Discrete-to-continuum description of protein dynamics: Models and comparative simulations

We propose and compare through simulations different ways of linking a continuum descriptiond of protein dynamics and translocation through tissue pores with the low-scale protein discrete structure and its inner in- teractions. At first we consider a model emerging from a version of the Cauchy-Born rule, written in terms of velocities. Then, we explore its variants, which account for the rate at which amino acids move relatively to the protein mass center. In representing the molecular morphology, such variants allow us to overcome the limits associated with the assumption of homogeneous deformation sustaining the Cauchy-Born rule, which appears to be appropriate essentially in confined environment, where fluctuations are bounded. The suggested variants in the discrete-to-continuum identification furnish a significant overall picture of protein mechanics. Our analysis paves the way to a continuum description of flowing molecular clusters.