Impact of Andreev Bound States within the Leads of a Quantum Dot Josephson Junction

This repository contains all the raw data and the code used to generate the figures of the article "Impact of Andreev Bound States within the Leads of a Quantum Dot Josephson Junction".

The plotting.ipynb notebook creates the majority of the figures. To run it you need to install proplot. Create a fresh python environment for it, since you might need to downgrade numpy to the 1.19.5 version and matplotlib to the 3.4.3 one. To install the relevant python packages and open the notebook you can download Anaconda and use the following terminal instructions:

conda create -n andreev-trimer python=3.10
conda activate andreev-trimer
conda install proplot
conda install jupyterlab xarray netcdf4 tqdm
jupyter lab
extraction-3D.ipynb extracts the charge degeneracy points from 3D charge stability diagram measurements. To run it you need to install scikit-image. If you want to export additional .gif images install imageio as well:

conda install scikit-image imageio

To visualize the 3D charge stability diagrams (Figure 5) you can use plotting-3D.ipynb. To run it you need to install pyvista. A dedicated environment is recommended. To install pyvista and run it with JupyterLab use the following instructions:

conda create -n pyvista python=3.9
conda activate pyvista
conda install nodejs
pip install jupyter pyvista trame
jupyter lab

Finally, simulations.ipynb computes all the theoretical simulations. To run it you need cython and you can install it in a dedicated environment using the following instructions:

conda create -n theory
conda activate theory
conda install jupyterlab matplotlib cython scipy
jupyter lab