Waveguide Quantum Electrodynamics: Tryptophans Entangled with Water as Data Qubits in a Microtubule

In this paper, we introduce waveguide Quantum Electrodynamics (wQED) for the description of tryptophans in microtubules representing data qubits for information storage and, possibly, information processing. We propose a Hamiltonian in wQED and derive Heisenberg equations for qubits and photons. Using the Heisenberg equations, we derive time-evolution equations for the probability of qubits and the distribution of photons both at zero and finite temperature. We then demonstrate the resultant sub-radiance with small decay rates, which is required to achieve robust data qubits for information storage by coupling tryptophan residues containing data qubits with water molecules as Josephson quantum filters (JQFs). We also describe an oscillation processes of qubits in a tubulin dimer through the propagation of excitations with changing decay rates of JQFs. Data qubits are found to retain initial values by adopting sub-radiant states involving entanglement with water degrees of freedom.