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 \emph{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.

翻译：容错量子计算的即将实现，将导致经典公钥基础设施的系统性崩溃，并迫切需要向后量子密码学过渡。然而，当前的标准化工作主要依赖于结构化的数学难题，这些难题可能仍然容易受到不可预见的算法突破的影响，这突显了对根本上正交的安全范式的迫切需求。在此，我们引入 \emph{Crypto-ncRNA} 作为一种受生物物理学启发的密码学原语，它利用非编码RNA折叠的热力学复杂性作为计算工作量放大器。通过利用RNA二级结构预测所固有的崎岖能量景观（这是一个难以快速求逆的问题），我们建立了一个独立于传统数论假设的安全基础。我们通过将折叠问题映射到二次无约束二进制优化模型来验证该方法，并展示了其针对包括量子近似优化算法在内的量子优化攻击的理论韧性。作为一种依赖于预共享种子的对称密钥封装与派生原语，Crypto-ncRNA 实现了与基于软件的高级加密标准实现相竞争的吞吐量。通过在标准流密码框架内使用生成的高熵密钥，其密文熵满足严格的NIST SP 800-22统计标准。这些发现不仅阐明了一条用于密码防御的新型生物计算路径，还为未来的物理实现提供了严格的算法蓝图，证明了生物系统的热力学复杂性为后量子时代保护数字基础设施提供了一个稳健且基于物理的前沿。