Aggregate Size Dependence of Amyloid Adsorption onto Charged Interfaces

This repository contains Jupyter Notebooks, as well as experimental and simulation data, for reproducing the work of the scientific paper Aggregate Size Dependence of Amyloid Adsorption onto Charged Interfaces published in ACS Langmuir (doi:10/chz9). This supporting information can be further accessed via Zenodo (doi:10/ch58).

The layout is as follows:

notebook.ipynb - Jupyter Notebook for compiling, running, and plotting all MC simulation data, experimental results, and results from the analytical line segment theory
notebook.html - Jupyter Notebook in HTML format
environment.yml - Environment file for setting up dependencies for Anaconda
mc/ - Directory with Monte Carlo data and C++ code
exp/ - Directory with QCM-D and AFM experimental data
md/ - Directory with Notebook for MD simulations using OpenMM and GROMACS input files.

To open this Notebook, install python via (Mini)conda and make sure all required packages are loaded by issuing the following terminal commands,

conda env create -f environment.yml
source activate surfacefibrils
jupyter-notebook notebook.ipynb

Alternatively, you may try the Launch Binder link at the top of this page which will automatically setup an online Jupyter environment and import the SI.

mlund/SI-surfacefibrils

Aggregate Size Dependence of Amyloid Adsorption onto Charged Interfaces