# equal contribution; * corresponding author
[54] Dong Hai-Long#, Zhang Chen#, Dai Liang, Zhang Yan, Zhang Xinghua*, Tan Zhi-Jie*, “The origin of different bending stiffness betweendouble-stranded RNA and DNA revealed by magnetic tweezers and simulations”, Nucleic Acids Research, accepted.[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
[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
[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
[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
[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 ——
[25] Liang Dai, and Patrick S. Doyle*.
“Universal knot spectra for confined polymers”,
Macromolecules 51, 6327 (2018).
DOI[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
[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
[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
[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
[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
[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
[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[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[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[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[1] Liang Dai*, and Qing Chen.
‘Comment on: “Quantum cooperative games”’,
Physics Letter A 328, 414 (2004).
DOI