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License: GNU General Public License v3.0
DNACoatedColloidsInteractions
License: GNU General Public License v3.0
##################################################################################### ## Welcome to the program that calculates (DNA-coated) colloidal interactions ##################################################################################### 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 ##################################################################################### ## INSTALLATION ##################################################################################### ## Requirements This code runs under python3 You may have to install: lmfit, joblib pip3 install lmfit pip3 install joblib ##################################################################################### ## TOOL 1: FIND THE POTENTIAL PROFILE OF INTERACTING PARTICLES (ANY KIND) ##################################################################################### ## 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 ##################################################################################### ## TOOL 2: LAUNCH A MELTING CURVE OF DNA COATED COLLOIDS ##################################################################################### ## 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 ##################################################################################### ## TOOL 3: FIND THE DIFFUSION COEFFICIENT OF DNA COATED COLLOIDS ##################################################################################### ## 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 ##################################################################################### ## OTHER INFORMATION ##################################################################################### 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.
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