Publications

# equal contribution; * corresponding author

2024

  • [60] 张智毓, 朱永健, 代亮 译, “识别纽结”. 物理, 53, 716-718(2024). Html

  • [59] Bin Zhu, Chenxi Zhang, Jiwei Wang, Chuandong Jia, Teng Lu*, Liang Dai*, and Tao Chen*. “Scaling Laws for Protein Folding under Confinement", The Journal of Physical Chemistry Letters, 15, 10138-10145 (2024). DOI

  • [58] Xinkai Zhao, Ziyu Li, Bingbing Cao, Yichao Jin, Wenxing Wang, Jing Tian, Liang Dai, Dan Sun, Ce Zhang. “A high-throughput system for drug screening based on the movement analysis of zebrafish”, Heliyon, 10, e36495 (2024). DOI

  • [57] Yibo Feng, Bingchen Che, Jiahao Fu, Yu Sun, Wenju Ma, Jing Tian, Liang Dai, Guangyin Jing, Wei Zhao*, Dan Sun*, and Ce Zhang*. “From Chips-in-Lab to Point-of-Care Live Cell Device: Development of a Microfluidic Device for on-Site Cell Culture and High-Throughput Drug Screening”, ACS Biomaterials Science & Engineering, 10(8), 5399-5408 (2024). DOI

  • [56] Qiyuan Qiu, Yongjian Zhu, Zhongtao Wu, Liang Dai*, “A simple and efficient algorithm to identify the chirality of polymer knots”, Chinese Journal of Polymer Science, 1-8 (2024). DOI

  • [55] Luwei Lu#, Qiyuan Qiu#, Yuyuan Lu, Lijia An*, Liang Dai*, “Knotting in Flexible-Semiflexible Block Copolymers”, Macromolecules, 57, 5330 (2024). DOI

  • [54] Hai-Long Dong#, Chen Zhang#, Liang Dai, Zhang Yan, Zhang Xinghua*, Tan Zhi-Jie*, “The origin of different bending stiffness between double-stranded RNA and DNA revealed by magnetic tweezers and simulations”, Nucleic Acids Research, 52, 2519–2529 (2024). DOI

2023

  • [53] Chen Zhang#, Jiaqing Hou#, Yang Zeng#, Liang Dai, Wei Zhao, Guangyin Jing, Dan Sun, Yaoyu Cao* and Ce Zhang*, “Optically Fabricated Gradient Nanochannel Array to Access Translocation Dynamics of T4-phage DNA Through Nanoconfinement”, Lap On a Chip, 23, 3811(2023) . DOI

  • [52] Fujia Tian#, Chen Zhang#, Erchi Zhou#, Hai-Long Dong, Zhi-Jie Tan, Xing-Hua Zhang*, and Liang Dai*, “Universality in RNA and DNA Deformations Induced by Salt, Temperature Change, Stretching Force, and Protein Binding”, Proceedings of the National Academy of Sciences USA, 120, 2218425120(2023). DOI

  • [51] 代亮*, “管子模型在高分子纽结体系中的构建和应用”, 中国科学:化学, 53, 693(2023) . DOI

  • [50] Bingchen Che, Dan Sun, Chen Zhang, Jiaqing Hou, Wei Zhao, Guangyin JING, Yuguang Mu, Yaoyu Cao, Liang Dai, Ce Zhang*, “Gradient Nano-confinement FacilitatesBinding of Transcriptional Factor NF-$\kappa$B to Histone- and Protamine- DNA complex”, Nano Letters, 23, 2388(2023). DOI

  • [49] Kaiyuan Yang, Houjing Huang, Olafs Vandans, Adithya Murali, Fujia Tian, Roland H.C.Yap*, Liang Dai*, “Applying Deep Reinforcement Learning to the HP Model for Protein Structure Prediction”, Physica A: Statistical Mechanics and its Applications 609, 128395(2023). DOI

2022

  • [48] Xiao-Cong Zhao#, Hai-Long Dong#, Xiao-Lu Li, Hong-Yu Yang, Xue-Feng Chen, Liang Dai, WenQiang Wu, Zhi-Jie Tan* and Xing-Hua Zhang*, “5-methyl-cytosine stabilizes DNA but hinders DNA hybridization revealed by magnetic tweezers and simulations”, Nucleic Acids Research, gkac1122(2022). DOI

  • [47] Yanwei Wang*, Qiyuan Qiu*, Arailym Yedilbayeva, Diana Kairula, and Liang Dai*, “Phase behavior of ion-containing polymers in polar solvents: Predictions from a liquid-state theory with local short-range interactions”, Polymers 14, 4421(2022). DOI

  • [46] Liang Sun, Simin Wang, Fujia Tian, Haoqi Zhu, and Liang Dai*, “Organizations of melittin peptides after spontaneous penetration into cell membranes”, Biophysical Journal, 121, 4368 (2022). DOI

  • [45] Simin Wang, Hongzhao Fan, Zhe Zhang, Liang Sun, Jialu Chen, Nuo Yang, Yanguang Zhou*, Bing Li*, Liang Dai*, “Resonant phonon modes induced by molecular rotations in α-pentaerythritol crystal”, Journal of Materials Chemistry C 10, 14431(2022). DOI

  • [44] Haoqi Zhu, Fujia Tian, Liang Sun, Yongjian Zhu, Qiyuan Qiu, Liang Dai*, “Computational Design of Extraordinarily Stable Peptide Structures Through Sidechain-Locked Knots”, The Journal of Physical Chemistry Letters, 13, 7741 (2022). DOI

  • [43] Jiang Du#, Hongmei Yin#, Haoqi Zhu#, Tiantian Wan, Binzhou Wang, Hongtao Qi, Yanfang Lu, Liang Dai*, and Tao Chen*. “Forming double-helix phase of single polymer chains by the cooperation between local structure and nonlocal attraction”, Physical Review Letters 128, 197801 (2022). DOI

  • [42] Xiao-Wei Qiang#, Chen Zhang#, Hai-Long Dong#, Fu-Jia Tian, Hang Fu, Ya-Jun Yang, Liang Dai*, Xing-Hua Zhang*, and Zhi-Jie Tan*. “Multivalent cations reverse the twist-stretch coupling of RNA”, Physical Review Letters 128, 108103 (2022). DOI

  • [41] Chen Zhang#, Fujia Tian#, Ying Lu, Bing Yuan, Zhi-Jie Tan, Xing-Hua Zhang*, and Liang Dai*. “Twist-diameter coupling drives DNA twist changes with salt and temperature”, Science Advances 8, eabn1384 (2022). DOI

  • [40] Yongjian Zhu, Haoqi Zhu, Fujia Tian, Qiyuan Qiu, and Liang Dai*. “Quantifying the effects of slit confinement on polymer knots using the tube model”, Physical Review E 105, 024501 (2022). DOI

2021

  • [39] Jialu Chen, Liang Sun, Simin Wang, Fujia Tian, Haoqi Zhu, Ruiqin Zhang, and Liang Dai*. “Crowding-Induced Polymer Trapping in a Channel”, Physical Review E 104, 054502 (2021). DOI

  • [38] Liang Dai*. “Tube model for polymer knots with excluded volume interactions and its application”, Macromolecules 54, 9299 (2021). DOI

  • [37] Simin Wang, Liang Sun, Bing Li, and Liang Dai*. “Atomistic Insights into the Anisotropic and Low Thermal Conductivity in Neopentyl Glycol Crystals: A Molecular Dynamics Study”, Journal of Physical Chemistry C 125, 15853 (2021). DOI

  • [36] Rajesh Kumar Sharma, Ishita Agrawal, Liang Dai, Patrick Doyle*, and Slaven Garaj*. “DNA Knot Malleability in Single-Digit Nanopores”, Nano Letters 21, 3772 (2021). DOI

  • [35] Yanchen Liu, He Zhu*, Hekang Zhu, Yang Ren, Yizhou Zhu, Yalan Huang, Liang Dai, Shuming Dou, Jie Xu, Cheng-Jun Sun, Xun-Li Wang, Yida Deng, Qunhui Yuan, Xingjun Liu, Junwei Wu*,Yanan Chen*, and Qi Liu*. “Modulating the Surface Ligand Orientation for Stabilized Anionic Redox in Li-Rich Oxide Cathodes”, Advanced Energy Materials 11, 2003479 (2021). DOI

  • [34] Haoqi Zhu#, Fujia Tian#, Liang Sun, Simin Wang, and Liang Dai*. “Revisiting the Non-monotonic Dependence of Polymer Knotting Probability on the Bending Stiffness”, Macromolecules 54, 1623 (2021). DOI

2020

  • [33] Luwei Lu#, Haoqi Zhu#, Yuyuan Lu, Lijia An*, and Liang Dai*. “Application of the tube model to explain the unexpected decrease in polymer bending energy induced by knot formation”, Macromolecules 53, 9443 (2020). DOI

  • [32] Ya-Jun Yang, Hai-Long Dong, Xiao-Wei Qiang, Hang Fu, Er-Chi Zhou, Chen Zhang, Lei Yin, Xuefeng Chen, Fuchao Jia, Liang Dai, Zhi-Jie Tan, and Xing-Hua Zhang*. “Cytosine methylation enhances DNA condensation revealed by equilibrium measurements using magnetic tweezers”, Journal of the American Chemical Society 142, 9203 (2020). DOI

  • [31] Liang Dai*. “Developing the tube theory for polymer knots”, Physical Review Research (Rapid Comm.) 2, 022014(R) (2020). DOI

  • [30] Olafs Vandans#, Kaiyuan Yang#, Zhongtao Wu, and Liang Dai*. “Identifying knot types of polymer conformations by machine learning”, Physical Review E 101, 022502 (2020). DOI, Featured in Physics, Editors’ Suggestion, Nature Research Highlight

  • [29] Hang Fu #, Chen Zhang#, Xiao-Wei Qiang#, Ya-Jun Yang, Liang Dai, Zhi-Jie Tan*, and Xing-Hua Zhang*. “Opposite effects of high-valent cations on the elasticities of DNA and RNA duplexes revealed by magnetic tweezers”, Physical Review Letters 124, 058101 (2020). DOI

2019

  • [28] Rajesh K. Sharma, Ishita Agrawal, Liang Dai, Patrick S. Doyle*, and Slaven Garaj*. “Complex DNA knots detected with a nanopore sensor”, Nature Communications 10, 4473 (2019). DOI

  • [27] Liang Dai, Beatrice W. Soh, and Patrick S. Doyle*. “Effects of side chains on polymer knots”, Macromolecules 52, 6792 (2019). DOI

  • [26] Beatrice W. Soh, Alexander R. Klotz, Liang Dai, and Patrick S. Doyle*. “Conformational State Hopping of Knots in Tensioned Polymer Chains”, ACS Macro Letters 8, 905 (2019). DOI

—— Since joining CityU ——

2018

  • [25] Liang Dai, and Patrick S. Doyle*. “Universal knot spectra for confined polymers”, Macromolecules 51, 6327 (2018). DOI

2017

  • [24] Liang Dai, J. J. Jones, A. R. Klotz, S. Levy and Patrick S. Doyle*. “Nanoconfinement greatly speeds up the nucleation and the annealing in single-DNA collapse”, Soft Matter 13, 6363 (2017). DOI

  • [23] Liang Dai, and Patrick S. Doyle*. “Invited paper: Trapping a Knot into Tight Conformations by Intra-Chain Repulsions”, Polymers 9, 57 (2017). DOI

2016

  • [22] Liang Dai, and Patrick S. Doyle*. “Effects of Intrachain Interactions on the Knot Size of a Polymer”, Macromolecules 49, 7581 (2016). DOI

  • [21] Liang Dai, C. Benjamin Renner, and Patrick S. Doyle*. “The polymer physics of single DNA confined in nanochannel”, Advances in colloid and interface science 232, 80 (2016). DOI

2015

  • [20] Liang Dai, C. Benjamin Renner, Jie Yan and Patrick S. Doyle*. “Coil-globule transition of a single semiflexible chain in slitlike confinement”, Scientific Reports 5, 18438 (2015). DOI

  • [19] Peiwen Cong, Liang Dai, Hu Chen, Johan R. C. van der Maarel, Patrick S. Doyle, and Jie Yan*. “Revisiting the Anomalous Bending Elasticity of Sharply Bent DNA”, Biophysical Journal 109, 2338 (2015). DOI

  • [18] Liang Dai#, C. Benjamin Renner#, and Patrick S. Doyle*. “Metastable knots in confined semiflexible chains”, Macromolecules 48, 2812 (2015). DOI

  • [17] Liang Dai, C. Benjamin Renner, and Patrick S. Doyle*. “Origin of metastable knots in flexible chains”, Physical Review Letters 114, 037801 (2015). DOI

2014

  • [16] Liang Dai#, C. Benjamin Renner#, and Patrick S. Doyle*. “Metastable tight knots in semiflexible chains”, Macromolecules 47, 6135 (2014). DOI

  • [15] Liang Dai, Johan R.C. van der Maarel, and Patrick S. Doyle*. “Extended de Gennes Regime of DNA Confined in a Nanochannel”, Macromolecules 47, 2445 (2014). DOI

2013

  • [14] Bing-Rui Zhou, Hanqiao Feng, Hidenori Kato, Liang Dai, Yuedong Yang, Yaoqi Zhou, and Yawen Bai*. “Structural insights into the histone H1-nucleosome complex”, Proceedings of the National Academy of Sciences USA 110, 19390 (2013). DOI

  • [13] C. Zhang, A. Hernandez-Garcia, K. Jiang, Z. Gong, D. Guttula, S. Y. Ng, P. Malar, J. van Kan, Liang Dai, P. Doyle, R. de Vries, and J. van der Maarel*. “Amplified stretch of bottlebrush-coated DNA in nanofluidic channels”, Nucleic Acids Research 41, e189 (2013). DOI

  • [12] C. Zhang#, D. Guttula#, F. Liu, P. Malar, S. Y. Ng, Liang Dai, P. Doyle, J. van Kan, and J. van der Maarel*. “Effect of H-NS on the elongation and compaction of single DNA molecules in a nanospace”, Soft Matter 9, 9593 (2013). DOI

  • [11] Liang Dai, and Patrick S. Doyle*. “Comparisons of a polymer in confinement versus applied force”, Macromolecules 46, 6336 (2013). DOI

  • [10] Liang Dai, Douglas R. Tree, Johan R.C. van der Maarel, Kevin D. Dorfman, and Patrick S. Doyle*. “Revisiting blob theory for DNA diffusivity in slitlike confinement”, Physical Review Letters 110, 168105 (2013). DOI

  • [9] Zhixiu Li, Yuedong Yang, Jian Zhan, Liang Dai, and Yaoqi Zhou*. “Energy functions in de novo protein design: current challenges and future prospects”, Annual Review of Biophysics 42, 315 (2013). DOI

2012

  • [8] Liang Dai, Siow Yee Ng, Patrick S. Doyle, and Johan R.C. van der Maarel*. “Conformation model of back-folding and looping of a single DNA molecule confined inside a nanochannel”, ACS Macro Letters 1, 1046, (2012). DOI

  • [7] Liang Dai, Johan R.C. van der Maarel and Patrick S. Doyle*. “Effect of nanoslit confinement on the knotting probability of circular DNA”, ACS Macro Letters 1, 732, (2012). DOI

  • [6] Liang Dai, Jeremy J. Jones, Johan R.C. van der Maarel and Patrick S. Doyle*. “A systematic study of DNA conformation in slitlike confinement”, Soft Matter 8, 2972, (2012). DOI

2011

  • [5] Liang Dai, and Yaoqi Zhou*. “Characterizing the Existing and Potential Structural Space of Proteins by Large-Scale Multiple Loop Permutations”, Journal of Molecular Biology 408, 585 (2011). DOI

2010

  • [4] Liang Dai, Yuedong Yang, Hyung Rae Kim, and Yaoqi Zhou*. “Improving computational protein design by using structure-derived sequence profile”, Proteins 78, 2338 (2010). DOI

2008

  • [3] Liang Dai, Yuguang Mu, Lars Nordenskiöld, and Johan R.C. van der Maarel*. “Molecular dynamics simulation of multivalent ion mediated DNA attraction”, Physical Review Letters 100, 118301 (2008). DOI

2007

  • [2] Liang Dai, Yuguang Mu, Lars Nordenskiöld, Alain Lapp and Johan R.C. van der Maarel*. “Charge structure and counterion distribution in hexagonal DNA liquid crystal”, Biophysical Journal 92, 947 (2007). DOI

2004

  • [1] Liang Dai*, and Qing Chen. ‘Comment on: “Quantum cooperative games”', Physics Letter A 328, 414 (2004). DOI