Computational Methods for the Parallel 3D Simulation of Biochemical Kinetics at the Microscopic Scale - Archive ouverte HAL Accéder directement au contenu
Communication Dans Un Congrès Lecture Notes in Computer Science Année : 2013

Computational Methods for the Parallel 3D Simulation of Biochemical Kinetics at the Microscopic Scale

Laurent Crépin
  • Fonction : Auteur correspondant
  • PersonId : 942388

Connectez-vous pour contacter l'auteur
Fabrice Harrouet
  • Fonction : Auteur
  • PersonId : 935423
Sébastien Kerdelo
  • Fonction : Auteur
  • PersonId : 833030
Jacques Tisseau
  • Fonction : Auteur
  • PersonId : 865438
Pascal Redou
  • Fonction : Auteur
  • PersonId : 890679

Résumé

This work takes place in the context of biochemical kinetics simulation for the understanding of complex biological systems such as hæmostasis. The classical approach, based on the numerical solving of differential systems, cannot satisfactorily handle local geometrical constraints, such as membrane binding events. To address this problem, we propose a particle-based system in which each molecular species is represented by a three-dimensional entity which diffuses and may undergo reactions. Such a system can be computationaly intensive, since a small time step and a very large number of entities are required to get significant results. Therefore, we propose a model that is suitable for parallel computing and that can especially take advantage of recent multicore and multiprocessor architectures. We present our particle-based system, detail the behaviour of our entities, and describe our parallel computing algorithms. Comparisons between simulations and theoretical results are exposed, as well as a performance evaluation of our algorithms.
Fichier principal
Vignette du fichier
2013m03d11_isbra2013_final.pdf (187.51 Ko) Télécharger le fichier
Origine : Fichiers produits par l'(les) auteur(s)
Loading...

Dates et versions

hal-00832448 , version 1 (10-06-2013)

Identifiants

Citer

Laurent Crépin, Fabrice Harrouet, Sébastien Kerdelo, Jacques Tisseau, Pascal Redou. Computational Methods for the Parallel 3D Simulation of Biochemical Kinetics at the Microscopic Scale. International Symposium on Bioinformatics Research and Applications (ISBRA) 2013, May 2013, Charlotte, United States. pp.28-39, ⟨10.1007/978-3-642-38036-5_7⟩. ⟨hal-00832448⟩
191 Consultations
267 Téléchargements

Altmetric

Partager

Gmail Facebook X LinkedIn More