Modeling of Nucleosome Clustering in Euchromatin Resulting from Interactions Between Reader Proteins

Joseph Wakim, PhD Candidate, Spakowitz Group, Stanford University
The Spakowitz lab is engaged in projects that address fundamental chemical and physical phenomena underlying a range of biological processes and soft-material applications. Current research in the lab focuses on four main research themes: chromosomal organization and dynamics, protein self-assembly, polymer membranes, and charge transport in conducting polymers. These broad research areas offer complementary perspectives on chemical and physical processes, and the lab leverages this complementarity throughout its research. The approach draws from a diverse range of theoretical and computational methods, including analytical theory of semiflexible polymers, polymer field theory, continuum elastic mechanics, Brownian dynamics simulation, equilibrium and dynamic Monte Carlo simulations, analytical theory and numerical simulations of reaction-diffusion phenomena, and machine-learning and data-science approaches. A common thread in the work is the need to capture phenomena over many length and time scales, and flexibility in research methodologies provides them with the critical tools to address these complex multidisciplinary problems.
Sponsored by the Center for Physical Genomics and Engineering at Northwestern University, the Cancer and Physical Sciences Program at the Robert H. Lurie Comprehensive Cancer Center, and NIH Grants T32GM142604 and U54CA268084
physicalgenomics.northwestern...