Author(s): Robert Benda; Eric Cancès; Virginie Ehrlacher; Benjamin Stamm
Published in: J Chem Phys. 156(16):164107, Issue 00000000, 2022, ISSN 0000-0000
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Force-Field-Enhanced Neural Network Interactions: from Local Equivariant Embedding to Atom-in-Molecule properties and long-range effects

Author(s): T. Plé, L. Lagardère, J.-P. Piquemal
Published in: Chem. Sci., 2023, ISSN 2041-6539
Publisher: The Royal Society of Chemistry’s
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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
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Development of the Quantum Inspired SIBFA Many-Body Polarizable Force Field: Enabling Condensed Phase Molecular Dynamics Simulations

Author(s): Sehr Naseem-Khan; Louis Lagardère; Christophe Narth; G. Andrés Cisneros; Pengyu Ren; Nohad Gresh; Jean-Philip Piquemal
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O(N) Stochastic Evaluation of Many-Body van der Waals Energies in Large Complex Systems

Author(s): Pier Paolo Poir; Louis Lagardère; Jean-Philip Piquemal
Published in: Journal of Chemical Theory and Computation, American Chemical Society,, 2022, Page(s) 8 (3), pp.1633-1645
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Efficient Extraction of Resonant States in Systems with Defects

Author(s): Ivan Duchemin; Luigi Genovese; Eloïse Letournel; Antoine Levitt; Simon Ruget
Published in: Journal of Computational Physics, Volume 477, 15 March 2023, 111928, Issue 13, 2023, ISSN 0021-9991
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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
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The Adaptive Biasing Force algorithm with non-conservative forces and related topics

Author(s): Tony Lelièvre, Lise Maurin, Pierre Monmarché
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Van der Waals interactions between two hydrogen atoms: The next orders

Author(s): Cancès, Éric; Coyaud, Rafaël; Scott, L. Ridgway
Published in: Comm. Math. Sci. Vol. 21, No. 4, Issue 11, 2023, Page(s) 915–948, ISSN 1945-0796
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Routine Molecular Dynamics Simulations Including Nuclear Quantum Effects: from Force Fields to Machine Learning Potentials

Author(s): Plé, Thomas; Mauger, Nastasia; Adjoua, Olivier; Jaffrelot-Inizan, Théo; Lagardère, Louis; Huppert, Simon; Piquemal, Jean-Philip
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Overlap-ADAPT-VQE: Practical Quantum Chemistry on Quantum Computers via Overlap-Guided Compact Ansätze

Author(s): C Feniou, M Hassan, D Traoré, E Giner, Y Maday, JP Piquemal
Published in: Commun.Phys. 6 (2023) 1, 192, Issue 6, 2023, Page(s) 192, ISSN 2399-3650
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Targeting the Major Groove of the Palindromic d(GGCGCC)2 Sequence by Oligopeptide Derivatives of Anthraquinone Intercalators

Author(s): Krystel El Hage; Giovanni Ribaudo; Louis Lagardère; Alberto Ongaro; Philippe H. Kahn; Luc Demange; Jean-Philip Piquemal; Giuseppe Zagotto; Nohad Gresh
Published in: "Journal of Chemical Information and Modeling, American Chemical Society, 2022, ⟨10.1021/acs.jcim.2c00337⟩", 2022
Publisher: JCIM
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On the Quantum Chemical Nature of Lead(II) “Lone Pair”

Author(s): Christophe Gourlaouen; Jean-Philip Piquemal
Published in: "Molecules, MDPI, 2022, 27 (1), pp.27. ⟨10.3390/molecules27010027⟩", 2022
Publisher: Molecules, 2022, 27(1), 27
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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
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An overview of a posteriori error estimation and post-processingmethods for nonlinear eigenvalue problems G Dusson

Author(s): G Dusson, Y Maday
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Open source variational quantum eigensolver extension of the quantum learning machine for quantum chemistry

Author(s): M Haidar, MJ Rančić, T Ayral, Y Maday, JP Piquemal
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Photoionization and core resonances from range-separated density-functional theory: General formalism and example of the beryllium atom

Author(s): Karno Schwinn; Felipe Zapata; Antoine Levitt; Éric Cancès; Eleonora Luppi; Julien Toulouse
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Convergence analysis of adaptive DIIS algorithms with application to electronic ground state calculations

Author(s): M. Chupin, M. S. Dupuy, G. Legendre, E. Séré
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An Efficient Gaussian-Accelerated Molecular Dynamics (GaMD) Multilevel Enhanced Sampling Strategy: Application to Polarizable Force Fields Simulations of Large Biological Systems

Author(s): Frédéric Célerse; Théo Jaffrelot Inizan; Louis Lagardère; Olivier Adjoua; Pierre Monmarché; Yinglong Miao; Etienne Derat; Jean-Philip Piquemal
Published in: Journal of Chemical Theory and Computation, American Chemical Society,, 2022, Page(s) 18 (2), pp.968-977
Publisher: ACS Publishing
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Martingale product estimators for sensitivity analysis in computational statistical physics Get access Arrow

Author(s): P. Plechac, G. Stoltz, T. Wang
Published in: IMA Journal of Numerical Analysis, Issue drac073, 2022, ISSN 1464-3642
Publisher: Oxford University Press
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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
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A Coq Formalization of Lebesgue Integration of Nonnegative Functions

Author(s): Sylvie Boldo; François Clément; François Clément; Florian Faissole; Vincent Martin; Micaela Mayero
Published in: "Journal of Automated Reasoning, Springer Verlag, In press, ⟨10.1007/s10817-021-09612-0⟩", 2022, Page(s) 66, 175–213
Publisher: Journal of Automated Reasoning
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Parallel Memory-Independent Communication Bounds for SYRK

Author(s): H. Al Daas, G. Ballard, L. Grigori, S. Kumar, K. Rouse
Published in: SPAA '23: Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, 2023, Page(s) Pages 391–401
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Quasi-stationary distribution for the Langevin process in cylindrical domains, part I: existence, uniqueness and long-time convergence

Author(s): Tony Lelièvre, Mouad Ramil, Julien Reygner
Published in: Stochastic Processes and their Applications., 2022, Page(s) Volume 144, Pages 173-201
Publisher: ScienceDirect
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Block subsampled randomized Hadamard transform for low-rank approximation on distributed architectures

Author(s): Oleg Balabanov, Matthias Beaupere, Laura Grigori, Victor Lederer
Published in: ICML'23: Proceedings of the 40th International Conference on Machine Learning, Issue Article No.: 66, 2023, Page(s) Pages 1564–1576
Publisher: ICML'23: Proceedings of the 40th International Conference on Machine Learning
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