Quantum-Nuclear DNA Computing: Using Nucleotide Spin States as Biological Quantum Bits for Molecular Calculations

Khaled Salah Mohamed

Hafiz Md. Hasan Babu

Combinatorics is a type of calculation that traditional computers have trouble handling and it is one such challenge. These calculations involve arranging elements in a way that achieves a particular objective. Deoxyribonucleic acid is the most stable type of nucleic acid (DNA). Each DNA strand forms helical structures, which are lengthy polymers made up of millions of nucleotides bonded together. Multi-Valued DNA computing is introduced based on the usage of DNA and molecular biology hardware instead of the typical silicon-based technology. It is already found that the quantum computation qubits produce large amounts of heat. On the other hand, DNA computation needs energy or heat to perform its expected operations. In this chapter, a heat transferring procedure for the Quantum-DNA computation system will be shown. A Multi-Valued Half Subtractor is a type of subtractor, an electronic circuit that performs the subtractions of ternary numbers.

Onur Pusuluk, Cemsinan Deliduman B

Quantum effects are mainly used for the determination of molecular shapes in molecular biology, but quantum information theory may be a more useful tool to understand the physics of life. Organic molecules and quantum circuits/protocols can be considered as hardware and software of living systems that are co-optimized during evolution. We try to model DNA replication in this sense as a multi-body entanglement swapping with a reliable qubit representation of the nucleotides. In our model molecular recognition of a nucleotide triggers an intrabase entanglement corresponding to a superposition state of different tautomer forms. Then, base pairing occurs by swapping intrabase entanglements with interbase entanglements. We examine possible realizations of quantum circuits to be used to obtain intrabase entanglement and swapping protocols to be employed to obtain interbase entanglement. Finally, we discuss possible ways for computational and experimental verification of the model.

Hafiz Md. Hasan Babu

L. Dang, Dung Van Lu, Nguyen Thi Phuong Bac

Jose Daniel Llopis

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.