Application of Recurrence Plot Analysis to Examine Dynamics of Biological Molecules on the Example of Aggregation of Seed Mucilage Components

Abstract

The goal of the research is to describe the aggregation process inside the mucilage produced by plant seeds using molecular dynamics (MD) combined with time series algorithmic analysis based on the recurrence plots. The studied biological molecules model is seed mucilage composed of three main polysaccharides, i.e. pectins, hemicellulose, and cellulose. The modeling of biological molecules is based on the assumption that a classical–quantum passage underlies the aggregation process in the mucilage, resulting from non-covalent interactions, as they affect the macroscopic properties of the system. The applied recurrence plot approach is an important tool for time series analysis and data mining dedicated to analyzing time series data originating from complex, chaotic systems. In the current research, we demonstrated that advanced algorithmic analysis of seed mucilage data can reveal some features of the dynamics of the system, namely temperature-dependent regions with different dynamics of increments of a number of hydrogen bonds and regions of stable oscillation of increments of a number of hydrophobic–polar interactions. Henceforth, we pave the path for automatic data-mining methods for the analysis of biological molecules with the intermediate step of the application of recurrence plot analysis, as the generalization of recurrence plot applications to other (biological molecules) datasets is straightforward.

Keywords

• time series analysis
• recurrence plot
• aggregation
• molecular dynamics
• seed mucilage
• classical–quantum passage