Quantifying biomolecular diffusion with a “spherical cow” model

The dynamics of biological polymers, including proteins, RNA, and DNA, occur in very high-dimensional spaces. Many naturally occurring polymers can navigate a vast phase space rapidly find their lowest free energy (folded) state. Thus, although the search process is stochastic, it not completely random. Instead, best described terms diffusion along downhill landscape. In this context, there have been many efforts to use simplified representations energetics, for which potential chosen be relatively smooth function with global minimum that corresponds folded That is, instead every type physical interaction, broad characteristics landscape are encoded approximate functions. We describe particular class models, called structure-based used explore diffusive properties biomolecular folding conformational rearrangements. These functions may regarded as spherical cow modeling molecular biophysics. discuss principles underlying these models provide an entry-level tutorial, adapted curricula physics non-physics majors.