From Tools to Insights: Molecular Dynamics in Mechanosensing

Website: compbiophysics.auburn.edu Abstract: Mechanical forces play a central role in biology, from cell adhesion and migration to host–pathogen interactions and tissue integrity. Over the past two decades, molecular dynamics simulations have evolved into a true computational microscope, allowing us to visualize and quantify biomolecular processes at spatial and temporal scales that are inaccessible to experiments alone. In this talk, I will discuss recent developments in this computational microscope, focusing on advances in the VMD and NAMD ecosystem and the integration of generalized Dynamic Network Analysis (gDNA). Together, these tools enable not only large-scale, high-performance simulations of biomolecules under force, but also the extraction of physically meaningful insights from complex dynamical data. I will show how this framework allows us to move beyond force–extension curves and single rupture events to identify allosteric communication pathways, load-bearing residues, and network-level mechanisms that govern mechanosensing. Overall, this talk will highlight how the transition from tools to insights is reshaping our understanding of protein mechanics and mechanosensing, and how computational biophysics can directly inform questions of evolution, function, and disease.