Spiral trajectories of asymmetric molecules

doi:10.1088/1674-1056/adcea0

中国物理B ›› 2025, Vol. 34 ›› Issue (8): 80507-080507.doi: 10.1088/1674-1056/adcea0

所属专题： SPECIAL TOPIC — A celebration of the 90th Anniversary of the Birth of Bolin Hao

Spiral trajectories of asymmetric molecules

Nan Sheng(盛楠)^1,†, Shiqi Sheng(盛世奇)^2,†, Yu-Song Tu(涂育松)³, Rong-Zheng Wan(万荣正)⁴, Zuo-Wei Wang(王作维)⁵, Zhanchun Tu(涂展春)^6,§, and Hai-Ping Fang(方海平)^2,‡

1 Shanghai Yonovate Technology Co., Ltd., Shanghai 200062, China;
2 School of Physics, East China University of Science and Technology, Shanghai 200237, China;
3 College of Physics Science and Technology, Yangzhou University, Jiangsu 225009, China;
4 Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China;
5 School of Mathematical, Physical and Computational Sciences, University of Reading, Whiteknights, Reading, RG6 6AX, United Kingdom;
6 School of Physics and Astronomy, Beijing Normal University, Beijing 100875, China

收稿日期:2025-03-11 修回日期:2025-04-09 接受日期:2025-04-21 出版日期:2025-07-17 发布日期:2025-07-17
通讯作者: Hai-Ping Fang, Zhanchun Tu E-mail:fanghaiping@ecust.edu.cn;tuzc@bnu.edu.cn
基金资助:
Project supported by the National Natural Science Foundation of China (Grant Nos. 12475032 and 12005062), the Supercomputing Center of the Chinese Academy of Sciences, Shanghai Snowlake Technology Co., Ltd., and the Shanghai Super-Computer Center of China.

Spiral trajectories of asymmetric molecules

1 Shanghai Yonovate Technology Co., Ltd., Shanghai 200062, China;
2 School of Physics, East China University of Science and Technology, Shanghai 200237, China;
3 College of Physics Science and Technology, Yangzhou University, Jiangsu 225009, China;
4 Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China;
5 School of Mathematical, Physical and Computational Sciences, University of Reading, Whiteknights, Reading, RG6 6AX, United Kingdom;
6 School of Physics and Astronomy, Beijing Normal University, Beijing 100875, China

Received:2025-03-11 Revised:2025-04-09 Accepted:2025-04-21 Online:2025-07-17 Published:2025-07-17
Contact: Hai-Ping Fang, Zhanchun Tu E-mail:fanghaiping@ecust.edu.cn;tuzc@bnu.edu.cn
Supported by:
Project supported by the National Natural Science Foundation of China (Grant Nos. 12475032 and 12005062), the Supercomputing Center of the Chinese Academy of Sciences, Shanghai Snowlake Technology Co., Ltd., and the Shanghai Super-Computer Center of China.

1. 2025-080507-SI.pdf(1839KB)

摘要/Abstract

摘要： Spiral patterns widely exist in both macroscopic and microscopic systems such as hearts, bacteria, and active matters but have never been reported at molecular length scale. The emergence of spiral patterns has considerable impacts on the trajectories of the objects and thus usually relates to various physical, chemical, biological and physiological processes. In this paper, we show that, down to the length scale of only several Angstroms, asymmetric molecules exhibit spiral patterns in their trajectories within finite time based on the under-damped Langevin equation and demonstrated by molecular dynamics simulation. The key to this observation lies in the asymmetric molecular architecture that leads to a translation-rotation coupling. This finding enriches the knowledge of spiral patterns to the molecular length scale, provides a new insight into the understanding of various processes at the molecular level, and may evoke new ideas on the understanding of the vortices in turbulence.

关键词: spiral pattern, asymmetric molecule, under-damped Langevin equation, translation-rotation coupling

Abstract: Spiral patterns widely exist in both macroscopic and microscopic systems such as hearts, bacteria, and active matters but have never been reported at molecular length scale. The emergence of spiral patterns has considerable impacts on the trajectories of the objects and thus usually relates to various physical, chemical, biological and physiological processes. In this paper, we show that, down to the length scale of only several Angstroms, asymmetric molecules exhibit spiral patterns in their trajectories within finite time based on the under-damped Langevin equation and demonstrated by molecular dynamics simulation. The key to this observation lies in the asymmetric molecular architecture that leads to a translation-rotation coupling. This finding enriches the knowledge of spiral patterns to the molecular length scale, provides a new insight into the understanding of various processes at the molecular level, and may evoke new ideas on the understanding of the vortices in turbulence.

Key words: spiral pattern, asymmetric molecule, under-damped Langevin equation, translation-rotation coupling

中图分类号: (Brownian motion)

05.40.Jc

02.70.Ns (Molecular dynamics and particle methods) 34.10.+x (General theories and models of atomic and molecular collisions and interactions (including statistical theories, transition state, stochastic and trajectory models, etc.))

Nan Sheng(盛楠), Shiqi Sheng(盛世奇), Yu-Song Tu(涂育松), Rong-Zheng Wan(万荣正), Zuo-Wei Wang(王作维), Zhanchun Tu(涂展春), and Hai-Ping Fang(方海平). Spiral trajectories of asymmetric molecules[J]. 中国物理B, 2025, 34(8): 80507-080507.

参考文献

[1] Davidenko J M, Pertsov A V, Salomonsz R, BaxterWand Jalife J 1992 Nature 355 349
[2] Christoph J, Chebbok M, Richter C, Schröder-Schetelig J, Bittihn P, Stein S, Uzelac I, Fenton F H, Hasenfuß G, Gilmour R F and Luther S 2018 Nature 555 667
[3] Parrish J K and Hamner W M 1997 Animals Groups in Three Dimensions: How Species Aggregate (Cambridge University Press)
[4] Cross M C and Hohenberg P C 1993 Rev. Mod. Phys. 65 851
[5] Ouyang Q and Flesselles J M 1996 Nature 379 143
[6] Sellwood J A 2014 Rev. Mod. Phys. 86 1
[7] Sagués F, Sancho J M and García-Ojalvo J 2007 Rev. Mod. Phys. 79 829
[8] Kruse K, Joanny J F, Jülicher F, Prost J and Sekimoto K 2004 Phys. Rev. Lett. 92 078101
[9] Park J S and Lee K J 1999 Phys. Rev. Lett. 83 5393
[10] von Kameke A, Huhn F, Muñuzuri A P and Pérez-Muñuzuri V 2013 Phys. Rev. Lett. 110 088302
[11] Surrey T, Nedelec F, Leibler S and Karsenti E 2001 Science 292 1167
[12] Sumino Y, Nagai K H, Shitaka Y, Tanaka D, Yoshikawa K, Chaté H and Oiwa K 2012 Nature 483 448
[13] Chen C, Liu S, Shi X Q, Chaté H and Wu Y 2017 Nature 542 210
[14] Wioland H, Woodhouse F G, Dunkel J, Kessler J O and Goldstein R E 2013 Phys. Rev. Lett. 110 268102
[15] Dombrowski C, Cisneros L, Chatkaew S, Goldstein R E and Kessler J O 2004 Phys. Rev. Lett. 93 098103
[16] Gray R A and Chattipakorn N 2005 Proc. Natl. Acad. Sci. USA 102 4672
[17] Lerma C and Glass L 2016 J. Physiol. 594 2445
[18] Baldzizhar A, Manuylova E, Marchenko R, Kryvalap Y and Carey M G 2016 Crit. Care Nurs. Clin. North Am. 28 317
[19] Kümmel F, ten Hagen B,Wittkowski R, Buttinoni I, Eichhorn R, Volpe G, Löwen H and Bechinger C 2013 Phys. Rev. Lett. 110 198302
[20] Krüger C, Klös G, Bahr C and Maass C C 2016 Phys. Rev. Lett. 117 048003
[21] Wang W, Duan W, Sen A and Mallouk T E 2013 Proc. Natl. Acad. Sci. USA 110 17744
[22] Harder J and Cacciuto A 2018 Phys. Rev. E 97 022603
[23] Fodor E, Nardini C, Cates M E, Tailleur J, Visco P and van Wijland F 2016 Phys. Rev. Lett. 117 038103
[24] Shi X and Ma Y 2010 Proc. Natl. Acad. Sci. USA 107 11709
[25] Fu X, Tang L H, Liu C, Huang J D, Hwa T and Lenz P 2012 Phys. Rev. Lett. 108 198102
[26] Wulfert R, Oechsle M, Speck T and Seifert U 2017 Phys. Rev. E 95 050103
[27] Bechinger C, Di Leonardo R, Löwen H, Reichhardt C, Volpe G and Volpe G 2016 Rev. Mod. Phys. 88 045006
[28] Marchetti M C, Joanny J F, Ramaswamy S, Liverpool T B, Prost J, Rao M and Simha R A 2013 Rev. Mod. Phys. 85 1143
[29] See supplemental materials for more information
[30] Shi G, Dang Y, Pan T, Liu X, Liu H, Li S, Zhang L, Zhao H, Li S, Han J, Tai R, Zhu Y, Li J, Ji Q, Mole R A, Yu D and Fang H 2016 Phys. Rev. Lett. 117 238102
[31] von Hansen Y, Gekle S and Netz R R 2013 Phys. Rev. Lett. 111 118103
[32] Chen L, Shi G, Shen J, Peng B, Zhang B, Wang Y, Bian F, Wang J, Li D, Qian Z, Xu G, Liu G, Zeng J, Zhang L, Yang Y, Zhou G, Wu M, Jin W, Li J and Fang H 2017 Nature 550 380
[33] Nosé S 1984 Mol. Phys. 52 255
[34] Hoover W G 1985 Phys. Rev. A 31 1695
[35] Abraham M J, Murtola T, Schulz R, Páll S, Smith J C, Hess B and Lindahl E 2015 SoftwareX 1–2 19
[36] Sheng N, Tu Y S, Guo P, Wan R Z, Wang Z W and Fang H P 2017 Sci. China Phys. Mech. Astron. 60 040511
[37] Kelly T R, Tellitu I and Sestelo J P 1997 Angew. Chem. Int. Ed. 36 1866
[38] Davis A P 1998 Angew. Chem. Int. Ed. 37 909
[39] Berridge M J and Irvine R F 1989 Nature 341 197
[40] Rodbell M 1980 Nature 284 17
[41] Campbell N A and Reece J B 2002 Biology (Benjamin Cummings)

Spiral trajectories of asymmetric molecules

Spiral trajectories of asymmetric molecules

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