Abstract:
RNA molecules play a fundamental role in biology, and their function is often tightly connected to their dynamics. Molecular dynamics (MD) simulations can be used to reconstruct RNA dynamics. However, MD simulations suffer from poor accuracy due to incorrect force field parametrizations and poor precision due to slow sampling. In the group, we develop and apply integrative methods and enhanced sampling techniques to tackle these two issues. I will provide an overview of recent applications, including enhanced sampling of RNA-Mg interactions, integration of cryogenic electron microscopy data, and development of force fields for modified nucleotides that tune RNA-protein interactions.