Toward modeling dynamics in biological suspensions with Roseanna Zia
Channel: LINXS
Date: 2023-11-22

1 November 2023
This webinar is part of the Antibodies in Solution webinar series at LINXS. Link: https://www.linxs.se/educational/toward-modeling-dynamics-in-biological-suspensions
Speaker: Roseanna Zia, University of Missouri, US
Title: Toward modeling dynamics in biological suspensions

Abstract
Although recent work showed that the speedup of bacterial protein synthesis with growth rate is driven by physical transport, diffusion alone is too slow to bring together matching translation molecules in crowded cytoplasm. Noting that knocking out interactions between ribosomal L12 and elongation factor Tu (EF-Tu) slows translation in vitro, we developed a physico-chemical model of the Escherichia coli cytoplasm including explicit EF-Tu·L12 interactions and elongation reaction kinetics. We found that these interactions shorten the time ribosomes must wait to test new tRNA, doubling elongation speed. In this talk, I focus on the development of our computational model to represent patchy colloidal interactions in a dense suspension, incorporating chemical kinetics from experimental data. I will also discuss our progress in merging this model with our parallelized Accelerated Stokesian dynamics, enabling accurate representation of very large polydisperse systems of interacting colloids.