# Crypto-ncRNA: a bio-inspired post-quantum cryptographic primitive exploiting RNA folding complexity

arXiv: https://arxiv.org/abs/2504.17878 · HTML: https://mlsanity.com/paper/2504.17878/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 5 of its 73 references that are in the map.
- First posted on arXiv 24 Apr 2025.

## Builds on (most cited first, 5 of 5)

- [LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search](https://mlsanity.com/paper/2001.04020/) (2019)
- [Quantum Physical Unclonable Functions: Possibilities and Impossibilities](https://mlsanity.com/paper/1910.02126/) (2019)
- [Review on DNA Cryptography](https://mlsanity.com/paper/1904.05528/) (2019)
- [Identifying Research Challenges in Post Quantum Cryptography Migration and Cryptographic Agility](https://mlsanity.com/paper/1909.07353/) (2019)
- [Physical Fault Injection and Side-Channel Attacks on Mobile Devices: A Comprehensive Analysis](https://mlsanity.com/paper/2105.04454/) (2021)

## Abstract (arXiv)

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.