Nanotube patterning may occur naturally upon the spontaneous self-assembly of biomolecules onto the surface of single-walled carbon nanotubes (SWNTs). It results in periodically alternating bands of surface properties, ranging from relatively hydrophilic to hydrophobic, along the axis of the nanotube. Single-chain mean field (SCMF) theory has been used to estimate the free energy of systems in which a surface patterned nanotube penetrates a phospholipid bilayer. In contrast to unpatterned nanotubes with uniform surface properties, certain patterned nanotubes have been identified that display a relatively low and approximately constant system free energy (<±10 kT) as the nanotube traverses through the bilayer. These observations support the hypothesis that the spontaneous self-assembly of biomolecules on the surface of SWNTs may facilitate nanotube transduction through cell membranes.