Fractal and complex network analyses of protein molecular dynamics

• Published in: arXiv.org 2014-08
• Main Authors: Yuan-Wu, Zhou, Jin-Long, Liu, Zu-Guo, Yu, Zhi-Qin Zhao, Vo Anh
• Format: Article
• Language: English
• Subjects: Energy; Fractal analysis; Fractal geometry; Fractals; Kinetic energy; Molecular dynamics; Parameters; Potential energy; Proteins; Time series; Variation; Visibility
• ISSN: 2331-8422
• DOI: 10.48550/arxiv.1403.4719

Based on protein molecular dynamics, we investigate the fractal properties of energy, pressure and volume time series using the multifractal detrended fluctuations analysis (MF-DFA) and the topological and fractal properties of their converted horizontal visibility graphs (HVGs). The energy parameters of protein dynamics we considered are bonded potential, angle potential, dihedral potential, improper potential, kinetic energy, Van der Waals potential, electrostatic potential, total energy and potential energy. The shape of the h(q) curves from MF-DFA indicates that these time series are multifractal. The numerical values of the exponent h(2) of MF-DFA show that the series of total energy and potential energy are non-stationary and anti-persistent; the other time series are stationary and persistent apart from series of pressure (with H approx 0.5 indicating the absence of long-range correlation). The degree distribution of their converted HVGs show that these networks are exponential. The results of fractal analysis show that fractality exists in these converted HVGs. For each energy, pressure or volume parameter, it is found that the values of h(2) of MF-DFA on the time series, exponent lambda of the exponential degree distribution and fractal dimension d_B of their converted HVGs do not change much for different proteins (indicating some universality). We also found that after taking average over all proteins, there is a linear relationship between < h(2)> (from MF-DFA on time series) and of the converted HVGs for different energy, pressure and volume.