We investigate ionization and heating of gas in the dense, shielded clumps/cores of molecular clouds bathed by an influx of energetic, charged cosmic rays (CRs). These molecular clouds have complex structures, with substantial variation in their physical properties over a wide range of length scales. The propagation and distribution of the CRs is thus regulated accordingly, in particular, by the magnetic fields threaded through the clouds and into the dense regions within. We have found that a specific heating rate reaching $10^{-26}$ erg cm$^{-3}$ s$^{-1}$ can be sustained in the dense clumps/cores for Galactic environments, and this rate increases with CR energy density. The propagation of CRs and heating rates in some star-forming filaments identified in IC 5146 are calculated, with the CR diffusion coefficients in these structures determined from magnetic field fluctuations inferred from optical and near-infrared polarizations of starlight, which is presumably a magnetic-field tracer. Our calculations indicate that CR heating can vary by nearly three orders of magnitude between different filaments within a cloud due to different levels of CR penetration. The CR ionization rate among these filaments is similar. The equilibrium temperature that could be maintained by CR heating alone is of order $1~{rm K}$ in a Galactic environment, but this value would be higher in strongly star-forming environments, thus causing an increase in the Jeans mass of their molecular clouds.
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