Fluorescent-Protein Spin Qubit

• Fluorescent-protein spin qubits are quantum two-level systems encoded in genetically engineered fluorescent proteins enabling integration with biological environments.
• Optical excitation and microwave techniques enable coherent initialization, manipulation, and high-contrast fluorescence readout in systems like EYFP, cryptochrome, and Venus YFP.
• These qubits offer practical quantum sensing applications by leveraging tunable photophysical properties and protein engineering to overcome solid-state interfacing limitations.

A fluorescent-protein spin qubit is a quantum two-level system encoded in the spin degree of freedom of a genetically encodable fluorescent protein chromophore, with initialization, coherent manipulation, and optical readout enabled through tailored photophysical and spin-resonant techniques. Unlike solid-state spin qubits in semiconductor or diamond hosts, fluorescent-protein spin qubits offer integration with biological systems, opening avenues for quantum sensing and information applications directly within complex biomolecular environments.

1. Principles and Motivation

Optically addressable spin qubits are foundational units for nanoscale sensors and quantum information applications, offering sensitivity to magnetic and electric fields, chemical environments, and temperature at the molecular scale. Traditional paradigms such as nitrogen-vacancy (NV) centers in diamond are limited in their ability to interface with biomolecules due to the bulk and surface chemistry of their host material. Fluorescent proteins, exemplified by Enhanced Yellow Fluorescent Protein (EYFP) and Venus Yellow Fluorescent Protein (YFP), are routinely used in bioimaging due to their genetic encodability, robust optical properties, and capacity for fusion to target biomolecules. Recent research demonstrates that engineered fluorescent proteins possess optically addressable spin states, establishing a protein-based qubit platform that overcomes the physical interfacing limitations of solid-state systems (Feder et al., 25 Nov 2024, Abrahams, 19 Aug 2025).

2. Physical Realization in Fluorescent Proteins

EYFP Triplet Spin Qubit

Fluorescent proteins such as EYFP exhibit a metastable triplet state, accessible via intersystem crossing from the fluorescent singlet excited state. Upon optical excitation, the protein transitions from its ground singlet state to the excited singlet manifold, followed by intersystem crossing to the lowest triplet state (T₁). The spin state encodes the qubit, with initialization and manipulation performed using resonant microwave pulses.

A key engineering advance is the optically activated delayed fluorescence (OADF) technique, in which a near-infrared (912 nm) laser pulse induces reverse intersystem crossing (RISC), transferring population from T₁ to a higher-lying triplet state (T₂) and then to the singlet manifold, emitting a background-free fluorescence photon that heralds the triplet spin state. This enables high-contrast (up to 44%), triggered spin readout that is orders of magnitude faster than the triplet's natural decay (Feder et al., 25 Nov 2024).

Radical Pair Spin Qubits in Cryptochrome

In cryptochrome proteins, optical excitation generates spin-correlated radical pairs (e.g., FAD•– and TrpH•+). The two radicals, separated by nanometer distances, occupy singlet and triplet spin states. Their dynamics are governed by a Hamiltonian with Zeeman and hyperfine interactions:

$$\hat{H} = g \mu_B \vec{B}_0 \cdot \hat{S} + \sum_{k} \hat{S} \cdot \mathbf{A}_k \cdot \hat{I}_k,$$

where the populations evolve under field-dependent rates. Fluorescence readout is achieved through spin-selective recombination pathways, and optically detected magnetic resonance (ODMR) is used for spin manipulation and detection (Meng et al., 23 Apr 2025).

Dimeric Excitonic Qubits in Venus YFP

Venus YFP dimers exhibit strong excitonic coupling between chromophores, yielding bright/dark excitonic states split by a negative Davydov energy. Photon antibunching, signifying single-quantum emission, coexists with this strong coupling, explained by rapid decoherence modeled via a Lindblad master equation:

$$\frac{d\rho}{dt} = -\frac{i}{\hbar}[H, \rho] + \sum_l \mathcal{L}(\rho, \gamma_l),$$

where $\rho$ is the density matrix and $\mathcal{L}$ denotes dissipative (dephasing and relaxation) channels (Abrahams, 19 Aug 2025).

3. Performance Metrics and Coherence Properties

The EYFP qubit exhibits key quantum performance parameters at liquid-nitrogen temperatures (Feder et al., 25 Nov 2024):

Metric	Value	Method
Spin-lattice relaxation ($T_1$)	$(141 \pm 5)\, \mu$s	Microwave spectroscopy
Spin coherence ($T_2$, CPMG)	$(16 \pm 2)\, \mu$s	Dynamical decoupling
AC magnetic field sensitivity	$$183\,\mathrm{fT}\,\mathrm{mol}^{1/2}\,\mathrm{Hz}^{-1/2}$$	Calculated upper bound
ODMR contrast (room temp, aqueous)	Up to $3\%$	Optically detected
DC field sensitivity (room temp)	$$93\,\mathrm{pT}\,\mathrm{mol}^{1/2}\,\mathrm{Hz}^{-1/2}$$	Measured upper bound

In Venus YFP dimers, coherence lifetimes at room temperature are limited to tens of femtoseconds due to rapid dephasing, but cryogenic cooling is predicted to extend them into the picosecond regime, potentially supporting quantum gate operations (Abrahams, 19 Aug 2025).

4. Integration with Biological Systems

Fluorescent-protein spin qubits offer direct genetic encodability and targeting within living cells. EYFP qubits expressed in human embryonic kidney 293T cells retain both optical spin-contrast and coherent microwave control, even amid the fluctuating and heterogeneous intracellular environment (Feder et al., 25 Nov 2024). This biological compatibility enables in situ nanoscale sensors of magnetic fields that traditional solid-state platforms cannot realize.

Radical-pair-based protein qubits (cryptochrome) are also tunable by protein engineering, with contrast and radical pair lifetimes modifiable via site-directed mutagenesis. This suggests a pathway toward highly specific, application-tailored quantum sensors for biomolecular environments (Meng et al., 23 Apr 2025).

5. Quantum Sensing and Information Applications

Fluorescent-protein spin qubits support several emerging applications:

• Magnetometry: EYFP spin qubits demonstrate AC and DC magnetic field sensitivities sufficient for detection in biological contexts, with sensitivity approaching the range of established solid-state quantum sensors (Feder et al., 25 Nov 2024).
• Spin-Photon Interfaces: High-contrast, on-demand optical readout via OADF or radical-pair recombination provides an avenue toward hybrid quantum networks linking stationary (spin) qubits and propagating (photon) qubits.
• Multiplexed Microscopy: Cryptochrome's ODMR contrast mechanism allows encoding supplementary spectral information through RF resonance rather than fluorescence emission wavelength, increasing information density in optical microscopy (Meng et al., 23 Apr 2025).
• Ultrafast Optical Control: In Venus dimers, strong excitonic coupling allows the use of bright/dark state populations as logical encoding bases. Rapid decoherence imposes practical limits at ambient temperature, but sub-picosecond manipulations or cryogenic operation could render coherent quantum gates viable (Abrahams, 19 Aug 2025).

6. Structural Principles and Tunability

The "bioexciton motif" (Editor's term) encapsulates the design principle by which protein architecture governs excitonic coupling strength, decoherence rates, and photophysical performance. In Venus YFP dimers, evolutionary optimization of chromophore orientation and spacing enables robust excitonic splitting, strong antibunching, and rapid dephasing. Adjusting these parameters via protein engineering or directed evolution allows fine control over qubit-relevant properties (Abrahams, 19 Aug 2025).

In cryptochrome and EYFP, the protein environment determines the accessibility, lifetime, and readout efficiency of the relevant spin states. Genetic modification provides a tunable handle over these properties without requiring changes in the microenvironment or external field strengths (Feder et al., 25 Nov 2024, Meng et al., 23 Apr 2025).

7. Prospects and Open Directions

Expansion of fluorescent-protein spin qubits as quantum sensors and quantum information primitives raises several practical and theoretical challenges:

• Extending Coherence: Attaining coherence lifetimes that exceed quantum gate times remains the foremost challenge; strategies include cryogenic operation, vibrational decoupling, and further protein engineering (Abrahams, 19 Aug 2025).
• Complex Environment Adaptation: Maintaining spin-contrast and coherence in vivo and in aqueous solution demonstrates robustness, but the limits imposed by intracellular fluctuations and chemical reactivity require further paper (Feder et al., 25 Nov 2024).
• Integration with Quantum Networks: The combination of bio-compatibility, optical readout, and tunable spin physics places fluorescent-protein spin qubits as candidates for interfacing biological nanotechnology with quantum photonics.
• Theoretical Modeling: Accurately capturing ultrafast dynamics, non-Markovian decoherence, and correlated noise requires advanced open quantum system modeling, beyond the standard Lindblad equation, including path-integral or QM/MM treatments (Abrahams, 19 Aug 2025).

A plausible implication is that continued improvements in protein design, combined with advanced optical and spin-resonance techniques, will enable fluorescent-protein spin qubits to complement and, in bio-integrative contexts, surpass traditional solid-state quantum sensing and computation platforms.