Scientific exploration converges on DNA's potential as a quantum computer, highlighting different facets of this concept. One study examines proton transfer's role during DNA strand separation and its link to mutagenic tautomers, suggesting a reevaluation of tautomer mutation mechanisms. Another investigates the possibility of constructing quantum logic gates using DNA, RNA, and proteins via proton-coupled electron transfer, proposing a new method for molecular computing. A third article explains how DNA could theoretically serve as a quantum computer due to oscillatory resonant quantum states, Josephson Junctions, and quantum informational cryptography, further positing that a central hydrogen bond in DNA functions like an ideal Josephson Junction.
I. Overview This document synthesizes information from three sources exploring the intersection of DNA, quantum computing, and molecular electronics. The sources discuss:
DNA Base Separation (DFT Modeling): A study using density functional theory (DFT) to model the separation of DNA bases (Guanine-Cytosine dimer), examining the effects on hydrogen bond lengths and energies during this process.
DNAtronics for Quantum Logic Gates: A proposal for using DNA, RNA, and proteins (DNAtronics, RNAtronics, and Proteintronics) as the basis for quantum logic gates, focusing on proton-coupled electron transfer (PCET) in residue pairs.
DNA as a Superconducting Quantum System: A theoretical framework describing DNA bases as exhibiting superconductivity through oscillatory resonant quantum states of electron and hole pairs, suggesting Josephson Junction behavior and potential for quantum teleportation.
II. Key Themes and Ideas
A. DNA Base Separation Dynamics
Asynchronous Separation: DFT calculations suggest that DNA base pairs (specifically G-C) do not split apart synchronously. One O-H-N hydrogen bond tends to maintain its equilibrium length while the bases rotate relative to each other. "The non-uniformity of the separation implies that the bases do not synchronously split apart, but instead separate asymmetrically."
Rotation about the R-group: The model constrains the R-group atom (where the base joins the DNA backbone), and the observed rotation during separation is physically consistent with this covalent link. "The rotation about the fixed R-group is physi-cally consistent since it is the only covalently bonded link between the base and the rest of the DNA."
Solvation Effects: The DFT calculations incorporate an implicit solvent model with a dielectric factor of 8.0, simulating the influence of water molecules and the protein interface expected during DNA-helicase interactions.
Molecular Dynamics Simulations: Simulations were conducted using the CHARMM36 force field to analyze the separation dynamics with a pulling force applied to the base pairs. The separation speed was estimated using linear regression on the hydrogen bond length time series.
Reaction Coordinate Analysis: The study uses reaction coordinate analysis to determine the synchronicity of proton transfers during base separation. The parameter α is used to quantify the separation of transfer events, with larger values indicating a greater separation.
B. DNAtronics, RNAtronics, and Proteintronics for Quantum Computing
Molecular Transistors: The paper proposes using molecular transistors based on DNA, RNA, and proteins to build quantum logic gates. "Herein, it is demonstrated that DNA, RNA, and protein are promising media for QCs, and one uses residue pairs, including nucleotide base pairs and amino acid pairs, via proton-coupled electron transfer to fabricate a quantum logic gate."
Qubit Implementation: Proton transfer between donor and acceptor states in residue pairs is suggested as a means to implement qubits. The energy barrier of a double-well potential energy surface is crucial for exhibiting distinct qubit states.
Logic Gate Realizations:DNA-CG (3-qubit): Toffoli gate
AT (2-qubit): SWAP gate and CNOT gate (depending on spin state and phosphate group charges)
AU and RNA-CG: CNOT gate and Toffoli gate, respectively
Amino acid pairs: 1-qubit gates satisfying Pauli-X, -Y, and -Z gates
Universal Quantum Logic Gates: The combination of these 1-, 2-, and 3-qubit gates is argued to fulfill the requirements for a universal quantum logic gate (Clifford group and T-phase gate). "Notably, our designated 1-, 2-, and 3-qubit gates fulfill the requirement of a universal quantum logic gate."
DiVincenzo's Criteria: The proposed molecular transistor-based QC is analyzed against DiVincenzo's criteria for reliable QCs, addressing scalability, qubit characterization, state initialization, decoherence times, universal quantum states, and qubit-specific measurement.
Experimental Methodology: The study utilizes DFT calculations with Gaussian 16 and the ALACANT program to calculate the transmission spectrum of electron transfer based on DFT-non-equilibrium green function (NEGF) theory. MD simulations were conducted using NAMD and the CHARMM27 force field.
Charge Distribution Analysis: The study employs Natural Bond Orbital (NBO) analysis using Gaussian to calculate the natural charge (NC) of each site in the nucleotide base pair for all charge states.
C. DNA as a Superconducting Quantum System
Oscillatory Resonant Quantum States: This paper posits that DNA bases exhibit superconductivity through a mechanism involving oscillatory resonant quantum states between electron and hole pairs within π orbitals. "In Fig. 1, we described the general oscillatory resonant quantum states process between electron and hole pairs forming in π orbitals."
Benzene Analogy: The aromaticity of benzene is used as a model to explain the correlated movement of electron and hole pairs in DNA bases.
Josephson Junctions: A-T and C-G base pairs are proposed to function as Josephson Junctions, with the hydrogen bonds acting as a nonlinear inductive element. "When the A-T or C-G composite systems enter the Josephson regime, the weak link is expected to act as a nonlinear inductive element because the Josephson current, a nonlinear function of the quantum phase, gives the current through it."
Superdense Coding for Perfect Teleportation: The study describes how DNA codons can be encoded to achieve superdense coding for quantum teleportation. It outlines a teleportation protocol to simulate a quantum computer based on DNA qubits.
Zero Momentum State: The study shows the zero momentum state (P=0) in A-T and C-G base pairs condensates in Table 1 with electron, proton, and neutron numbers.
Hamiltonian: Shows the Hamiltonian for the pairs T-A, G-C, and C-G and the respective evolution operator.
Classical and Quantum Information Hybridization: This paper defines purines and pyrimidines as quantum states.
III. Implications and Potential Applications
Novel Computing Paradigms: These studies suggest radical new approaches to computing, leveraging the inherent properties of biomolecules for quantum-level operations.
Nanomedicine: Residue pair-based computing elements may find applications in nanomedicine, potentially for diagnostics or targeted therapies.
Nanoelectronics: The findings could contribute to the development of new nanoelectronic devices based on molecular transistors and quantum phenomena in DNA.
Quantum Information Processing: The research explores fundamental aspects of quantum information processing, including qubit implementation, quantum logic gates, and quantum teleportation, using biological systems.
IV. Caveats and Considerations
Theoretical Nature: Much of this work is theoretical, relying on computational modeling and simulations. Experimental validation is crucial.
Complexity: The complexity of biological systems poses significant challenges to controlling and manipulating these molecular-level quantum phenomena.
Decoherence: Maintaining coherence in quantum systems is a major hurdle. The study of decoherence and dephasing in these biomolecular systems is essential.
Scalability: Scaling up these molecular-level quantum devices to create practical quantum computers remains a significant challenge.
Citation:
Slocombe, L., Winokan, M., Al-Khalili, J. et al. Proton transfer during DNA strand separation as a source of mutagenic guanine-cytosine tautomers. Commun Chem 5, 144 (2022). https://doi.org/10.1038/s42004-022-00760-x
Sheu, S., Hsu, H., & Yang, D. (2021). Quantum Logic gates based on DNAtronics, RNAtronics, and proteintronics. Advanced Intelligent Systems, 3(7). https://doi.org/10.1002/aisy.202000273
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