论文标题
用量子退火折叠晶格蛋白
Folding lattice proteins with quantum annealing
论文作者
论文摘要
量子退火是一种获得良好近似解决方案解决困难优化问题的有前途的方法。将蛋白质序列折叠到其最小能源结构中代表了这样的问题。为了测试此任务的新算法和技术,基于晶格的HP模型非常适合,因为尽管它简单起见,但它还是一个巨大的挑战。 HP模型在相邻而不是直接结合疏水残基之间具有有利的相互作用。在这里,我们为定制用于量子退火的晶格蛋白折叠的新型自旋表示。随着分布式编码在晶格上,它与较早的尝试折叠基于链生长技术的量子退火器上的晶格蛋白的尝试不同。通过我们的编码,设计的哈密顿量具有在Ising型灭气器上计算所需的二次结构,而无需引入任何辅助自旋变量。该属性极大地促进了对长链的研究。该方法对于将旋转系统限制为链式配置所需的参数的变化是可靠的,并且在解决方案质量方面表现良好。对结果进行了评估,该结果与HP链的现有确切结果,最多$ n = 30 $珠的珠子(100%命中率),从而超过了经典的模拟退火。此外,该方法使我们能够以$ n = 48 $和$ n = 64 $ hp链的恢复最低的已知能量,其命中率相似。这些结果是通过常用的杂种量子古典方法获得的。对于纯量子退火,我们的方法成功折叠了$ n = 14 $ hp链。计算是在D-Wave优势量子退火器上进行的。
Quantum annealing is a promising approach for obtaining good approximate solutions to difficult optimization problems. Folding a protein sequence into its minimum-energy structure represents such a problem. For testing new algorithms and technologies for this task, the minimal lattice-based HP model is well suited, as it represents a considerable challenge despite its simplicity. The HP model has favorable interactions between adjacent, not directly bound hydrophobic residues. Here, we develop a novel spin representation for lattice protein folding tailored for quantum annealing. With a distributed encoding onto the lattice, it differs from earlier attempts to fold lattice proteins on quantum annealers, which were based upon chain growth techniques. With our encoding, the Hamiltonian by design has the quadratic structure required for calculations on an Ising-type annealer, without having to introduce any auxiliary spin variables. This property greatly facilitates the study of long chains. The approach is robust to changes in the parameters required to constrain the spin system to chain-like configurations, and performs very well in terms of solution quality. The results are evaluated against existing exact results for HP chains with up to $N=30$ beads with 100% hit rate, thereby also outperforming classical simulated annealing. In addition, the method allows us to recover the lowest known energies for $N=48$ and $N=64$ HP chains, with similar hit rates. These results are obtained by the commonly used hybrid quantum-classical approach. For pure quantum annealing, our method successfully folds an $N=14$ HP chain. The calculations were performed on a D-Wave Advantage quantum annealer.