Improving the efficiency of BD algorithms for biological systems simulations

David Marreiro, Yuzhou Tang, Shela Aboud, Eric Jakobsson, Marco Saraniti

Research output: Contribution to journalArticle

3 Scopus citations

Abstract

In this work, an error analysis methodology is applied to the study of various integration schemes used in Brownian Dynamics simulations of ion channels. Three algorithms have been compared for the integration of the full Langevin Equation [1]. A first-order Euler scheme [2], the Verlet-like algorithm proposed by [3], and a novel Predictor/Corrector (PC) scheme [4] have been implemented and analyzed using our assessment methodology [5]. Our results show that a significant increase in the integration timestep, and a subsequent reduction in computational cost and improvement in efficiency, can be achieved with the second order Verlet-like and PC schemes, while maintaining an excellent accuracy for the description of both structure and dynamics of the electrolyte solution. This work extends the analysis developed in [5] to dynamic properties of the solution as well as structural aspects of inhomogeneous systems such as a lipid membrane.

Original languageEnglish (US)
Pages (from-to)377-380
Number of pages4
JournalJournal of Computational Electronics
Volume6
Issue number1-3
DOIs
StatePublished - Sep 1 2007
Externally publishedYes

Keywords

  • Brownian dynamics
  • Ion channels
  • Langevin equation
  • Modeling

ASJC Scopus subject areas

  • Electronic, Optical and Magnetic Materials
  • Atomic and Molecular Physics, and Optics
  • Modeling and Simulation
  • Electrical and Electronic Engineering

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