This paper presents a mathematical model for the manipulation of proteins using insulator-based dielectrophoresis (iDEP) and direct current (DC) electric fields. Simulations via COMSOL v4.1 Multiphysics® software are implemented to study the response of moderately sized proteins on a lab-on-a-chip platform. The geometry of the device is incorporated in a model that solves current and mass conservation equations within an array of circular insulating silicon posts embedded in a channel. Both micro- and nano-scale geometries are utilized to investigate the protein concentration distributions in the iDEP device. Our results indicate that the trapping of proteins is independent of the scale with respect to the geometry of a device as long as the applied electric field remains constant. DC voltage dependency on concentration distributions has also been explored in both micro- and nano-scale device geometries. To achieve DEP trapping of the proteins, nano-scale geometry is a better selection, as the voltage necessary to generate the required electric field (2.5 MV/cm) is 105× lower compared with the voltage required to generate the same field in the micro-scale device.