Developing physics-based models for molecular simulation requires fitting many unknown parameters to experimental datasets of diverse properties. Model development typically proceeds according to the trial-and-error tinkering of individual researchers, and the procedures by which parameters are chosen are often opaque and irreproducible. This erects significant barriers to extending and...
In the nucleus, essential biological processes rely on proteins diffusing through and interacting with a complex network of nucleic acid polymers. To better understand this dynamic interplay requires an advanced imaging platform that simultaneously tracks single-molecule dynamics and the local chromatin environment in live cells. In this talk, I will present our work that combines...
We carry out molecular dynamics simulations of peptides confined within aqueous nanodroplets and investigate the influence of the temperature-dependent properties of the nanodroplets on peptide folding, localization within the nanodroplet, and secondary structure. Recent computational studies from our group have revealed the emergence of thermodynamic and structural anomalies in liquid water...
One way to glue objects together at the nanoscale or microscale is by ligand-receptor interactions, where short sticky hair-like ligands stick to receptors on another surface, much like velcro on the nanoscale. Such interactions are common in biological systems, such as white blood cells, virus particles, cargo in the nuclear pore complex, etc, and they are also useful in materials science,...
