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.

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.

Lobachevsky crystallography made real through carbon pseudospheres.

We realize Lobachevsky geometry in a simulation lab, by producing a carbon-based energetically stable molecular structure, arranged in the shape of a Beltrami pseudosphere. We find that this structure: (i) corresponds to a non-Euclidean crystallographic group, namely a loxodromic subgroup of SL(2, Z); (ii) has an unavoidable singular boundary, that we fully take into account. Our approach, substantiated by extensive numerical simulations of Beltrami pseudospheres of different size, might be applied to other surfaces of constant negative Gaussian curvature, and points to a general procedure to generate them. Our results also pave the way to test certain scenarios of the physics of curved spacetimes owing to graphene's unique properties.

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.

Non-adiabatic ab initio molecular dynamics of supersonic beam epitaxy of silicon carbide at room temperature.

In this work, we investigate the processes leading to the room-temperature growth of silicon carbide thin films by supersonic molecular beam epitaxy technique. We present experimental data showing that the collision of fullerene on a silicon surface induces strong chemical-physical perturbations and, for sufficient velocity, disruption of molecular bonds, and cage breaking with formation of nanostructures with different stoichiometric character. We show that in these out-of-equilibrium conditions, it is necessary to go beyond the standard implementations of density functional theory, as ab initio methods based on the Born-Oppenheimer approximation fail to capture the excited-state dynamics. In particular, we analyse the Si-C(60) collision within the non-adiabatic nuclear dynamics framework, where stochastic hops occur between adiabatic surfaces calculated with time-dependent density functional theory. This theoretical description of the C(60) impact on the Si surface is in good agreement with our experimental findings.

Effects of co-exposure to extremely low frequency (ELF) magnetic fields and benzene or benzene metabolites determined in vitro by the alkaline comet assay.

In the present study, we investigated in vitro the possible genotoxic and/or co-genotoxic activity of 50 Hz (power frequency) magnetic fields (MF) by using the alkaline single-cell microgel-electrophoresis (comet) assay. Sets of experiments were performed to evaluate the possible interaction between 50 Hz MF and the known leukemogen benzene. Three benzene hydroxylated metabolites were also evaluated: 1,2-benzenediol (1,2-BD, catechol), 1,4-benzenediol (1,4-BD, hydroquinone), and 1,2,4-benzenetriol (1,2,4-BT). MF (1 mT) were generated by a system consisting of a pair of parallel coils in a Helmholtz configuration. To evaluate the genotoxic potential of 50 Hz MF, Jurkat cell cultures were exposed to 1 mT MF or sham-exposed for 1h. To evaluate the co-genotoxic activity of MF, the xenobiotics (benzene, catechol, hydroquinone, and 1,2,4-benzenetriol) were added to Jurkat cells subcultures at the beginning of the exposure time. In cell cultures co-exposed to 1 mT (50 Hz) MF, benzene and catechol did not show any genotoxic activity. However, co-exposure of cell cultures to 1 mT MF and hydroquinone led to the appearance of a clear genotoxic effect. Moreover, co-exposure of cell cultures to 1 mT MF and 1,2,4-benzenetriol led to a marked increase in the genotoxicity of the ultimate metabolite of benzene. The possibility that 50 Hz (power frequency) MF might interfere with the genotoxic activity of xenobiotics has important implications, since human populations are likely to be exposed to a variety of genotoxic agents concomitantly with exposure to this type of physical agent.