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A self-consistent numerical model for silicon-based field effect nanowire biosensors is developed to study the impact of various surface-related physical and chemical processes, including transport of semiconductor carriers and electrolyte mobile ions, protonation and deprotonation of surface charge groups, and charges, and orientations and surface binding dynamics of immobilized biomolecules. It is shown that the sensing signal levels are affected by the gate biasing points, nonlinear screening from both electrolytes and surface charge groups, as well as the biomolecule charges and orientations. The critical role of the nanowire surface heterogeneity in determining the sensing input dynamic range is indicated based on correlations with experimental data.