TimeSOAP: Tracking high-dimensional fluctuations in complex molecular systems via time variations of SOAP spectra

Many molecular systems and physical phenomena are controlled by local fluctuations and microscopic dynamical rearrangements of the constitutive interacting units that are often difficult to detect. This is the case, for example, of phase transitions, phase equilibria, nucleation events, and defect propagation, to mention a few. A detailed comprehension of local atomic environments and of their dynamic rearrangements is essential to understand such phenomena and also to draw structure-property relationships useful to unveil how to control complex molecular systems. Considerable progress in the development of advanced structural descriptors [e.g., Smooth Overlap of Atomic Position (SOAP), etc.] has certainly enhanced the representation of atomic-scale simulations data. However, despite such efforts, local dynamic environment rearrangements still remain difficult to elucidate. Here, exploiting the structurally rich description of atomic environments of SOAP and building on the concept of time-dependent local variations, we developed a SOAP-based descriptor, TimeSOAP (tSOAP), which essentially tracks time variations in local SOAP environments surrounding each molecule (i.e., each SOAP center) along ensemble trajectories. We demonstrate how analysis of the time-series tSOAP data and of their time derivatives allows us to detect dynamic domains and track instantaneous changes of local atomic arrangements (i.e., local fluctuations) in a variety of molecular systems. The approach is simple and general, and we expect that it will help shed light on a variety of complex dynamical phenomena. (c) 2023 Author(s).

Automated summary

Many molecular systems and physical phenomena are controlled by difficult-to-detect local fluctuations and microscopic dynamical rearrangements. In this study, a SOAP-based descriptor called tSOAP is developed to track time variations in local atomic environments and detect dynamic domains in molecular systems. This simple and general approach is expected to shed light on complex dynamical phenomena.