QuantumDNA: A python package for analyzing quantum charge dynamics in DNA and exploring its biological relevance

Abstract

The study of DNA charge dynamics is a highly interdisciplinary field that bridges physics, chemistry, biology, and medicine, and plays a critical role in processes such as DNA damage detection, protein-DNA interactions, and DNA-based nanotechnology. However, despite significant progress in each of these areas, knowledge often remains inaccessible to researchers in other scientific communities, limiting the broader impact of advances across disciplines. To bridge this gap, we present QuantumDNA, an open-source Python package for simulating DNA charge transfer and excited state dynamics using quantum physical methods. QuantumDNA combines an efficient Linear Combination of Atomic Orbitals (LCAO) approach combined with tight-binding models and incorporates open quantum systems techniques to account for environmental effects. This approach allows for a rapid yet sufficiently accurate analysis of large DNA ensembles, enabling statistical studies of genetic and epigenetic phenomena. To ensure accessibility, the package features a graphical user interface, making it suitable for researchers across disciplines.

Program summary

Program Title: QuantumDNA

CPC Library link to program files: https://doi.org/10.17632/5mw48c7gbb.1

Developer's repository link: https://github.com/dehe1011/QuantumDNA

Licensing provisions: BSD 3-clause

Programming language: Python

Nature of the Problem: Over the past 60 years, a variety of advanced simulation methods have been employed to explore charge dynamics of DNA. However, most of these approaches are computationally too expensive for the large-scale statistical screening required in genetics and epigenetics. Therefore, theoretical and computational results are often restricted to specialized fields, limiting their accessibility and reproducibility to researchers across disciplines. Solution Method: QuantumDNA combines computational methods from quantum physics and theoretical chemistry to facilitate high-throughput analysis of DNA charge dynamics with sufficient accuracy. Unlike computationally expensive ab initio methods, it utilizes the efficiency of LCAO and TB models to simulate charge dynamics while considering environmental effects, making simulations more accessible and encouraging interdisciplinary research. Additional comments: QuantumDNA is an open-source package featuring a graphical user interface, tutorial Jupyter notebooks, and a dedicated documentation website. The package also supports CPU parallel computing.