Our work aims to develop multi-scale computational procedures for simulating the dielectrophoretic behavior of biomolecules in micro/nano-fluidics, which combine electrohydrodynamics with molecular theories for the macromolecule polarization caused by the distortion of the counterion cloud. Molecular dynamics is used to simulate the transport of a flexible polyelectrolyte suspended in a solvent, with or without added salt, under the action of electric fields. We used a model with explicit solvent atoms that includes hydrodynamic interactions and finite atom size effects naturally. The poly-electrolyte is modeled as a negatively charged freely-jointed bead-spring chain and its responses in dc and ac fields are studied in details. We developed a procedure to compute the dipole moments of the molecule and the surrounding double layer, which are required for the multi-scale simulation of dielectrophoretic phenomena in nanochannels.