ESR 5: Zhengyue Zhang

Molecular Mechanism/Quantum Mechanism Study on Nucleic Acids Structure and Dynamics

LightDyNAmics Research

I am studying the riboswitch structure and dynamics features by implementing Molecular Mechanics (MM) and Quantum Mechanics (QM) simulations. By comparing MM, QM simulations and the experimental data, I am going to evaluate the nucleic acids force field quality. I will explore more MM and QM techniques on more nucleic acid cases in my further PhD period.

Scientific Background

Bachelor’s study: Zhejiang University, China. Majoring in Bioinformatics and having internships on Molecular Dynamics (MD) simulations and docking.

Master’s study: Utrecht University, the Netherlands. Molecular & Cellular Life Sciences program. Having the internship on docking, supervised by Prof. Alexandre Bonvin, and the internship on nucleic acids structure and dynamics study, supervised by Prof. Jiri Sponer.

Scientific Publications

Zhengyue Zhang (ESR5), Jennifer Vögele, Klaudia Mráziková, Holger Kruse, Xiaohui Cang, Jens Wöhnert, Miroslav Krepl, Jiří Šponer
(2021) Phosphorothioate Substitutions in RNA Structure Studied by Molecular Dynamics Simulations, QM/MM Calculations, and NMR Experiments. The Journal of Physical Chemistry B