Publications

Selected papers and research artifacts with direct access to paper, preprint, code, and archived releases.

2026

Collective Variable-Guided Engineering of the Free-Energy Surface of a Small Peptide

Muralika Medaparambath, Alexander Zhilkin, Dan Mendels

Journal of Chemical Information and Modeling, article

Uses CV-FEST and HLDA on short molecular dynamics trajectories to guide mutation analysis in CLN025, connecting collective-variable structure to mutation-induced shifts in peptide free-energy landscapes.

Paper DOI arXiv

Guiding Peptide Kinetics via Collective-Variable Tuning of Free-Energy Barriers

Alexander Zhilkin, Muralika Medaparambath, Dan Mendels

Journal of Chemical Theory and Computation, recent paper

Introduces a framework for rationally modifying free-energy surfaces to control conformational transition rates, using HLDA-based collective variables derived from limited metastable-state sampling.

Details Paper DOI arXiv

2025

Enhancing Bayesian Network Discovery by Sampling Markov Equivalent DAGs

Alexander Zhilkin

Master's thesis, University of Helsinki, Master's thesis

Introduces a Markov Equivalent Step for Bayesian network structure discovery MCMC, improving convergence and exploration of complex network-structure posteriors.

Thesis GitHub

Scaling Up Bayesian DAG Sampling

Daniele Nikzad, Alexander Zhilkin, Juha Harviainen, Jack Kuipers, Giusi Moffa, Mikko Koivisto

arXiv preprint

Presents more efficient Bayesian DAG sampling methods, including faster basic graph moves and approximate parent-set pruning to improve scalability.

arXiv