Many crucial biomolecular processes, such as ligand dissociation and conformational switching, occur via multiple competing transition pathways. While standard rare-event sampling methodologies provide rigorous estimates of the global transition rate, they typically collapse the underlying mechanistic heterogeneity i...
Dibyendu Maity, Shaheerah Shahid, Sayari Bhattacharya et al.· Journal of Chemical Theory a...· 1 citation
A lightweight, engine-agnostic adaptive sampling framework that iteratively launches short trajectory ensembles across either fixed or on-the-fly machine-learned (ML) collective-variable (CV) spaces, and shows how lineage-aware exploratory ensembles can seamlessly seed unbiased production trajectories for the construct...
Dibyendu Maity, Rupak Majumdar, Suman Chakrabarty· Journal of Chemical Physics· 0 citations
A central theme is emphasised: that generative AI delivers speed and breadth, while physics-based simulation supplies thermodynamic rigour, and that their integration, rather than either alone, defines the most promising path forward.
Sutanu Mukhopadhyay, Suman Chakrabarty· Chemical Communications· 0 citations
It is demonstrated that PDZ2 allostery arises from the coupling between pre-existing structural heterogeneity and ligand-induced network reorganization, providing a mechanistic framework for understanding PDZ regulation and guiding allosteric modulator design.
