Europhys. Lett.
Volume 75, Number 3, August 2006
Page(s) 503 - 509
Section Interdisciplinary physics and related areas of science and technology
Published online 05 July 2006
Europhys. Lett., 75 (3), pp. 503-509 (2006)
DOI: 10.1209/epl/i2006-10129-2

Causal relations in molecular dynamics from the multi-variate autoregressive model

A. Gorecki1, J. Trylska2 and B. Lesyng1, 2

1  Department of Biophysics, Institute of Experimental Physics, Warsaw University Zwirki i Wigury 93, 02-089 Warsaw, Poland
2  Interdisciplinary Centre for Mathematical and Computational Modelling Pawinskiego 5A, 02-106 Warsaw, Poland

received 16 March 2006; accepted in final form 13 June 2006
published online 5 July 2006

We show that Granger-type causality analysis can be applied to determine correlations between atomic motions. A multivariate autoregressive model and directed transfer functions were applied to analyze the causality in the dynamics of a linear chain of atoms and the malonaldehyde molecule. The presented methodology is promising, can be applied in post-processing of classical and quantum-classical molecular dynamics data, and to study the mechanisms of functioning of biomolecular systems.

87.15.Aa - Theory and modeling; computer simulation.
31.15.Qg - Molecular dynamics and other numerical methods.
05.45.Tp - Time series analysis.

© EDP Sciences 2006