Semiempirical model for the ion impact ionization of complex biological media

Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment

This roadmap reviews the new, highly interdisciplinary research field studying the behavior of condensed matter systems exposed to radiation. The Review highlights several recent advances in the field and provides a roadmap for the development of the field over the next decade. Condensed matter systems exposed to radiation can be inorganic, organic, or biological, finite or infinite, composed of different molecular species or materials, exist in different phases, and operate under different thermodynamic conditions. Many of the key phenomena related to the behavior of irradiated systems are very similar and can be understood based on the same fundamental theoretical principles and computational approaches. The multiscale nature of such phenomena requires the quantitative description of the radiation-induced effects occurring at different spatial and temporal scales, ranging from the atomic to the macroscopic, and the interlinks between such descriptions. The multiscale nature of the effects and the similarity of their manifestation in systems of different origins necessarily bring together different disciplines, such as physics, chemistry, biology, materials science, nanoscience, and biomedical research, demonstrating the numerous interlinks and commonalities between them. This research field is highly relevant to many novel and emerging technologies and medical applications.

On the Thermal Behavior during Spatial Anisotropic Femtoseconds Laser-DNA Interaction: The Crucial Role of Hermite Polynomials

A novel analytical formalism based on the quantum heat transport equation is proposed for the interaction of fs-laser pulses with deoxyribonucleic acid (DNA) strands. The formalism has the intensity of the laser beam and the interaction time between the laser and the DNA as input parameters. To this end, the thermal distribution generated in the irradiated DNA strands was introduced by splitting the laser beam into transverse Hermite-Gauss modes. To achieve this goal, a new powerful mathematical model was developed and applied. Fluctuations in laser intensity were taken into account by modeling them as superpositions of Hermite-Gauss laser modes. These analyses were carried out for a laser pulse duration of 100 fs, where a tiny heat-affected zone is expected, with positive predicted effects on the stability and repeatability of this technology. The main conclusion is that the laser beam spatial distribution intensity plays an essential role in the generation of the shape and magnitude of the thermal field at the junction of the irradiated DNA strands. The model may prove useful in modeling laser beam processing under significant intensity fluctuations. There are at least two main areas of application for the present model of heat transfer from laser to DNA: (i) the study of DNA elongation without destroying the target information (for a sample temperature variation lower than 10 K; in the case of H[1,y]); and (ii) cancer treatment (especially of skin tissue), where we should obtain a temperature variation higher than 10 K (but lower than 30 K; in the case of H[2,y], H[4,y]), in order to eradicate the diseased cells.

Energy Deposition around Swift Carbon-Ion Tracks in Liquid Water

Energetic carbon ions are promising projectiles used for cancer radiotherapy. A thorough knowledge of how the energy of these ions is deposited in biological media (mainly composed of liquid water) is required. This can be attained by means of detailed computer simulations, both macroscopically (relevant for appropriately delivering the dose) and at the nanoscale (important for determining the inflicted radiobiological damage). The energy lost per unit path length (i.e., the so-called stopping power) of carbon ions is here theoretically calculated within the dielectric formalism from the excitation spectrum of liquid water obtained from two complementary approaches (one relying on an optical-data model and the other exclusively on ab initio calculations). In addition, the energy carried at the nanometre scale by the generated secondary electrons around the ion's path is simulated by means of a detailed Monte Carlo code. For this purpose, we use the ion and electron cross sections calculated by means of state-of-the art approaches suited to take into account the condensed-phase nature of the liquid water target. As a result of these simulations, the radial dose around the ion's path is obtained, as well as the distributions of clustered events in nanometric volumes similar to the dimensions of DNA convolutions, contributing to the biological damage for carbon ions in a wide energy range, covering from the plateau to the maximum of the Bragg peak.

Irradiation-driven molecular dynamics simulation of the FEBID process for Pt(PF3)4

This paper presents a detailed computational protocol for the atomistic simulation of formation and growth of metal-containing nanostructures during focused electron beam-induced deposition (FEBID). The protocol is based upon irradiation-driven molecular dynamics (IDMD), a novel and general methodology for computer simulations of irradiation-driven transformations of complex molecular systems by means of the advanced software packages MBN Explorer and MBN Studio. Atomistic simulations performed following the formulated protocol provide valuable insights into the fundamental mechanisms of electron-induced precursor fragmentation and the related mechanism of nanostructure formation and growth using FEBID, which are essential for the further advancement of FEBID-based nanofabrication. The developed computational methodology is general and applicable to different precursor molecules, substrate types, and irradiation regimes. The methodology can also be adjusted to simulate the nanostructure formation by other nanofabrication techniques using electron beams, such as direct electron beam lithography. In the present study, the methodology is applied to the IDMD simulation of the FEBID of Pt(PF3)4, a widely studied precursor molecule, on a SiO2 surface. The simulations reveal the processes driving the initial phase of nanostructure formation during FEBID, including the nucleation of Pt atoms and the formation of small metal clusters on the surface, followed by their aggregation and the formation of dendritic platinum nanostructures. The analysis of the simulation results provides spatially resolved relative metal content, height, and growth rate of the deposits, which represents valuable reference data for the experimental characterization of the nanostructures grown by FEBID.

A Mathematical Radiobiological Model (MRM) to Predict Complex DNA Damage and Cell Survival for Ionizing Particle Radiations of Varying Quality

Predicting radiobiological effects is important in different areas of basic or clinical applications using ionizing radiation (IR); for example, towards optimizing radiation protection or radiation therapy protocols. In this case, we utilized as a basis the ‘MultiScale Approach (MSA)’ model and developed an integrated mathematical radiobiological model (MRM) with several modifications and improvements. Based on this new adaptation of the MSA model, we have predicted cell-specific levels of initial complex DNA damage and cell survival for irradiation with ¹¹Β, ¹²C, ¹⁴Ν, ¹⁶Ο, ²⁰Νe, ⁴⁰Αr, ²⁸Si and ⁵⁶Fe ions by using only three input parameters (particle’s LET and two cell-specific parameters: the cross sectional area of each cell nucleus and its genome size). The model-predicted survival curves are in good agreement with the experimental ones. The particle Relative Biological Effectiveness (RBE) and Oxygen Enhancement Ratio (OER) are also calculated in a very satisfactory way. The proposed integrated MRM model (within current limitations) can be a useful tool for the assessment of radiation biological damage for ions used in hadron-beam radiation therapy or radiation protection purposes.

Excitation and ionisation cross-sections in condensed-phase biomaterials by electrons down to very low energy: application to liquid water and genetic building blocks

A model is presented for computing electron-impact electronic excitation and ionisation cross-sections for arbitrary condensed-phase biomaterials in a wide energy range, showing a general good agreement with the available experimental data.

Multiscale simulation of the focused electron beam induced deposition process

Focused electron beam induced deposition (FEBID) is a powerful technique for 3D-printing of complex nanodevices. However, for resolutions below 10 nm, it struggles to control size, morphology and composition of the structures, due to a lack of molecular-level understanding of the underlying irradiation-driven chemistry (IDC). Computational modeling is a tool to comprehend and further optimize FEBID-related technologies. Here we utilize a novel multiscale methodology which couples Monte Carlo simulations for radiation transport with irradiation-driven molecular dynamics for simulating IDC with atomistic resolution. Through an in depth analysis of [Formula: see text] deposition on [Formula: see text] and its subsequent irradiation with electrons, we provide a comprehensive description of the FEBID process and its intrinsic operation. Our analysis reveals that simulations deliver unprecedented results in modeling the FEBID process, demonstrating an excellent agreement with available experimental data of the simulated nanomaterial composition, microstructure and growth rate as a function of the primary beam parameters. The generality of the methodology provides a powerful tool to study versatile problems where IDC and multiscale phenomena play an essential role.

Proton transport modeling in a realistic biological environment by using TILDA-V

Whether it is in radiobiology to identify DNA lesions or in medicine to adapt the radiotherapeutic protocols, a detailed understanding of the radiation-induced interactions in living matter is required. Monte Carlo track-structure codes have been successfully developed to describe these interactions and predict the radiation-induced energy deposits at the nanoscale level in the medium of interest. In this work, the quantum-mechanically based Monte Carlo track-structure code TILDA-V has been used to compute the slowing-down of protons in water and DNA. Stopping power and range are then reported and compared with existing data. Then, a first application of TILDA-V to cellular irradiations is also reported in order to highlight the absolute necessity of taking into account a realistic description of the cellular environment in microdosimetry.

First principles simulation of damage to solvated nucleotides due to shock waves

We present a first-principles molecular dynamics study of the effect of shock waves (SWs) propagating in a model biological medium. We find that the SW can cause chemical modifications through varied and complex mechanisms, in particular, phosphate-sugar and sugar-base bond breaks. In addition, the SW promotes the dissociation of water molecules, thus enhancing the ionic strength of the medium. Freed protons can hydrolyze base and sugar rings previously opened by the shock. However, many of these events are only temporary, and bonds reform rapidly. Irreversible damage is observed for pressures above 15-20 GPa. These results are important to gain a better understanding of the microscopic damage mechanisms underlying cosmic-ray irradiation in space and ion-beam cancer therapy.

Energy Spectra of Protons and Generated Secondary Electrons around the Bragg Peak in Materials of Interest in Proton Therapy

The number and energy of secondary electrons generated around the trajectories of swift protons interacting with biological materials are highly relevant in proton therapy, due to the prominent role of low-energy electrons in the production of biodamage. For a given material, electron energy distributions are determined by the proton energy; and it is imperative that the distribution of proton energy at depths around the Bragg peak region be described as accurately as possible. With this objective, we simulated the energy distributions of proton beams of clinically relevant energies (50-300 MeV) at depths around the Bragg peak in liquid water and the water-equivalent polymer poly(methyl methacrylate) (PMMA). By using a simple model, this simulation has been conveniently extended to account for nuclear fragmentation reactions, providing depth-dose curves in excellent agreement with available experimental data. Special care has been taken to describe the electronic excitation spectrum of the target, taking into account its condensed phase nature. A predictive formula has been obtained for the mean value and the width of the proton energy distribution at the Bragg peak depth, quantities which are found to grow linearly with the initial energy of the beam, in good agreement with available data. To accurately characterize (in number and energy) the electrons generated around the proton paths, the energy distributions of the latter at each depth have been convoluted with the energy-dependent ionization inverse mean free paths. This results in a number of low-energy electrons around the Bragg peak larger than when only the proton beam average energy at the given depths is considered. The convoluted ionization inverse mean free path closely resembles the Bragg curve shape. The average energy of the secondary electrons is nearly constant (∼55 eV for liquid water and ∼43 eV for PMMA) in the plateau of the Bragg curve, independent of the proton incident energy and suddenly decaying once the Bragg peak is reached. These findings highlight the importance of a precise calculation of the proton beam energy distribution as a function of the target depth to reliably characterize the secondary electrons generated around the Bragg peak region.

Simple and universal model for electron-impact ionization of complex biomolecules

We present a simple and universal approach to calculate the total ionization cross section (TICS) for electron impact ionization in DNA bases and other biomaterials in the condensed phase. Evaluating the electron impact TICS plays a vital role in ion-beam radiobiology simulation at the cellular level, as secondary electrons are the main cause of DNA damage in particle cancer therapy. Our method is based on extending the dielectric formalism. The calculated results agree well with experimental data and show a good comparison with other theoretical calculations. This method only requires information of the chemical composition and density and an estimate of the mean binding energy to produce reasonably accurate TICS of complex biomolecules. Because of its simplicity and great predictive effectiveness, this method could be helpful in situations where the experimental TICS data are absent or scarce, such as in particle cancer therapy.

Low-energy electron inelastic mean free paths for liquid water

We improve the Mermin-Penn algorithm (MPA) for determining the energy loss function (ELF) within the dielectric formalism. The present algorithm is applicable not only to real metals, but also to materials that have an energy gap in the excitation spectrum. Applying the improved MPA to liquid water, we show that the present algorithm is able to address the ELF overestimation at the energy gap, and the calculated results are in good agreement with experimental data.

Radiation track, DNA damage and response-a review

The purpose of this paper has been to review the current status and progress of the field of radiation biophysics, and draw attention to the fact that physics, in general, and radiation physics in particular, with the aid of mathematical modeling, can help elucidate biological mechanisms and cancer therapies. We hypothesize that concepts of condensed-matter physics along with the new genomic knowledge and technologies and mechanistic mathematical modeling in conjunction with advances in experimental DNA (Deoxyrinonucleic acid molecule) repair and cell signaling have now provided us with unprecedented opportunities in radiation biophysics to address problems in targeted cancer therapy, and genetic risk estimation in humans. Obviously, one is not dealing with 'low-hanging fruit', but it will be a major scientific achievement if it becomes possible to state, in another decade or so, that we can link mechanistically the stages between the initial radiation-induced DNA damage; in particular, at doses of radiation less than 2 Gy and with structural changes in genomic DNA as a precursor to cell inactivation and/or mutations leading to genetic diseases. The paper presents recent development in the physics of radiation track structure contained in the computer code system KURBUC, in particular for low-energy electrons in the condensed phase of water for which we provide a comprehensive discussion of the dielectric response function approach. The state-of-the-art in the simulation of proton and carbon ion tracks in the Bragg peak region is also presented. The paper presents a critical discussion of the models used for elastic scattering, and the validity of the trajectory approach in low-electron transport. Brief discussions of mechanistic and quantitative aspects of microdosimetry, DNA damage and DNA repair are also included as developed by the authors' work.

Revealing the mechanism of the low-energy electron yield enhancement from sensitizing nanoparticles

We provide a physical explanation for the enhancement of the low-energy electron production by sensitizing nanoparticles due to irradiation by fast ions. It is demonstrated that a significant increase in the number of emitted electrons arises from the collective electron excitations in the nanoparticle. We predict a new mechanism of the yield enhancement due to the plasmon excitations and quantitatively estimate its contribution to the electron production. Revealing the nanoscale mechanism of the electron yield enhancement, we provide an efficient tool for evaluating the yield of the emitted electron from various sensitizers. It is shown that the number of low-energy electrons generated by the gold and platinum nanoparticles of a given size exceeds that produced by the equivalent volume of water and by other metallic (e.g., gadolinium) nanoparticles by an order of magnitude. This observation emphasizes the sensitization effect of the noble-metal nanoparticles and endorses their application in novel technologies of cancer therapy with ionizing radiation.

Angular and energy distributions of electrons produced in arbitrary biomaterials by proton impact

We present a simple method for obtaining reliable angular and energy distributions of electrons ejected from arbitrary condensed biomaterials by proton impact. Relying on a suitable description of the electronic excitation spectrum and a physically motivated relation between the ion and electron scattering angles, it yields cross sections in rather good agreement with experimental data in a broad range of ejection angles and energies, by only using as input the target composition and density. The versatility and simplicity of the method, which can be also extended to other charged particles, make it especially suited for obtaining ionization data for any complex biomaterial present in realistic cellular environments.