Normand Mousseau
Professeur de physique et titulaire de la Chaire UdeM
Matériaux complexes, énergie et ressources naturelles

La technique d’Activation et de Relaxation (ART)

Les premières méthodes numériques pour trouver des chemins de diffusion remontent au années 1970 et 1980 et ont été développées dans la communauté de physico-chimie. Ces méthodes permettaient de traiter des molécules de quelques atomes. La technique d’activation et de relaxation (\emphActivation-Relaxation Technique ou ART et ART nouveau), mise au point par Barkema et moi-même en 1996, fut la première méthode pour la recherche de chemins de transition \emphouverts pour des grands systèmes, i.e. plusieurs centaines ou milliers d’atomes. Cette méthode et d’autres similaires proposées par la suite par d’autres groupes sont maintenant utilisées régulièrement en physique, en chimie et en science des matériaux et ont été incorporées dans de nombreux codes distribués à travers le monde. En constant développement, ART nouveau se maintient parmi les méthodes les plus efficaces de recherche de chemins de diffusion (Machado-Charry et coll., 2011).

Au cours des 10 dernières années, ART nouveau a été au coeur de mes recherche et m’a permis de faire des contributions originales et importantes dans de nombreux domaines dont : les matériaux amorphes, la diffusion de défauts dans les semiconducteurs et les métaux, le repliement et l’agrégation des protéines, etc. Ces méthode est également la base pour de nombreux algorithmes que j’ai développés depuis 10 ans incluant : POP-ART (Chubynsky et coll., 2006), une méthode qui couple la dynamique moléculaire et ART nouveau ; ART holographique (Dupuis et NM, 2012), un algorithme multiéchelle pour le repliement de protéines ; ARTIST (Yun et coll., 2006), un algorithme activité en coordonnées internes ; et ART cinétique (El-Mellouhi, Lewis et Mousseau, 2008), discuté ci-dessous. ART nouveau est utilisé par de nombreux groupes à travers le monde, notamment en Chine, en France, aux Pays-bas et aux États-Unis.

Quelques-uns de mes travaux sur le sujet



  • P. Ganster, L. K. Béland, N. Mousseau, First stages of silicon oxidation with the activation relaxation technique, Physical Review B 86, 075408 (2012).
    Résumé : Using the art nouveau method, we study the initial stages of silicon oxide formation. After validating the method's parameters with the characterization of point defects diffusion mechanisms in pure Stillinger-Weber silicon, which allows us to recover some known results and to detail vacancy and self-interstitial diffusion paths, the method is applied onto a system composed of an oxygen layer deposited on a silicon substrate. We observe the oxygen atoms as they move rapidly into the substrate. From these art nouveau simulations, we extract the energy barriers of elementary mechanisms involving oxygen atoms and leading to the formation of an amorphouslike silicon oxide. We show that the kinetics of formation can be understood in terms of the energy barriers between various coordination environments.
    Mots-clés : ART.


  • N. Mousseau, L. K. Béland, P. Brommer, J. - F. Joly, F. El-Mellouhi, E. Machado-Charry, et al., The Activation-Relaxation Technique: ART Nouveau and Kinetic ART, Journal of Atomic, Molecular, and Optical Physics 2012, 925278 (2012).
    Résumé : The evolution of many systems is dominated by rare activated events that occur on timescale ranging from nanoseconds to the hour or more. For such systems, simulations must leave aside the full thermal description to focus specifically on mechanisms that generate a configurational change. We present here the activation relaxation technique (ART), an open-ended saddle point search algorithm, and a series of recent improvements to ART nouveau and kinetic ART, an ART-based on-the-fly off-lattice self-learning kinetic Monte Carlo method.
    Mots-clés : ART.


  • J. - F. St-Pierre, N. Mousseau, Large loop conformation sampling using the activation relaxation technique, ART-nouveau method, Proteins: Structure, Function, and Bioinformatics 80, 1883-1894 (2012).
    Résumé : We present an adaptation of the ART-nouveau energy surface sampling method to the problem of loop structure prediction. This method, previously used to study protein folding pathways and peptide aggregation, is well suited to the problem of sampling the conformation space of large loops by targeting probable folding pathways instead of sampling exhaustively that space. The number of sampled conformations needed by ART nouveau to find the global energy minimum for a loop was found to scale linearly with the sequence length of the loop for loops between 8 and about 20 amino acids. Considering the linear scaling dependence of the computation cost on the loop sequence length for sampling new conformations, we estimate the total computational cost of sampling larger loops to scale quadratically compared to the exponential scaling of exhaustive search methods. Proteins 2012; © 2012 Wiley Periodicals, Inc.
    Mots-clés : ART, flexibilite.


  • N. Mousseau, E. Machado-Charry, L. K. Béland, D. Caliste, L. Genovese, T. Deutsch, et al., Optimized energy landscape exploration using the ab initio based activation-relaxation technique, The Journal of Chemical Physics 135, 034102 (2011).
    Résumé : Unbiased open-ended methods for finding transition states are powerful tools to understand diffusion and relaxation mechanisms associated with defect diffusion, growth processes, and catalysis. They have been little used, however, in conjunction with ab initio packages as these algorithms demanded large computational effort to generate even a single event. Here, we revisit the activation-relaxation technique (ART nouveau) and introduce a two-step convergence to the saddle point, combining the previously used Lanczós algorithm with the direct inversion in interactive subspace scheme. This combination makes it possible to generate events (from an initial minimum through a saddle point up to a final minimum) in a systematic fashion with a net 300–700 force evaluations per successful event. ART nouveau is coupled with BigDFT, a Kohn-Sham density functional theory (DFT) electronic structure code using a wavelet basis set with excellent efficiency on parallel computation, and applied to study the potential energy surface of C20 clusters, vacancydiffusion in bulk silicon, and reconstruction of the 4H-SiC surface.
    Mots-clés : ART.


  • M. - R. Yun, R. Lavery, N. Mousseau, K. Zakrzewska, P. Derreumaux, ARTIST: An activated method in internal coordinate space for sampling protein energy landscapes, Proteins: Structure, Function, and Bioinformatics 63, 967-975 (2006).
    Résumé : We present the first applications of an activated method in internal coordinate space for sampling all-atom protein conformations, the activation–relaxation technique for internal coordinate space trajectories (ARTIST). This method differs from all previous internal coordinate-based studies aimed at folding or refining protein structures in that conformational changes result from identifying and crossing well-defined saddle points connecting energy minima. Our simulations of four model proteins containing between 4 and 47 amino acids indicate that this method is efficient for exploring conformational space in both sparsely and densely packed environments, and offers new perspectives for applications ranging from computer-aided drug design to supramolecular assembly. Proteins 2006. © 2006 Wiley-Liss, Inc.
    Mots-clés : ART, flexibilite.
    Pièce jointe 90.pdf 410.3 ko
  • Malek, Rachid, Mousseau, Normand, Barkema, Gerard T., dans Advances in materials theory and modeling - bridging over multiple length and time scale, Bulatov, Vasily, Colombo, Luciano, Cleri, Fabrizio, Lewis, Laurent J., Mousseau, Normand, Éd. (Materials Research Society, Symposium proceedings, 2001), vol. 677, p. AA8.4.
    Mots-clés : ART.


  • G. T. Barkema, N. Mousseau, Event-Based Relaxation of Continuous Disordered Systems, Physical Review Letters 77, 4358-4361 (1996).
    Résumé : A computational approach is presented to obtain energy-minimized structures in glassy materials. This approach, the activation-relaxation technique (ART), achieves its efficiency by focusing on significant changes in the microscopic structure (events). The application of ART is illustrated with two examples: the structure of amorphous silicon and the structure of Ni80P20, a metallic glass.
    Mots-clés : ART.
mardi 1er juillet 2014

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