UCLA

RNA-protein binding is important in many biological processes. These processes depend on the structural properties of the RNA, DNA and proteins involved. In this thesis we have investigated the nature of these interactions at the scale of coarse grained interactions, in atomistic detail and with analytical continuum theories. By exploring the dynamics of these biopolymers at these different scales, we hope to shed light on the important phenomena and characteristics that govern the biological processes involved.

First we show that the structural flexibility of these polymers affects he binding energy measured in MD simulations and can help understand the different packaging scenarios in in-vitro viral reconstitution. Then using analytical models we show how flexibility can aid it non-specific binding given the strength of interaction compared to thermal energy between the binding of polymers.

We finish this thesis by looking at coarse grained brownian dynamics simulations for the bonds in a chain to represent the non-linear viscoelastic behavior of proteins deforming under force. We see both equilibrium mechanical induced melting of the chain and a dynamical phase transition in the response of the chain under a varying drive amplitude and frequency of and AC applied force out of equilibrium. Using the model to understand the dynamics of a deformable chain under force, we explore how this model can provide insight into the binding of deformable structure forming chains that mimic biopolymers like RNA, DNA and proteins.