Application of the Hilbert-Huang transform to the analysis of molecular dynamics simulations
Application of the Hilbert-Huang transform to the analysis of molecular dynamics simulations
The Hilbert-Huang transform (HHT) is a new method for the analysis of nonstationary signals that allows a signal's frequency and amplitude to be evaluated with excellent time resolution. In this paper, the HHT method is described, and its performance is compared with the Fourier methods of spectral analysis. The HHT is then applied to the analysis of molecular dynamics simulation trajectories, including enhanced sampling trajectories produced by reversible digitally filtered molecular dynamics. Amplitude-time, amplitude-frequency, and amplitude-frequency-time spectra are all produced with the method and compared to equivalent results obtained using wavelet analysis. The wavelet and HHT analysis yield qualitatively similar results, but the HHT provides a better match to physical intuition than the wavelet transform. Moreover the HHT method is able to show the flow of energy into low-frequency vibrations during conformational change events and is able to identify frequencies appropriate for amplification by digital filters including the observation of a 10 cm(-1) shift in target frequency.
empirical mode decomposition, numerical-integration, systems
4869-4876
Phillips, Stephen C.
47610c30-a543-4bac-a96a-bc1fce564a59
Gledhill, Robert J.
de6cab60-d1f3-4f64-978c-3fc464aa277e
Essex, Jonathan W.
1f409cfe-6ba4-42e2-a0ab-a931826314b5
Edge, Colin M.
7cb32b1b-4e31-4d58-becc-c65d76dc9370
19 June 2003
Phillips, Stephen C.
47610c30-a543-4bac-a96a-bc1fce564a59
Gledhill, Robert J.
de6cab60-d1f3-4f64-978c-3fc464aa277e
Essex, Jonathan W.
1f409cfe-6ba4-42e2-a0ab-a931826314b5
Edge, Colin M.
7cb32b1b-4e31-4d58-becc-c65d76dc9370
Phillips, Stephen C., Gledhill, Robert J., Essex, Jonathan W. and Edge, Colin M.
(2003)
Application of the Hilbert-Huang transform to the analysis of molecular dynamics simulations.
Journal of Physical Chemistry A, 107 (24), .
(doi:10.1021/jp0261758).
Abstract
The Hilbert-Huang transform (HHT) is a new method for the analysis of nonstationary signals that allows a signal's frequency and amplitude to be evaluated with excellent time resolution. In this paper, the HHT method is described, and its performance is compared with the Fourier methods of spectral analysis. The HHT is then applied to the analysis of molecular dynamics simulation trajectories, including enhanced sampling trajectories produced by reversible digitally filtered molecular dynamics. Amplitude-time, amplitude-frequency, and amplitude-frequency-time spectra are all produced with the method and compared to equivalent results obtained using wavelet analysis. The wavelet and HHT analysis yield qualitatively similar results, but the HHT provides a better match to physical intuition than the wavelet transform. Moreover the HHT method is able to show the flow of energy into low-frequency vibrations during conformational change events and is able to identify frequencies appropriate for amplification by digital filters including the observation of a 10 cm(-1) shift in target frequency.
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e-pub ahead of print date: 23 May 2003
Published date: 19 June 2003
Keywords:
empirical mode decomposition, numerical-integration, systems
Identifiers
Local EPrints ID: 20065
URI: http://eprints.soton.ac.uk/id/eprint/20065
ISSN: 1089-5639
PURE UUID: 659fb1ed-15e8-4ae4-86b7-38b0ac3ef754
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Date deposited: 24 Feb 2006
Last modified: 16 Mar 2024 02:59
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Author:
Stephen C. Phillips
Author:
Robert J. Gledhill
Author:
Colin M. Edge
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