PACKMOL: A Package for Building Initial Configurations for Molecular Dynamics Simulations

Adequate initial configurations for molecular dynamics simulations consist of arrangements of molecules distributed in space in such a way to approximately represent the system`s overall structure. In order that the simulations are not disrupted by large van der Waals repulsive interactions, atoms from different molecules Must keep safe pairwise distances. Obtaining Such a molecular arrangement can be considered it packing problem: Each type molecule must satisfy spatial constraints related to the geometry of the system, and the distance between atoms of different molecules Must be greater than some specified tolerance. We have developed a code able to pack millions of atoms. grouped in arbitrarily complex molecules, inside a variety of three-dimensional regions. The regions may be intersections of spheres, ellipses, cylinders, planes, or boxes. The user must provide only the structure of one molecule of each type and the geometrical constraints that each type of molecule must satisfy. Building complex mixtures, interfaces, solvating biomolecules in water, other solvents, or mixtures of solvents, is straight forward. In addition. different atoms belonging to the same molecule may also be restricted to different spatial regions, in Such a way that more ordered molecular arrangements call be built, as micelles. lipid double-layers, etc. The packing time for state-of-the-art molecular dynamics systems varies front a few seconds to a few Minutes in a personal Computer. The input files are simple and Currently compatible with PDB, Tinker, Molden, or Moldy coordinate files. The package is distributed as free software and call be downloaded front http://www.ime.unicamp.br/similar to martinez/packmol/. (C) 2009 Wiley Periodicals. Inc. J Comput Chem 30: 2157-2164, 2009

Cellular automata and non-static image processing for embodied robot systems on a massively parallel processor array

Huelse, M, Barr, D R W, Dudek, P: Cellular Automata and non-static image processing for embodied robot systems on a massively parallel processor array. In: Adamatzky, A et al. (eds) AUTOMATA 2008, Theory and Applications of Cellular Automata. Luniver Press, 2008, pp. 504-510. Sponsorship: EPSRC

Simulation of field-induced structural formation and transition in electromagnetorheological suspensions

A computer simulation method has been used to study the three-dimensional structural formation and transition of eleetromagnetorheological (EMR) suspensions under compatible electric and magnetic fields. When the fields are applied simultaneously and perpendicularly to each other, the particles rapidly arrange into single layer structures parallel to both fields. In each layer, there is a two-dimensional hexagonal lattice. The single layers then combine together to form thicker sheetlike structures. With the help of the thermal fluctuations, the thicker structures relax into three-dimensional close-packed structures, which may be face-centered cubic (fcc), hexagonal close-packed (hup) lattices, or, more probably, the mixture of them, depending on the initial configurations and the thermal fluctuations. On the other hand, if the electric field is applied first to induce the body-centered tetragonal (bct) columns in the system, and then the magnetic field is applied in the perpendicular direction, the bet to fee structure transition is observed in a very short time. Following that, the structure keeps on evolving due to the demagnetization effect and finally forms close-packed structures with fee and hcp lattice character. The simulation results are in agreement with the theoretical and experimental results.

Analysis of Agonist and Antagonist Effects on Thyroid Hormone Receptor Conformation by Hydrogen/Deuterium Exchange

Thyroid hormone receptors (TRs) are ligand-gated transcription factors with critical roles in development and metabolism. Although x-ray structures of TR ligand-binding domains (LBDs) with agonists are available, comparable structures without ligand (apo-TR) or with antagonists are not. It remains important to understand apo-LBD conformation and the way that it rearranges with ligands to develop better TR pharmaceuticals. In this study, we conducted hydrogen/deuterium exchange on TR LBDs with or without agonist (T(3)) or antagonist (NH(3)). Both ligands reduce deuterium incorporation into LBD amide hydrogens, implying tighter overall folding of the domain. As predicted, mass spectroscopic analysis of individual proteolytic peptides after hydrogen/deuterium exchange reveals that ligand increases the degree of solvent protection of regions close to the buried ligand-binding pocket. However, there is also extensive ligand protection of other regions, including the dimer surface at H10-H11, providing evidence for allosteric communication between the ligand-binding pocket and distant interaction surfaces. Surprisingly, C-terminal activation helix H12, which is known to alter position with ligand, remains relatively protected from solvent in all conditions suggesting that it is packed against the LBD irrespective of the presence or type of ligand. T(3), but not NH(3), increases accessibility of the upper part of H3-H5 to solvent, and we propose that TR H12 interacts with this region in apo-TR and that this interaction is blocked by T(3) but not NH(3.) We present data from site-directed mutagenesis experiments and molecular dynamics simulations that lend support to this structural model of apo-TR and its ligand-dependent conformational changes. (Molecular Endocrinology 25: 15-31, 2011)

On the Denaturation Mechanisms of the Ligand Binding Domain of Thyroid Hormone Receptors

The ligand binding domain (LBD) of nuclear hormone receptors adopts a very compact, mostly alpha-helical structure that binds specific ligands with very high affinity. We use circular dichroism spectroscopy and high-temperature molecular dynamics Simulations to investigate unfolding of the LBDs of thyroid hormone receptors (TRs). A molecular description of the denaturation mechanisms is obtained by molecular dynamics Simulations of the TR alpha and TR beta LBDs in the absence and in the presence of the natural ligand Triac. The Simulations Show that the thermal unfolding of the LBD starts with the loss of native contacts and secondary Structure elements, while the Structure remains essentially compact, resembling a molten globule state. This differs From most protein denaturation simulations reported to date and suggests that the folding mechanism may start with the hydrophobic collapse of the TR LBDs. Our results reveal that the stabilities of the LBDs of the TR alpha and TR beta Subtypes are affected to different degrees by the binding of the isoform selective ligand Triac and that ligand binding confers protection against thermal denaturation and unfolding in a subtype specific manner. Our Simulations indicate two mechanisms by which the ligand stabilizes the LBD: (1) by enhancing the interactions between H8 and H 11, and the interaction of the region between H I and the Omega-loop with the core of the LBD, and (2) by shielding the hydrophobic H6 from hydration.

Molecular Basis of the Thermostability and Thermophilicity of Laminarinases: X-ray Structure of the Hyperthermostable Laminarinase from Rhodothermus marinus and Molecular Dynamics Simulations

Glycosyl hydrolases are enzymes capable of breaking the glycosidic linkage of polysaccharides and have considerable industrial and biotechnological applications. Driven by the later applications, it is frequently desirable that glycosyl hydrolases display stability and activity under extreme environment conditions, such as high temperatures and extreme pHs. Here, we present X-ray structure of the hyperthermophilic laminarinase from Rhodothermus marinus (RmLamR) determined at 1.95 angstrom resolution and molecular dynamics simulation studies aimed to comprehend the molecular basis, for the thermal stability of this class of enzymes. As most thermostable proteins, RmLamR contains a relatively large number of salt bridges, which are not randomly distributed on the structure. On the contrary, they form clusters interconnecting beta-sheets of the catalytic domain. Not all salt bridges, however, are beneficial for the protein thermostability: the existence of charge-charge interactions permeating the hydrophobic core of the enzymes actually contributes to destabilize the structure by facilitating water penetration into hydrophobic cavities, as can be seen in the case of mesophilic enzymes. Furthermore, we demonstrate that the mobility of the side-chains is perturbed differently in each class of enzymes. The side-chains of loop residues surrounding the catalytic cleft in the mesophilic laminarinase gain mobility and obstruct the active site at high temperature. By contrast, thermophilic laminarinases preserve their active site flexibility, and the active-site cleft remains accessible for recognition of polysaccharide substrates even at high temperatures. The present results provide structural insights into the role played by salt-bridges and active site flexibility on protein thermal stability and may be relevant for other classes of proteins, particularly glycosyl hydrolases.

Orthogonal packing of identical rectangles within isotropic convex regions

A mixed integer continuous nonlinear model and a solution method for the problem of orthogonally packing identical rectangles within an arbitrary convex region are introduced in the present work. The convex region is assumed to be made of an isotropic material in such a way that arbitrary rotations of the items, preserving the orthogonality constraint, are allowed. The solution method is based on a combination of branch and bound and active-set strategies for bound-constrained minimization of smooth functions. Numerical results show the reliability of the presented approach. (C) 2010 Elsevier Ltd. All rights reserved.

The boundedness of penalty parameters in an augmented Lagrangian method with constrained subproblems

Augmented Lagrangian methods are effective tools for solving large-scale nonlinear programming problems. At each outer iteration, a minimization subproblem with simple constraints, whose objective function depends on updated Lagrange multipliers and penalty parameters, is approximately solved. When the penalty parameter becomes very large, solving the subproblem becomes difficult; therefore, the effectiveness of this approach is associated with the boundedness of the penalty parameters. In this paper, it is proved that under more natural assumptions than the ones employed until now, penalty parameters are bounded. For proving the new boundedness result, the original algorithm has been slightly modified. Numerical consequences of the modifications are discussed and computational experiments are presented.

Molekulardynamik-Simulation zur Struktur von SiO 2-Oberflächen mit adsorbiertem Wasser

In der vorliegenden Arbeit werdenMolekulardynamik-Simulationen zur Untersuchung derstatischen Eigenschaften von amorphenSiliziumdioxidoberflächen (Siliziumdioxid) durchgeführt. Da das von van Beest, Kramer und van Santen vorgeschlagene,sogenannte BKS-Potential für Bulksysteme optimiert wurde und an Oberflächen deutlichandere Ladungsverteilungenauftreten als im Bulk, ist die Anwendbarkeit diesesPotentials für Oberflächensystemefraglich. Aus diesem Grund haben wir untersucht, inwieweitsich die Oberflächeneigenschaften von Systemen, die mit Hilfe des BKS-Potentials äquilibriertwurden, durch ein Nachrelaxieren mit einer ab-initio-Simulation (Car-Parrinello-Methode)ändern. Mit Hilfe der Kombination aus BKS- und Car-Parrinello-Methode (CPMD)konnten wir feststellen, daß sich die Systeme aufgrund des Nachrelaxierens in z-Richtungweiter ausdehnen. Desweiteren zeigte sich insbesondere bei kleinen Ringen (kommen nur ander Oberfläche vor), daß es deutliche Abweichungen in den Geometrien (Atomabstände,Winkel usw.) zwischen der reinen BKS- und der kombinierten BKS-CPMD-Methode gibt. Anhand vonCPMD-Simulationen konnten wir zeigen, daß es durch die Wechselwirkung eines Wassermolekülsmit einem 2er-Ring zum Aufbrechen dieser Ringstruktur und zur Bildung von zweiSilanolgruppen (SiOH) kommt. Desweiteren stellten wir fest, daß es sich hierbei um eineexotherme Reaktion (Energiedifferenz 1.6 eV) handelt, für die eineEnergiebarriere von 1.1 eV überwunden werden muß. Ferner ergab sich, daß die an der Bildung des2er-Ringes beteiligten, stark deformierten Tetraeder nach dem Aufbrechen dieserRingstruktur eine nahezu ideale Tetraederform annehmen.

Thermal relaxation for particle systems in interaction with several bosonic heat reservoirs

The present thesis is concerned with the study of a quantum physical system composed of a small particle system (such as a spin chain) and several quantized massless boson fields (as photon gasses or phonon fields) at positive temperature. The setup serves as a simplified model for matter in interaction with thermal "radiation" from different sources. Hereby, questions concerning the dynamical and thermodynamic properties of particle-boson configurations far from thermal equilibrium are in the center of interest. We study a specific situation where the particle system is brought in contact with the boson systems (occasionally referred to as heat reservoirs) where the reservoirs are prepared close to thermal equilibrium states, each at a different temperature. We analyze the interacting time evolution of such an initial configuration and we show thermal relaxation of the system into a stationary state, i.e., we prove the existence of a time invariant state which is the unique limit state of the considered initial configurations evolving in time. As long as the reservoirs have been prepared at different temperatures, this stationary state features thermodynamic characteristics as stationary energy fluxes and a positive entropy production rate which distinguishes it from being a thermal equilibrium at any temperature. Therefore, we refer to it as non-equilibrium stationary state or simply NESS. The physical setup is phrased mathematically in the language of C*-algebras. The thesis gives an extended review of the application of operator algebraic theories to quantum statistical mechanics and introduces in detail the mathematical objects to describe matter in interaction with radiation. The C*-theory is adapted to the concrete setup. The algebraic description of the system is lifted into a Hilbert space framework. The appropriate Hilbert space representation is given by a bosonic Fock space over a suitable L2-space. The first part of the present work is concluded by the derivation of a spectral theory which connects the dynamical and thermodynamic features with spectral properties of a suitable generator, say K, of the time evolution in this Hilbert space setting. That way, the question about thermal relaxation becomes a spectral problem. The operator K is of Pauli-Fierz type. The spectral analysis of the generator K follows. This task is the core part of the work and it employs various kinds of functional analytic techniques. The operator K results from a perturbation of an operator L0 which describes the non-interacting particle-boson system. All spectral considerations are done in a perturbative regime, i.e., we assume that the strength of the coupling is sufficiently small. The extraction of dynamical features of the system from properties of K requires, in particular, the knowledge about the spectrum of K in the nearest vicinity of eigenvalues of the unperturbed operator L0. Since convergent Neumann series expansions only qualify to study the perturbed spectrum in the neighborhood of the unperturbed one on a scale of order of the coupling strength we need to apply a more refined tool, the Feshbach map. This technique allows the analysis of the spectrum on a smaller scale by transferring the analysis to a spectral subspace. The need of spectral information on arbitrary scales requires an iteration of the Feshbach map. This procedure leads to an operator-theoretic renormalization group. The reader is introduced to the Feshbach technique and the renormalization procedure based on it is discussed in full detail. Further, it is explained how the spectral information is extracted from the renormalization group flow. The present dissertation is an extension of two kinds of a recent research contribution by Jakšić and Pillet to a similar physical setup. Firstly, we consider the more delicate situation of bosonic heat reservoirs instead of fermionic ones, and secondly, the system can be studied uniformly for small reservoir temperatures. The adaption of the Feshbach map-based renormalization procedure by Bach, Chen, Fröhlich, and Sigal to concrete spectral problems in quantum statistical mechanics is a further novelty of this work.

Symbolic Dynamics in the Free-Fall Equal-Mass Three-Body Problem

The paper has been presented at the 12th International Conference on Applications of Computer Algebra, Varna, Bulgaria, June, 2006

Personnalité et compétences en emploi : comparaison de la capacité prévisionnelle de deux configurations de la personnalité

Certaines études récentes confirment que les tests de personnalité sont largement utilisés à des fins de sélection dans les organisations nord-américaines et que leur fréquence d’utilisation continue de croître (Boudrias, Pettersen, Longpré, & Plunier, 2008; Rothstein & Goffin, 2006). Or, les résultats des recherches portant sur le lien prévisionnel entre la personnalité et le rendement global au travail sont peu convaincants (Morgeson et al., 2007b; Murphy & Dzieweczynski, 2005). La présente thèse vise à vérifier si une amélioration des liens prédictifs entre la personnalité et le rendement au travail pourrait être obtenue en modifiant la façon d’opérationnaliser les variables prévisionnelles issues des inventaires de personnalité et en précisant les critères à prédire de manière à les rendre plus spécifiques et mieux arrimés. Pour ce faire, la capacité prévisionnelle d’une approche centrée sur le critère, c’est-à-dire l’utilisation de composites de traits de personnalité, est comparée à l’approche traditionnelle centrée sur le prédicteur, dans ce cas-ci, les cinq grands facteurs de personnalité (Big Five). D’autre part, le rendement au travail est opérationnalisé sous l’angle des compétences en emploi, ce qui permet d’en différencier les dimensions et d’augmenter la spécificité des critères. Des hypothèses précisant les facteurs de personnalité qui devraient permettre de prédire chacune des compétences évaluées sont testées. De plus, des hypothèses précisant les traits de personnalité servant à créer les variables composites sont aussi testées. Finalement, une hypothèse portant sur la comparaison de la puissance prévisionnelle des deux approches est mise à l’épreuve. L’échantillon de la recherche est composé de 225 employés occupant divers emplois au sein d’une grande organisation québécoise. Ils ont complété un inventaire de personnalité au travail dans le cadre des processus de sélection de l’organisation. Leur supérieur immédiat a effectué une évaluation de leurs compétences et de leur rendement au moins six (6) mois après leur embauche. Les résultats démontrent que la maîtrise des compétences est mieux prédite par une approche centrée sur le prédicteur (c’est-à-dire les Big Five) que par une approche centrée sur le critère (c’est-à-dire les variables composites). En effet, seules trois hypothèses portant sur le lien entre certains facteurs de personnalité et les compétences se sont avérées partiellement soutenues. Les résultats d’analyses statistiques supplémentaires, réalisées a posteriori afin de mieux comprendre les résultats, laissent supposer la présence de variables modératrices, dont, notamment, les caractéristiques situationnelles. En somme, il nous semble plus probable d’arriver, dans le futur, à trouver une méthode structurée de création des variables composites qui permettrait d’obtenir des liens prévisionnels plus puissants que de découvrir des variables composites qui seraient elles-mêmes généralisables à tous les emplois et à toutes les organisations. Par ailleurs, nous encourageons les praticiens à porter attention à la façon d’utiliser les données de personnalité. Pour le moment, il semble que les facteurs de personnalité permettent de prédire, en partie, le rendement futur en emploi. Or, les preuves empiriques concernant l’efficacité d’autres approches demeurent relativement rares et, surtout, insuffisantes pour guider fidèlement les praticiens à travers les choix nécessaires à leur utilisation.

The Met Office unified model global atmosphere 4.0 and JULES global land 4.0 configurations

We describe Global Atmosphere 4.0 (GA4.0) and Global Land 4.0 (GL4.0): configurations of the Met Office Unified Model and JULES (Joint UK Land Environment Simulator) community land surface model developed for use in global and regional climate research and weather prediction activities. GA4.0 and GL4.0 are based on the previous GA3.0 and GL3.0 configurations, with the inclusion of developments made by the Met Office and its collaborators during its annual development cycle. This paper provides a comprehensive technical and scientific description of GA4.0 and GL4.0 as well as details of how these differ from their predecessors. We also present the results of some initial evaluations of their performance. Overall, performance is comparable with that of GA3.0/GL3.0; the updated configurations include improvements to the science of several parametrisation schemes, however, and will form a baseline for further ongoing development.

Design and analysis of hull configurations for a low-cost, autonomous underwater robot as an enabling technology for system of system applications

The objective of this research is to model and analyze candidate hull configurations for a low-cost, modular, autonomous underwater robot. As the computational power and speed of microprocessors continue to progress, we are seeing a growth in the research, development, and the utilization of underwater robots. The number of applications is broadening in the R&D and science communities, especially in the area of multiple, collaborative robots. These underwater collaborative robots represent an instantiation of a System of Systems (SoS). While each new researcher explores a unique application, control method, etc. a new underwater robot vehicle is designed, developed, and deployed. This sometimes leads to one-off designs that are costly. One limit to the wide-scale utilization of underwater robotics is the cost of development. Another limit is the ability to modify the configuration for new applications and evolving requirements. Consequently, we are exploring autonomous underwater vehicle (AUV) hull designs towards the goal of modularity, vehicle dexterity, and minimizing the cost. In our analysis, we have employed 3D solid modeling tools and finite element methods. In this paper we present our initial results and discuss ongoing work.

Irregular satellites of Jupiter: capture configurations of binary-asteroids

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)