Symplectic reduction and topology for applications in classical molecular dynamics

This paper aims to introduce readers with backgrounds in classical molecular dynamics to some ideas in geometric mechanics that may be useful. This is done through some simple but specific examples: (i) the separation of the rotational and internal energies in an arbitrarily floppy N-body system and (ii) the reduction of the phase space accompanying the change from the laboratory coordinate system to the center of mass coordinate system relevant to molecular collision dynamics. For the case of two-body molecular systems constrained to a plane, symplectic reduction is employed to demonstrate explicitly the separation of translational, rotational, and internal energies and the corresponding reductions of the phase space describing the dynamics for Hamiltonian systems with symmetry. Further, by examining the topology of the energy-momentum map, a unified treatment is presented of the reduction results for the description of (i) the classical dynamics of rotating and vibrating diatomic molecules, which correspond to bound trajectories and (ii) the classical dynamics of atom-atom collisions, which correspond to scattering trajectories. This provides a framework for the treatment of the dynamics of larger N-body systems, including the dynamics of larger rotating and vibrating polyatomic molecular systems and the dynamics of molecule-molecule collisions.