Biomolecular modeling and its associated analytical software simulation tools have a significant role in the rapid progress of bio-inspired semiconductor technologies. This paper presents the implementation of logic gates using molecular modeling of a cytosine-based single-walled nanotube. Density functional theory in and the nonequilibrium Green’s function-based first-principles approach are used to perform the quantum mechanical calculations for the electronic transmission within the nanotube. The gated cytosine single-walled nanotube shows high current-voltage response during room-temperature operation where the electrode voltage is kept at ± 0.02 V. This is a first attempt towards the circuit-level modeling of logic gates using a cytosine nanotube. The quantum transport phenomenon of this analytical model is investigated using an atomistic software simulation technique. The basic logic gates and XNOR gate are implemented with the study of the current-voltage characteristics. The maximum current observed during the simulation process is 52.6 μA. Moreover, the local device density at different energy levels proves the candidature of cytosine nanotubes as logic gates. The transmission spectrum analysis also confirms the high channel conductivity at the central scattering region of the nanotube.