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Analysis of single-molecule diffusion movement in cell membrance based on unsupervised learning methods: Different effects of cholesterol on flowability of model membrane and living cell membrane

Tan Jin-Peng Zhang Wan-Ting Xu Cheng Lu Xue-Mei Zhu Wen-Sheng Yang Kai Yuan Bing

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Analysis of single-molecule diffusion movement in cell membrance based on unsupervised learning methods: Different effects of cholesterol on flowability of model membrane and living cell membrane

Tan Jin-Peng, Zhang Wan-Ting, Xu Cheng, Lu Xue-Mei, Zhu Wen-Sheng, Yang Kai, Yuan Bing
cstr: 32037.14.aps.73.20240915
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  • Single molecular tracking is a valuable approach to investigate the dynamic processes and molecular interactions in soft matter systems, particularly in biological systems. However, understanding the complexity of single molecule motion behaviors in biological systems remains a significant challenge. To address this issue, we propose a two-step classification method based on unsupervised learning to efficiently identify and classify single molecule trajectories. Firstly, we employ an entropy-constrained least square method to distinguish between confined (e.g., immobile) and unconfined diffusion trajectories. Subsequently, statistical tests are utilized to categorize the unconfined trajectories into different diffusion modes such as sub-diffusion, normal diffusion, and super-diffusion.By applying this method, we analyze the diffusion motion of single molecules in both DOPC model cell membranes and living cell membranes while uncovering their distinct responses to cholesterol composition. Our findings demonstrate that both model membranes and living cell membranes exhibit diverse molecular diffusion modes. Specifically, in the DOPC model membrane system, the presence of cholesterol components impedes lipid diffusion within the membrane. The degree of inhibition is positively correlated with the amount of cholesterol present. For instance, as the cholesterol content in the membrane increases from 0 to 20% (DOPC:Chol = 4∶1) and 50% (DOPC:Chol = 1∶1), there is an increase in the proportion of molecules, exhibiting confined diffusion and sub-diffusion (from 55% to 45%), while there is a decrease in the proportion of molecules, displaying normal diffusion and super-diffusion (from 45% to 35%). The ensemble diffusion coefficient of molecules in the membrane significantly decreases, which can be attributed to both a decrease in velocity among fast-moving molecules. Interestingly, after using MeβCD to remove cholesterol, the single-molecule mobility within the DOPC/Chol composite membrane system is restored to a level similar to that of the pure DOPC membrane.Conversely, in the living cell membrane system, the diffusion coefficient values of molecules are significantly lower than those observed in the model membrane system; furthermore, the removal of cholesterol further slows down the molecular diffusion rate. This study contributes to understanding the intricacies of biomolecular motility and its dependence on environmental factors from a perspective of single molecular motion.
      Corresponding author: Yang Kai, yangkai@suda.edu.cn ; Yuan Bing, yuanbing@sslab.org.cn
    • Funds: Project supported by the National Natural Science Foundation of China (Grant Nos. 12274307, 32230063, 12347102, 22307090, 22203059), the Basic and Applied Basic Research Foundation of Guangdong Province, China (Grant No. 2023A1515011610), the Natural Science Foundation of Jiangsu Province, China (Grant No. BK20210100), and the Program of Jiangsu Key Laboratory of Frontier Material Physics and Devices, China (Grant No. KJS2131).
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    Jacobson K, Liu P, Lagerholm B C 2019 Cell 177 806Google Scholar

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    He W, Song H, Su Y, et al. 2016 Nat. Commun. 7 11701Google Scholar

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    Golan Y, Sherman E 2017 Nat. Commun. 8 15851Google Scholar

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    Subczynski W K, Pasenkiewicz-Gierula M, Widomska J, Mainali L, Raguz M 2017 Cell Biochem. Biophys. 75 369Google Scholar

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    van Meer G, Voelker D R, Feigenson G W 2008 Nat. Rev. Mol. Cell Biol. 9 112Google Scholar

    [6]

    Liu Y, Zheng X, Guan D, Jiang X, Hu G 2022 ACS Nano 16 16054Google Scholar

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    Lyman E 2021 Biophys. J. 120 1777Google Scholar

    [8]

    Zhang X, Barraza K M, Beauchamp J L 2018 P. Natl. Acad. Sci. USA 115 3255Google Scholar

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    Chakraborty S, Doktorova M, Molugu T R, et al. 2020 P. Natl. Acad. Sci. USA 117 21896Google Scholar

    [10]

    Pohnl M, Trollmann M F W, Bockmann R A 2023 Nat. Commun. 14 8038Google Scholar

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    Fernandez-Perez E J, Sepulveda F J, Peters C, et al. 2018 Front. Aging Neurosci. 10 226Google Scholar

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    Doole F T, Kumarage T, Ashkar R, Brown M F 2022 J. Membr. Biol. 255 385Google Scholar

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    Byfield F J, Aranda-Espinoza H, Romanenko V G, Rothblat G H, Levitan I 2004 Biophys. J. 87 3336Google Scholar

    [14]

    Yang S T, Kreutzberger A J B, Lee J, Kiessling V, Tamm L K 2016 Chem. Phys. Lipids 199 136Google Scholar

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    Norregaard K, Metzler R, Ritter C M, Berg-Sorensen K, Oddershede L B 2017 Chem. Rev. 117 4342Google Scholar

    [16]

    Ge F, Du Y, He Y 2022 ACS Nano 16 5325Google Scholar

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    Chen P Y, Yue H, Zhai X B, Huang Z H, Ma G H, Wei W, Yan L T 2019 Sci. Adv. 5 eaaw3192Google Scholar

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    Jeon J H, Javanainen M, Martinez-Seara H, Metzler R, Vattulainen I 2016 Phys. Rev. X 6 021006Google Scholar

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    Xu C, Yang K, Yuan B 2023 J. Phys. Chem. Lett. 14 854Google Scholar

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    Xu C, Ma W, Wang K, He K, Chen Z, Liu J, Yang K, Yuan B 2020 J. Phys. Chem. Lett. 11 4834Google Scholar

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    Pinholt H D, Bohr S S R, Iversen J F, Boomsma W, Hatzakis N S 2021 P. Natl. Acad. Sci. USA 118 e2104624118Google Scholar

    [22]

    Muñoz-Gil G, Garcia-March M A, Manzo C, Martín-Guerrero J D, Lewenstein M 2020 New J. Phys. 22 013010Google Scholar

    [23]

    Cherstvy A G, Thapa S, Wagner C E, Metzler R 2019 Soft Matter 15 2526Google Scholar

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    Granik N, Weiss L E, Nehme E, Levin M, Chein M, Perlson E, Roichman Y, Shechtman Y 2019 Biophys. J. 117 185Google Scholar

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    Janczura J, Kowalek P, Loch-Olszewska H, Szwabinski J, Weron A 2020 Phys. Rev. E 102 032402Google Scholar

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    Barkai E, Garini Y, Metzler R 2012 Phys. Today 65 29Google Scholar

    [27]

    Krapf D, Metzler R 2019 Phys. Today 72 48Google Scholar

    [28]

    Wu J F, Xu C, Ye Z F, Chen H B, Wang Y P, Yang K, Yuan B 2023 Small 19 2301713Google Scholar

    [29]

    Yamamoto E, Akimoto T, Kalli A C, Yasuoka K, Sansom M S P 2017 Sci. Adv. 3 e1601871Google Scholar

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    Feder T J, Brust-Mascher I, Slattery J P, Baird B, Webb W W 1996 Biophys. J. 70 2767Google Scholar

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    Briane V, Kervrann C, Vimond M 2018 Phys. Rev. E 97 062121Google Scholar

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    Lanoiselée Y, Sikora G, Grzesiek A, Grebenkov D S, Wylomanska A 2018 Phys. Rev. E 98 062139Google Scholar

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    Sikora G, Teuerle M, Wylomanska A, Grebenkov D 2017 Phys. Rev. E 96 022132Google Scholar

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    Saxton M J, Jacobson K 1997 Annu. Rev. Biophys. Biomol. Struct. 26 373Google Scholar

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    Kusumi A, Sako Y, Yamamoto M 1993 Biophys. J. 65 2021Google Scholar

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    Saxton M J 1993 Biophys. J. 64 1766Google Scholar

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    Shannon C E 1948 Bell Syst. Tech. J. 27 379Google Scholar

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    Wright S J, Tenny M J 2004 Siam J. Optim. 14 1074Google Scholar

    [39]

    Raja M A Z, Ahmed U, Zameer A, Kiani A K, Chaudhary N I 2019 Neural. Comput. Appl. 31 447Google Scholar

    [40]

    Zhang Y, Yao F, Iu H H C, Fernando T, Wong K P 2013 J. Mod. Power Syst. Clean Energy 1 231Google Scholar

    [41]

    Weron A, Janczura J, Boryczka E, Sungkaworn T, Calebiro D 2019 Phys. Rev. E 99 042149Google Scholar

    [42]

    Hubicka K, Janczura J 2020 Phys. Rev. E 101 022107Google Scholar

    [43]

    Xu R, Zhang W T, Jin T, Tu W, Xu C, Wei Y, Han W, Yang K, Yuan B 2024 ACS Appl. Mater. Interfaces 16 6813Google Scholar

    [44]

    Li L, Ji J, Song F, Hu J 2023 J. Mol. Biol. 435 167787Google Scholar

    [45]

    Li L, Hou R H, Shi X H, et al. 2024 Commun. Phys. 7 174Google Scholar

    [46]

    Gao J, Hou R, Li L, Hu J 2021 Front. Mol. Biosci. 8 811711Google Scholar

    [47]

    陆越, 马建兵, 滕翠娟, 陆颖, 李明, 徐春华 2018 物理学报 67 088201Google Scholar

    Lu Y, Ma J B, Teng C J, Lu Y, Li M, Xu C H 2018 Acta Phys. Sin. 67 088201Google Scholar

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  • 图 1  单分子扩散运动的不同模式 (a)模拟运动模型的MSD曲线, 即定向扩散(蓝色)、正常扩散(红色)、异常扩散(绿色)和受限扩散(黑色), 横坐标为滞后时间(lag time); (b)采用“两步归类法”对单分子轨迹进行识别和分类的步骤, 第一步区分受限扩散与非受限扩散, 第二步将非受限扩散进一步区分

    Figure 1.  Different modes of single-molecule diffusion. (a) Simulated mean square displacement (MSD) curves depicting directed diffusion (blue), normal diffusion (red), anomalous diffusion (green), and confined diffusion (black). (b) The “two-step classification method” employed to identify and classify single-molecule trajectories: the first step involves distinguishing between confined and unconfined diffusion, followed by further differentiation of unconfined diffusion in the second step.

    图 2  不同模型膜体系内单分子扩散运动分析, 即利用“两步归类法”将其分为受限扩散(Confined diffusion)、亚扩散(Sub-diffusion)、正常扩散(Normal diffusion)、超扩散(Super-diffusion) 4个子群, 分别计算其单分子轨迹的时间平均MSD并作出其分布. 轨迹数目见表1

    Figure 2.  Analysis of single lipid diffusion in various model membrane systems using the “two-step classification method”. Trajectories were categorized into four subgroups, namely confined diffusion, sub-diffusion, normal diffusion, and super-diffusion. The time-averaged MSD of individual trajectories was calculated to obtain the distribution. The number of trajectories is presented in Table 1.

    图 3  B16活细胞膜(MeβCD处理前或处理后)内单分子扩散运动分析, 即利用“两步归类法”将其分为受限扩散(Confined diffusion)、亚扩散(Sub-diffusion)、正常扩散(Normal diffusion) 3个子群, 分别计算其单分子轨迹的时间平均MSD并作出其分布, 轨迹数目见表2

    Figure 3.  Analysis of single-molecule diffusion in live cell membranes (before or after MeβCD treatment). This analysis employs a two-step classification method to divide the data into subgroups of confined diffusion, sub-diffusion, and normal diffusion. The time-averaged MSD is calculated for individual trajectories and its distribution is plotted. The number of trajectories analyzed is provided in Table 2.

    图 4  不同体系内DLα值分布, 包括纯DOPC膜(包含1324条轨迹)、DOPC∶Chol = 1∶1混合膜(2347条轨迹)、活细胞膜经MeβCD处理之前(1436条轨迹)和之后(784条轨迹), 其中插图中横坐标以对数形式显示

    Figure 4.  Distribution of DL and α values in different systems: pure DOPC membrane (1324 trajectories), DOPC∶Chol = 1∶1 mixed membrane (2347 trajectories), living cell membrane before MeβCD treatment (1436 trajectories), and after MeβCD treatment (784 trajectories). The horizontal coordinate is presented logarithmically in the inset.

    表 1  不同模型膜体系内单脂质分子轨迹分类及相应的系综扩散系数和异常指数数值, 其中轨迹长度为60帧

    Table 1.  Classification of single lipid trajectories in different model membrane systems and corresponding ensemble diffusion coefficient and anomaly index values. The trajectory length is 60 frames.

    Subgroup Control +MeβCD
    DOPC DOPC:CHOL
    = 4∶1
    DOPC:CHOL
    = 1∶1
    DOPC DOPC:CHOL
    = 4∶1
    DOPC:CHOL
    = 1∶1
    Trajectory
    number
    Confined 282 383 497 293 334 330
    Sub-diffusion 943 1143 1036 947 799 811
    Normal diffusion 318 294 290 305 200 207
    Super-diffusion 667 577 524 647 448 449
    Proportion/% Confined 12.76 15.98 21.18 13.37 18.75 18.36
    Sub-diffusion 42.67 47.68 44.14 43.20 44.86 45.13
    Normal diffusion 14.39 12.27 12.36 13.91 11.23 11.52
    Super-diffusion 30.18 24.07 22.33 29.52 25.15 24.99
    Diffusion coefficient
    DL/(μm2·s–1)
    Confined 0.045 0.032 0.029 0.064 0.034 0.061
    Sub-diffusion 1.086 0.582 0.308 0.805 0.784 0.717
    Normal diffusion 2.421 1.581 0.870 2.100 2.051 1.781
    Super-diffusion 4.149 3.211 1.444 3.908 3.650 3.381
    Anomaly
    index (α)
    Confined 0.116 0.094 0.068 0.207 0.099 0.171
    Sub-diffusion 0.709 0.629 0.512 0.629 0.635 0.614
    Normal diffusion 0.909 0.869 0.916 0.948 0.910 0.874
    Super-diffusion 1.133 1.103 1.178 1.141 1.132 1.132
    DownLoad: CSV

    表 2  经MeβCD去除胆固醇前后活细胞膜内单分子轨迹分类及相应的系综扩散系数和异常指数数值, 其中轨迹长度为20帧

    Table 2.  Classification of single-molecule trajectory in living cell membranes before and after cholesterol depletion by MeβCD, along with corresponding ensemble-averaged diffusion coefficient and anomaly index values. The trajectory length is 20 frames.

    Subgroup Control +MeβCD
    Trajectory
    number
    Confined 452 304
    Sub-diffusion 645 377
    Normal diffusion 339 103
    Proportion/% Confined 31.48 38.78
    Sub-diffusion 44.92 48.09
    Normal diffusion 23.61 13.14
    Diffusion coefficient
    DL/(μm2·s–1)
    Confined 0.017 0.011
    Sub-diffusion 0.069 0.040
    Normal diffusion 0.465 0.260
    Anomaly
    index (α)
    Confined 0.146 0.095
    Sub-diffusion 0.437 0.461
    Normal diffusion 0.983 0.861
    DownLoad: CSV
  • [1]

    Jacobson K, Liu P, Lagerholm B C 2019 Cell 177 806Google Scholar

    [2]

    He W, Song H, Su Y, et al. 2016 Nat. Commun. 7 11701Google Scholar

    [3]

    Golan Y, Sherman E 2017 Nat. Commun. 8 15851Google Scholar

    [4]

    Subczynski W K, Pasenkiewicz-Gierula M, Widomska J, Mainali L, Raguz M 2017 Cell Biochem. Biophys. 75 369Google Scholar

    [5]

    van Meer G, Voelker D R, Feigenson G W 2008 Nat. Rev. Mol. Cell Biol. 9 112Google Scholar

    [6]

    Liu Y, Zheng X, Guan D, Jiang X, Hu G 2022 ACS Nano 16 16054Google Scholar

    [7]

    Lyman E 2021 Biophys. J. 120 1777Google Scholar

    [8]

    Zhang X, Barraza K M, Beauchamp J L 2018 P. Natl. Acad. Sci. USA 115 3255Google Scholar

    [9]

    Chakraborty S, Doktorova M, Molugu T R, et al. 2020 P. Natl. Acad. Sci. USA 117 21896Google Scholar

    [10]

    Pohnl M, Trollmann M F W, Bockmann R A 2023 Nat. Commun. 14 8038Google Scholar

    [11]

    Fernandez-Perez E J, Sepulveda F J, Peters C, et al. 2018 Front. Aging Neurosci. 10 226Google Scholar

    [12]

    Doole F T, Kumarage T, Ashkar R, Brown M F 2022 J. Membr. Biol. 255 385Google Scholar

    [13]

    Byfield F J, Aranda-Espinoza H, Romanenko V G, Rothblat G H, Levitan I 2004 Biophys. J. 87 3336Google Scholar

    [14]

    Yang S T, Kreutzberger A J B, Lee J, Kiessling V, Tamm L K 2016 Chem. Phys. Lipids 199 136Google Scholar

    [15]

    Norregaard K, Metzler R, Ritter C M, Berg-Sorensen K, Oddershede L B 2017 Chem. Rev. 117 4342Google Scholar

    [16]

    Ge F, Du Y, He Y 2022 ACS Nano 16 5325Google Scholar

    [17]

    Chen P Y, Yue H, Zhai X B, Huang Z H, Ma G H, Wei W, Yan L T 2019 Sci. Adv. 5 eaaw3192Google Scholar

    [18]

    Jeon J H, Javanainen M, Martinez-Seara H, Metzler R, Vattulainen I 2016 Phys. Rev. X 6 021006Google Scholar

    [19]

    Xu C, Yang K, Yuan B 2023 J. Phys. Chem. Lett. 14 854Google Scholar

    [20]

    Xu C, Ma W, Wang K, He K, Chen Z, Liu J, Yang K, Yuan B 2020 J. Phys. Chem. Lett. 11 4834Google Scholar

    [21]

    Pinholt H D, Bohr S S R, Iversen J F, Boomsma W, Hatzakis N S 2021 P. Natl. Acad. Sci. USA 118 e2104624118Google Scholar

    [22]

    Muñoz-Gil G, Garcia-March M A, Manzo C, Martín-Guerrero J D, Lewenstein M 2020 New J. Phys. 22 013010Google Scholar

    [23]

    Cherstvy A G, Thapa S, Wagner C E, Metzler R 2019 Soft Matter 15 2526Google Scholar

    [24]

    Granik N, Weiss L E, Nehme E, Levin M, Chein M, Perlson E, Roichman Y, Shechtman Y 2019 Biophys. J. 117 185Google Scholar

    [25]

    Janczura J, Kowalek P, Loch-Olszewska H, Szwabinski J, Weron A 2020 Phys. Rev. E 102 032402Google Scholar

    [26]

    Barkai E, Garini Y, Metzler R 2012 Phys. Today 65 29Google Scholar

    [27]

    Krapf D, Metzler R 2019 Phys. Today 72 48Google Scholar

    [28]

    Wu J F, Xu C, Ye Z F, Chen H B, Wang Y P, Yang K, Yuan B 2023 Small 19 2301713Google Scholar

    [29]

    Yamamoto E, Akimoto T, Kalli A C, Yasuoka K, Sansom M S P 2017 Sci. Adv. 3 e1601871Google Scholar

    [30]

    Feder T J, Brust-Mascher I, Slattery J P, Baird B, Webb W W 1996 Biophys. J. 70 2767Google Scholar

    [31]

    Briane V, Kervrann C, Vimond M 2018 Phys. Rev. E 97 062121Google Scholar

    [32]

    Lanoiselée Y, Sikora G, Grzesiek A, Grebenkov D S, Wylomanska A 2018 Phys. Rev. E 98 062139Google Scholar

    [33]

    Sikora G, Teuerle M, Wylomanska A, Grebenkov D 2017 Phys. Rev. E 96 022132Google Scholar

    [34]

    Saxton M J, Jacobson K 1997 Annu. Rev. Biophys. Biomol. Struct. 26 373Google Scholar

    [35]

    Kusumi A, Sako Y, Yamamoto M 1993 Biophys. J. 65 2021Google Scholar

    [36]

    Saxton M J 1993 Biophys. J. 64 1766Google Scholar

    [37]

    Shannon C E 1948 Bell Syst. Tech. J. 27 379Google Scholar

    [38]

    Wright S J, Tenny M J 2004 Siam J. Optim. 14 1074Google Scholar

    [39]

    Raja M A Z, Ahmed U, Zameer A, Kiani A K, Chaudhary N I 2019 Neural. Comput. Appl. 31 447Google Scholar

    [40]

    Zhang Y, Yao F, Iu H H C, Fernando T, Wong K P 2013 J. Mod. Power Syst. Clean Energy 1 231Google Scholar

    [41]

    Weron A, Janczura J, Boryczka E, Sungkaworn T, Calebiro D 2019 Phys. Rev. E 99 042149Google Scholar

    [42]

    Hubicka K, Janczura J 2020 Phys. Rev. E 101 022107Google Scholar

    [43]

    Xu R, Zhang W T, Jin T, Tu W, Xu C, Wei Y, Han W, Yang K, Yuan B 2024 ACS Appl. Mater. Interfaces 16 6813Google Scholar

    [44]

    Li L, Ji J, Song F, Hu J 2023 J. Mol. Biol. 435 167787Google Scholar

    [45]

    Li L, Hou R H, Shi X H, et al. 2024 Commun. Phys. 7 174Google Scholar

    [46]

    Gao J, Hou R, Li L, Hu J 2021 Front. Mol. Biosci. 8 811711Google Scholar

    [47]

    陆越, 马建兵, 滕翠娟, 陆颖, 李明, 徐春华 2018 物理学报 67 088201Google Scholar

    Lu Y, Ma J B, Teng C J, Lu Y, Li M, Xu C H 2018 Acta Phys. Sin. 67 088201Google Scholar

    [48]

    Gao J, Hou R, Hu W, et al. 2024 J. Phys. Chem. B 128 4735Google Scholar

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  • supplement 2024年73卷188702补充材料.pdf supplement
    supplement 2024年73卷188702补充材料-模型膜和活细胞膜内单分子运动轨迹的扩散系数、异常指数、位移的三维分布视频.gif supplement
Metrics
  • Abstract views:  2026
  • PDF Downloads:  84
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Publishing process
  • Received Date:  02 July 2024
  • Accepted Date:  31 July 2024
  • Available Online:  15 August 2024
  • Published Online:  20 September 2024

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