Inelastic electron injection in a water chain

Rizzi, Valerio; Todorov, Tchavdar N.; Kohanoff, Jorge

doi:10.1038/srep45410

Cited by 8 publications

(3 citation statements)

References 22 publications

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“…Although CEID is still rather young and costly, it has emerged as a powerful tool for problems in which the transfer of energy between electrons and nuclei is crucial. A cost-effective alternative that limits the nuclear motion to harmonic phonons, named Effective CEID, has been proposed recently [81], and applied to inelastic electron transport in water chains [89]. It is important to remark that none of these methods is presently mature enough to allow for the dynamical simulation of the dissociative electron attachment process.…”

Section: Modelling the Dynamics Of Deamentioning

confidence: 99%

Interactions between low energy electrons and DNA: a perspective from first-principles simulations

Kohanoff¹,

McAllister²,

Tribello³

et al. 2017

J. Phys.: Condens. Matter

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Abstract. DNA damage caused by irradiation has been studied for many decades. Such studies allow us to better assess the dangers posed by radiation, and to increase the efficiency of the radiotherapies that are used to combat cancer. A full description of the irradiation process involves multiple size and time scales. It starts from the interaction of radiation -either photons or swift ions -with the biological medium. Such interactions cause electronic excitation and ionisation. The two main products of ionising radiation are thus electrons and radicals. Both of these species can cause damage to biological molecules, in particular DNA. In the long run, this molecular level damage can prevent cells from replicating and can hence lead to cell death. For a long time it was assumed that the main actors in the damage process were the radicals. However, experiments in a seminal paper by the group of Leon Sanche in 2000 showed that low-energy electrons (LEE), such as those generated when ionising biological targets, can also cause bond breaks in biomolecules, in particular strand breaks in plasmid DNA [1]. These results prompted a significant amount of experimental and theoretical work aimed at elucidating the role played by LEE in DNA damage.In this Topical Review we provide a general overview of the problem. We discuss experimental findings and theoretical results hand in hand with the aim of describing the physics and chemistry that occurs during the process of radiation damage, from the initial stages of electronic excitation, through the inelastic propagation of electrons in the medium, the interaction of electrons with DNA, and the chemical end-point effects on DNA. A very important aspect of this discussion is the consideration of a realistic, physiological environment. The role played by the aqueous solution and the amino acids from the histones in chromatin must be considered. Moreover, thermal fluctuations must be incorporated when studying these phenomena. Hence, a special place in this Topical Review is occupied by our recent first-principles molecular dynamics simulations that address the issue of how the environment favours or prevents LEEs from causing damage to DNA. We finish by summarising the conclusions achieved so far, and by suggesting a number of possible directions for further study.

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Section: Modelling the Dynamics Of Deamentioning

confidence: 99%

Interactions between low energy electrons and DNA: a perspective from first-principles simulations

Kohanoff¹,

McAllister²,

Tribello³

et al. 2017

J. Phys.: Condens. Matter

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“…We are not aware of methodologies described in the literature to simulate such irradiation by real-time TDDFT (RT-TDDFT). Rizzi et al (57) attempted to simulate electron injection into small water chains, comparing two methodologies: one using an electron pulse and another a steady stream of electrons. They highlighted the difficulties of controlling injection conditions, but they paved the way for more realistic simulations in the future.…”

Section: Electron Dynamics Simulationsmentioning

confidence: 99%

First-Principles Simulations of Biological Molecules Subjected to Ionizing Radiation

Omar

Hasnaoui

Lande

2021

Annu. Rev. Phys. Chem.

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Ionizing rays cause damage to genomes, proteins, and signaling pathways that normally regulate cell activity, with harmful consequences such as accelerated aging, tumors, and cancers but also with beneficial effects in the context of radiotherapies. While the great pace of research in the twentieth century led to the identification of the molecular mechanisms for chemical lesions on the building blocks of biomacromolecules, the last two decades have brought renewed questions, for example, regarding the formation of clustered damage or the rich chemistry involving the secondary electrons produced by radiolysis. Radiation chemistry is now meeting attosecond science, providing extraordinary opportunities to unravel the very first stages of biological matter radiolysis. This review provides an overview of the recent progress made in this direction, focusing mainly on the atto- to femto- to picosecond timescales. We review promising applications of time-dependent density functional theory in this context.

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“…This formalism shows a good description of thermal equilibration between electrons and phonons, and electronic transport in open systems. 27 Nevertheless, it is still expensive for an ab initio setting such as DFT, and even more in the context of transport calculations.…”

Section: Introductionmentioning

confidence: 99%

A simple approximation to the electron–phonon interaction in population dynamics

Bustamante

Todorov

Sánchez

et al. 2020

The Journal of Chemical Physics

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The modelling of coupled electron-ion dynamics including a quantum description of the nuclear degrees of freedom has remained a costly and technically difficult practice. The Kinetic Model for electron-phonon interaction provides an efficient approach to this problem, for systems evolving with low amplitude fluctuations, in a quasi-stationary state. We propose in this work an extension of the Kinetic Model to include the effect of coherences, which are absent from the original approach. The new scheme, referred to as Liouville von Neumann -Kinetic Equation (or LvN+KE), is implemented here in the context of a tight-binding Hamiltonian and employed to model the broadening, caused by the nuclear vibrations, of the electronic absorption bands of an atomic wire. The results, which show close agreement with the predictions given by Fermi's Golden Rule, serve as a validation of the methodology. Thereafter, the method is applied to the electron-phonon interaction in transport simulations, adopting to this end the driven Liouville von Neumann equation to model open quantum boundaries. In this case the LvN+KE model qualitatively captures the Joule heating effect and Ohm's law. It however exhibits numerical discrepancies with respect to the results based on Fermi's Golden Rule, attributable to the fact that the quasi-stationary state is defined taking into consideration the eigenstates of the closed system rather than those of the open boundaries system. The simplicity and numerical efficiency of this approach and its ability to capture the essential physics of the electron-phonon coupling make it an attractive route to first-principles electron-ion dynamics.

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Inelastic electron injection in a water chain

Cited by 8 publications

References 22 publications

Interactions between low energy electrons and DNA: a perspective from first-principles simulations

Interactions between low energy electrons and DNA: a perspective from first-principles simulations

First-Principles Simulations of Biological Molecules Subjected to Ionizing Radiation

A simple approximation to the electron–phonon interaction in population dynamics

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