Ion-Type Dependence of DNA Electronic Excitation in Water under Proton, α-Particle, and Carbon Ion Irradiation: A First-Principles Simulation Study

Shepard, Christopher; Kanai, Yosuke

doi:10.1021/acs.jpcb.3c05446

Cited by 4 publications

(4 citation statements)

References 83 publications

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“…RT-TDDFT offers a direct nonperturbative approach to examining how the electronic stopping dynamics change for complex heterogeneous systems with different high-energy ions beyond the usual linear response theory. 133 Although we do not wish to dwell on the computational details of RT-TDDFT simulation in this Perspective, let us discuss a few practical considerations. These simulations of DNA in the water represent some of the largest first-principles quantum dynamics simulations with more than 11,000 electrons.…”

Section: Novel Insights From Rt-tddft Simulationmentioning

confidence: 99%

“…49 The RT-TDDFT approach enables us to move beyond such a linear response theory description, allowing us to examine how the electronic stopping power changes with α-particles and carbon ions as the irradiating high-energy particles. 132 Figure 3 shows the stopping power for the Side path as a function of the ion velocity for protons, α-particles, and carbon ions. The stopping power changes considerably but not as predicted by the linear response theory, according to which the stopping power scales quadratically with the ion charge and the stopping power peak position depends only on the target matter (i.e., DNA/water).…”

Section: Novel Insights From Rt-tddft Simulationmentioning

confidence: 99%

“…In addition to having various contradicting experimental measurements, − widely used models based on the linear response theory fail to predict the electronic stopping power change with the projectile ion type . The RT-TDDFT approach enables us to move beyond such a linear response theory description, allowing us to examine how the electronic stopping power changes with α-particles and carbon ions as the irradiating high-energy particles Figure shows the stopping power for the Side path as a function of the ion velocity for protons, α-particles, and carbon ions.…”

Section: Novel Insights From Rt-tddft Simulationmentioning

confidence: 99%

“…For both α-particles and carbon ions, the linear response theory underestimates the stopping power by as much as 40% at velocities close to the stopping power peak while also failing to predict the correct peak velocity. RT-TDDFT offers a direct nonperturbative approach to examining how the electronic stopping dynamics change for complex heterogeneous systems with different high-energy ions beyond the usual linear response theory …”

Section: Novel Insights From Rt-tddft Simulationmentioning

confidence: 99%

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Real-Time Time-Dependent Density Functional Theory for Simulating Nonequilibrium Electron Dynamics

Xu,

Carney,

Zhou

et al. 2024

J. Am. Chem. Soc.

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The explicit real-time propagation approach for time-dependent density functional theory (RT-TDDFT) has increasingly become a popular first-principles computational method for modeling various time-dependent electronic properties of complex chemical systems. In this Perspective, we provide a nontechnical discussion of how this first-principles simulation approach has been used to gain novel physical insights into nonequilibrium electron dynamics phenomena in recent years. Following a concise overview of the RT-TDDFT methodology from a practical standpoint, we discuss our recent studies on the electronic stopping of DNA in water and the Floquet topological phase as examples. Our discussion focuses on how RT-TDDFT simulations played a unique role in deriving new scientific understandings. We then discuss existing challenges and some new advances at the frontier of RT-TDDFT method development for studying increasingly complex dynamic phenomena and systems.

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Section: Novel Insights From Rt-tddft Simulationmentioning

confidence: 99%

Section: Novel Insights From Rt-tddft Simulationmentioning

confidence: 99%

Section: Novel Insights From Rt-tddft Simulationmentioning

confidence: 99%

Section: Novel Insights From Rt-tddft Simulationmentioning

confidence: 99%

See 2 more Smart Citations

Real-Time Time-Dependent Density Functional Theory for Simulating Nonequilibrium Electron Dynamics

Xu,

Carney,

Zhou

et al. 2024

J. Am. Chem. Soc.

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Quantitative analysis of dose dependent DNA fragmentation in dry pBR322 plasmid using long read sequencing and Monte Carlo simulations

Beaudier,

Zein,

Chatzipapas

et al. 2024

Sci Rep

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Exposure to ionizing radiation can induce genetic aberrations via unrepaired DNA strand breaks. To investigate quantitatively the dose–effect relationship at the molecular level, we irradiated dry pBR322 plasmid DNA with 3 MeV protons and assessed fragmentation yields at different radiation doses using long-read sequencing from Oxford Nanopore Technologies. This technology applied to a reference DNA model revealed dose-dependent fragmentation, as evidenced by read length distributions, showing no discernible radiation sensitivity in specific genetic sequences. In addition, we propose a method for directly measuring the single-strand break (SSB) yield. Furthermore, through a comparative study with a collection of previous works on dry DNA irradiation, we show that the irradiation protocol leads to biases in the definition of ionizing sources. We support this scenario by discussing the size distributions of nanopore sequencing reads in the light of Geant4 and Geant4-DNA simulation toolkit predictions. We show that integrating long-read sequencing technologies with advanced Monte Carlo simulations paves a promising path toward advancing our comprehension and prediction of radiation-induced DNA fragmentation.

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Efficient exact exchange using Wannier functions and other related developments in planewave-pseudopotential implementation of RT-TDDFT

Shepard,

Zhou,

Bost

et al. 2024

The Journal of Chemical Physics

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The plane-wave pseudopotential (PW-PP) formalism is widely used for the first-principles electronic structure calculation of extended periodic systems. The PW-PP approach has also been adapted for real-time time-dependent density functional theory (RT-TDDFT) to investigate time-dependent electronic dynamical phenomena. In this work, we detail recent advances in the PW-PP formalism for RT-TDDFT, particularly how maximally localized Wannier functions (MLWFs) are used to accelerate simulations using the exact exchange. We also discuss several related developments, including an anti-Hermitian correction for the time-dependent MLWFs (TD-MLWFs) when a time-dependent electric field is applied, the refinement procedure for TD-MLWFs, comparison of the velocity and length gauge approaches for applying an electric field, and elimination of long-range electrostatic interaction, as well as usage of a complex absorbing potential for modeling isolated systems when using the PW-PP formalism.

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Ion-Type Dependence of DNA Electronic Excitation in Water under Proton, α-Particle, and Carbon Ion Irradiation: A First-Principles Simulation Study

Cited by 4 publications

References 83 publications

Real-Time Time-Dependent Density Functional Theory for Simulating Nonequilibrium Electron Dynamics

Real-Time Time-Dependent Density Functional Theory for Simulating Nonequilibrium Electron Dynamics

Quantitative analysis of dose dependent DNA fragmentation in dry pBR322 plasmid using long read sequencing and Monte Carlo simulations

Efficient exact exchange using Wannier functions and other related developments in planewave-pseudopotential implementation of RT-TDDFT

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