This paper presents the use of a physical model and numerical simulation in the investigation of traveling electric fields on capillary electrophoresis (CE) chips. The principal material transport mechanisms of electrokinetic migration, ionic concentration, fluid flow, and diffusion are all taken into consideration. Traditionally, the high electric field strength required for the separation of biological samples by microfluiclic devices has involved the application of high external voltages. In contrast, this study presents a proposal for samples separation by means of a moving electric field within a low voltage-driven CE chip. Under this proposal, the separation channel is partitioned into a series of smaller separation zones by means of electrode pairs. This paper considers two different electrode configurations, namely arranged along a single side of the separation channel, and arranged on two sides of the separation channel. The quality of the separation achieved with these two configurations is then compared with the traditional straight separation channel approach. The results confirm that the proposed method is successful in maintaining an adequate field strength for separation purposes in a low-voltage driven CE chip. Furthermore, it is determined that the best separation results are obtained using electrodes arranged along both sides of the separation channel.