DNA has been proposed as a chemical platform for computing and data storage, paving the way for building DNA-based computers. Recently, DNA has been hypothesized as an ideal quantum computer with the base pairs working as Josephson junctions. There are still major challenges to be overcome in these directions, but they do not prevent deviceful perspectives of the main problem. The present paper explores DNA base pairs as elementary units for a scalable nuclear magnetic resonance quantum computer (NMRQC). First, it presents an overview of the proton transfer (PT) mechanism during the prototropic tautomerism in the base pairs, scoring the current stage. Second, as a proof-of-principle, the paper examines these molecular structures as quantum processing units (QPUs) of a biochemical quantum device. For the model proposed here, it is theoretically demonstrated that the nuclear spins involved in the PT of base pairs can be deterministically prepared in a superposition of triplet states. Under appropriate conditions, the proton dynamics provides the minimal two-qubit entanglement required for quantum computing. The dynamics between the canonical and tautomeric quantum states (CQS and TQS, respectively) is determined from a thermally dependent Watson-Crick quantum superposition (WCQS); i.e., |WCQS> = a(T)|CQS> + b(T)|TQS> with |a(T)|^2 + |b(T)|^2 = 1. If the DNA structure is sufficiently protected to avoid environment-induced decoherence of the confined-proton quantum states, quantum information can be successfully encoded in several base pairs along the coiled double strand. As a potential applicability, a crystalline DNA device could be employed for quantum computing and cryptography controlled by a sequence of Ramsey pulses. Finally, this study critically evaluates these possibilities toward a proof-of-concept of a DNA-based quantum computer.
DNA has been proposed as a chemical platform for computing and data storage, paving the way for building DNA-based computers. Recently, DNA has been hypothesized as an ideal quantum computer with the base pairs working as Josephson junctions. There are still major challenges to be overcome in these directions, but they do not prevent deviceful perspectives of the main problem. The present paper explores DNA base pairs as elementary units for a scalable nuclear magnetic resonance quantum computer (NMRQC). First, it presents an overview of the proton transfer (PT) mechanism during the prototropic tautomerism in the base pairs, scoring the current stage. Second, as a proof-of-principle, the paper examines these molecular structures as quantum processing units (QPUs) of a biochemical quantum device. For the model proposed here, it is theoretically demonstrated that the nuclear spins involved in the PT of base pairs can be deterministically prepared in a superposition of triplet states. Under appropriate conditions, the proton dynamics provides the minimal two-qubit entanglement required for quantum computing. The dynamics between the canonical and tautomeric quantum states (CQS and TQS, respectively) is determined from a thermally dependent Watson-Crick quantum superposition (WCQS); i.e., |WCQS> = a(T)|CQS> + b(T)|TQS> with |a(T)|^2 + |b(T)|^2 = 1. If the DNA structure is sufficiently protected to avoid environment-induced decoherence of the confined-proton quantum states, quantum information can be successfully encoded in several base pairs along the coiled double strand. As a potential applicability, a crystalline DNA device could be employed for quantum computing and cryptography controlled by a sequence of Ramsey pulses. Finally, this study critically evaluates these possibilities toward a proof-of-concept of a DNA-based quantum computer.
This paper establishes a rigorous theoretical and analytical framework positioning the double-helix Deoxyribonucleic Acid (DNA) molecule as a functional topological quantum computing system. Traditional molecular biology fails to address the thermodynamic paradox regarding the absolute informational fidelity of genetic transmission against high thermal noise within the intracellular medium (T ≈ 310 K). We propose a quantum bio-cryptographic model where nucleotide base pairs function as highly entangled qubits protected by non-local Quantum Error Correction (QEC) stabilizer codes. By analyzing the density matrix dynamics under localized environmental perturbations via the Lindblad master equation, we demonstrate that non-local quantum correlations suppress thermal dephasing. This mathematical architecture bridges functional quantum mechanics with structural genetics, providing an analytical blueprint for advanced bio-computing and computer-verified topological data storage.
DNA computation (DNAC) has been proposed to solve the satisfiability (SAT) problem due to operations in parallel on extremely large numbers of strands. This paper attempts to treat the DNA-based bio-molecular solution for the SAT problem from the quantum mechanical perspective with a purpose to explore the relationship between DNAC and quantum computation (QC). To achieve this goal, it first builds up the correspondence of operations between QC and DNAC. Then it gives an example for the case of two variables and three clauses for details of this theory. It also demonstrates a three-qubit experiment for solving the simplest SAT problem with a single variable on a liquid-state nuclear magnetic resonance ensemble to verify this theory. Some discussions are made for the potential application and for further exploration of the present work.
DNA, deoxyribonucleic acid, carrying encoded genetic information at molecular level, is the most significant discovery in the history of genetics. Previous researches on DNA included topics of bases, base-pairing, hydrogen bonds, structure, base sequence, dynamics, replication and mutation. DNA must duplicate itself, and so DNA structure and DNA replication are the fundamental problems. Watson and Crick described the structure and the mechanism for replication of DNA. Other authors focused their studies on DNA replication. DNA molecules are micro-entities ruled by laws of quantum mechanics, but the mechanisms, found previously of DNA forming and replicating, were not explored by applying quantum mechanics. Here we show that controlled by quantum mechanics, the quantum state of DNA is a bio-quantum-entangled state, the mechanism of DNA forming and replicating is a process of bio-quantum entangling, de-entangling and re-entangling. This bio-quantum mechanical result is different from the conventional biochemical descriptions of DNA structure and replication. DNA genetics is bio-quantum genetics in nature. With this deep understanding, reform and progress should be expected for further development of genetics.
We propose a novel theoretical framework for a hybrid DNA–quantum computing system based on electron–positron spin-entangled pairs embedded within the chiral architecture of DNA molecules. Utilizing the spin-1/2 nature of both particles, this two-qubit entanglement structure interfaces with the quantum chiral environment of DNA, enabling controlled spin interactions, photonic readout via annihilation, and logic gate operations induced by chirality shifts (e.g., B–Z DNA transitions). This model integrates concepts from chiral-induced spin selectivity (CISS), quantum entanglement, and DNA computing, offering a pathway toward bio-quantum logic gates, memory, and information transmission. We discuss potential mechanisms for initialization, operation, and measurement, supported by over twenty relevant studies across quantum physics, spintronics, and molecular biology.
Molecular biology explains function of molecules by their geometrical and electronical structures that are mainly determined by utilization of quantum effects in chemistry. However, further quantum effects are not thought to play any significant role in the essential processes of life. On the contrary, consideration of quantum circuits/protocols and organic molecules as software and hardware of living systems that are co-optimized during evolution, may be useful to overcome the difficulties raised by biochemical complexity and to understand the physics of life. In this sense, we review quantum information-theoretic approaches to the process of DNA replication and propose a new model in which 1) molecular recognition of a nucleobase is assumed to trigger an intrabase entanglement corresponding to a superposition of different tautomer forms and 2) pairing of complementary nucleobases is described by swapping intrabase entanglements with interbase entanglements. We examine possible biochemical realizations of quantum circuits/protocols to be used to obtain intrabase and interbase entanglements. We deal with the problem of cellular decoherence by using the theory of decoherence-free subspaces and subsystems. Lastly, we discuss feasibility of the computational or experimental verification of the model and future research directions.
We present a comprehensive quantum-inspired DNA computing framework implemented in IcsDNA using the InChroSil Virtual Machine [11], a production-ready DNA computing platform. Our approach extends the classical four-letter nucleotide alphabet {A, G, C, T} into a four-dimensional complex Hilbert space ℋ! , enabling superposition states, entanglement between nucleotide pairs, and quantum gate operations adapted to the biological domain. The framework introduces novel adaptations of fundamental quantum computing primitives, including Pauli gates, Hadamard transforms, rotation operators, and Bell-state generation, to a quaternary (base-4) nucleotide encoding. We further implement quantum-inspired algorithms for DNA sequence alignment, pattern matching via Grover-like amplitude amplification, Fourier analysis of genomic sequences, and quantum error correction for DNA storage integrity. The system provides both a high-level C++ object-oriented stack and a C API for integration into bioinformatics pipelines. Experimental evaluation demonstrates the applicability of quantum-inspired techniques to probabilistic genomic analysis, DNA-based cryptographic key generation, and fault-tolerant DNA data storage with decoherence simulation.