Multiscale approach predictions for biological outcomes in ion-beam cancer therapy

10 págs.; 4 figs. 1 tab. ; Open Access funded by Creative Commons Atribution Licence 4.0Ion-beam therapy provides advances in cancer treatment, offering the possibility of excellent dose localization and thus maximising cell-killing within the tumour. The full potential of such therapy can only be realised if the fundamental mechanisms leading to lethal cell damage under ion irradiation are well understood. The key question is whether it is possible to quantitatively predict macroscopic biological effects caused by ion radiation on the basis of physical and chemical effects related to the ion-medium interactions on a nanometre scale. We demonstrate that the phenomenon-based MultiScale Approach to the assessment of radiation damage with ions gives a positive answer to this question. We apply this approach to numerous experiments where survival curves were obtained for different cell lines and conditions. Contrary to other, in essence empirical methods for evaluation of macroscopic effects of ionising radiation, the MultiScale Approach predicts the biodamage based on the physical effects related to ionisation of the medium, transport of secondary particles, chemical interactions, thermo-mechanical pathways of biodamage, and heuristic biological criteria for cell survival. We anticipate this method to give great impetus to the practical improvement of ion-beam cancer therapy and the development of more efficient treatment protocols.We acknowledge the financial support received from the European Union Seventh Framework Programme (PEOPLE2013-ITN-ARGENT project) under grant agreement no. 608163.Peer Reviewe

Irradiation driven molecular dynamics: A review

This paper reviews Irradiation Driven Molecular Dynamics (IDMD) - a novel computational methodology for atomistic simulations of the irradiation driven transformations of complex molecular systems implemented in the MBN Explorer software package. Within the IDMD framework, various quantum processes occurring in irradiated systems are treated as random, fast and local transformations incorporated into the classical MD framework in a stochastic manner with the probabilities elaborated on the basis of quantum mechanics. Major transformations of irradiated molecular systems (such as topological changes, redistribution of atomic partial charges, alteration of interatomic interactions) and possible paths of their further reactive transformations can be simulated by means of MD with reactive force fields, in particular with the reactive CHARMM (rCHARMM) force field implemented in MBN Explorer. This paper reviews the general concept of the IDMD methodology and the rCHARMM force field and provides several exemplary case studies illustrating the utilization of these methods.Comment: 12 pages, 8 figures. Review paper to be published in Eur. Phys. J.

Interplay of the volume and surface plasmons in the electron energy loss spectra of C60_{60}

The results of a joint experimental and theoretical investigation of the C60 collective excitations in the process of inelastic scattering of electrons are presented. The shape of the electron energy loss spectrum is observed to vary when the scattering angle increases. This variation arising due to the electron diffraction of the fullerene shell is described by a new theoretical model which treats the fullerene as a spherical shell of a finite width and accounts for the two modes of the surface plasmon and for the volume plasmon as well. It is shown that at small angles, the inelastic scattering cross section is determined mostly by the symmetric mode of the surface plasmon, while at larger angles, the contributions of the antisymmetric surface plasmon and the volume plasmon become prominent.Comment: 11 pages, 3 figure

Hybridization-related correction to the jellium model for fullerenes

We introduce a new type of correction for a more accurate description of fullerenes within the spherically symmetric jellium model. This correction represents a pseudopotential which originates from the comparison between an accurate ab initio calculation and the jellium model calculation. It is shown that such a correction to the jellium model allows one to account, at least partly, for the sp2-hybridization of carbon atomic orbitals. Therefore, it may be considered as a more physically meaningful correction as compared with a structureless square-well pseudopotential which has been widely used earlier.Comment: 16 pages, 10 figure

Surface softening in metal-ceramic sliding contacts: An experimental and numerical investigation

This study investigates the tribolayer properties at the interface of ceramic/metal (i.e., WC/W) sliding contacts using various experimental approaches and classical atomistic simulations. Experimentally, nanoindentation and micropillar compression tests, as well as adhesion mapping by means of atomic force microscopy, are used to evaluate the strength of tungsten?carbon tribolayers. To capture the influence of environmental conditions, a detailed chemical and structural analysis is performed on the worn surfaces by means of XPS mapping and depth profiling along with transmission electron microscopy of the debris particles. Experimentally, the results indicate a decrease in hardness and modulus of the worn surface compared to the unworn one. Atomistic simulations of nanoindentation on deformed and undeformed specimens are used to probe the strength of the WC tribolayer and despite the fact that the simulations do not include oxygen, the simulations correlate well with the experiments on deformed and undeformed surfaces, where the difference in behavior is attributed to the bonding and structural differences of amorphous and crystalline W-C. Adhesion mapping indicates a decrease in surface adhesion, which based on chemical analysis is attributed to surface passivation

Roadmap on dynamics of molecules and clusters in the gas phase

This roadmap article highlights recent advances, challenges and future prospects in studies of the dynamics of molecules and clusters in the gas phase. It comprises nineteen contributions by scientists with leading expertise in complementary experimental and theoretical techniques to probe the dynamics on timescales spanning twenty order of magnitudes, from attoseconds to minutes and beyond, and for systems ranging in complexity from the smallest (diatomic) molecules to clusters and nanoparticles. Combining some of these techniques opens up new avenues to unravel hitherto unexplored reaction pathways and mechanisms, and to establish their significance in, e.g. radiotherapy and radiation damage on the nanoscale, astrophysics, astrochemistry and atmospheric science

Lethal DNA damages caused by ion-induced shock waves in cells

The elucidation of fundamental mechanisms underlying ion-induced radiation damage of biological systems is crucial for the advancement of radiotherapy with ion beams and for radiation protection in space. The study of ion-induced biodamage using the phenomenon-based MultiScale Approach to the physics of radiation damage with ions (MSA) has led to the prediction of nanoscale shock waves (SW) that are created by ions in the biological medium at the high linear energy transfer (LET). The high-LET regime corresponding to energy losses higher than 1 keV/nm is typical for ions heavier than carbon in biological media at the Bragg peak region. This paper reveals that the thermomechanical stress of the DNA molecule by the ion-induced SW becomes the dominant mechanism of complex DNA damage at the high-LET ion irradiation. Damage of the DNA molecule in water caused by the ion-induced SW is studied by means of reactive molecular dynamics simulations. Five projectile ions (C, O, Si, Ar, and Fe) at the Bragg peak energies are considered. Simulations reveal that Ar and, especially, Fe ions induce multiple bond breakages in a DNA segment containing 20 base pairs. The DNA damage produced in segments of such size leads to complex irreparable lesions in a cell. This makes the SW-induced thermomechanical stress the dominant mechanism of complex DNA damage at the high-LET ion irradiation. A detailed theory for evaluating the DNA damage caused by ions at high-LET is formulated and integrated into the MSA formalism. The theoretical analysis reveals that a single ion hitting a cell nucleus at high-LET is sufficient to produce highly complex, lethal damages to a cell by the SW-induced thermomechanical stress. A good agreement of the calculated cell survival probabilities with experimental data obtained for the cell irradiation with iron ions provides strong experimental evidence of the ion-induced SW effect.Comment: 28 pages, 15 figure

Ion-impact-induced multifragmentation of liquid droplets

6 pags., 4 figs.Abstract: An instability of a liquid droplet traversed by an energetic ion is explored theoretically. This instability is brought about by the predicted shock wave induced by the ion. An observation of multifragmentation of small droplets traversed by ions with high linear energy transfer is suggested to demonstrate the existence of shock waves. A number of effects are analysed in effort to find the conditions for such an experiment to be signifying. The presence of shock waves crucially affects the scenario of radiation damage with ions since the shock waves significantly contribute to the thermomechanical damage of biomolecules as well as the transport of reactive species. While the scenario has been upheld by analyses of biological experiments, the shock waves have not yet been observed directly, regardless of a number of ideas of experiments to detect them were exchanged at conferences. Graphical abstract: [Figure not available: see fulltext.].We appreciate the support of FP7 ITN-ARGENT (Grant Agreement No. 608163). E.S. is indebted to G. Sushko and P. de Vera for their assistance in modeling shock waves using the MBN Explorer packagePeer Reviewe

Photoionization of multishell fullerenes studied by ab initio and model approaches*

11 págs.; 7 figs.; 1 tab. Part of the collections Topical Issue: Atomic Cluster Collisions (7th International Symposium)Photoionization of two buckyonions, C@C and C@C, is investigated by means of time-dependentdensity-functional theory (TDDFT). The TDDFT-based photoabsorption spectrum ofC@C, calculated in a broad photon energy range, resemblesthe sum of spectra of the two isolated fullerenes, thus illustrating the absence of strongplasmonic coupling between the fullerenes which was proposed earlier. The calculatedspectrum of the smaller buckyonion, C@C, differs significantly from the sum of the crosssections of the individual fullerenes because of strong geometrical distortion of thesystem. The contribution of collective electron excitations arising in individualfullerenes is evaluated by means of plasmon resonance approximation (PRA). An extension ofthe PRA formalism is presented, which allows for the study of collective electronexcitations in multishell fullerenes under photon impact. An advanced analysis ofphotoionization of buckyonions, performed using modern computational and analyticalapproaches, provides valuable information on the response of complex molecular systems tothe external electromagnetic field. c EDP Sciences, Società Italiana di Fisica, Springer-Verlag 2016A.V. acknowledges the support by the FP7 Multi-ITN Project “ARGENT” (Grant agreement No. 608163). A.V.K. acknowledges the support from the Alexander von Humboldt FoundationPeer Reviewe