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Updated: Jun 24, 2025

Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
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Predicting Long-Time-Scale Kinetics under Variable Experimental Conditions with Kinetica.jl
Joe Gilkes1,2, Mark T Storr3, Reinhard J Maurer1,4
1Department of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL Coventry, U.K.
Abstract:
Predicting the degradation processes of molecules over long time scales is a key aspect of industrial materials design. However, it is made computationally challenging by the need to construct large networks of chemical reactions that are relevant to the experimental conditions that kinetic models must mirror, with every reaction requiring accurate kinetic data. Here, we showcase Kinetica.jl, a new software package for constructing large-scale chemical reaction networks in a fully automated fashion by exploring chemical reaction space with a kinetics-driven algorithm; coupled to efficient machine-learning models of activation energies for sampled elementary reactions, we show how this approach readily enables generation and kinetic characterization of networks containing ∼103 chemical species and ≃104-105 reactions. Symbolic-numeric modeling of the generated reaction networks is used to allow for flexible, efficient computation of kinetic profiles under experimentally realizable conditions such as continuously variable temperature regimes, enabling direct connection between bottom-up reaction networks and experimental observations. Highly efficient propagation of long-time-scale kinetic profiles is required for automated reaction network refinement and is enabled here by a new discrete kinetic approximation. The resulting Kinetica.jl simulation package therefore enables automated generation, characterization, and long-time-scale modeling of complex chemical reaction systems. We demonstrate this for hydrocarbon pyrolysis simulated over time scales of seconds, using transient temperature profiles representing those of tubular flow reactor experiments.
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