Spatial and temporal separation in overdamped systems

Abstract

Due to their small sizes molecular systems are often overdamped. Conformational changes in these molecules are a consequence of the separation of the energy input between the different displacements and velocities of the different functional sites of the molecule. We show how a simple mechanical device, that splits the forces between the different parts of the system, can achieve spatial (displacements) and temporal (velocities) separation. As a result of the overdamped nature of the motion, the equations can be decoupled by introducing a damping center. As a particular example, we briefly discuss myosin II, a motor protein responsible for the contraction of skeletal muscles.