Persistent homology analysis of ion aggregation and hydrogen-bonding network

TL;DR

This paper introduces persistent homology, a novel mathematical method, to quantitatively analyze the topological structures of ion aggregation and hydrogen-bonding networks, revealing distinct morphological features in different systems.

Contribution

The study applies persistent homology to ion and water networks, providing a new, topology-based approach that does not rely on predefined bond lengths and can measure structural features directly.

Findings

NaCl and KSCN solutions show distinguishable topological features.

KSCN exhibits increasing diversity and size of local circle structures with concentration.

NaCl shows decreasing average circle size and more uniform structures as concentration increases.

Abstract

Despite the great advancement of experimental tools and theoretical models, a quantitative characterization of the microscopic structures of ion aggregates and its associated water hydrogen-bonding networks still remains a challenging problem. In this paper, a newly-invented mathematical method called persistent homology is introduced, for the first time, to quantitatively analyze the intrinsic topological properties of ion aggregation systems and hydrogen-bonding networks. Two most distinguishable properties of persistent homology analysis of assembly systems are as follows. First, it does not require a predefined bond length to construct the ion or hydrogen network. Persistent homology results are determined by the morphological structure of the data only. Second, it can directly measure the size of circles or holes in ion aggregates and hydrogen-bonding networks. To validate our model, we consider two well-studied systems, i.e., NaCl and KSCN solutions, generated from molecular dynamics simulations. They are believed to represent two morphological types of aggregation, i.e., local clusters and extended ion network. It has been found that the two aggregation types have distinguishable topological features and can be characterized by our topological model very well. For hydrogen-bonding networks, KSCN systems demonstrate much more dramatic variations in their local circle structures with the concentration increase. A consistent increase of large-sized local circle structures is observed and the sizes of these circles become more and more diverse. In contrast, NaCl systems show no obvious increase of large-sized circles. Instead a consistent decline of the average size of circle structures is observed and the sizes of these circles become more and more uniformed with the concentration increase.