We present a geant4 Monte Carlo simulation of cosmic-ray (CR) hadronic interactions in a spherical molecular cloud ($\sim 5400M_{\odot }$, 13 concentric shells, $r^{-1.2}$ density profile) using six primary CR species, protons, alpha particles, carbon, oxygen, silicon, and iron, drawn from galprop-helmod local interstellar spectra over $1\mathrm{GeV}{\mathrm{nuc}}^{-1}$ to $1\mathrm{PeV}{\mathrm{nuc}}^{-1}$, the hadronic interaction regime in which pion production and nuclear spallation dominate the secondary particle output. We compute, for the first time within this framework, radial energy deposition profiles, per-layer secondary production rates, and the differential physical flux of all emerging stable secondaries for the full nuclear CR composition. Energy deposition scales as $Z^2$, with the secondary cascade dominating $\ge 92\%$ of the deposited energy in the dense core for all species. Alpha particles produce the highest integrated gamma-ray flux ($0.125{\mathrm{cm}}^{-2}{\mathrm{s}}^{-1}{\mathrm{sr}}^{-1}$ above 100 MeV), followed by protons ($6.71\times {10}^{-2}{\mathrm{cm}}^{-2}{\mathrm{s}}^{-1}{\mathrm{sr}}^{-1}$); together, they account for $\approx 96\%$ of the total emerging gamma-ray and neutrino fluxes. A robust composition-diagnostic signature emerges in the neutrino sector: the ${\nu }_e/{\overline{\nu }}_e$ ratio above 100 MeV decreases from $\approx 6.4$ for protons, driven by the ${\pi }^{+}/{\pi }^{-}\approx 8–11$ charge asymmetry, to $\approx 2.8$ for $N=Z$ nuclei (C, O, Si), directly encoding the isospin content of the primary CR beam in an observable flux ratio. Secondary nuclear clusters ($d$, $t$, ${}^3\mathrm{He}$, $\alpha$, and heavier ions up to $Z=26$) emerge exclusively for nuclei heavier than protons, contributing at the $\approx 32\%$ level of the secondary proton flux for light clusters, while heavy-ion fragments remain 1 to 2 orders of magnitude below the secondary proton channel.

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• Cosmic ray composition & spectra
• Cosmic rays & astroparticles