Defining, Calculating, and Converging Observables of a Kinetic Transition Network.
Journal of chemical theory and computation
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Swinburne, T. D., & Wales, D. (2020). Defining, Calculating, and Converging Observables of a Kinetic Transition Network.. Journal of chemical theory and computation, 16 (4), 2661-2679. https://doi.org/10.1021/acs.jctc.9b01211
Kinetic transition networks (KTNs) of local minima and transition states are able to capture the dynamics of numerous systems in chemistry, biology, and materials science. However, extracting observables is numerically challenging for large networks and generally will be sensitive to additional computational discovery. To have any measure of convergence for observables, these sensitivities must be regularly calculated. We present a matrix formulation of the discrete path sampling framework for KTNs, deriving expressions for branching probabilities, transition rates, and waiting times. Using the concept of the quasi-stationary distribution, a clear hierarchy of expressions for network observables is established, from exact results to steady-state approximations. We use these results in combination with the graph transformation method to derive the sensitivity, with respect to perturbations of the known KTN, giving explicit terms for the pairwise sensitivity and discussing the pathwise sensitivity. These results provide guidelines for converging the network, with respect to additional sampling, focusing on the estimates obtained for the overall rate coefficients between product and reactant states. We demonstrate this procedure for transitions in the double-funnel landscape of the 38-atom Lennard-Jones cluster.
External DOI: https://doi.org/10.1021/acs.jctc.9b01211
This record's URL: https://www.repository.cam.ac.uk/handle/1810/316897
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