SURPRISES: when ab initio meets statistics in extended systems

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.

Computational methods for 2D materials modelling

Materials with thickness ranging from a few nanometers to a single atomic layer present unprecedented opportunities to investigate new phases of matter constrained to the two-dimensional plane. Particle-particle Coulomb interaction is dramatically affected and shaped by the dimensionality reduction, driving well-established solid state theoretical approaches to their limit of applicability. Methodological developments in theoretical modelling and computational algorithms, in close interaction with experiments, led to the discovery of the extraordinary properties of two-dimensional materials, such as high carrier mobility, Dirac cone dispersion and bright exciton luminescence, and inspired new device design paradigms. This review aims to describe the computational techniques used to simulate and predict the optical, electronic and mechanical properties of two-dimensional materials, and to interpret experimental observations. In particular, we discuss in detail the particular challenges arising in the simulation of two-dimensional constrained fermions and quasiparticles, and we offer our perspective on the future directions in this field.

The Resonant and Normal Auger Spectra of Ozone

In this work, we outline a general method for calculating Auger spectra in molecules, which accounts for the underlying symmetry of the system. This theory starts from Fano’s formulation of the interaction between discrete and continuum states, and it generalizes this formalism to deal with the simultaneous presence of several intermediate quasi-bound states and several non-interacting decay channels. Our theoretical description is specifically tailored to resonant autoionization and Auger processes, and it explicitly includes the incoming wave boundary conditions for the continuum states and an accurate treatment of the Coulomb repulsion. This approach is implemented and applied to the calculation of the K−LL Auger and autoionization spectra of ozone, which is a C2v symmetric molecule, whose importance in our atmosphere to filter out radiation has been widely confirmed. We also show the effect that the molecular point group and, in particular, the localization of the core-hole in the oxygen atoms related by symmetry operations, has on the electronic structure of the Auger states and on the spectral lineshape by comparing our results with the experimental data.

Relative Role of 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 appropriate protection in manned space missions rely on the accurate understanding of the energy delivery to cells that damages 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 obtained the energy and momentum transfer excitation spectrum (the energy-loss function, ELF) of liquid water (the main constituent of biological tissues), which was in excellent agreement with experimental data. The inelastic scattering cross sections obtained from this ELF, together with the elastic scattering cross sections derived by considering the condensed phase nature of the medium, were 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 such as ionization, excitation, and dissociative electron attachment (DEA). The latter are strongly correlated with cellular death, which is scored in sensitive volumes with the size of two DNA convolutions. The sizes of the clusters of damaging events for a wide range of carbon-ion energies, from those relevant to hadrontherapy up to those for 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.

Tetrapeptide unfolding dynamics followed by core-level spectroscopy: a first-principles approach

In this work we demonstrate that core level analysis is a powerful tool for disentangling the dynamics of a model polypeptide undergoing conformational changes in solution and disulphide bond formation. In particular, we present computer simulations within both initial and final state approximations of 1s sulphur core level shifts (S1s CLS) of the CYFC (cysteine-phenylalanine-tyrosine-cysteine) tetrapeptide for different folding configurations. Using increasing levels of accuracy, from Hartree-Fock and density functional theory to configuration interaction via a multiscale algorithm capable of reducing drastically the computational cost of electronic structure calculations, we find that distinct peptide arrangements present S1s CLS sizeably different (in excess of 0.5 eV) with respect to the reference disulfide bridge state. This approach, leading to experimentally detectable signals, may represent an alternative to other established spectroscopic techniques.

Tunable band gap in hydrogenated quasi-free-standing graphene

We show by angle-resolved photoemission spectroscopy that a tunable gap in quasi-free-standing monolayer graphene on Au can be induced by hydrogenation. The size of the gap can be controlled via hydrogen loading and reaches approximately 1.0 eV for a hydrogen coverage of 8%. The local rehybridization from sp(2) to sp(3) in the chemical bonding is observed by X-ray photoelectron spectroscopy and X-ray absorption and allows for a determination of the amount of chemisorbed hydrogen. The hydrogen induced gap formation is completely reversible by annealing without damaging the graphene. Calculations of the hydrogen loading dependent core level binding energies and the spectral function of graphene are in excellent agreement with photoemission experiments. Hydrogenation of graphene gives access to tunable electronic and optical properties and thereby provides a model system to study hydrogen storage in carbon materials.