Net ionization and net capture cross-section calculations are presented for proton collisions from methane molecules and the DNA/RNA nucleobases adenine, cytosine, guanine, thymine, and uracil. We use the recently introduced independent-atom-model pixel counting method to calculate these cross sections in the 10 keV to 10 MeV impact energy range and compare them with results obtained from the simpler additivity rule, a previously used complete-neglect-of-differential-overlap method, and with experimental data and previous calculations where available. It is found that all theoretical results agree reasonably well at high energies, but deviate significantly in the low-to-intermediate energy range. In particular, the pixel counting method which takes the geometrical overlap of atomic cross sections into account is the only calculation that is able to describe the measurements for capture in proton-methane collisions down to 10 keV impact energy. For the nucleobases it also yields a significantly smaller cross section in this region than the other models. New measurements are urgently required to test this prediction.
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