Author

P. Tiwary

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Open access Sep 2026

Topology, Energy Landscapes and Folding Kinetics of RNA Hairpins

Many RNAs occupy multiple inter-converting structures in order to perform key biological functions. Characterizing RNA conformational ensembles is therefore critical to illuminating the mechanisms by which RNAs fold, unfold, and undergo precise structural rearrangements in response to cellular signals. However, resolvi...

Anjali R. Verma, P. Tiwary, Yun-Rui Qiu · bioRxiv · 0 citations

#machine learning Preprint Sep 2026

SPIBER: Reconstructing Free Energy Landscapes from Short, Unconverged Trajectories with Generative Flow Networks

Molecular systems have many degrees of freedom, but their metastable behavior can often be described by a few collective variables. Identifying these variables and estimating free energies along them from limited simulation data remains a challenging, important problem. Separate short trajectories may sample different...

Venkata Sai Sreyas Adury, P. Tiwary · 0 citations

Review Aug 2026

Expanding Protein Structure Prediction into Conformational State Space

It is argued that structure prediction should be reformulated as a state-space inference problem: recovering not one conformation's coordinates but accessible states, their energetic and kinetic relationships, context dependence, and responses to perturbations.

Devlina Chakravarty, Justin J. Miller, Da Teng et al. · 0 citations