Author

Z. F. Brotzakis

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Preprint Oct 2026

MD-LLM-2: A Transferable Language Model of Molecular Dynamics with Physical Conditioning and Explicit Path Probabilities

Molecular dynamics (MD) simulations model the motion of proteins between conformational states, but crossing free energy barriers and sampling multiple thermodynamic conditions remain computationally costly. We recently introduced MD-LLM-1, which showed that language models can generate conformational trajectories at l...

Mhd Hussein Murtada, Z. F. Brotzakis, Michele Vendruscolo · 0 citations

#protein folding Open access Oct 2026

Anneal-MaxCal: kinetic ensembles from a Markov model learned along a solute-tempering ladder

A full characterisation of a molecular system requires its metastable states, their populations and their intercon-version rates. Molecular Dynamics can in principle provide this characterisation but is limited by sampling and by force-field inaccuracies. Enhanced sampling addresses the first problem, but typically req...

Z. F. Brotzakis, N. Rekatsinas · bioRxiv · 0 citations