# Data and Source Code for "Quantifying Dissipation in Actomyosin Networks"


## General Information

### Contact Information

* ###### Carlos Floyd: csfloyd@umd.edu
* ###### Garegin A. Papoian: gpapoian@umd.edu
* ###### Christopher Jarzynski: cjarzyns@umd.edu

### Data Creation Information

Data was collected/generated from 2018-08-14 to 2018-08-17 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)

Additionally, please cite the data files:

Floyd C, Papoian GA, Jarzynski C (2018) Quantifying dissipation in actomyosin networks [Data files]. (DOI to be added before embargo is lifted)



### Funding Source

This work was supported by the following grants:
* NSF 1632976
* NSF DMR-1506969
* NSF CHE-1800418

## Data Format & Overview

### Inventory

1. LL.zip
2. LM.zip
3. LH.zip
4. ML.zip
5. MM.zip
6. MH.zip
7. HL.zip
8. HM.zip
9. HH.zip
10. src.zip
11. README.md

### Description

The data is organized into 9 folders, representing the pairings of 3 conditions of cross-linker concentration and 3 conditions of myosin minifilament concentration.  The first letter of each 2 letter folder name stands for Low (0.1 micromolar ), Medium (0.2 micromolar), or High (0.4 micromolar) myosin minifilament concentration, and the second letter stands for Low (0.1 micromolar), Medium (1.0 micromolar), or High (5.0 micromolar) alpha-actinin concentration.

Within each of the 9 conditions are 10 trials, each representing a different stochastic trajectory of actomyosin network self-organization for the given concentrations.  Within each trial folder are:

* input files (system.txt and chemistry.txt)
* a bash script to run the job (.sh)
* the standard out file from the run (.out)
* an Output folder

The Output folder is where the data collected during the simulation is kept.  These are text files with the .traj extension, representing a trajectory of different quantities measured at 1 second intervals.  The formats of each .traj file are slightly different from each other, so analysis code for each should in general be written separately.  Note that unfortunately the tensions.traj output files did not record the tensions on the cross-linkers or motors in this study, due to a bug.

#### 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.  Here we indicate the format of the dissipation.traj and HRCD.traj files, which are not included in that documentation.  Please contact the authors if further information is needed in this regard.

### dissipation.traj

This file is divided into pairs of two lines, each representing a timestep.  The format for each pair of lines is:

```
timestep time
delGDiss delGChemDiss delCMechDiss delGChem delGMech
```

Here the delG values are cumulative, so to obtain the instantaneous rates, simply take the difference between consecutive values.  These meanings of these quantities are discussed in the manuscript, and the units are in kT assuming T = 298 Kelvin.

### HRCD.traj

This stands for high resolution chemical dissipation, meaning that the delGChem (note this is delGChem, not delGChemDiss, despite the filename indicating dissipation) for each reaction is tracked individually.  Each reaction is given a reacID, which are specified in the chemistry.txt input file.  In that file, the second object of each reaction line is: delG0:reacID.  delG0 refers to the standard state change in Gibbs free energy for that reaction (adjusted according to the formula used to compute delG as discussed in the manuscript), and reacID is the unique string given to identify the reaction in the HRCD.traj file.  For binding reactions, the reacID of the unbinding reaction is generated by appending the string "off" to the binding reacID.  The reacIDs of the reactions and their contribution to the change in Gibbs free energy are appended in HRCD.traj in the order in which they first occur.  The format of the HRCD.traj file is then:



```
timestep time
reacID1 reacID2 reacID3 ...
delGChem1 delGChem2 delGChem3 ...
```

Here the delG values are cumulative, so to obtain the instantaneous rates, sipmly take the difference between consecutive values.  These meanings of these quantities are discussed in the manuscript, and the units are in kT assuming T = 298 Kelvin.

### Source Code

The file src.zip contains a compressed folder named src, which contains the code version used to generate the results presented in the manuscript.  With this repository, please consult the documentation available at medyan.org for information on installing and running the code.  Contact the authors if additional information is needed.