Welcome to the QuantumDNA Jupyter Notebook Tutorials! These tutorials and demonstrations are designed to help users explore and understand the functionalities of the qDNA package through practical examples.
The tutorials are located in the tutorials folder. Among them, the notebook PRE_2024 reproduces all the figures presented in the reference paper [1].
Additionally, the tutorials folder includes the following tutorials, covering various aspects of qDNA:
| Tutorial Name | Description |
|---|---|
1_Tight_Binding_Parameters |
Learn to use the Linear Combination of Atomic Orbitals (LCAO) approach with Slater–Koster two-center interaction integrals and Harrison-type expressions. |
2_Tight_Binding_Method |
Explore predefined and custom tight-binding models. This tutorial demonstrates calculating time-averaged exciton populations in a Fishbone Ladder Model (FLM) and simulating charge transfer in the Fenna-Matthews-Olson (FMO) complex in green sulfur bacteria, showcasing how qDNA can define custom models. |
3_Environment_Simulation |
Discover how to model DNA excited-state relaxation and environmental interactions using dephasing and thermalization models from Quantum Biology. |
4_Visualization |
Learn how to use qDNA's predefined plotting routines for visualizing results effectively. |
5_Evaluation |
Perform calculations for various observables, such as estimated exciton lifetimes, average charge separation, and dipole moments. This tutorial also demonstrates the use of qDNA's parallelization capabilities. |
These tutorials provide hands-on examples and explanations to help you effectively use the qDNA package. For each tutorial, navigate to the corresponding .ipynb file in the tutorials folder and follow the provided instructions.