smarbach / dnacoatedcolloidsinteractions Goto Github PK

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## Welcome to the program that calculates (DNA-coated) colloidal interactions
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This program was created by Sophie Marbach on August 5th, 2021. 
Special thanks to Brennan Sprinkle for providing a plug in to calculate lubrication forces (used for Tool #3). 

Please cite relevant manuscripts or software versions if you use this software:

####### DNA Coated colloids interactions publication ########
Comprehensive view of microscopic interactions between DNA-coated colloids
F Cui, S Marbach, JA Zheng, M Holmes-Cerfon, DJ Pine
Nature communications 13 (1), 1-10

####### DNA Coated colloids interactions software ########
S Marbach (2022), “DNA Coated Colloids Interactions”, v1.0, Zenodo, doi.org/10.5281/zenodo.6383258.

####### DNA Coated colloids diffusion publications ########
The Nanocaterpillar's Random Walk: Diffusion With Ligand-Receptor Contacts
S Marbach, JA Zheng, M Holmes-Cerfon
Soft Matter D1SM01544C; arXiv preprint arXiv:2110.03112

Can mass change the diffusion coefficient of DNA-coated colloids?
S Marbach, M Holmes-Cerfon
arXiv preprint arXiv:2112.05266

####### DNA Coated colloids diffusion software ########
S Marbach (2022), “DNA Coated Colloids Interactions”,  --- to be released

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## INSTALLATION
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## Requirements

This code runs under python3
You may have to install: lmfit, joblib
pip3 install lmfit
pip3 install joblib

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## TOOL 1: FIND THE POTENTIAL PROFILE OF INTERACTING PARTICLES (ANY KIND)
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## To just launch a potential profile calculations for your favorite DNA coated colloids then you can simply run one!

To do that run the Launch_energyProfile.py in the analysis folder. 
The program will output a plot with the energy profile and will break down the contributions between steric, binding, van der Waals etc. 

In command line

cd analysis/
python3 Launch_energyProfile.py 

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## TOOL 2: LAUNCH A MELTING CURVE OF DNA COATED COLLOIDS
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## To simulate a melting curve simply run the example in the analysis folder

To do that simply run the Launch_MeltingCurve.py with your favorite python program (located in the analysis/ folder). It should output melting curve information and an .eps plot of the melting curve. 

The program does 3 runs to refine the analysis around the melting transition that takes a total of ~1min on a standard computer. 

In command line

cd analysis/ 
python3 Launch_meltingCurve.py

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## TOOL 3: FIND THE DIFFUSION COEFFICIENT OF DNA COATED COLLOIDS
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## To compute the diffusion coefficient of DNA-coated colloids simply run the example in the analysis folder

To do that simply run the Launch_DiffusionCurve.py with your favorite python program (located in the analysis/ folder). 
It should output 3 plots (and some information detailed in the code):
- MyDiffusionSimulation_DiffusionPlot.eps = diffusion coefficients with temperature for a set of particle densities
- MyDiffusionSimulation_percentage = relative difference between 2 diffusion coefficients (corresponding to 2 different particle densities) with temperature
- MyDiffusionSimulation_NumberOfBounds = number of bonds with temperature for the chosen particle

The program does 2 runs to refine the analysis around the melting transition that takes a total of ~1min on a standard computer. 

In command line

cd analysis/ 
python3 Launch_DiffusionCurve.py


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## OTHER INFORMATION
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The program also saves data as defaultSave.pickle (and for diffusion as MyDiffusionSimulation_DiffusionProperties.pickle). 
The details of the content of this pickle file will be explained further in a subsequent release.