tokens: and along with the dust distribution, it sets the thermal profile of the disk. Likewise, UV and X-ray photons dominate the chemistry in the upper layers through molecular ionization and photodissociation. Given that photodissociating photons play a considerable role in the disk chemistry, we use a large number of photon packages for the X-rays and the UV frequencies to minimize the photon noise in the Monte Carlo simulation. We run the simulations using 5 × 10 6 photon packages for the optical and longer wavelengths, but we include a refinement factor of 10 3 for Ly α photons, 5 × 10 3 for UV photons, and 10 6 for X-rays. By using the refinement factor, we increase the number of photon packages in the respective spectral window by the corresponding refinement value. Even using a refinement for the UV photons, the dust opacity does not let the UV photons reach the midplane. Nevertheless, the UV flux reaching the midplane and its associated photodissociation rate are negligible compared to the optical irradiation and the gas-phase chemistry, so it does not change our final results. Further, Agúndez et al. ( 2018 ) show that FUV photodissociation rates for T Tauri disks are negligible for z / r 0.3 at 100 au. In our basic or benchmark model, the surface density, Σ basic , follows the self-similar solution from Lynden-Bell Pringle ( 1974 ), i.e.,where r e is the radius of the exponential cutoff, r 0 is the characteristic radius for the disk, and Σ 0 is the surface density of the disk at r = r 0 . In our basic model, the gas and dust components have the same profiles, where Σ 0 is the only changing value. For the disk with the dust substructure, we add the ring and the gap as modulations of the self-similar solution. Those modulations are further discussed in Section 2.1.1 . We aim to include how the gas and the distinct dust populations alter the chemistry and physical conditions in the disk. So, we set different vertical distributions for them, but with the same functional form. Both gas and dust have vertical Gaussian distributions (Armitage 2010 ):where and h is the scale height, which we vary for each population. Particularly for the gas, the aspect ratio is set to be h / r = 0.08 at r = 100 au. The scale height also has a radial dependence through a power law with a flaring index ψ :The flaring index is a common value for the gas and dust populations. We set it with a value of ψ = 1.22. Besides the gas, we include two main dust populations differentiated by the grain size they represent and an additional third component only within the inner 3.5 au. The two main populations are composed of a mixture of 80% silicates and 20% graphite. The optical opacities where taken from Draine Lee ( 1984 ), while the X-rays opacities come from the prescription in Bethell Bergin ( 2011 ). Both dust populations follow a grain size distribution with a standard power law, n ( a ) ∝ a −3.5 , which is taken from Mathis et al. ( 1977 ). We also set a
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