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In the present report, we have simulated the FET based silicon nanowire biosensor and studied the effect of nanowire length and radius on the different functional characteristics of the silicon nanowire biosensor. We have used BioSensorLab open source simulation tool for the present investigation. Particularly, we have studied the effect of nanowire length and radius on conductance modulation with respect to target molecule density, conductance modulation with respect to buffer ion concentration, nanowire surface potential with respect to pH, signal to noise ratio (SNR) with respect to receptor density, settling time with respect to analyte concentration and density of captured molecule with respect to detection time. We have taken into account the electrostatic interaction between receptor molecules and target biomolecules, which is based on the Diffusion-Capture model. The results suggested that the higher conductance modulation can be achieved at the higher target molecule density with a larger radius of the silicon nanowire. On the other hand, maximum conductance modulation is observed at the lower radius of the silicon nanowire with lower buffer ion concentration. The simulation results suggested that the surface potential of the nanowire tends to decrease as the pH increases for both cases (nanowire length and radius). No significant effect on the signal to noise ratio due to the change in the nanowire length and radius was observed. It is observed that the nanowire length does not affect the settling time; however, change in the nanowire radius shows the significant effect on the settling time. In the nutshell, the nanowire length and radius significantly affect the performance parameters of the FET based silicon nanowire biosensor.