Skip to content
University of Maryland LibrariesDigital Repository at the University of Maryland
    • Login
    View Item 
    •   DRUM
    • College of Computer, Mathematical & Natural Sciences
    • Physics
    • Physics Research Works
    • View Item
    •   DRUM
    • College of Computer, Mathematical & Natural Sciences
    • Physics
    • Physics Research Works
    • View Item
    JavaScript is disabled for your browser. Some features of this site may not work without it.

    Data for "Membrane-MEDYAN: Simulating Deformable Vesicles Containing Complex Cytoskeletal Networks"

    Thumbnail
    View/Open
    Simulation inputs and results of filament growing in an initially spherical membrane vesicle, with initially randomly seeded actin filaments. (138.2Mb)
    No. of downloads: 6

    Simulation inputs and results of filament growing in an initially spherical membrane vesicle, with initially bundled actin filaments. (41.82Mb)
    No. of downloads: 3

    Inputs and outputs for bundle protrusion simulations with different numbers of actin filaments and different G-Actin concentrations. (338.7Mb)
    No. of downloads: 4

    Inputs and outputs for bundle protrusion simulations with different incident angles and different membrane rigidities. (652.4Mb)
    No. of downloads: 6

    The code necessary to compile membrane-MEDYAN, which was used to generate the results presented in the manuscript. (2.865Mb)
    No. of downloads: 29

    General description (5.533Kb)
    No. of downloads: 12

    External Link(s)
    https://doi.org/10.1021/acs.jpcb.1c02336
    Date
    2021
    Author
    Ni, Haoran
    Papoian, Garegin A.
    Advisor
    Papoian, Garegin A.
    DRUM DOI
    https://doi.org/10.13016/iyni-9spg
    Metadata
    Show full item record
    Abstract
    The plasma membrane defines the shape of the cell and plays an indispensable role in bridging intra- and extra-cellular environments. Mechanochemical interactions between plasma membrane and cytoskeleton are vital for cell biomechanics and mechanosensing. A computational model that comprehensively captures the complex, cell-scale cytoskeleton-membrane dynamics is still lacking. In this work, we introduce a triangulated membrane model that accounts for membrane's elastic properties, as well as for membrane-filament steric interactions. The corresponding force-field was incorporated into the active biological matter simulation platform, MEDYAN ("Mechanochemical Dynamics of Active Networks"). Simulations using the new model shed light on how actin filament bundling affects generation of tubular membrane protrusions. In particular, we used membrane-MEDYAN simulations to investigate protrusion initiation and dynamics while varying geometries of filament bundles, membrane rigidities and local G-Actin concentrations. We found that bundles' protrusion propensities sensitively depend on the synergy between bundle thickness and inclination angle at which the bundle approaches the membrane. The new model paves the way for simulations of biological systems involving intricate membrane-cytoskeleton interactions, such as occurring at the leading edge and the cortex, eventually helping to uncover the fundamental principles underlying the active matter organization in the vicinity of the membrane.
    Notes
    This contains the source code and data set used for the paper "Membrane-MEDYAN: Simulating Deformable Vesicles Containing Complex Cytoskeletal Networks".
    URI
    http://hdl.handle.net/1903/27200
    Collections
    • Physics Research Works
    • UMD Data Collection

    DRUM is brought to you by the University of Maryland Libraries
    University of Maryland, College Park, MD 20742-7011 (301)314-1328.
    Please send us your comments.
    Web Accessibility
     

     

    Browse

    All of DRUMCommunities & CollectionsBy Issue DateAuthorsTitlesSubjectsThis CollectionBy Issue DateAuthorsTitlesSubjects

    My Account

    LoginRegister
    Pages
    About DRUMAbout Download Statistics

    DRUM is brought to you by the University of Maryland Libraries
    University of Maryland, College Park, MD 20742-7011 (301)314-1328.
    Please send us your comments.
    Web Accessibility