Physical chemist combining neutron scattering and biomolecular simulations to understand biophysical processes at the molecular level and accelerate drug design.
C₁₀H₁₅N₂⁺ Protonated nicotine cation
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Person
I’m Matěj Červenka, a physical chemist based in Prague. I study at UCT Prague and work at IOCB Prague in the group built by Pavel Jungwirth, where research has taken me from the computer to neutron and synchrotron facilities across Europe. In 2026, I was awarded the Via Chimica prize for my work in physical chemistry.
Outside the lab, I spend as much time as possible windsurfing. That usually means chasing wind around Europe, loading far too much gear into a car, and slowly converting a van into something better suited for the job.
The problem
Our goal is to obtain an experimentally grounded molecular picture of noncovalent interactions in aqueous solution. Neutron diffraction with isotopic substitution (NDIS) provides structural constraints, while simulations provide the atomistic interpretation. By testing and improving molecular dynamics against NDIS — and by benchmarking force-field MD against AIMD and MLP-MD — we can build more reliable models for biomolecular simulations and, ultimately, support simulation-guided drug design.
NDIS is uniquely suited to studying solution structure because isotopic substitution changes neutron-scattering contrast and helps isolate selected intermolecular correlations, especially those involving hydrogen-containing molecules in water.
Scattering data are ensemble-averaged and do not directly give a unique three-dimensional molecular picture. Atomistic simulations are therefore needed to interpret the experiment in terms of hydration structure, molecular association, and specific interaction motifs.
Classical MD can misrepresent important interactions in solution. We therefore use NDIS as an experimental benchmark, improve FFMD where needed, and compare its performance with higher-level approaches such as AIMD and MLP-MD.
The same interactions that can be studied in simple aqueous systems also appear in biomolecules, where they affect solvation, molecular recognition, and ligand binding. Better validated solution-phase models can therefore improve biomolecular simulations and provide more reliable input for drug-design applications.
Selected writing
With B. L. Shanks, P. E. Mason, P. Jungwirth. Empirical strength of aqueous cation–π contacts; ECC in CHARMM36.
With H. W. Sullivan, B. L. Shanks, M. P. Hoepfner. Artifact-free RDFs with uncertainty.
With Vitek, Mason, Gale, Marsalek, Jungwirth. Localized electrons becoming a bronze metallic band.
From LinkedIn
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