qantumdna:一个python包,用于分析DNA中的量子电荷动力学并探索其生物学相关性

IF 7.2 2区 物理与天体物理 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS
Dennis Herb , Marco Trenti , Marilena Mantela , Constantinos Simserides , Joachim Ankerhold , Mirko Rossini
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引用次数: 0

摘要

DNA电荷动力学的研究是一个高度跨学科的领域,它连接了物理学、化学、生物学和医学,在DNA损伤检测、蛋白质-DNA相互作用和基于DNA的纳米技术等过程中起着关键作用。然而,尽管这些领域都取得了重大进展,但其他科学界的研究人员往往无法获得这些知识,从而限制了跨学科进展的更广泛影响。为了弥补这一差距,我们提出了QuantumDNA,这是一个开源的Python包,用于使用量子物理方法模拟DNA电荷转移和激发态动力学。量子dna结合了一种有效的原子轨道线性组合(LCAO)方法,结合了紧密结合模型,并结合了开放量子系统技术来解释环境影响。这种方法允许对大的DNA集合进行快速而足够准确的分析,使遗传和表观遗传现象的统计研究成为可能。为了确保可访问性,该软件包具有图形用户界面,使其适合跨学科的研究人员。程序摘要程序标题:QuantumDNACPC库链接到程序文件:https://doi.org/10.17632/5mw48c7gbb.1Developer's存储库链接:https://github.com/dehe1011/QuantumDNALicensing条款:BSD 3-clause编程语言:python问题的性质:在过去的60年里,各种先进的模拟方法被用来探索DNA的电荷动力学。然而,对于遗传学和表观遗传学所需的大规模统计筛选来说,这些方法中的大多数在计算上过于昂贵。因此,理论和计算结果往往局限于专门领域,限制了跨学科研究人员的可及性和可重复性。解决方法:QuantumDNA结合了量子物理和理论化学的计算方法,以促进DNA电荷动力学的高通量分析,并具有足够的准确性。与计算昂贵的从头开始方法不同,它利用LCAO和TB模型的效率来模拟电荷动力学,同时考虑环境影响,使模拟更容易获得并鼓励跨学科研究。附加说明:QuantumDNA是一个开源软件包,具有图形用户界面、教程Jupyter笔记本和专用文档网站。该软件包还支持CPU并行计算。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
QuantumDNA: A python package for analyzing quantum charge dynamics in DNA and exploring its biological relevance
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.
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来源期刊
Computer Physics Communications
Computer Physics Communications 物理-计算机:跨学科应用
CiteScore
12.10
自引率
3.20%
发文量
287
审稿时长
5.3 months
期刊介绍: The focus of CPC is on contemporary computational methods and techniques and their implementation, the effectiveness of which will normally be evidenced by the author(s) within the context of a substantive problem in physics. Within this setting CPC publishes two types of paper. Computer Programs in Physics (CPiP) These papers describe significant computer programs to be archived in the CPC Program Library which is held in the Mendeley Data repository. The submitted software must be covered by an approved open source licence. Papers and associated computer programs that address a problem of contemporary interest in physics that cannot be solved by current software are particularly encouraged. Computational Physics Papers (CP) These are research papers in, but are not limited to, the following themes across computational physics and related disciplines. mathematical and numerical methods and algorithms; computational models including those associated with the design, control and analysis of experiments; and algebraic computation. Each will normally include software implementation and performance details. The software implementation should, ideally, be available via GitHub, Zenodo or an institutional repository.In addition, research papers on the impact of advanced computer architecture and special purpose computers on computing in the physical sciences and software topics related to, and of importance in, the physical sciences may be considered.
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