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Crypto-ncRNA: Non-coding RNA (ncRNA) Based Encryption Algorithm

Xu Wang, Yiquan Wang, Tin-yeh Huang

TL;DR

The paper tackles quantum-era cryptography by exploiting the conformational entropy and intrinsic unclonability of non-coding RNA to create post-quantum secure keys and ciphertexts. It introduces Crypto-ncRNA, a four-tier framework that encodes data into RNA codons using Base64 indices, applies RNA secondary structure folding (LinearFold) to create $4^N$ dynamic configurations, and derives quantum-resistant keys via PBKDF2-HMAC-SHA256 with a $256$-bit salt to produce a $32$-byte session key, then encrypts with ChaCha20 and verifies integrity. Benchmark results show encryption/decryption speeds are slightly below AES but exceed RSA, with ciphertext entropy near $8$ bits per byte and all 15 NIST SP 800-22 tests passing, alongside a cryptographic correctness rate of $100ackslash%$ across data lengths up to $10^6$ bytes. The work presents a promising, scalable path for post-quantum cryptography by fusing biomolecular PUFs with conventional crypto primitives and suggests future work in deep-learning-driven RNA structure prediction to further enhance security in real-world deployments.

Abstract

In the looming post-quantum era, traditional cryptographic systems are increasingly vulnerable to quantum computing attacks that can compromise their mathematical foundations. To address this critical challenge, we propose crypto-ncRNA-a bio-convergent cryptographic framework that leverages the dynamic folding properties of non-coding RNA (ncRNA) to generate high-entropy, quantum-resistant keys and produce unpredictable ciphertexts. The framework employs a novel, multi-stage process: encoding plaintext into RNA sequences, predicting and manipulating RNA secondary structures using advanced algorithms, and deriving cryptographic keys through the intrinsic physical unclonability of RNA molecules. Experimental evaluations indicate that, although crypto-ncRNA's encryption speed is marginally lower than that of AES, it significantly outperforms RSA in terms of efficiency and scalability while achieving a 100% pass rate on the NIST SP 800-22 randomness tests. These results demonstrate that crypto-ncRNA offers a promising and robust approach for securing digital infrastructures against the evolving threats posed by quantum computing.

Crypto-ncRNA: Non-coding RNA (ncRNA) Based Encryption Algorithm

TL;DR

The paper tackles quantum-era cryptography by exploiting the conformational entropy and intrinsic unclonability of non-coding RNA to create post-quantum secure keys and ciphertexts. It introduces Crypto-ncRNA, a four-tier framework that encodes data into RNA codons using Base64 indices, applies RNA secondary structure folding (LinearFold) to create dynamic configurations, and derives quantum-resistant keys via PBKDF2-HMAC-SHA256 with a -bit salt to produce a -byte session key, then encrypts with ChaCha20 and verifies integrity. Benchmark results show encryption/decryption speeds are slightly below AES but exceed RSA, with ciphertext entropy near bits per byte and all 15 NIST SP 800-22 tests passing, alongside a cryptographic correctness rate of across data lengths up to bytes. The work presents a promising, scalable path for post-quantum cryptography by fusing biomolecular PUFs with conventional crypto primitives and suggests future work in deep-learning-driven RNA structure prediction to further enhance security in real-world deployments.

Abstract

In the looming post-quantum era, traditional cryptographic systems are increasingly vulnerable to quantum computing attacks that can compromise their mathematical foundations. To address this critical challenge, we propose crypto-ncRNA-a bio-convergent cryptographic framework that leverages the dynamic folding properties of non-coding RNA (ncRNA) to generate high-entropy, quantum-resistant keys and produce unpredictable ciphertexts. The framework employs a novel, multi-stage process: encoding plaintext into RNA sequences, predicting and manipulating RNA secondary structures using advanced algorithms, and deriving cryptographic keys through the intrinsic physical unclonability of RNA molecules. Experimental evaluations indicate that, although crypto-ncRNA's encryption speed is marginally lower than that of AES, it significantly outperforms RSA in terms of efficiency and scalability while achieving a 100% pass rate on the NIST SP 800-22 randomness tests. These results demonstrate that crypto-ncRNA offers a promising and robust approach for securing digital infrastructures against the evolving threats posed by quantum computing.

Paper Structure

This paper contains 48 sections, 4 equations, 4 figures, 8 tables, 1 algorithm.

Table of Contents

  1. Introduction
  2. Method (details in Appendix B)
  3. Results (details in Appendix D)
  4. Conclusion
  5. Theoretical Foundations of the Crypto-ncRNA Framework
  6. RNA-Intrinsic Physical Unclonable Functions
  7. Verification and Key Generation Process using RNA-based PUFs
  8. Technical Specifications of the crypto-ncRNA Framework
  9. Data Encoding & RNA Sequence Synthesis
  10. Base64 Preprocessing
  11. Process
  12. Technical Details
  13. Advantages
  14. Codon Mapping
  15. Process
  16. ...and 33 more sections

Figures (4)

  • Figure 1: The Framework of Crypto-ncRNA Algorithm
  • Figure 2: Summary of Algorithm(s) Comparation and Tesing Results
  • Figure 3: ncRNA-based Physical Unclonable Function (PUF) Workflow
  • Figure 4: Verification and Key Generation Process using RNA-based PUFs Workflow