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25
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Introduction
Luc-Henri Jolly currently works at the Institut Parisien de Chimie Physique et Théorique - Parisian Institute for Theoretical and Physical Chemistry, French National Centre for Scientific Research. Luc-Henri does research in Solid State Physics, Condensed Matter Physics and Computational Physics. He also has strong skills in system management of clusters under Linux. His current project is 'Tinker-HP, a massively parallel software for new generation polarizable molecular dynamics.', where he works on vectorization and optimization on modern architectures. He received the Atos-Fourier Award 2018 in HPC with Tinker-HP.
Additional affiliations
July 2003 - June 2016
January 2019 - present
September 2014 - present
Publications
Publications (25)
This living paper reviews the present High Performance Computing (HPC) capabilities of the Tinker-HP molecular modeling package. We focus here on the reference, double precision, massively parallel molecular dynamics engine present in Tinker-HP and dedicated to perform large scale simulations. We show how it can be adapted to recent Intel Central P...
Following our previous work (Chem. Sci. 2021, 12, 4889−4907), we study the structural dynamics of the SARS-CoV-2 Main Protease dimerization interface (apo dimer) by means of microsecond adaptive sampling molecular dynamics simulations (50 μs) 10 using the AMOEBA polarizable force field (PFF). This interface is structured by a complex H-bond network...
Following our previous work (Chem. Sci., 2021, 12, 4889 – 4907), we study the structural dynamics of the SARS-CoV-2 Main Protease dimerization interface (apo dimer) by means of microsecond adaptive sampling molecular dynamics simulations (50 microseconds) using the AMOEBA polarizable force field (PFF). This interface is structured by a complex H-bo...
Following our previous work (Chem. Sci., 2021, 12, 4889 – 4907), we study the structural dynamics of the SARS-CoV-2 Main Protease dimerization interface (apo dimer) by means of microsecond adaptive sampling molecular dynamics simulations (50 microseconds) using the AMOEBA polarizable force field (PFF). This interface is structured by a complex H-bo...
We provide an unsupervised adaptive sampling strategy capable of producing μs-timescale molecular dynamics (MD) simulations of large biosystems using many-body polarizable force fields (PFF). The global exploration problem is decomposed into a set of separate MD trajectories that can be restarted within a selective process to achieve sufficient pha...
We present the extension of the Tinker-HP package (Lagard\`ere et al., Chem. Sci., 2018,9, 956-972) to the use of Graphics Processing Unit (GPU) cards to accelerate molecular dynamics simulations using polarizable many-body force fields. The new high-performance module allows for an efficient use of single- and multi-GPU architectures ranging from...
We present the extension of the Tinker-HP package (Lagardère et al., Chem. Sci., 2018,9, 956-972) to the use of Graphics Processing Unit (GPU) cards to accelerate molecular dynamics simulations using polarizable many-body force fields. The new high-performance module allows for an efficient use of single-and multi-GPUs archi-1 arXiv:2011.01207v1 [p...
We provide a new unsupervised adaptive sampling strategy capable of producing microsecondtimescale molecular dynamics (MD) simulations using many-body polarizable force fields (PFF) on modern supercomputers. The global exploration problem is decomposed into a set of separate MD trajectories that can be restarted within an iterative/selective proces...
We provide an unsupervised adaptive sampling strategy capable of producing microseconds-timescale molecular dynamics (MD) simulations of large biosystems using many-body polarizable force fields (PFF). The global exploration problem is decomposed into a set of separate MD trajectories that can be restarted within a selective process to achieve suff...
Using polarizable (AMOEBA) and non-polarizable (CHARMM) force fields, we compare the relative free energy stability of two extreme conformations of the HIV-1 NCp7 nucleocapsid that had been previously experimentally advocated to prevail in solution. Using accelerated sampling techniques, we show that they differ in stability by no more than 0.75-1....
The Human Immunodeficiency Virus Type 1 nucleocapsid 7 (NCp7) is a multi-functional protein formed by N-terminal and C-terminal domains surrounding two Zn-fingers, linked by a stretch of basic residues, which play a key role in the viral replica-tion. We report the first NCp7 polarizable molecular dynamics (MD) study using the AMOEBA force field co...
The Human Immunodeficiency Virus Type 1 nucleocapsid 7 (NCp7) is a multi-functional protein formed by N-terminal and C-terminal domains surrounding two Zn-fingers, linked by a stretch of basic residues, which play a key role in the viral replica-tion. We report the first NCp7 polarizable molecular dynamics (MD) study using the AMOEBA force field co...
This living paper reviews the present High Performance Computing (HPC) capabilities of the Tinker-HP molecular modeling package. We focus here on the reference, double precision, massively parallel molecular dynamics engine present in Tinker-HP and dedicated to perform large scale simulations. We show how it can be adapted to recent Intel Central P...
We present Tinker-HP, a massively MPI parallel package dedicated to classical molecular dynamics (MD) and to multiscale simulations, using advanced polarizable force fields (PFF) encompassing distributed multipoles electrostatics. Tinker-HP is an evolution of the popular Tinker package code that conserves its simplicity of use and its reference dou...
Since the PAH hypothesis has been proposed for interpreting the UIR bands, the question of the intensity of the 3.3 mum has been largely debated. An in-depth study of the CH fragment using density functional theory (DFT) is presented that shows the striking difference of the dipole moment functions mu = f (rCH) between the neutral CH and the ionize...
Non-empirical calculations of a Cr2O3
unit, taken as an initial model of chromium oxide clusters, interacting with ions and (small models of) molecules present in natural seawater have been carried out. The results obtained for the isolated oxide unit show that the coupling between the unpaired 3d electrons of the two chromium atoms has a negligibl...
FORTRAN tools have been designed to support well-structures, modular, route-independent and easily interfaceable programming. This set of tools, which creates a kind of low-level object-oriented programming environment, is refered to as OSIPE (Open Structured Interfaceable Programming Environment). Its main role is to transform meaningful FORTRAN v...
The structure and stability of the rutile structure of SiO2 and GeO2 and of three other putative hexacoordinated polymorphs, namely the anatase, pyrite and α-PbO2 structures, have been investigated by the Periodic Hartree-Fock method. The optimized structural parameters and equation-of-state coefficients of these four polymorphs are reported. -Auth...
La transition observee au dessus de 100 GPa entre les phases stishovite et de type CaCl 2 de la silice a ete etudiee theoriquement par la methode Hartree-Fock periodique. Le mecanisme de cette transition de phase met en jeu le mode B 1g (Γ 3 + ) de rotation des octaedres SiO 6 autour de leur axe C2 paralelle a c. La frequence de ce mode diminue qua...
The periodic Hartree-Fock method has been used to sample the potential energy hypersurface of CaO to determine a collective reaction pathway between the low-pressure (NaCl) and high-pressure (CsCl) phases. The predicted transition pressure, 68 GPa, is in good agreement with both experimental data and previous theoretical studies. At low pressure th...
Silicon is tetracoordinated in most silica polymorphs except stishovite, in which it is hexacoordinated. Pseudopotential periodic Hartree-Fock calculations have been performed to study a possible reaction pathway between cristobalite and stishovite. The calculated transition pressure (6 GPa) is consistent with the stishovite synthesis pressure rang...
Split valence basis sets adapted to Durand and Barthelat core pseudopotentials have been optimized for the three first rows of the main group elements. The reliability of these PS-21G basis functions has been checked by performing test calculations on about 30 small molecule and crystalline systems. These studies indicate a satisfactory overall agr...