publications

  1. Pengbo Song, Qiaojing Huang, Wenyu Li, Maodong Li* and Zhirong Liu*. Decomposition of forces in protein: Methodology and general properties. J. Chem. Inf. Model. 64 (18), 7108-7121 (2024).
  2. Zhirong Liu*. Accelerating kinetics with time-reversal path sampling. Molecules 28 (24), 8147/1-12 (2023).
  3. Yingqi Wang, Zijian Wang, Ting Cheng, and Zhirong Liu*. Carrier mobility of two-dimensional Dirac materials: the influence of optical phonon scattering. Phys. Chem. Chem. Phys. 25 (35), 23491-23501 (2023). (This article is part of the themed collection: 2023 PCCP HOT Articles)
  4. Zijian Wang and Zhirong Liu*. Novel piezoelectricity in two-dimensional metallic/semimetallic materials with out-of-plane polarization. J. Phys. Chem. Lett. 14 (33), 7549-7555 (2023).
  5. Junwei He and Zhirong Liu*.  Dirac cones in bipartite square-octagon lattice: A theoretical approach. J. Chem. Phys. 159 (4), 044713/1-16 (2023).
  6. Zun Wang#, Hongfei Wu#, Lixin Sun, Xinheng He, Zhirong Liu, Bin Shao*, Tong Wang*, and Tie-Yan Liu.  Improving machine learning force fields for molecular dynamics simulations with fine-grained force metrics. J. Chem. Phys. 159 (3), 035101/1-12 (2023). (Cover Paper)
  7. Chen Yang#, Yanwei Li#, Shuyao Zhou, Yilin Guo, Chuancheng Jia, Zhirong Liu, Kendall N. Houk*, Yonatan Dubi*, and Xuefeng Guo*. Real-time monitoring of reaction stereochemistry through single-molecule observations of chirality-induced spin selectivity. Nat. Chem. 15 (7), 972-979 (2023).
  8. Chen Yang#, Yilin Guo#, Shuyao Zhou, Zhirong Liu, Zitong Liu,* Deqing Zhang, and Xuefeng Guo*. A tunable single-molecule light-emitting diode with single-photon precision. Adv. Mater. 35 (16), 2209750/1-10 (2023).
  9. Qiaojing Huang, Limin Chen, Luhua Lai*, and Zhirong Liu*. Intrinsic disorder and allosteric regulation. Book Chapter in "Structure and Intrinsic Disorder in Enzymology" edited by Munishwar Nath Gupta and Vladimir N. Uversky (Elsevier, 2023, ISBN: 978-0-323-99533-7), p.327-352 (2023).
  10. Zhaoxi Sun*, Qiaole He, Zhihao Gong, Payam Kalhor, Zhe Huai*, and Zhirong Liu. A general picture of cucurbit[8]uril host–guest binding: Recalibrating bonded interactions. Molecules 28 (7), 3124/1-43 (2023).
  11. Zhaoxi Sun*, Lei Zheng, Zuo-Yuan Zhang, Yalong Cong , Mao Wang, Xiaohui Wang*, Jingjing Yang, Zhirong Liu, and Zhe Huai*. Molecular modelling of ionic liquids: situations when charge scaling seems insufficient.  Molecules 28 (2), 800/1-19 (2023).
  12. Zhaoxi Sun*, Mao Wang, Qiaole He, and Zhirong Liu. Molecular modeling of ionic liquids: Force-field validation and thermodynamic perspective from large-scale fast-growth solvation free energy calculations. Adv. Theory Simul. 5 (9), 2200274/1-21 (2022).
  13. Zhaoxi Sun*, Zhihao Gong, Lei Zheng, Payam Kalhor, Zhe Huai*, Zhirong Liu. Molecular modelling of ionic liquids: General guidelines on fixed-charge force fields for balanced descriptions. J. Ionic Liquids 2 (2), 100043/1-16 (2022).
  14. Xiao Liu*, Lei Zheng, Yalong Cong, Zhihao Gong, Zhixiang Yin, John Z. H. Zhang*, Zhirong Liu, Zhaoxi Sun*. Comprehensive evaluation of end‑point free energy techniques in carboxylated‑pillar[6]arene host–guest binding: II. regression and dielectric constant. J. Comput.-Aided Mol. Des. 36 (12), 879-894 (2022).
  15. Zhaoxi Sun*, Lei Zheng, Kai Wang, Zhe Huai, Zhirong Liu. Primary vs secondary: Directionalized guest coordination in β-cyclodextrin derivatives. Carbohydr. Polym. 297, 120050/1-13 (2022).
  16. Xiangyu Dou, Hongjun Jin, Tongyue Wu, Jianbin Huang, Bin Zhang*, Zhirong Liu, Tao Chen*, and Yun Yan*. Physical insight into the conditions required in the solid-phase molecular self-assembly of SDS revealed by coarse-grained molecular dynamics simulation. J. Phys. Chem. B 126 (33), 6345-6353 (2022).
  17. Mingyao Li, Shuyao Zhou, Shizhao Ren, Lei Zhang, Bing Yin, Cong Zhao, Zhirong Liu, Chuancheng Jia*, Xuefeng Guo*. Precise edge functionalization and tailoring of graphene via solvent-controlled reactions. Carbon 197, 519-525 (2022).
  18. Xiaohui Wang, Bin Chong, Zhaoxi Sun, Hao Ruan, Yingguang Yang, Pengbo Song, and Zhirong Liu*. More is simpler: decomposition of ligand-binding affinity for proteins being disordered. Protein Sci. 31 (7), e4375 (2022).
  19. Huanyan Fu, Cong Zhao, Jie Cheng, Shuyao Zhou, Peizhen Peng, Jie Hao, Zhirong Liu, Xike Gao*, Chuancheng Jia* and Xuefeng Guo*.  Dipole-improved gating of azulene-based single-molecule transistors. J. Mater. Chem. C 10 (20), 7803-7809 (2022).
  20. Dingkai Su, Shuyao Zhou, Hiroshi Masai, Zihao Liu, Ce Zhou, Chen Yang, Zhizhou Li, Susumu Tsuda, Zhirong Liu*, Jun Terao* and Xuefeng Guo*. Stochastic binding dynamics of a photoswitchable single supramolecular complex. Adv. Sci. 9 (13), 2200022/1-9 (2022).
  21. Caiyao Yang, Ping chuan Shen, Qi Ou, Qian Peng, Shuyao Zhou, Jinshi Li, Zhirong Liu, Zujin Zhao, Anjun Qin, Zhigang Shuai*, Ben Zhong Tang*, Xuefeng Guo*. Complete deciphering of the dynamic stereostructures of a single aggregation-induced emission molecule. Matter 5 (4), 1224-1234 (2022).
  22. Qiaojing Huang, Luhua Lai*, and Zhirong Liu*. Quantitative analysis of dynamic allostery. J. Chem. Inf. Model. 62 (10), 2538-2549 (2022).
  23. Qiaojing Huang, Yanyan Wang, Zhirong Liu*, and Luhua Lai*. The regulatory roles of intrinsically disordered linker in VRN1-DNA phase separation. Int. J. Mol. Sci. 23 (9), 4594/1-12 (2022).
  24. Zi-Le Wang, Zhirong Liu*, Wenhui Duan*, and Zhi-Feng Huang*. Control of phase ordering and elastic properties in phase field crystals through three-point direct correlation. Phys. Rev. E 105 (4), 044802/1-14 (2022).
  25. Yilin Guo, Chen Yang, Shuyao Zhou, Zhirong Liu*, and Xuefeng Guo*. A single-molecule memristor based on an electric-field-driven dynamical structure reconfiguration. Adv. Mater. 34 (36), 2204827/1-9 (2022).
  26. Yilin Guo, Chen Yang, Huiping Li, Lei Zhang, Shuyao Zhou, Xin Zhu, Huanyan Fu, Zhizhou Li, Zhirong Liu, Chuancheng Jia, Zitong Liu*, Wenguang Zhu*, Fanyang Mo*, Deqing Zhang* and Xuefeng Guo*. Accurate single-molecule kinetic isotope effects. J. Am. Chem. Soc. 144 (7), 3146-3153 (2022).
  27. Zijian Wang, Ting Cheng*, and Zhirong Liu*. Dirac cones, elastic properties, and carrier mobility of the FeB2 monolayer: the effects of symmetry. J. Phys. Chem. C 126 (1), 617-624 (2022).
  28. Citian Wang, Ting Cheng, Zhirong Liu, Feng Liu*, and Huaqing Huang*. Structural amorphization-induced topological order. Phys. Rev. Lett. 128 (5), 056401/1-7 (2022).
  29. Irene Ai*, Zhirong Liu*. Brief history of thermal techniques in ancient china. Univ. Chem. 37 (1), 2103052/1-8 (2022). http://www.dxhx.pku.edu.cn/CN/Y2022/V37/I1/2103052
  30. Ting Cheng, Luzhao Sun, Zhirong Liu, Feng Ding, Zhongfan Liu. Roles of transition metal substrates in graphene chemical vapor deposition growth. Acta Phys. -Chim. Sin. 38 (1), 2012006 (2022).
  31. Na Xin, Chen Hu, Hassan Al Sabea, Miao Zhang, Chenguang Zhou, Linan Meng, Chuancheng Jia, Yao Gong, Yu Li, Guojun Ke, Xiaoyan He, Pramila Selvanathan, Lucie Norel, Mark A. Ratner, Zhirong Liu*, Shengxiong Xiao*, Stéphane Rigaut*, Hong Guo*, and Xuefeng Guo*. Tunable symmetry-breaking-induced dual functions in stable and photoswitched single-molecule junctions.  J. Am. Chem. Soc. 143 (49), 20811-20817 (2021).
  32. Chen Yang, Lei Zhang, Chenxi Lu, Shuyao Zhou, Xingxing Li, Yanwei Li, Yang Yang, Yu Li, Zhirong Liu, Jinlong Yang, K. N. Houk*, Fanyang Mo*, and Xuefeng Guo*. Unveiling the full reaction path of the Suzuki-Miyaura cross-coupling in a single-molecule junction. Nat. Nanotech. 16 (11), 1214-1223 (2021).
  33. Zhirong Liu*. Possible applications of machine learning in cluster research. Chemistry (Huaxue Tongbao) 84 (11), 1205-1209 (2021).
  34. Zhaoxi Sun*, Zhe Huai, Qiaole He, and Zhirong Liu. A general picture of Cucurbit[8]uril host–guest binding. J. Chem. Inf. Model. 61 (12), 6107-6134 (2021).
  35. Zhaoxi Sun* and Zhirong Liu. BAR-based multi-dimensional nonequilibrium pulling for indirect construction of QM/MM free energy landscapes: varying the QM region. Adv. Theory Simul. 4 (10), 2100185 (2021).
  36. Yanyan Wang, Huabin Zhou, Xiangyu Sun, Qiaojing Huang, Siyang Li, Zhirong Liu, Changsheng Zhang and Luhua Lai*. Disordered region governs VRN1 and DNA liquid-like phase separation. J. Mol. Biol. 433 (22), 167269/1-15 (2021).
  37. Qiaojing Huang, Pengbo Song, Yixin Chen, Zhirong Liu*, and Luhua Lai*. Allosteric type and pathways are governed by the forces of protein-ligand binding. J. Phys. Chem. Lett. 12 (22), 5404-5412 (2021). (Media report: Protein Allosteric Regulation Type Can Now Be Predicted, see /en/news/129069.htm)
  38. Ting Cheng, Luzhao Sun, Zhirong Liu, Feng Ding*, and Zhongfan Liu*. Theoretical calculation boosting the chemical vapor deposition growth of graphene film. APL Mater.  9 (6), 060906/1-8 (2021).
  39. Ting Cheng, Zhirong Liu, Feng Ding*, and Zhongfan Liu*. The mechanism of graphene vapor-solid growth on insulating substrates. ACS Nano 15 (4), 7399-7408 (2021).
  40. Bin Chong, Yingguang Yang, Zi-Le Wang, Han Xing, and Zhirong Liu*. Reinforcement learning to boost molecular docking upon protein conformational ensemble. Phys. Chem. Chem. Phys. 23 (11), 6800-6806 (2021). (Media report: Artificial Intelligence has Solved a Bottleneck of Virtual Screening upon Intrinsically Disordered Proteins, see /en/news/134120.htm)
  41. Chen Yang, Zitong Liu, Yanwei Li, Shuyao Zhou, Chenxi Lu, Yilin Guo, Melissa Ramirez, Qingzhu Zhang, Yu Li, Zhirong Liu, K. N. Houk, Deqing Zhang, Xuefeng Guo.  Electric field–catalyzed single-molecule Diels-Alder reaction dynamics. Sci. Adv. 7 (4), eabf0689 (2021).
  42. Ting Cheng, Zhongfan Liu, and Zhirong Liu*. High elastic moduli, controllable bandgap and extraordinary carrier mobility in single-layer diamond. J. Mater. Chem. C 8 (39), 13819-13826 (2020).
  43. Zi-Le Wang, Zhirong Liu*, Zhi-Feng Huang*, and Wenhui Duan*. Minimal phase-field crystal modeling of vapor-liquid-solid coexistence and transitions. Phys. Rev. Mater. 4 (10), 103802/1-13 (2020).
  44. Bin Chong, Yingguang Yang, Chenguang Zhou, and Zhirong Liu*. Ensemble-based thermodynamics of the fuzzy binding between intrinsically disordered proteins and small molecule ligands. J. Chem. Inf. Model. 60 (10), 4967-4974 (2020).
  45. Qi Sun, Ting Cheng, Zhirong Liu, Limin Qi*. A cobalt silicate modified BiVO4 photoanode for efficient solar water oxidation. Appl. Catal. B: Environ. 277, 119189 (2020).
  46. Qiaojing Huang, Maodong Li, Luhua Lai*, and Zhirong Liu*. Allostery of multidomain proteins with disordered linkers. Curr. Opin. Struct. Biol. 62, 175-182 (2020).
  47. Songtao Tian and Zhirong Liu*. Emergence of income inequality: origin, distribution and possible policies. Physica A 537, 122767/1-14 (2020).
  48. Hengxin Tan, Menglei Li*, Haitao Liu, Zhirong Liu*, Yuanchang Li*, and Wenhui Duan. Two-dimensional ferromagnetic-ferroelectric multiferroics in violation of the d0 rule. Phys. Rev. B 99 (19), 195434/1-6 (2019).
  49. Miao Yu, Yixin Chen, Zi-Le Wang, and Zhirong Liu*. Fluctuation correlations as major determinants of structure- and dynamics-driven allosteric effects. Phys. Chem. Chem. Phys. 21 (9), 5200-5214 (2019).
  50. Junwen Xiong, Meng Gao, Jingjing Zhou, Sen Liu, Zhengding Su, Zhirong Liu, and Yongqi Huang. The influence of intrinsic folding mechanism of an unfoldedprotein on the coupled folding-binding process duringtarget recognition. Proteins: Struct. Funct. Bioinform. 87 (4), 265-275 (2019).
  51. Luhao Zhang, MaoDong Li and Zhirong Liu*. A comprehensive ensemble model for comparing the allosteric effect of ordered and disordered proteins. PLOS Comput. Biol. 14 (12), e1006393/1-22 (2018).
  52. Miao Yu, Xiaomin Ma, Huaiqing Cao, Bin Chong, Luhua Lai, and Zhirong Liu*. Singular value decomposition for the correlation of atomic fluctuations with arbitrary angle. Proteins: Struct. Funct. Bioinform. 86 (10), 1075-1087 (2018).
  53. Bin Chong, Maodong Li, Tong Li, Miao Yu, Yugang Zhang, and Zhirong Liu*. Conservation of potentially druggable cavities in intrinsically disordered proteins. ACS Omega 3 (11), 15643-15652 (2018).
  54. Maodong Li, Huaiqing Cao, Luhua Lai, and Zhirong Liu*. Disordered linkers in mutli-domain allosteric proteins: entropic effect to favor the open state or enhanced local concentration to favor the closed state? Protein Sci. 27 (9), 1600-1610 (2018).
  55. Xuejiao Wang, Maodong Li, Pengbo Song, Xiaolin Lv, Zhirong Liu*, Jianbin Huang*, and Yun Yan*. Reversible manipulation of supramolecular chirality using host-guest dynamics between β-cyclodextrin and alkyl amines. Chem. Eur. J. 24 (52), 13734-13739 (2018).
  56. Ting Cheng, Congwei Tan, Shuqing Zhang, Teng Tu, Hailin Peng*, and Zhirong Liu*. Raman spectra and strain effects in bismuth oxychalcogenides. J. Phys. Chem. C 122 (34), 19970-19980 (2018).
  57. Xiewen Wen, Hailong Chen, Tianmin Wu, Zhihao Yu, Qirong Yang, Jingwen Deng, Zhengtang Liu, Xin Guo, Jianxin Guan, Xiang Zhang, Yongji Gong, Jiangtan Yuan, Zhuhua Zhang, Chongyue Yi, Xuefeng Guo, Pulickel M. Ajayan*, Wei Zhuang*, Zhirong Liu*, Jun Lou*, and Junrong Zheng*. Ultrafast probes of electron-hole transitions between two atomic layers. Nat. Commun. 9, 1859/1-9 (2018).
  58. Zi-Le Wang, Zhirong Liu*, and Zhi-Feng Huang*. Angle-adjustable density field formulation for the modeling of crystalline microstructure. Phys. Rev. B 97 (18), 180102(R)/1-6 (2018).
  59. Zi-Le Wang, Zhi-Feng Huang*, and Zhirong Liu*. Elastic constants of stressed and unstressed materials in the phase field crystal model. Phys. Rev. B 97 (14), 144112/1-14 (2018).
  60. Shishu Zhang, Na Zhang, Yan Zhao, Ting Cheng, Xiaobo Li, Rui Feng, Hua Xu, Zhirong Liu, Jin Zhang and Lianming Tong. Spotting the differences in two-dimensional materials – the Raman scattering perspective. Chem. Soc. Rev. 47 (9), 3217-3240 (2018).
  61. Xiaoyun Zhang, Jian-Hua Wang, Dan Tan, Qiang Li, Maodong Li, Zhou Gong, Chun Tang, Zhirong Liu, Meng-Qiu Dong, and Xiaoguang Lei. Carboxylate-selective chemical cross-linkers for mass spectrometric analysis of protein structures. Anal. Chem. 90 (2), 1195-1201 (2018).
  62. Jing Liang, Jin Zhang, Zhenzhu Li, Hao Hong, Jinhuan Wang, Zhihong Zhang, Xu Zhou, Ruixi Qiao, Jiyu Xu, Peng Gao, Zhirong Liu, Zhongfan Liu, Zhipei Sun, Sheng Meng, Kaihui Liu, and Dapeng Yu. Monitoring local strain vector in atomic-layered MoSe2 by second-Harmonic generation. Nano Lett. 17 (12), 7539-7543 (2017).
  63. Ting Cheng, Haifeng Lang, Zhenzhu Li, Zhongfan Liu, and Zhirong Liu*. Anisotropic carrier mobility in two-dimensional materials with tilted Dirac cones: theory and application. Phys. Chem. Chem. Phys. 19 (35), 23942-23950 (2017).
  64. Xiong Zhou, Fabian Bebensee, Mingmei Yang, Regine Bebensee, Fang Cheng, Yang He, Qian Shen, Jian Shang, Zhirong Liu, Flemming Besenbacher, Trolle Linderoth, and Kai Wu. Steering surface reaction at specific sites with self-assembly strategy. ACS Nano 11 (9), 9397-9404 (2017).
  65. Zeyu Jiang, Zhirong Liu*, Yuanchang Li*, and Wenhui Duan*. Scaling universality between band gap and exciton binding energy of two-dimensional semiconductors. Phys. Rev. Lett. 118 (26), 266401/1-6 (2017).
  66. Shuqing Zhang, Nannan Mao, Juanxia Wu, Lianming Tong*, Jin Zhang*, and Zhirong Liu*. In-plane uniaxial strain in black phosphorus enables the identification of crystalline orientation. Small 13 (30), 1700466/1-9 (2017).
  67. Zhenzhu Li, Zhongfan Liu and Zhirong Liu*. Movement of Dirac points and band gaps in graphyne under rotating strain. Nano Res. 10 (6), 2005-2020 (2017).
  68. Ruiqi Zhao, Xiaolei Zhao, Zhirong Liu, Feng Ding and Zhongfan Liu. Controlling the orientations of h-BN during growth on transition metals by chemical vapor deposition. Nanoscale 9 (10), 3561-3567 (2017).
  69. Na Xin, Jinying Wang, Chuancheng Jia, Zitong Liu, Xisha Zhang, Chenmin Yu, Mingliang Li, Shuopei Wang, Yao Gong, Hantao Sun, Guanxin Zhang, Zhirong Liu, Guangyu Zhang, Jianhui Liao, Deqing Zhang, and Xuefeng Guo. Stereoelectronic effect-induced conductance switching in aromatic chain single-molecule junctions. Nano Lett. 17 (2), 856-861 (2017).
  70. Haifeng Lang, Shuqing Zhang, and Zhirong Liu*. Mobility anisotropy of two-dimensional semiconductors. Phys. Rev. B 94 (23), 235306/1-8 (2016).
  71. Maodong Li, Tanlin Sun, Fan Jin, Daqi Yu, and Zhirong Liu*. Dimension conversion and scaling of disordered protein chains. Mol. Biosys. 12 (9), 2932-2940 (2016).
  72. Hue Sun Chan* and Zhirong Liu*. Thermodynamics and kinetics of TopoII action: A consensus on T-segment curvature selection? Comment on “Disentangling DNA Molecules” by Alexander Vologodskii. Phys. Life Rev.18, 135-138 (2016).
  73. Shuqing Zhang, Jinying Wang, Zhenzhu Li, Ruiqi Zhao, Lianming Tong, Zhongfan Liu, Jin Zhang* and Zhirong Liu*. Raman spectra and corresponding strain effects in graphyne and graphdiyne. J. Phys. Chem. C120 (19), 10605-10613 (2016).
  74. Chuancheng Jia, Agostino Migliore, Na Xin, Shaoyun Huang, Jinying Wang, Qi Yang, Shuopei Wang, Hongliang Chen, Duoming Wang, Boyong Feng, Zhirong Liu, Guangyu Zhang, Da-Hui Qu, He Tian, Mark A. Ratner, H. Q. Xu, Abraham Nitzan, Xuefeng Guo. Covalently bonded single-molecule junctions with stable and reversible photoswitched conductivity. Science 352 (6292), 1443-1445 (2016).
  75. Huaiqing Cao, Yongqi Huang*, and Zhirong Liu*. Interplay between binding affinity and kinetics in protein-protein interactions. Proteins: Struct. Funct. Bioinform. 84 (7), 920-933 (2016).
  76. Maodong Li and Zhirong Liu*. Dimensions, energetics and denaturant effects of protein unstructured state. Protein Sci. 25 (3), 734-747 (2016).
  77. Lin Zhou, Lei Liao, Jinying Wang, Jingwen Yu, Denghua Li, Qin Xie, Zhirong Liu,Yanlian Yang, Xuefeng Guo, and Zhongfan Liu. Substrate-induced graphene chemistry for 2D superlattices with tunable periodicities. Adv. Mater. 28 (11), 2148-2154 (2016). 
  78. Chen Yu, Xiaogang Niu, Fan Jin, Zhirong Liu, Changwen Jin, and Luhua Lai. Structure-based inhibitor design for the intrinsically disordered protein c-Myc. Sci. Rep. 6, 22298/1-11 (2016).
  79. Zeren Lin and Zhirong Liu*. Spin-1 Dirac-Weyl fermions protected by bipartite symmetry. J. Chem. Phys. 143(21), 214109/1-8 (2015).
  80. Ruiqi Zhao, Feifei Li, Zhirong Liu, Zhongfan Liu and Feng Ding. The transition metal surface passivated edges of hexagonal boron nitride (h-BN) and the mechanism of h-BN’s chemical vapor deposition (CVD) growth.Phys. Chem. Chem. Phys. 17 (43), 29327-29334 (2015).
  81. Huaqing Huang, Zhirong Liu, Hongbin Zhang, Wenhui Duan, and David Vanderbilt. Emergence of a Chern-insulating state from a semi-Dirac dispersion. Phys. Rev. B 92 (16), 161115/1-6 (2015).
  82. Huaqing Huang, Zhaoyou Wang, Nannan Luo, Zhirong Liu, Rong Lu, Jian Wu, and Wenhui Duan. Time-reversal symmetry protected chiral interface states between quantum spin and quantum anomalous Hall insulators. Phys. Rev. B 92 (7), 075138/1-14 (2015).
  83. Zhirong Liu* and Hue Sun Chan*. Consistent rationalization of type-2 topoisomerases' unknotting, decatenating, supercoil-relaxing actions and their scaling relation. J. Phys.: Condens. Matter. 27 (35), 354103/1-13 (2015).
  84. Jinying Wang, Shibin Deng, Zhongfan Liu, and Zhirong Liu*. The rare two-dimensional materials with Dirac cones. Natl. Sci. Rev. 2 (1), 22-39 (2015).
  85. Yugang Zhang, Huaiqing Cao, and Zhirong Liu*. Binding cavities and druggability of intrinsically disordered proteins. Protein Sci. 24 (5), 688-705 (2015).  (cover paper)
  86. Zhenzhu Li, Jinying Wang, and Zhirong Liu*. Intrinsic carrier mobility of Dirac cones: the limitations of deformation potential theory. J. Chem. Phys. 141 (14), 144107/1-9 (2014).
  87. Zhirong Liu* and Yongqi Huang. Advantages of proteins being disordered. Protein. Sci. 23 (5), 539-550 (2014).
  88. Jinying Wang, Shuqing Zhang, Jingyuan Zhou, Rong Liu, Ran Du, Hua Xu, Zhongfan Liu*, Jin Zhang*, and Zhirong Liu*. Identifying sp-sp2 carbon materials by Raman and infrared spectroscopies. Phys. Chem. Chem. Phys. 16 (23), 11303-11309 (2014).
  89. Lin Zhou, Liming Zhang, Lei Liao, Mingmei Yang, Qin Xie, Hailin Peng, Zhirong Liu, and Zhongfan Liu. Photochemical modification of graphene. Acta Chim. Sinica 72 (3), 289-300 (2014).
  90. Limin Xu, Lingxiang Jiang, Markus Drechsler, Yu Sun, Zhirong Liu, Jianbin Huang, Ben Zhong Tang, Zhibo Li, Martien A. Cohen Stuart, and Yun Yan. Self-assembly of ultralong polyion nanoladders facilitated by ionic recognition and molecular stiffness. J. Am. Chem. Soc. 136 (5) 1942-1947 (2014).
  91. Zhirong Liu*, Jinying Wang, and Jianlong Li. Dirac cones in two-dimensional systems: from hexagonal to square lattices. Phys. Chem. Chem. Phys. 15 (43), 18855-18862 (2013).
  92. Jinying Wang, Huaqing Huang, Wenhui Duan, and Zhirong Liu*. Identifying Dirac cones in carbon allotropes with square symmetry. J. Chem. Phys. 139 (18), 184701/1-6 (2013).
  93. Fan Jin, Chen Yu, Luhua Lai*, and Zhirong Liu*. Ligand clouds around protein clouds: a scenario of ligand binding with intrinsically disordered proteins. PLoS Comput. Biol. 9 (10), e1003249/1-11 (2013). (cover paper)
  94. Chuancheng Jia, Jinying Wang, Changjiang Yao, Yang Cao, Yuwu Zhong, Zhirong Liu, Zhongfan Liu, and Xuefeng Guo. Conductance Switching and Mechanisms in Single-Molecule Junctions. Angew. Chem. Int. Ed. 52(33), 8666-8670 (2013).
  95. Jinying Wang, Ruiqi Zhao, Zhongfan Liu*, and Zhirong Liu*. Widely tunable carrier mobility of boron-nitride-embedded graphene. Small 9 (8), 1373-1378 (2013).
  96. Jinying Wang, Ruiqi Zhao, Mingmei Yang, Zhongfan Liu*, and Zhirong Liu*. Inverse relationship between carrier mobility and band gap in graphene. J. Chem. Phys. 138 (8), 084701/1-5 (2013).  (cover paper)
  97. Mingmei Yang, Ruiqi Zhao, Jinying Wang, Liming Zhang, Qin Xie, Zhongfan Liu, and Zhirong Liu*. Bandgap opening in Janus-type mosaic graphene. J. Appl. Phys. 113 (8), 084313/1-6 (2013).
  98. Lin Zhou, Lushan Zhou, Mingmei Yang, Di Wu, Lei Liao, Kai Yan, Qin Xie, Zhirong Liu, Hailin Peng, and Zhongfan Liu. Free radical reactions in two dimensions: a case study on photochlorination of graphene. Small 9(8), 1388-1396 (2013).
  99. Liming Zhang, Lin Zhou, Mingmei Yang, Zhirong Liu, Qin Xie, Hailin Peng, and Zhongfan Liu. Photo-induced free radical modification of graphene. Small 9 (8), 1134-1143 (2013).
  100. Huaqing Huang, Wenhui Duan, and Zhirong Liu*. The existence/absence of Dirac cones in graphynes. New J. Phys. 15 (2), 023004/1-13 (2013). (selected by the journal editors for inclusion in the exclusive "Highlights of 2013" collection.)
  101. Fan Jin and Zhirong Liu*. Inherent relationships among different biophysical prediction methods for intrinsically disordered proteins. Biophys. J. 104 (2), 488-495 (2013).
  102. Zhirong Liu* and Yongqi Huang. Evidences for the unfolding mechanism of three-dimensional domain swapping. Protein Sci. 22 (3), 280-286 (2013).
  103. Yongqi Huang and Zhirong Liu*. Do intrinsically disordered proteins possess high specificity in protein–protein interactions? Chem. Eur. J. 19 (14), 4462-4467 (2013).
  104. Huaqing Huang, Yuanchang Li, Zhirong Liu, Jian Wu, and Wenhui Duan, Comment on "Structural and electronic properties of T graphene: a two-dimensional carbon allotrope with tetrarings". Phys. Rev. Lett. 110(2), 029603 (2013).
  105. Ruiqi Zhao, Jinying Wang, Mingmei Yang, Zhongfan Liu*, and Zhirong Liu*. Graphene quantum dots embedded in a hexagonal BN sheet: identical influences of zigzag/armchair edges. Phys. Chem. Chem. Phys. 15 (3), 803-806 (2013).
  106. Ruiqi Zhao, Jinying Wang, Mingmei Yang, Zhongfan Liu*, and Zhirong Liu*. BN-embedded graphene with a ubiquitous gap opening. J. Phys. Chem. C 116 (39), 21098-21103 (2012).
  107. Yongqi Huang, Xue Kang, Bing Xia, and Zhirong Liu*. Mechanism of 3D domain swapping for Mpro-C: clues from molecular simulations. Acta Phys. -Chim. Sin. 28 (10), 2411-2417 (2012).
  108. Iskra Staneva, Yongqi Huang, Zhirong Liu, and Stefan Wallin. Binding of two intrinsically disordered peptides to a multi-specific protein: a combined Monte Carlo and molecular dynamics study. PLoS Comput. Biol. 8 (9), e1002682/1-9 (2012).
  109. Yongqi Huang, Huaiqing Cao, and Zhirong Liu*. Three-dimensional domain swapping in the protein structure space. Proteins: Struct. Funct. Bioinform. 80 (6), 1610-1619 (2012).
  110. Mingmei Yang, Lin Zhou, Jinying Wang, Zhongfan Liu*, and Zhirong Liu*. Evolutionary chlorination of graphene: from charge-transfer complex to covalent bonding and non-bonding. J. Phys. Chem. C 116 (1), 844-850 (2012).
  111. Jinying Wang, Zhongfan Liu, and Zhirong Liu*. First-principles study of the transport behavior of zigzag graphene nanoribbons tailored by strain. AIP Adv. 2 (1), 012103/1-7 (2012). (Has been selected for the January 16, 2012 issue of Virtual Journal of Nanoscale Science & Technology.)
  112. Fangping Ouyang, Shenglin Peng, Zhongfan Liu*, and Zhirong Liu*. Bandgap opening in graphene antidot lattices: the missing half. ACS Nano 5 (5), 4023-4030 (2011).
  113. Hue Sun Chan, Zhuqing Zhang, Stefan Wallin, and Zhirong Liu. Cooperativity, local-nonlocal coupling, and nonnative interactions: principles of protein folding from coarse-grained models. Annu. Rev. Phys. Chem. 62, 301-326 (2011).
  114. Yongqi Huang and Zhirong Liu*. Anchoring intrinsically disordered proteins to multiple targets: lessons from N-terminus of the p53 protein. Int. J. Mol. Sci. 12 (2), 1410-1430 (2011).
  115. Shaogang Hao, Zhirong Liu, Junqiang Lu, and Gang Zhou. Editorial: Theoretical modeling and computational simulation of electronic properties of nanomaterials. J. Nanomater. 2011, 408581/1-2 (2011).
  116. J. Lin, N. Wang, Y. Li, Z. Liu, S. Tian, L. Zhao, Y. Zheng, S. Liu, S. Li, C. Jin, and B. Xia. LEC-BiFC: a new method for rapid assay of protein interaction. Biotechnic & Histochemistry 86 (4), 272-279 (2011).
  117. Chaoye Wu, Wenhui Duan, Xiao-Wen Zhang, and Zhirong Liu*. Effects of hydrostatic pressure on Pb(Zr1-xTix)O3 near the morphotropic phase boundary. J. Appl. Phys. 108 (12), 124102/1-5 (2010).
  118. Peng Wang, Zhirong Liu, Feng Lin, Gang Zhou, Jian Wu, Wenhui Duan, Bing-Lin Gu, and S. B. Zhang, Optimizing photoelectrochemical properties of TiO2 by chemical codoping. Phys. Rev. B 82 (19) , 193103/1-4 (2010).
  119. Yongqi Huang and Zhirong Liu*. Nonnative interactions in coupled folding and binding processes of intrinsically disordered proteins. PLoS ONE 5 (11), e15375/1-10 (2010).
  120. Yongqi Huang and Zhirong Liu*. Smoothing molecular interactions: the "kinetic buffer" effect of intrinsically disordered proteins. Proteins: Struct. Funct. Bioinform. 78 (16), 3251-3259 (2010).
  121. Jia Li, Zuanyi Li, Gang Zhou, Zhirong Liu, Jian Wu, Bing-Lin Gu, Jisoon Ihm, and Wenhui Duan. Spontaneous edge-defect formation and defect-induced conductance suppression in graphene nanoribbons. Phys. Rev. B 82(11), 115410 (2010).
  122. Yang Li, Xiaowei Jiang, Zhongfan Liu, and Zhirong Liu*. Strain effects in graphene and graphene nanoribbons: the underlying mechanism. Nano Res. 3 (8), 545-556 (2010).
  123. Yongqi Huang and Zhirong Liu*. Intrinsically disordered proteins: the new sequence-structure-function relations. Acta Phys. -Chim. Sin.26 (8), 2061-2072 (2010).
  124. Zhirong Liu, Lynn Zechiedrich, and Hue Sun Chan. Action at hooked or twisted–hooked DNA juxtapositions rationalizes unlinking preference of type-2 topoisomerases. J. Mol. Biol. 400 (5), 963-982 (2010).
  125. Meng Gao, Xin-Qiu Yao, Zhen-Su She, Zhi-Rong Liu*, and Huai-Qiu Zhu*. Intermediate structure and slow hydration water dynamics in protein folding process. Acta Phys. -Chim. Sin. 26 (7), 1998-2006 (2010).
  126. Zhirong Liu, Lynn Zechiedrich, and Hue Sun Chan. Local site preference rationalizes disentangling by DNA topoisomerases. Phys. Rev. E. 81 (3), 031902/1-4 (2010).
  127. Yifei Qi, Yongqi Huang, Huanhuan Liang, Zhirong Liu*, and Luhua Lai*. Folding simulations of a de novo designed protein with a βαβ fold. Biophys. J. 98 (2), 321-329 (2010).
  128. Zhirong Liu, Richard W. Deibler, Hue Sun Chan, and Lynn Zechiedrich. The why and how of DNA unlinking. Nucleic Acids Res. 37 (3), 661-671 (2009). (cover paper)
  129. Yongqi Huang and Zhirong Liu*. Kinetic advantage of intrinsically disordered proteins in coupled folding-binding process: a critical assessment of the "fly-casting" mechanism. J. Mol. Biol. 393 (5), 1143-1159 (2009). [422 (1), 156 (2012).]
  130. Yu Yang, Jia Li, Zhirong Liu, Gang Zhou, Jian Wu, Wenhui Duan, Peng Jiang, Jin-Feng Jia, Qi-Kun Xue, Bing-Lin Gu, and S. B. Zhang. Activated dissociation of O2 on Pb(111) surfaces by Pb adatoms. Phys. Rev. B 80(7), 073406/1-4 (2009).
  131. Artem Badasyan, Zhirong Liu and Hue Sun Chan. Interplaying roles of native topology and chain length in marginally cooperative and noncooperative Int. J. Quantum Chem. 109 (14), 3482-3499 (2009).
  132. Allison Ferguson, Zhirong Liu and Hue Sun Chan. Desolvation barrier effects are a likely contributor to the remarkable diversity in the folding rates of small proteins. J. Mol. Biol. 389 (3), 619-636 (2009). [Corrigendum: 392 (1), 242 (2009).]
  133. Fawei Zheng, Gang Zhou, Zhirong Liu, Jian Wu, Wenhui Duan, Bing-Lin Gu and S. B. Zhang. Half metallicity along the edge of zigzag boron nitride nanoribbons. Phys. Rev. B 78 (20), 205415/1-5 (2008).
  134. Artem Badasyan, Zhirong Liu and Hue Sun Chan. Probing possible downhill folding: native contact topology likely places a significant constraint on the folding cooperativity of proteins with ~40 residues. J. Mol. Biol. 384 (2), 512-530 (2008).
  135. Bing Huang, Zuanyi Li, Zhirong Liu, Gang Zhou, Shaogang Hao, Jian Wu, Bing-Lin Gu, and Wenhui Duan. Adsorption of gas molecules on graphene nanoribbons and its implication for nanoscal J. Phys. Chem. C 112(35), 13442-13446 (2008).
  136. Fawei Zheng, Zhirong Liu, Jian Wu, Wenhui Duan, and Bing-Lin Gu. Scaling law of the giant Stark effect in boron nitride nanoribbons and nanotubes. Phys. Rev. B 78 (8), 085423/1-5 (2008).
  137. Zhirong Liu and Hue Sun Chan. Efficient chain moves for Monte Carlo simulations of a wormlike DNA model: excluded volume, supercoils, site juxtapositions, knots, and comparisons with random-flight and lattice models. J. Chem. Phys. 128 (14), 145104/1-31 (2008). [Corrigendum: 131 (4), 049902 (2009).]
  138. Jie Yu, ZhongqingWu, Zhirong Liu, Qimin Yan, JianWu and Wenhui Duan. Phase diagram of ferroelectric BaTiO3 ultrathin films under open-circuit conditions J. Phys.: Condens. Matter 20 (13), 135203/1-6 (2008).
  139. Zhongqing Wu, Ningdong Huang, Zhirong Liu, Jian Wu, Wenhui Duan, and Bing-Lin Gu. Unusual vortex structure in ultrathin Pb(Zr0.5Ti0.5)O3 films. J. Appl. Phys. 101 (1), 014112/1-5 (2007).
  140. Rong Lü and Zhirong Liu. Current and shot noise in a quantum dot coupled to ferromagnetic leads in the Kondo regime. Chinese Phys. Lett. 24 (1), 195-198 (2007).
  141. Wenhui Duan, Zhi-Rong Liu. Theoretical modeling and simulations of perovskite ferroelectrics: from phenomenological approaches to ab initio. Current Opin. Solid State & Mater. Sci. 10 (1), 40-51 (2006).
  142. Zhirong Liu, Jennifer K. Mann, E. Lynn Zechiedrich, and Hue Sun Chan. Topological information embodied in local juxtaposition geometry provides a statistical mechanical basis for unknotting by type-2 DNA topoisomerases. J. Mol. Biol. 361 (2), 268-285 (2006). (cover paper)
  143. Zhirong Liu, E. Lynn Zechiedrich, and Hue Sun Chan. Inferring global topology from local juxtaposition geometry: interlinking polymer rings and ramifications for topoisomerase action. Biophys. J. 90 (7), 2344-2355 (2006).
  144. Zhirong Liu and Hue Sun Chan. Solvation and desolvation effects in protein folding: native flexibility, kinetic cooperativity and enthalpic barriers under isostability conditions. Phys. Biol. 2 (4), S75-S85 (2005).
  145. Zhirong Liu and Hue Sun Chan. Desolvation is a likely origin of robust enthalpic barriers to protein folding. J. Mol. Biol. 349 (4), 872-889 (2005).
  146. Hüseyin Kaya, Zhirong Liu, and Hue Sun Chan. Chevron behavior and isostable enthalpic barriers in protein folding: successes and limitations of simple Gō-like modeling. Biophys. J. 89 (1), 520-535 (2005).
  147. Rong Lü and Zhi-Rong Liu. Time-dependent electron transport through molecular quantum dots in the presence of external irradiation. J. Phys.: Condens. Matter 17 (37), 5859-5867 (2005).
  148. Guang-Ming Zhang, Rong Lü, Zhi-Rong Liu, and Lu Yu. Swapping Kondo resonances in coupled double quantum dots. Phys. Rev. B 72 (7), 73308/1-4 (2005).
  149. Zhongqing Wu, Ningdong Huang, Zhirong Liu, Jian Wu, Wenhui Duan, Bing-Lin Gu, and Xiao-Wen Zhang. Ferroelectricity in Pb(Zr0.5Ti0.5)O3 thin films: Critical thickness and 180° stripe domains. Phys. Rev. B 70 (10), 104108/1-4 (2004).
  150. Y. Wang, Y. L. Cheng, K. C. Cheng, H. L. W. Chan, C. L. Choy, and Z. R. Liu. In-plane dielectric properties of epitaxial 0.65Pb(Mg1/3Nb2/3)O3-0.35PbTiO3 thin films in a very wide frequency range. Appl. Phys. Lett. 85(9), 1580-1582 (2004).
  151. Zhi-Rong Liu, Jian Wu, and Wenhui Duan. Electronic-structure theory of crystalline insulators under a homogeneous electric field. Phys. Rev. B 69 (8), 085117/1-7 (2004).
  152. Z. -R. Liu and H. Gao. A differential cluster variation method for analysis of spinodal decomposition in alloys. Eur. Phys. J. B 37 (3), 369-374 (2004).
  153. Zhi-Rong Liu, Huajian Gao, Long-Qing Chen and K. J. Cho. Patterned nanostructure in AgCo/Pt/MgO(001) thin film. Phys. Rev. B 68 (3), 35429/1-7 (2003).
  154. Ningdong Huang, Zhirong Liu, Zhongqing Wu, Jian Wu, Wenhui Duan, Bing-Lin Gu, and Xiao-Wen Zhang. Huge enhancement of electromechanical responses in compositionally modulated Pb(Zr1-xTix)O3. Phys. Rev. Lett. 91 (6), 67602/1-4 (2003).
  155. Zhongqing Wu, Wenhui Duan, Zhirong Liu, Bing-Lin Gu and Xiao-Wen Zhang. Effect of tunneling frequency on relaxor behavior. Microelectronic Engineering 66 (1-4), 676-682 (2003).
  156. Yu Wang, Zhirong Liu, Helen L. W. Chan and Chung Loong Choy. A Phenomenological Explanation to the Dielectric Aging Mechanism of a Lead Magnesium Niobate-Based Ceramic. Jpn. J. Appl. Phys. 42 (2A), 515-519 (2003).
  157. Zhongqing Wu, Wenhui Duan, Zhirong Liu, Bing-Lin Gu and Xiao-Wen Zhang. Multiple tunneling channels order-disorder ferroelectric model and field-induced phase transition in relaxors. Phys Rev. B 65 (17), 174119/1-5 (2002).
  158. Z. -R. Liu, W. Duan, B. -L. Gu, and X. -W. Zhang. Stochastic resonance induced by random fields in ferroelectrics. Europhys. Lett. 55 (1), 1-5 (2001).
  159. Zhi-Rong Liu, Wenhui Duan, Bing-Lin Gu, and Xiao-Wen Zhang. Soft modes in order-disorder ferroelectrics. Appl. Phys. Lett. 79 (9), 1333-1335 (2001).
  160. Zhi-Rong Liu, Yong Zhang, Bing-Lin Gu, and Xiao-Wen Zhang. The proportion of frozen local polarization in relaxor ferroelectrics. J. Phys.: Condens. Matter 13 (5), 1133-1139 (2001).
  161. J. S. Liu, Z. R. Liu, H. Zheng, J. Ni, B. L. Gu, and X. W. Zhang. Monte Carlo simulation of domains and mesoscopic structures in perovskite relaxor ferroelectric Pb(Mg1/3Nb2/3)O3. Ferroelectrics 252 (1-4), 375-382 (2001).
  162. J. S. Liu, Z. R. Liu, H. Zheng, B. L. Gu, and X. W. Zhang. A unified picture of the ordered domains in relaxor ferroelectric lead magnesium niobate. Ferroelectrics 261 (1-4), 813-818 (2001).
  163. Zhi-Rong Liu, Bing-Lin Gu, and Xiao-Wen Zhang. Eight-potential-well order-disorder ferroelectric model and effects of random fields. Appl. Phys. Lett. 77 (21), 3447-3449 (2000).
  164. Zhi-Rong Liu, Bing-Lin Gu, and Xiao-Wen Zhang. Effects of ac field amplitude on the dielectric susceptibility of relaxors. Phys. Rev. B 62 (1), 1-4 (2000).
  165. Zhi-Rong Liu, Jian-She Liu, Bing-Lin Gu, and Xiao-Wen Zhang. Cluster-variation-method studies on the atomic ordering in complex perovskite alloys. Phys. Rev. B 61 (18), 11918-11921 (2000).
  166. Xiao-Wen Zhang, Xi Liu, Zhi-Rong Liu, and Bing-Lin Gu. Dielectric nonlinearity of relaxor ferroelectric ceramics at low ac-drive amplitudes. J. Phys.: Condens. Matter 12 (27), 5929-5937 (2000).
  167. Rong Lü, Jia-Lin Zhu, Zhi-Rong Liu, Lee Chang, and Bing-Lin Gu. Spin Tunnelling of trigonal and hexagonal ferromagnets in an arbitrarily directed magnetic field. J. Phys.: Condens. Matter 12 (20), 4503-4522 (2000).
  168. Zhi-Rong Liu, Bing-Lin Gu, Hong Gui, and Xiao-Wen Zhang. Transient ordered phases with different structure types along a phase-decomposition path. Phys. Rev. B 59 (1), 16-19 (1999).
  169. Bing-Lin Gu, Hong Gui, Zhi-Rong Liu, and Xiao-Wen Zhang. Possible order-disorder phase diagrams in (A'xA"1-x)BO3 and A(B'xB"1-x)O3 complex perovskites. J. Appl. Phys. 85 (4), 2408-2413 (1999).
  170. Xiao-Wen Zhang, Hong Gui, Zhi-Rong Liu, and Bing-Lin Gu. Phase transition of ergodic space shrinking in succession and relaxor ferroelectrics. Phys. Lett. A 251 (3), 219-222 (1999).
Copyright: College of Chemistry and Molecular Engineering, Peking University, China
Address: the Chemistry Building, Peking University, Beijing 100871, China
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