QuantumDNA Jupyter Notebook Tutorials

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.

Overview

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.
6_Reproduce_Papers	This tutorial guides you through reproducing results from research papers [2-7] using the qDNA package.

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Getting Started

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.

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References

[1] D. Herb, M. Rossini and J. Ankerhold, Ultrafast excitonic dynamics in DNA: Bridging correlated quantum dynamics and sequence dependence. Physical Review E 109, 064413 (2024).

[2] Mantela, Marilena and Lambropoulos, Konstantinos and Simserides, Constantinos, Charge transport properties of ideal and natural DNA segments, as mutation detectors. Physical Chemistry Chemical Physics 25, 7750--7762 (2023).

[3] Simserides, Constantinos, A systematic study of electron or hole transfer along DNA dimers, trimers and polymers. Chemical Physics 440, 31--41 (2014).

[4] Bittner, Eric R., Frenkel exciton model of ultrafast excited state dynamics in AT DNA double helices. Journal of Photochemistry and Photobiology A: Chemistry 190, 328--334 (2007).

[5] Bittner, Eric R., Lattice theory of ultrafast excitonic and charge-transfer dynamics in DNA. The Journal of Chemical Physics 125, 094909 (2006).

[6] Giese, Bernd and Amaudrut, Jérôme and Köhler, Anne-Kathrin and Spormann, Martin and Wessely, Stephan, Direct observation of hole transfer through DNA by hopping between adenine bases and by tunnelling. Nature 412, 318--320 (2001).

[7] Giese, Bernd and Wessely, Stephan and Spormann, Martin and Lindemann, Ute and Meggers, Eric and Michel-Beyerle, Maria E., On the Mechanism of Long-Range Electron Transfer through DNA. Angewandte Chemie International Edition 38, 996--998 (1999).