Structure-Informed Bayesian Inference of Anomalous Transport and Hidden Molecular Trapping in Amorphous Media

Abstract

Molecular diffusion in fluctuating amorphous and macromolecular media governs key transport processes across soft-matter physics, energy storage, and biological membranes. Extracting localized trapping states from single-particle tracking trajectories remains a fundamental challenge; because thermal structural breathing continuously reconfigures pore boundaries, conventional geometric algorithms suffer from severe systematic biases, erroneously merging distinct localized states during cyclic molecular returns. Here, we address this deadlock by shifting the paradigm from local geometric recurrence to a structure-informed Bayesian regularization. Leveraging discrete Morse theory, we extract the time-invariant topological skeleton of the fluctuating host matrix to construct robust, gas-specific physical priors that account for individual molecular dimensions. Trajectory steps are sequentially partitioned via a two-stage probabilistic refinement that dynamically adapts to the transport landscape. Benchmarked against a rigorous environment where synthetic particles explore the actual interconnected matrix graph, our approach eliminates systemic biases, restricting macroscopic trapping parameter deviations to just a few percent under optimal linear $O(N)$ computational scaling. Applied to hydrogen and methane transport within a type-I kerogen matrix, serving as a prototype for highly tortuous, flexible macromolecular networks, the method successfully decodes the hidden microscopic mechanisms of confined diffusion. To ensure immediate broad impact, the documented open-source code and data are made publicly available, offering an accessible strategy readily adaptable to a broad spectrum of tracking phenomena, from ion transport in battery polymers to protein trafficking within cellular environments.