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Mesoscale simulation of biomembranes with FreeDTS

Author

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  • Weria Pezeshkian

    (University of Copenhagen)

  • John H. Ipsen

    (University of Southern Denmark, Campusvej 55)

Abstract

We present FreeDTS software for performing computational research on biomembranes at the mesoscale. In this software, a membrane is represented by a dynamically triangulated surface equipped with vertex-based inclusions to integrate the effects of integral and peripheral membrane proteins. Several algorithms are included in the software to simulate complex membranes at different conditions such as framed membranes with constant tension, vesicles and high-genus membranes with various fixed volumes or constant pressure differences and applying external forces to membrane regions. Furthermore, the software allows the user to turn off the shape evolution of the membrane and focus solely on the organization of proteins. As a result, we can take realistic membrane shapes obtained from, for example, cryo-electron tomography and backmap them into a finer simulation model. In addition to many biomembrane applications, this software brings us a step closer to simulating realistic biomembranes with molecular resolution. Here we provide several interesting showcases of the power of the software but leave a wide range of potential applications for interested users.

Suggested Citation

  • Weria Pezeshkian & John H. Ipsen, 2024. "Mesoscale simulation of biomembranes with FreeDTS," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-44819-w
    DOI: 10.1038/s41467-024-44819-w
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    References listed on IDEAS

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    1. Theresa Louise Boye & Kenji Maeda & Weria Pezeshkian & Stine Lauritzen Sønder & Swantje Christin Haeger & Volker Gerke & Adam Cohen Simonsen & Jesper Nylandsted, 2017. "Annexin A4 and A6 induce membrane curvature and constriction during cell membrane repair," Nature Communications, Nature, vol. 8(1), pages 1-11, December.
    2. Alexander Mühleip & Rasmus Kock Flygaard & Rozbeh Baradaran & Outi Haapanen & Thomas Gruhl & Victor Tobiasson & Amandine Maréchal & Vivek Sharma & Alexey Amunts, 2023. "Structural basis of mitochondrial membrane bending by the I–II–III2–IV2 supercomplex," Nature, Nature, vol. 615(7954), pages 934-938, March.
    3. Hanumantha Rao Vutukuri & Masoud Hoore & Clara Abaurrea-Velasco & Lennard Buren & Alessandro Dutto & Thorsten Auth & Dmitry A. Fedosov & Gerhard Gompper & Jan Vermant, 2020. "Active particles induce large shape deformations in giant lipid vesicles," Nature, Nature, vol. 586(7827), pages 52-56, October.
    4. Mohsen Sadeghi & Frank Noé, 2020. "Large-scale simulation of biomembranes incorporating realistic kinetics into coarse-grained models," Nature Communications, Nature, vol. 11(1), pages 1-13, December.
    5. Larissa Heinrich & Davis Bennett & David Ackerman & Woohyun Park & John Bogovic & Nils Eckstein & Alyson Petruncio & Jody Clements & Song Pang & C. Shan Xu & Jan Funke & Wyatt Korff & Harald F. Hess &, 2021. "Whole-cell organelle segmentation in volume electron microscopy," Nature, Nature, vol. 599(7883), pages 141-146, November.
    6. Weria Pezeshkian & Melanie König & Tsjerk A. Wassenaar & Siewert J. Marrink, 2020. "Backmapping triangulated surfaces to coarse-grained membrane models," Nature Communications, Nature, vol. 11(1), pages 1-9, December.
    7. Rikhia Ghosh & Vahid Satarifard & Reinhard Lipowsky, 2023. "Different pathways for engulfment and endocytosis of liquid droplets by nanovesicles," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
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