Adaptative algorithms for molecular simulation


Speciality : Mathématiques et Informatique

30/05/2012 - 14:00 Mlle Svetlana Artemova (Université de Grenoble) Grand Amphi de l'INRIA Rhône-Alpes, Montbonnot

Keywords :
  • algorithmes adaptatifs
  • nanoscience
Molecular simulations have become an essential tool in biology, chemistry and physics. Unfortunately, they still remain computationally challenging.
In this dissertation, we propose algorithms that accelerate molecular simulations by clustering particles into rigid bodies.
We first study several neighbor-search algorithms for large rigid bodies, and show that hierarchy-based algorithms may provide significant speedups.
Accordingly, we propose a technique to build a hierarchical representation of an arbitrary molecular graph. We show how this technique can be used in adaptive torsion-angle mechanics, a simulation method that describes molecules as articulated rigid bodies.
Finally, we introduce ARPS – Adaptively Restrained Particle Simulations – a mathematically-grounded method able to switch positional degrees of freedom on and off. We propose two switching strategies, and illustrate the advantages of ARPS on various examples. In particular, we show how ARPS allow us to smoothly trade between precision and speed, and efficiently compute correct static equilibrium properties on molecular systems.


  • Mr Stéphane Redon (Chargé de recherche - INRIA )


  • Mr Mark Tuckerman (Professeur - New York University )
  • Mr Tony Lelièvre (Professeur - Ecole des Ponts - Paris )


  • Mr Richard Lavery (Directeur de Recherche - CNRS )
  • Mme Marie-Paule Cani (Professeur - Grenoble INP )
  • Brigitte Bidegaray-Fesquet (Chargé de Recherche - CNRS/LJK )
  • Mr Serge Crouzy (Directeur de recherche - CEA Grenoble )
  • Mr Matej Praprotnik (Assistant Professeur of Physics - National Institute of Chemistry - Slovénie )