The existence of two types of internal friction—wet and dry—is revisited, and a simple protocol is proposed for distinguishing between the two types and extracting the appropriate internal friction coefficient. The scheme requires repeatedly stretching a polymer molecule and measuring the average work dissipated in the process by applying the Jarzynski equality. The internal friction coefficient is then estimated from the average dissipated work in the extrapolated limit of zero solvent viscosity. The validity of the protocol is established through analytical calculations on a one-dimensional free-draining Hookean spring-dashpot model for a polymer, and Brownian dynamics simulations of (a) a single-mode nonlinear spring-dashpot model for a polymer and (b) a finitely extensible bead-spring chain with cohesive intrachain interactions, both of which incorporate fluctuating hydrodynamic interactions. Well-established single-molecule manipulation techniques, such as optical tweezerbased pulling, can be used to implement the suggested protocol experimentally.
- Biomolecular dynamics
- Fluctuation Theorems
- Polymer conformation changes
- Brownian dynamics simulations
- Nonequilibrium and irreversible thermodynamics