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    Luc-henri Jolly

    ABSTRACT
    Un protocole specifique pour l'etude des transitions de phase par la methode hartree-fock periodique (simulation du chemin reactionnel par un mode de deplacement collectif des atomes) a ete mis au point en vue de calculer les... more
    Un protocole specifique pour l'etude des transitions de phase par la methode hartree-fock periodique (simulation du chemin reactionnel par un mode de deplacement collectif des atomes) a ete mis au point en vue de calculer les pressions de transition et l'energie d'activation des transitions displacives et, dans certains cas, des transitions reconstructives. Ce protocole a ete applique a cao. La pression de transition obtenue (68 gpa) est proche des valeurs experimentales disponibles et l'etude cinetique de la transformation revele une boucle d'hysteresis. L'etude des polymorphes de sio#2 et geo#2 montre une difference entre ces deux composes. Pour sio#2, les phases les plus stables a basse pression sont toujours les phases tetracoordonnees. La transition de phase cristobalite-stishovite, ou la coordination du silicium passe de 4 a 6, est prevue aux environs de 6 gpa. Une transition vers une phase de type cacl#2 est predite aux environs de 100 gpa, impliquant l'extinction du mode b#1#g de rotation des octaedres de sio#6, ainsi qu'une transition ordre-desordre a haute temperature. Par contre, pour geo#2, les phases de type pbo#2 et pyrite, hexacoordonnees, sont les plus stables a haute pression. En conclusion, ce protocole fournit des resultats coherents et possede des qualites predictives certaines, au moins en ce qui concerne les mineraux etudies. Une exploitation cinetique des resultats est ensuite possible, et l'extension des techniques utilisees a des structures plus complexes peut etre envisagee a moyen terme
    ABSTRACT
    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... more
    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 Processing Unit (CPU) petascale architectures. First, we discuss the new set of Intel Advanced Vector Extensions 512 (Intel AVX-512) instructions present in recent Intel processors (e.g., the Intel Xeon Scalable and Intel Xeon Phi 2nd generation processors) allowing for larger vectorization enhancements. These instructions constitute the central source of potential computational gains when using the latest processors, justifying important vectorization efforts for developers. We then briefly review the organization of the Tinker-HP code and identify the computational hotspots which require Intel AVX-512 optimization and we propose a general...
    Sorbonne Université, Institut des Sciences d Sorbonne Université, Institut Parisien de Ch 2622, Paris, France Sorbonne Université, Laboratoire de Chimi France. E-mail: jpp@lct.jussieu.fr Universita di Pisa, Dipartimento di Chimic... more
    Sorbonne Université, Institut des Sciences d Sorbonne Université, Institut Parisien de Ch 2622, Paris, France Sorbonne Université, Laboratoire de Chimi France. E-mail: jpp@lct.jussieu.fr Universita di Pisa, Dipartimento di Chimic MATHCCES, Department of Mathematics Germany The University of Texas at Austin, Departm Department of Chemistry, Wayne State Uni Department of Chemistry, University of No Cite this: Chem. Sci., 2018, 9, 956
    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.... more
    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 research laboratories to modern pre-exascale supercomputer centers. After detailing an analysis of our general scalable strategy that relies on OpenACC and CUDA, we discuss the various capabilities of the package. Among them, the multi-precision possibilities of the code are discussed. If an efficient double precision implementation is provided to preserve the possibility of fast reference computations, we show that a lower precision arithmetic is preferred providing a similar accuracy for molecular dynamics while exhibiting superior performances. As Tinker-HP is mainly dedicated to accelerate simulations using new generation point dipole ...
    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.... more
    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 research laboratories to modern pre-exascale supercomputer centers. After detailing an analysis of our general scalable strategy that relies on OpenACC and CUDA, we discuss the various capabilities of the package. Among them, the multi-precision possibilities of the code are discussed. If an efficient double precision implementation is provided to preserve the possibility of fast reference computations, we show that a lower precision arithmetic is preferred providing a similar accuracy for molecular dynamics while exhibiting superior performances. As Tinker-HP is mainly dedicated to accelerate simulations using new generation point dipole ...
    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... more
    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 Processing Unit (CPU) petascale architectures. First, we discuss the new set of Intel Advanced Vector Extensions 512 (Intel AVX-512) instructions present in recent Intel processors (e.g., the Intel Xeon Scalable and Intel Xeon Phi 2nd generation processors) allowing for larger vectorization enhancements. These instructions constitute the central source of potential computational gains when using the latest processors, justifying important vectorization efforts for developers. We then briefly review the organization of the Tinker-HP code and identify the computational hotspots which require Intel AVX-512 optimization and we propose a general...
    Un protocole specifique pour l'etude des transitions de phase par la methode hartree-fock periodique (simulation du chemin reactionnel par un mode de deplacement collectif des atomes) a ete mis au point en vue de calculer les... more
    Un protocole specifique pour l'etude des transitions de phase par la methode hartree-fock periodique (simulation du chemin reactionnel par un mode de deplacement collectif des atomes) a ete mis au point en vue de calculer les pressions de transition et l'energie d'activation des transitions displacives et, dans certains cas, des transitions reconstructives. Ce protocole a ete applique a cao. La pression de transition obtenue (68 gpa) est proche des valeurs experimentales disponibles et l'etude cinetique de la transformation revele une boucle d'hysteresis. L'etude des polymorphes de sio#2 et geo#2 montre une difference entre ces deux composes. Pour sio#2, les phases les plus stables a basse pression sont toujours les phases tetracoordonnees. La transition de phase cristobalite-stishovite, ou la coordination du silicium passe de 4 a 6, est prevue aux environs de 6 gpa. Une transition vers une phase de type cacl#2 est predite aux environs de 100 gpa, impliquant ...
    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... more
    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 quand la pression augmente. Aux basses pressions la surface d'energie potentielle presente un minimum unique correspondant a la forme stishovite, tandis qu'au dela de 80 GPa, deux puits de potentiel symetriques apparaissent
    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... more
    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-bond network that is only stable at physiological pH. Structural correlations analysis between its residues and the catalytic site confirms the presence of a buried allosteric site. However, noticeable differences in allosteric connectivity are observed between PFFs and non-PFFs. Interfacial polarizable water molecules are shown to appear at the heart of this discrepancy, since they are connected to the global interface H-bond network and able to adapt their dipole moment (and dynamics) to their diverse local physico-chemical micro-environments. The water-interface many-body interactions appear to drive the interface volume fluctuations and ...
    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... more
    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 process to achieve sufficient phase-space sampling within large biosystems, while accurate statistical properties can be obtained through debiasing. With this pleasingly parallel setup, the Tinker-HP package can be powered by an arbitrary large number of GPUs (Graphics Processing Unit) cards available on pre-exascale supercomputers, reducing to days explorations that would have taken years. We applied the approach to the urgent problem of the modeling of the SARS–CoV–2 Main protease (Mpro) dimer. A 15.14 microsecond high-resolution all-atom simulation (AMOEBA PFF) of its apo state is provided and compared to other available long-timescale non-PF...
    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... more
    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 replication. We report the first NCp7 polarizable molecular dynamics (MD) study using the AMOEBA force field complemented by non-polarizable CHARMM simulations. Specifically, we compared the relative free-energy stability of two extreme conformations: a compact one having two aromatic residues from each finger, partially stacked, denoted A; and an unfolded one, with the two residues apart, denoted B. Each of these conformations had been previously experimentally advocated to prevail in solution. We compared their theoretical relative free-energy stability using accelerated MD sampling techniques (Steered MD and Umbrella Sampling) and showed that there was a low free energy difference between them. As A and B do not differ in stability by more than 1...
    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.... more
    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 double precision implementation for CPUs. Grounded on interdisciplinary efforts with applied mathematics, Tinker-HP allows for long polarizable MD simulations on large systems up to millions of atoms. We detail in the paper the newly developed extension of massively parallel 3D spatial decomposition to point dipole polarizable models as well as their coupling to efficient Krylov iterative and non-iterative polarization solvers. The design of the code allows the use of various computer systems ranging from laboratory workstations to modern petascale supercomputers with thousands of cores. Tinker-HP proposes therefore the first high-performance...
    Research Interests:
    ABSTRACT
    ABSTRACT
    ... Table 3. Mulliken population analysis TiOa difference electron density Ti 0 Apical bond Equatorial bond Ti drf3;, Ti 3rf Ti 34 Ti 3rf.;,,2 Ti 34, Ti ... Catlow C. R, A., Freeman CM and Royle RL, Physica 131B ... 577, Quantum Chemistry... more
    ... Table 3. Mulliken population analysis TiOa difference electron density Ti 0 Apical bond Equatorial bond Ti drf3;, Ti 3rf Ti 34 Ti 3rf.;,,2 Ti 34, Ti ... Catlow C. R, A., Freeman CM and Royle RL, Physica 131B ... 577, Quantum Chemistry Program Exhange, Indiana University, Indiana (1988 ...
    Abstract 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-21 G basis functions has been checked by... more
    Abstract 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-21 G basis functions has been checked by performing test calculations on about ...