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.
M. Herbst, A. Levitt, A robust and efficient line search for self-consistent field iterations,Journal of Computational Physics Vol. 459, No. 15, 2022. Science Direct link
M.-S. Dupuy, A. Levitt, Finite-size effects in response functions of molecular systems, SMAI Journal of Computational Mathematics, in press, 2022.
I. Duchemin, L. Genovese, E. Letournel, A. Levitt, S. Ruget, Efficient extraction of resonant states in systems with defects, Journal of Computational Physics, in press, 2022.
D. Loco, J.-P. Piquemal, Polarizable Multiscale Dynamics for probing solvent and complex environments, Photochemistry, Vol. 50, pp. 382–398, in press (publication 2022/12/09). RSC link
K. El Hage, G. Ribaudo , L. Lagardère, A. Ongaro, P. H. Kahn, L. Demange, J.-P. Piquemal, G. Zagotto, N. Gresh. Targeting the Major Groove of the Palindromic d(GGCGCC)2 Sequence by Oligopeptide Derivatives of Anthraquinone Intercalators, J. Chem. Inf. Model., 2022. ACD Publishing link
S. Naseem Kahn, L. Lagardère, C. Narth, G. A. Cisneros, P. Ren, N. Gresh, J.-P. Piquemal. Development of the Quantum Inspired SIBFA Many-Body Polarizable ForceField: I. Enabling Condensed Phase Molecular Dynamics Simulations, Chem. Theory Comput. Vol. 18, No. 6, pp. 3607–3621, 2022. ACS Publishing
P. P. Poier, T. Jaffrelot Inizan, O. Adjoua, L. Lagardère, J.-P. Piquemal. Accurate Deep Learning-aided Density-free Strategy for Many-Body Dispersion-corrected Density Functional Theory, J. Phys. Chem. Lett., Vol. 13, No. 19, pp. 4381–4388, 2022. ACS Publishing link
P. Poier, L. Lagardère, J.-P. Piquemal. O(N) Stochastic Evaluation of Many-Body van der Waals Energies in Large Complex Systems, Theory Comput., Vol. 8, No. 3, pp.1633–1645, 2022. ACS Publishing link
F. Célerse, T. Jaffrelot Inizan, L. Lagardère, O. Adjoua, P. Monmarché, Y. Miao, E. Derat, J.-P. Piquemal. An Efficient Gaussian-Accelerated Molecular Dynamics (GaMD) Multilevel Enhanced Sampling Strategy: Application to Polarizable Force Fields Simulations of Large Biological Systems, J. Chem. Theory Comput. Vol. 18, No. 2, pp. 968–977, 2022. ACS Publishing link
C. Gourlaouen, J.-P. Piquemal. On the Quantum Chemical Nature of Lead(II) “Lone Pair”, Molecules Vol. 27, No.1 , 2022. NCBI link
E. Cancès, G. Dusson, G. Kemlin and A. Levitt. Practical error bounds for properties in plane-wave electronic structure calculations, accepted in SIAM Journal on Scientific Computing Vol.44, No. 5, 2022. SIAM link
K. Schwinn, F. Zapata, A. Levitt, E. Cancès, E. Luppi and J. Toulouse. Photoionization and core resonances from range-separated density-functional theory: General formalism and example of the beryllium atom , J. Chem. Phys. Vol. 156, 224106, 2022. AIP Publishing link
T. Lelièvre, L. Maurin, P. Monmarché. The Adaptive Biasing Force algorithm with non-conservative forces and related topics , ESAIM: M2AN, Vol. 56, No. 2, pp. 529 – 564, 2022. ESAIM link
F. Célerse, T. Jaffrelot Inizan, L. Lagardère, O. Adjoua, P. Monmarché, Y. Miao, E. Derat, J.-P. Piquemal. An Efficient GaMD Multi-Level Enhanced Sampling Strategy: Application to Polarizable Force Fields Simulations of Large Biological Systems, J. Chem. Theory Comput. Vol. 18, No. 2, pp. 968–977, 2022. ACS Publications link
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, in press (publication 2023/03/01). 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
D. R. Rehn, Z. Rinkevicius, M. F. Herbst and others. Gator: a Python-driven program for spectroscopy simulations using correlated wave functions, WIREs Vol. 11, No. 6, pp. WIREs link, 2021.
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

R. Benda, G. Zucchi, E. Cancès, B. Lebental. Insights into the ππ – ππ interaction driven non-covalent functionalization of carbon nanotubes of various diameters by conjugated fluorene and carbazole copolymers. AIP The Journal of Chemical Physics 2020, Vol. 152, No. 6. AIP 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

E. Polack, Y. Maday, A. Savin. FLEIM: A stable, accurate and robust extrapolation method at infinity for computing the ground state of electronic Hamiltonians, 2021.
M. S. Dupuy, K. Thicke.Dissociation limit of the H2 molecule in the particle-hole random phase approximation, 2022.
P. Monmarché. An entropic approach for Hamiltonian Monte Carlo: the idealized case, 2022.
I. Duchemin, L. Genovese, E. Letournel, A. Levitt, S. Ruget. Efficient extraction of resonant states in systems with defects, 2022.
S. Boldo, F. Clément, V. Martin, M. Mayero, H. Mouhcine. Lebesgue Induction and Tonelli’s Theorem in Coq, 2022.
H. Al Daas, G. Ballard, L. Grigori, S. Kumar, K. Rouse. Tight Memory-Independent Parallel Matrix Multiplication Communication Lower Bounds, 2022.
H. Al Daas, G. Ballard, L. Grigori, S. Kumar, K. Rouse. Communication Lower Bounds and Optimal Algorithms for Multiple Tensor-Times-Matrix Computation, 2022.
O. Balabanov and L. Grigori. Randomized block Gram-Schmidt process for solution of linear systems and eigenvalue problems, 2022.
T. Jaffrelot Inizan, T. Plé, O. Adjoua, P. Ren, H. Gökcan, O. Isayev, L. Lagardère, J.-P. Piquemal. Open Source Variational Quantum Eigensolver Extension of the Quantum Learning Machine (QLM) for Quantum Chemistry, 2022.
W. Sennane, J.-P. Piquemal, M.J. Rančić. Calculating the ground state energy of benzene under spatial deformations with noisy quantum computing,2022.
N. Mauger, T. Plé, L. Lagardère, S. Huppert, J.-P. Piquemal.Improving Condensed Phase Water Dynamics with Explicit Nuclear Quantum Effects: the Polarizable Q-AMOEBA Force Field,2022.
M. F. Herbst, A. Levitt, E. Cancès. DFTK: A Julian approach for simulating electrons in solids, 2021.
M-S. Dupuy, A. Levitt. Finite-size effects in response functions of molecular systems , 2021.
Y. Maday, C. Marcati. Analyticity and hp discontinuous Galerkin approximation of nonlinear Schr\” odinger eigenproblems , 2021.
Y. Maday, C. Marcati. Weighted analyticity of Hartree-Fock eigenfunctions, 2021.
A. F. De Guerny. The influence of periodic edge conditions for the simulation of some quantities of interest for separative chemistry, thesis defended in April 2021.
M. Blel, V. Ehrlacher, T. Lelièvre. Influence of sampling on the convergence rates of greedy algorithms for parameter-dependent random variables, 2021.
A. Durmus, A. Enfroy, É. Moulines, G. Stoltz. Uniform minorization condition and convergence bounds for discretizations of kinetic Langevin dynamics, 2021.
I. Sekkat, G. Stoltz. Removing the mini-batching error in Bayesian inference using Adaptive Langevin dynamics, 2021.
E. Camrud, D. P. Herzog, G. Stoltz, M. Gordina. Weighted L2-contractivity of Langevin dynamics with singular potentials, 2021.
L. Journel, P. Monmarché. Convergence of the kinetic annealing for general potentials, 2021.
H. Vroylandt, L. Goudenège, P. Monmarché, F. Pietrucci et B. Rotenberg. Likelihood-based parametric estimator for memory kernels in molecular dynamics, 2021.
E. Cancès, R. Coyaud and L. Ridgway Scott. Van der Waals interactions between two hydrogen atoms: The next orders, Comm. Math. Sci., in press, 2021
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.