Data for "Membrane-MEDYAN: Simulating Deformable Vesicles Containing Complex Cytoskeletal Networks"
| dc.contributor.advisor | Papoian, Garegin A. | |
| dc.contributor.author | Ni, Haoran | |
| dc.contributor.author | Papoian, Garegin A. | |
| dc.date.accessioned | 2021-07-02T18:14:21Z | |
| dc.date.available | 2021-07-02T18:14:21Z | |
| dc.date.issued | 2021 | |
| dc.description | This contains the source code and data set used for the paper "Membrane-MEDYAN: Simulating Deformable Vesicles Containing Complex Cytoskeletal Networks". | en_US |
| dc.description.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. | en_US |
| dc.description.sponsorship | NSF CHE-1800418 | en_US |
| dc.description.uri | https://doi.org/10.1021/acs.jpcb.1c02336 | |
| dc.identifier | https://doi.org/10.13016/iyni-9spg | |
| dc.identifier.uri | http://hdl.handle.net/1903/27200 | |
| dc.relation.isAvailableAt | College of Computer, Mathematical & Natural Sciences | en_us |
| dc.relation.isAvailableAt | Physics | en_us |
| dc.relation.isAvailableAt | Digital Repository at the University of Maryland | en_us |
| dc.relation.isAvailableAt | University of Maryland (College Park, MD) | en_us |
| dc.subject | MEDYAN | en_US |
| dc.subject | membrane | en_US |
| dc.subject | cytoskeleton | en_US |
| dc.subject | active matter | en_US |
| dc.subject | simulation | en_US |
| dc.title | Data for "Membrane-MEDYAN: Simulating Deformable Vesicles Containing Complex Cytoskeletal Networks" | en_US |
| dc.type | Dataset | en_US |
Files
Original bundle
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- Name:
- vesicle-random.zip
- Size:
- 138.27 MB
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- Unknown data format
- Description:
- Simulation inputs and results of filament growing in an initially spherical membrane vesicle, with initially randomly seeded actin filaments.
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- Name:
- vesicle-bundle.zip
- Size:
- 41.82 MB
- Format:
- Unknown data format
- Description:
- Simulation inputs and results of filament growing in an initially spherical membrane vesicle, with initially bundled actin filaments.
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- Name:
- fil-num-conc.zip
- Size:
- 338.71 MB
- Format:
- Unknown data format
- Description:
- Inputs and outputs for bundle protrusion simulations with different numbers of actin filaments and different G-Actin concentrations.
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- Name:
- mem-angle-rigid.zip
- Size:
- 652.48 MB
- Format:
- Unknown data format
- Description:
- Inputs and outputs for bundle protrusion simulations with different incident angles and different membrane rigidities.
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- Name:
- medyan-e4c9e7a0786bd2939a88f241e9e3076574dd3520.zip
- Size:
- 2.87 MB
- Format:
- Unknown data format
- Description:
- The code necessary to compile membrane-MEDYAN, which was used to generate the results presented in the manuscript.
License bundle
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