Study of molecular transport through a single nanopore in the membrane of a giant unilamellar vesicle using COMSOL simulation

  • Mohammad Abu Sayem KaralEmail author
  • Md. Kamrul Islam
  • Zaid Bin Mahbub
Original Article


The antimicrobial peptide (AMP) magainin 2 induces nanopores in the lipid membranes of giant unilamellar vesicles (GUVs), as observed by the leakage of water-soluble fluorescent probes from the inside to the outside of GUVs through the pores. However, molecular transport through a single nanopore has not been investigated in detail yet and is studied in the present work by simulation. A single pore was designed in the membrane of a GUV using computer-aided design software. Molecular transport, from the outside to the inside of GUV through the nanopore, of various fluorescent probes such as calcein, Texas-Red Dextran 3000 (TRD-3k), TRD-10k and TRD-40k was then simulated. The effect of variation in GUV size (diameter) was also investigated. A single exponential growth function was fitted to the time course of the fluorescence intensity inside the GUV and the corresponding rate constant of molecular transport was calculated, which decreases with an increase in the size of fluorescent probe and also with an increase in the size of GUV. The rate constant found by simulation agrees reasonably well with reported experimental results for inside-to-outside probe leakage. Based on Fick’s law of diffusion an analytical treatment is developed for the rate constant of molecular transport that supports the simulation results. These investigations contribute to a better understanding of the mechanism of pore formation using various membrane-active agents in the lipid membranes of vesicles and the biomembranes of cells.


Molecular transport Rate constant of molecular transport COMSOL simulation Nanopore Lipid membrane of GUV Fluorescent probes 



This work was supported partly by the Grants from Directorate of Advisory, Extension and Research Services (CASR) of BUET (R-01/2017/2310-73, 316-4), Ministry of Science and Technology (39.00.0000.’s-370, 39.00.0000.’s-450, 39.00.0000.’s-7), Ministry of Education (7.20.0000.004.033.020. 2016.1478) and ICT Division (39.00.0000. of Bangladesh to Mohammad Abu Sayem Karal. The authors are thankful to Abdul Halim Bhuiyan, Assistant Professor, Department of Mathematics, BUET for valuable discussion.

Compliance with ethical standards

Conflict of interest

The authors declare no conflict of interest.

Supplementary material

249_2019_1412_MOESM1_ESM.docx (158 kb)
Supplementary material 1 (DOCX 157 kb)


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Copyright information

© European Biophysical Societies' Association 2019

Authors and Affiliations

  • Mohammad Abu Sayem Karal
    • 1
    Email author
  • Md. Kamrul Islam
    • 1
  • Zaid Bin Mahbub
    • 2
  1. 1.Department of PhysicsBangladesh University of Engineering and TechnologyDhakaBangladesh
  2. 2.Department of Mathematics and PhysicsNorth South UniversityDhakaBangladesh

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