# Data and Source Code for "Membrane-MEDYAN: Simulating Deformable Vesicles Containing Complex Cytoskeletal Networks"


## General Information

### Contact Information

* ###### Haoran Ni: haoranni@umd.edu
* ###### Garegin A. Papoian: gpapoian@umd.edu

### Data Creation Information

Data was collected/generated from 2019-10-15 to 2019-10-31 using the MEDYAN software package.

### Sharing and Access

The code provided here is versioned from MEDYAN source code and made available for academic and research purposes only. By downloading the MEDYAN source code or this version code you agree to the terms of the MEDYAN license [medyan.org/medyanlicense.txt](http://medyan.org/medyanlicense.txt). MEDYAN Copyright 2015-16 Papoian Lab

Any academic or research works resulting in a publication that has used any of the MEDYAN distributions’ source code must cite the following paper:

Popov K, Komianos J, Papoian GA (2016)
MEDYAN: Mechanochemical Simulations of
Contraction and Polarity Alignment in Actomyosin
Networks. PLoS Comput Biol 12(4): e1004877.
doi:10.1371/journal.pcbi.1004877

Data files are available for reuse under the CC0 license; more information can be found at [creativecommons.org](https://creativecommons.org/publicdomain/zero/1.0/).

When using these data or the version code, please cite the original paper:

(citation to be added before the embargo is lifted)



### Funding Source

This work was supported by the following grants:
* NSF CHE-1800418

## Data Format & Overview

### Inventory

1. vesicle-random.zip
1. vesicle-bundle.zip
1. fil-num-conc.zip
1. angle-mem-rigid.zip
1. medyan-3e5ed64c58810bf8844afed5684fea82e1d1c60b.zip
1. README.md

### Description

#### Actin network growth in vesicle

`vesicle-random.zip` and `vesicle-bundle.zip` contain the simulation inputs and results of filament growing in an initially spherical membrane vesicle, corresponding to initially randomly seeded actin filaments and initially bundled actin filaments, respectively.
Each folder includes the following files:

- input files (`system.txt`, `chemistry.txt` and (bundle only) `fil.txt`)
- output trajectory files (`*.traj`)

#### Actin bundle protrusion

`fil-num-conc.zip` contains inputs and outputs for bundle protrusion simulations with different numbers of actin filaments and different G-Actin concentrations. Each simulation is located in a folder named `m.n`, where `m` is the serial ID of simulation configuration (illustrated in the table below), and `n` indicates the trial number under the same configuration. The configuration IDs are listed in the following table, where each row corresponds to a certain number of filaments in the bundle, and each column represents a certain number of G-Actin monomers in the simulation volume (6 cubic micron).

| G-Actin copy number | 100,000 | 200,000 | 240,000 | 300,000 | 400,000 |
|---------------------|---------|---------|---------|---------|---------|
| 4 filaments         |      11 |         |         |         |         |
| 7 filaments         |      16 |      17 |      18 |      19 |      20 |
| 10 filaments        |      21 |      22 |      23 |      24 |      25 |
| 14 filaments        |      26 |      27 |      28 |      29 |      30 |

Each folder contains the following files:

- input files (`system.txt`, `chemistry.txt` and `fil.txt`)
- snapshot trajectory file (`snapshot.traj`)

`angle-mem-rigid.zip` contains inputs and outputs for bundle protrusion simulations with different incident angles and different membrane rigidities. Each simulation is located in a folder named `m.n`, where `m` is the serial ID of simulation configuration (illustrated in the table below), and `n` indicates the trial number under the same configuration. The configuration IDs are listed in the following table, where each row corresponds to a certain incident angle α, and each column represents a certain membrane rigidity characterized by a dimensionless parameter χ (explained in detail in the main text).

|                     | χ = 1/sqrt(2) | χ = 1 | χ = sqrt(2) |
|---------------------|---------------|-------|-------------|
| α = 0°              |             1 |     2 |           3 |
| α = 17.5°           |             5 |     6 |           7 |

Each folder contains the following files:

- input files (`system.txt`, `chemistry.txt` and `fil.txt`)
- snapshot trajectory file (`snapshot.traj`)

#### Source code

The file `medyan-3e5ed64c58810bf8844afed5684fea82e1d1c60b.zip` contains the code necessary to compile membrane-MEDYAN, which was used to generate the results presented in the manuscript. With this repository, please consult the documentation available at medyan.org for information on building and running the code. Contact the authors if additional information is needed.

#### Additional Documentation

The format of most of these output files, as well as of the input files, can be found in the documentation available at medyan.org.  However, additional information on membrane configuration is included in `snapshot.traj`, which is documented below.  Please contact the authors if further information is needed in this regard.

**`snapshot.traj`**
In each snapshot, a membrane represented by triangular mesh will be printed using the following format.

```
MEMBRANE <membrane-id> <membrane-type> <number-of-vertices> <number-of-triangles>
vertex_0_x vertex_0_y vertex_0_z
vertex_1_x vertex_1_y vertex_1_z
...
triangle_0_v0_index triangle_0_v1_index triangle_0_v2_index
triangle_1_v0_index triangle_1_v1_index triangle_1_v2_index
...
```