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|
Causal relations in molecular dynamics from the multi-variate autoregressive model
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
Accepted: 13 June 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.
PACS: 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
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