Extreme-scale Mathematically-based Computational Chemistry

Pubblicazioni

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

Autori: Laura Grigori, Sever Hirstoaga, Julien Salomon
Pubblicato in: Computers and Mathematics with Applications, Numero Volume 130, 2023, Pagina/e Pages 137-148, ISSN 1873-7668
Editore: 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

Autori: 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
Pubblicato in: Journal of Chemical Theory and Computation, Numero 17/4, 2021, Pagina/e 2034-2053, ISSN 1549-9618
Editore: 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

Autori: A. Anciaux-Sekadrian, M. Corral-Valero,T. Lelièvre, M. Moreaud, T. Pigeon, P. Raybaud, G. Stoltz
Pubblicato in: Journal of Chemical Theory and Computation, Numero 19(12), 2023, Pagina/e 3538–3550, ISSN 1549-9618
Editore: American Chemical Society
DOI: 10.1021/acs.jctc.3c00280

On basis set optimisation in quantum chemistry

Autori: E Cancès, G Dusson, G Kemlin, L Vidal
Pubblicato in: ESAIM: Proceedings and Surveys 73, Numero irregular, 2023, Pagina/e 07-129, ISSN 2267-3059
Editore: EDP Sciences
DOI: 10.1051/proc/202373107

Multiple projection MCMC algorithms on submanifolds

Autori: Lelièvre, Tony; Stoltz, Gabriel; Zhang, Wei
Pubblicato in: IMA Journal of Numerical Analysis, drac006, 2022
Editore: IMA Journal of Numerical Analysis, drac006
DOI: 10.48550/arxiv.2003.09402

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

Autori: Michael F. Herbst; Antoine Levitt
Pubblicato in: Journal of Computational Physics, Numero 00219991, 2022, Pagina/e Volume 459, ISSN 0021-9991
Editore: Academic Press
DOI: 10.48550/arxiv.2109.14018

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

Autori: E. Cancès, G. Dusson, Y. Maday, B. Stamm, M. Vohralík.
Pubblicato in: IMA Journal of Numerical Analysis, 2020, ISSN 0000-0000
Editore: 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.

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

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

Autori: P. P. Poier, L. Lagardère, J.-P. Piquemal
Pubblicato in: Phys. Chem. Lett, Numero 14, 6, 2023, Pagina/e 1609–1617, ISSN 1948-7185
Editore: American Chemical Society
DOI: 10.1021/acs.jpclett.2c03722

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

Autori: Tony Lelièvre; Mouad Ramil; Julien Reygner
Pubblicato in: Journal of Evolution Equations, 2022, Pagina/e volume 22, Article number: 38
Editore: 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

Autori: Z. Belkacemi, M. Bianciotto, P. Gkeka, T. Lelièvre, H. Minoux, G. Stoltz,
Pubblicato in: The Journal of Chemical Physics, Numero 159, 2023, Pagina/e 024122, ISSN 1089-7690
Editore: AIP Publishing
DOI: 10.48550/arxiv.2306.02935

Extending the regime of linear response with synthetic forcings

Autori: R. Spacek, G. Stoltz
Pubblicato in: Multiscale Modeling and Simulation 21 (4), 1602-1643 1 2023, Numero Quarterly, 2023, Pagina/e 602-1643, ISSN 1540-3459
Editore: Society for Industrial and Applied Mathematics
DOI: 10.1137/23m1557611

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

Autori: 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
Pubblicato in: Chem. Sc., Numero 13, 2022, Pagina/e 3674-3687, ISSN 2041-6539
Editore: The Royal Society of Chemistry’s
DOI: 10.1039/d1sc05892d

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

Autori: E. Cancès, M. Herbst, G. Kemlin, A. Levitt, B. Stamm
Pubblicato in: Letters in Mathematical Physics, Numero 113, article number 21, 2023, Pagina/e 1–32., ISSN 1573-0530
Editore: Springer
DOI: 10.1007/s11005-023-01645-3

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

Autori: Michael F. Herbst, Antoine Levitt, Eric Cancès
Pubblicato in: JuliaCon Proceedings, Numero 3, 69, 2021, ISSN 2642-4029
Editore: Cambridge MA: JuliaCon
DOI: 10.21105/jcon.00069

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

Autori: Tony Lelièvre, Lise Maurin, Pierre Monmarché
Pubblicato in: ESAIM: M2AN 56 (, 2022, Pagina/e 529–564
Editore: ESAIM: M2AN
DOI: 10.48550/arxiv.2102.09957

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

Autori: L.-H. Jolly, A. Duran, L. Lagardère, J. W. Ponder, P. Ren, J.-P. Piquemal.
Pubblicato in: Living Journal of Computational Molecular Science, University of Colorado Boulder, 2019, ISSN 0000-0000
Editore: 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

Autori: T. Lelièvre, G. Robin, I. Sekkat, G. Stoltz, G. Victorino Cardoso
Pubblicato in: ESAIM: PROCEEDINGS AND SURVEYS, Numero Vol. 73, p. 238-256, 2023, Pagina/e p. 238-256, ISSN 2267-3059
Editore: EDP Sciences
DOI: 10.48550/arxiv.2205.02818

Weighted L2-contractivity of Langevin dynamics with singular potentials

Autori: E. Camrud, D. P. Herzog, G. Stoltz, M. Gordina,
Pubblicato in: Nonlinearity, 2022, Pagina/e 35, 998
Editore: IOP Publishing
DOI: 10.48550/arxiv.2104.10574

Convergence analysis of direct minimization and self-consistent iterations

Autori: Eric Cancès, Gaspard Kemlin, Antoine Levitt
Pubblicato in: SIAM Journal on Matrix Analysis and Applications, Numero Volume 42, Numero 1, 2020, Pagina/e 243–274. (32 pages), ISSN 0895-4798
Editore: Society for Industrial and Applied Mathematics
DOI: 10.1137/20m1332864

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

Autori: P. P. Poier, L. Lagardère, J.-P. Piquemal
Pubblicato in: J. Chem. Phys., Numero 159, 154109, 2023, ISSN 1089-7690
Editore: AIP Publishing
DOI: 10.1063/5.0166476

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

Autori: 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
Pubblicato in: WIREs Computational Molecular Science, 2021, Pagina/e Volume11, Numero6
Editore: WIREs Computational Molecular Science
DOI: 10.1002/wcms.1528

Overdamped limit at stationarity for non-equilibrium Langevin diffusions

Autori: Pierre Monmarché, Mouad Ramil
Pubblicato in: Electron. Commun, 2022
Editore: Project Euclid
DOI: 10.1214/22-ecp447

Building Kohn-Sham potentials for ground and excited states

Autori: Louis Garrigue
Pubblicato in: Archive for Rational Mechanics and Analysis volume 245, pages949–1003 (2022), 2022, Pagina/e volume 245, pages949–1003 (2022)
Editore: Springer
DOI: 10.48550/arxiv.2101.01127

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

Autori: I. Chollet, L. Lagardère, J.-P. Piquemal
Pubblicato in: J. Chem. Theory. Comput., Numero 19, 10, 2023, Pagina/e 2887–2905, ISSN 1549-9618
Editore: American Chemical Society
DOI: 10.1021/acs.jctc.3c00015

Coherent Electronic Transport in Periodic Crystals

Autori: Eric Cancès; Clotilde Fermanian Kammerer; Antoine Levitt; Sami Siraj-Dine
Pubblicato in: Annales Henri Poincaré volume 22, 2021, Pagina/e pages 2643–2690
Editore: Springer
DOI: 10.1007/s00023-021-01026-3

Nonlinear compressive reduced basis approximation for PDE's A

Autori: A Cohen, C Farhat, A Somacal, Y Maday
Pubblicato in: Comptes Rendus Mécanique, 2023, Pagina/e pp. 1-18, ISSN 1873-7234
Editore: 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.

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

Accurate biomolecular simulations account for electronic polarization.

Autori: J. Melcr, J.-P. Piquemal
Pubblicato in: Frontiers in Molecular Biosciences, Frontiers Media, 2019, 6, pp.143., 2019, ISSN 0000-0000
Editore: Frontiers in Molecular Biosciences
DOI: 10.3389/fmolb.2019.00143

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

Autori: R. Boto, F. Peccati, R. Laplaza, C. Quan, A. Carbone, J.-P. Piquemal, Y. Maday, J. Contreras-Garcia
Pubblicato in: Journal of Chemical Theory and Computation, American Chemical Society, Numero 00000000, 2020, ISSN 0000-0000
Editore: 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

Autori: Eric Cancès, Geneviève Dusson, Gaspard Kemlin , Antoine Levitt
Pubblicato in: SIAM Journal on Scientific Computing, Numero Vol. 44, Iss. 5, 2022, ISSN 1064-8275
Editore: Society for Industrial and Applied Mathematics
DOI: 10.1137/21m1456224

Hypocoercivity with Schur complements

Autori: Bernard, Etienne; Fathi, Max; Levitt, Antoine; Stoltz, Gabriel
Pubblicato in: Annales Henri Lebesgue, 2022, Pagina/e Annales Henri Lebesgue, Volume 5 (2022), pp. 523-557
Editore: Annales Henri Lebesgue
DOI: 10.48550/arxiv.2003.00726

Numerical algorithms for high-performance computational science

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

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

Autori: E. Cancès, G. Dusson, Y. Maday, B. Stamm, M. Vohralík
Pubblicato in: Mathematics of Computation, 2020, ISSN 0025-5718
Editore: 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

Autori: M Hassan, Y Maday, Y Wang
Pubblicato in: ESAIM: M2AN, Numero 57, 2023, Pagina/e 545–583, ISSN 2804-7214
Editore: Springer link
DOI: 10.1051/m2an/2022099

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

Autori: Éric Cancès; Louis Garrigue; David Gontier
Pubblicato in: PHYSICAL REVIEW B, Numero 11, Phys. Rev. B 107, Numero 15,, 2023, Pagina/e 155403, ISSN 2469-9969
Editore: American Physical Society (APS)
DOI: 10.1103/physrevb.107.155403

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

Autori: Ehrlacher, Virginie; Fuente-Ruiz, Maria; Lombardi, Damiano
Pubblicato in: Molecules, 2022
Editore: Molecules
DOI: 10.48550/arxiv.2011.09725

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

Autori: Virginie Ehrlacher; Maria Fuente Ruiz; Damiano Lombardi
Pubblicato in: SIAM Journal on Scientific Computing, Society for Industrial and Applied Mathematics, In press, 2021, Pagina/e Vol. 44, Iss. 210.1137/20M1381472
Editore: SIAM
DOI: 10.1137/20m1381472

On basis set optimization in quantum chemistry

Autori: E. Cancès, G. Dusson, G. Kemlin, L. Vidal
Pubblicato in: ESAIM: Proceedings and Surveys, Numero Vol. 73, 2023, Pagina/e 107-129, ISSN 2267-3059
Editore: 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

Autori: S. Naseem Kahn, L. Lagardère, C. Narth, G. A. Cisneros, P. Ren, N. Gresh, J.-P. Piquemal,
Pubblicato in: J. Chem. Theory Comput, Numero 18, 6, 2022, Pagina/e 3607–3621, ISSN 1549-9618
Editore: American Chemical Society
DOI: 10.1021/acs.jctc.2c00029

Convergence of the kinetic annealing for general potentials

Autori: L. Journel, P. Monmarché
Pubblicato in: Electron. J. Probab, Numero vol. 27article no. 159, 2022, Pagina/e pp. 1–37, ISSN 1083-6489
Editore: Institute of Mathematical Statistics
DOI: 10.1214/22-ejp891

Extension of the trotterized unitary coupled cluster to triple excitations

Autori: M Haidar, MJ Rancic, Y Maday, JP Piquemal
Pubblicato in: The Journal of Physical Chemistry, Numero A 127 (15), 2023, Pagina/e 3543-3550, ISSN 1089-7690
Editore: AIP Publishing
DOI: 10.1021/acs.jpca.3c01753

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

Autori: M. F. Herbst, A. Levitt, E. Cancès.
Pubblicato in: Faraday Discussions, 2020, ISSN 0000-0000
Editore: Faraday Discussions
DOI: 10.1039/d0fd00048e

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

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

Numerical quadrature in the Brillouin zone for periodic Schrödinger operators

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

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

Autori: Tony Lelièvre, Gabriel Stoltz, Wei Zhang.
Pubblicato in: Chemical Communications. Numero 49, 2020, ISSN 0000-0000
Editore: Chemical Communications
DOI: 10.1039/d0cc01938k

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

Autori: Inass Sekkat, Gabriel Stoltz
Pubblicato in: Journal of Machine Learning Research 24, Numero 8 times annually, 2023, Pagina/e 1-58, ISSN 2642-4029
Editore: Microtome Publishing
DOI: 10.48550/arxiv.2105.10347

Implementation of Geometry Dependent Charge Flux into Polarizable AMOEBA+ Potential

Autori: C. Liu, J.-P. Piquemal, P. Ren.
Pubblicato in: Journal of Physical Chemistry Letters, American Chemical Society, 2019, ISSN 0000-0000
Editore: ACS Publications
DOI: 10.1021/acs.jpclett.9b03489

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

Autori: Michael F. Herbst; Antoine Levitt
Pubblicato in: Journal of Physics: Condensed Matter, Numero 1361648X, 2020, ISSN 1361-648X
Editore: IOP SCIENCE
DOI: 10.1088/1361-648x/abcbdb

Scaling limits for the generalized Langevin equation

Autori: G. Pavliotis, G. Stoltz, U. Vaes
Pubblicato in: Springer Link, Numero 00000000, 2020, ISSN 0000-0000
Editore: Springer Link
DOI: 10.1007/s00332-020-09671-4

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

Autori: Pier Paolo Poier; Théo Jaffrelot Inizan; Olivier Adjoua; Louis Lagardère; Jean-Philip Piquemal
Pubblicato in: Journal of Physical Chemistry Letters, American Chemical Society,, 2022, Pagina/e pp.4381-4388
Editore: 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

Autori: S. Naseem-Khan,J.-P. Piquemal, G. A. Cisneros
Pubblicato in: J. Chem. Phys., Numero 155, 194103, 2021, ISSN 1089-7690
Editore: AIP Publishing
DOI: 10.1063/5.0072380

Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field

Autori: 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
Pubblicato in: Journal of Chemical Theory and Computation, Numero 17/4, 2021, Pagina/e 2323-2341, ISSN 1549-9618
Editore: American Chemical Society
DOI: 10.1021/acs.jctc.0c01286

Adaptive Hierarchical Subtensor Partitioning for Tensor Compression

Autori: Virginie Ehrlacher, Laura Grigori, Damiano Lombardi, Hao Song
Pubblicato in: SIAM Journal on Scientific Computing, Numero 43/1, 2021, Pagina/e A139-A163, ISSN 1064-8275
Editore: Society for Industrial and Applied Mathematics
DOI: 10.1137/19m128689x

Ab initio canonical sampling based on variational inference

Autori: A. Castellano, F. Bottin, J. Bouchet, A. Levitt, G. Stoltz
Pubblicato in: Physical Review B, Numero 106, 2022, Pagina/e L161110, ISSN 2469-9969
Editore: 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

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

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

Autori: T. Lelièvre, M. Ramil and J. Reygner
Pubblicato in: MRS Communications, 2022, Pagina/e Vol. 12, pp. 454–459
Editore: Springer
DOI: 10.1557/s43579-022-00207-3

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

Autori: E. Cancès, L. Garrigue, D. Gontier
Pubblicato in: SIAM Journal on Mathematicla Analysis, Numero Vol. 55, Iss. 3, 2023, ISSN 1095-7154
Editore: Society for Industrial and Applied Mathematics Publications
DOI: 10.1137/22m1478446

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

Autori: Jad Dabaghi, Virginie Ehrlacher, Christoph Strössner
Pubblicato in: Journal of Computational Physics, Numero Volume 480, 2023, Pagina/e 112017, ISSN 0021-9991
Editore: Academic Press
DOI: 10.1016/j.jcp.2023.112017

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

Autori: E. Cancès, R. Coyaud, L.R. Scott
Pubblicato in: Communications Mathematical Sciences, Numero 21, 2023, Pagina/e 915–948, ISSN 1945-0796
Editore: International Press
DOI: 10.48550/arxiv.2007.04227

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

Autori: Virginie Ehrlacher, Tony Lelièvre, Pierre Monmarché
Pubblicato in: The Annals of Applied Probability, Numero 32(5), 2022, Pagina/e 3850-3888, ISSN 2168-8737
Editore: 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

Autori: J. Toulouse, K. Schwinn, F. Zapata, A. Levitt, E. Cancès and E. Luppi
Pubblicato in: J. Chem. Phys., Numero Volume 157, Numero 24 (244104), 2022, ISSN 1089-7690
Editore: AIP Publising
DOI: 10.1063/5.0134645

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

Autori: M. S. Dupuy
Pubblicato in: Journal of Computational Physics, Numero 00000000, 2021, ISSN 0000-0000
Editore: ScienceDirect
DOI: 10.1016/j.jcp.2021.110510

A parareal Monte Carlo algorithm for parabolic problems hybrid

Autori: J Dabaghi, Y Maday, A Zoia
Pubblicato in: Journal of Computational and Applied Mathematics 420, 114800, Numero 420, 2023, Pagina/e 114800, ISSN 0377-0427
Editore: Elsevier BV
DOI: 10.1016/j.cam.2022.114800

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

Autori: D. Loco, I. Chataignier, J.-P. Piquemal, R. Spezia
Pubblicato in: Chem. Phys. Chem., Numero Volume23, Numero18, e202200349, 2022, ISSN 1439-7641
Editore: Chemistry Europe
DOI: 10.1002/cphc.202200349

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

Autori: 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
Pubblicato in: J. Chem. Science Chem. Sci., 2021,12,, Numero 20416539, 2021, Pagina/e 4889-4907, ISSN 2041-6539
Editore: Publishing
DOI: 10.26434/chemrxiv.13003166.v2

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

Autori: 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
Pubblicato in: Physical Chemistry Chemical Physics, Numero Numero 47 Phys. Chem. Chem. Phys., 2022, 24 (47), 2022, Pagina/e 28700-28781, ISSN 1463-9076
Editore: Royal Society of Chemistry
DOI: 10.1039/d2cp02827a

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

Autori: T. Hoang Ngoc Minh, G. Stoltz, B. Rotenberg
Pubblicato in: The Journal of Chemical Physics, Numero Vol. 158, Numero 10, 2023, Pagina/e 4103, ISSN 1089-7690
Editore: AIP Publishing
DOI: 10.1063/5.0139258

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

Autori: Trinidad Novoa; Rubén Laplaza; Francesca Peccati; Franck Fuster; Julia Contreras-García
Pubblicato in: Journal of Chemical Information and Modeling, Numero 4, 2023, ISSN 1549-9596
Editore: 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.

Autori: P. Monmarché, J. Weisman, L. Lagardère, J.-P. Piquemal.
Pubblicato in: AIP The Journal of Chemical Physics, 2020, ISSN 0000-0000
Editore: AIP The Journal of Chemical Physics
DOI: 10.1063/5.0005060

Directed message passing based on attention for prediction of molecular properties

Autori: G Chen, Y Maday
Pubblicato in: Computational Materials Science, Numero Volume 229, 2023, Pagina/e 112443, ISSN 0927-0256
Editore: 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

Autori: 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
Pubblicato in: The Journal of Physical Chemistry Letters, 2021, Pagina/e 12, 26, 6218–6226, ISSN 1948-7185
Editore: American Chemical Society
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Mobility Estimation for Langevin Dynamics Using Control Variates

Autori: G. A. Pavliotis, G. Stoltz, U. Vaes,
Pubblicato in: Mutiscale Modeling & Simulation, Numero Vol. 21 Numero 2, 2023, Pagina/e 680-715, ISSN 1540-3467
Editore: Society for Industrial and Applied Mathematics
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Analysis of an Adaptive Biasing Force method based on self-interacting dynamics

Autori: Michel Benaïm, Charles-Edouard Bréhier, Pierre Monmarché
Pubblicato in: Electronic Journal of Probability, Numero Vol.25 • 2020, 2020, ISSN 0000-0000
Editore: 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.

Autori: P. El Darazi, L. El Khoury, K. El Hage, R. Maroun, Z. Hobaika, J.-P. Piquemal, N. Gresh.
Pubblicato in: Theoretical and Computational Chemistry, 2019, ISSN 0000-0000
Editore: Theoretical and Computational Chemistry
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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

Autori: O. Gorynina, F. Legoll, T. Lelièvre, D. Perez
Pubblicato in: Comptes Rendus Mécanique, 2023, Pagina/e pp. 1-25, ISSN 1873-7234
Editore: Académie des sciences_ Institut de France
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Quantifying the error of the core-valence separation approximation.

Autori: M. F. Herbst, T. Fransson.
Pubblicato in: The Journal of Chemical Physics, Numero Volume 153, Numero 5 > 10.1063/5.0013538, 2020, ISSN 0000-0000
Editore: The Journal of Chemical Physics
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Chasing Collective Variables Using Autoencoders and Biased Trajectories

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

Autori: Alfonsi, Aur��lien; Coyaud, Rafa��l; Ehrlacher, Virginie
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Reconciling NMR Structures of the HIV-1 Nucleocapsid Protein (NCp7) using Extensive Polarizable Force Field Free-Energy Simulations.

Autori: 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.
Pubblicato in: Journal of Chemical Theory and Computation, 2020, ISSN 0000-0000
Editore: Journal of Chemical Theory and Computation
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Some Formal Tools for Computer Arithmetic: Flocq and Gappa

Autori: S. Boldo, G. Melquiond
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Editore: IEEE 28th Symposium on Computer Arithmetic (ARITH)
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Improving Condensed Phase Water Dynamics with Explicit Nuclear Quantum Effects: the Polarizable Q-AMOEBA Force Field

Autori: N. Mauger, T. Plé, L. Lagardère, S. Huppert, J.-P. Piquemal, J.
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Editore: Chemistry Europe
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Scalable Hybrid Deep Neural Networks/Polarizable Potentials Biomolecular Simulations including long-range effects

Autori: T. Jaffrelot Inizan, T. Plé, O. Adjoua, P. Ren, H. Gökcan, O. Isayev, L. Lagardère, J.-P. Piquemal
Pubblicato in: Chem. Sci., Numero 14, 2023, Pagina/e 5438-5452, ISSN 2041-6539
Editore: The Royal Society of Chemistry’s
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Geometric ergodicity of the Bouncy Particle Sampler

Autori: Alain Durmus, Arnaud Guillin, Pierre Monmarché
Pubblicato in: The Annals of Applied Probability, Numero 30/5, 2020, ISSN 1050-5164
Editore: Institute of Mathematical Statistics
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Factorized structure of the long-range two-electron integrals tensor and its application in quantum chemistry

Autori: S. Badreddine, I. Chollet, L. Grigori
Pubblicato in: Journal of Computational Physics, Numero Vol. 493, 112460, 2023, ISSN 0021-9991
Editore: 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

Autori: Robert Benda, Gaël Zucchi, Eric Cancès, Bérengère Lebental
Pubblicato in: AIP The Journal of Chemical Physics, Numero Volume 152, Numero 6 > 10.1063/1.5133634, 2020, ISSN 0000-0000
Editore: AIP The Journal of Chemical Physics
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Bounding the Round-Off Error of the Upwind Scheme for Advection

Autori: L. B. Salem-Knapp, S. Boldo, W. Weens
Pubblicato in: IEEE Transactions on Emerging Topics in Computing, 2022, Pagina/e vol. 10, no. 3, pp. 1253-1262
Editore: 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

Autori: L. El-Khoury, K. El Hage, J.-P. Piquemal, S. Fermandjian, R. Maroun, N. Gresh, Z. Hobaika.
Pubblicato in: PeerJ Physical Chemistry, PeerJ, 2019, 1, pp.e6., 2019, ISSN 0000-0000
Editore: PeerJ Physical Chemistry
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Multi-center decomposition of molecular densities: a mathematical perspective

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

Autori: T. Plé, L. Lagardère, J.-P. Piquemal
Pubblicato in: Chem. Sci., 2023, ISSN 2041-6539
Editore: The Royal Society of Chemistry’s
DOI: 10.1039/d3sc02581k

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

Autori: R. Laplaza, F. Peccati, R. Boto, C. Quan, A. Carbone, J.-P. Piquemal, Y. Maday, J. Contreras-Garcia
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Editore: WIREs Computational Molecular Science
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Development of the Quantum Inspired SIBFA Many-Body Polarizable Force Field: Enabling Condensed Phase Molecular Dynamics Simulations

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

Autori: Pier Paolo Poir; Louis Lagardère; Jean-Philip Piquemal
Pubblicato in: Journal of Chemical Theory and Computation, American Chemical Society,, 2022, Pagina/e 8 (3), pp.1633-1645
Editore: ACS Publishing
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Efficient Extraction of Resonant States in Systems with Defects

Autori: Ivan Duchemin; Luigi Genovese; Eloïse Letournel; Antoine Levitt; Simon Ruget
Pubblicato in: Journal of Computational Physics, Volume 477, 15 March 2023, 111928, Numero 13, 2023, ISSN 0021-9991
Editore: Academic Press
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High-resolution mining of the SARS-CoV-2 main protease conformational space: supercomputer-driven unsupervised adaptive sampling

Autori: 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
Pubblicato in: Chemical Science, Numero 12/13, 2021, Pagina/e 4889-4907, ISSN 2041-6520
Editore: Royal Society of Chemistry
DOI: 10.1039/d1sc00145k

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

Autori: Tony Lelièvre, Lise Maurin, Pierre Monmarché
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Editore: ESAIM: M2AN
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Van der Waals interactions between two hydrogen atoms: The next orders

Autori: Cancès, Éric; Coyaud, Rafaël; Scott, L. Ridgway
Pubblicato in: Comm. Math. Sci. Vol. 21, No. 4, Numero 11, 2023, Pagina/e 915–948, ISSN 1945-0796
Editore: International Press of Boston
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Routine Molecular Dynamics Simulations Including Nuclear Quantum Effects: from Force Fields to Machine Learning Potentials

Autori: Plé, Thomas; Mauger, Nastasia; Adjoua, Olivier; Jaffrelot-Inizan, Théo; Lagardère, Louis; Huppert, Simon; Piquemal, Jean-Philip
Pubblicato in: J. Chem. Theory. Comput., Numero 11, 2023, Pagina/e 1432–1445, ISSN 1549-9618
Editore: American Chemical Society
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Overlap-ADAPT-VQE: Practical Quantum Chemistry on Quantum Computers via Overlap-Guided Compact Ansätze

Autori: C Feniou, M Hassan, D Traoré, E Giner, Y Maday, JP Piquemal
Pubblicato in: Commun.Phys. 6 (2023) 1, 192, Numero 6, 2023, Pagina/e 192, ISSN 2399-3650
Editore: Nature Research publishing
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Targeting the Major Groove of the Palindromic d(GGCGCC)2 Sequence by Oligopeptide Derivatives of Anthraquinone Intercalators

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

Autori: Christophe Gourlaouen; Jean-Philip Piquemal
Pubblicato in: "Molecules, MDPI, 2022, 27 (1), pp.27. ⟨10.3390/molecules27010027⟩", 2022
Editore: Molecules, 2022, 27(1), 27
DOI: 10.3390/molecules27010027

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

Autori: Ting Wang, Gabriel Stoltz, Petr Plechac
Pubblicato in: ESAIM: Mathematical Modelling and Numerical Analysis (ESAIM: M2AN), Numero Volume 55, 2021, 2021, Pagina/e S593 - S623, ISSN 0000-0000
Editore: edp sciences
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An overview of a posteriori error estimation and post-processingmethods for nonlinear eigenvalue problems G Dusson

Autori: G Dusson, Y Maday
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Editore: Academic Press
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Open source variational quantum eigensolver extension of the quantum learning machine for quantum chemistry

Autori: M Haidar, MJ Rančić, T Ayral, Y Maday, JP Piquemal
Pubblicato in: Wiley Interdisciplinary Reviews: Computational Molecular Science, Numero e1664, 2023, ISSN 1759-0876
Editore: John Wiley & Sons Inc.
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Photoionization and core resonances from range-separated density-functional theory: General formalism and example of the beryllium atom

Autori: Karno Schwinn; Felipe Zapata; Antoine Levitt; Éric Cancès; Eleonora Luppi; Julien Toulouse
Pubblicato in: J. Chem. Phys. 156, 224106, Numero 10897690, 2022, ISSN 1089-7690
Editore: AIP
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Convergence analysis of adaptive DIIS algorithms with application to electronic ground state calculations

Autori: M. Chupin, M. S. Dupuy, G. Legendre, E. Séré
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Editore: EDP Sciences
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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

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

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

Autori: P. Plechac, G. Stoltz, T. Wang
Pubblicato in: IMA Journal of Numerical Analysis, Numero drac073, 2022, ISSN 1464-3642
Editore: Oxford University Press
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A New Way for Probing Bond Strength

Autori: J. Klein, H. Khartabil, J.C. Boisson, J. Contreras-Garcia, J.-P. Piquemal, E. Henon.
Pubblicato in: Journal of Physical Chemistry A, American Chemical Society, Numero 124 (9), pp.1850-1860, 2020, ISSN 0000-0000
Editore: Journal of Physical Chemistry A, American Chemical Society
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A Coq Formalization of Lebesgue Integration of Nonnegative Functions

Autori: Sylvie Boldo; François Clément; François Clément; Florian Faissole; Vincent Martin; Micaela Mayero
Pubblicato in: "Journal of Automated Reasoning, Springer Verlag, In press, ⟨10.1007/s10817-021-09612-0⟩", 2022, Pagina/e 66, 175–213
Editore: Journal of Automated Reasoning
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Parallel Memory-Independent Communication Bounds for SYRK

Autori: H. Al Daas, G. Ballard, L. Grigori, S. Kumar, K. Rouse
Pubblicato in: SPAA '23: Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, 2023, Pagina/e Pages 391–401
Editore: ACM Digital Library
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Quasi-stationary distribution for the Langevin process in cylindrical domains, part I: existence, uniqueness and long-time convergence

Autori: Tony Lelièvre, Mouad Ramil, Julien Reygner
Pubblicato in: Stochastic Processes and their Applications., 2022, Pagina/e Volume 144, Pages 173-201
Editore: ScienceDirect
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Block subsampled randomized Hadamard transform for low-rank approximation on distributed architectures

Autori: Oleg Balabanov, Matthias Beaupere, Laura Grigori, Victor Lederer
Pubblicato in: ICML'23: Proceedings of the 40th International Conference on Machine Learning, Numero Article No.: 66, 2023, Pagina/e Pages 1564–1576
Editore: ICML'23: Proceedings of the 40th International Conference on Machine Learning
DOI: 10.48550/arxiv.2210.11295

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