Journal Publications

• Large language models for reticular chemistry

Z. Zheng, N. Rampal, T. Jaffrelot Inizan, C. Borgs, J. Chayes, O. M. Yaghi

Nat Rev Mater, in press

• Machine Learned Potential for High-Throughput Phonon Calculations of Metal-Organic Frameworks

A. M. Elena, P. Divakar Kamath, T. Jaffrelot Inizan, A. S. Rosen, F. Zanca, K. A. Persson

arXiv, submitted

• AMOEBA Polarizable Molecular Dynamics Simulations of Guanine Quadruplexes: from the c-Kit Proto-oncogene to HIV-1

D. El Ahdab, L. Lagardère, Z. Hobaika, T. Jaffrelot Inizan, F. Célerse, N. Gresh, R. G Maroun, J-P. Piquemal

    arXiv, submitted

• Advancing Force Fields Parameterization: A Directed Graph Attention Networks Approach

G. Chen, T. Jaffrelot Inizan, T. Plé, L. Lagardère, J-P. Piquemal, Y. Maday

J. Chem. Theory Comput., 20, 13, 5558–5569, 2024

• Incorporating Neural Networks into the AMOEBA Polarizable Force Field 

Y. Wang*, T. Jaffrelot Inizan*, C. Liu, J-P. Piquemal, P. Ren

J. Phys. Chem. B, 10, 128, 2381-2388, 2024

• High-resolution Molecular Dynamics Simulations of the Pyruvate Kinase Muscle Isoform 1 and 2 (PKM1/2)

Q. Delobelle, T. Jaffrelot Inizan, O. Adjoua, L. Lagardere, F. Celerse, V. Marechal, J-P. Piquemal

Chem. Eur. J., e202402534, 2024.

• Scalable hybrid deep neural networks/polarizable potentials biomolecular simulations including long-range effects

T. Jaffrelot Inizan, T. Ple, P. Ren, H. Gokcan, O. Isayev, O. Adjoua, L. Lagardere, J-P. Piquemal

Chemical Science 14 (20), 5438-5452, 2023

• Routine molecular dynamics simulations including nuclear quantum effects: from force fields to machine learning potentials

T. Plé, N. Mauger, O. Adjoua, T. Jaffrelot Inizan, L. Lagardère, S. Huppert, J-P. Piquemal

J. Chem. Theory Comput., 19, 5, 1432–1445, 2023

• Accurate Deep Learning-Aided Density-Free Strategy for Many-Body Dispersion-Corrected Density Functional Theory

P. P. Poier, T. Jaffrelot Inizan, O. Adjoua, L. Lagardère, J-P. Piquemal

J. Phys. Chem. Lett., 13, 19, 4381–4388, 2022

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

T. Jaffrelot Inizan*, F. Célerse*,  L. Lagardère, O. Adjoua, P. Monmarché, Y. Miao, E. Derat, J-P. Piquemal

J. Chem. Theory Comput., 18, 2, 968–977, 2022

• Computationally driven discovery of SARS-CoV-2 M pro inhibitors: from design to experimental validation

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. L. 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., J. W Ponder, L. Lagardère, J-P. Piquemal, D. Sabbadin

Chemical Science, 13, 3674-3687, 2022

• How Robust Is the Reversible Steric Shielding Strategy for Photoswitchable Organocatalysts?

S. Gallarati, R. Fabregat, V. Juraskova, T. Jaffrelot Inizan, C. Corminboeuf

J. Org. Chem., 87, 14, 8849–8857, 2022

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

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, J-P. Piquemal

Chemical Science 12 (13), 4889-4907, 2021

• Interfacial water many-body effects drive structural dynamics and allosteric interactions in SARS-CoV-2 main protease dimerization interface

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

J. Phys. Chem. Lett., 12, 26, 6218–6226, 2021

• Tinker-HP: Accelerating molecular dynamics simulations of large complex systems with advanced point dipole polarizable force fields using GPUs and multi-GPU systems

O. Adjoua, L. Lagardère, L-H. Jolly, A. Durocher, T. Very, I. Dupays, Z. Wang, T. Jaffrelot Inizan, F. Célerse, P. Ren, J. W Ponder, J-P. Piquemal

J. Chem. Theory Comput., 17, 4, 2034–2053, 2021

• Binding and 2D organization of arginine on Cu (110)

R. Totani, C. Méthivier, D. Costa, T. Jaffrelot Inizan, C-M. Pradier, V. Humblot

Applied Surface Science, 509, 144865, 2020