3 papers
physics.bio-ph2026
Collective Variable-Guided Engineering of the Free-Energy Surface of a Small Peptide
Muralika Medaparambath, Alexander Zhilkin, Dan Mendels
Engineering the free-energy surfaces (FES) of proteins and peptides is central to controlling conformational ensembles and their responses to perturbations. However, predicting how…
physics.bio-ph2026
Guiding Peptide Kinetics via Collective-Variable Tuning of Free-Energy Barriers
Alexander Zhilkin, Muralika Medaparambath, Dan Mendels
While recent advances in AI have transformed protein structure prediction, protein function is also strongly influenced by the thermodynamic and kinetic features encoded in its und…
cs.LG2025
Scaling Up Bayesian DAG Sampling
Daniele Nikzad, Alexander Zhilkin, Juha Harviainen +3
Bayesian inference of Bayesian network structures is often performed by sampling directed acyclic graphs along an appropriately constructed Markov chain. We present two techniques…