2021/12/22 by Adu Offei-Danso, Ali Hassanali, Offei-Danso, Adu +3 · 1 citation
Biochemistry, Genetics and Molecular Biology · Materials Science · Physics and Astronomy · #FOS: Physical sciences #Machine Learning in Materials Science #Materials Science (cond-mat.mtrl-sci) #Protein Structure and Dynamics #Soft Condensed Matter (cond-mat.soft) #Spectroscopy and Quantum Chemical Studies
paper · pdf · doi:10.48550/arxiv.2112.11894
openalex publication_date 2021/12/22 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
The microscopic description of the local structure of water remains an open challenge. Here, we adopt an agnostic approach to understanding water's hydrogen bond network using data harvested from molecular dynamics simulations of an empirical water model. A battery of state-of-the-art unsupervised data-science techniques are used to characterize the free energy landscape of water starting from encoding the water environment using local-atomic descriptors, through dimensionality reduction and finally the use of advanced clustering techniques. Analysis of the free energy at ambient conditions was found to be consistent with a rough single basin and independent of the choice of the water model. We find that the fluctuations of the water network occur in a high-dimensional space which we characterize using a combination of both atomic descriptors and chemical-intuition based coordinates. We demonstrate that a combination of both types of variables are needed in order to adequately capture the complexity of the fluctuations in the hydrogen bond network at different length-scales both at room temperature and also close to the critical point of water. Our results provide a general framework for examining fluctuations in water under different conditions.