@article{xia_persistent_2018,
abstract = {Despite the great advancement of experimental tools and theoretical models, a quantitative characterization of the microscopic structures of ion aggregates and their 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. The 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-bonding 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 networks. It has been found that the two aggregation types have distinguishable topological features and can be characterized by our topological model very well. Further, we construct two types of networks, i.e., O-networks and H2O-networks, for analyzing the topological properties of hydrogen-bonding networks. It is found that for both models, {KSCN} systems demonstrate much more dramatic variations in their local circle structures with a 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 the circle structures is observed and the sizes of these circles become more and more uniform with a concentration increase. As far as we know, these unique intrinsic topological features in ion aggregation systems have never been pointed out before. More importantly, our models can be directly used to quantitatively analyze the intrinsic topological invariants, including circles, loops, holes, and cavities, of any network-like structures, such as nanomaterials, colloidal systems, biomolecular assemblies, among others. These topological invariants cannot be described by traditional graph and network models.},
author = {Xia, Kelin},
date = {2018-05-16},
doi = {10.1039/C8CP01552J},
issn = {1463-9084},
journaltitle = {Physical Chemistry Chemical Physics},
keywords = {1 - Biophysical chemistry, 1 - Biophysics, 1 - Crystal structure, 1 - Hydrogen-bonding network, 1 - Ion aggregation, 1 - Molecular dynamics, 2 - Betti function, 2 - Clustering, 2 - Persistent homology, 3 - Molecular dynamic simulation, 3 - Networks},
langid = {english},
note = {Publisher: The Royal Society of Chemistry},
number = {19},
pages = {13448--13460},
shortjournal = {Phys. Chem. Chem. Phys.},
title = {Persistent homology analysis of ion aggregations and hydrogen-bonding networks},
url = {https://pubs.rsc.org/en/content/articlelanding/2018/cp/c8cp01552j},
urldate = {2020-11-10},
volume = {20}
}