arXiv subjects

Pablo de Vera

Publications and source records attributed to Pablo de Vera.

17 recordsLinked to original sources

arXiv2026

Proposal of a consistent value for the mean excitation energy of liquid water using advanced modeling, detailed simulations and precission proton Bragg curves

Protontherapy precision depends on accurately knowing the stopping power of liquid water, as it is the most abundant component of soft body tissues. Difficulties when working with volatile liquids have led to a long-standing debate regarding the values of the stopping power and the mean excitation energy $I$ of liquid water. The equivalence between the stopping power of liquid water and amorphous ice per unit mass density across all clinically relevant proton energies opens the possibility to obtain a reliable estimation of the $I$-value of liquid water. In this work, we employ two complementary theoretical methodologies to assess the proton stopping power of water. The MELF-GOS (Mermin Energy Loss Function - Generalized Oscillator Strengths) approach, based on the perturbative dielectric formalism, serves as an accurate reference for sufficiently high energies, while the novel non-perturbative TDDFT-Penn (time-dependent density functional theory - Penn) method ensures accuracy for energies even below the stopping maximum. These stopping-power values were incorporated into the simulation code SEICS (Simulation of Energetic Ions and Clusters through Solids) to evaluate proton Bragg curves from $1$ to $230$ MeV. Comparisons with available precise depth-dose measurements provide critical insights that help establish the consistent value $I = 79.4$ eV for liquid water, providing robust physical grounds for improving range prediction for treatment planning.

physics.med-ph↗

arXiv2024

Assessing the electronic excitation spectra of chromium, palladium and samarium from their stopping quantities

The electronic excitation spectrum of a material characterises the response to external electromagnetic perturbations through its energy loss function (ELF), which is obtained from several experimental sources that usually do not completely agree among them. In this work, we assess the available ELF of three metals, namely chromium, palladium, and samarium, by using the dielectric formalism to calculate relevant stopping quantities, such as the stopping cross sections for protons and alpha particles, as well as the corresponding electron inelastic mean free paths. The comparison of these quantities (as calculated from different sets of ELF) with the available experimental data for each of the analyzed metals highlights the promising capability of the recently proposed reverse Monte Carlo method for the determination of the ELF. This work also analyzes the contribution of different electronic shells to the electronic excitation spectra of these materials, and reveals the important role that the excitation of "semi-core" bands plays on the energy loss mechanism for these metals.

cond-mat.mtrl-sci↗

arXiv2024

Simulation of depth-dose curves and water equivalent ratios of energetic proton beams in cortical bone

We have determined the depth-dose curve, the penetration range, and the water equivalent ratio (WER), for proton beams of clinical energies in cortical bone, by means of a detailed and accurate simulation that combines molecular dynamics and Monte Carlo techniques. The fundamental input quantities (stopping power and energy loss straggling) for the simulation were obtained from a reliable electronic excitation spectrum of the condensed-phase target, which takes into account the organic and mineral phases that form it. Our simulations with these inputs, that are in excellent agreement with the scarce data available for a cortical bone target, deviate from simulations performed using other stopping quantities, such as those provided by the International Commission on Radiation Units and Measurements (ICRU) in its widely used Report 49. The results of this work emphasize the importance of an accurate determination of the stopping quantities of cortical bone in order to advance towards the millimetric precision for the proton penetration ranges and deposited dose needed in radiotherapy.

physics.med-ph↗

arXiv2021

Simulating the nanometric track-structure of carbon ion beams in liquid water at energies relevant for hadrontherapy

The nanometric track-structure of energetic ion beams in biological media determines the direct physical damage to living cells, which is one of the main responsibles of their killing or inactivation during radiotherapy treatments or under cosmic radiation bombardment. In the present work, detailed track-structure Monte Carlo simulations, performed with the code SEED (Secondary Electron Energy Deposition), are presented for carbon ions in a wide energy range in liquid water. Liquid water is the main constituent of biological tissues, and carbon ions are one of the most promising projectiles currently available for ion beam cancer therapy. The simulations are based on accurate cross sections for the different elastic and inelastic events determining the interaction of charged particles with condensed-phase materials. The latter are derived from the ab initio calculation of the electronic excitation spectrum of liquid water by means of time-dependent density functional theory (TDDFT), which is then used within the dielectric formalism to obtain inelastic electronic cross sections for both carbon ions and secondary electrons. Both the ionisation cross sections of water by carbon ions and the excitation and ionisation cross sections for electron impact are obtained in very good agreement with known experimental data. The elastic scattering cross sections for electrons in condensed-phase water are also obtained from ab initio calculations by solving the Dirac-Hartree-Fock equation. The detailed simulations fed with reliable cross sections allow to assess the contribution of different physical mechanisms (electronic excitation, ionisation and dissociative electron attachment -DEA-) to the carbon ion-induced direct biodamage.

cond-mat.soft↗

arXiv2021

Calculated energy loss of swift light ions in platinum and gold: importance of the target electronic excitation spectrum

Understanding and predicting the energy loss of swift ions in metals is important for many applications of charged particle beams, such as analysis and modification of materials, and recently for modelling metal nanoparticle radiosensitisation in ion beam cancer therapy. We have calculated the stopping power of the transition metals Pt and Au for protons and alpha particles in a wide energy range, using the dielectric formalism, which realistically accounts for the excitation spectrum of each metal through the Mermin Energy Loss Function - Generalised Oscillator Strength methodology. For each combination of projectile, energy and target, we have considered: (i) the equilibrium charge state of the projectile through the target, (ii) the energy-loss due to electron capture and loss processes, and (iii) the energy loss resulting from the polarisation of the projectile's electronic cloud due to the self-induced electric field. Our calculated stopping powers show a fairly good agreement with the available experimental data for platinum and gold, particularly the most recent ones around the stopping power maximum, which validates the methodology we have used to be further extended to other transition metals. For the materials studied (platinum and gold), two commonly used and different sources of the experimental excitation spectrum yield comparable calculated stopping powers and mean excitation energies, the latter being closer to the most recent data provided in a recent ICRU Report than to previous compilations. Despite the small differences in the sources of excitation spectra of these metals, they lead to practically the same stopping power results as far as they reproduce the main excitation features of the material and fulfil physically motivated sum rules.

cond-mat.other↗

arXiv2021

Electronic excitation spectra of cerium oxides: from ab initio dielectric response functions to Monte Carlo charge transport simulations

Nanomaterials made of the cerium oxides CeO$_2$ and Ce$_2$O$_3$ have a broad range of applications, from catalysts in automotive, industrial or energy operations to promising materials to enhance hadrontherapy effectiveness in oncological treatments. To elucidate the physico-chemical mechanisms involved in these processes, it is of paramount importance to know the electronic excitation spectra of these oxides, which are obtained here through high-accuracy linear-response time-dependent density functional theory calculations. In particular, the macroscopic dielectric response functions $\barε$ of both bulk CeO$_2$ and Ce$_2$O$_3$ are derived, which compare remarkably well with the available experimental data. These results stress the importance of appropriately accounting for local field effects to model the dielectric function of metal oxides. Furthermore, we reckon the materials energy loss functions $\mbox{Im} (-1/\barε)$, including the accurate evaluation of the momentum transfer dispersion from first-principles. In this respect, by using a Mermin-type parametrization we are able to model the contribution of different electronic excitations to the dielectric loss function. Finally, from the knowledge of the electron inelastic mean free path, together with the elastic mean free path provided by the relativistic Mott theory, we carry out statistical Monte Carlo (MC) charge transport simulations to reproduce the major features of the reported experimental reflection electron energy loss (REEL) spectra of cerium oxides. The good agreement with REEL experimental data strongly supports our approach based on MC modelling informed by ab initio calculated electronic excitation spectra in a broad range of momentum and energy transfers.

cond-mat.mtrl-sci↗

arXiv2020

Molecular dynamics simulations of sodium nanoparticle deposition on magnesium oxide

The interaction of mass-selected atomic clusters and nanoparticles with surfaces attracts strong interest in view of fundamental research and technological applications. Understanding dynamics of the deposition process is important for controlling structure and functioning of deposited nanoparticles on a substrate, but experimental techniques can usually observe only the final outcome of the deposition process. In this paper, the deposition of 4 nm-sized sodium nanoparticles on an experimentally relevant magnesium oxide substrate is studied by means of classical molecular dynamics simulations. An empirical force field is derived which accounts for the interaction of highly polarizable Na atoms with the surface, reproducing the results of previously reported quantum mechanics/molecular mechanics simulations. Molecular dynamics simulations permit exploring the dynamics of deposited nanoparticles on long timescales on the order of hundreds of picoseconds, thus enabling the analysis of energy relaxation mechanisms and the evolution of nanoparticle structure up to its thermalization with the substrate. Several nanoparticle characteristics, such as internal structure, contact angle, and aspect ratio are studied in a broad deposition energy range from the soft landing to multi-fragmentation regimes.

physics.atm-clus↗

arXiv2020

On the relative role of the physical mechanisms on complex biodamage induced by carbon irradiation

The effective use of swift ion beams in cancer treatment (known as hadrontherapy) as well as an appropriate protection in manned space missions rely on the accurate understanding of energy delivery to cells damaging their genetic information. The key ingredient characterizing the response of a medium to the perturbation induced by charged particles is its electronic excitation spectrum. By using linear response time-dependent density functional theory, we obtain the energy and momentum transfer excitation spectrum (the energy-loss function, ELF) of liquid water (main constituent of biological tissues), in excellent agreement with experimental data. The inelastic scattering cross sections obtained from this ELF, together with the elastic scattering cross sections derived considering the condensed phase nature of the medium, are used to perform accurate Monte Carlo simulations of the energy deposited by swift carbon ions in liquid water and carried away by the generated secondary electrons producing inelastic events (ionization, excitation, and dissociation electron attachment, DEA), strongly correlated with cellular death, which are scored in sensitive volumes having the size of two DNA convolutions. The sizes of clusters of damaging events for a wide range of carbon ion energies, from those relevant to hadrontherapy up to cosmic radiation, predict with unprecedented statistical accuracy the nature and relative magnitude of the main inelastic processes contributing to radiation biodamage, confirming that ionization accounts for the vast majority of complex damage. DEA, typically regarded as a very relevant biodamage mechanism, surprisingly plays a minor role in carbon-ion induced clusters of harmful events.

physics.bio-ph↗

arXiv2020

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

Electronic excitations and ionisations produced by electron impact are key processes in the radiation-induced damage mechanisms in materials of biological relevance, underlying important medical and technological applications, including radiotherapy, radiation protection in manned space missions and nanodevice fabrication techniques. However, experimentally measuring all the necessary electronic interaction cross-sections for every relevant material is an arduous task, so it is necessary having predictive models, sufficiently accurate yet easily implementable. In this work we present a model, based on the dielectric formalism, to provide reliable ionisation and excitation cross-sections for electron-impact on complex biomolecular media, taking into account their condensed-phase nature. We account for the indistinguishability and exchange between the primary beam and excited electrons, for the molecular electronic structure effects in the electron binding, as well as for higher-order corrections to the first Born approximation. The resulting approach yields total ionisation cross-sections, energy distributions of secondary electrons, and total electronic excitation cross-sections for condensed-phase biomaterials, once the electronic excitation spectrum is known, either from experiments or from a predictive model. The results of this methodology are compared with the available experimental data in water and DNA/RNA molecular building blocks, showing a very good agreement and a great predictive power in a wide range of electron incident energies, from the large values characteristic of electron beams down to excitation threshold. The proposed model constitutes a very useful procedure for computing the electronic interaction cross-sections for arbitrary biological materials in a wide range of electron incident energies.

physics.chem-ph↗

arXiv2020

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 modelling is a tool to comprehend and further optimise FEBID-related technologies. Here we utilise 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 W(CO)$_6$ deposition on SiO$_2$ and its subsequent irradiation with electrons, we provide a comprehensive description of the FEBID process and its intrinsic operation. Our analysis reveals that these simulations deliver unprecedented results in modelling 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.

cond-mat.mtrl-sci↗

arXiv2019

Reactive molecular dynamics simulations of organometallic compound W(CO)6 fragmentation

Irradiation- and collision-induced fragmentation studies provide information about geometry, electronic properties and interactions between structural units of various molecular systems. Such knowledge brings insights into irradiation-driven chemistry of molecular systems which is exploited in different technological applications. An accurate atomistic-level simulation of irradiation-driven chemistry requires reliable models of molecular fragmentation which can be verified against mass spectrometry experiments. In this work fragmentation of a tungsten hexacarbonyl, W(CO)$_6$, molecule is studied by means of reactive molecular dynamics simulations. The quantitatively correct fragmentation picture including different fragmentation channels is reproduced. We show that distribution of the deposited energy over all degrees of freedom of the parent molecule leads to thermal evaporation of CO groups and the formation of W(CO)$_n^+$ ($n = 0-5$) fragments. Another type of fragments, WC(CO)$_n^+$ ($n = 0-4$), is produced due to cleavage of a C--O bond as a result of the localized energy deposition. Calculated fragment appearance energies are in good agreement with experimental data. These fragmentation mechanisms have a general physical nature and should take place in radiation-induced fragmentation of different molecular and biomolecular systems.

physics.chem-ph↗

arXiv2018

Electron inelastic mean free paths in condensed matter down to a few electronvolts

A method is reported for a simple, yet reliable, calculation of electron inelastic mean free paths in condensed phase insulating and conducting materials, from the very low energies of hot electrons up to the high energies characteristic of electron beams. Through a detailed consideration of the energy transferred by the projectile in individual and collective electronic excitations, as well as ionizations, together with the inclusion of higher order corrections to the results provided by the dielectric formalism, inelastic mean free paths are calculated for water, aluminum, gold and copper in excellent agreement with the available experimental data, even at the elusive very low energy region. These results are important due to the crucial role played by low energy electrons in radiobiology (owing to their relevant effects in biodamage), and also in order to assess the not yet elucidated disagreement between older and recent measurements of low energy electron mean free paths in metals (which are relevant for low energy electron transport and effects in nanostructured devices).

cond-mat.other↗

arXiv2018

Transport of secondary electrons through coatings of ion-irradiated metallic nanoparticles

The transport of low-energy electrons through the coating of a radiosensitizing metallic nanoparticle under fast ion irradiation is analyzed theoretically and numerically. As a case study, we consider a poly(ethylene glycol)-coated gold nanoparticle of diameter 1.6~nm excited by a carbon ion in the Bragg peak region in water as well as by more energetic carbon ions. The diffusion equation for low-energy electrons emitted from a finite-size spherical source representing the surface of the metal core is solved to obtain the electron number density as a function of radial distance and time. Information on the atomistic structure and composition of the coating is obtained from molecular dynamics simulations performed with the MBN Explorer software package. Two mechanisms of low-energy electron production by the metallic core are considered: the relaxation of plasmon excitations and collective excitations of valence $d$ electrons in individual atoms of gold. Diffusion coefficients and characteristic lifetimes of electrons propagating in gold, water, and poly(ethylene glycol) are obtained from relativistic partial wave analysis and the dielectric formalism, respectively. On this basis, the number of electrons released through the organic coating into the surrounding aqueous medium and the number of hydroxyl radicals produced are evaluated. The largest increase of the radical yield due to low-energy electrons is observed when the nanoparticle is excited by an ion with energy significantly exceeding that in the Bragg peak region. It is also shown that the water content of the coating, especially near the surface of the metal core, is crucial for the production of hydroxyl radicals.

physics.atm-clus↗

arXiv2017

The effect of ion-induced shock waves on the transport of reacting species around energetic ion tracks

The passage of energetic ions through tissue initiates a series of physico-chemical events, which lead to biodamage. The study of this scenario using a multiscale approach brought about the theoretical prediction of shock waves initiated by energy deposited within ion tracks. These waves are being explored in this letter in different aspects. The radial dose that sets their initial conditions is calculated using diffusion equations extended to include the effect of energetic $δ$-electrons. The resulting shock waves are simulated by means of reactive classical molecular dynamics. The simulations predict a characteristic distribution of reactive species which may have a significant contribution to biodamage, and also suggests experimental means to detect the shock waves.

physics.bio-ph↗

arXiv2017

Radial doses around energetic ion tracks and the onset of shock waves on the nanoscale

Energetic ions lose their energy in tissue mainly by ionising its molecules. This produces secondary electrons which transport this energy radially away from the ion path. The ranges of most of these electrons do not exceed a few nanometres, therefore large energy densities (radial doses) are produced within a narrow region around the ion trajectory. Large energy density gradients correspond to large pressure gradients and this brings about shock waves propagating away from the ion path. Previous works have studied these waves by molecular dynamics simulations investigating their damaging effects on DNA molecules. However, these simulations where performed assuming that all energy lost by ions is deposited uniformly in thin cylinders around their path. In the present work the radial dose distributions, calculated by solving the diffusion equation for the low energy electrons and complemented with a semi-empirical inclusion of more energetic $δ$-electrons, are used to set up initial conditions for the shock wave simulation. The effect of these energy distributions vs. stepwise energy distributions in tracks on the strength of shock waves induced by carbon ions both in the Bragg peak region and out of it is studied by molecular dynamics simulations.

physics.bio-ph↗

arXiv2016

Molecular dynamics study of accelerated ion-induced shock waves in biological media

We present a molecular dynamics study of the effects of carbon- and iron-ion induced shock waves in DNA duplexes in liquid water. We use the CHARMM force field implemented within the MBN Explorer simulation package to optimize and equilibrate DNA duplexes in liquid water boxes of different sizes and shapes. The translational and vibrational degrees of freedom of water molecules are excited according to the energy deposited by the ions and the subsequent shock waves in liquid water are simulated. The pressure waves generated are studied and compared with an analytical hydrodynamics model which serves as a benchmark for evaluating the suitability of the simulation boxes. The energy deposition in the DNA backbone bonds is also monitored as an estimation of biological damage, something which lies beyond the possibilities of the analytical model.

physics.bio-ph↗

arXiv2015

Comparative analysis of the secondary electron yield from carbon nanoparticles and pure water medium

The production of secondary electrons generated by carbon nanoparticles and pure water medium irradiated by fast protons is studied by means of model approaches and Monte Carlo simulations. It is demonstrated that due to a prominent collective response to an external field, the nanoparticles embedded in the medium enhance the yield of low-energy electrons. The maximal enhancement is observed for electrons in the energy range where plasmons, which are excited in the nanoparticles, play the dominant role. Electron yield from a solid carbon nanoparticle composed of fullerite, a crystalline form of C60 fullerene, is demonstrated to be several times higher than that from liquid water. Decay of plasmon excitations in carbon-based nanosystems thus represents a mechanism of increase of the low-energy electron yield, similar to the case of sensitizing metal nanoparticles. This observation gives a hint for investigation of novel types of sensitizers to be composed of metallic and organic parts.

physics.atm-clus↗