We show that indirect spin-spin interactions between effective spin-1/2 systems can be realized in two parallel one-dimensional optical lattices loaded with polar molecules and/or Rydberg atoms. The effective spin can be encoded into low-energy rotational states of polar molecules or long-lived states of Rydberg atoms, tightly trapped in a deep optical lattice. The spin-spin interactions can be mediated by Rydberg atoms, placed in a parallel shallow optical lattice, interacting with the effective spins by charge-dipole (for polar molecules) or dipole-dipole (for Rydberg atoms) interaction. Indirect
XX, Ising, and
XXZ interactions with interaction coefficients ${J}^{\ensuremath{\perp}}$ and
Jzz sign varying with interspin distance can be realized, in particular, the ${J}_{1}\ensuremath{-}{J}_{2} XXZ$ model with frustrated ferro-(antiferro-)magnetic nearest (next-nearest) neighbor interactions.
We study the possibility to use interaction between a polar molecule in the ground electronic and vibrational state and a Rydberg atom to construct two-qubit gates between molecular qubits and to coherently control molecular states. A polar molecule within the electron orbit in a Rydberg atom can either shift the Rydberg state, or form a Rydberg molecule. Both the atomic shift and the Rydberg molecule states depend on the initial internal state of the polar molecule, resulting in molecular state dependent van der Waals or dipole-dipole interaction between Rydberg atoms. Rydberg atoms mediated interaction between polar molecules can be enhanced up to 10(3) times. We describe how the coupling between a polar molecule and a Rydberg atom can be applied to coherently control molecular states, and specifically, to individually address molecules in an optical lattice, and to non-destructively readout molecular qubits.