Normand Mousseau
Professor of Physics and Academic director
of the Trottier Energy Institute

The Activation-Relaxation Technique

While the first numerical methods for finding transition states (saddle points) go back to the 1970s and 1980s, with work in the physical chemistry community, ART, developed by Barkema and I in 1996, was the first open-ended search method for transition states designed for large systems, i.e. hundreds and thousands of atoms instead of a few atoms. ART, ART nouveau (an improved algorithm proposed by Malek and I in 2000) and similar methods by other groups are now routinely used in chemistry, physics and materials science around the world and are incorporated in many standard codes.

ART has been an important tool in my research, as it allowed me to make original and fundamental contributions in a number of fields including : amorphous materials, defect diffusion in semiconductors and metals, protein folding and flexibility, protein aggregation, etc. This includes identifying diffusion and folding mechanisms, characterization of the energy landscape, sampling of configurational space and the identification of new low-energy structures. This method has also formed the basis for a number of accelerated algorithms that I have developed over the years including POP-ART, that couples MD and ART, holographic ART (Dupuis and NM, 2012), for multiscale protein folding, and kinetic ART (El-Mellouhi, NM and Lewis, 2008), described below. With these methods, I have established myself as one of the world’s leading developers of accelerated algorithms. ART nouveau is currently used by a number of groups around the world, notably in China, France, the Netherlands and the USA.

Selected work

  • N. Salles, N. Richard, N. Mousseau, A. Hemeryck, Strain-driven diffusion process during silicon oxidation investigated by coupling density functional theory and activation relaxation technique, The Journal of Chemical Physics 147, 054701 (2017).
    Tags: ART.

  • P. Ganster, L. K. Béland, N. Mousseau, First stages of silicon oxidation with the activation relaxation technique, Physical Review B 86, 075408 (2012).
    Abstract: 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.
    Tags: 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).
    Abstract: 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.
    Tags: ART, flexibilite.

  • 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).
    Abstract: 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.
    Tags: ART.

  • 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).
    Abstract: 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.
    Tags: 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).
    Abstract: 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.
    Tags: ART, flexibilite.
    Attachment 90.pdf 410.3 kb
  • Malek, Rachid, Mousseau, Normand, Barkema, Gerard T., in Advances in materials theory and modeling - bridging over multiple length and time scale, Bulatov, Vasily, Colombo, Luciano, Cleri, Fabrizio, Lewis, Laurent J., Mousseau, Normand, Eds. (Materials Research Society, Symposium proceedings, 2001), vol. 677, p. AA8.4.
    Tags: ART.

  • G. T. Barkema, N. Mousseau, Event-Based Relaxation of Continuous Disordered Systems, Physical Review Letters 77, 4358-4361 (1996).
    Abstract: 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.
    Tags: ART.
Tuesday 1 July 2014

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