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Rik S. Breebaart

Publications and source records attributed to Rik S. Breebaart.

3 recordsLinked to original sources

Discovering Reaction Mechanisms with Transition Path Sampling-Based Active Learning of Machine-Learned Potentials

Machine-learned interatomic potentials (MLPs) provide near density functional theory (DFT) accuracy at reduced computational cost, but their reliability depends on representative training data and often deteriorates in transition-state regions governing rare events. We introduce an active-learning framework in which Transition Path Sampling (TPS) serves as a targeted data-generation engine for constructing MLPs accurate in barrier regions. TPS generates ensembles of unbiased reactive trajectories, and a committee-based uncertainty estimate identifies configurations for selective DFT labeling and retraining. Iterating this cycle systematically refines the potential energy surface in dynamically relevant regions, without the need of prior knowledge of the mechanism. Applied to electrochemical CO$_2$ reduction to CO on copper in explicit water, the approach removes nonphysical artifacts present in early models, achieves near-DFT energy and force accuracy, and enables stable long-time sampling of reactive pathways. Extended TPS simulations reveal multiple dynamically accessible protonation mechanisms. This work establishes TPS as an efficient and principled active-learning strategy for reactive molecular simulations at electrochemical interfaces.

physics.chem-ph↗

Combining multiple interface set path ensembles with MBAR reweighting

We introduce a method to compute the reweighted path ensemble by combining transition interface sampling simulations conditioned on different collective variables. The approach is based on the Multistate Bennett Acceptance Ratio (MBAR) methodology applied to entire trajectories. Illustrating the technique with simple 2D potential models and a more complex host-guest system, we show that the statistics can significantly improve compared to a straightforward combination.

cond-mat.stat-mech↗

Understanding Reaction Mechanisms from Start to Finish

Understanding mechanisms of rare but important events in complex molecular systems, such as protein folding or ligand (un)binding, requires accurately mapping transition paths from an initial to a final state. The committor is the ideal reaction coordinate for this purpose, but calculating it for high-dimensional, nonlinear systems has long been considered intractable. Here, we introduce an iterative path sampling strategy for computing the committor function for systems with high free energy barriers. We start with an initial guess to define isocommittor interfaces for transition interface sampling. The resulting path ensemble is then reweighted and used to train a neural network, yielding a more accurate committor model. This process is repeated until convergence, effectively solving the long-standing circular problem in enhanced sampling where a good reaction coordinate is needed to generate efficient sampling, and vice-versa. The final, converged committor model can be interrogated to extract mechanistic insights. We demonstrate the power of our method on a benchmark 2D potential and a more complex host-guest (un)binding process in explicit solvent.

physics.chem-ph↗