Author

P. Tiwary

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Open access Sep 2026

Topology, Energy Landscapes and Folding Kinetics of RNA Hairpins

A de novo hierarchical multiscale computational framework that integrates diverse secondary and tertiary structure generation, adaptive unbiased molecular dynamics, a generative AI model termed latent thermodynamic flows (LaTF), and Markov state modeling to efficiently map global RNA folding landscapes and associated d...

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