Jupyter Notebook Tutorials

These tutorials and demonstrations are designed to help users explore and understand the functionalities of the QuantumDNA package through practical examples.

For a detailed description of the classes and functions used in these tutorials, visit the API documentation.

Overview

The Jupyter notebooks in the tutorials folder provide demonstrations of various features and functionalities of the QuantumDNA package. Each tutorial focuses on a specific aspect, helping you get started.

Tutorials

Below is a list of available tutorials. Click on each to access the detailed notebook:

Descriptions

Tight Binding Parameters

Learn the Linear Combination of Atomic Orbitals (LCAO) approach using Slater–Koster integrals and Harrison-type expressions.

Tight_Binding_Method

Explore predefined and custom tight-binding models. Includes calculating time-averaged exciton populations in the Fishbone Ladder Model (FLM) and simulating charge transfer in the Fenna-Matthews-Olson (FMO) complex.

Environment_Simulation

Model DNA excited-state relaxation and environmental interactions. This tutorial covers dephasing and thermalization models inspired by Quantum Biology.

Visualization

Learn how to use built-in plotting routines for visualization. Learn to create custom visualizations tailored to your data.

Evaluation

Perform calculations for observables like exciton lifetimes, average charge separation, and dipole moments. Includes parallelization features for efficient computation.

Reproduce Papers

Reproduce the plots from the papers [GWS+99], [GAK+01], [Bit06], [Bit07], [Sim14] and [MLS23] using the QuantumDNA package. This tutorial demonstrates how to obtain results that have already been published elsewhere.

PRE2024

Reproduces all the figures presented in the reference paper [HRA24]. This serves as a comprehensive example of QuantumDNA’s visualization and analysis features.

Getting Started

These tutorials provide examples to guide you through using the QuantumDNA package. To get started:

  1. Navigate to the tutorials folder and open the desired .ipynb file as Jupyter notebook.

  2. Follow the instructions provided in the notebook to run the cells.

  3. Refer to the API documentation for deeper insights into the functions and classes used in the tutorials.

Tips for Using the Tutorials

  • Run in a Jupyter Environment: Ensure you have Jupyter Notebook or JupyterLab installed to execute the tutorials interactively.

  • Dependencies: Before starting, confirm that all dependencies for QuantumDNA are installed. Check the requirements/requirements.txt file in the repository for details.

  • Explore Further: Modify and experiment with the code to deepen your understanding of the concepts.

We hope these tutorials will help you!