Publications & Preprints for EMC2
Publications
HAL Link / Other link
- M. S. Dupuy. Variational projector-augmented wave method: a full-potential approach for electronic structure calculations in solid-state physics, Journal of Computational Physics, Vol. 442, 2021. Science Direct link
- M. Chupin, M. S. Dupuy, G. Legendre, E. Séré. Convergence analysis of adaptive DIIS algorithms with application to electronic ground state calculations, ESIAM:M2AN, Vol. 55, No. 6, 2021. EDP Sciences link
- L. B. Salem-Knapp, S. Boldo and W. Weens, Bounding the Round-Off Error of the Upwind Scheme for Advection, IEEE Transactions on Emerging Topics in Computing, Vol. 10, No. 3, pp. 1253-1262, 2022. IEEE Xplore link
- S. Boldo, G. Melquiond, Some Formal Tools for Computer Arithmetic: Flocq and Gappa, IEEE 28th Symposium on Computer Arithmetic (ARITH), pp. 111-114, 2021. IEEE Xplore link
- J. Demmel, L. Grigori, A. Rusciano. An improved analysis and unified perspective on deterministic and randomized low rank matrix approximations, SIAM Journal on Matrix Analysis and Applications, in press, 2022.
- O. Balabanov, L. Grigori. Randomized Gram-Schmidt process with application to GMRES, SIAM Journal on Scientific Computing Vol. 44, No. 3, pp. 1450-1474, in press, 2022.
- D. Frenkiel, L. Grigori and M. Beaupère. Higher-order QR with tournament pivoting for tensor compression, SIAM Journal on Matrix Analysis and Applications, in press, 2022.
- P. Monmarché, M. Ramil. Overdamped limit at stationarity for non-equilibrium Langevin diffusions, Electron. Commun. Probab.Vol. 27, 2022. Project Euclid link
- J. Dabaghi, Y. Maday, A. Zoia. A hybrid parareal Monte Carlo algorithm for parabolic problems, 2021. Journal of Computational and Applied Mathematics Vo. 420, . Science Direct link
- L. Garrigue. Building Kohn-Sham potentials for ground and excited states, Archive for Rational Mechanics and Analysis Vol. 245, pp. 949–1003. Springer link
- K. Schwinn, F. Zapata, A. Levitt, E. Cancès, E. Luppi and J. Toulouse. Mathematical foundations for the Parallel Replica algorithm applied to the underdamped Langevin dynamics . The Journal Chemical Physics Vol 156, 2022. AIP link
- T. Lelièvre, M. Ramil and J. Reygner. Mathematical foundations for the Parallel Replica algorithm applied to the underdamped Langevin dynamics . MRS Communications Vol. 12, pp. 454–459, 2022. Springer link
- T. Lelièvre, M. Ramil and J. Reygner. A probabilistic study of the kinetic Fokker-Planck equation in cylindrical domains. Journal of Evolution Equations Vol. 22, Article number: 38, 2022. Springer link
- T. Lelièvre, L. Maurin, P. Monmarché. The Adaptive Biasing Force algorithm with non-conservative forces and related topics. ESAIM: Mathematical Modelling and Numerical Analysis, Vol. 56, No 2, pp. 129-164, 2022. ESAIM Link
- T. Lelièvre, M. Ramil and J. Reygner. Quasi-stationary distribution for the Langevin process in cylindrical domains, part I: existence, uniqueness and long-time convergence. Stochastic Processes and their Applications. Vol. 144, pp. 173-201, 2022. Science direct link
- Z. Belkacemi, P. Gkeka, T. Lelièvre, G. Stoltz. Chasing Collective Variables using Autoencoders and biased trajectories. J. Chem. Theory Comput., Vol. 18, 1, pp. 59–78, 2022. ACS Publications
- E. Bernard, M. Fathi, A. Levitt and G. Stoltz. Hypocoercivity with Schur complements, Annales Henri Lebesgue, Vol 5, pp. 523-557, 2022. AHL link
- E. Camrud, D. P. Herzog, G. Stoltz, M. Gordina. Weighted L2-contractivity of Langevin dynamics with singular potentials. IOP Publising Vol. 35, No. 2, pp. 998-1035, 2022. IOP link
- R. Benda, E. Cancès, V. Ehrlacher, B. Stamm. Multi-center decomposition of molecular densities: a mathematical perspective . The Journal of Chemical Physics, 156(16), pp. 164107, 2022. AIP link
- A. Alfonsi, R. Coyaud, V. Ehrlacher. Constrained overdamped Langevin dynamics for symmetric multimarginal optimal transportation. Mathematical Models and Methods in Applied Sciences Vol. 32, No. 03, pp. 403-455, 2022. MAS link
- S. Boldo, F. Clément, F. Faissole, V. Martin and M. Mayero. A Coq Formalization of Lebesgue Integration of Nonnegative Functions. J Autom Reasoning Vol. 66, pp. 175–213, 2022. Springer link
- V. Ehrlacher, M. Fuente-Ruiz, D. Lombardi. SoTT: greedy approximation of a tensor as a sum of Tensor Trains. SIAM Journal on Scientific Computing Vol. 44, Iss. 210.1137/20M1381472, 2021. SIAM Publications link
- F. Legoll, T. Lelièvre, U. Sharma. An adaptive parareal algorithm: application to the simulation of molecular dynamics trajectories. SIAM Journal on Scientific Computing Vol. 44, Iss. 110.1137/21M1412979, 2021. SIAM link
- 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. Interfacial Water Many-body Effects Drive Structural Dynamics and Allosteric interactions in SARS-CoV-2 Main Protease Dimerization Interface. J. Phys. Chem. Lett. 12, 26, 6218–6226, 2021. ACS Publications
- N. Mauger, T. Plé, L. Lagardère, S. Bonella, E. Mangaud, J.-P. Piquemal, S. Huppert. Nuclear Quantum Effects in liquid water at near classical computational cost using the adaptive Quantum Thermal Bath. J. Phys. Chem. Lett., 12, 34, pp. 8285–8291, 2021. ACS Publications link
- D. Loco, L. Lagardère, O. Adjoua, J.-P. Piquemal. Atomistic Polarizable embeddings: energy, dynamics, spectroscopy and reactivity. Acc. Chem. Res. 54, 13, pp. 2812–2822, 2021. ACS Publications link
- R. A. Corrigan, G. Qi, T. Casavant, A. Thiel, J. Lynn, B. Walker, L. Lagardère, J.-P. Piquemal, J. W. Ponder, P. Ren, M. J. Schnieders. Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field. J. Chem. Theory Comput, Vol. 17, No. 4, pp. 2323–2341, 2021. ACS Publications link
- E. Cancès, C. Fermanian Kammerer, A. Levitt, S. Siraj-Dine. Coherent electronic transport in periodic crystals, Ann. Henri Poincaré Vol. 22, pp. 2643–2690, 2021. Springer link
- V. Ehrlacher, L. Grigori, D. Lombardi and Hao Song. Adaptative hierarchical subtensor partitioning for tensor compression, 2021. SIAM link
- R. A. Corrigan, G. Qi, T. Casavant, A. Thiel, J. Lynn, B. Walker, L. Lagardère, J-P. Piquemal, J. W. Ponder, P. Ren, M. J. Schnieders, J. Chem. Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field, 2021. ACS Publications link
- O. Adjoua, L. Lagardère, L-H. Jolly, Arnaud Durocher, Z. Wang, T. Very, I. Dupays, T. Jaffrelot Inizan, F. Célerse, P. Ren, J. Ponder, J-P. Piquemal. Tinker-HP: Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields Using GPUs and Multi-GPU Systems, 2021. ACS Publications link
- T. Jaffrelot Inizan, F. Célerse, O. Adjoua, D. El Ahdab, L-H. Jolly, C. Liu, P. Ren, M. Montes, N. Lagarde, L. Lagardère, P. Monmarché et J-P. Piquemal. High-Resolution Mining of SARS-CoV-2 Main Protease Conformational Space: Supercomputer-Driven Unsupervised Adaptive Sampling, 2021. Chemical Science link
- T. Wang, G. Stoltz, P. Plechac. Convergence of the likelihood ratio method for linear response of non-equilibrium stationary states, 2021. ESAIM link
- V. Ehrlacher, L. Grigori, D. Lombardi, H. Song. Adaptive hierarchical subtensor partitioning for tensor compression, 2021. SIAM link
- M. F. Herbst, A. Levitt. Black-box inhomogeneous preconditioning for self-consistent field iterations in density functional theory. Journal of Physics: Condensed Matter, 2020, Volume 33, Number 8. IOP Science link
- A. Durmus, A. Guillin, P. Monmarché. Geometric ergodicity of the bouncy particle sampler, 2020.
- M. Benaïm, Charles-E. Bréhier et P. Monmarché. Analysis of an Adaptive Biasing Force method based on self-interacting dynamics, 2020.
- E. Cancès, G. Kemlin, A. Levitt. Convergence analysis of direct minimization and self-consistent iterations. SIAM Jounal on Matrix Analysis and Applications Vol. 42, No. 1, 2021 , SIAM link
- R. Benda, G. Zucchi, E. Cancès, B. Lebental. Insights into the π – π interaction driven non-covalent functionalization of carbon nanotubes of various diameters by conjugated fluorene and carbazole copolymers. 2020, AIP link
- T. Lelièvre, G. Stoltz, W. Zhang. Multiple projection MCMC algorithms on submanifolds, IMA Journal of Numerical Analysis, drac006, 2020. IMA link
- E. Cancès, V. Ehrlacher, D. Gontier, A. Levitt, D. Lombardi. Numerical quadrature in the Brillouin zone for periodic Schrödinger operators. 2020, Springer link
- Dongarra, Laura Grigori, Nicholas J. Higham. Numerical algorithms for high-performance computational science. 2020, Royal Society link
- D. Loco, R. Spezia, F. Cartier, I. Chataignier, J.-P. Piquemal. Solvation Effects Drive the Selectivity in Diels-Alder Reaction Under Hyperbaric Conditions. 2020, RSC link
- G. Pavliotis, G. Stoltz, U. Vaes. Scaling limits for the generalized Langevin equation. Journal of Nonlinear Science, 31, no. 8. 2020, Springer link
- S. Nassem-Khan, N. Gresh, A. Misquitta, J.-P. Piquemal. An Assessment of SAPT and Supermolecular EDAs Approaches for the Development of Separable and Polarizable force fields. 2020, ACS Publications link
- M. F. Herbst, T. Fransson. Quantifying the error of the core-valence separation approximation. 2020, AIP publications link
- M. F. Herbst, A. Levitt, E. Cancès. A posteriori error estimation for the non-self consistent Kohn-Sham equations. 2020, RSC link
- E. Cancès, G. Dusson, Y. Maday, B. Stamm, M. Vohralík. Post-processing of the planewave approximation of Schrödinger equations. Part I: linear operators. IMA Journal of Numerical Analysis, Vol. 41, No. 4, pp. 2423–2455. 2020, Oxford Academic link
- R. Laplaza, F. Peccati, R. Boto, C. Quan, A. Carbone, J.-P. Piquemal, Y. Maday, J. Contreras-Garcia. NCIPLOT and the analysis of noncovalent interactions using the reduced density gradient. WIREs Computational Molecular Science, 2020, Wiley Online Library link.
- P. Monmarché, J. Weisman, L. Lagardère, J.-P. Piquemal. Velocity jump processes: an alternative to multi-time-step methods for faster and accurate molecular dynamics simulations. Journal of Chemical Physics, American Institute of Physics, 2020, arXiv link.
- P. El Darazi, L. El Khoury, K. El Hage, R. G. Maroun, Z. Hobaika, J.-P. Piquemal, N. Gresh. Quantum-Chemistry based design of halobenzene derivatives with augmented affinities for the HIV-1 viral G4/C16 base-pair. Frontiers in Chemistry, Frontiers Vol 8, pp. 440, 2020, arXiv link.
- R. Boto, F. Peccati, R. Laplaza, C. Quan, A. Carbone, J.-P. Piquemal, Y. Maday, J. Contreras-Garcia. NCIPLOT4: fast, robust and quantitative analysis of noncovalent interactions. Journal of Chemical Theory and Computation, American Chemical Society, 2020, ACS Publications link.
- D. Loco, R. Spezia, F. Cartier, I. Chataignier, J.-P. Piquemal. Solvation Effects Drive the Selectivity in Diels-Alder Reaction Under Hyperbaric Conditions. Chemical Communications, Royal Society of Chemistry, Vol 56, pp. 6632-6635, 2022 Royal Society of Chemistry link.
- E. Cancès, G. Dusson, Y. Maday, B. Stamm, M. Vohralík. Guaranteed a posteriori bounds for eigenvalues and eigenvectors: multiplicities and clusters. Mathematics of Computation, American Mathematical Society, In press, 2020.
- 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. Reconciling NMR Structures of the HIV-1 Nucleocapsid Protein (NCp7) using Extensive Polarizable Force Field Free-Energy Simulations. Journal of Chemical Theory and Computation, American Chemical Society, 2020, ACS Publications link.
- J. Klein, H. Khartabil, J.C. Boisson, J. Contreras-Garcia, J.-P. Piquemal, E. Henon. A New Way for Probing Bond Strength. Journal of Physical Chemistry A, American Chemical Society Vol. 124 (9), pp.1850-1860, 2020 ACS Publications link.
- P. P. Paolo, L. Lagardère, J.-P. Piquemal, F. Jensen. Molecular Dynamics using Non-variational Polarizable Force Fields: Theory, Periodic Boundary Conditions Implementation and Application to the Bond Capacity Model, 2019, ACS publications link
- C. Liu, J.-P. Piquemal, P. Ren. Implementation of Geometry Dependent Charge Flux into Polarizable AMOEBA+ Potential. Journal of Physical Chemistry Letters, American Chemical Society, 2019. ACS Publications link.
- J. Melcr, J.-P. Piquemal. Accurate biomolecular simulations account for electronic polarization. Frontiers in Molecular Biosciences, Frontiers Media, Vol. 6, pp.143, 2019. Frontiers In link.
- L. El-Khoury, K. El Hage, J.-P. Piquemal, S. Fermandjian, R. Maroun, N. Gresh, Z. Hobaika. Spectrometric and computational studies of the binding of HIV-1 integrase inhibitors to viral DNA extremities. PeerJ Physical Chemistry, PeerJ, Vol. 1, pp.e6, 2019. PeerJ link.
- L-H. Jolly, A. Duran, L. Lagardère, J. W. Ponder, P. Ren, J.-P. Piquemal. Raising the Performance of the Tinker-HP Molecular Modeling Package [Article v1.0]. Living Journal of Computational Molecular Science, University of Colorado Boulder, Vol. 1 (2), 2019 LiveCoMS link.
- Poier Pier Paolo, L. Lagardère, J.-P. Piquemal, F. Jensen. Molecular Dynamics using Non-variational Polarizable Force Fields: Theory, Periodic Boundary Conditions Implementation and Application to the Bond Capacity Model. Journal of Chemical Theory and Computation, American Chemical Society, 2019, ACS Publication link.
Preprints
- V. Ehrlacher, M. Fuente-Ruiz, D. Lombardi. CP-TT: using TT-SVD to greedily construct a Canonical Polyadic tensor approximation, 2021.
- V. Ehrlacher, T. Lelièvre and P. Monmarché. Adaptive force biasing algorithms: new convergence results and tensor approximations of the bias, 2021.
- M. Beaupère, L. Grigori. Communication avoiding low rank approximation based on QR with tournament pivoting, 2021.
- L. Grigori, S. Kumar. Parallel Tensor Train through Hierarchical Decomposition, 2021.