A Central Partition of Molecular Conformational Space. V. The Hypergraph of 3D Partition Sequences

TL;DR

This paper introduces an algorithmic method to aggregate and compactly represent the conformational space of molecules using hypergraphs derived from molecular dynamics data.

Contribution

It presents a novel hypergraph-based approach for aggregating and efficiently encoding molecular conformational space from trajectory data.

Findings

Hypergraph representation enables efficient enumeration of relevant molecular conformations.

The method significantly reduces data complexity for conformational analysis.

Provides a systematic way to analyze molecular dynamics trajectories.

Abstract

In a previous work a procedure was decribed for dividing the $3 \times N$-dimensional conformational space of a molecular system into a number of discrete cells, this partition allowed the building of a combinatorial structure from data sampled in molecular dynamics trajectories: the graph of cells or G, encoding the set of cells in conformational space that are visited by the system in its thermal wandering. The information in G however, is encoded in a great number of fragments that must be aggregated. We describe here the algorithmic procedures 1) for aggregating the information from G into an hypergraph allowing to enumerate the relevant cells from conformational space, and 2) for puttting the data in a very compact format.