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A numerical study on the operation of Si nanowire (NW) biosensors in charge-based sensing is presented. The simulation is built on physical models that, upon numerical convergence, coherently account for Fermi-Dirac, Poisson-Boltzman, site-binding and Gouy-Chapman-Stern theories in self-consistent manner. The method enables us to disentangle the impact of key design and experimental setup factors and assess their contribution to the sensitivity, linearity, and stability of such sensors. Our results quantitatively show SiNW sensor is significantly more stable when biased through solution gate than back gate; dense functional group at oxide surface and good SAM coverage are essential to linear and sensitive detection of uniformly distributed targets; compared to high concentration target detection, the effect of NW surface-to-volume ratio (S/V ) plays a more profound role in biomolecule detection when targets are at very low concentration, in which case, optimal S/V exists for a maximum sensitivity. Arbitrary down scaling beyond such S/V point may have reverse effect on sensor sensitivity.