All atoms are treated as point particles with atomic masses according to their atom types (H, C, N, and O).
Silicon and carbon atoms are treated on the same footing by characterizing each with their corresponding orbitals.
The non-local atoms are treated by discrete atomistic lattice statics in the areas where severe plastic deformations occur.
The cluster of carbon atoms is treated as the atoms of diamond tool, and the several layers of monocrystalline germanium are deemed to be the substrate.
This is followed by a high-resolution search, in which all atoms are treated explicitly, and backbone and side chain degrees of freedom are simultaneously optimized.
In the mobile H group these hydrogen atoms are treated as non-isotopic; the number of these mobile isotopic hydrogen atoms is appended to the "exchangeable isotopic hydrogen atoms" part of the isotopic layer.
In many methods the ligand, usually a small molecule with up to dozens of atoms, is treated as flexible, but the flexibility of the protein/receptor (for simplicity, herein protein and receptor are synonymous), depending on their complexity and size, which can reach dozens of thousands of atoms, is still treated in a more restricted manner.
An example is depicted in Figure 16b, where (a) the atoms are treated classically, (b) d nk = 0 for the given diabatic states, and (c) the large value of the electronic coupling V nk implies that the system evolves on the initially populated adiabatic electronic state.
The single valence, or outer-shell, electron of each alkali atom is treated explicitly, while all the others are considered part of the smeared-out core.
Each polar atom is treated as a dipole with a direction.
