Publications

(^#Equal contribution; ^*Corresponding author; Names in bold represent our group members)

Jump to: Book Chapters, Others, 2024, 2023, 2022, 2021, 2020, 2019, 2018, 2010-2017

Book Chapters

1. Xubo Lin^*. Chapter 21 Molecular Dynamics Simulations of Intrinsically Disordered, Fuzzy Complexes, and Phase Separated Protein States. The Three Functional States of Proteins: Structured, Intrinsically Disordered, and Phase Separated (Edited by Timir Tripathi and Vladimir N. Uversky), Academic Press (Elsevier), 2024, in press.
2. Xubo Lin^*. Chapter 27 Applications of molecular dynamics simulations in drug discovery. Advances in Protein Molecular and Structural Biology Methods (Edited by Timir Tripathi and Vikash Kumar Dubey), Academic Press (Elsevier), 2022, 455-465. (PDF)
3. 李洋, 林绪波, 顾宁. 第8章 纳米材料作用于细胞膜的模拟研究, 生物医用纳米材料对细胞的作用(顾宁、许海燕等编著), 科学出版社, 2014, 246-285.
4. 柳东芳, 熊菲, 林绪波, 柏婷婷, 顾宁. 第6章 磁性纳米材料的表面修饰及其对生物膜的作用, 生物医用磁性纳米材料与器件(顾宁等编著), 化学工业出版社, 2013, 139-164.

Others

1. Siya Zhang#, Hongyin Wang#, Xuan Tao#, Zhongwen Chen, Ilya Levental, Xubo Lin^*. Palmitoylation of PD-L1 Regulates Its Membrane Orientation and Immune Evasion. Submitted.
2. Liuyan Yang#, Mingdong Liu#, Yunhui Liu, Xubo Lin^*, Yu-Zhong Zhang^*, Qing-Tao Shen^*. Structural variability of the mitochondrial protein import gate. Submitted.
3. Xiaoqian Lin, Xubo Lin^*. Regulate PD-L1’s Membrane Orientation Thermodynamics with Hydrophobic Nanoparticles. In preparation.
4. Shuo Ma, Xubo Lin^*. Computer Simulation of Nanoparticle-Mediated Membrane Fusion. In preparation.
5. Hongyan Kang#* Guiqin Yan#, Xiaoqian Lin#, Jiaxin Yin, Jiao Liu, Zhilan Deng, Jiaxin Guo, Jinyan Lu, Xubo Lin, Anqiang Sun, Xiaoyan Deng, Yubo Fan*. The arrangement of the aortic endothelial glycocalyx and its interaction with the low-density lipoproteins (LDL). Submitted.
6. Jin Zhou#, Guanhuier Wang#, Yue Zhou#, Xubo Lin, Zhenmin Zhao, Yumeng Xue, Yang An, Hui Shao, Ying Wang, Sen Hou, Lizhen Wang, Yubo Fan*. Synthetic vesicles with improved cartilage matrix affinity and extended retention promote early osteoarthritis recovery and repair of fullthickness cartilage defects. Submitted.

2024

J51. Xiu Li, Yuan He, Yuxuan Wang, Kaidong Lin, Xubo Lin^*. CHARMM36 All-atom Gas Model for Lipid Nanobubble Simulation. Journal of Chemical Information and Modeling, 2024, 64, 7503-7512. (Supplementary Cover)

J50. Yuxin Sun#, Xuan Tao#, Yaping Han#, Xubo Lin, Rui Tian, Haodong Wang, Pei Chang, Qiming Sun, Liang Ge^*, Min Zhang^*. A dual role of ERGIC-localized Rabs in TMED10-mediated unconventional protein secretion. Nature Cell Biology, 2024, 26, 1077-1092.

J49. Yue Zhou#, Yumeng Xue#, Xubo Lin, Menglong Duan, Weili Hong, Lina Geng Jin Zhou^*, Yubo Fan^*. Smartphone-based Polydiacetylene Colorimetric Sensor for Point-of-care Diagnosis of Bacterial Infections. Smart Materials in Medicine, 2024, 5, 140-152.

2023

J48. 林开东, 林晓倩, 林绪波^*. 靶向PD-L1蛋白的计算机辅助药物筛选, 物理学报, 2023, 72, 240501.

J47. Xiao Wang, Yang Liu, Mingxi Li, Yongxu Ju, Jian Tang, Tiandong Chen, Xubo Lin, Ning Gu, Fang Yang^*. Neuroinflammation catching nanobubbles for microglia-neuron unit modulation against epilepsy. Biomaterials, 2023, 302, 122302.

J46. Yifei Zhou, Xubo Lin^*. Binding Kinetics of Ten Small-Molecule Drug Candidates on SARS-CoV-2 3CLpro Revealed by Biomolecular Simulations. Medicine in Novel Technology and Devices, 2023, 20, 100257. (Selected as Cover and “Editor Choice Paper”)

J45. Xiaoqian Lin#, Kaidong Lin#, Shiqi He, Yue Zhou, Xiu Li, Xubo Lin^*. Membrane Domain Anti-Registration Induces an Intrinsic Transmembrane Potential. Langmuir, 2023, 39, 11621–11627.

J44. Hui Shao, Jin Zhou^*, Xiaoqian Lin, Yue Zhou, Yumeng Xue, Weili Hong, Xubo Lin, Xiaoling Jia^*, Yubo Fan^*. Bio-inspired Peptide-conjugated Liposomes for Enhanced Planktonic Bacteria Killing and Biofilm Eradication. Biomaterials, 2023, 300, 122183.

2022

J43. Jing He, Wen Pang, Bobo Gu, Xubo Lin, Jian Ye^*. The Stiffness-Dependent Tumor Cell Internalization of Liquid Metal Nanoparticles. Nanoscale, 2022, 14, 16902-16917.

J42. Akkaranunt Supakijsilp, Jing He, Xubo Lin^*, Jian Ye^*. Molecular dynamics simulation insights into the cellular uptake of elastic nanoparticles through human pulmonary surfactant. RSC Advances, 2022, 12, 24222-24231.

J41. Xiu Li, Shiying Zhou, Xubo Lin^*. Molecular View on the Impact of DHA Molecules on Physical Properties of Model Cell Membrane. Journal of Chemical Information and Modeling, 2022, 62, 2421-2431. (PDF)

J40. Chan Wang, Ying Liu, Xuecheng Qu, Bojing Shi, Qiang Zheng, Xubo Lin, Shengyu Chao, Changyong Wang, Jin Zhou, Yu Sun, Gengsheng Mao, Zhou Li^*. Ultra‐stretchable and Fast Self‐healing Ionic Hydrogel in Cryogenic Environments for Artificial Nerve Fiber. Advanced Materials, 2022, 34, 2105416. (ESI Highly Cited Papers)

J39. Baocai Ma, Zuoheng Zhang, Yan Li, Xubo Lin^*, Ning Gu^*. Evaluation of Interactions between SARS-CoV-2 RBD and Full-length ACE2 with Coarse-Grained Molecular Dynamics Simulations. Journal of Chemical Information and Modeling, 2022, 62, 936-944. (PDF)

2021

J38. Xiaoqian Lin, Xubo Lin^*. Designing amphiphilic Janus nanoparticles with tunable lipid raft affinity via molecular dynamics simulation. Biomaterials Science, 2021, 9, 8249-8258. (PDF)

J37. Xiaoqian Lin, Xubo Lin^*. Surface Ligand Rigidity Modulates Lipid Raft Affinity of Ultra-small Hydrophobic Nanoparticles: Insights from Molecular Dynamics Simulations. Nanoscale, 2021, 13, 9825-9833. (PDF)

J36. Lingbing Yang, Xubo Lin, Jin Zhou, Sen Hou, Xuewei Bi, Li Yang, Linhao Li^*, Yubo Fan^*. Cell Membrane-Biomimetic Coating via Click-Mediated Liposome Fusion for Mitigating the Foreign-Body Reaction. Biomaterials, 2021, 271, 120768. (PDF)

J35. Xubo Lin^*. Current Advances in Computational and Experimental Approaches for Nanoparticle-Drug Conjugates (Editorial). Current Topics in Medicinal Chemistry, 2021, 21, 90-91. (PDF)

2020

J34. Xubo Lin^*, Alemayehu A. Gorfe^*. Transmembrane Potential of Physiologically Relevant Model Membranes: Effects of Membrane Asymmetry. Journal of Chemical Physics, 2020, 153, 105103. (PDF)

J33. Jiebo Li#, Zhen Chi#, Ruzhan Qin, Li Yan, Xubo Lin, Mingjun Hu^*, Guangcun Shan^*, Hailong Chen^*, Yu-Xiang Weng. Hydrogen Bond Interaction Promotes Flash Energy Transport at MXene-Solvent Interface. Journal of Physical Chemistry C, 2020, 124, 10306-10314.

J32. Fangzhou Hu, Borislav Angelov, Shuang Li, Na Li, Xubo Lin^*, Aihua Zou^*. Single‐molecule study of peptides with the same amino acid composition but different sequences using an aerolysin nanopore. ChemBioChem, 2020, 21, 2467-2473. (PDF)

J31. Min Zhang#, Lei Liu#, Xubo Lin, Ying Li, Shulin Li, Yuxin Sun, Di Zhang, Xiachen Lv, Liang Ge^*. A translocation pathway for vesicle-mediated unconventional protein secretion. Cell, 2020, 181, 637-652.e15. (PDF)

J30. Xiaoqian Lin#, Xiu Li#, Xubo Lin^*. A Review on Applications of Computational Methods in Drug Screening and Design. Molecules. 2020, 25, 1375. (Invited Review, ESI Highly Cited Papers) (PDF)

J29. Xiaoqian Lin, Xubo Lin^*, Ning Gu^*. Optimization of hydrophobic nanoparticles to better target lipid rafts with molecular dynamics simulations. Nanoscale, 2020, 12, 4101-4109. (PDF)

2019

J28. Jiebo Li#, Qi Zhang#, Li Yan, Guorong Wu, Mingjun Hu^*, Xubo Lin^*, Kaijun Yuan^*, Xueming Yang. Ultrafast Flash Energy Conductance at MXene-Surfactant Interface and Its Molecular Origins. Advanced Materials Interfaces, 2019, 6, 1901461. (PDF)

J27. Siya Zhang, Xubo Lin^*. Lipid Acyl Chain cis Double Bond Position Modulates Membrane Domain Registration/Anti-registration. Journal of the American Chemical Society, 2019, 141, 15884-15890. (F1000Prime Recommended) (PDF)

J26. Fujia Tian, Xubo Lin^*, Russell P. Valle, Yi Y. Zuo^*, Ning Gu^*. Poly(amidoamine) Dendrimer as a Respiratory Nanocarrier: Insights from Experiments and Molecular Dynamics Simulations. Langmuir, 2019, 35, 5364-5371. (Supplementary Cover) (PDF)

J25. Xubo Lin^* and Alemayehu A. Gorfe^*. Understanding Membrane Domain-Partitioning Thermodynamics of Transmembrane Domains with Potential of Mean Force Calculations. Journal of Physical Chemistry B, 2019, 123(5), 1009-1016. (PDF)

2018

J24. Yang Wang#, Cecylia Severin Lupala#, Haiguang Liu*, Xubo Lin^*. Identification of Drug Binding Sites and Action Mechanisms with Molecular Dynamics Simulations. Current Topics in Medicinal Chemistry, 2018, 18, 2268-2277. (Invited Review) (PDF)

J23. Xubo Lin, Hongyin Wang#, Zhichao Lou#, Meng Cao#, Zuoheng Zhang, Ning Gu^*. Roles of PIP2 in the membrane binding of MIM I-BAR: insights from molecular dynamics simulations. FEBS Letters, 2018, 592, 2533-2542. (PDF)

J22. Xubo Lin, Vinay Nair, Yong Zhou, Alemayehu A. Gorfe^*. Membrane Potential and Dynamics in a Ternary Lipid Mixture: Insights from Molecular Dynamics Simulations. Physical Chemistry Chemical Physics, 2018, 20, 15841-15851. (PDF)

J21. Xubo Lin, Alemayehu A. Gorfe^*, Ilya Levental^*. Protein Partitioning into Ordered Membrane Domains: Insights from Simulations. Biophysical Journal, 2018, 114, 1936-1944. (PDF)

2010-2017:

J20. Joseph H. Lorent, Barbara Diaz-Rohrer, Xubo Lin, Kevin Spring, Alemayehu A. Gorfe, Kandice R. Levental, Ilya Levental*. Structural determinants and functional consequences of protein affinity for membrane rafts. Nature Communications, 2017, 8, 1219.

J19. Zuoheng Zhang#, Xubo Lin#, Ning Gu*. Effects of temperature and PEG grafting density on the translocation of PEGylated nanoparticles across asymmetric lipid membrane. Colloids and Surfaces B: Biointerfaces, 2017, 160, 92-100.

J18. Yue Zhang, Zhichao Lou, Xubo Lin, Qiwei Wang, Meng Cao, Ning Gu*. Optimizing purification process of MIM-I-BAR domain by introducing atomic force microscope and dynamics simulations. Colloids and Surfaces B: Biointerfaces, 2017, 157, 391-397.

J17. Hui Ding, Xianhua Gui, Xubo Lin, Ruhua Chen, Tieliang Ma, Yunlu Sheng, Hourong Cai, Yan Fen*. The Prognostic Effect of MAC30 Expression on Patients with Non-Small Cell Lung Cancer Receiving Adjuvant Chemotherapy. Technology in Cancer Research & Treatment, 2017, 16, 645-653.

J16. Xubo Lin, Joseph H. Lorent, Allison D. Skinkle, Kandice R. Levental, M. Neal Waxham, Alemayehu A. Gorfe, Ilya Levental. Domain Stability in Biomimetic Membranes Driven by Lipid Polyunsaturation. Journal of Physical Chemistry B, 2016, 120, 11930-11941.

J15. Xubo Lin#, Siya Zhang#, Hui Ding, Ilya Levental, Alemayehu A. Gorfe. The aliphatic chain of cholesterol modulates bilayer interleaflet coupling and domain registration. FEBS Letters, 2016, 590, 3368-3374.

J14. Dandan Sun, Xubo Lin, Zuoheng Zhang, Ning Gu*. Impact of Shock-induced Lipid Nanobubble Collapse on a Phospholipid Membrane. Journal of Physical Chemistry C, 2016, 120, 18803-18810.

J13. Kandice R. Levental, Joseph H. Lorent, Xubo Lin, Allison Skinkle, Michal Surma, Emily Stockenbojer, Alemayehu A. Gorfe, Ilya Levental*. Polyunsaturated lipids regulate membrane domain stability by tuning membrane order. Biophysical Journal, 2016, 110, 1800-1810.

J12. Hui Ding, Xianhua Gui, Xubo Lin, Ruhua Chen, Hourong Cai, Yan Fen, Yunlu Sheng. Prognostic Value of MAC30 Expression in Human Pure Squamous Cell Carcinomas of the Lung. Asian Pacific Journal of Cancer Prevention, 2016, 17, 2705-2710.

J11. Ruhua Chen, Yan Fen, Xubo Lin, Tieliang Ma, Hourong Cai, Hui Ding*. Overexpression of MAC30 is Resistant to Platinum-Based Chemotherapy in Patients with Non-Small Cell Lung Cancer. Technology in Cancer Research & Treatment, 2016, 15, 815-820.

J10. Xubo Lin, Zhenlong Li, Alemayehu A. Gorfe*. Reversible Effects of Peptide Concentration and Lipid Composition on H-Ras Lipid Anchor Clustering. Biophysical Journal, 2015, 109, 2467-2470.

J9. Xubo Lin, Yi Y. Zuo, Ning Gu*. Shape Affects the Interactions of Nanoparticles with Pulmonary Surfactant. Science China Materials, 2015, 58, 28-37.

J8. Meng Cao, Ziqi Ye, Xubo Lin, Ning Gu*. 转移消失蛋白研究进展. Chinese Science Bulletin, 2015, 60, 356-366. (In Chinese)

J7. Xubo Lin, Ning Gu*. Surface properties of encapsulating hydrophobic nanoparticles regulate the main phase transition temperature of lipid bilayers: A simulation study. Nano Research, 2014, 7, 1195-1204.

J6. Xubo Lin, Tingting Bai, Yi Y. Zuo, Ning Gu*. Promote Potential Applications of Nanoparticles as Respiratory Drug Carrier: Insights from Molecular Dynamics Simulations. Nanoscale, 2014, 6, 2759-2767.

J5. Dandan Sun, Xubo Lin, Ning Gu*. Cholesterol Affects C60 Translocation across Lipid Bilayers. Soft Matter, 2014, 10, 2160-2168.

J4. Ning Gu*, Xubo Lin. 医学纳米颗粒对类细胞膜作用的仿真研究进展. Progress in Biochemistry and Biophysics, 2013, 40, 918-924.

J3. Xubo Lin, Changling Wang, Meng Wang, Kun Fang and Ning Gu*. Computer Simulation of the Effects of Nanoparticles’ Adsorption on the Properties of Supported Lipid Bilayer. Journal of Physical Chemistry C, 2012, 116, 17960-17968.

J2. Xubo Lin, Yang Li and Ning Gu*. Molecular Dynamics Simulations of the Interactions of Charge-neutral PAMAM Dendrimers with Pulmonary Surfactant. Soft Matter, 2011, 7, 3882-3888 (Selected by Virtual Journal of Biological Physics Research, 2011, Volume 21, Issue 8; Reported by Obesity, Fitness and Wellness Week and HighBeam Research)

J1. Xubo Lin, Yang Li, and Ning Gu*. Nanoparticle’s Size Effect on Its Translocation across a Lipid Bilayer: A Molecular Dynamics Simulation. Journal of Computational and Theoretical Nanoscience, 2010, 7, 269-276.