Computational molecular engineering

Alex Zhilkin

PhD student in computational molecular engineering at the Technion.

I am Alex Zhilkin, a PhD student at the Technion – Israel Institute of Technology, working in the Mendels Lab for Computational Molecular Engineering. I develop computational methods for molecular simulation, collective variables, free-energy surfaces, and machine learning.

Before the Technion, I completed an MSc in Theoretical and Computational Methods at the University of Helsinki. I also have around 10 years of software engineering experience, including technical leadership on a game development project at Netflix. That background shapes my interest in methods that are mathematically grounded and practical enough to become real tools.

Research

My current work studies how low-dimensional collective variables and local molecular fluctuations can explain and guide peptide kinetics. I use CV-FEST and HLDA to connect limited metastable-state sampling with free-energy barriers, conformational change, and mutation-dependent unfolding rates.

Featured Paper

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

Alexander Zhilkin, Muralika Medaparambath, Dan Mendels

Journal of Chemical Theory and Computation, 2026

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

Earlier Work

My earlier research focused on Bayesian network structure discovery, especially sampling Markov equivalent DAGs and acyclic moral orientations.

Software

I co-authored lammps.js, which compiles LAMMPS to WebAssembly for interactive molecular simulation in the browser. A lightweight example is available here: open the lammps.js demo.

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