Electronic Excitation Dynamics in DNA under Proton and α-Particle Irradiation

Atomic-Scale Simulations of Chemical Damage in Neoprene under Noble Gas Ion Irradiation

The molecular simulation is an effective approach for investigating the effects of energetic ion irradiation on polymers. However, there is a lack of relevant studies on atomic structural changes and quantitative analysis. This study utilizes an inelastic thermal spike model and reactive molecular dynamics simulations to investigate the damage mechanisms of noble gas ion irradiation in neoprene rubber. The ion track structure and chemical damage mechanism are systematically studied. The radiolytic products are observed to form a distinctive core-shell structure with a threshold in electronic energy loss (Se). Subtle chemical structural changes are noted in the track shell, in stark contrast to the pronounced damage observed in the track core. Additionally, the four distinct types of repeating units in the neoprene molecular chain are found to significantly influence both the structure and the yield of the radiolytic products. The extent of chemical damage is further quantitatively analyzed. A remarkable linear relationship is verified between damage cross sections (σ) and Se. Moreover, the activation energy associated with the same chemical structure is found to remain constant. These results are in alignment with previous experimental studies. This work provides an effective and accurate simulation method for studying radiolytic mechanisms in polymers.

Effects of BPQ binding on the nonadiabatic dynamics of excited electrons in poly(dG)-poly(dC) DNA under proton irradiation

The interaction between DNA and small molecules is important for understanding the mechanisms of DNA-based multifunctional devices and has been extensively studied. However, there are few reports on such interactions in irradiation environments. Here, we investigate the nonadiabatic dynamic behaviors of excited electrons in double-stranded DNA bound to BPQ molecule upon proton irradiation, focusing on the energy deposition and electronic excitation dynamics as protons traverse the DNA along different channels. Our results reveal that the presence of BPQ significantly influences charge migration and DNA damage, with notable differences between CGvdW and CGcovalent adducts. The energy deposition process is highly dependent on charge density, and guanine exhibits higher excitation propensity than cytosine due to its structural characteristics. The BPQ molecule enhances DNA charge migration and promotes damage through secondary electron migration. These findings provide insights into the nonadiabatic dynamics of DNA under ionizing radiation and have implications for designing targeted electrophilic organics to improve radiotherapy efficacy.

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

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.

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

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.

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

Understanding how the electronic excitation of DNA changes in response to different high-energy particles is central to advancing ion beam cancer therapy and other related approaches, such as boron neutron capture therapy. While protons have been the predominant ions of choice in ion beam cancer therapy, heavier ions, particularly carbon ions, have drawn significant attention over the past decade. Carbon ions are expected to transfer larger amounts of energy according to linear response theory. However, molecular-level details of the electronic excitation under heavier ion irradiation remain unknown. In this work, we use real-time time-dependent density functional theory simulations to examine the quantum-mechanical details of DNA electronic excitations in water under proton, α-particle, and carbon ion irradiation. Our results show that the energy transfer does indeed increase for the heavier ions, while the excitation remains highly conformal. However, the increase in the energy transfer rate, measured by electronic stopping power, does not match the prediction by the linear response model, even when accounting for the velocity dependence of the irradiating ion's charge. The simulations also reveal that while the number of holes generated on DNA increases for heavier ions, the increase is only partially responsible for the larger stopping power. Larger numbers of highly energetic holes formed from the heavier ions also contribute significantly to the increased electronic stopping power.

Use of Gaussian-Type Functions for Describing Fast Ion-Matter Irradiation with Time-Dependent Density Functional Theory

The electronic stopping power is an observable property that quantifies the ability of swift ions to penetrate matter to transfer energy to the electron cloud. The recent literature has proven the value of Real-Time Time-Dependent Density Functional Theory to accurately evaluate this property from first-principles, but questions remain regarding the capability of computer codes relying on atom-centered basis functions to capture the physics at play. In this Perspective, we draw attention to the fact that irradiation by swift ions triggers electron emission into the continuum, especially at the Bragg peak. We investigate the ability of Gaussian atomic orbitals (AOC), which were fitted to mimic continuum wave functions, to improve electronic stopping power predictions. AOC are added to standard correlation-consistent basis sets or STO minimal basis sets. Our benchmarks for water irradiation by fast protons clearly advocate for the use of AOC, especially near the Bragg peak. We show that AOC only need to be placed on the molecules struck by the ion. The number of AOC that are added to the usual basis set is relatively small compared to the total number of atomic orbitals, making the use of such a basis set an excellent choice from a computational cost point of view. The optimum basis set combination is applied for the calculation of the stopping power of a proton in water with encouraging agreement with experimental data.

Stretching effects on non-adiabatic electron dynamic behavior in poly(dG)-poly(dC) DNA upon the proton irradiation

The electronic excitations caused by DNA when exposed to ion radiation is essential to DNA damage. In this paper, we investigated the energy deposition and electron excitation process of DNA with reasonable stretching range upon proton irradiation based on time-dependent density functional theory. Stretching changes the strength of hydrogen bonding between the DNA base pairs, which in turn affects the Coulomb interaction between the projectile and DNA. As a semi-flexible molecule, the way of energy deposition is weakly sensitive to the stretching rate of DNA. However, the increase of stretching rate causes the increase of charge density along the trajectory channel, sequentially resulting in an increase in proton resistance along the intruding channel. The Mulliken charge analysis indicates that the guanine base and guanine ribose are ionized, meanwhile the cytosine base and cytosine ribose are reduced at all stretching rates. In a few femtoseconds, there exists an electron flow passing through the guanine ribose, guanine, cytosine base and the cytosine ribose in turn. This electron flow increases electron transfer and DNA ionization, promoting the side chain damage of the DNA upon ion irradiation. Our results provide a theoretical insight for deciphering the physical mechanism of the early stage of the irradiation process, and are also of great significance for the study of particle beam cancer therapy in different biological tissues.

Electronic Excitation Response of DNA to High-Energy Proton Radiation in Water

The lack of molecular-level understanding for the electronic excitation response of DNA to charged particle radiation, such as high-energy protons, remains a fundamental scientific bottleneck in advancing proton and other ion beam cancer therapies. In particular, the dependence of different types of DNA damage on high-energy protons represents a significant knowledge void. Here we employ first-principles real-time time-dependent density functional theory simulation, using a massively parallel supercomputer, to unravel the quantum-mechanical details of the energy transfer from high-energy protons to DNA in water. The calculations reveal that protons deposit significantly more energy onto the DNA sugar-phosphate side chains than onto the nucleobases, and greater energy transfer is expected onto the DNA side chains than onto water. As a result of this electronic stopping process, highly energetic holes are generated on the DNA side chains as a source of oxidative damage.

The contribution of inner electron excitation to the electronic stopping power of palladium for protons

The electronic stopping power of palladium (Pd) for protons is investigated based on time-dependent density functional theory combined with Ehrenfest molecular dynamics simulations. The electronic stopping power of Pd with explicitly considering inner electrons for protons is calculated and the excitation mechanism for the inner electrons of Pd is revealed. The velocity proportionality of the low-energy stopping power of Pd is reproduced. Our study verified that the inner electron excitation contributes significantly to the electronic stopping power of Pd in the high energy range, which is strongly dependent on the impact parameter. The electronic stopping power obtained from the off-channeling geometry is in quantitative agreement with the experimental data in a wide velocity range, and the discrepancy around the stopping maximum is further reduced by considering the relativistic correction on the binding energy of inner electrons. The velocity dependence of the mean steady-state charge of protons is quantified, and the results showed that the participation of 4p-electrons reduces the mean steady-state charge of protons, and consequently decreases the electronic stopping power of Pd in the low energy range.

Dynamic interplay between thionine and DNA under carbon ion irradiation: a real-time first-principles study

Understanding the interactions between deoxyribonucleic acid (DNA) and photosensitizer under ion irradiation benefits the development of aptasensors, DNA biosensors and cancer diagnosis. Using real-time time-depended density functional theory, by simulating high-energy C ion passing through DNA with poly(dG)·poly(dC) sequence and that with embedded thionine (3,7-diamino-5-phenothiazinium, TH), we compared the electronic stopping power (ESP), evolution of the structure and charge, and absorption spectrum. TH inserting leads the increase in space charge density, a larger electron de-excitation and a larger ESP, but the speed corresponding to the maximum ESP is almost same. When C ion passes through TH-DNA, the structure of TH slightly changes and there still exists noncovalent interaction between TH and DNA, but the absorption coefficient depends on the electron occupied state of TH when the ion passes through. These results indicate that at low radiation doses, TH still can be a DNA detector, although its response wavelength and intensity have been slightly changed, and provide a theoretical reference to improve the possible application of phenothiazine dye in DNA biosensor under ion irradiation.

Nonlinear electronic excitation in water under proton irradiation: a first principles study

Nonlinear dynamics of electronic excitation bridge physical and physicochemical stages of water radiolysis under proton irradiation, a multi-scale physicochemical process that is fundamental to a wide range of technological and medical applications of high-energy protons. We study the spatial and temporal changes to the excited holes generated in this ionization event using first-principles theory simulation. A significant majority of holes are formed in the immediate vicinity of the irradiating proton paths, and these holes decay rapidly, while secondary excitations are simultaneously induced in regions farther away. While the hole population remains constant, the observed spatially spreading hole distribution cannot be described as concentration-dependent diffusion current. Compared to the primary excitation induced by the irradiating protons, the secondary excitation farther away is somewhat less energetic. The first-principles theory simulation here provides a detailed description of how the primary excitation by proton radiation precedes the formation of cationic holes, which undergo ultrafast chemical processes in water radiolysis.

Mixed stochastic-deterministic time-dependent density functional theory: application to stopping power of warm dense carbon

Warm dense matter (WDM) describes an intermediate phase, between condensed matter and classical plasmas, found in natural and man-made systems. In a laboratory setting, WDM is often created dynamically. It is typically laser or pulse-power generated and can be difficult to characterize experimentally. Measuring the energy loss of high energy ions, caused by a WDM target, is both a promising diagnostic and of fundamental importance to inertial confinement fusion research. However, electron coupling, degeneracy, and quantum effects limit the accuracy of easily calculable kinetic models for stopping power, while high temperatures make the traditional tools of condensed matter, e.g. time-dependent density functional theory (TD-DFT), often intractable. We have developed a mixed stochastic-deterministic approach to TD-DFT which provides more efficient computation while maintaining the required precision for model discrimination. Recently, this approach showed significant improvement compared to models when compared to experimental energy loss measurements in WDM carbon. Here, we describe this approach and demonstrate its application to warm dense carbon stopping across a range of projectile velocities. We compare direct stopping-power calculation to approaches based on combining homogeneous electron gas response with bound electrons, with parameters extracted from our TD-DFT calculations.

Simulating electronic excitation and dynamics with real-time propagation approach to TDDFT within plane-wave pseudopotential formulation

We give a perspective on simulating electronic excitation and dynamics using the real-time propagation approach to time-dependent density functional theory (RT-TDDFT) in the plane-wave pseudopotential formulation. RT-TDDFT is implemented in various numerical formalisms in recent years, and its practical application often dictates the most appropriate implementation of the theory. We discuss recent developments and challenges, emphasizing numerical aspects of studying real systems. Several applications of RT-TDDFT simulation are discussed to highlight how the approach is used to study interesting electronic excitation and dynamics phenomena in recent years.

First Principles Dynamics Study of Excited Hole Relaxation in DNA

A recent theoretical work showed that ion irradiation generates excited holes deep within the valence band of DNA. In this work, we investigate the excited hole relaxation toward HOMO using a first-principles computational method following such ionization events. The excited hole relaxation is found to depend significantly on the energetic position of the excited hole generated. The relaxation process is found to be an order of magnitude slower for holes that are generated deeper than 20 eV than those generated within 10 eV, where the probability for the initial ionization events is the highest. However, the excited holes that are generated in different spatial moieties such as DNA nucleotide bases and phosphate backbones do not show noticeable differences in terms of the relaxation time. Our work also shows that decoherence due to nuclei dynamics slows down the relaxation by a factor of two or more. At the same time, the relaxation time is found to be less than a couple of picoseconds, much shorter than typical timescales associated with chemical bond dissociation.

PyRad: A software shell for simulating radiolysis with Qball package

The assessment of the radiolytic stability of media is an important task in the fields of nuclear power engineering and radiochemistry. Such studies must be carried out in special laboratory conditions with the use of sources of ionizing radiation, which may increase personal doses of the staff. In addition, difficulties arise in studying the products of irradiated media. While it is impossible to abandon experiments to obtain reliable results in this area, computational methods of quantum chemistry can reduce the number of experiments and help understand the mechanisms of the reactions that occur during radiolysis. Here we would like to present a software shell of the Qb@ll program performing time-dependent density functional theory simulations of the radiolysis process.

First-Principles Simulations of Biological Molecules Subjected to Ionizing Radiation

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.

Dynamical transition orbitals: A particle-hole description in real-time TDDFT dynamics

We expand the concept of natural transition orbitals in the context of real-time time-dependent density functional theory (RT-TDDFT) and show its application in practical calculations. Kohn-Sham single-particle wavefunctions are propagated in RT-TDDFT simulation, and physical properties remain invariant under their unitary transformation. In this work, we exploit this gauge freedom and expand the concept of natural transition orbitals, which is widely used in linear-response TDDFT, for obtaining a particle-hole description in RT-TDDFT simulation. While linear-response TDDFT is widely used to study electronic excitation, RT-TDDFT can be employed more generally to simulate non-equilibrium electron dynamics. Studying electron dynamics in terms of dynamic transitions of particle-hole pairs is, however, not straightforward in the RT-TDDFT simulation. By constructing natural transition orbitals through projecting time-dependent Kohn-Sham wave functions onto occupied/unoccupied eigenstate subspaces, we show that linear combinations of a pair of the resulting hole/particle orbitals form a new gauge, which we refer to as dynamical transition orbitals. We demonstrate the utility of this framework to analyze RT-TDDFT simulations of optical excitation and electronic stopping dynamics in the particle-hole description.

Early Events in Radiobiology: Isolated and Cluster DNA Damage Induced by Initial Cations and Nonionizing Secondary Electrons

Radiobiological damage is principally triggered by an initial cation and a secondary electron (SE). We address the fundamental questions: What lesions are first produced in DNA by this cation or nonionizing SE? What are their relative contributions to isolated and potentially lethal cluster lesions? Five monolayer films of dry plasmid DNA deposited on graphite or tantalum substrates are bombarded by 0.1-100 eV electrons in a vacuum. From measurements of the current transmitted through the films, 3.5 and 4.5 cations per incident 60 and 100 eV electrons, respectively, are estimated to be produced and stabilized within DNA. Damage analysis at 6, 10, 20, 30, 60, and 100 eV indicates that essentially all lesions, but preferentially cluster damages, are produced by non-ionizing or weakly ionizing electrons of energies below 12 eV. Most of these lesions are induced within femtosecond times, via transient anions and electron transfer within DNA, with little contributions from the numerous cations.

Interactions of Single Particle with Organic Matters: A Facile Bottom-Up Approach to Low Dimensional Nanostructures

A particle induces a pack of chemical reactions in nanospace: chemical reactions confined into extremely small space provide an ultimate technique for the nanofabrication of organic matter with a variety of functions. Since the discovery of particle accelerators, an extremely high energy density can be deposited, even by a single isolated particle with MeV-ordered kinetic energy. However, this was considered to cause severe damages to organic molecules due to its relatively small bond energies, and lack of ability to control the reactions precisely to form the structures while retaining physico-chemical molecular functionalities. Practically, the severely damaged area along a particle trajectory: a core of a particle track has been simply visualized for the detection/dosimetry of an incident particle to the matters, or been removed to lead nanopores and functionalized by refilling/grafting of fresh organic/inorganic materials. The use of intra-track reactions in the so-called “penumbra” or “halo” area of functional organic materials has been realized and provided us with novel and facile protocols to provide low dimensional nano-materials with perfect size controllability in the 21st century. These protocols are now referred to as single particle nanofabrication technique (SPNT) and/or single particle triggered linear polymerization technique (STLiP), paving the way towards a new approach for nanomaterials with desired functionalities from original molecules. Herein, we report on the extremely wide applicability of SPNT/STLiP protocols for the future development of materials for opto-electronic, catalytic, and biological applications among others.

First-Principles Modeling of Electronic Stopping in Complex Matter under Ion Irradiation

Electronic stopping refers to the dynamical energy-transfer process to electrons in matter from highly energetic charged particles such as high-velocity protons. We discuss recent progress in theoretical studies of electronic stopping in condensed matter under ion irradiation, focusing on modern electronic structure theory's role in enabling the study of electronic excitation dynamics that result from the energy transfer. In the last few decades, first-principles simulation approaches based on real-time time-dependent density functional theory have greatly advanced the field. While linear response theory is widely used to study electronic stopping processes, especially for simple solids, novel first-principles dynamics approaches now allow us to study chemically complex systems and also yield detailed descriptions of electronic excitations at the molecular scale. Outstanding challenges for further advancement of electronic stopping modeling are also discussed from the viewpoint of electronic structure theory.

The physical stage of radiolysis of solvated DNA by high-energy-transfer particles: insights from new first principles simulations

Electron dynamics simulations based on density functional theory are carried out on nanometric molecular systems to decipher the primary processes following irradiation of bio-macromolecules by high energy transfer charged particles.