Normand Mousseau
Professor of Physics and Chair
Université de Montréal

1989-2013

  • J. - F. Joly, N. Mousseau, S. Roorda, Identification of a regime change in the microscopic relaxation of ion-implanted amorphous silicon using the kinetic ART method, Physical Review B (no date).
    Tags: soumis.

2016

2015



  • S. Côté, V. Binette, E.  S. Salnikov, B. Bechinger, N. Mousseau, Probing the Huntingtin 1-17 Membrane Anchor on a Phospholipid Bilayer by Using All-Atom Simulations, Biophysical Journal 108, 1187-1198 (2015).
    Abstract: Mislocalization and aggregation of the huntingtin protein are related to Huntington?s disease. Its first exon?more specifically the first 17 amino acids (Htt17)?is crucial for the physiological and pathological functions of huntingtin. It regulates huntingtin?s activity through posttranslational modifications and serves as an anchor to membrane-containing organelles of the cell. Recently, structure and orientation of the Htt17 membrane anchor were determined using a combined solution and solid-state NMR approach. This prompted us to refine this model by investigating the dynamics and thermodynamics of this membrane anchor on a POPC bilayer using all-atom, explicit solvent molecular dynamics and Hamiltonian replica exchange. Our simulations are combined with various experimental measurements to generate a high-resolution atomistic model for the huntingtin Htt17 membrane anchor on a POPC bilayer. More precisely, we observe that the single α-helix structure is more stable in the phospholipid membrane than the NMR model obtained in the presence of dodecylphosphocholine detergent micelles. The resulting Htt17 monomer has its hydrophobic plane oriented parallel to the bilayer surface. Our results further unveil the key residues interacting with the membrane in terms of hydrogen bonds, salt-bridges, and nonpolar contributions. We also observe that Htt17 equilibrates at a well-defined insertion depth and that it perturbs the physical properties?order parameter, thickness, and area per lipid?of the bilayer in a manner that could favor its dimerization. Overall, our observations reinforce and refine the NMR measurements on the Htt17 membrane anchor segment of huntingtin that is of fundamental importance to its biological functions.
    Tags: amyloide.

  • C. Eugène, N. Mousseau, Aggregation process of Abeta(1-40) with non-Abeta amyloid component of alpha-synuclein, Journal of Physics: Conference Series 640, 012008 (2015).


  • C. Guo, S. Côté, N. Mousseau, G. Wei, Distinct Helix Propensities and Membrane Interactions of Human and Rat IAPP1–19 Monomers in Anionic Lipid Bilayers, The Journal of Physical Chemistry B 119, 3366-3376 (2015).
    Abstract: Islet amyloid polypeptide, IAPP or amylin, is a 37-residue peptide hormone coexpressed with insulin by pancreatic ?-cells. The aggregation of human IAPP (hIAPP) into amyloid deposits is associated with type II diabetes. Substantial evidence suggests that the interaction of anionic membranes with hIAPP may facilitate peptide aggregation and the N-terminal 1?19 fragment (IAPP1?19) plays an important role in peptide?membrane interaction. As a first step to understand how structural differences between human and rat IAPP peptides in membranes may influence the later oligomerization process, we have investigated the structures and orientations of hIAPP1?19 and the less toxic rIAPP1?19 (i.e., the H18R mutant of hIAPP1?19) monomers in anionic POPG bilayers by performing replica exchange molecular dynamics (REMD) simulations. On the basis of ?20 ?s REMD simulations started from a random coil conformation of the peptide placed in water, we find that unfolded h(r)IAPP1?19 can insert into the bilayers and the membrane-bound peptide stays mainly at the lipid head?tail interface. hIAPP1?19 displays higher helix propensity than rIAPP1?19, especially in the L12?L16 region. The helix is oriented parallel to the bilayer surface and buried in the membrane 0.3?0.8 nm below the phosphorus atoms, consistent with previous electron paramagnetic resonance data. The helical conformation is an amphiphilic helix with its hydrophilic and hydrophobic faces pointing, respectively, to the lipid head and tail regions. The H18R substitution enhances the electrostatic interactions of IAPP1?19 with the membrane, while it weakens the intrapeptide interactions crucial for helix formation, thus leading to lower helix propensity of rIAPP1?19. Implications of our simulation results on the membrane-mediated IAPP1?19 oligomerization are discussed.

  • S. Jain, G. T. Barkema, N. Mousseau, C. - M. Fan, M. van Huis, Strong Long-Range Relaxations of Structural Defects in Graphene Simulated Using a New Semi-Empirical Potential, The Journal of Physical Chemistry C 119, 9646-9655 (2015).

  • N. Mousseau, La politique québécoise de l'énergie: un pass en avant, trois en arrrière, Revue Vie Économique 6, 1-9 (2015).
  • N. Mousseau, in Sortir le Québec du pétrole, (Ianik Marcil, Montréal, 2015), p. 103-110.

  • N. Mousseau, La maîtrise de l’énergie, une approche intégrée permettant au Québec de transformer à la fois sa consommation énergétique et de faire face à ses responsabilités environnementales, Cahier de la Chaire de recherche en développement des collectivités (CRDC), Série Conférences , 15-22 (2015).

  • N. Mousseau, Science, politique et changements climatiques, Philo & Cie 11, 50-53 (2015).

  • N. Mousseau, Politique énergétique du Québec: la nécessité d’une référence de marché sur la valeur de l’électricité au Québec, L’Énergique 9, 6-9 (2015).
  • N. Mousseau, in Creuser jusqu'où? Extractivisme et limites à la croissance, (Yves-Marie Abraham et David Murray, Montréal, 2015), p. 183-201.

  • N. Mousseau, P. Brommer, J. - F. Joly, L. K. Béland, F. El-Mellouhi, G. K. N'Tsouaglo, et al., Following atomistic kinetics on experimental timescales with the kinetic Activation-Relaxation Technique, Computational Materials Science 100, 111-123 (2015).

  • N. Mousseau, P. - O. Pineau, Mémoire présenté à la Commission des transports et de l’environnement du Québec dans le cadre de ses auditions sur le document de consultation intitulé « Cible de réduction d’émissions de gaz à effet de serre du Québec pour 2030 » (2015) (available at http://normandmousseau.com/publications/174.pdf).

  • G. K. N'Tsouaglo, L. K. Béland, J. - F. Joly, P. Brommer, N. Mousseau, P. Pochet, Probing potential energy surface exploration strategies for complex systems, J. Chem. Theory Comput. 11, 1970-1977 (2015).
    Abstract: The efficiency of minimum-energy configuration searching algorithms is closely linked to the energy landscape structure of complex systems. Here we characterize this structure by following the time evolution of two systems, vacancy aggregation in Fe and energy relaxation in ion-bombarded c-Si, using the kinetic Activation-Relaxation Technique (k-ART), an off-lattice kinetic Monte Carlo (KMC) method, and the well-known Bell-Evans-Polanyi (BEP) principle. We also compare the efficiency of two methods for handling non-diffusive flickering states -- an exact solution and a Tabu-like approach that blocks already visited states. Comparing these various simulations allow us to confirm that the BEP principle does not hold for complex system since forward and reverse energy barriers are completely uncorrelated. This means that following the lowest available energy barrier, even after removing the flickering states, leads to rapid trapping: relaxing complex systems requires crossing high-energy barriers in order to access new energy basins, in agreement with the recently proposed replenish-and-relax model [Béland et al., PRL 111, 105502 (2013)] This can be done by forcing the system through these barriers with Tabu-like methods. Interestingly, we find that following the fundamental kinetics of a system, though standard KMC approach, is at least as efficient as these brute-force methods while providing the correct kinetics information.
    Tags: ARTc.


  • J. Nasica-Labouze, P. H. Nguyen, F. Sterpone, O. Berthoumieu, N. - V. Buchete, S. Coté, et al., Amyloid β Protein and Alzheimer’s Disease: When Computer Simulations Complement Experimental Studies, Chemical Reviews 115, 3518-3563 (2015).

  • C. Potvin, N. Mousseau, et 58 co-auteurs, Agir sur les changements climatique. Les solutions d'univeritaires canadiens et canadiennes/Acting on climate change. Solutions from Canadian Scholars (Dialogues pour un Canada vert/Dialogues for a sustainable Canada, 2015; http://normandmousseau.com/publications/173a.pdf).

  • B. Rousseau, V. Timoshevskii, N. Mousseau, M. Côté, K. Zaghib, A novel intercalation cathode material for sodium-based batteries, Electrochemistry Communications 52, 9-12 (2015).

  • M. Trochet, L. K. Béland, P. Brommer, J. - F. Joly, N. Mousseau, Diffusion of point defects in crystalline silicon using the kinetic ART method, Phys. Rev. B 91, 224106 (2015).

2014



  • L. K. Béland, E. Machado-Charry, P. Pochet, N. Mousseau, Strain effects and intermixing at the Si surface: Importance of long-range elastic corrections in first-principles calculations, Phys. Rev. B 90, 155302 (2014).


  • P. Brommer, L. K. Béland, J. - F. Joly, N. Mousseau, Understanding long-time vacancy aggregation in iron: A kinetic activation-relaxation technique study, Phys. Rev. B 90, 134109 (2014).


  • S. Côté, G. Wei, N. Mousseau, Atomistic mechanisms of huntingtin N-terminal fragment insertion on a phospholipid bilayer revealed by molecular dynamics simulations, Proteins: Structure, Function, and Bioinformatics 82, 1409-1427 (2014).
    Abstract: The huntingtin protein is characterized by a segment of consecutive glutamines (QN) that is responsible for its fibrillation. As with other amyloid proteins, misfolding of huntingtin is related to Huntington's disease through pathways that can involve interactions with phospholipid membranes. Experimental results suggest that the N-terminal 17-amino-acid sequence (httNT) positioned just before the QN region is important for the binding of huntingtin to membranes. Through all-atom explicit solvent molecular dynamics simulations, we unveil the structure and dynamics of the httNTQN fragment on a phospholipid membrane at the atomic level. We observe that the insertion dynamics of this peptide can be described by four main steps—approach, reorganization, anchoring, and insertion—that are very diverse at the atomic level. On the membrane, the httNT peptide forms a stable α-helix essentially parallel to the membrane with its nonpolar side-chains—mainly Leu-4, Leu-7, Phe-11 and Leu-14—positioned in the hydrophobic core of the membrane. Salt-bridges involving Glu-5, Glu-12, Lys-6, and Lys-15, as well as hydrogen bonds involving Thr-3 and Ser-13 with the phospholipids also stabilize the structure and orientation of the httNT peptide. These observations do not significantly change upon adding the QN region whose role is rather to provide, through its hydrogen bonds with the phospholipids' head group, a stable scaffold facilitating the partitioning of the httNT region in the membrane. Moreover, by staying accessible to the solvent, the amyloidogenic QN region could also play a key role for the oligomerization of httNTQN on phospholipid membranes. Proteins 2014; 82:1409–1427. © 2014 Wiley Periodicals, Inc.
    Tags: amyloide.

  • C. Eugène, R. Laghaei, N. Mousseau, Early oligomerization stages for the non-amyloid component of alpha-synuclein amyloid, J. Chem. Phys. 141, 135103 (2014).

  • R. Lanoue, N. Mousseau, Maîtriser notre avenir énergétique. Pour le bénéfice économique, environnemental et social de tous (Commission sur les enjeux énergétiques du Québec, 2014; http://consultationenergie.gouv.qc.ca), 310 pp.
  • N. Mousseau, et 18 co-auteurs, Éléments d’une stratégie énergétique pour lʼest du Canada/ Elements of an Eastern Canada Energy Strategy (Montréal, 2014).

  • N. Mousseau, in Resources, empire and Labour. Crises, lessons and alternatives., D. Leadbeater, Eds. (Fernwood Publishing, Black Point, NS, 2014), p. 112-123.


  • F. Sterpone, S. Melchionna, P. Tuffery, S. Pasquali, N. Mousseau, T. Cragnolini, et al., The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems, Chemical Society Reviews 43, 4871-4893 (2014).
    Abstract: The OPEP coarse-grained protein model has been applied to a wide range of applications since its first release 15 years ago. The model, which combines energetic and structural accuracy and chemical specificity, allows the study of single protein properties, DNA-RNA complexes, amyloid fibril formation and protein suspensions in a crowded environment. Here we first review the current state of the model and the most exciting applications using advanced conformational sampling methods. We then present the current limitations and a perspective on the ongoing developments.

2013



  • L. K. Béland, Y. Anahory, D. Smeets, M. Guihard, P. Brommer, J. - F. Joly, et al., Replenish and Relax: Explaining Logarithmic Annealing in Ion-Implanted c-Si, Physical Review Letters 111, 105502 (2013).
    Abstract: We study ion-damaged crystalline silicon by combining nanocalorimetric experiments with an off-lattice kinetic Monte Carlo simulation to identify the atomistic mechanisms responsible for the structural relaxation over long time scales. We relate the logarithmic relaxation, observed in a number of disordered systems, with heat-release measurements. The microscopic mechanism associated with this logarithmic relaxation can be described as a two-step replenish and relax process. As the system relaxes, it reaches deeper energy states with logarithmically growing barriers that need to be unlocked to replenish the heat-releasing events leading to lower-energy configurations.
    Tags: ARTc.


  • L. K. Béland, N. Mousseau, Long-time relaxation of ion-bombarded silicon studied with the kinetic activation-relaxation technique: Microscopic description of slow aging in a disordered system, Physical Review B 88, 214201 (2013).
    Abstract: Diffusion and relaxation of defects in bulk systems is a complex process that can only be accessed directly through simulations. We characterize the mechanisms of low-temperature aging in self-implanted crystalline silicon, a model system used extensively to characterize both amorphization and return to equilibrium processes, over 11 orders of magnitudes in time, from 10 ps to 1 s, using a combination of molecular dynamics and kinetic activation-relaxation technique simulations. These simulations allow us to reassess the atomistic mechanisms responsible for structural relaxations and for the overall logarithmic relaxation, a process observed in a large number of disordered systems and observed here over the whole simulation range. This allows us to identify three microscopic regimes, annihilation, aggregation, and reconstruction, in the evolution of defects and to propose atomistic justification for an analytical model of logarithmic relaxation. Furthermore, we show that growing activation barriers and configurational space exploration are kinetically limiting the system to a logarithmic relaxation. Overall, our long-time simulations do not support the amorphous cluster model but point rather to a relaxation driven by elastic interactions between defect complexes of all sizes.


  • J. - F. Joly, L. K. Béland, P. Brommer, N. Mousseau, Contribution of vacancies to relaxation in amorphous materials: A kinetic activation-relaxation technique study, Physical Review B 87, 144204 (2013).
    Abstract: The nature of structural relaxation in disordered systems such as amorphous silicon (a-Si) remains a fundamental issue in our attempts at understanding these materials. While a number of experiments suggest that mechanisms similar to those observed in crystals, such as vacancies, could dominate the relaxation, theoretical arguments point rather to the possibility of more diverse pathways. Using the kinetic activation-relaxation technique, an off-lattice kinetic Monte Carlo method with on-the-fly catalog construction, we resolve this question by following 1000 independent vacancies in a well-relaxed a-Si model at 300 K over a timescale of up to one second. Less than one percent of these survive over this period of time and none diffuse more than once, showing that relaxation and diffusion mechanisms in disordered systems are fundamentally different from those in the crystal.
    Tags: Amorphe.

  • N. Mousseau, coll., De la réduction des gaz à effet de serre à l’indépendance énergétique/From Greenhouse Gas Reduction to Québec’s Energy Self-sufficiency (Commission sur les enjeux énergéiques du Québec/Quebec Commission on Energy Issues, 2013; http://consultationenergie.gouv.qc.ca), 83/86 pp.

  • N. Mousseau, in L’énergie à découvert, Mosseri, Rémy, Jeandel, Catherine, Eds. (CNRS Éditions, Paris, 2013), p. 345.
  • Mousseau, Normand, La science et l'excès, Philo & Cie , 43-47 (2013).
  • J. Nasica-Labouze, N. Mousseau, in Alzheimer’s Disease : Insights into Low Molecular Weight and Cytotoxic Aggregates from In Vitro and Computer Experiments, P. Derreumaux, Eds. (Imperial College Press, 2013), p. 209-237.

2012



  • P. Brommer, N. Mousseau, Comment on “Mechanism of Void Nucleation and Growth in bcc Fe: Atomistic Simulations at Experimental Time Scales”, Physical Review Letters 108, 219601 (2012).
    Abstract: A Comment on the Letter by Yue Fan et al., Phys. Rev. Lett. 106, 125501 (2011). The authors of the Letter offer a reply.


  • Y. Chebaro, P. Jiang, T. Zang, Y. Mu, P. H. Nguyen, N. Mousseau, et al., Structures of Aβ17–42 Trimers in Isolation and with Five Small-Molecule Drugs Using a Hierarchical Computational Procedure, The Journal of Physical Chemistry B 116, 8412-8422 (2012).
    Abstract: The amyloid-? protein (A?) oligomers are believed to be the main culprits in the cytoxicity of Alzheimer?s disease (AD) and p3 peptides (A?17?42 fragments) are present in AD amyloid plaques. Many small-molecule or peptide-based inhibitors are known to slow down A? aggregation and reduce the toxicity in vitro, but their exact modes of action remain to be determined since there has been no atomic level of A?(p3)?drug oligomers. In this study, we have determined the structure of A?17?42 trimers both in aqueous solution and in the presence of five small-molecule inhibitors using a multiscale computational study. These inhibitors include 2002-H20, curcumin, EGCG, Nqtrp, and resveratrol. First, we used replica exchange molecular dynamics simulations coupled to the coarse-grained (CG) OPEP force field. These CG simulations reveal that the conformational ensemble of A?17?42 trimer can be described by 14 clusters with each peptide essentially adopting turn/random coil configurations, although the most populated cluster is characterized by one peptide with a ?-hairpin at Phe19?Leu31. Second, these 14 dominant clusters and the less-frequent fibril-like state with parallel register of the peptides were subjected to atomistic Autodock simulations. Our analysis reveals that the drugs have multiple binding modes with different binding affinities for trimeric A?17?42 although they interact preferentially with the CHC region (residues 17?21). The compounds 2002-H20 and Nqtrp are found to be the worst and best binders, respectively, suggesting that the drugs may interfere at different stages of A? oligomerization. Finally, explicit solvent molecular dynamics of two predicted Nqtrp?A?17?42 conformations describe at atomic level some possible modes of action for Nqtrp.


  • S. Côté, R. Laghaei, P. Derreumaux, N. Mousseau, Distinct Dimerization for Various Alloforms of the Amyloid-Beta Protein: Aβ1–40, Aβ1–42, and Aβ1–40(D23N), The Journal of Physical Chemistry B 116, 4043-4055 (2012).
    Abstract: The Amyloid-beta protein is related to Alzheimer?s disease, and various experiments have shown that oligomers as small as the dimer are cytotoxic. Two alloforms are mainly produced: A?1?40 and A?1?42. They have very different oligomer distributions, and it was recently suggested, from experimental studies, that this variation may originate from structural differences in their dimer structures. Little structural information is available on the A? dimer, however, and to complement experimental observations, we simulated the folding of the wild-type A?1?40 and A?1?42 dimers as well as the mutated A?1?40(D23N) dimer using an accurate coarse-grained force field coupled to Hamiltonian-temperature replica exchange molecular dynamics. The D23N variant impedes the salt-bridge formation between D23 and K28 seen in the wild-type A?, leading to very different fibrillation properties and final amyloid fibrils. Our results show that the A?1?42 dimer has a higher propensity than the A?1?40 dimer to form ?-strands at the central hydrophobic core (residues 17?21) and at the C-terminal (residues 30?42), which are two segments crucial to the oligomerization of A?. The free energy landscape of the A?1?42 dimer is also broader and more complex than that of the A?1?40 dimer. Interestingly, D23N also impacts the free energy landscape by increasing the population of configurations with higher ?-strand propensities when compared against A?40. In addition, while A?1?40(D23N) displays a higher ?-strand propensity at the C-terminal, its solvent accessibility does not change with respect to the wild-type sequence. Overall, our results show the strong impact of the two amino acids Ile41-Ala42 and the salt-bridge D23?K28 on the folding of the A? dimer.


  • S. Côté, G. Wei, N. Mousseau, All-Atom Stability and Oligomerization Simulations of Polyglutamine Nanotubes with and without the 17-Amino-Acid N-Terminal Fragment of the Huntingtin Protein, The Journal of Physical Chemistry B 116, 12168-12179 (2012).
    Abstract: Several neurodegenerative diseases are associated with the polyglutamine (polyQ) repeat disorder in which a segment of consecutive glutamines in the native protein is produced with too many glutamines. Huntington?s disease, for example, is related to the misfolding of the Huntingtin protein which occurs when the polyQ segment has more than approximately 36 glutamines. Experimentally, it is known that the polyQ segment alone aggregates into ?-rich conformations such as amyloid fibrils. Its aggregation is modulated by the number of glutamine residues as well as by the surrounding amino acid sequences such as the 17-amino-acid N-terminal fragment of Huntingtin which increases the aggregation rate. Little structural information is available, however, regarding the first steps of aggregation and the atomistic mechanisms of oligomerization are yet to be described. Following previous coarse-grained replica-exchange molecular dynamics simulations that show the spontaneous formation of a nanotube consisting of two intertwined antiparallel strands (Laghaei, R.; Mousseau, N. J. Chem. Phys.2010, 132, 165102), we study this configuration and some extensions of it using all-atom explicit solvent MD simulations. We compare two different lengths for the polyQ segment, 40 and 30 glutamines, and we investigate the impact of the Huntingtin N-terminal residues (httNT). Our results show that the dimeric nanotubes can provide a building block for the formation of longer nanotubes (hexamers and octamers). These longer nanotubes are characterized by large ?-sheet propensities and a small solvent exposure of the main-chain atoms. Moreover, the oligomerization between two nanotubes occurs through the formation of protein/protein H-bonds and can result in an elongation of the water-filled core. Our results also show that the httNT enhances the structural stability of the ?-rich seeds, suggesting a new mechanism by which it can increase the aggregation rate of the amyloidogenic polyQ sequence.
    Tags: amyloide.


  • L. Dupuis, N. Mousseau, Understanding the EF-hand closing pathway using non-biased interatomic potentials, The Journal of Chemical Physics 136, 035101 (2012).
    Abstract: The EF-hand superfamily of proteins is characterized by the presence of calcium binding helix-loop-helix structures. Many of these proteins undergo considerable motion responsible for a wide range of properties upon binding but the exact mechanism at the root of this motion is not fully understood. Here, we use an unbiased accelerated multiscale simulation scheme, coupled with two force fields — CHARMM-EEF1 and the extended OPEP — to explore in details the closing pathway, from the unbound holo state to the closed apo state, of two EF-hand proteins, the Calmodulin and Troponin C N-terminal nodules. Based on a number of closing simulations for these two sequences, we show that the EF-hand β-scaffold, identified as crucial by Grabarek for the EF-hand opening driven by calcium binding, is also important in closing the EF-hand. We also show the crucial importance of the phenylalanine situated at the end of first EF-hand helix, and identify an intermediate state modulating its behavior, providing a detailed picture of the closing mechanism for these two representatives of EF-hand proteins.
    Tags: flexibilite.


  • 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. Joly, L. K. Béland, P. Brommer, F. El-Mellouhi, N. Mousseau, Optimization of the Kinetic Activation-Relaxation Technique, an off-lattice and self-learning kinetic Monte-Carlo method, Journal of Physics: Conference Series 341, 012007 (2012).
    Abstract: We present two major optimizations for the kinetic Activation-Relaxation Technique (k-ART), an off-lattice self-learning kinetic Monte Carlo (KMC) algorithm with on-the-fly event search THAT has been successfully applied to study a number of semiconducting and metallic systems. K-ART is parallelized in a non-trivial way: A master process uses several worker processes to perform independent event searches for possible events, while all bookkeeping and the actual simulation is performed by the master process. Depending on the complexity of the system studied, the parallelization scales well for tens to more than one hundred processes. For dealing with large systems, we present a near order 1 implementation. Techniques such as Verlet lists, cell decomposition and partial force calculations are implemented, and the CPU time per time step scales sublinearly with the number of particles, providing an efficient use of computational resources.


  • E. Machado-Charry, P. Boulanger, L. Genovese, N. Mousseau, P. Pochet, Tunable magnetic states in hexagonal boron nitride sheets, Applied Physics Letters 101, 132405 (2012).
    Abstract: Magnetism in two dimensional atomic sheets has attracted considerable interest as its existence could allow the development of electronic and spintronic devices. The existence of magnetism is not sufficient for devices, however, as states must be addressable and modifiable through the application of an external drive. We show that defects in hexagonal boron nitride present a strong interplay between the N-N distance in the edge and the magnetic moments of the defects. By stress-induced geometry modifications, we change the ground statemagnetic moment of the defects. This control is made possible by the triangular shape of the defects as well as the strong spin localisation in the magnetic state.

  • N. Mousseau, Enjeux de l’exploitation du gaz et de l’huile de schiste (rapport) (Conseil scientifique région d’Île-de-France, 2012; http://normandmousseau.com/publications/144.pdf), 33 pp.

  • N. Mousseau, Le défi des ressources minières (Éditions MultiMondes, 2012), 275 pp.


  • 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.
  • Mousseau, Normand, in Sortir de l’économie du désastre : austérité, inégalités, résistance, Élie, Bernard, Vaillancourt, Claude, Eds. (M Éditeur, 2012), p. 131-144.
  • Mousseau, Normand, in L'État du Québec 2013, Fahmy, Miriam, Eds. (Boréal, 2012), p. 429-435.


  • J. Nasica-Labouze, N. Mousseau, Kinetics of Amyloid Aggregation: A Study of the GNNQQNY Prion Sequence, PLoS Comput Biol 8, e1002782 (2012).
    Abstract: Author SummaryProtein aggregation plays an important pathological role in numerous neurodegenerative diseases such as Alzheimer's, Parkinson's, Creutzfeldt-Jakob, the Prion disease and diabetes mellitus. In most cases, misfolded proteins are involved and aggregate irreversibly to form highly ordered insoluble macrostructures, called amyloid fibrils, which deposit in the brain. Studies have revealed that all proteins are capable of forming amyloid fibrils that all share common structural features and therefore aggregation mechanisms. The toxicity of amyloid aggregates is however not attributed to the fibrils themselves but rather to smaller more disordered aggregates, oligomers, forming parallel to or prior to fibrils. Understanding the assembly process of these amyloid oligomers is key to understanding their toxicity mechanism in order to devise a possible treatment strategy targeting these toxic aggregates. Our approach here is to computationally study the aggregation dynamics of a 20-mer of an amyloid peptide GNNQQNY from a prion protein. Our findings suggest that the assembly is a spontaneous process that can be described as a complex nucleation and growth mechanism and which can lead to two classes of morphologies for the aggregates, one of which resembles a protofibril-like structure. Such numerical studies are crucial to understanding the details of fast biological processes and complement well experimental studies.


  • J. - F. St-Pierre, A. Bunker, T. Róg, M. Karttunen, N. Mousseau, Molecular Dynamics Simulations of the Bacterial ABC Transporter SAV1866 in the Closed Form, The Journal of Physical Chemistry B 116, 2934-2942 (2012).
    Abstract: The ATP binding cassette (ABC) transporter family of proteins contains members involved in ATP-mediated import or export of ligands at the cell membrane. For the case of exporters, the translocation mechanism involves a large-scale conformational change that involves a clothespin-like motion from an inward-facing open state, able to bind ligands and adenosine triphosphate (ATP), to an outward-facing closed state. Our work focuses on SAV1866, a bacterial member of the ABC transporter family for which the structure is known for the closed state. To evaluate the ability of this protein to undergo conformational changes at physiological temperature, we first performed conventional molecular dynamics (MD) on the cocrystallized adenosine diphosphate (ADP)-bound structure and on a nucleotide-free structure. With this assessment of SAV1866?s stability, conformational changes were induced by steered molecular dynamics (SMD), in which the nucleotide binding domains (NBD) were pushed apart, simulating the ATP hydrolysis energy expenditure. We found that the transmembrane domain is not easily perturbed by large-scale motions of the NBDs.
    Tags: flexibilite.


  • 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.


  • S. Talon, N. Mousseau, G. Peslherbe, F. Bertrand, P. Gauthier, L. Kadem, et al., Proceedings of the High Performance Computing Symposium 2011, Journal of Physics: Conference Series 341, 011001 (2012).
    Abstract: HPCS (High Performance Computing Symposium) is a multidisciplinary conference that focuses on research involving High Performance Computing and its application. Attended by Canadian and international experts and renowned researchers in the sciences, all areas of engineering, the applied sciences, medicine and life sciences, mathematics, the humanities and social sciences, it is Canada's pre-eminent forum for HPC. The 25th edition was held in Montréal, at the Université du Québec à Montréal, from 15–17 June and focused on HPC in Medical Science. The conference was preceded by tutorials held at Concordia University, where 56 participants learned about HPC best practices, GPU computing, parallel computing, debugging and a number of high-level languages. 274 participants from six countries attended the main conference, which involved 11 invited and 37 contributed oral presentations, 33 posters, and an exhibit hall with 16 booths from our sponsors. The work that follows is a collection of papers presented at the conference covering HPC topics ranging from computer science to bioinformatics. They are divided here into four sections: HPC in Engineering, Physics and Materials Science, HPC in Medical Science, HPC Enabling to Explore our World and New Algorithms for HPC. We would once more like to thank the participants and invited speakers, the members of the Scientific Committee, the referees who spent time reviewing the papers and our invaluable sponsors. To hear the invited talks and learn about 25 years of HPC development in Canada visit the Symposium website: http://2011.hpcs.ca/lang/en/conference/keynote-speakers/ Enjoy the excellent papers that follow, and we look forward to seeing you in Vancouver for HPCS 2012! Gilles Peslherbe Chair of the Scientific Committee Normand Mousseau Co-Chair of HPCS 2011 Suzanne Talon Chair of the Organizing Committee The PDF also contains photographs from the conference banquet.

2011



  • L. K. Béland, P. Brommer, F. El-Mellouhi, J. - F. Joly, N. Mousseau, Kinetic activation-relaxation technique, Physical Review E 84, 046704 (2011).
    Abstract: We present a detailed description of the kinetic activation-relaxation technique (k-ART), an off-lattice, self-learning kinetic Monte Carlo (KMC) algorithm with on-the-fly event search. Combining a topological classification for local environments and event generation with ART nouveau, an efficient unbiased sampling method for finding transition states, k-ART can be applied to complex materials with atoms in off-lattice positions or with elastic deformations that cannot be handled with standard KMC approaches. In addition to presenting the various elements of the algorithm, we demonstrate the general character of k-ART by applying the algorithm to three challenging systems: self-defect annihilation in c-Si (crystalline silicon), self-interstitial diffusion in Fe, and structural relaxation in a-Si (amorphous silicon).
    Tags: ARTc.


  • S. Côté, P. Derreumaux, N. Mousseau, Distinct Morphologies for Amyloid Beta Protein Monomer: Aβ1–40, Aβ1–42, and Aβ1–40(D23N), Journal of Chemical Theory and Computation 7, 2584-2592 (2011).
    Abstract: Numerous experimental studies indicate that amyloid beta protein (A?) oligomers as small as dimers trigger Alzheimer?s disease. Precise solution conformation of A? monomer is missing since it is highly dynamic and aggregation prone. Such a knowledge is however crucial to design drugs inhibiting oligomers and fibril formation. Here, we determine the equilibrium structures of the A?1?40, A?1?42, and A?1?40(D23N) monomers using an accurate coarse-grained force field coupled to Hamiltonian-temperature replica exchange molecular dynamics simulations. We observe that even if these three alloforms are mostly disordered at the monomeric level, in agreement with experiments and previous simulations on A?1?40 and A?1?42, striking morphological differences exist. For instance, A?1?42 and A?1?40(D23N) have higher ?-strand propensities at the C-terminal, residues 30?42, than A?1?40. The D23N mutation enhances the conformational freedom of the residues 22?29 and the propensity for turns and ?-strands in the other regions. It also changes the network of contacts; the N-terminal (residues 1?16) becoming more independent from the rest of the protein, leading to a less compact morphology than the wild-type sequence. These structural properties could explain in part why the kinetics and the final amyloid products vary so extensively between the A?1?40 and the A?1?40(D23N) peptides.


  • A. Kerrache, N. Mousseau, L. J. Lewis, Crystallization of amorphous silicon induced by mechanical shear deformations, Physical Review B 84, 014110 (2011).
    Abstract: We investigate the response of amorphous silicon (a-Si) to external mechanical shear deformations using classical molecular dynamics simulations and the empirical environment dependent interatomic potential [Phys. Rev. B 56, 8542 (1997)]. In agreement with previous results, we find that, at low shear velocity and low temperature, shear deformations increase disorder and defect density. At low shear and high temperature, the deformations are found to induce crystallization, demonstrating a dynamical transition associated with both shear rate and temperature. The properties of a-Si under shear deformations and the extent at which the system crystallizes are analyzed in terms of the potential energy difference between the sheared and nonsheared material, as well as the fraction of defects and the number of particles that possess a crystalline environment.


  • A. Kerrache, N. Mousseau, L. J. Lewis, Amorphous silicon under mechanical shear deformations: Shear velocity and temperature effects, Physical Review B 83, 134122 (2011).
    Abstract: Mechanical shear deformations lead, in some cases, to effects similar to those resulting from ion irradiation. Here we characterize the effects of shear velocity and temperature on amorphous silicon (a-Si) modeled using classical molecular-dynamics simulations based on the empirical environment-dependent interatomic potential (EDIP). With increasing shear velocity at low temperature, we find a systematic increase in the internal strain leading to the rapid appearance of structural defects (fivefold-coordinated atoms). The impacts of externally applied strain can be almost fully compensated by increasing the temperature, allowing the system to respond more rapidly to the deformation. In particular, we find opposite power-law relations between the temperature and the shear velocity and the deformation energy. The spatial distribution of defects is also found to depend strongly on temperature and strain velocity. For low temperature or high shear velocity, defects are concentrated in a few atomic layers near the center of the cell, while with increasing temperature or decreasing shear velocity, they spread slowly throughout the full simulation cell. This complex behavior can be related to the structure of the energy landscape and the existence of a continuous energy-barrier distribution.
    Tags: Amorphe.


  • R. Laghaei, N. Mousseau, G. Wei, Structure and Thermodynamics of Amylin Dimer Studied by Hamiltonian-Temperature Replica Exchange Molecular Dynamics Simulations, The Journal of Physical Chemistry B 115, 3146-3154 (2011).
    Abstract: The loss of the insulin-producing ?-cells in the pancreatic islets of Langerhans, responsible for type-II diabetes, is associated with islet amyloid deposits. The main component of these deposits is the amyloid fibrils formed by the 37-residue human islet amyloid polypeptide (hIAPP also known as amylin). Although the fibrils are well characterized by cross ? structure, the structure of the transient oligomers formed in the early stage of aggregation remains elusive. In this study, we apply the Hamiltonian-temperature replica exchange molecular dynamics to characterize the structure and thermodynamics of a full-length hIAPP dimer in both the presence and the absence of the Cys2?Cys7 disulfide bond. We compare these results with those obtained on the monomeric and dimeric forms of rat IAPP (rIAPP) with a disulfide bridge which differ from the hIAPP by 6 amino acids in the C-terminal region, but it is unable to form fibrils. Using a coarse-grained protein force field (OPEP?the Optimized Potential for Efficient peptide structure Prediction) running for a total of 10?28 ?s per system studied, we show that sequences sample α-helical structure in the N-terminal region but that the length of this secondary element is shorter and less stable for the chains without the disulfide bridge (residues 5?16 for hIAPP with the bridge vs 10?16 for hIAPP without the bridge). This α-helix is known to be an important transient stage in the formation of oligomers. In the C-terminal, the amyloidogenic region of hIAPP, ?-strands are seen for residues 17?26 and 30?35. On the contrary, no significant ?-sheet content in the C-terminal is observed for either the monomeric or the dimeric rIAPP. These numerical results are fully consistent with recent experimental findings that the N-terminal residues are not part of the fibril by forming α-helical structure but rather play a significant role in stabilizing the amyloidogenic region available for the fibrillation.


  • M. - C. Marinica, F. Willaime, N. Mousseau, Energy landscape of small clusters of self-interstitial dumbbells in iron, Physical Review B 83, 094119 (2011).
    Abstract: The activation-relaxation technique nouveau (ARTn), a method for the systematic search of the minima and saddle-point configurations, is applied to the study of interstitial-cluster defects in iron. Some simple modifications to improve the efficiency of the ARTn method for these types of applications are proposed. The energy landscapes at 0 K of defect clusters with up to four self-interstitial atoms obtained using the Ackland-Mendelev potential for iron are presented. The efficiency of the method is demonstrated in the case of monointerstitials. The number of different bound configurations increases very rapidly with cluster size from di- to quadri-interstitials. All these clusters can be analyzed as assemblies of dumbbells mostly with ⟨110⟩ orientation. The lowest-energy configurations found with the present method and potential are made of parallel dumbbells. The mechanisms associated with the lowest saddle-point energies are analyzed. They include local rearrangements that do not contribute to long-range diffusion. The translation-rotation mechanism is confirmed for the migration of mono- and di-interstitials. For the tri-interstitial the migration is dominated by three mechanisms that do not involve the lowest-energy configuration. The migration of quadri-interstitials occurs by an on-site reorientation of the dumbbells in the ⟨111⟩ direction, followed by the conventional easy glide. Finally, the minimum energy paths are investigated for the transformation toward the lowest-energy configuration of two specific clusters, including a quadri-interstitial cluster with a ring configuration, which was shown to exhibit an unexpected low mobility in previous molecular-dynamics simulations.

  • N. Mousseau, Comment gérer les ressources naturelles pour le bénéfice de leurs propriétaires ?, Revue Vie Économique 3 (2011) (available at http://normandmousseau.com/publications/140.pdf).


  • 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.
  • Mousseau, Normand, Eds., Mousseau, Normand, Eds. Nuclear Energy after Fukushima / L’Énergie nucléaire après Fukushima, La Physique au Canada/Physics in Canada 67 (2011).


  • J. Nasica-Labouze, M. Meli, P. Derreumaux, G. Colombo, N. Mousseau, A Multiscale Approach to Characterize the Early Aggregation Steps of the Amyloid-Forming Peptide GNNQQNY from the Yeast Prion Sup-35, PLoS Comput Biol 7, e1002051 (2011).
    Abstract: Author Summary The formation of amyloid fibrils is associated with many neurodegenerative diseases such as Alzheimer's, Creutzfeld-Jakob, Parkinson's, the Prion disease and diabetes mellitus. In all cases, proteins misfold to form highly ordered insoluble aggregates called amyloid fibrils that deposit intra- and extracellularly and are resistant to proteases. All proteins are believed to have the instrinsic capability of forming amyloid fibrils that share common specific structural properties that have been observed by X-ray crystallography and by NMR. However, little is known about the aggregation dynamics of amyloid assemblies, and their toxicity mechanism is therefore poorly understood. It is believed that small amyloid oligomers, formed on the aggregation pathway of full amyloid fibrils, are the toxic species. A detailed atomic characterization of the oligomerization process is thus necessary to further our understanding of the amyloid oligomer's toxicity. Our approach here is to study the aggregation dynamics of a 7-residue amyloid peptide GNNQQNY through a combination of numerical techniques. Our results suggest that this amyloid sequence can form fibril-like structures and is polymorphic, which agrees with recent experimental observations. The ability to fully characterize and describe the aggregation pathway of amyloid sequences numerically is key to the development of future drugs to target amyloid oligomers.
    Tags: amyloide.


  • J. - F. St-Pierre, M. Karttunen, N. Mousseau, T. Róg, A. Bunker, Use of Umbrella Sampling to Calculate the Entrance/Exit Pathway for Z-Pro-Prolinal Inhibitor in Prolyl Oligopeptidase, Journal of Chemical Theory and Computation 7, 1583-1594 (2011).
    Abstract: Prolyl oligopeptidase (POP), a member of the prolyl endopeptidase family, is known to play a role in several neurological disorders. Its primary function is to cleave a wide range of small oligopeptides, including neuroactive peptides. We have used force biased molecular dynamics simulation to study the binding mechanism of POP. We examined three possible binding pathways using Steered Molecular Dynamics (SMD) and Umbrella Sampling (US) on a crystal structure of porcine POP with bound Z-pro-prolinal (ZPP). Using SMD, an exit pathway between the first and seventh blade of the ?-propeller domain of POP was found to be a nonviable route. US on binding pathways through the ?-propeller tunnel and the TYR190-GLN208 flexible loop at the interface between both POP domains allowed us to isolate the flexible loop pathway as the most probable. Further analysis of that pathway suggests a long-range covariation of the interdomain H-bond network, which indicates the possibility of large-scale domain reorientation observed in bacterial homologues and hypothesized to also occur in human POP.

2010



  • H. Kallel, N. Mousseau, F. Schiettekatte, Evolution of the Potential-Energy Surface of Amorphous Silicon, Physical Review Letters 105, 045503 (2010).
    Abstract: The link between the energy surface of bulk systems and their dynamical properties is generally difficult to establish. Using the activation-relaxation technique, we follow the change in the barrier distribution of a model of amorphous silicon as a function of the degree of global relaxation. We find that while the barrier-height distribution, calculated from the initial minimum, is a unique function that depends only on the level of relaxation, the reverse-barrier height distribution, calculated from the final state, is independent of global relaxation, following a different function. Moreover, the resulting gained or released energy distribution is a simple convolution of these two distributions indicating that the activation and relaxation parts of the elementary relaxation mechanism are completely independent. This characterized energy landscape can be used to explain nanocalorimetry measurements.
    Tags: Amorphe.
    Attachment Full Text PDF 302 kb (source)


  • R. Laghaei, N. Mousseau, Spontaneous formation of polyglutamine nanotubes with molecular dynamics simulations, The Journal of Chemical Physics 132, 165102 (2010).
    Abstract: Expansion of polyglutamine (polyQ) beyond the pathogenic threshold (35–40 Gln) is associated with several neurodegenerative diseases including Huntington’s disease, several forms of spinocerebellar ataxias and spinobulbar muscular atrophy. To determine the structure of polyglutamine aggregates we perform replica-exchange molecular dynamics simulations coupled with the optimized potential for effective peptide forcefield. Using a range of temperatures from 250 to 700 K, we study the aggregation kinetics of the polyglutamine monomer and dimer with chain lengths from 30 to 50 residues. All monomers show a similar structural change at the same temperature from α -helical structure to random coil, without indication of any significant β -strand. For dimers, by contrast, starting from random structures, we observe spontaneous formation of antiparallel β -sheets and triangular and circular β -helical structures for polyglutamine with 40 residues in a 400 ns 50 temperature replica-exchange molecular dynamics simulation (total integrated time 20 μ s ). This ∼ 32 Å diameter structure reorganizes further into a tight antiparallel double-stranded ∼ 22 Å nanotube with 22 residues per turn close to Perutz’ model for amyloid fibers as water-filled nanotubes. This diversity of structures suggests the existence of polymorphism for polyglutamine with possibly different pathways leading to the formation of toxic oligomers and to fibrils.
    Tags: amyloide.
    Attachment Full Text PDF 851.2 kb (source)


  • R. Laghaei, N. Mousseau, G. Wei, Effect of the Disulfide Bond on the Monomeric Structure of Human Amylin Studied by Combined Hamiltonian and Temperature Replica Exchange Molecular Dynamics Simulations, The Journal of Physical Chemistry B 114, 7071-7077 (2010).
    Abstract: The human Islet amyloid polypeptide (hIAPP or amylin) is a 37-residue peptide hormone that is normally cosecreted with insulin by the pancreatic ?-cells. In patients with type 2 diabetes, hIAPP deposits as amyloid fibrils in the extracellular spaces of the pancreatic islets. Recent experimental studies show that the intramolecular disulfide bond between Cys2 and Cys7 plays a central role in the process of fibril formation. However, the effect of the disulfide bond on the intrinsic structural properties of monomeric hIAPP is yet to be determined. In this study, we characterize the atomic structure and the thermodynamics of full-length hIAPP in the presence and absence of a disulfide bond using extensive combined Hamiltonian and temperature replica exchange molecular dynamics simulations (HT-REMD) with a coarse grained protein force field. Our simulations show that HT-REMD is more efficient in sampling than temperature REMD. On the basis of a total simulation time of 28 ?s, we find that, although native hIAPP (in the presence of a disulfide bond) essentially adopts a disordered conformation in solution, consistent with the signal measured by ultraviolet-circular dichroism (UV-CD) spectroscopy, it also transiently samples α-helical structure for residues 5?16. In comparison with the N-terminal region, the C-terminal region is highly disordered and populates a much lesser content of isolated ?-strand conformation for residues 22?26 and 30?35. Moreover, the absence of the disulfide bond greatly decreases the extent of helix formed throughout residues 5?9 in favor of random coil and ?-sheet structure. Implications of the stabilization of N-terminal helical structure by disulfide bond on the initialization of hIAPP amyloid formation are discussed.

  • N. Mousseau, La révolution des gaz de schiste (Éditions MultiMondes, 2010), 161 pp.

2009



  • Y. Chebaro, X. Dong, R. Laghaei, P. Derreumaux, N. Mousseau, Replica Exchange Molecular Dynamics Simulations of Coarse-grained Proteins in Implicit Solvent, The Journal of Physical Chemistry B 113, 267-274 (2009).
    Abstract: Current approaches aimed at determining the free energy surface of all-atom medium-size proteins in explicit solvent are slow and are not sufficient to converge to equilibrium properties. To ensure a proper sampling of the configurational space, it is preferable to use reduced representations such as implicit solvent and/or coarse-grained protein models, which are much lighter computationally. Each model must be verified, however, to ensure that it can recover experimental structures and thermodynamics. Here we test the coarse-grained implicit solvent OPEP model with replica exchange molecular dynamics (REMD) on six peptides ranging in length from 10 to 28 residues: two alanine-based peptides, the second ?-hairpin from protein G, the Trp-cage and zinc-finger motif, and a dimer of a coiled coil peptide. We show that REMD-OPEP recovers the proper thermodynamics of the systems studied, with accurate structural description of the ?-hairpin and Trp-cage peptides (within 1?2 Å from experiments). The light computational burden of REMD-OPEP, which enables us to generate many hundred nanoseconds at each temperature and fully assess convergence to equilibrium ensemble, opens the door to the determination of the free energy surface of larger proteins and assemblies.


  • Y. Chebaro, N. Mousseau, P. Derreumaux, Structures and Thermodynamics of Alzheimer’s Amyloid-β Aβ(16−35) Monomer and Dimer by Replica Exchange Molecular Dynamics Simulations: Implication for Full-Length Aβ Fibrillation, The Journal of Physical Chemistry B 113, 7668-7675 (2009).
    Abstract: Many proteins display a strand-loop-strand motif in their amyloid fibrillar states. For instance, the amyloid ?-protein, A?1?40, associated with Alzheimer?s disease, displays a loop at positions 22?28 in its amyloid fibril state. It has been suggested that this loop could appear early in the aggregation process, but quantitative information regarding its presence in small oligomers remains scant. Because residues 1?15 are disordered in A?1?42 fibrils and A?10?35 forms fibrils in vitro, we select the peptide A?16?35, centered on residues 22?28 and determine the structures and thermodynamics of the monomer and dimer using coarse-grained implicit solvent replica exchange molecular dynamics simulations. Our simulations totalling 5 ?s for the monomer and 12 ?s for the dimer show no sign of strong secondary structure signals in both instances and the significant impact of dimerization on the global structure of A?16?35. They reveal however that the loop 22?28 acts as a quasi-independent unit in both species. The loop structure ensemble we report in A?16?35 monomer and dimer has high similarity to the loop formed by the A?21?30 peptide in solution and, to a lesser extent, to the loop found in A?1?40 fibrils. We discuss the implications of our findings on the assembly of full-length A?.


  • Y. Lu, P. Derreumaux, Z. Guo, N. Mousseau, G. Wei, Thermodynamics and dynamics of amyloid peptide oligomerization are sequence dependent, Proteins: Structure, Function, and Bioinformatics 75, 954-963 (2009).
    Abstract: Aggregation of the full-length amyloid-β (Aβ) and β2-microglobulin (β2m) proteins is associated with Alzheimer's disease and dialysis-related amyloidosis, respectively. This assembly process is not restricted to full-length proteins, however, many short peptides also assemble into amyloid fibrils in vitro. Remarkably, the kinetics of amyloid-fibril formation of all these molecules is generally described by a nucleation-polymerization process characterized by a lag phase associated with the formation of a nucleus, after which fibril elongation occurs rapidly. In this study, we report using long molecular dynamics simulations with the OPEP coarse-grained force field, the thermodynamics and dynamics of the octamerization for two amyloid 7-residue peptides: the β2m83-89 NHVTLSQ and Aβ16-22 KLVFFAE fragments. Based on multiple trajectories run at 310 K, totaling 2.2 μs (β2m83-89) and 4.8 μs (Aβ16-22) and starting from random configurations and orientations of the chains, we find that the two peptides not only share common but also very different aggregation properties. Notably, an increase in the hydrophobic character of the peptide, as observed in Aβ16-22 with respect to β2m83-89 impacts the thermodynamics by reducing the population of bilayer β-sheet assemblies. Higher hydrophobicity is also found to slow down the dynamics of β-sheet formation by enhancing the averaged lifetime of all configuration types (CT) and by reducing the complexity of the CT transition probability matrix. Proteins 2009. © 2008 Wiley-Liss, Inc.
    Attachment 116.pdf 560 kb

  • N. Mousseau, L’avenir du Québec passe par l’indépendance énergétique (Éditions MultiMondes, 2009), 184 pp.

  • Mousseau, Normand, in Avez-vous peur du nucléaire ? Vous devriez peut-être.., par Julie Lemieux, (Éditions MultiMondes, 2009), p. 202.

2008



  • X. Dong, W. Chen, N. Mousseau, P. Derreumaux, Energy landscapes of the monomer and dimer of the Alzheimer’s peptide Aβ(1–28), The Journal of Chemical Physics 128, 125108 (2008).
    Abstract: The cytoxicity of Alzheimer’s disease has been linked to the self-assembly of the 40 ∕ 42 amino acid of the amyloid- β ( A β ) peptide into oligomers. To understand the assembly process, it is important to characterize the very first steps of aggregation at an atomic level of detail. Here, we focus on the N-terminal fragment 1–28, known to form fibrilsin vitro. Circular dichroism and NMR experiments indicate that the monomer of A β ( 1 – 28 ) is α -helical in a membranelike environment and random coil in aqueous solution. Using the activation-relaxation technique coupled with the OPEP coarse grained force field, we determine the structures of the monomer and of the dimer of A β ( 1 – 28 ) . In agreement with experiments, we find that the monomer is predominantly random coil in character, but displays a non-negligible β -strand probability in the N-terminal region. Dimerization impacts the structure of each chain and leads to an ensemble of intertwined conformations with little β -strand content in the region Leu17-Ala21. All these structural characteristics are inconsistent with the amyloidfibril structure and indicate that the dimer has to undergo significant rearrangement en route to fibril formation.
    Attachment Full Text PDF 1.9 Mb (source)


  • F. El-Mellouhi, N. Mousseau, L. J. Lewis, Kinetic activation-relaxation technique: An off-lattice self-learning kinetic Monte Carlo algorithm, Physical Review B 78, 153202 (2008).
    Abstract: Many materials science phenomena are dominated by activated diffusion processes and occur on time scales that are well beyond the reach of standard molecular-dynamics simulations. Kinetic Monte Carlo (KMC) schemes make it possible to overcome this limitation and achieve experimental time scales. However, most KMC approaches proceed by discretizing the problem in space in order to identify, from the outset, a fixed set of barriers that are used throughout the simulations, limiting the range of problems that can be addressed. Here, we propose a flexible approach—the kinetic activation-relaxation technique (k-ART)—which lifts these constraints. Our method is based on an off-lattice, self-learning, on-the-fly identification and evaluation of activation barriers using ART and a topological description of events. Using this method, we demonstrate that elastic deformations are determinant to the diffusion kinetics of vacancies in Si and are responsible for their trapping.
    Tags: ARTc.
    Attachment Full Text PDF 168.3 kb (source)


  • K. Levasseur-Smith, N. Mousseau, Numerical characterization of the Ga interstitial self-diffusion mechanisms in GaAs, Journal of Applied Physics 103, 113502 (2008).
    Abstract: Recent diffusion experiments by Bracht and Brotzmann [H. Bracht and S. Brotzmann, Phys. Rev. B71, 115216 (2005)] show that the dominant charge states for Ga I diffusion in GaAs should be 0 and + 1 with surprisingly high enthalpy barriers of 5.45 ± 0.12 and 5.80 ± 0.32 eV , respectively. Using the activation-relaxation technique, coupled with the ab initio code SIESTA, we identify possible migration pathways and barriers for these two charge states. In the + 1 charge state, we observe two different migration paths between tetrahedral sites surrounded by Ga atoms ( tetra [ Ga − Ga ] ) , implicating either a tetrahedral interstitial surrounded by As atoms ( tetra [ Ga − As ] ) or a ⟨ 111 ⟩ -oriented split configuration, with total barriers of 1.4 and 1.3 eV, respectively. Including formation energy, the enthalpy barriers that we find are lower than the experimentally derived values. We analyze the possible causes and the significance of this discrepancy and offer a partial explanation based on the correction method used for finite-size effects.
    Attachment Full Text PDF 365.9 kb (source)


  • C. Liang, P. Derreumaux, N. Mousseau, G. Wei, The β-Strand-Loop-β-Strand Conformation Is Marginally Populated in β2-Microglobulin (20–41) Peptide in Solution as Revealed by Replica Exchange Molecular Dynamics Simulations, Biophysical Journal 95, 510-517 (2008).
    Abstract: Solid-state NMR study shows that the 22-residue K3 peptide (Ser20-Lys41) from β2-microglobulin (β2m) adopts a β-strand-loop-β-strand conformation in its fibril state. Residue Pro32 has a trans conformation in the fibril state of the peptide, while it adopts a cis conformation in the native state of full-length β2m. To get insights into the structural properties of the K3 peptide, and determine whether the strand-loop-strand conformation is encoded at the monomeric level, we run all-atom explicit solvent replica exchange molecular dynamics on both the cis and trans variants. Our simulations show that the conformational space of the trans- and cis-K3 peptides is very different, with 1% of the sampled conformations in common at room temperature. In addition, both variants display only 0.3–0.5% of the conformations with β-strand-loop-β-strand character. This finding, compared to results on the Alzheimer's Aβ peptide, suggests that the biases toward aggregation leading to the β-strand-loop-β-strand conformation in fibrils are peptide-dependent.


  • A. Melquiond, X. Dong, N. Mousseau, P. Derreumaux, Role of the Region 23-28 in Aβ Fibril Formation: Insights from Simulations of the Monomers and Dimers of Alzheimers Peptides Aβ40 and Aβ42, Current Alzheimer Research 5, 244-250 (2008).

  • N. Mousseau, Au bout du pétrole. Tout ce que vous devez savoir sur la crise énergétique (Éditions MultiMondes, 2008), 156 pp.
  • N. Mousseau, P. Derreumaux, Exploring energy landscapes of protein folding and aggregation, Frontiers in Bioscience: A Journal and Virtual Library 13, 4495-4516 (2008).
    Abstract: Human diseases, such as Alzheimer's and Creutzfeldt-Jakob's are associated with misfolding and aggregation of specific proteins into amyloid fibrils sharing a generic cross-beta structure. The self-assembly process is complex, but once a nucleus is formed, rapid fibril formation occurs. Insight into the structures of the oligomers during the lag phase, varying between hours and days, is very difficult experimentally because these species are transient, and numerically using all-atom molecular dynamics because the time scale explored is on the order of 10-100 ns. It is therefore important to develop simplified protein models and alternative methods to sample more efficiently the conformational space. In the past few years, we have developed the activation-relaxation technique (ART nouveau) coupled to the OPEP coarse-grained force field. This review reports the application of ART-OPEP on protein folding and aggregation.
    Attachment 109.pdf 1.1 Mb
  • N. Mousseau, in Raisons d’être : Le sens à l’épreuve de la science et de la religion, Solange Lefebvre, Eds. (Les Presses de l’Université de Montréal, 2008), p. 39-50.
  • Mousseau, Normand, in L'état du Québec 2009, Fahmy, Miriam, Eds. (Fides, (chapitre invité), 2008), p. 609-613.


  • W. Song, G. Wei, N. Mousseau, P. Derreumaux, Self-Assembly of the β2-Microglobulin NHVTLSQ Peptide Using a Coarse-Grained Protein Model Reveals a β-Barrel Species, The Journal of Physical Chemistry B 112, 4410-4418 (2008).
    Abstract: Although a wide variety of proteins can assemble into amyloid fibrils, the structure of the early oligomeric species on the aggregation pathways remains unknown at an atomic level of detail. In this paper we report, using molecular dynamics simulations with the OPEP coarse-grained force field, the free energy landscape of a tetramer and a heptamer of the ?2-microglobulin NHVTLSQ peptide. On the basis of a total of more than 17 ns trajectories started from various states, we find that both species are in equilibrium between amorphous and well-ordered aggregates with cross-?-structure, a perpendicular bilayer ?-sheet, and, for the heptamer, six- or seven-stranded closed and open ?-barrels. Moreover, analysis of the heptamer trajectories shows that the perpendicular bilayer ?-sheet is one possible precursor of the ?-barrel, but that this barrel can also be formed from a twisted monolayer ?-sheet with successive addition of chains. Comparison with previous aggregation simulations and the fact that nature constructs transmembrane ?-sheet proteins with pores open the possibility that ?-barrels with small inner diameters may represent a common intermediate during the early steps of aggregation.


  • J. - F. St-Pierre, N. Mousseau, P. Derreumaux, The complex folding pathways of protein A suggest a multiple-funnelled energy landscape, The Journal of Chemical Physics 128, 045101 (2008).
    Abstract: Folding proteins into their native states requires the formation of both secondary and tertiary structures. Many questions remain, however, as to whether these form into a precise order, and various pictures have been proposed that place the emphasis on the first or the second level of structure in describing folding. One of the favorite test models for studying this question is the B domain of protein A, which has been characterized by numerous experiments and simulations. Using the activation-relaxation technique coupled with a generic energy model (optimized potential for efficient peptide structure prediction), we generate more than 50 folding trajectories for this 60-residue protein. While the folding pathways to the native state are fully consistent with the funnel-like description of the free energy landscape, we find a wide range of mechanisms in which secondary and tertiary structures form in various orders. Our nonbiased simulations also reveal the presence of a significant number of non-native β and α conformations both on and off pathway, including the visit, for a non-negligible fraction of trajectories, of fully ordered structures resembling the native state of nonhomologous proteins.
    Tags: flexibilite.
    Attachment Full Text PDF 1.1 Mb (source)
  • G. Wei, W. Song, P. Derreumaux, N. Mousseau, Self-assembly of amyloid-forming peptides by molecular dynamics simulations, Frontiers in Bioscience: A Journal and Virtual Library 13, 5681-5692 (2008).
    Abstract: Protein aggregation is associated with many neurodegenerative diseases. Understanding the aggregation mechanisms is a fundamental step in order to design rational drugs interfering with the toxic intermediates. This self-assembly process is however difficult to observe experimentally, which gives simulations an important role in resolving this problem. This study shows how we can proceed to gain knowledge about the first steps of aggregation. We first start by characterizing the free energy surface of the Abeta (16-22) dimer, a well-studied system numerically, using molecular dynamics simulations with OPEP coarse-grained force field. We then turn to the study of the NHVTLSQ peptide in 4-mers and 16-mers, extracting information on the onset of aggregation. In particular, the simulations indicate that the peptides are mostly random coil at room temperature, but can visit diverse amyloid-competent topologies, albeit with a low probability. The fact that the 16-mers constantly move from one structure to another is consistent with the long lag phase measured experimentally, but the rare critical steps leading to the rapid formation of amyloid fibrils still remain to be determined.
    Attachment 110.pdf 989.2 kb

2007



  • M. - A. Brière, M. V. Chubynsky, N. Mousseau, Self-organized criticality in the intermediate phase of rigidity percolation, Physical Review E 75, 056108 (2007).
    Abstract: Experimental results for covalent glasses have highlighted the existence of a self-organized phase due to the tendency of glass networks to minimize internal stress. Recently, we have shown that an equilibrated self-organized two-dimensional lattice-based model also possesses an intermediate phase in which a percolating rigid cluster exists with a probability between zero and one, depending on the average coordination of the network. In this paper, we study the properties of this intermediate phase in more detail. We find that microscopic perturbations, such as the addition or removal of a single bond, can affect the rigidity of macroscopic regions of the network, in particular, creating or destroying percolation. This, together with a power-law distribution of rigid cluster sizes, suggests that the system is maintained in a critical state on the rigid-floppy boundary throughout the intermediate phase, a behavior similar to self-organized criticality, but, remarkably, in a thermodynamically equilibrated state. The distinction between percolating and nonpercolating networks appears physically meaningless, even though the percolating cluster, when it exists, takes up a finite fraction of the network. We point out both similarities and differences between the intermediate phase and the critical point of ordinary percolation models without self-organization. Our results are consistent with an interpretation of recent experiments on the pressure dependence of Raman frequencies in chalcogenide glasses in terms of network homogeneity.


  • P. Derreumaux, N. Mousseau, Coarse-grained protein molecular dynamics simulations, The Journal of Chemical Physics 126, 025101 (2007).
    Abstract: A limiting factor in biological science is the time-scale gap between experimental and computational trajectories. At this point, all-atom explicit solventmolecular dynamics (MD) are clearly too expensive to explore long-range protein motions and extract accurate thermodynamics of proteins in isolated or multimeric forms. To reach the appropriate time scale, we must then resort to coarse graining. Here we couple the coarse-grained OPEP model, which has already been used with activated methods, to MD simulations. Two test cases are studied: the stability of three proteins around their experimental structures and the aggregation mechanisms of the Alzheimer’s A β 16 – 22 peptides. We find that coarse-grained isolated proteins are stable at room temperature within 50 ns time scale. Based on two 220 ns trajectories starting from disordered chains, we find that four A β 16 – 22 peptides can form a three-stranded β sheet. We also demonstrate that the reptation move of one chain over the others, first observed using the activation-relaxation technique, is a kinetically important mechanism during aggregation. These results show that MD-OPEP is a particularly appropriate tool to study qualitatively the dynamics of long biological processes and the thermodynamics of molecular assemblies.
    Tags: flexibilite.
    Attachment Full Text PDF 516.5 kb (source)


  • F. El-Mellouhi, N. Mousseau, Ab-initio simulations of self-diffusion mechanisms in semiconductors, Physica B: Condensed Matter 401–402, 658-661 (2007).
    Abstract: We present an application of SIEST-A-RT that combines the activation relaxation technique, ART nouveau, and the local-basis ab-initio code SIESTA, to study self-defect migration pathways in semiconductors. SIESTA provides reliable descriptions of defect properties in semiconductors directly comparable to experiment as well as, once combined with ART nouveau, a detailed description of their possible migration mechanisms. We use this package to characterize the properties of vacancies in silicon and GaAs, such as relaxation geometries, formation energies at low and high temperature, diffusion mechanisms and migration barriers. We show here that diffusion in bulk semiconductors is a rich and complex phenomenon that depends not only on the geometry of the defect and the surrounding lattice but also on its charge.


  • M. - A. Malouin, F. El-Mellouhi, N. Mousseau, Gallium self-interstitial relaxation in GaAs: An ab initio characterization, Physical Review B 76, 045211 (2007).
    Abstract: Ga interstitials in GaAs (IGa) are studied using the local-orbital ab initio code SIESTA in a supercell of 216+1 atoms. Starting from eight different initial configurations, we find five metastable structures: the two tetrahedral sites in addition to the 110-split[Ga-As], 111-split[Ga-As], and 110-split[Ga-Ga]. Studying the competition between various configuration and charges of IGa at T=0K, we find that predominant gallium interstitials in GaAs are charged +1, neutral, or at most −1 depending on doping conditions and prefer to occupy the tetrahedral configuration where it is surrounded by Ga atoms. Our results are in excellent agreement with recent experimental results concerning the dominant charge of IGa, underlining the importance of finite size effects in the calculation of defects.
    Attachment Full Text PDF 414.6 kb (source)


  • A. Melquiond, J. - C. Gelly, N. Mousseau, P. Derreumaux, Probing amyloid fibril formation of the NFGAIL peptide by computer simulations, The Journal of Chemical Physics 126, 065101 (2007).
    Abstract: Amyloidfibril formation, as observed in Alzheimer’s disease and type II diabetes, is currently described by a nucleation-condensation mechanism, but the details of the process preceding the formation of the nucleus are still lacking. In this study, using an activation-relaxation technique coupled to a generic energy model, we explore the aggregation pathways of 12 chains of the hexapeptide NFGAIL. The simulations show, starting from a preformed parallel dimer and ten disordered chains, that the peptides form essentially amorphous oligomers or more rarely ordered β -sheet structures where the peptides adopt a parallel orientation within the sheets. Comparison between the simulations indicates that a dimer is not a sufficient seed for avoiding amorphous aggregates and that there is a critical threshold in the number of connections between the chains above which exploration of amorphous aggregates is preferred.
    Attachment Full Text PDF 450.2 kb (source)

  • G. Wei, N. Mousseau, P. Derreumaux, Computational Simulations of the Early Steps of Protein Aggregation, Prion 1, 3-8 (2007).
    Abstract: There is strong evidence that the oligomers of key proteins, formed during the early steps of aggregation, could be the primary toxic species associated with human neurodegenerative diseases, such as Alzheimer's and prion diseases. Here, we review recent progress in the development of computational approaches in order to understand the structures, dynamics and free energy surfaces of oligomers. We also discuss possible research directions for the coming years.

2006



  • G. Boucher, N. Mousseau, P. Derreumaux, Aggregating the amyloid Aβ11–25 peptide into a four-stranded β-sheet structure, Proteins: Structure, Function, and Bioinformatics 65, 877-888 (2006).
    Abstract: We present a detailed analysis of the structural properties of one monomer of Aβ11–25 as well as of the aggregation mechanisms for four chains of Aβ11–25 using the activation–relaxation technique coupled with a generic energy potential. Starting from a random distribution of these four chains, we find that the system assembles rapidly into a random globular state that evolves into three- and four-stranded antiparallel β-sheets. The aggregation process is considerably accelerated by the presence of preformed dimers. We also find that the reptation mechanism already identified in shorter peptides plays a significant role here in allowing the structure to reorganize without having to fully dissociate. Proteins 2006. © 2006 Wiley-Liss, Inc.


  • W. Chen, N. Mousseau, P. Derreumaux, The conformations of the amyloid-β (21–30) fragment can be described by three families in solution, The Journal of Chemical Physics 125, 084911 (2006).
    Abstract: Alzheimer’s disease has been linked to the self-assembly of the amyloid- β protein of 40 and 42 residues. Although monomers are in equilibrium with higher-order species ranging from dimers to heptamers, structural knowledge of the monomeric amyloid- β ( A β ) peptides is an important issue. Recent experimental data have shown that the fragment (21–30) is protease-resistant within full-length A β peptides and displays two structural families in solution. Because the details of the A β 21 – 30 structures found using distinct force fields and protocols differ at various degrees from those of the NMRstructures, we revisit the conformational space of this peptide using the activation-relaxation technique (ART nouveau) coupled with a coarse-grained force field (OPEP v.3.0). We find that although A β 21 – 30 does not have a secondary structure, it dominantly populates three structural families, with a loop spanning residues Val24-Lys28. The first two families, which differ in the nature of the electrostatic interactions, satisfy the five interproton rotating frame nuclear Overhauser effect spectroscopy (ROESY) distances and superpose well onto the NMRstructures. The third family, which cannot be seen by ROESY NMR experiments, displays a more open structure. This numeric study complements the experimental results by providing a much more detailed description of the dominant structures. Moreover, it provides further evidence of the capability of ART OPEP in providing a reliable conformational picture of peptides in solution.


  • M. V. Chubynsky, M. - A. Brière, N. Mousseau, Self-organization with equilibration: A model for the intermediate phase in rigidity percolation, Physical Review E 74, 016116 (2006).
    Abstract: Recent experimental results for covalent glasses suggest the existence of an intermediate phase attributed to the self-organization of the glass network resulting from the tendency to minimize its internal stress. However, the exact nature of this experimentally measured phase remains unclear. We modified a previously proposed model of self-organization by generating a uniform sampling of stress-free networks. In our model, studied on a diluted triangular lattice, an unusual intermediate phase appears, in which both rigid and floppy networks have a chance to occur, a result also observed in a related model on a Bethe lattice by Barré et al. [Phys. Rev. Lett. 94, 208701 (2005)]. Our results for the bond-configurational entropy of self-organized networks, which turns out to be only about 2% lower than that of random networks, suggest that a self-organized intermediate phase could be common in systems near the rigidity percolation threshold.
    Attachment Full Text PDF 202.6 kb (source)


  • M. V. Chubynsky, H. Vocks, G. T. Barkema, N. Mousseau, Exploiting memory in event-based simulations, Journal of Non-Crystalline Solids 352, 4424-4429 (2006).
    Abstract: Few simulation methods have succeeded in sampling efficiently the phase space of complex systems with a dynamics dominated by activated events. In order to address this limitation, we have recently introduced an activated algorithm based on a mixture of the activation-relaxation technique and molecular dynamics (the properly obeying probability activation relaxation technique, POP-ART). We show here that the basic implementation of POP-ART is only as fast as MD in sampling the phase space of a complex material, amorphous silicon at 600 K. However, as the activation moves are locally defined, it is possible to use a number of tricks that can increase significantly sampling efficiency of POP-ART. We consider an approach, the memory kernel, based on avoiding recently encountered moves and show using a simple model that this introduces very little bias while ensuring a significant gain over standard Monte Carlo in sampling the phase space of this model. Incorporating the memory kernel into POP-ART improves considerably its efficiency in sampling the phase space of amorphous silicon as compared to standard POP-ART and molecular dynamics.


  • F. El-Mellouhi, N. Mousseau, Charge-dependent migration pathways for the Ga vacancy in GaAs, Physical Review B 74, 205207 (2006).
    Abstract: Using a combination of the local-basis ab initio program SIESTA and the activation-relaxation technique we study the diffusion mechanisms of the gallium vacancy in GaAs. Vacancies are found to diffuse to the second neighbor using two different mechanisms, as well as to the first and fourth neighbors following various mechanisms. We find that the height of the energy barrier is sensitive to the Fermi level and generally increases with the charge state. Migration pathways themselves can be strongly charge dependent and may appear or disappear as a function of the charge state. These differences in transition state and migration barrier are explained by the charge transfer that takes place during the vacancy migration.
    Attachment Full Text PDF 576.9 kb (source)


  • F. El-Mellouhi, N. Mousseau, Thermally activated charge reversibility of gallium vacancies in GaAs, Journal of Applied Physics 100, 083521 (2006).
    Abstract: The dominant charge state for the Ga vacancy in GaAs has been the subject of a long debate, with experiments suggesting − 1 , − 2 , or − 3 as the best answer. We revisit this problem using ab initio calculations to compute the effects of temperature on the Gibbs free energy of formation, and we find that the thermal dependence of the Fermi level and of the ionization levels lead to a reversal of the preferred charge state as the temperature increases. Calculating the concentrations of gallium vacancies based on these results, we reproduce two conflicting experimental measurements, showing that these can be understood from a single set of coherent local density approximation results when thermal effects are included.
    Attachment Full Text PDF 738 kb (source)


  • A. Melquiond, N. Mousseau, P. Derreumaux, Structures of soluble amyloid oligomers from computer simulations, Proteins: Structure, Function, and Bioinformatics 65, 180-191 (2006).
    Abstract: Alzheimer's, Parkinson's, and Creutzfeldt-Jakob's neurodegenerative diseases are all linked with the assembly of normally soluble proteins into amyloid fibrils. Because of experimental limitations, structural characterization of the soluble oligomers, which form early in the process of fibrillogenesis and are cytotoxic, remains to be determined. In this article, we study the aggregation paths of seven chains of the shortest amyloid-forming peptide, using an activitated method and a reduced atomic representation. Our simulations show that disordered KFFE monomers ultimately form three distinct topologies of similar energy: amorphous oligomers, incomplete rings with β-barrel character, and cross-β-sheet structures with the meridional but not the equatorial X-ray fiber reflections. The simulations also shed light on the pathways from misfolded aggregates to fibrillar-like structures. They also underline the multiplicity of building blocks that can lead to the formation of the critical nucleus from which rapid growth of the fibril occurs. Proteins 2006. © 2006 Wiley-Liss, Inc.
    Attachment 91.pdf 1 Mb

2005



  • P. Beaucage, N. Mousseau, Liquid–liquid phase transition in Stillinger–Weber silicon, Journal of Physics: Condensed Matter 17, 2269 (2005).
    Abstract: It was recently demonstrated that Stillinger–Weber silicon undergoes a liquid–liquid first-order phase transition deep into the supercooled region (Sastry and Angell 2003 Nat. Mater. 2 739). Here we study the effects of perturbations on this phase transition. We show that the order of the liquid–liquid transition changes with negative pressure. We also find that the liquid–liquid transition disappears when the three-body term of the potential is strengthened by as little as 5%. This implies that the details of the potential could affect strongly the nature and even the existence of the liquid–liquid phase.


  • P. Beaucage, N. Mousseau, Nucleation and crystallization process of silicon using the Stillinger-Weber potential, Physical Review B 71, 094102 (2005).
    Abstract: We study the homogeneous nucleation process in Stillinger-Weber silicon in the canonical ensemble. A clear first-order transition from the liquid to crystal phase is observed thermodynamically with kinetic and structural evidence of the transformation. At 0.75Tm, the critical cluster size is about 175 atoms. The lifetime distribution of clusters as a function of the maximum size they reach follows an inverse Gaussian distribution as was predicted recently from the classical theory of nucleation (CNT). However, while there is a qualitative agreement with the CNT, the free-energy curve obtained from the simulations differs significantly from the theoretical predictions, suggesting that the low-density liquid phase found recently could play a role at the interface between the crystallite and the surrounding liquid during the nucleation process.


  • F. El-Mellouhi, N. Mousseau, Self-vacancies in gallium arsenide: An ab initio calculation, Physical Review B 71, 125207 (2005).
    Abstract: We report here a reexamination of the static properties of vacancies in GaAs by means of first-principles density-functional calculations using localized basis sets. Our calculated formation energies yields results that are in good agreement with recent experimental and ab initio calculation and provide a complete description of the relaxation geometry and energetic for various charge states of vacancies from both sublattices. Gallium vacancies are stable in the 0, −, −2, −3 charge states, but V−3Ga remains the dominant charge state for intrinsic and n-type GaAs, confirming results from positron annihilation. Interestingly, arsenic vacancies show two successive negative-U transitions making only +1, −1, and −3 charge states stable, while the intermediate defects are metastable. The second transition (−/−3) brings a resonant bond relaxation for V−3As similar to the one identified for silicon and GaAs divacancies.
    Attachment Full Text PDF 447.6 kb (source)


  • A. Melquiond, G. Boucher, N. Mousseau, P. Derreumaux, Following the aggregation of amyloid-forming peptides by computer simulations, The Journal of Chemical Physics 122, 174904 (2005).
    Abstract: There is experimental evidence suggesting that the toxicity of neurodegenerative diseases such as Alzheimer’s disease may result from the soluble intermediate oligomers. It is therefore important to characterize extensively the early steps of oligomer formation at atomic level. As these structures are metastable and short lived, experimental data are difficult to obtain and they must be complemented with numerical simulations. In this work, we use the activation-relaxation technique coupled with a coarse-grained energy model to study in detail the mechanisms of aggregation of four lys–phe–phe–glu (KFFE) peptides. This is the shortest peptide known to form amyloidfibrilsin vitro. Our simulations indicate that four KFFE peptides adopt a variety of oligomeric states (tetramers, trimers, and dimers) with various orientations of the chains in rapid equilibrium. This conformational distribution is consistent with all-atom molecular-dynamics simulations in explicit solvent and is sequence dependent; as seen experimentally, the lys–pro–gly–glu (KPGE) peptides adopt disordered structures in solution. Our unbiased simulations also indicate that the assembly process is much more complex than previously thought and point to intermediate structures which likely are kinetic traps for longer chains.
    Tags: amyloide.
    Attachment Full Text PDF 734.8 kb (source)


  • N. Mousseau, P. Derreumaux, G. Gilbert, Navigation and analysis of the energy landscape of small proteins using the activation–relaxation technique, Physical Biology 2, S101 (2005).
    Abstract: The resolution of the protein folding problem has been tied to the development of a detailed understanding of the configurational energy or of the free energy landscape associated with these molecules. Using the activation–relaxation technique and a simplified energy model, we present here a detailed analysis of the energy landscape of 16-residue peptide that folds into a β-hairpin. Our results support the concept of an energy landscape with an effective topology consistent with a scale-free network.


  • N. Mousseau, P. Derreumaux, Exploring the Early Steps of Amyloid Peptide Aggregation by Computers, Accounts of Chemical Research 38, 885-891 (2005).
    Abstract: The assembly of normally soluble proteins into amyloid fibrils is a hallmark of neurodegenerative diseases. Because protein aggregation is very complex, involving a variety of oligomeric metastable intermediates, the detailed aggregation paths and structural characterization of the intermediates remain to be determined. Yet, there is strong evidence that these oligomers, which form early in the process of fibrillogenesis, are cytotoxic. In this paper, we review our current understanding of the underlying factors that promote the aggregation of peptides into amyloid fibrils. We focus here on the structural and dynamic aspects of the aggregation as observed in state-of-the-art computer simulations of amyloid-forming peptides with an emphasis on the activation?relaxation technique.


  • N. Mousseau, M. F. Thorpe, Proceedings of the Workshop on Flexibility in biomolecules, Physical Biology 2, null (2005).
    Abstract: Flexibility in biomolecules is an important determinant of biological functionality. Almost all enzymatic and chemical reactions involve a significant conformational change of the protein and, in general, of the associated ligand. The motions that lead to these conformational changes can be large and occur on time scales that are long compared with thermal vibrations; standard molecular dynamics must therefore be augmented by new approaches. This workshop (http:// biophysics.asu.edu/workshop_2005/index.html) was held in Tempe, Arizona, USA from 15–18 May 2005, and brought together biochemists, chemists, computer scientists, mathematicians and physicists, in an effort to identify and promote the most promising approaches for studying flexibility in biomolecules and biomolecular complexes. The 12 papers that are published in this volume represent a good cross section of the work presented at the workshop. The first papers focus on understanding the structure of the energy landscape of small proteins using full-atom description and various methods allowing a faster sampling of the phase space. The second series of papers focuses more directly on flexibility of biomolecules using topological tools. The third group of papers uses simplified representations in order to address flexibility on a large scale involving thousands of residues. This collection sets out what we think are some of the more promising theoretical approaches currently being explored to study flexibility in biomolecules. We believe that they will be useful to anybody interested in studying this fascinating problem, that is likely to remain challenging for many years to come.
    Attachment Full Text PDF 35.4 kb (source)
  • Santini, Sébastien, Wei, Guanghong, Mousseau, Normand, Derreumaux, Philippe, in Amyloid and Amyloidosis : from molecular dissection to therapeutics, Grateau, G., Kyle R., Skinner, M., Eds. (Life Sciences/CRC Press, 2005), p. 200-203.


  • H. Vocks, M. V. Chubynsky, G. T. Barkema, N. Mousseau, Activated sampling in complex materials at finite temperature: The properly obeying probability activation-relaxation technique, The Journal of Chemical Physics 123, 244707 (2005).
    Abstract: While the dynamics of many complex systems is dominated by activated events, there are very few simulation methods that take advantage of this fact. Most of these procedures are restricted to relatively simple systems or, as with the activation-relaxation technique (ART), sample the conformation space efficiently at the cost of a correct thermodynamical description. We present here an extension of ART, the properly obeying probability ART (POP-ART), that obeys detailed balance and samples correctly the thermodynamic ensemble. Testing POP-ART on two model systems, a vacancy and an interstitial in crystalline silicon, we show that this method recovers the proper thermodynamical weights associated with the various accessible states and is significantly faster than molecular dynamics in the simulations of a vacancy below 700 K.
    Attachment Full Text PDF 330.9 kb (source)

2004



  • P. Derreumaux, G. Wei, S. Santini, N. Mousseau, Early steps of amyloid-petide oligomerisation explored by simulations, Neurobiology of Aging 25, S143 (2004).


  • D. A. Drabold, N. Mousseau, Eds., D. A. Drabold, N. Mousseau, Eds. A Workshop in Honour of Professor Mike Thorpe’s 60th Birthday : Flexibility in Complex Materials : Glasses, Amorphous and Proteins, Journal of Physics: Condensed Matter 16, null (2004).
    Abstract: This volume is the outcome of a three-day meeting held 7-10 August, 2004 in St Adèle, Québec honouring Michael F Thorpe, Foundation Professor of Physics, Chemistry and Biophysics at Arizona State University. Michael Thorpe has made many important contributions to condensed matter physics, broadly defined. From the famous Weaire and Thorpe Hamiltonian in 1971 [1] to rigidity percolation theory [2] and flexibility in proteins [3], he has always provided highly original solutions to difficult problems. He has also demonstrated an uncommon gift for selecting and solving problems of remarkably broad significance (for example, rigidity theory is now a powerful tool in glasses, microelectronics and proteins). Throughout his career, Mike has also made a point of establishing contact with scientists from all disciplines and origins, organizing tens of conferences and maintaining a very active visitor's program both at Michigan State University, where he spent 25 years, and, now, at Arizona State University, where he moved a year ago. It is therefore not surprising that the participants, all with scientific or personal links with Mike, usually both, came from Europe, Asia and North America to celebrate the 60th birthday of an eminent physicist and friend. Reflecting the impact of Mike's work across the traditional scientific boundaries, the meeting included contributions ranging from studies of concrete by Ed Garboczi (NIST), a hybrid VCA/CPA treatment of the Hubbard model presented by Sir Roger Elliott (Oxford) to the assembly process of viral capsids by Brandon Hespenheide (ASU). Especially memorable talks were given by Rafael Barrio (with his photogenic striped imperial fish), Alex Kolobov (presenting impressive scientific results using equally impressive computer graphics), and Dick Zallen, for a remarkably good `roast' of the honoree and work with his daughter (a molecular biologist) on biophysics. The meeting had an unusual warmth befitting the birthday celebration, and was also by any measure a scientific success, with innumerable questions and discussions among this diverse group, and the scholarly contributions in this volume. We thank the participants, and Dr Richard Palmer, the Publisher of Journal of Physics: Condensed Matter and his staff for working to make this volume appear very quickly, thereby increasing the value of the papers to the community. We would also thank the Office of the vice-president for research at Université de Montréal, the Department of Physics and Astronomy at Arizona State University, the Department of Physics and Astronomy at Ohio University and the Canada Research Chair Program for financial assistance that made the meeting more enjoyable. We were both pleased to be part of this delightful occasion, and wish to take this last opportunity to wish Mike a happy birthday, and urge him to even greater achievements in coming years. Bibliography [1] Weaire D and Thorpe M F 1971 Electronic Properties of an Amorphous Solid: I. A Simple Tight Binding Theory Phys. Rev. B 4 2508--20 [2] Thorpe M F 1983 Continuous Deformations in Random Networks J. Non-Cryst. Solids 57 355-70 [3] Jacobs D J, Rader A J, Kuhn L A and Thorpe M F 2001 Protein Flexibilty Predictions using Graph Theory Proteins 44 150-65


  • F. El-Mellouhi, N. Mousseau, P. Ordejón, Sampling the diffusion paths of a neutral vacancy in silicon with quantum mechanical calculations, Physical Review B 70, 205202 (2004).
    Abstract: We report a first-principles study of vacancy-induced self-diffusion in crystalline silicon. Starting from a fully relaxed configuration with a neutral vacancy, we proceed to search for local diffusion paths. The diffusion of the vacancy proceeds by hops to first nearest neighbor with an energy barrier of 0.40eV in agreement with experimental results. Competing mechanisms are identified, such as the reorientation, and the recombination of dangling bonds by Wooten-Winer-Weaire process.
    Attachment Full Text PDF 338.7 kb (source)


  • N. Mousseau, G. T. Barkema, Binary continuous random networks, Journal of Physics: Condensed Matter 16, S5183 (2004).
    Abstract: Many properties of disordered materials can be understood by looking at idealized structural models, in which the strain is as small as is possible in the absence of long-range order. For covalent amorphous semiconductors and glasses, such an idealized structural model, the continuous random network, was introduced 70 years ago by Zachariasen. In this model, each atom is placed in a crystal-like local environment, with perfect coordination and chemical ordering, yet longer-range order is nonexistent. Defects, such as missing or added bonds, or chemical mismatches, however, are not accounted for. In this paper we explore under what conditions the idealized CRN model without defects captures the properties of the material, and under what conditions defects are an inherent part of the idealized model. We find that the density of defects in tetrahedral networks does not vary smoothly with variations in the interaction strengths, but jumps from close to zero to a finite density. Consequently, in certain materials, defects do not play a role except for being thermodynamical excitations, whereas in others they are a fundamental ingredient of the ideal structure.
    Attachment Full Text PDF 129.1 kb (source)


  • S. Santini, N. Mousseau, P. Derreumaux, In Silico Assembly of Alzheimer's Aβ16-22 Peptide into β-Sheets, Journal of the American Chemical Society 126, 11509-11516 (2004).
    Abstract: Recent studies suggest that soluble oligomers of amyloid-forming peptides have toxic effects in cell cultures. In this study, the folding of three Alzheimer's A ?16-22 peptides have been simulated with the activation?relaxation technique and a generic energy model. Starting from randomly chosen states, the predicted lowest energy structure superposes within 1 Å rms deviation from its conformation within the fibrils. This antiparallel structure is found to be in equilibrium with several out-of-register antiparallel ?-sheets and mixed parallel?antiparallel ?-sheets, indicating that full structural order in the fibrils requires larger aggregates. Folding involves the formation of dimers followed by the addition of a monomer and proceeds through a generalized mechanism between disordered and native alignments of ?-strands.


  • S. Santini, G. Wei, N. Mousseau, P. Derreumaux, Pathway Complexity of Alzheimer's β-Amyloid Aβ16-22 Peptide Assembly, Structure 12, 1245-1255 (2004).
    Abstract: Recent studies suggest that both soluble oligomers and insoluble fibrils have toxic effects in cell cultures, raising the interest in determining the first steps of the assembly process. We have determined the aggregation mechanisms of Aβ16-22 dimer using the activation-relaxation technique and an approximate free energy model. Consistent with the NMR solid-state analysis, the dimer is predicted to prefer an antiparallel β sheet structure with the expected registry of intermolecular hydrogen bonds. The simulations, however, locate three other antiparallel minima with nonnative β sheet registries and one parallel β sheet structure, slightly destabilized with respect to the ground state. This result is significant because it can explain the observed dependency of β sheet registry on pH conditions. We also find that assembly of Aβ16-22 into dimers follows multiple routes, but α-helical intermediates are not obligatory. This indicates that destabilization of α-helical intermediates is unlikely to abolish oligomerization of Aβ peptides.


  • G. Wei, N. Mousseau, P. Derreumaux, Exploring the early steps of aggregation of amyloid-forming peptide KFFE, Journal of Physics: Condensed Matter 16, S5047 (2004).
    Abstract: It has been shown recently that even a tetrapeptide can form amyloid fibrils sharing all the characteristics of amyloid fibrils built from large proteins. Recent experimental studies also suggest that the toxicity observed in several neurodegenerative diseases, such as Alzheimer's disease and Creutzfeldt–Jakob disease, is not only related to the mature fibrils themselves, but also to the soluble oligomers formed early in the process of fibrillogenesis. This raises the interest in studying the early steps of the aggregation process. Although fibril formation follows the nucleation–condensation process, characterized by the presence of lag phase, the exact pathways remain to be determined. In this study, we used the activation–relaxation technique and a generic energy model to explore the process of self-assembly and the structures of the resulting aggregates of eight KFFE peptides. Our simulations show, starting from different states with a preformed antiparallel dimer, that eight chains can self-assemble to adopt, with various orientations, four possible distant oligomeric well-aligned structures of similar energy. Two of these structures show a double-layer β-sheet organization, in agreement with the structure of amyloid fibrils as observed by x-ray diffraction; another two are mixtures of dimers and trimers. Our results also suggest that octamers are likely to be below the critical size for nucleation of amyloid fibrils for small peptides.
    Attachment Full Text PDF 999.2 kb (source)


  • G. Wei, N. Mousseau, P. Derreumaux, Complex folding pathways in a simple β-hairpin, Proteins: Structure, Function, and Bioinformatics 56, 464-474 (2004).
    Abstract: The determination of the folding mechanisms of proteins is critical to understand the topological change that can propagate Alzheimer and Creutzfeld-Jakobs diseases, among others. The computational community has paid considerable attention to this problem; however, the associated time scale, typically on the order of milliseconds or more, represents a formidable challenge. Ab initio protein folding from long molecular dynamics simulations or ensemble dynamics is not feasible with ordinary computing facilities and new techniques must be introduced. Here we present a detailed study of the folding of a 16-residue β-hairpin, described by a generic energy model and using the activation-relaxation technique. From a total of 90 trajectories at 300 K, three folding pathways emerge. All involve a simultaneous optimization of the complete hydrophobic and hydrogen bonding interactions. The first two pathways follow closely those observed by previous theoretical studies (folding starting at the turn or by interactions between the termini). The third pathway, never observed by previous all-atom folding, unfolding, and equilibrium simulations, can be described as a reptation move of one strand of the β-sheet with respect to the other. This reptation move indicates that non-native interactions can play a dominant role in the folding of secondary structures. Furthermore, such a mechanism mediated by non-native hydrogen bonds is not available for study by unfolding and Gō model simulations. The exact folding path followed by a given β-hairpin is likely to be influenced by its sequence and the solvent conditions. Taken together, these results point to a more complex folding picture than expected for a simple β-hairpin. Proteins 2004;9999:000–000. © 2004 Wiley-Liss, Inc.
    Attachment 71.pdf 550.8 kb


  • G. Wei, N. Mousseau, P. Derreumaux, Sampling the Self-Assembly Pathways of KFFE Hexamers, Biophysical Journal 87, 3648-3656 (2004).
    Abstract: The formation of amyloid fibrils is often encountered in Alzheimer’s disease, type II diabetes, and transmissible spongiform encephalopathies. In the last few years, however, mounting evidence has suggested that the soluble oligomers of amyloid-forming peptides are also cytotoxic agents. Understanding the early pathway steps of amyloid self-assembly at atomic detail might therefore be crucial for the development of specific inhibitors to prevent amyloidosis in humans. Using the activation-relaxation technique and a generic energy model, we study in detail the aggregation of a hexamer of KFFE peptide. Our simulations show that a monomer remains disordered, but that six monomers placed randomly in an open box self-associate to adopt, with various orientations, three possible distant low-energy structures. Two of these structures show a double-layer β-sheet organization, in agreement with the structure of amyloid fibrils as observed by x-ray diffraction, whereas the third one consists of a barrel-like curved single-layer hexamer. Based on these results, we propose a bidirectional growth mode of amyloid fibril, involving alternate lateral and longitudinal growths.

2003



  • N. Mousseau, S. I. Simdyankin, M. - A. Brière, E. R. Hunt, in AIP Conference Proceedings, (AIP Publishing, 2003), vol. 676, p. 32-43.
    Abstract: Arrays of coupled chaotic elements have been used as models for studying a wide range of phenomena such as synchronization and pattern formation in biological and physical systems. We present experimental and numerical results showing that these arrays can also help us understand the origin of the stretched exponential dynamics observed in glasses and other complex systems. Stretched exponential behavior has been measured over many decades in a 1D array of coupled diode‐resonators, just above a crisis‐induced intermittency transition. Similar results are obtained numerically in an array of identical chaotic oscillators, confirming the chaotic origin of this universal behavior. In these systems, we find that the fundamental physical quantity associated with stretched exponentials is not the auto‐correlation function but, rather, the distribution of times spent in dynamical traps. Here, we review these results and discuss their relation with other systems. We will also present results obtained on higher dimensional networks.
  • Mousseau, Normand, Beaucage, Philippe, Valiquette, Francis, in (invited paper). (MRS Spring Meeting, San Francisco, 2003), p. .
  • Santini, Sébastien, Wei, Guanghong, Mousseau, Normand, Derreumaux, Philippe, Exploring the Folding Pathways of Proteins through Energy Landscape Sampling: Application to Alzheimer's β-Amyloid Peptide, Internet Electronic Journal of Molecular Design 2, 564-577 (2003).


  • S. I. Simdyankin, N. Mousseau, Relationship between dynamical heterogeneities and stretched exponential relaxation, Physical Review E 68, 041110 (2003).
    Abstract: We identify dynamical heterogeneities as an essential prerequisite for stretched exponential relaxation in dynamically frustrated systems. This heterogeneity takes the form of ordered domains of finite but diverging lifetime for particles in atomic or molecular systems, or spin states in magnetic materials. At the onset of the dynamical heterogeneity, the distribution of time intervals spent in such domains or traps becomes stretched exponential at long times. We rigorously show that once this is the case the autocorrelation function of the renewal process formed by these time intervals is also a stretched exponential at long times.
    Attachment Full Text PDF 361.6 kb (source)


  • F. Valiquette, N. Mousseau, Energy landscape of relaxed amorphous silicon, Physical Review B 68, 125209 (2003).
    Abstract: We analyze the structure of the energy landscape of a well-relaxed 1000-atom model of amorphous silicon using the activation-relaxation technique (ART nouveau). Generating more than 40 000 events starting from a single minimum, we find that activated mechanisms are local in nature, that they are distributed uniformly throughout the model, and that the activation energy is limited by the cost of breaking one bond, independently of the complexity of the mechanism. The overall shape of the activation-energy-barrier distribution is also insensitive to the exact details of the configuration, indicating that well-relaxed configurations see essentially the same environment. These results underscore the localized nature of relaxation in this material.
    Attachment Full Text PDF 370 kb (source)


  • G. Wei, P. Derreumaux, N. Mousseau, Sampling the complex energy landscape of a simple β-hairpin, The Journal of Chemical Physics 119, 6403-6406 (2003).
    Abstract: The folding trajectories of a 16-residue β-hairpin are studied using the activation–relaxation technique with a generic energymodel. From more than 70 trajectories, three folding pathways emerge. All involve a simultaneous optimization of the complete hydrophobic and hydrogen bondinginteractions. The first two follow closely those observed by previous theoretical studies, while the third can be described as a reptation move of one strand of the β-sheet with respect to the other. This reptation move indicates that non-native interactions can play a dominant role in the folding of secondary structures.
    Attachment Full Text PDF 273.7 kb (source)

2002



  • N. Mousseau, G. T. Barkema, S. M. Nakhmanson, Recent developments in the study of continuous random networks, Philosophical Magazine Part B 82, 171-183 (2002).
    Abstract: Abstract We report on recent progress in the development of new techniques to generate high-quality models of continuous random networks, which are used as models for elemental and binary tetrahedral semiconductors such as amorphous Si and amorphous GaAs. The availability of such models has allowed us to look at a number of outstanding issues regarding their electronic properties, the fundamental role of defects and dynamics. We describe briefly our modifications made to the Wooten-Winer-Weaire bond-switching algorithm, allowing us to produce low-strain amorphous and paracrystalline networks of up to 10000 atoms. Then some of the structural and electronic properties of these models are presented. We also discuss briefly some recent results on the recrystallization of amorphous networks.
    Attachment Full Text PDF 1.1 Mb (source)
  • Mousseau, Normand, Derreumaux, Philippe, Sampling methods for protein folding, Trends in Chemical Physics 10, 235-240 (2002).


  • S. I. Simdyankin, N. Mousseau, E. R. Hunt, Characterization of the stretched-exponential trap-time distributions in one-dimensional coupled map lattices, Physical Review E 66, 066205 (2002).
    Abstract: Stretched-exponential distributions and relaxation responses are encountered in a wide range of physical systems such as glasses, polymers, and spin glasses. As found recently, this type of behavior occurs also for the distribution function of a certain trap time in a number of coupled dynamical systems. We analyze a one-dimensional mathematical model of coupled chaotic oscillators that reproduces an experimental setup of coupled diode resonators and identify the necessary ingredients for stretched-exponential distributions.
    Attachment Full Text PDF 207.6 kb (source)


  • G. Wei, N. Mousseau, P. Derreumaux, Exploring the energy landscape of proteins: A characterization of the activation-relaxation technique, The Journal of Chemical Physics 117, 11379-11387 (2002).
    Abstract: Finding the global energy minimum region of a polypeptide chain, independently of the starting conformation and in a reasonable computational time, is of fundamental interest. As the energy landscape of proteins is very rugged, sampling is hindered by the vast number of minima existing on this multidimensional landscape. In this study, we use activation-relaxation technique (ART) to explore the energy landscape of a series of peptidemodels with 14, 26, and 28 amino acids.Peptides are modeled by a reduced off-lattice representation and a simplified OPEP-like (optimized potential for efficient peptide-structure prediction) energymodel. ART defines moves directly in the energy landscape and can generate with equal efficiency events with root-mean-square deviation as small as 0.1 or as large as 4 Å. Our results show that (i) ART trajectories are reversible and provide real activated paths; (ii) ART simulations converge to the same low-energy minimum region, for a wide range of starting configurations; (iii) ART method can sample the phase space effectively, going through many hyper-basins, and can generate significant moves in a single event. Possible applications of ART method to biomolecules are discussed.
    Attachment Full Text PDF 563.1 kb (source)

2001



  • G. T. Barkema, N. Mousseau, The activation–relaxation technique: an efficient algorithm for sampling energy landscapes, Computational Materials Science 20, 285-292 (2001).
    Abstract: Activated processes, i.e., rare events requiring thermal fluctuations many times larger than the average thermal energy, play a central role in controlling the relaxation and diffusion mechanisms of disordered materials such as amorphous and glassy solids, polymers and bio-molecules. As the time scales involved are much longer than those associated with thermal vibrations, these processes cannot be studied efficiently with standard real-space methods such as molecular dynamics (MD). They can be investigated much more efficiently by working in the potential energy space. Instead of defining moves in terms of atomic displacements, the activation–relaxation technique (ART) follows paths directly in the energy landscape, from local minima to adjacent saddle points, giving full freedom for the system to create events of any complexity. In this paper, we review the technique in detail and present some recent applications to amorphous semiconductors and glasses.
  • G. T. Barkema, N. Mousseau, Vink, Richard L. C., Biswas, Partha, in Amorphous and Heterogeneous Silicon-Based Films-2001, Joyce, James B., Cohen, J. David, Hanna, Jun-ichi, Collins, Robert W., Stutzman, Martin, Eds. (Proceedings of the Materials Research Society, 2001), vol. 661, p. A28.1.
  • V. Bulatov, L. Colombo, F. Cléri, L. J. Lewis, N. Mousseau, Eds., Advances in materials theory and modeling - bridging over multiple length and time scale V. Bulatov, L. Colombo, F. Cléri, L. J. Lewis, N. Mousseau, Eds. (Materials Research Society, Symposium proceedings, 2001).
  • 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.


  • N. Mousseau, G. T. Barkema, Fast bond-transposition algorithms for generating covalent amorphous structures, Current Opinion in Solid State and Materials Science 5, 497-502 (2001).
    Abstract: Continuous random network (CRN) models are often used as models for elemental and binary tetrahedral semiconductors such as a-Si and a-GaAs. Here, we review algorithms to generate CRN models. We discuss their structural properties and compare with those models obtained via different computational approaches, as well as with experiment. Additionally, we discuss current results towards the generation of para-crystalline models.


  • N. Mousseau, P. Derreumaux, G. T. Barkema, R. Malek, Sampling activated mechanisms in proteins with the activation–relaxation technique, Journal of Molecular Graphics and Modelling 19, 78-86 (2001).
    Abstract: The activated dynamics of proteins occur on time scales of milliseconds and longer. Standard all-atom molecular dynamics simulations are limited to much shorter times, of the order of tens of nanoseconds. Therefore, many activated mechanisms that are crucial for long-time dynamics will not be observed in such molecular dynamics simulation; different methods are required. Here, we describe in detail the activation–relaxation technique (ART) that generates directly activated mechanisms. The method is defined in the configurational energy landscape and defines moves in a two step fashion: (a) a configuration is first brought from a local minimum to a nearby first-order saddle point (the activation); and (b) the configuration is relaxed to a new metastable state (the relaxation). The method has already been applied to a wide range of problems in condensed matter, including metallic glasses, amorphous semiconductors and silica glass. We review the algorithm in detail, discuss some previously published results and present simulations of activated mechanisms for a two-helix bundle protein using an all-atom energy function.


  • S. M. Nakhmanson, P. M. Voyles, N. Mousseau, G. T. Barkema, D. A. Drabold, Realistic models of paracrystalline silicon, Physical Review B 63, 235207 (2001).
    Abstract: We present a procedure for the preparation of physically realistic models of paracrystalline silicon based on a modification of the bond-switching method of Wooten, Winer, and Weaire. The models contain randomly oriented c−Si grains embedded in a disordered matrix. Our technique creates interfaces between the crystalline and disordered phases of Si with an extremely low concentration of coordination defects. The resulting models possess structural and vibrational properties comparable with those of good continuous random network models of amorphous silicon and display realistic optical properties, correctly reproducing the electronic band gap of amorphous silicon. The largest of our models also shows the best agreement of any atomistic model structure that we tested with fluctuation microscopy experiments, indicating that this model has a degree of medium-range order closest to that of the real material.
    Attachment Full Text PDF 227.1 kb (source)


  • R. L. C. Vink, G. T. Barkema, W. F. van der Weg, N. Mousseau, Fitting the Stillinger–Weber potential to amorphous silicon, Journal of Non-Crystalline Solids 282, 248-255 (2001).
    Abstract: Modifications are proposed to the Stillinger–Weber (SW) potential, an empirical interaction potential for silicon. The modifications are specifically intended to improve the description of the amorphous phase and are obtained by a direct fit to the amorphous structure. The potential is adjusted to reproduce the location of the transverse optic (TO) and transverse acoustic (TA) peaks of the vibrational density of states (VDOS), properties insensitive to the details of experimental preparation. These modifications also lead to excellent agreement with structural properties. Comparison with other empirical potentials shows that amorphous silicon configurations generated with the modified potential have overall better vibrational and structural properties.

2000



  • G. T. Barkema, N. Mousseau, High-quality continuous random networks, Physical Review B 62, 4985-4990 (2000).
    Abstract: The continuous random network (CRN) model is an idealized model for perfectly coordinated amorphous semiconductors. The quality of a CRN can be assessed in terms of topological and configurational properties, including coordination, bond-angle distributions, and deformation energy. Using a variation on the sillium approach proposed 14 years ago by Wooten, Winer, and Weaire, we present 1000-atom and 4096-atom configurations with a degree of strain significantly less than the best CRN available at the moment and comparable to experimental results. The low strain is also reflected in the electronic properties. The electronic density of state obtained from ab initio calculation shows a perfect band gap, without any defect, in agreement with experimental data.
    Tags: Amorphe.


  • R. Malek, N. Mousseau, Dynamics of Lennard-Jones clusters: A characterization of the activation-relaxation technique, Physical Review E 62, 7723-7728 (2000).
    Abstract: The potential energy surface of Lennard-Jones clusters is investigated using the activation-relaxation technique (ART). This method defines events in the configurational energy landscape as a two-step process: (a) a configuration is first activated from a local minimum to a nearby saddle-point and (b) is then relaxed to a new minimum. Although ART has been applied with success to a wide range of materials such as a−Si, a−SiO2 and binary Lennard-Jones glasses, questions remain regarding the biases of the technique. We address some of these questions in a detailed study of ART-generated events in Lennard-Jones clusters, a system for which much is already known. In particular, we study the distribution of saddle-points, the pathways between configurations, and the reversibility of paths. We find that ART can identify all trajectories with a first-order saddle point leaving a given minimum, is fully reversible, and samples events following the Boltzmann weight at the saddle point.
    Attachment Full Text PDF 74.5 kb (source)


  • N. Mousseau, G. T. Barkema, Activated mechanisms in amorphous silicon: An activation-relaxation-technique study, Physical Review B 61, 1898-1906 (2000).
    Abstract: At low temperatures, dynamics in amorphous silicon occurs through a sequence of discrete activated events that locally reorganize the topological network. Using the activation-relaxation technique, a database containing over 8000 such events is generated, and the events are analyzed with respect to their energy barrier and asymmetry, displacement and volume expansion/contraction. Special attention is paid to those events corresponding to diffusing coordination defects. The energetics is not clearly correlated with the displacement, nor with the defect density in well-relaxed configurations. We find however some correlation with the local volume expansion: it tends to increase by about 4eV/Å3. The topological properties of these events are also studied; they show an unexpectedly rich diversity.
    Attachment Full Text PDF 218.7 kb (source)


  • N. Mousseau, G. T. Barkema, S. W. de Leeuw, Elementary mechanisms governing the dynamics of silica, The Journal of Chemical Physics 112, 960-964 (2000).
    Abstract: A full understanding of glasses requires an accurate atomistic picture of the complex activated processes that constitute the low-temperature dynamics of these materials. To this end, we generate over five thousand activated events in a model silicaglass, using the activation–relaxation technique; these atomistic mechanisms are analyzed and classified according to their activation energies, their topological properties and their spatial extent. We find that these are collective processes, involving ten to hundreds of atoms with a continuous range of activation energies; that diffusion and relaxation occurs through the creation, annihilation and motion of single dangling bonds; and that silicon and oxygen have essentially the same diffusivity.
    Attachment Full Text PDF 248.6 kb (source)


  • Y. Song, R. Malek, N. Mousseau, Optimal activation and diffusion paths of perfect events in amorphous silicon, Physical Review B 62, 15680-15685 (2000).
    Abstract: Knowledge of the dynamics in amorphous silicon that occurs through a sequence of discrete activated events is essential to predict many of the associated physical and chemical properties. Using the recently introduced nudged elastic band method of Jónsson, Mills, and Jacobsen and a modified empirical Stillinger-Weber potential, we investigate, in detail, 802 perfect events generated with the activation-relaxation technique. We find that a large number of the high-energy events contain, in fact, two or more “subevents.” With this result included, the average barrier height goes down to about 3.0 eV, in line with experimental values and we also find that the bond-exchange mechanism of Wooten, Winer, and Weaire is, by far, the most important one for nondefect based dynamics in a-Si.
    Attachment Full Text PDF 84.1 kb (source)

1999

1998



  • G. T. Barkema, N. Mousseau, Identification of Relaxation and Diffusion Mechanisms in Amorphous Silicon, Physical Review Letters 81, 1865-1868 (1998).
    Abstract: The dynamics of amorphous silicon at low temperatures can be characterized by a sequence of discrete activated events, through which the topological network is locally reorganized. Using the activation-relaxation technique, we create more than 8000 events, providing an extensive database of relaxation and diffusion mechanisms. The generic properties of these events—size, number of atoms involved, activation energy, etc.—are discussed and found to be compatible with experimental data. We introduce a topological classification of events and apply it to study those events involving only fourfold coordinated atoms. For these, we identify and present in detail three dominant mechanisms.


  • G. Boisvert, N. Mousseau, L. J. Lewis, Surface diffusion coefficients by thermodynamic integration: Cu on Cu(100), Physical Review B 58, 12667-12670 (1998).
    Abstract: The rate of diffusion of a Cu adatom on the Cu(100) surface is calculated using thermodynamic integration within the transition state theory. The results are found to be in excellent agreement with the essentially exact values from molecular-dynamics simulations. The activation energy and related entropy are shown to be effectively independent of temperature, thus establishing the validity of the Arrhenius law over a wide range of temperatures. Our study demonstrates the equivalence of diffusion rates calculated using thermodynamic integration within the transition state theory and direct molecular-dynamics simulations.


  • L. J. Lewis, N. Mousseau, Tight-binding molecular-dynamics studies of defects and disorder in covalently bonded materials, Computational Materials Science 12, 210-241 (1998).
    Abstract: Tight-binding (TB) molecular dynamics (MD) has emerged as a powerful method for investigating the atomic-scale structure of materials – in particular the interplay between structural and electronic properties – bridging the gap between empirical methods which, while fast and efficient, lack transferability, and ab initio approaches which, because of excessive computational workload, suffer from limitations in size and run times. In this short review article, we examine several recent applications of TBMD in the area of defects in covalently bonded semiconductors and the amorphous phases of these materials.


  • N. Mousseau, G. T. Barkema, Traveling through potential energy landscapes of disordered materials: The activation-relaxation technique, Physical Review E 57, 2419-2424 (1998).
    Abstract: A detailed description of the activation-relaxation technique (ART) is presented. This method defines events in the configurational energy landscape of disordered materials such as amorphous semiconductors, glasses and polymers, in a two-step process: first, a configuration is activated from a local minimum to a nearby saddle point; next, the configuration is relaxed to a new minimum; this allows for jumps over energy barriers much higher than what can be reached with standard techniques. Such events can serve as basic steps in equilibrium and kinetic Monte Carlo schemes.
    Attachment Full Text PDF 113.9 kb (source)
  • Mousseau, Normand, Barkema, Gerard T., in Proceedings of the HLRZ workshop 1997 "Monte Carlo approach to biopolymers and protein folding", Grassberger, Peter, Barkema, Gerard T., Nadler, A., Eds. (World Scientific, 1998), p. 321.

1997



  • N. Mousseau, Multiple phase changes induced by frustration in randomly connected cellular automata, Journal of Physics A: Mathematical and General 30, 2995 (1997).
    Abstract: Frustration is introduced in randomly connected totalistic cellular automata via mixing rules leading to incompatible periods. As the respective concentration of rules is varied, these cellular automata go through eight phases, many of which with symmetries different from the two rules mixed in. The complex phase diagram so created is similar to those seen in frustrated systems in static equilibrium. It shows that a minimized free energy is not necessary for frustration to produce this rich behaviour.


  • N. Mousseau, Comment on “Systematic approach to generate near-perfect periodic continuous random network models: Application to amorphous Si3N4”, Physical Review B 56, 14190-14191 (1997).
    Abstract: Ouyang and Ching [Phys. Rev. B 54, R15 594 (1996)] have recently proposed a very elegant algorithm for building amorphous networks. Their algorithm, though, leaves strong remnants of cubic symmetry and cannot provide satisfactory amorphous models.
    Attachment Full Text PDF 20.7 kb (source)


  • N. Mousseau, Avalanche distribution in the Feder and Feder model: Effects of quenched disorder, Physical Review E 55, 3682-3685 (1997).
    Abstract: The Feder and Feder earthquake model shows an integrated size distribution of events that decays as a power law when averaged over realizations with different initial conditions. The question remains as to what is the distribution for a single realization. Small amounts of quenched disorder can break the symmetries of the Feder and Feder model, introduce stochasticity in the dynamics, and allow for self-averaging. The introduction of weak frozen spatial disorder reveals a dynamical behavior very different from what is seen by ensemble averaging. The resulting integrated size distribution seems to be a function of the logarithm of the size, P(n)∼(log n10)-ν.
    Attachment Full Text PDF 84.9 kb (source)


  • N. Mousseau, L. J. Lewis, Topology of Amorphous Tetrahedral Semiconductors on Intermediate Length Scales, Physical Review Letters 78, 1484-1487 (1997).
    Abstract: Using the recently proposed “activation-relaxation technique,” we develop a structural model for a-GaAs almost free of odd-membered rings, i.e., wrong bonds, having an almost perfect coordination of four. This model is found to be superior to structures from tight-binding or quantum molecular dynamics simulations. Comparing with a-Si, as described by a Polk-type continuous random network, we find that the cost of wrong bonds is such that the two materials should have different topologies. Our study provides direct information on the intermediate-range topology of amorphous tetrahedral semiconductors.
    Attachment Full Text PDF 95.2 kb (source)


  • N. Mousseau, L. J. Lewis, Structural, electronic, and dynamical properties of amorphous gallium arsenide: A comparison between two topological models, Physical Review B 56, 9461-9468 (1997).
    Abstract: We present a detailed study of the effect of local chemical ordering on the structural, electronic, and dynamical properties of amorphous gallium arsenide. Using the recently proposed “activation-relaxation technique” and empirical potentials, we have constructed two 216-atom tetrahedral continuous random networks with different topological properties, which were further relaxed using tight-binding molecular dynamics. The first network corresponds to the traditional amorphous Polk-type network randomly decorated with Ga and As atoms. The second is an amorphous structure with a minimum of wrong (homopolar) bonds, and therefore a minimum of odd-membered atomic rings, and thus corresponds to the Connell-Temkin model. By comparing the structural, electronic, and dynamical properties of these two models, we show that the Connell-Temkin network is energetically favored over Polk, but that most properties are little affected by the differences in topology. We conclude that most indirect experimental evidence for the presence (or absence) of wrong bonds is much weaker than previously believed and that only direct structural measurements, i.e., of such quantities as partial radial distribution functions, can provide quantitative information on these defects in a−GaAs.
    Attachment Full Text PDF 179.8 kb (source)
  • Mousseau, Normand, Lewis, Laurent J., Structure of amorphous semiconductors on intermediate length scales, Disorder in Materials Newsletter (1997).


  • Y. G. Rubo, M. F. Thorpe, N. Mousseau, Strain broadening of the magnetization steps in diluted magnetic semiconductors, Physical Review B 56, 13094-13102 (1997).
    Abstract: We show that the bond-length mismatch in magnetic solid alloys (diluted magnetic semiconductors) results in fluctuations of the exchange constants between neighboring magnetic ions. We present the theory of these fluctuations and analyze their effect on the broadening of magnetization steps observed in these materials. We conclude that the effect is quantitatively comparable to the effect of the Dzyaloshinski-Moriya interaction, but produces a different behavior of the magnetization curve, which gives a possibility to distinguish between these mechanisms experimentally.
    Attachment Full Text PDF 192.1 kb (source)

1996



  • 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.


  • N. Mousseau, On the phase diagram of frustrated (quasi-)periodic cellular automata, Journal of Physics A: Mathematical and General 29, 3021 (1996).
    Abstract: We introduce and study frustrated cellular automata (CA) obtained by quenching competing Chaté - Manneville rules. A period-two (P2) rule and a quasi-periodic one with period close to three (QP3) are frozen at random on the lattice sites. We find that the periodic and quasi-periodic cycles are resilient to internal frustration as well as to external unbounded noise. A low concentration of impurities improves the (quasi-)periodicity of the CA, damping the chaotic background noise significantly. Starting from pure QP3 CA, a first phase transition happens at a concentration of rule P2, , leading to a macroscopic fixed point. A second phase transition, at , brings the P2 phase. Although macroscopically stable, the central phase displays a stretched exponential relaxation of the site - site autocorrelations, indicating the presence of a new type of glass with slow dynamics superimposed on the natural cyclic dynamics of the CA rules. These results appear to be quite general and are found for many pairs of rules.


  • N. Mousseau, Synchronization by Disorder in Coupled Systems, Physical Review Letters 77, 968-971 (1996).
    Abstract: Effects of quenched disorder on a coupled map model of earthquakes are studied. In its original version, this model is known to display a self-organized critical distribution of avalanches. However, when some finite amount of quenched disorder is introduced, the bulk sites synchronize fully and a single stable system-wide avalanche appears. This synchronization is found for a wide band of disorder and goes against some recent predictions about integrate-and-fire models.
  • Mousseau, Normand, Disorder-induced synchronization in coupled-map lattices, J. de Physique I (Paris) , 58 (1996).

1995



  • N. Mousseau, M. F. Thorpe, Size-mismatch disorder at the surface of semiconductors, Physical Review B 52, 2660-2667 (1995).
    Abstract: We study the effects of size-mismatch disorder on the surface relaxation of semiconductor solid solutions. Assuming a Kirkwood-type potential, we obtain an analytic solution for the nearest-neighbor distances and their distributions as a function of the distance from the surface as well as the displacements at the (111) and (100) surfaces. This solution is also valid for bond-mismatch disorder and is checked against computer simulations for two-dimensional triangular networks along (10) and (11) surfaces. Predictions are made for the topography of the (111) surface of a SiGe alloy.
    Attachment Full Text PDF 471 kb (source)


  • R. W. Wang, M. F. Thorpe, N. Mousseau, Length mismatch in random semiconductor alloys. IV. General multinary compounds, Physical Review B 52, 17191-17198 (1995).
    Abstract: We generalize previous theory on the length-mismatch problem in random semiconductor alloys to deal with an arbitrary number of components on each sublattice. We also calculate the lengthdistribution functions for any two sites in the crystalline alloy. It is found that the properly scaled length-distribution functions are independent of the types of atomic species, and the first and second moments of the distributions are calculated. We illustrate these results with computer simulations performed on SixGe1−x, and apply these results to the pseudoternary alloy Cd1−x−yMnxZnyTe.
    Attachment Full Text PDF 295.8 kb (source)

1994



  • S. Sen, N. Mousseau, G. Overney, Onset of avalanches in granular media, Physical Review E 49, 4712-4715 (1994).
    Abstract: Marginal stability and avalanches at angles Θ≥Θaval are associated with granular media (GM) subject to special conditions. We study the Newtonian dynamics of random size-mismatched hard-core-like disks in a two-dimensional box which confirm claims that avalanches in GM are restricted to a few topmost boundary layers. We find that the velocity profile of the top layer grains, which obey ‖v‖∝tγ, typically with 3.5≤γ, signal the onset of an avalanche in GM. Our studies suggest that the dynamics of a single particle in a cosine potential in the presence of a linear field well describes the onset of motion of a top layer grain.
    Attachment Full Text PDF 390.6 kb (source)

1993



  • N. Mousseau, M. F. Thorpe, Structural model for crystalline and amorphous Si-Ge alloys, Physical Review B 48, 5172-5178 (1993).
    Abstract: There are serious contradictions between extended x-ray-absorption fine structure (EXAFS) measurements of the Si-Ge and Ge-Ge bond lengths in both crystalline and amorphous silicon-germanium alloys, and in theoretical and simulation predictions. In particular, results from EXAFS experiments show that the Si-Ge and Ge-Ge bond lengths are independent of the alloy composition, indicating that there is no topological rigidity in the lattice. These EXAFS results on Si-Ge alloys are in sharp disagreement with all previous EXAFS results on III-V and II-VI semiconductor alloys. We discuss the implications of the EXAFS results regarding the local and global structure of the alloys. We also propose a structural model to serve as a focus for further experiments. In order to satisfy the overall floppiness of the network, we suggest that the Si-Ge samples may contain a large density of planar cracks, lined with hydrogen, and separated by ∼10 Å. Some measurements that could confirm (or discredit) this model are suggested.
    Attachment Full Text PDF 380.1 kb (source)

1992



  • N. Mousseau, M. F. Thorpe, Length distributions in metallic alloys, Physical Review B 45, 2015-2022 (1992).
    Abstract: We use the embedded-atom potential of Johnson to compute the length-distribution functions for a large number of fcc binary metallic alloys. From these distributions, we extract the mean lengths of the nearest-neighbor bonds, which compare well with recent extended x-ray-absorption fine-structure (EXAFS) experiments in NixAu1-x. In other cases, where EXAFS results are not available, we compare our results with the mean lattice parameter as determined by diffraction experiments. While the embedded-atom potential is accurate for some alloys (e.g., Ni-Au), we show that for alloys containing Pt, a simple central-force model is superior. The embedded-atom potential of Johnson predicts an unexpected contraction of the Au-Au distance in Ag-rich Au-Ag alloys. We point out that an important characteristic of any alloy potential is its ability to get the single and double defects correct.


  • N. Mousseau, M. F. Thorpe, Length mismatch in random semiconductor alloys. III. Crystalline and amorphous SiGe, Physical Review B 46, 15887-15893 (1992).
    Abstract: In the third paper of this series on the length mismatch problem, we study binary semiconductor alloys in both their crystalline and amorphous forms. We have concentratred on SiGe alloys. Applying the theory developed in paper I, we obtain the mean length for both nearest and next-nearest neighbors as well as the nearest-neighbor length distribution for the crystalline alloy. We show that the theoretical results fall within the limits set by experiment. We check our analytical results against computer simulations. We examine the effect of amorphization on the internal strain, using the Wooten, Winer, and Weaire model, and find that the disorders due to the length mismatch and due to amorphization decouple.
    Attachment Full Text PDF 390.3 kb (source)

1991



  • N. Mousseau, L. J. Lewis, Dynamical models of hydrogenated amorphous silicon, Physical Review B 43, 9810-9817 (1991).
    Abstract: The results of our molecular-dynamics simulation of bulk hydrogenated amorphous silicon using empirical potentials are presented. More specifically, we discuss a dynamical procedure for incorporating hydrogen into a pure amorphous silicon matrix, which is derived from the concept of floating bonds put forward by Pantelides [Phys. Rev. Lett. 57, 2979 (1986)]. The structures resulting from this model are compared with those obtained with use of a static approach recently developed by us. This method exhibits considerable improvement over the previous one and, in particular, unambiguously reveals the strain-relieving role of hydrogen. While the former model leads to substantial overcoordination, the present one results in almost perfect tetrahedral bonding, with an average coordination number Z=4.03, the lowest value ever achieved using a Stillinger-Weber potential. The simulations are also used to calculate the vibrational densities of states, which are found to be in good accord with corresponding neutron-scattering measurements.
    Attachment Full Text PDF 349.5 kb (source)

1990



  • N. Mousseau, L. J. Lewis, Computer models for amorphous silicon hydrides, Physical Review B 41, 3702-3707 (1990).
    Abstract: A procedure for generating fully coordinated model structures appropriate to hydrogenated amorphous semiconductors is described. The hydrogen is incorporated into an amorphous matrix using a bond-switching process similar to that proposed by Wooten, Winer, and Weaire, which ensures that fourfold coordination is preserved. After each inclusion of hydrogen, the structure is relaxed using a finite-temperature Monte Carlo algorithm. The method is applied to a-Si:H at various hydrogen concentrations. The resulting model structures are found to be in excellent agreement with recent neutron-scattering measurements on a sample with 12 at. % H. Our prescription, which is essentially nonlocal, allows great flexibility and can easily be extended to related systems.
    Attachment Full Text PDF 309 kb (source)

1989

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