Quantifying Energetic and Entropic Pathways in Molecular Systems.
J Phys Chem B
; 126(21): 3950-3960, 2022 06 02.
Article
em En
| MEDLINE
| ID: mdl-35605180
ABSTRACT
When examining dynamics occurring at nonzero temperatures, both energy and entropy must be taken into account to describe activated barrier crossing events. Furthermore, good reaction coordinates need to be constructed to describe different metastable states and the transition mechanisms between them. Here we use a physics-based machine learning method called state predictive information bottleneck (SPIB) to find nonlinear reaction coordinates for three systems of varying complexity. SPIB is able to correctly predict an entropic bottleneck for an analytical flat-energy double-well system and identify the entropy- and energy-dominated pathways for an analytical four-well system. Finally, for a simulation of benzoic acid permeation through a lipid bilayer, SPIB is able to discover the entropic and energetic barriers to the permeation process. Given these results, we thus establish that SPIB is a reasonable and robust method for finding the important entropy, energy, and enthalpy barriers in physical systems, which can then be used to enhance the understanding and sampling of different activated mechanisms.
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Simulação de Dinâmica Molecular
/
Bicamadas Lipídicas
Tipo de estudo:
Prognostic_studies
Idioma:
En
Ano de publicação:
2022
Tipo de documento:
Article