发表论文

2024

71. Yongfeng Ye, Lirong Zheng, Liang Hong, Victoria García Sakai, Nicolas R. de Souza, Dahong Teng, Bin Wu, Yichao Xu, Jinzhen Cai*, and Zhuo Liu*.
Direct Observation of the Mutual Coupling Effect in the Protein–Water–Glycerol Mixture by Combining Neutron Scattering and Selective Deuteration
J. Phys. Chem. B 2024, 128, 2, 405–414

70. Zheng Lirong, Zhou Bingxin, Wu Banghao, Huang Juan, Tyagi Madhusudan, Sakai Victoria García, Yamada Takeshi, O’Neill Hugh, Zhang Qiu, Hong Liang.
Decoupling of the Onset of Anharmonicity between a Protein and Its Surface Water around 200 K
eLife 13:RP95665

69. Lirong Zheng, Bingxin Zhou, Yu Yang, bing zan, Bozitao Zhong, Banghao Wu, Yan Feng, Qian Liu and Liang Hong.
Mn2+-Induced Structural Flexibility Enhances the Entire Catalytic Cycle and the Cleavage of Mismatches in Prokaryotic Argonaute Proteins
Chemical Science, 2024, Advance Article.

2023

68. Chao Hu, Song Li, Chenxing Yang, Jun Chen, Yi Xiong, Guisheng Fan, Hao Liu, Liang Hong.
ScaffoldGVAE: Scaffold Generation and Hopping of Drug Molecules via a Variational Autoencoder Based on Multi-View Graph Neural Networks.
Journal of Cheminformatics, 15, 91 (2023).

67. Song Li, Chao Hu, Song Ke, Chenxing Yang, Jun Chen, Yi Xiong, Hao Liu, Liang Hong.
LS-MolGen: Ligand-and-Structure Dual-driven Deep Reinforcement Learning for Target-specific Molecular Generation Improves Binding Affinity and Novelty.
J. Chem. Inf. Model. 2023, 63, 13, 4207–4215.

66. Lei Zhang, Yuanxi Yu, Liumin Suo, Wei Zhuang, Lunhua He, Xiaohua Zhang, Liang Hong and Pan Tan.
The evolution of anionic nanoclusters at the electrode interface in water-in-salt electrolytes.
Phys. Chem. Chem. Phys., 2023, 25, 10301-10312.

65. Yanyan Xue, Jun Li, Dian Chen, Xizhu Zhao, Liang Hong and Yu Liu.
Observation of structural switch in nascent SAM-VI riboswitch during transcription at single-nucleotide and single-molecule resolution.
Nature Communications, 14, 2320 (2023).

64. Liqi Kang, Pan Tan, Liang Hong.
人工智能时代下的酶工程.
合成生物学, 2023.

63. Fan Jiang, Jiahao Bian, Hao Liu, Song Li, Xue Bai, Lirong Zheng, Sha Jin, Zhuo Liu, Guang-Yu Yang, Liang Hong.
Creatinase: Using Increased Entropy to Improve Activity and Thermostability.
The Journal of Physical Chemistry B, 2023, 127, 12, 2671–2682.

62. Mingchen Li, Liqi Kang, Yi Xiong, Yu Guang Wang, Guisheng Fan, Pan Tan, Liang Hong.
SESNet: sequence-structure feature-integrated deep learning method for data-efficient protein engineering.
Journal of Cheminformatics, 15, 12 (2023).

2022

61. Weishu Zhao, Bozitao Zhong, Lirong Zheng, Pan Tan, Yinzhao Wang, Hao Leng, Nicolas de Souza, Zhuo Liu, Liang Hong, and Xiang Xiao.
Proteome-wide 3D structure prediction provides insights into the ancestral metabolism of ancient archaea and bacteria.
Nature Communications, 13, 7861 (2022).

60. Jun Li, Xiaoyu Zhang, Liang Hong, and Yu Liu.
Entropy Driving the Mg2+-Induced Folding of TPP Riboswitch RNA.
The Journal of Physical Chemistry B, 2022, 126, 46, 9457–9464.

59. Zhiqiang Hu, Wenfeng Liu, Chenbin Zhang, Jiawen Huang, Shaoting Zhang, Huiqun Yu, Yi Xiong, Hao Liu, Song Ke, Liang Hong.
SAM-DTA: A Sequence-Agnostic Model for Drug-Target Binding Affinity Prediction.
Briefings in Bioinformatics, 24, 1 (2022).

58. Bingxin Zhou, Outongyi Lv, Kai Yi, Xinye Xiong, Pan Tan, Liang Hong, Yu Guang Wang.
Lightweight Equivariant Graph Representation Learning for Protein Engineering.
Accepted at NeurIPS Workshop on Machine Learning for Structural Biology, 2022.

57. Lei Zhang, Zhuo Liu, Chenxing Yang, Victoria García Sakai, Madhusudan Tyagi, Liang Hong
Conduction mechanism in graphene oxide membranes with varied water content: From proton hopping dominant to ion diffusion dominant.
ACS Nano, 2022, 16, 9, 13771–13782.

56. J. Li , J. Xie , A. Godec , K. R. Weninger , C. Liu , J. C. Smith, and L. Hong
Non-ergodicity of a globular protein extending beyond its functional timescale
Chemical Science, 2022, 13, 9668-9677.

55. L. Zheng, H. Lu, B. Zan, S. Li, H. Liu, Z. Liu, J. Huang, Y. Liu, F. Jiang, Q. Liu, Yan Feng, and L. Hong
Loosely-packed Dynamical Structures with Partially-melted Surface Being the Key for Thermophilic Argonaute Proteins Achieving High DNA-cleavage Activity
Nucleic Acids Research, gkac565, 2022.

54. J. Liang, P. Tan, Y. Zhao, L. Li, S. Jin, L. Hong, and Z. Xu
Superscalability of the random batch Ewald method
The Journal of Chemical Physics, 156, 014114 (2022)

53. R. Li, Z. Liu, F. Jiang, Y. Zhao, G. Yang and L. Hong
Enhancement of Thermal Stability of Proteinase K by Biocompatible Cholinium-based Ionic Liquids
Physical Chemistry Chemical Physics, 2022, 24, 13057-13065

52. Y. Yu, C. Yang, M. Baggioli, A. E. Phillips, A. Zaccone, L. Zhang, R. Kajimoto, M. Nakamura, D. Yu, L. Hong
The ω3 scaling of the vibrational density of states in quasi-2D nanoconfined solids
Nature Communications, 13, 3649 (2022).

51. L. Zheng, Z. Liu, Q. Zhang, S. Li, J. Huang, L. Zhang, B. Zan, M. Tyagi, H. Cheng, T. Zuo, V. G. Sakai, T. Yamada,C. Yang, P. Tan, F. Jiang, H. Chen, W. Zhuang, L. Hong
Universal Dynamical Onset in Water at Distinct Material Interfaces
Chemical Science, 2022, 13, 4341.

50. S. Li, P. Tan, J. Li, M. Tang, and L. Hong
Many-body effect renders universal subdiffusion to water on different proteins
Physical Review Research, 4, L22003 (2022).

2021

49. X. Qian, D. Han, L. Zheng, J. Chen, M. Tyag, Q. Li, F. Du, S. Zheng, X. Huang*, S. Zhang, J. Shi, H. Huang, X. Shi, J. Chen, H Qin, J. Bernholc, X. Chen, L. Q Chen, L. Hong, Q. M. Zhang
High-entropy polymer produces a giant electrocaloric effect at low fields
Nature, 600.7890 (2021): 664-669.

48. Z. Lin, M. Mao, C. Yang, Y. Tong, Q. Li, J. Yue, G. Yang, L. Hong, X. Yu, L. Gu, X. Huang, L. Suo and L. Chen
Amorphous anion-rich titanium polysulfides for aluminum-ion batteries
Science Advances, 7, no. 35 (2021): eabg6314

47. J. Li, X. Hu, T. Neusius, X. Cheng, M.D. Smith, A. Godec, L. Hong, R. Metzler, J.C. Smith
Reply to: Insufficient evidence for ageing in protein dynamics
Nature Physics, 17, 775–776 (2021)

46. P. Tan, J. Yue, Y. Yu, B. B. Liu, T. Liu; L. Zheng, L. He, X. Zhang, L. Suo, L. Hong
Solid-like Nano-Anion-Cluster Constructs Free Lithium-ion Conducting Super-Fluid Framework in Water-in-salt Electrolyte.
The Journal of Physical Chemistry C, (2021), 125, 22, 11838–11847

2020

45. R. Li, Z. Liu, L. Li, J. Huang, T. Yamada, V. G. Sakai, P. Tan and L. Hong
Anomalous sub-diffusion of water in biosystems: From hydrated protein powders to concentrated protein solution to living cells
Structural Dynamics,7, no. 5 (2020): 054703.

44. Z. Dominik, P. Tan, L. Hong, D. D. Bari, V. G. Sakai, and J. Peters.
Differences between calcium rich and depleted α-lactalbumin investigated by molecular dynamics simulations and incoherent neutron scattering
Physical Review E, 101, no. 3 (2020): 032415

43. M. Yu, P. Tan, Y. Ye, D. J. Voneshen, X. Xing and L. Hong
One Dimensional Nature of Protein Low Energy Vibrations 
Physical Review Research, 2, no. 3 (2020): 032050.

42. P. Tan, J. Huang, E. Mamontov, V.G. Sakai, F. Merzel, Z. Liu, Y. Ye, L. Hong
Decoupling between translation and rotation of water in the proximity of a protein molecule
Physical Chemistry Chemical Physics, 22, no. 32 (2020): 18132-18140.

41. L. Liu, S. Jiang, M. Xing, C. Chen, C. Lai, N. Li, G. Liu, D. Wu, H. Gao, L. Hong, P. Tan, S. Chen, Z. Deng, G. Wu, L. Wang
Structural Analysis of an l-Cysteine Desulfurase from an Ssp DNA Phosphorothioation System. 
mBio, 11, no. 2 (2020).

40. Z. Liu, C. Yang, L. Zhang, Y. Yu, M. Yu, V.G Sakai, M. S. Tyagi, T. Yamada, L. He, X. Zhang, L. Hong
Heterogeneity of Water Molecules on the Free Surface of Thin Reduced Graphene Oxide Sheets
The Journal of Physical Chemistry C, 2020 124 (20), 11064-11074

2019

39. L. Zheng, L. Hong
Combining Neutron Scattering, Deuteration Technique, and Molecular Dynamics Simulations to Study Dynamics of Protein and Its Surface Water Molecules
Chinese Journal of Polymer Science, 37:1083–1091

38. K. L. Ngai, L. Hong, S. Capaccioli, A. Paciaroni
Uncovering a novel transition in the dynamics of proteins in the dry state
Journal of Molecular Liquids, 286:110810

37. T. Zuo, C. Ma, G. Jiao, Z. Han, S. Xiao, H. Liang, L. Hong, D. Bowron, A. Soper, C. C. Han, H. Cheng
Water/Cosolvent Attraction Induced Phase Separation: A Molecular Picture of Cononsolvency
Macromolecules, 52:457-464

36. P. Tan, J. Li, L. Hong
Statistical properties for diffusive motion of hydration water on protein surface
Physica B: Condensed Matter, 562:1-5

35. X. Ma, Q. Wang, Y. Li, P. Tan, H. Wu, P. Wang, X. Dong, L. Hong, and G. Meng
How BamA recruits OMP substrates via poly-POTRAs domain
The FASEB Journal, 33:13063-14842

2018

34. Z. Liu, C. Yang, J. Huang, G. Ciampalini, J. Li, V. G. Sakai, M. Tyagi, H. ONeill, Q. Zhang, S. Capacciol, K. L. Ngai, and L. Hong
Direct Experimental Characterization of Contributions from Self-motion of Hydrogen and from Interatomic Motion of Heavy Atoms to Protein Anharmonicity
Journal of Physical Chemistry B, 122.43 (2018): 9956-9961.

33. P. Tan, Z. Fu, L. Petridis, S. Qian, J. Li and L. Hong
A two-fold structural classification method for determining the accurate ensemble of protein structures
Communications in Computational Physics, 25:1010-1023

32. Z. Liu, Sara Lemmonds, J. Huang, M. Tyagi, L. Hong and N. Jain
Entropic Contribution to Enhanced Thermal Stability in the Thermostable P450 CYP119
Proceedings of the National Academy of Sciences,115.43 (2018): E10049-E10058. 

31. P. Tan, Y. Liang, Q. Xu, E. Mamontov, J. Li, X. Xing, and L. Hong
Gradual crossover from subdiffusion to normal diffusion: A many-body effect in protein surface water.
Physical Review Letters,120, 248101 (2018). (Editors' suggestion, Featured in Physics)

30. J. C. Smith, P. Tan, L. Petridis, L. Hong.
Dynamic Neutron Scattering by Biological Systems.
Annual Review of Biophysics, 47, 335-354 (2018)

2017

29. H. O’neill, S. V. Pingali, L. Petridis, J. He, E. Mamontov, L. Hong, V. Urban, B. Evans, P. Langan, J. C. Smith. 
Dynamics of Water Bound to Crystalline Cellulose.
Science Reports, 2017, 7 (1), 11840.

28. C. Xia, J. Li, B. Kou, Y. Cao, Z. Li, X. Xiao, Y. Fu, T. Xiao, L. Hong, J. Zhang, W. Kob, Y. Wang.
Origin of Noncubic Scaling Law in Disordered Granular Packing.
Physical Review Letters, 118 (2017) 238002.

27. Z. Liu, J. Huang, M. Tyagi, H. O’Neill, Q. Zhang, E. Mamontov, N. Jain, Yujie Wang, Jie Zhang, Jeremy C. Smith, and L. Hong
Dynamical Transition of Collective Motions in Dry Protein.
Physical Review Letters, 119 (2017), 048101.

26. L. Zhang, J. Zheng, Y. Q. Wang, L. Zhang, Z. H. Jin, L. Hong, Y. J. Wang and J. Zhang
Experimental studies of vibrational modes in a two-dimensional amorphous solid.
Nature Communications, 8: 67 (2017).

2016

25. X. Hu, L. Hong, M. Smith, T. Neusius, X. Cheng, and J.C. Smith.
The Dynamics of Single Protein Molecules is Nonequilibrium and Self-Similar over Thirteen Decades in Time.
Nature Physics, 12, 171–174 (2016)

24. D. Vural, X. Hu, B. Lindner, N. Jain, Y. Miao, X. Cheng, Z. Liu, L. Hong, and J. C. Smith.
Quasielastic neutron scattering in biology: Theory and applications.
Biochim. Biophys. Acta, 2016.

23. L. Hong, N. Jain, X. Cheng, A. Bernal, M. Tyagi, and J. C. Smith.
Determination of functional collective motions in a protein at atomic resolution using coherent neutron scattering.
Science Advances, Vol. 2, no. 10, e1600886, pp. 1–8, 14 Oct 2016.

22. G. K. Dhindsa, D. Bhowmik, M. Goswami, H. O’Neill, E. Mamontov, B. G. Sumpter, L. Hong, P. Ganesh, and X.-q. Chu
Enhanced Dynamics of Hydrated tRNA on Nanodiamond Surfaces: A Combined Neutron Scattering and MD Simulation Study.
J. Phys. Chem. B, DOI: 10.1021/acs.jpcb.6b07511 (2016).

21. C. D. Ferrier, A. Kisliuk, L. Hong, G. C. Jr, G. Carini, G. D’Angelo, C. Alba-Simionesco, V. N. Novikov, and A. P. Sokolov. 
Why many polymers are so fragile: A new perspective.
J. Chem. Phys, vol. 145, no. 15, p. 154901, 2016.

来上海交大之前

2015

20. D. Vural, L. Hong, J. C. Smith, and H. R. Glyde.
Motional displacements in proteins: The origin of wave-vector-dependent values. 
Phys. Rev. E, vol. 91, no. 5, pp. 1–11, 2015.

2014

19. L. Hong, M. Sharp, S. Poblete, R. Bhiel, X. Cheng, D. Richter and J. C. Smith.
Detailed structure and dynamics of a compact state of a multidomain protein, the mercuric ion reductase, in aqueous solution.
Biophys. J.,107, 393,(2014).

18. L. Hong, L. Petridis and J. C. Smith.
Biomolecular Structure and Dynamics with Neutrons: The View from Simulation.
Isr. J.Chem. 54, 1264 (2014).

17. L. Hong, N. Smolin and J. C. Smith.
De Gennes Narrowing Describes the Relative Motion of Protein Domains.
Physical Review Letters, 112, 158102 (2014).

2013

16. Y. Miao, L. Hong, Z. Yi and J. C. Smith.
Zaccai Resilience and Site-specific Hydration in a Globular Protein.
The European Physical Journal E, 36, 9885 (2013).

15. L. Hong, D.C. Glass, J.D. Nickels, Z. Yi, T. Madhusudan, H. O’Neill, A. P. Sokolov and J.C. Smith.
Elastic and conformational softness of a globular protein.
Physical Review Letters, 110, 028104 (2013).

2012

14.Y.L. Miao, Z. Yi, D.C. Glass, L. Hong, M. Tyagi, J. Baudry, N. Jain and J.C. Smith. 
Temperature-Dependent Dynamical Transitions of Different Classes of Amino Acid Residue in a Globular Protein.
J. Am. Chem. Soc. 134, 19576 (2012).

13. J.D. Nickels, H. O’Neill, L. Hong, M. Tyagi, G. Ehlers, K. Weiss, Q. Zhang, Z. Yi, E. Mamontov, J.C. Smith and A.P. Sokolov.
Dynamics of Protein and its Hydration Water: Neutron Scattering Studies on Fully Deuterated GFP.
Biophys. J. 103, 1566 (2012).

12. L. Hong, X. Cheng, D.C. Glass, and J.C. Smith.
Surface hydration amplifies single-well protein atom diffusion propagating into the macromolecular core.
Physical Review Letters, 108, 238102 (2012).

2011

11. L. Hong, N. Smolin, B. Lindner, A.P. Sokolov, and J.C. Smith.
Three classes of motion in the dynamic neutron scattering susceptibility of a globular protein.
Physical Review Letters, 107, 148102 (2011).

10. L. Hong, V.N. Novikov, and A.P. Sokolov.
Dynamic heterogeneities, boson peak, and activation volume in glass-forming liquids.
Phys. Rev. E, 83, 061508 (2011).

9. L. Hong, V.N. Novikov, and A.P. Sokolov.
Is there any connection between fragility of glass forming systems and dynamic heterogeneity /cooperativity.
J. Non-Cryst. Solids, 357, 351 (2011).

2010

8. L. Hong, B. Begen, A. Kisliuk, V.N. Novikov, and A.P. Sokolov.
Influence of pressure on fast picosecond relaxation in glass-forming materials.
Phys. Rev. B, 81, 104207 (2010).

2009

7. L. Hong, P.D. Gujrati, V.N. Novikov, and A.P. Sokolov.
Molecular cooperativity in the dynamics of glass-forming systems: A new insight.
J. Chem. Phys., 131, 194511 (2009).

6. L. Hong, B. Begen, A. Kisliuk, S. Pawlus, M. Paluch, and A.P. Sokolov.
Influence of pressure on quasielastic scattering in glasses: Relationship to the boson peak.
Physical Review Letters., 102, 145502 (2009).

2008

5. L. Hong, B. Begen, A. Kisliuk, C. Alba-Simionesco, V.N. Novikov, and A.P Sokolov.
Pressure and density dependence of the boson peak in polymers.
Phys. Rev. B, 78,134201 (2008).

4. G. Carini Jr, G. Carini, G. D’Angelo, G. Tripodo, A. Bartolotta, G. Salvato, and L. Hong.
Low temperature Specific heat of heterocyclic polymer networks: Effect of network density.
Phil. Mag., 88, 3999 (2008).

3. S. Pawlus, K. Kunal, L. Hong, and A.P. Sokolov.
Influence of molecular weight on dynamic crossover temperature in linear polymers.
Polymer, 49, 2918 (2008).

2006

2. L. Hong, Z. Liu, X.T. Zhang, and S.K. Hark.
Self-catalytic growth of single-phase AlGaN alloy nanowires by chemical vapor deposition.
Appl. Phys. Lett., 89, 193105 (2006).

1. L. Hong, Z.R. Wang, and S.K. Hark.
Relationship of the SERRS of CV and the concentration of Ag colloids. 
Chin. J.Light Scattering, 18, 21 (2006).