title: Internal dissipation of a polymer.
abstract: The dynamics of flexible polymer molecules are often assumed to be governed by hydrodynamics of the solvent. However there is considerable evidence that internal dissipation of a polymer contributes as well. Here we investigate the dynamics of a single chain in the absence of solvent to characterize the nature of this internal friction. We model the chains as freely hinged but with localized bond angles and threefold symmetric dihedral angles. We show that the damping is close but not identical to Kelvin damping, which depends on the first temporal and second spatial derivative of monomer position. With no internal potential between monomers, the magnitude of the damping is small for long wavelengths and weakly damped oscillatory time dependent behavior is seen for a large range of spatial modes. When the size of the internal potential is increased, such oscillations persist, but the damping becomes larger. However underdamped motion is present even with quite strong dihedral barriers for long enough wavelengths.
authors.affiliation: Department of Physics, University of California, Santa Cruz, California 95064, USA.
authors.forename: J M
authors.initials: JM
authors.lastname: Deutsch
mesh_terms: D000465:Algorithms; D001703:Biophysics / Q000379:methods*; D003198:Computer Simulation; D008962:Models, Theoretical; D016011:Normal Distribution; D009991:Oscillometry / Q000379:methods; D011108:Polymers / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry; D013696:Temperature; D013997:Time Factors; D014783:Viscosity
chemical_list: D011108:Polymers; D012997:Solvents