2025/04/24 by Xu Wang, Wang, Xu, Yiquan Wang +4
Biochemistry, Genetics and Molecular Biology · Computer Science · #Artificial Intelligence (cs.AI) #Cryptography and Security (cs.CR) #DNA and Biological Computing #FOS: Computer and information sciences #Physical Unclonable Functions (PUFs) and Hardware Security #RNA and protein synthesis mechanisms
paper · pdf · doi:10.48550/arxiv.2504.17878
openalex publication_date 2025/04/24 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/30
The imminent realization of fault-tolerant quantum computing precipitates a systemic collapse of classical public-key infrastructure and necessitates an urgent transition to post-quantum cryptography. However, current standardization efforts predominantly rely on structured mathematical problems that may remain vulnerable to unforeseen algorithmic breakthroughs, highlighting a critical need for fundamentally orthogonal security paradigms. Here, we introduce Crypto-ncRNA as a biophysically inspired cryptographic primitive that exploits the thermodynamic complexity of non-coding RNA folding as a computational work-factor amplifier. By leveraging the rugged energy landscape inherent to RNA secondary structure prediction, a problem intractable to rapid inversion, we establish a security foundation independent of conventional number-theoretic assumptions. We validate this approach by mapping the folding problem to a Quadratic Unconstrained Binary Optimization model and demonstrate theoretical resilience against quantum optimization attacks including the Quantum Approximate Optimization Algorithm. Functioning as a symmetric key encapsulation and derivation primitive dependent on pre-shared seeds, Crypto-ncRNA achieves throughputs competitive with software-based Advanced Encryption Standard implementations. By utilizing the generated high-entropy keys within a standard stream cipher framework, it exhibits ciphertext entropy that satisfies rigorous NIST SP 800-22 statistical standards. These findings not only articulate a novel bio-computational pathway for cryptographic defense but also provide a rigorous algorithmic blueprint for future physical realization, demonstrating that the thermodynamic complexity of biological systems offers a robust and physically grounded frontier for securing digital infrastructure in the post-quantum era.