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 (τSOAP), 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 τSOAP 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.
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7 June 2023
Research Article|
June 01 2023
TimeSOAP: Tracking high-dimensional fluctuations in complex molecular systems via time variations of SOAP spectra
Special Collection:
Machine Learning Hits Molecular Simulations
Cristina Caruso
;
Cristina Caruso
(Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Validation, Visualization, Writing – original draft)
1
Department of Applied Science and Technology, Politecnico di Torino
, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
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Annalisa Cardellini
;
Annalisa Cardellini
(Conceptualization, Investigation, Methodology, Supervision, Writing – original draft)
2
Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland, Polo Universitario Lugano
, Campus Est, Via la Santa 1, 6962 Lugano-Viganello, Switzerland
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Martina Crippa
;
Martina Crippa
(Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Visualization, Writing – original draft)
1
Department of Applied Science and Technology, Politecnico di Torino
, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
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Daniele Rapetti
;
Daniele Rapetti
(Conceptualization, Data curation, Formal analysis, Investigation, Methodology)
1
Department of Applied Science and Technology, Politecnico di Torino
, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
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Giovanni M. Pavan
Giovanni M. Pavan
a)
(Conceptualization, Funding acquisition, Investigation, Resources, Supervision, Writing – review & editing)
1
Department of Applied Science and Technology, Politecnico di Torino
, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
2
Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland, Polo Universitario Lugano
, Campus Est, Via la Santa 1, 6962 Lugano-Viganello, Switzerland
a)Author to whom correspondence should be addressed: [email protected]
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a)Author to whom correspondence should be addressed: [email protected]
J. Chem. Phys. 158, 214302 (2023)
Article history
Received:
February 18 2023
Accepted:
May 15 2023
Citation
Cristina Caruso, Annalisa Cardellini, Martina Crippa, Daniele Rapetti, Giovanni M. Pavan; TimeSOAP: Tracking high-dimensional fluctuations in complex molecular systems via time variations of SOAP spectra. J. Chem. Phys. 7 June 2023; 158 (21): 214302. https://doi.org/10.1063/5.0147025
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