Rational Construction of Stochastic Numerical Methods for Molecular Sampling

In this article, we focus on the sampling of the configurational Gibbs-Boltzmann distribution, that is, the calculation of averages of functions of the position coordinates of a molecular $N$-body system modelled at constant temperature. We show how a formal series expansion of the invariant measure of a Langevin dynamics numerical method can be obtained in a straightforward way using the Baker-Campbell-Hausdorff lemma. We then compare Langevin dynamics integrators in terms of their invariant distributions and demonstrate a superconvergence property (4th order accuracy where only 2nd order would be expected) of one method in the high friction limit; this method, moreover, can be reduced to a simple modification of the Euler-Maruyama method for Brownian dynamics involving a non-Markovian (coloured noise) random process. In the Brownian dynamics case, 2nd order accuracy of the invariant density is achieved. All methods considered are efficient for molecular applications (requiring one force evaluation per timestep) and of a simple form. In fully resolved (long run) molecular dynamics simulations, for our favoured method, we observe up to two orders of magnitude improvement in configurational sampling accuracy for given stepsize with no evident reduction in the size of the largest usable timestep compared to common alternative methods

Efficacité de la formation par Apprentissages par Problèmes (APP) pour l'acquisition des compétences scientifiques et techniques en Cursus Master Ingénierie

International audienceThe aim of this paper is to introduce problem based learning (PBL) as one of the solutions to the lack of satisfaction as regards the traditional teaching (explicit teaching) of disciplinary skills expected from an engineer. The experiment is led in a bachelor's degree in Sciences for the Engineer, within a Master's degree Engineering Program (CMI) on the course entitled Study of mechanical systems. The method held to estimate the efficiency of PBL is based on diverse criteria of efficiency such as learning gain, transfer of knowledge. The partial results obtained show that PBL is effective on the acquisition of disciplinary skills.Cet article a pour objet l'apprentissage par problèmes (APP) qui est une des solutions possible, à partir du constat de non satisfaction de l'enseignement traditionnel (explicite) vis à vis des compétences disciplinaires attendues d'un ingénieur. L'expérimentation est menée en licence sciences pour l'ingénieur dans un Cursus Master Ingénierie (CMI) sur l'UE étude des systèmes mécaniques. La méthode retenue pour évaluer l'efficacité du dispositif en APP est fondée sur divers critères de l'efficacité (exemples : gain d'apprentissage, transfert des connaissances,…). Les résultats partiels obtenus montrent que le dispositif en APP est efficace sur l'acquisition des compétences disciplinaires

The multiscale coarse-graining method. VI. Implementation of three-body coarse-grained potentials

Journal ArticleMany methodologies have been proposed to build reliable and computationally fast coarse-grained potentials. Typically, these force fields rely on the assumption that the relevant properties of the system under examination can be reproduced using a pairwise decomposition of the effective coarse-grained forces. In this work it is shown that an extension of the multiscale coarse-graining technique can be employed to parameterize a certain class of two-body and three-body force fields from atomistic configurations. The use of explicit three-body potentials greatly improves the results over the more commonly used two-body approximation. The method proposed here is applied to develop accurate one-site coarse-grained water models

Alcune osservazioni sul F 46 Kn., 11-12

In this contribution we consider the additions and conjectures proposed by Wilamowitz to F 46 K. 11-12 (= F 6 Sn.; F 5 Jouan-van Looy) that belong to the Euripides' tragedy Alexandros. The criticism, starting from the publication of the Strasbourg Papyrus, has accepted almost unanimously his proposals, but it has often underlined the need to be careful towards these hypotheses for the lacunosity of the verses. Applying the results of my doctoral thesis to the implicit stage direction during actor's entrance, that F 46 K, 11-12 contains, the aim of my paper is to propose some reflections on Wilamowitz's integrations and conjectures through a new approach to the text: generally each linguistic segment of the stage directions of actor's entrances depends not only on linguistic factors, but also on performative and dialogical factors and some sentence's segments have greater autonomy respect to the formularity that this type of implicit captions presents in Euripides. The argument is based on the application of the most important principles of pragmatics, of language's philosophy and dependence's grammar, which supports and enriches philological analysis. The implicit stage directions in entrance's scenes are informative-descriptive sentences and for this characteristic they can be considered a small drama in the drama, as it is a statement that accompanies and describes an action of movement of entrances on the scene. This approach, thanks to the results of a systematic research on implicit announcement captions of entrances in Euripides' tragedies can be applicated to the fragmentaries tragedy in order to argue new evidences for or against the conjectures and additions contemplated by the scholars and highlight new possible hypotheses. This research ultimately proves that the formularity of Euripidean entry announcements and the author's linguistic choices depend strictly on the staging.In this contribution we consider the additions and conjectures proposed by Wilamowitz to F 46 K. 11-12 (= F 6 Sn.; F 5 Jouan-van Looy) that belong to the Euripides' tragedy Alexandros. The criticism, starting from the publication of the Strasbourg Papyrus, has accepted almost unanimously his proposals, but it has often underlined the need to be careful towards these hypotheses for the lacunosity of the verses. Applying the results of my doctoral thesis to the implicit stage direction during actor's entrance, that F 46 K, 11-12 contains, the aim of my paper is to propose some reflections on Wilamowitz's integrations and conjectures through a new approach to the text: generally each linguistic segment of the stage directions of actor's entrances depends not only on linguistic factors, but also on performative and dialogical factors and some sentence's segments have greater autonomy respect to the formularity that this type of implicit captions presents in Euripides. The argument is based on the application of the most important principles of pragmatics, of language's philosophy and dependence's grammar, which supports and enriches philological analysis. The implicit stage directions in entrance's scenes are informative-descriptive sentences and for this characteristic they can be considered a small drama in the drama, as it is a statement that accompanies and describes an action of movement of entrances on the scene. This approach, thanks to the results of a systematic research on implicit announcement captions of entrances in Euripides' tragedies can be applicated to the fragmentaries tragedy in order to argue new evidences for or against the conjectures and additions contemplated by the scholars and highlight new possible hypotheses. This research ultimately proves that the formularity of Euripidean entry announcements and the author's linguistic choices depend strictly on the staging

Numerical Studies of the Structure and Dynamics of Polymers

In this thesis we studied several aspects of polymer dynamics simulations. The first part of the thesis deals with the crystallization in polymeric materials; there, it is shown that a single molecule in solution is able to reach its equilibrium configuration, which represents the minimum of the free energy landscape. For the first time, an analytical model is proposed to take into account the effects related to the short length of the loop at the crystal boundaries. The second part of the thesis is devoted to develop faster stochastic algorithms for the integration of the equation of motion; our attention is addressed in particular toward symplectic integration schemes, which allow to achieve longer time steps. The last part of the thesis tackles the problem of glass transition, proposing a possible universal scaling which is able to link the fast, local motions of the polymer, with its slow, structural properties

Análise das influências do fenômeno El Niño 2015-16 sobre a Região Sul do Brasil

TCC(graduação) - Universidade Federal de Santa Catarina. Centro de Ciências Físicas e Matemáticas. Meteorologia.A atuação do fenômeno El Niño no Sul do Brasil é relacionada a um aumento significativo da precipitação e da temperatura média na Região. Essas mudanças no padrão do clima podem causar grandes impactos econômicos e sociais, principalmente com o aumento das enchentes. O El Niño de 2015-16, um dos mais fortes já registrados, também apresentou, no geral, características típicas de um El Niño canônico, mas com variações de um mês para outro. Portanto, é importante analisar as condições atmosféricas sobre a Região Sul e seu desenvolvimento ao longo deste evento. Assim, será apresentada uma visão geral dos efeitos esperados para o Sul do Brasil durante o fenômeno El Niño. Desse modo, a pesquisa foca principalmente em analisar como o El Niño de 2015-16 afetou o Sul do Brasil, e como ele se compara aos demais. A passagem de frentes frias e a formação CCMs nesse período também são estudadas. A observação dos jatos (de altos e baixos níveis) é necessária já que os mesmos interferem no desenvolvimento e progressão desses sistemas.El Niño effects in Southern Brazil tend to be related to a significant positive anomaly in precipitation and mean average temperature. These changes in the pattern of the area's climate can cause economic and social impacts for its inhabitants, especially when it comes to flooding. As for the 2015-16 El Niño event, which was one of the strongest on record, it can be observed typical canonical El Niño effects for Southern Brazil, although with big variations from one month to another. Therefore, it's important to analyze the atmospheric conditions over the Region and their development throughout that event. Therefore, a general analysis of El Niño effects in Southern Brazil is presented. The research focus mainly in the way the 2015-16 El Niño event affected Southern Brazil and how it compares to the climatology of El Niño patterns. The characteristics and development of cold fronts during this period are also studied, as well as the development of Mesoscale Convective Systems, such as the MCCs (Mesoscale Convective Complex). The analysis of the subtropical and low-level jets is necessary since they interfere in the formation and progression of fronts

Simulazione Numerica dei Processi di Cristallizzazione nei Materiali Polimerici

Una simulazione numerica di tipo "molecular dynamics" è stata condotta allo scopo di studiare i processi di cristallizzazione nei materiali polimerici in soluzione. Il programma di simulazione è stato sviluppato in modo originale durante il lavoro di tesi. Il polimero è stato modellizzato come una catena di sfere rigide, utilizzando potenziali relativi ad angoli di legame, distanza di legame, angoli di torsione e potenziale Lennard-Jones per le interazioni a lungo raggio; l'effetto del solvente è descritto da forze viscose e casuali attraverso l'equazione di Langevin.Si sono svolti studi dettagliati sulla fase liquida in equilibrio, quindi si è proceduto ad una serie di quench al fine di ottenere la fase cristallina. Si è inoltre verificata la stabilità di alcune possibili fasi cristalline