Abstract

The equations of motion are derived for the dynamical folding of charged molecular strands, modeled as flexible continuous filamentary distributions of interacting rigid charge conformations. These equations are nonlocal when the screened Coulomb interactions, or Lennard-Jones potentials between pairs of charges, are included. The nonlocal dynamics is derived in the convective representation of continuum motion by using modified Euler-Poincar and Hamilton-Pontryagin variational formulations. In the absence of nonlocal interactions, the equations recover the classical Kirchhoff theory of elastic rods. The motion equations in the convective representation are shown to arise by a classical Lagrangian reduction associated to the symmetry group of the system. This approach uses the process of affine Euler-Poincar reduction initially developed for complex fluids. On the Hamiltonian side, the Poisson bracket of the molecular strand is obtained by reduction of the canonical symplectic structure on the phase space. Time permitting, the dynamics of multibouquets will also be presented.