Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, 91405, Orsay, France.
Institut du Développement et des Ressources en Informatique Scientifique, Rue John von Neumann, B.P. 167, 91403, Orsay, France and Maison de la Simulation, CEA, CNRS, Université Paris-Saclay, 91191, Gif-sur-Yvette, France.
Phys Chem Chem Phys. 2020 Apr 15;22(15):7747-7758. doi: 10.1039/d0cp00165a.
The primary processes that occur following direct irradiation of bio-macromolecules by ionizing radiation determine the multiscale responses that lead to biomolecular lesions. The so-called physical stage loosely describes processes of energy deposition and molecular ionization/excitation but remains largely elusive. We propose a new approach based on first principles density functional theory to simulate energy deposition in large and heterogeneous biomolecules by high-energy-transfer particles. Unlike traditional Monte Carlo approaches, our methodology does not rely on pre-parametrized sets of cross-sections, but captures excitation, ionization and low energy electron emission at the heart of complex biostructures. It furthermore gives access to valuable insights on ultrafast charge and hole dynamics on the femtosecond time scale. With this new tool, we reveal the mechanisms of ionization by swift ions in microscopic DNA models and solvated DNA comprising almost 750 atoms treated at the DFT level of description. We reveal a so-called ebb-and-flow ionization mechanism in which polarization of the irradiated moieties appears as a key feature. We also investigate where secondary electrons produced by irradiation localize on chemical moieties composing DNA. We compare irradiation of solvated DNA by light (H+, and He2+) vs. heavier (C6+) ions, highlighting the much higher probability of double ionization with the latter. Our methodology constitutes a stepping stone towards a greater understanding of the chemical stage and more generally towards the multiscale modelling of radiation damage in biology using first principles.
电离辐射直接辐照生物大分子后发生的主要过程决定了导致生物分子损伤的多尺度响应。所谓的物理阶段松散地描述了能量沉积和分子电离/激发的过程，但在很大程度上仍难以捉摸。我们提出了一种新的方法，基于第一性原理密度泛函理论，来模拟高能转移粒子在大尺寸和异质生物分子中的能量沉积。与传统的蒙特卡罗方法不同，我们的方法不依赖于预先参数化的截面集，而是在复杂生物结构的核心中捕捉激发、电离和低能电子发射。它还可以深入了解超快电荷和空穴在飞秒时间尺度上的动力学。有了这个新工具，我们揭示了在微观 DNA 模型和包含近 750 个原子的溶剂化 DNA 中，快离子的电离机制。我们揭示了一种所谓的“潮起潮落”电离机制，其中辐照部分的极化是一个关键特征。我们还研究了辐照产生的次级电子在构成 DNA 的化学部分上的定位。我们比较了溶剂化 DNA 被光（H+和 He2+）和较重的（C6+）离子的辐照，突出了后者发生双电离的可能性高得多。我们的方法是朝着更好地理解化学阶段迈进的一步，更广泛地说，是朝着使用第一性原理对生物学中的辐射损伤进行多尺度建模迈进的一步。
