Studying nuclear chromatin as an “active glassy” material
Supervisor: Dr. Yu Shi
Project Description (Abstract):
The cell nucleus can both preserve genome integrity and alter DNA configuration to regulate gene expression in response to external stimuli. Such seemingly contradictory properties is achieved by the hierarchical organization of DNA. However, comprehending how molecular dynamics interact with overall nuclear behavior is challenging due to the nucleus's heterogeneous nature. Often, a single model is insufficient to fully describe the entire nucleus. This project aims to quantitatively compare the dynamics of nucleosomes—the fundamental units of DNA packaging—with the dynamics observed in glassy systems. Students will focus on analyzing single-molecule imaging data and apply machine learning techniques to identify the contributions of various biological processes within the cell nucleus. They will also explore how biophysical models can be used to accurately represent and predict these molecular motions.
Example Reference:
Daugird, T.A., Shi, Y., Holland, K.L. et al. Correlative single molecule lattice light sheet imaging reveals the dynamic relationship between nucleosomes and the local chromatin environment. Nat Commun 15, 4178 (2024).
