Quantum intelligence on protein folding pathways

doi:10.1088/1674-1056/ab5fbe

中国物理B ›› 2020, Vol. 29 ›› Issue (1): 18702-018702.doi: 10.1088/1674-1056/ab5fbe

• SPECIAL TOPIC—Recent advances in thermoelectric materials and devices • 上一篇下一篇

Quantum intelligence on protein folding pathways

Wen-Wen Mao(毛雯雯), Li-Hua Lv(吕丽花), Yong-Yun Ji(季永运), You-Quan Li(李有泉)

1 Zhejiang Province Key Laboratory of Quantum Technology&Device and Department of Physics, Zhejiang University, Hangzhou 310027, China;
2 Department of Physics, Wenzhou University, Wenzhou 325035, China;
3 Collaberative Innovation Center of Advance Microstructure, Nanjing University, Nanjing 210008, China

收稿日期:2019-12-04 出版日期:2020-01-05 发布日期:2020-01-05
通讯作者: You-Quan Li E-mail:yqli@zju.edu.cn
基金资助:
Project supported by the National Key Research and Development Program of China (Grant No. 2017YFA0304304) and the National Natural Science Foundation of China (Grant No. 11935012).

Quantum intelligence on protein folding pathways

Wen-Wen Mao(毛雯雯)¹, Li-Hua Lv(吕丽花)¹, Yong-Yun Ji(季永运)², You-Quan Li(李有泉)^1,3

1 Zhejiang Province Key Laboratory of Quantum Technology&Device and Department of Physics, Zhejiang University, Hangzhou 310027, China;
2 Department of Physics, Wenzhou University, Wenzhou 325035, China;
3 Collaberative Innovation Center of Advance Microstructure, Nanjing University, Nanjing 210008, China

Received:2019-12-04 Online:2020-01-05 Published:2020-01-05
Contact: You-Quan Li E-mail:yqli@zju.edu.cn
Supported by:
Project supported by the National Key Research and Development Program of China (Grant No. 2017YFA0304304) and the National Natural Science Foundation of China (Grant No. 11935012).

摘要/Abstract

摘要： We study the protein folding problem on the base of our quantum approach by considering the model of protein chain with nine amino-acid residues. We introduce the concept of distance space and its projections on a XY-plane, and two characteristic quantities, one is called compactness of protein structure and another is called probability ratio involving shortest path. The concept of shortest path enables us to reduce the 388×388 density matrix to a 2×2 one from which the von Neumann entropy reflecting certain quantum coherence feature is naturally defined. We observe the time evolution of average distance and compactness solved from the classical random walk and quantum walk, we also compare the features of the time-dependence of Shannon entropy and von Neumann entropy. All the results not only reveal the fast quantum folding time but also unveil the existence of quantum intelligence hidden behind in choosing protein folding pathways.

关键词: protein folding, quantum walk, shortest pathways, mean first passage time

Abstract: We study the protein folding problem on the base of our quantum approach by considering the model of protein chain with nine amino-acid residues. We introduce the concept of distance space and its projections on a XY-plane, and two characteristic quantities, one is called compactness of protein structure and another is called probability ratio involving shortest path. The concept of shortest path enables us to reduce the 388×388 density matrix to a 2×2 one from which the von Neumann entropy reflecting certain quantum coherence feature is naturally defined. We observe the time evolution of average distance and compactness solved from the classical random walk and quantum walk, we also compare the features of the time-dependence of Shannon entropy and von Neumann entropy. All the results not only reveal the fast quantum folding time but also unveil the existence of quantum intelligence hidden behind in choosing protein folding pathways.

Key words: protein folding, quantum walk, shortest pathways, mean first passage time

中图分类号: (Folding dynamics)

87.15.hm

03.67.Ac (Quantum algorithms, protocols, and simulations) 05.40.Fb (Random walks and Levy flights)

毛雯雯, 吕丽花, 季永运, 李有泉. Quantum intelligence on protein folding pathways[J]. 中国物理B, 2020, 29(1): 18702-018702.

Wen-Wen Mao(毛雯雯), Li-Hua Lv(吕丽花), Yong-Yun Ji(季永运), You-Quan Li(李有泉). Quantum intelligence on protein folding pathways[J]. Chin. Phys. B, 2020, 29(1): 18702-018702.

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Quantum intelligence on protein folding pathways

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