Author

Saifuddin Syed

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#machine learning Preprint Sep 2026

METALICA: METAdynamics and repLICA exchange for enhanced diffusion sampling

METALICA, which implements Metadynamics on a pretrained diffusion model via Replica Exchange, is introduced, which implements Metadynamics on a pretrained diffusion model via Replica Exchange and accumulates a bias potential along a Collective Variable, repels new samples from previous ones through biased sampling, and...

Alireza Omidi, Jiajun He, Jörg Gsponer et al. · 1 citation

Open access Jul 2026

De Novo Design of Protein Switches with Diffusion-Based Ensemble Sampling

Diff-Switch is introduced, a framework for sampling switch-like backbone ensembles from pretrained protein diffusion models that preserves local domain geometry while encouraging diversity in global domain arrangements along user-specified collective variables, inspired by metadynamics.

Alireza Omidi, Jiajun He, Jennifer M. Bui et al. · bioRxiv · 0 citations