Extreme-scale Mathematically-based Computational Chemistry

Publicaciones

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

Autores: Laura Grigori, Sever Hirstoaga, Julien Salomon
Publicado en: Computers and Mathematics with Applications, Edición Volume 130, 2023, Página(s) Pages 137-148, ISSN 1873-7668
Editor: 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

Autores: 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
Publicado en: Journal of Chemical Theory and Computation, Edición 17/4, 2021, Página(s) 2034-2053, ISSN 1549-9618
Editor: 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

Autores: A. Anciaux-Sekadrian, M. Corral-Valero,T. Lelièvre, M. Moreaud, T. Pigeon, P. Raybaud, G. Stoltz
Publicado en: Journal of Chemical Theory and Computation, Edición 19(12), 2023, Página(s) 3538–3550, ISSN 1549-9618
Editor: American Chemical Society
DOI: 10.1021/acs.jctc.3c00280

On basis set optimisation in quantum chemistry

Autores: E Cancès, G Dusson, G Kemlin, L Vidal
Publicado en: ESAIM: Proceedings and Surveys 73, Edición irregular, 2023, Página(s) 07-129, ISSN 2267-3059
Editor: EDP Sciences
DOI: 10.1051/proc/202373107

Multiple projection MCMC algorithms on submanifolds

Autores: Lelièvre, Tony; Stoltz, Gabriel; Zhang, Wei
Publicado en: IMA Journal of Numerical Analysis, drac006, 2022
Editor: IMA Journal of Numerical Analysis, drac006
DOI: 10.48550/arxiv.2003.09402

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

Autores: Michael F. Herbst; Antoine Levitt
Publicado en: Journal of Computational Physics, Edición 00219991, 2022, Página(s) Volume 459, ISSN 0021-9991
Editor: Academic Press
DOI: 10.48550/arxiv.2109.14018

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

Autores: E. Cancès, G. Dusson, Y. Maday, B. Stamm, M. Vohralík.
Publicado en: IMA Journal of Numerical Analysis, 2020, ISSN 0000-0000
Editor: 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.

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

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

Autores: P. P. Poier, L. Lagardère, J.-P. Piquemal
Publicado en: Phys. Chem. Lett, Edición 14, 6, 2023, Página(s) 1609–1617, ISSN 1948-7185
Editor: American Chemical Society
DOI: 10.1021/acs.jpclett.2c03722

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

Autores: Tony Lelièvre; Mouad Ramil; Julien Reygner
Publicado en: Journal of Evolution Equations, 2022, Página(s) volume 22, Article number: 38
Editor: 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

Autores: Z. Belkacemi, M. Bianciotto, P. Gkeka, T. Lelièvre, H. Minoux, G. Stoltz,
Publicado en: The Journal of Chemical Physics, Edición 159, 2023, Página(s) 024122, ISSN 1089-7690
Editor: AIP Publishing
DOI: 10.48550/arxiv.2306.02935

Extending the regime of linear response with synthetic forcings

Autores: R. Spacek, G. Stoltz
Publicado en: Multiscale Modeling and Simulation 21 (4), 1602-1643 1 2023, Edición Quarterly, 2023, Página(s) 602-1643, ISSN 1540-3459
Editor: Society for Industrial and Applied Mathematics
DOI: 10.1137/23m1557611

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

Autores: 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
Publicado en: Chem. Sc., Edición 13, 2022, Página(s) 3674-3687, ISSN 2041-6539
Editor: The Royal Society of Chemistry’s
DOI: 10.1039/d1sc05892d

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

Autores: E. Cancès, M. Herbst, G. Kemlin, A. Levitt, B. Stamm
Publicado en: Letters in Mathematical Physics, Edición 113, article number 21, 2023, Página(s) 1–32., ISSN 1573-0530
Editor: Springer
DOI: 10.1007/s11005-023-01645-3

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

Autores: Michael F. Herbst, Antoine Levitt, Eric Cancès
Publicado en: JuliaCon Proceedings, Edición 3, 69, 2021, ISSN 2642-4029
Editor: Cambridge MA: JuliaCon
DOI: 10.21105/jcon.00069

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

Autores: Tony Lelièvre, Lise Maurin, Pierre Monmarché
Publicado en: ESAIM: M2AN 56 (, 2022, Página(s) 529–564
Editor: ESAIM: M2AN
DOI: 10.48550/arxiv.2102.09957

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

Autores: L.-H. Jolly, A. Duran, L. Lagardère, J. W. Ponder, P. Ren, J.-P. Piquemal.
Publicado en: Living Journal of Computational Molecular Science, University of Colorado Boulder, 2019, ISSN 0000-0000
Editor: 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

Autores: T. Lelièvre, G. Robin, I. Sekkat, G. Stoltz, G. Victorino Cardoso
Publicado en: ESAIM: PROCEEDINGS AND SURVEYS, Edición Vol. 73, p. 238-256, 2023, Página(s) p. 238-256, ISSN 2267-3059
Editor: EDP Sciences
DOI: 10.48550/arxiv.2205.02818

Weighted L2-contractivity of Langevin dynamics with singular potentials

Autores: E. Camrud, D. P. Herzog, G. Stoltz, M. Gordina,
Publicado en: Nonlinearity, 2022, Página(s) 35, 998
Editor: IOP Publishing
DOI: 10.48550/arxiv.2104.10574

Convergence analysis of direct minimization and self-consistent iterations

Autores: Eric Cancès, Gaspard Kemlin, Antoine Levitt
Publicado en: SIAM Journal on Matrix Analysis and Applications, Edición Volume 42, Edición 1, 2020, Página(s) 243–274. (32 pages), ISSN 0895-4798
Editor: Society for Industrial and Applied Mathematics
DOI: 10.1137/20m1332864

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

Autores: P. P. Poier, L. Lagardère, J.-P. Piquemal
Publicado en: J. Chem. Phys., Edición 159, 154109, 2023, ISSN 1089-7690
Editor: AIP Publishing
DOI: 10.1063/5.0166476

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

Autores: 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
Publicado en: WIREs Computational Molecular Science, 2021, Página(s) Volume11, Edición6
Editor: WIREs Computational Molecular Science
DOI: 10.1002/wcms.1528

Overdamped limit at stationarity for non-equilibrium Langevin diffusions

Autores: Pierre Monmarché, Mouad Ramil
Publicado en: Electron. Commun, 2022
Editor: Project Euclid
DOI: 10.1214/22-ecp447

Building Kohn-Sham potentials for ground and excited states

Autores: Louis Garrigue
Publicado en: Archive for Rational Mechanics and Analysis volume 245, pages949–1003 (2022), 2022, Página(s) volume 245, pages949–1003 (2022)
Editor: Springer
DOI: 10.48550/arxiv.2101.01127

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

Autores: I. Chollet, L. Lagardère, J.-P. Piquemal
Publicado en: J. Chem. Theory. Comput., Edición 19, 10, 2023, Página(s) 2887–2905, ISSN 1549-9618
Editor: American Chemical Society
DOI: 10.1021/acs.jctc.3c00015

Coherent Electronic Transport in Periodic Crystals

Autores: Eric Cancès; Clotilde Fermanian Kammerer; Antoine Levitt; Sami Siraj-Dine
Publicado en: Annales Henri Poincaré volume 22, 2021, Página(s) pages 2643–2690
Editor: Springer
DOI: 10.1007/s00023-021-01026-3

Nonlinear compressive reduced basis approximation for PDE's A

Autores: A Cohen, C Farhat, A Somacal, Y Maday
Publicado en: Comptes Rendus Mécanique, 2023, Página(s) pp. 1-18, ISSN 1873-7234
Editor: 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.

Autores: Poier Pier Paolo, L. Lagardère, J.-P. Piquemal, F. Jensen.
Publicado en: Journal of Chemical Theory and Computation, American Chemical Society, 2019, ISSN 0000-0000
Editor: Journal of Chemical Theory and Computation, American Chemical Society
DOI: 10.1021/acs.jctc.9b00721

Accurate biomolecular simulations account for electronic polarization.

Autores: J. Melcr, J.-P. Piquemal
Publicado en: Frontiers in Molecular Biosciences, Frontiers Media, 2019, 6, pp.143., 2019, ISSN 0000-0000
Editor: Frontiers in Molecular Biosciences
DOI: 10.3389/fmolb.2019.00143

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

Autores: R. Boto, F. Peccati, R. Laplaza, C. Quan, A. Carbone, J.-P. Piquemal, Y. Maday, J. Contreras-Garcia
Publicado en: Journal of Chemical Theory and Computation, American Chemical Society, Edición 00000000, 2020, ISSN 0000-0000
Editor: 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

Autores: Eric Cancès, Geneviève Dusson, Gaspard Kemlin , Antoine Levitt
Publicado en: SIAM Journal on Scientific Computing, Edición Vol. 44, Iss. 5, 2022, ISSN 1064-8275
Editor: Society for Industrial and Applied Mathematics
DOI: 10.1137/21m1456224

Hypocoercivity with Schur complements

Autores: Bernard, Etienne; Fathi, Max; Levitt, Antoine; Stoltz, Gabriel
Publicado en: Annales Henri Lebesgue, 2022, Página(s) Annales Henri Lebesgue, Volume 5 (2022), pp. 523-557
Editor: Annales Henri Lebesgue
DOI: 10.48550/arxiv.2003.00726

Numerical algorithms for high-performance computational science

Autores: Dongarra, Laura Grigori, Nicholas J. Higham
Publicado en: Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Edición Volume 378 Edición 2166 pp.20190066. ⟨10.1098/rsta.2019.0), 2020, ISSN 0000-0000
Editor: The Royal Society Publishing
DOI: 10.1098/rsta.2019.0066

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

Autores: E. Cancès, G. Dusson, Y. Maday, B. Stamm, M. Vohralík
Publicado en: Mathematics of Computation, 2020, ISSN 0025-5718
Editor: 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

Autores: M Hassan, Y Maday, Y Wang
Publicado en: ESAIM: M2AN, Edición 57, 2023, Página(s) 545–583, ISSN 2804-7214
Editor: Springer link
DOI: 10.1051/m2an/2022099

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

Autores: Éric Cancès; Louis Garrigue; David Gontier
Publicado en: PHYSICAL REVIEW B, Edición 11, Phys. Rev. B 107, Edición 15,, 2023, Página(s) 155403, ISSN 2469-9969
Editor: American Physical Society (APS)
DOI: 10.1103/physrevb.107.155403

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

Autores: Ehrlacher, Virginie; Fuente-Ruiz, Maria; Lombardi, Damiano
Publicado en: Molecules, 2022
Editor: Molecules
DOI: 10.48550/arxiv.2011.09725

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

Autores: Virginie Ehrlacher; Maria Fuente Ruiz; Damiano Lombardi
Publicado en: SIAM Journal on Scientific Computing, Society for Industrial and Applied Mathematics, In press, 2021, Página(s) Vol. 44, Iss. 210.1137/20M1381472
Editor: SIAM
DOI: 10.1137/20m1381472

On basis set optimization in quantum chemistry

Autores: E. Cancès, G. Dusson, G. Kemlin, L. Vidal
Publicado en: ESAIM: Proceedings and Surveys, Edición Vol. 73, 2023, Página(s) 107-129, ISSN 2267-3059
Editor: 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

Autores: S. Naseem Kahn, L. Lagardère, C. Narth, G. A. Cisneros, P. Ren, N. Gresh, J.-P. Piquemal,
Publicado en: J. Chem. Theory Comput, Edición 18, 6, 2022, Página(s) 3607–3621, ISSN 1549-9618
Editor: American Chemical Society
DOI: 10.1021/acs.jctc.2c00029

Convergence of the kinetic annealing for general potentials

Autores: L. Journel, P. Monmarché
Publicado en: Electron. J. Probab, Edición vol. 27article no. 159, 2022, Página(s) pp. 1–37, ISSN 1083-6489
Editor: Institute of Mathematical Statistics
DOI: 10.1214/22-ejp891

Extension of the trotterized unitary coupled cluster to triple excitations

Autores: M Haidar, MJ Rancic, Y Maday, JP Piquemal
Publicado en: The Journal of Physical Chemistry, Edición A 127 (15), 2023, Página(s) 3543-3550, ISSN 1089-7690
Editor: AIP Publishing
DOI: 10.1021/acs.jpca.3c01753

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

Autores: M. F. Herbst, A. Levitt, E. Cancès.
Publicado en: Faraday Discussions, 2020, ISSN 0000-0000
Editor: Faraday Discussions
DOI: 10.1039/d0fd00048e

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

Autores: Daniele Loco; Louis Lagardère; Olivier Adjoua; Jean-Philip Piquemal; Jean-Philip Piquemal; Jean-Philip Piquemal
Publicado en: "Accounts of Chemical Research, American Chemical Society, 2021, ⟨10.1021/acs.accounts.0c00662⟩", 2021
Editor: ACS
DOI: 10.1021/acs.accounts.0c00662

Numerical quadrature in the Brillouin zone for periodic Schrödinger operators

Autores: Eric Cancès, Virginie Ehrlacher, David Gontier, Antoine Levitt, Damiano Lombardi
Publicado en: Springer Link, Edición Numerische Mathematik volume 144, pages479–526(2020), 2020, ISSN 0000-0000
Editor: Springer Link
DOI: 10.1007/s00211-019-01096-w

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

Autores: Tony Lelièvre, Gabriel Stoltz, Wei Zhang.
Publicado en: Chemical Communications. Edición 49, 2020, ISSN 0000-0000
Editor: Chemical Communications
DOI: 10.1039/d0cc01938k

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

Autores: Inass Sekkat, Gabriel Stoltz
Publicado en: Journal of Machine Learning Research 24, Edición 8 times annually, 2023, Página(s) 1-58, ISSN 2642-4029
Editor: Microtome Publishing
DOI: 10.48550/arxiv.2105.10347

Implementation of Geometry Dependent Charge Flux into Polarizable AMOEBA+ Potential

Autores: C. Liu, J.-P. Piquemal, P. Ren.
Publicado en: Journal of Physical Chemistry Letters, American Chemical Society, 2019, ISSN 0000-0000
Editor: ACS Publications
DOI: 10.1021/acs.jpclett.9b03489

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

Autores: Michael F. Herbst; Antoine Levitt
Publicado en: Journal of Physics: Condensed Matter, Edición 1361648X, 2020, ISSN 1361-648X
Editor: IOP SCIENCE
DOI: 10.1088/1361-648x/abcbdb

Scaling limits for the generalized Langevin equation

Autores: G. Pavliotis, G. Stoltz, U. Vaes
Publicado en: Springer Link, Edición 00000000, 2020, ISSN 0000-0000
Editor: Springer Link
DOI: 10.1007/s00332-020-09671-4

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

Autores: Pier Paolo Poier; Théo Jaffrelot Inizan; Olivier Adjoua; Louis Lagardère; Jean-Philip Piquemal
Publicado en: Journal of Physical Chemistry Letters, American Chemical Society,, 2022, Página(s) pp.4381-4388
Editor: 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

Autores: S. Naseem-Khan,J.-P. Piquemal, G. A. Cisneros
Publicado en: J. Chem. Phys., Edición 155, 194103, 2021, ISSN 1089-7690
Editor: AIP Publishing
DOI: 10.1063/5.0072380

Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field

Autores: 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
Publicado en: Journal of Chemical Theory and Computation, Edición 17/4, 2021, Página(s) 2323-2341, ISSN 1549-9618
Editor: American Chemical Society
DOI: 10.1021/acs.jctc.0c01286

Adaptive Hierarchical Subtensor Partitioning for Tensor Compression

Autores: Virginie Ehrlacher, Laura Grigori, Damiano Lombardi, Hao Song
Publicado en: SIAM Journal on Scientific Computing, Edición 43/1, 2021, Página(s) A139-A163, ISSN 1064-8275
Editor: Society for Industrial and Applied Mathematics
DOI: 10.1137/19m128689x

Ab initio canonical sampling based on variational inference

Autores: A. Castellano, F. Bottin, J. Bouchet, A. Levitt, G. Stoltz
Publicado en: Physical Review B, Edición 106, 2022, Página(s) L161110, ISSN 2469-9969
Editor: 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

Autores: Sehr Naseem-Khan, Nohad Gresh, Alston J. Misquitta, Jean-Philip Piquemal
Publicado en: Journal of Chemical Theory and Computation, 2020, ISSN 1549-9618
Editor: American Chemical Society
DOI: 10.1021/acs.jctc.0c01337

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

Autores: T. Lelièvre, M. Ramil and J. Reygner
Publicado en: MRS Communications, 2022, Página(s) Vol. 12, pp. 454–459
Editor: Springer
DOI: 10.1557/s43579-022-00207-3

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

Autores: E. Cancès, L. Garrigue, D. Gontier
Publicado en: SIAM Journal on Mathematicla Analysis, Edición Vol. 55, Iss. 3, 2023, ISSN 1095-7154
Editor: Society for Industrial and Applied Mathematics Publications
DOI: 10.1137/22m1478446

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

Autores: Jad Dabaghi, Virginie Ehrlacher, Christoph Strössner
Publicado en: Journal of Computational Physics, Edición Volume 480, 2023, Página(s) 112017, ISSN 0021-9991
Editor: Academic Press
DOI: 10.1016/j.jcp.2023.112017

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

Autores: E. Cancès, R. Coyaud, L.R. Scott
Publicado en: Communications Mathematical Sciences, Edición 21, 2023, Página(s) 915–948, ISSN 1945-0796
Editor: International Press
DOI: 10.48550/arxiv.2007.04227

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

Autores: Virginie Ehrlacher, Tony Lelièvre, Pierre Monmarché
Publicado en: The Annals of Applied Probability, Edición 32(5), 2022, Página(s) 3850-3888, ISSN 2168-8737
Editor: 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

Autores: J. Toulouse, K. Schwinn, F. Zapata, A. Levitt, E. Cancès and E. Luppi
Publicado en: J. Chem. Phys., Edición Volume 157, Edición 24 (244104), 2022, ISSN 1089-7690
Editor: AIP Publising
DOI: 10.1063/5.0134645

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

Autores: M. S. Dupuy
Publicado en: Journal of Computational Physics, Edición 00000000, 2021, ISSN 0000-0000
Editor: ScienceDirect
DOI: 10.1016/j.jcp.2021.110510

A parareal Monte Carlo algorithm for parabolic problems hybrid

Autores: J Dabaghi, Y Maday, A Zoia
Publicado en: Journal of Computational and Applied Mathematics 420, 114800, Edición 420, 2023, Página(s) 114800, ISSN 0377-0427
Editor: Elsevier BV
DOI: 10.1016/j.cam.2022.114800

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

Autores: D. Loco, I. Chataignier, J.-P. Piquemal, R. Spezia
Publicado en: Chem. Phys. Chem., Edición Volume23, Edición18, e202200349, 2022, ISSN 1439-7641
Editor: Chemistry Europe
DOI: 10.1002/cphc.202200349

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

Autores: 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
Publicado en: J. Chem. Science Chem. Sci., 2021,12,, Edición 20416539, 2021, Página(s) 4889-4907, ISSN 2041-6539
Editor: Publishing
DOI: 10.26434/chemrxiv.13003166.v2

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

Autores: 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
Publicado en: Physical Chemistry Chemical Physics, Edición Edición 47 Phys. Chem. Chem. Phys., 2022, 24 (47), 2022, Página(s) 28700-28781, ISSN 1463-9076
Editor: Royal Society of Chemistry
DOI: 10.1039/d2cp02827a

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

Autores: T. Hoang Ngoc Minh, G. Stoltz, B. Rotenberg
Publicado en: The Journal of Chemical Physics, Edición Vol. 158, Edición 10, 2023, Página(s) 4103, ISSN 1089-7690
Editor: AIP Publishing
DOI: 10.1063/5.0139258

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

Autores: Trinidad Novoa; Rubén Laplaza; Francesca Peccati; Franck Fuster; Julia Contreras-García
Publicado en: Journal of Chemical Information and Modeling, Edición 4, 2023, ISSN 1549-9596
Editor: 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.

Autores: P. Monmarché, J. Weisman, L. Lagardère, J.-P. Piquemal.
Publicado en: AIP The Journal of Chemical Physics, 2020, ISSN 0000-0000
Editor: AIP The Journal of Chemical Physics
DOI: 10.1063/5.0005060

Directed message passing based on attention for prediction of molecular properties

Autores: G Chen, Y Maday
Publicado en: Computational Materials Science, Edición Volume 229, 2023, Página(s) 112443, ISSN 0927-0256
Editor: 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

Autores: 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
Publicado en: The Journal of Physical Chemistry Letters, 2021, Página(s) 12, 26, 6218–6226, ISSN 1948-7185
Editor: American Chemical Society
DOI: 10.1021/acs.jpclett.1c01460

Mobility Estimation for Langevin Dynamics Using Control Variates

Autores: G. A. Pavliotis, G. Stoltz, U. Vaes,
Publicado en: Mutiscale Modeling & Simulation, Edición Vol. 21 Edición 2, 2023, Página(s) 680-715, ISSN 1540-3467
Editor: Society for Industrial and Applied Mathematics
DOI: 10.1137/22m1504378

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

Autores: Michel Benaïm, Charles-Edouard Bréhier, Pierre Monmarché
Publicado en: Electronic Journal of Probability, Edición Vol.25 • 2020, 2020, ISSN 0000-0000
Editor: Electronic Journal of Probability
DOI: 10.1214/20-ejp490

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

Autores: P. El Darazi, L. El Khoury, K. El Hage, R. Maroun, Z. Hobaika, J.-P. Piquemal, N. Gresh.
Publicado en: Theoretical and Computational Chemistry, 2019, ISSN 0000-0000
Editor: Theoretical and Computational Chemistry
DOI: 10.3389/fchem.2020.00440

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

Autores: O. Gorynina, F. Legoll, T. Lelièvre, D. Perez
Publicado en: Comptes Rendus Mécanique, 2023, Página(s) pp. 1-25, ISSN 1873-7234
Editor: Académie des sciences_ Institut de France
DOI: 10.48550/arxiv.2212.10508

Quantifying the error of the core-valence separation approximation.

Autores: M. F. Herbst, T. Fransson.
Publicado en: The Journal of Chemical Physics, Edición Volume 153, Edición 5 > 10.1063/5.0013538, 2020, ISSN 0000-0000
Editor: The Journal of Chemical Physics
DOI: 10.1063/5.0013538

Chasing Collective Variables Using Autoencoders and Biased Trajectories

Autores: Zineb Belkacemi; Paraskevi Gkeka; Tony Lelièvre; Gabriel Stoltz
Publicado en: "Journal of Chemical Theory and Computation, American Chemical Society, 2022, 18 (1), pp.59-78. ⟨10.1021/acs.jctc.1c00415⟩", 2022
Editor: ACS Publishing
DOI: 10.1021/acs.jctc.1c00415

Constrained overdamped Langevin dynamics for symmetric multimarginal optimal transportation

Autores: Alfonsi, Aur��lien; Coyaud, Rafa��l; Ehrlacher, Virginie
Publicado en: MAS Mathematical Models and Methods in Applied Sciences, Edición 02182025, 2022, Página(s) Vol. 32, No. 03, pp. 403-455, ISSN 0218-2025
Editor: World Scientific Publishing Co
DOI: 10.1142/s0218202522500105

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

Autores: 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.
Publicado en: Journal of Chemical Theory and Computation, 2020, ISSN 0000-0000
Editor: Journal of Chemical Theory and Computation
DOI: 10.1021/acs.jctc.9b01204

Some Formal Tools for Computer Arithmetic: Flocq and Gappa

Autores: S. Boldo, G. Melquiond
Publicado en: IEEE 28th Symposium on Computer Arithmetic (ARITH), 2021, pp. 111-114, 2021, Página(s) pp. 111-114
Editor: IEEE 28th Symposium on Computer Arithmetic (ARITH)
DOI: 10.1109/arith51176.2021.00031

Improving Condensed Phase Water Dynamics with Explicit Nuclear Quantum Effects: the Polarizable Q-AMOEBA Force Field

Autores: N. Mauger, T. Plé, L. Lagardère, S. Huppert, J.-P. Piquemal, J.
Publicado en: J. Phys. Chem. B, 126, 43, Edición 126, 43, 2022, Página(s) 8813–8826, ISSN 1439-7641
Editor: Chemistry Europe
DOI: 10.1021/acs.jpcb.2c04454

Scalable Hybrid Deep Neural Networks/Polarizable Potentials Biomolecular Simulations including long-range effects

Autores: T. Jaffrelot Inizan, T. Plé, O. Adjoua, P. Ren, H. Gökcan, O. Isayev, L. Lagardère, J.-P. Piquemal
Publicado en: Chem. Sci., Edición 14, 2023, Página(s) 5438-5452, ISSN 2041-6539
Editor: The Royal Society of Chemistry’s
DOI: 10.1039/d2sc04815a

Geometric ergodicity of the Bouncy Particle Sampler

Autores: Alain Durmus, Arnaud Guillin, Pierre Monmarché
Publicado en: The Annals of Applied Probability, Edición 30/5, 2020, ISSN 1050-5164
Editor: Institute of Mathematical Statistics
DOI: 10.1214/19-aap1552

Factorized structure of the long-range two-electron integrals tensor and its application in quantum chemistry

Autores: S. Badreddine, I. Chollet, L. Grigori
Publicado en: Journal of Computational Physics, Edición Vol. 493, 112460, 2023, ISSN 0021-9991
Editor: Academic Press
DOI: 10.1016/j.jcp.2023.112460

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

Autores: Robert Benda, Gaël Zucchi, Eric Cancès, Bérengère Lebental
Publicado en: AIP The Journal of Chemical Physics, Edición Volume 152, Edición 6 > 10.1063/1.5133634, 2020, ISSN 0000-0000
Editor: AIP The Journal of Chemical Physics
DOI: 10.1063/1.5133634

Bounding the Round-Off Error of the Upwind Scheme for Advection

Autores: L. B. Salem-Knapp, S. Boldo, W. Weens
Publicado en: IEEE Transactions on Emerging Topics in Computing, 2022, Página(s) vol. 10, no. 3, pp. 1253-1262
Editor: IEEE Transactions on Emerging Topics in Computing
DOI: 10.1109/tetc.2022.3191472

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

Autores: L. El-Khoury, K. El Hage, J.-P. Piquemal, S. Fermandjian, R. Maroun, N. Gresh, Z. Hobaika.
Publicado en: PeerJ Physical Chemistry, PeerJ, 2019, 1, pp.e6., 2019, ISSN 0000-0000
Editor: PeerJ Physical Chemistry
DOI: 10.7717/peerj-pchem.6

Multi-center decomposition of molecular densities: a mathematical perspective

Autores: Robert Benda; Eric Cancès; Virginie Ehrlacher; Benjamin Stamm
Publicado en: J Chem Phys. 156(16):164107, Edición 00000000, 2022, ISSN 0000-0000
Editor: AIP
DOI: 10.48550/arxiv.2109.03304

Force-Field-Enhanced Neural Network Interactions: from Local Equivariant Embedding to Atom-in-Molecule properties and long-range effects

Autores: T. Plé, L. Lagardère, J.-P. Piquemal
Publicado en: Chem. Sci., 2023, ISSN 2041-6539
Editor: The Royal Society of Chemistry’s
DOI: 10.1039/d3sc02581k

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

Autores: R. Laplaza, F. Peccati, R. Boto, C. Quan, A. Carbone, J.-P. Piquemal, Y. Maday, J. Contreras-Garcia
Publicado en: WIREs Computational Molecular Science, Edición 00000000, 2020, ISSN 0000-0000
Editor: WIREs Computational Molecular Science
DOI: 10.1002/wcms.1497

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

Autores: Sehr Naseem-Khan; Louis Lagardère; Christophe Narth; G. Andrés Cisneros; Pengyu Ren; Nohad Gresh; Jean-Philip Piquemal
Publicado en: 18, 6, 3607–3621 Article associé dans chemistry news, 2022
Editor: Chemistry News
DOI: 10.48550/arxiv.2201.00804

O(N) Stochastic Evaluation of Many-Body van der Waals Energies in Large Complex Systems

Autores: Pier Paolo Poir; Louis Lagardère; Jean-Philip Piquemal
Publicado en: Journal of Chemical Theory and Computation, American Chemical Society,, 2022, Página(s) 8 (3), pp.1633-1645
Editor: ACS Publishing
DOI: 10.1021/acs.jctc.1c01291

Efficient Extraction of Resonant States in Systems with Defects

Autores: Ivan Duchemin; Luigi Genovese; Eloïse Letournel; Antoine Levitt; Simon Ruget
Publicado en: Journal of Computational Physics, Volume 477, 15 March 2023, 111928, Edición 13, 2023, ISSN 0021-9991
Editor: Academic Press
DOI: 10.1016/j.jcp.2023.111928

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

Autores: 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
Publicado en: Chemical Science, Edición 12/13, 2021, Página(s) 4889-4907, ISSN 2041-6520
Editor: Royal Society of Chemistry
DOI: 10.1039/d1sc00145k

The Adaptive Biasing Force algorithm with non-conservative forces and related topics

Autores: Tony Lelièvre, Lise Maurin, Pierre Monmarché
Publicado en: ESAIM: M2AN, 2022, Página(s) Vol. 56, No. 2, pp. 529 - 564
Editor: ESAIM: M2AN
DOI: 10.1051/m2an/2022010

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

Autores: Cancès, Éric; Coyaud, Rafaël; Scott, L. Ridgway
Publicado en: Comm. Math. Sci. Vol. 21, No. 4, Edición 11, 2023, Página(s) 915–948, ISSN 1945-0796
Editor: International Press of Boston
DOI: 10.1137/15m1021878

Routine Molecular Dynamics Simulations Including Nuclear Quantum Effects: from Force Fields to Machine Learning Potentials

Autores: Plé, Thomas; Mauger, Nastasia; Adjoua, Olivier; Jaffrelot-Inizan, Théo; Lagardère, Louis; Huppert, Simon; Piquemal, Jean-Philip
Publicado en: J. Chem. Theory. Comput., Edición 11, 2023, Página(s) 1432–1445, ISSN 1549-9618
Editor: American Chemical Society
DOI: 10.1021/acs.jctc.2c01233

Overlap-ADAPT-VQE: Practical Quantum Chemistry on Quantum Computers via Overlap-Guided Compact Ansätze

Autores: C Feniou, M Hassan, D Traoré, E Giner, Y Maday, JP Piquemal
Publicado en: Commun.Phys. 6 (2023) 1, 192, Edición 6, 2023, Página(s) 192, ISSN 2399-3650
Editor: Nature Research publishing
DOI: 10.1038/s42005-023-01312-y

Targeting the Major Groove of the Palindromic d(GGCGCC)2 Sequence by Oligopeptide Derivatives of Anthraquinone Intercalators

Autores: Krystel El Hage; Giovanni Ribaudo; Louis Lagardère; Alberto Ongaro; Philippe H. Kahn; Luc Demange; Jean-Philip Piquemal; Giuseppe Zagotto; Nohad Gresh
Publicado en: "Journal of Chemical Information and Modeling, American Chemical Society, 2022, ⟨10.1021/acs.jcim.2c00337⟩", 2022
Editor: JCIM
DOI: 10.1021/acs.jcim.2c00337

On the Quantum Chemical Nature of Lead(II) “Lone Pair”

Autores: Christophe Gourlaouen; Jean-Philip Piquemal
Publicado en: "Molecules, MDPI, 2022, 27 (1), pp.27. ⟨10.3390/molecules27010027⟩", 2022
Editor: Molecules, 2022, 27(1), 27
DOI: 10.3390/molecules27010027

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

Autores: Ting Wang, Gabriel Stoltz, Petr Plechac
Publicado en: ESAIM: Mathematical Modelling and Numerical Analysis (ESAIM: M2AN), Edición Volume 55, 2021, 2021, Página(s) S593 - S623, ISSN 0000-0000
Editor: edp sciences
DOI: 10.1051/m2an/2020050

An overview of a posteriori error estimation and post-processingmethods for nonlinear eigenvalue problems G Dusson

Autores: G Dusson, Y Maday
Publicado en: Journal of Computational Physics, Edición Volume 491, 2023, Página(s) 112352, ISSN 0021-9991
Editor: Academic Press
DOI: 10.1016/j.jcp.2023.112352

Open source variational quantum eigensolver extension of the quantum learning machine for quantum chemistry

Autores: M Haidar, MJ Rančić, T Ayral, Y Maday, JP Piquemal
Publicado en: Wiley Interdisciplinary Reviews: Computational Molecular Science, Edición e1664, 2023, ISSN 1759-0876
Editor: John Wiley & Sons Inc.
DOI: 10.1002/wcms.1664

Photoionization and core resonances from range-separated density-functional theory: General formalism and example of the beryllium atom

Autores: Karno Schwinn; Felipe Zapata; Antoine Levitt; Éric Cancès; Eleonora Luppi; Julien Toulouse
Publicado en: J. Chem. Phys. 156, 224106, Edición 10897690, 2022, ISSN 1089-7690
Editor: AIP
DOI: 10.1063/5.0091073

Convergence analysis of adaptive DIIS algorithms with application to electronic ground state calculations

Autores: M. Chupin, M. S. Dupuy, G. Legendre, E. Séré
Publicado en: ESAIM: M2AN, Edición 28047214, 2021, Página(s) 2785-2825, ISSN 2804-7214
Editor: EDP Sciences
DOI: 10.1051/m2an/2021069

An Efficient Gaussian-Accelerated Molecular Dynamics (GaMD) Multilevel Enhanced Sampling Strategy: Application to Polarizable Force Fields Simulations of Large Biological Systems

Autores: Frédéric Célerse; Théo Jaffrelot Inizan; Louis Lagardère; Olivier Adjoua; Pierre Monmarché; Yinglong Miao; Etienne Derat; Jean-Philip Piquemal
Publicado en: Journal of Chemical Theory and Computation, American Chemical Society,, 2022, Página(s) 18 (2), pp.968-977
Editor: ACS Publishing
DOI: 10.1021/acs.jctc.1c01024

Martingale product estimators for sensitivity analysis in computational statistical physics Get access Arrow

Autores: P. Plechac, G. Stoltz, T. Wang
Publicado en: IMA Journal of Numerical Analysis, Edición drac073, 2022, ISSN 1464-3642
Editor: Oxford University Press
DOI: 10.1093/imanum/drac073

A New Way for Probing Bond Strength

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

A Coq Formalization of Lebesgue Integration of Nonnegative Functions

Autores: Sylvie Boldo; François Clément; François Clément; Florian Faissole; Vincent Martin; Micaela Mayero
Publicado en: "Journal of Automated Reasoning, Springer Verlag, In press, ⟨10.1007/s10817-021-09612-0⟩", 2022, Página(s) 66, 175–213
Editor: Journal of Automated Reasoning
DOI: 10.48550/arxiv.2104.05256

Parallel Memory-Independent Communication Bounds for SYRK

Autores: H. Al Daas, G. Ballard, L. Grigori, S. Kumar, K. Rouse
Publicado en: SPAA '23: Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, 2023, Página(s) Pages 391–401
Editor: ACM Digital Library
DOI: 10.1145/3558481.3591072

Quasi-stationary distribution for the Langevin process in cylindrical domains, part I: existence, uniqueness and long-time convergence

Autores: Tony Lelièvre, Mouad Ramil, Julien Reygner
Publicado en: Stochastic Processes and their Applications., 2022, Página(s) Volume 144, Pages 173-201
Editor: ScienceDirect
DOI: 10.1016/j.spa.2021.11.005

Block subsampled randomized Hadamard transform for low-rank approximation on distributed architectures

Autores: Oleg Balabanov, Matthias Beaupere, Laura Grigori, Victor Lederer
Publicado en: ICML'23: Proceedings of the 40th International Conference on Machine Learning, Edición Article No.: 66, 2023, Página(s) Pages 1564–1576
Editor: ICML'23: Proceedings of the 40th International Conference on Machine Learning
DOI: 10.48550/arxiv.2210.11295

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