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This paper reports on a comprehensive study of an ultra-relativistic positron beam deflection by an oriented quasi-mosaic crystal. The analysis was carried out for the positron energy of 530 MeV incident on the quasi-mosaic bent Si(111) crystal. This particular case was chosen because it has recently been studied experimentally at the Mainz Microtron MAMI. The results of the relativistic molecular dynamics simulations were compared with the experimental observations and a good agreement was found. The presence of planar channeling, de-channeling, volume reflection and volume capture processes in the angular distribution of deflected positrons for different beam-crystal alignments has been studied. Predictions have been made for certain crystal orientations for which experimental data are lacking.

In this paper we present a novel scheme for the controlled generation of of tunable narrowband gamma-ray radiation by ultra-relativistic positron beams inside acoustically driven periodically bent crystals. A novel acoustic crystalline undulator is presented, in which excitation of a silicon single crystal along the (100) planar direction by a piezoelectric transducer periodically modulates the crystal lattice in the [100] axial direction. An ultra-relativistic positron beam is directed diagonally into the crystal and propagates along the (110) planes. The lattice modulation forces the positrons to follow periodic trajectories,resulting in the emission of undulator radiation in the MeV range. A computational methodology for the design and development of such acoustically based light sources is presented together with the results of simulations demonstrating the favourable properties of the proposed technology. The longitudinal acoustic strains induced in the crystal by high-frequency piezoelectric elements are calculated by finite element simulations. The resulting bending profiles of the deformed crystal planes are used as geometrical conditions in the relativistic molecular dynamics simulations that calculate the positron trajectories and the spectral distribution of the emitted radiation. The results show a strong enhancement of the emitted radiation within a narrow spectral band defined by the bending period, demonstrating the feasibility and potential of the proposed technology., Comment: 32 pages, 11 figures, submitted to Phys. Rev. - Accel. Beams

In this study, we conduct atomistic-level molecular dynamics simulations on fixed-sized silicon-germanium (Si$_{1-x}$Ge$_{x}$) crystals to elucidate the effects of dopant concentration and temperature on the crystalline inter-planar distances. Our calculations consider a range of Ge dopant concentrations between pure Si (0%) and 15%, and for both the optimised system state and a temperature of 300 K. We observe a linear relationship between Ge concentration and inter-planar distance and lattice constant, in line with the approximation of Vegard's Law, and other experimental and computational results. These findings will be employed in conjunction with future studies to establish precise tolerances for use in crystal growth, crucial for the manufacture of crystals intended for emerging gamma-ray crystal-based light source technologies.

The feasibility of gamma-ray light sources based on the channeling phenomenon of ultra-relativistic electrons and positrons in oriented single crystals is demonstrated using rigorous numerical modeling. Case studies are presented for 10 GeV and sub-GeV $e^{-}/e^{+}$ beams incident on $10^{-1}-10^0$ mm thick diamond and silicon crystals. It is shown that for moderate values of the beam average current ($\lesssim 10$ $\mu$A) the average photon flux in the energy range $10^0-10^2$ MeV emitted within the $10^1-10^3$ $\mu$rad cone and 1 \% bandwidth can be on the level of $10^{10}$ photon/s for electrons and $10^{10}-10^{12}$ photon/s for positrons. These values are higher than the fluxes available at modern laser-Compton gamma ray light sources., Comment: 24 pages (RevTex), 8 figures

A comprehensive numerical investigation has been conducted on the angular distribution and spectrum of radiation emitted by 855 MeV electron and positron beams while traversing a 'quasi-mosaic' bent silicon (111) crystal. This interaction of charged particles with a bent crystal gives rise to various phenomena such as channeling, dechanneling, volume reflection, and volume capture. The crystal's geometry, emittance of the collimated particle beams, as well as their alignment with respect to the crystal, have been taken into account as they are essential for an accurate quantitative description of the processes. The simulations have been performed using a specialized relativistic molecular dynamics module implemented in the MBN Explorer package. The angular distribution of the particles after traversing the crystal has been calculated for beams of different emittances as well as for different anticlastic curvatures of the bent crystals. For the electron beam, the angular distributions of the deflected particles and the spectrum of radiation obtained in the simulations are compared with the experimental data collected at the Mainz Microtron facility. For the positron beam such calculations have been performed for the first time. We predict significant differences in the angular distributions and the radiation spectra for positrons versus electrons., Comment: 17 pages, 9 figures. Submitted to: J. Phys. B: At. Mol. Opt. Phys

This paper reviews the new highly interdisciplinary research field studying the behavior of condensed matter systems exposed to radiation. The paper highlights several relevant examples of recent advances in the field and provides a roadmap for the development of the field in the next decade. Condensed matter systems exposed to radiation may have very different natures, being inorganic, organic or biological, finite or infinite, be composed of many different molecular species or materials, existing in different phases (solid, liquid, gaseous or plasma) and operating under different thermodynamic conditions. The essential and novel element of this research is that, despite the vast diversity of such systems, many of the key phenomena related to the behavior of irradiated systems (such as radiation-induced damage, mechanisms of damage repair and control, radiation protection, etc.) are very similar and can be understood based on the same fundamental theoretical principles and computational approaches. One of the essential features of the aforementioned phenomena concerns their multiscale nature as the manifestation of the radiation-induced effects occurring at different spatial and temporal scales ranging from the atomic to the macroscopic. The multiscale nature of the effects and similarity of their manifestation in systems of different origins necessarily brings together different disciplines, such as physics, chemistry, biology, materials and nano-science, and biomedical research, demonstrating numerous interlinks and commonalities between them. This research field is highly relevant to many novel and emerging technologies and medical applications., Comment: Roadmap paper; 376 pages, 32 figures. Submitted to Chemical Reviews

Exploration of the structure formation and dynamics of animate and inanimate matter on the nanometer scale is a highly interdisciplinary field of rapidly emerging research. It is relevant for various molecular and nanoscale systems of different origins and compositions and concerns numerous phenomena originating from physics, chemistry, biology, and materials science. This topical issue presents a collection of research papers devoted to different aspects of the Dynamics of Systems on the Nanoscale. Some of the contributions discuss specific applications of the research results in several modern and emerging technologies, such as controlled nanofabrication with charged particle beams or the design and practical realization of novel gamma-ray crystal-based light sources. Most works presented in this topical issue were reported at the joint Sixth International Conference "Dynamics of Systems on the Nanoscale" and the tenth International Symposium "Atomic Cluster Collisions" (DySoN-ISACC 2021), which were held in Santa Margherita Ligure, Italy, in October 2021., Comment: Editorial for the topical issue "Dynamics of Systems on the Nanoscale (2021)" of the European Physical Journal D; see https://epjd.epj.org/component/toc/?task=topic&id=1616

Atomic cluster-based networks represent a promising architecture for the realization of neuromorphic computing systems, which may overcome some of the limitations of the current computing paradigm. The formation and breakage of synapses between the clusters are of utmost importance for the functioning of these computing systems. This paper reports the results of molecular dynamics simulations of synapse (bridge) formation at elevated temperatures and thermal breaking processes between 2.8 nanometer-sized Au$_{1415}$ clusters deposited on a carbon substrate, a model system. Crucially, we find that the bridge formation process is driven by the diffusion of gold atoms along the substrate, however small the gap between the clusters themselves. The complementary simulations of the bridge-breaking process reveal the existence of a threshold bias voltage to activate bridge rupture via Joule heating. These results provide an atomistic-level understanding of the fundamental dynamical processes occurring in neuromorphic cluster arrays.

Neuromorphic computing systems may be the future of computing and cluster-based networks are a promising architecture for the realization of these systems. The creation and dissolution of synapses between the clusters are of great importance for their function. In this work, we model the thermal breakage of a gold nanofilament located between two gold nanoparticles via molecular dynamics simulations to study on the mechanisms of neuromorphic nanoparticle-based devices. We employ simulations of Au nanowires of different lengths ($2-8$ nm), widths ($0.4-0.8$ nm) and shapes connecting two Au$_{1415}$ nanoparticles (NPs) and monitor the evolution of the system via a detailed structural identification analysis. We found that atoms of the nanofilament gradually aggregate towards the clusters, causing the middle of the wire to gradually thin and then break. Most of the system remains crystalline during this process but the center is molten. The terminal NPs increase the melting point of the NWs by fixing the middle wire and act as recrystallization areas. We report a strong dependence on the width of the NWs, but also their length and structure. These results may serve as guidelines for the realization of cluster-based neuromorphic computing systems.

This study presents the results of atomistic structural characterisation of 3.7 nm diameter gold nanoparticles (NP) coated with polymer polyethylene glycol (PEG)-based ligands of different lengths (containing $2-14$ monomers) and solvated in water. The system size and composition are selected in connection to several experimental studies of radiosensitisation mechanisms of gold NPs. The coating structure and water distribution near the NP surface are characterised on the atomistic level by means of molecular dynamics simulations. The results of simulations carried out in this study, combined with the results of our recent study [J. Phys. Chem. A 126 (2022) 2170] and those from the field of polymer physics, are used to calculate key structural parameters of the coatings of radiosensitising gold NPs. On this basis, connections between the coating structure and distribution of water are established for different NP sizes as well as lengths and surface densities of coating molecules. The quantitative analysis of water distribution in the vicinity of coated metal NPs can be used to evaluate the radiosensitising effectiveness of a particular NP system based on the proximity of water to the NP metal core, which should impact the production of hydroxyl radicals and reactive oxygen species in the vicinity of metal NPs exposed to ionising radiation.

The angular distribution function of multiple scattering experienced by 855 MeV electrons passing through an amorphous silicon plate and an oriented silicon crystal has been studied by means of relativistic molecular dynamics simulations using two types of the potentials that describe electron-atom interaction. The differences in the angular distributions of the beam particles in both media are analysed. The results obtained are compared to the experimental data and to the results of Monte Carlo simulations., Comment: 9 pages, 4 figures

We review achievements made in recent years in the field of numerical modeling of ultra-relativistic projectiles propagation in oriented crystals, radiation emission and related phenomena. This topic is highly relevant to the problem of designing novel gamma-ray light sources based on the exposure of oriented crystals to the beams of ultra-relativistic charged particles. The paper focuses on the approaches that allow for advanced computation exploration beyond the continuous potential and the binary collisions frameworks. A comprehensive description of the multiscale all-atom relativistic molecular dynamics approach implemented in the MBN Explorer package is given. Several case studies related to modeling of ultra-relativistic projectiles (electrons, positron and pions) channeling and photon emission in oriented straight, bent and periodically bent crystals are presented. In most cases, the input data used in the simulations, such as crystal orientation and thickness, the bending radii, periods and amplitudes, as well as the energies of the projectiles, have been chosen to match the parameters used in the accomplished and the ongoing experiments. Wherever available the results of calculations are compared with the experimental data and/or the data obtained by other numerical means., Comment: 60 pages, 34 figures

A computational approach combining dispersion-corrected density functional theory (DFT) and classical molecular dynamics is employed to characterize the geometrical and thermo-mechanical properties of a recently proposed 2D transition metal dihalide NiCl$_2$. The characterization is performed using a classical interatomic force field whose parameters are determined and verified through the comparison with the results of DFT calculations. The developed force field is used to study the mechanical response, thermal stability, and melting of a NiCl$_2$ monolayer on the atomistic level of detail. The 2D NiCl$_2$ sheet is found to be thermally stable at temperatures below its melting point of ~695 K. At higher temperatures, several subsequent structural transformations of NiCl$_2$ are observed, namely a transition into a porous 2D sheet and a 1D nanowire. The computational methodology presented through the case study of NiCl$_2$ can also be utilized to characterize other novel 2D materials, including recently synthesized NiO$_2$, NiS$_2$, and NiSe$_2$.

Irradiation-driven fragmentation and chemical transformations of molecular systems play a key role in nanofabrication processes where organometallic compounds break up due to the irradiation with focused particle beams. In this study, reactive molecular dynamics simulations have been performed to analyze the role of the molecular environment on the irradiation-induced fragmentation of molecular systems. As a case study, we consider the dissociative ionization of iron pentacarbonyl, Fe(CO)$_5$, a widely used precursor molecule for focused electron beam-induced deposition. In connection to recent experiments, the irradiation-induced fragmentation dynamics of an isolated Fe(CO)$_5^+$ molecule is studied and compared with that of a Fe(CO)$_5^+$ molecule embedded into an argon cluster. The appearance energies of different fragments of an isolated Fe(CO)$_5^+$ agree with the recent experimental data. For Fe(CO)$_5^+$ embedded into an argon cluster, the simulations reproduce the experimentally observed suppression of Fe(CO)$_5^+$ fragmentation and provide an atomistic-level understanding of this effect. Understanding irradiation-driven fragmentation patterns for molecular systems in environments facilitates the advancement of atomistic models of irradiation-induced chemistry processes involving complex molecular systems., Comment: 10 pages, 5 figures

Physical mechanisms of structural transformations in deposited metallic clusters exposed to an electron beam of a transmission electron microscope (TEM) are studied theoretically and computationally. Recent TEM experiments with size-selected Au$_{923}$ clusters softly deposited on a carbon substrate showed that the clusters undergo structural transformations from icosahedron to decahedron and face-center cubic (fcc) structures upon exposure to a 200-keV electron beam. In this paper, we demonstrate that the relaxation of collective electronic (plasmon) excitations formed in deposited metal clusters can induce the experimentally observed structural transformations. Such excitations in the clusters are formed mainly due to the interaction with low-energy secondary electrons emitted from a substrate. The characteristic occurrence times for plasmon-induced energy relaxation events are several orders of magnitude shorter than those for the momentum transfer events by energetic primary electrons to atoms of the cluster. The theoretical analysis is complemented by molecular dynamics simulations, which show that an icosahedral Au$_{923}$ cluster softly deposited on graphite is transformed into an fcc-like structure due to the vibrational excitation of the cluster., Comment: 14 pages, 10 figures

Methodology is developed that incorporates the radiation reaction force into the relativistic molecular dynamics framework implemented in the MBN Explorer software package. The force leads to a gradual decrease in the projectile's energy E due to the radiation emission. This effect is especially strong for ultra-relativistic projectiles passing through oriented crystals where they experience the action of strong electrostatic fields as has been shown in recent experiments. A case study has been carried out for the initial approbation of the methodology developed. Simulations of the processes of planar channeling and photon emission have been performed for 150 GeV positrons in a 200 microns thick single oriented Si(110) crystal. Several regimes for the decrease in E have been established and characterized. Further steps in developing the code to include the necessary quantum corrections are identified and possible algorithmic modifications are proposed., Comment: 19 pages, 6 figures

The feasibility of gamma-ray light sources based on the channeling phenomenon of ultrarelativistic electrons and positrons in oriented crystals that are periodically bent with Small Amplitude and Short Period (SASP) is demonstrated by means of rigorous numerical modelling that accounts for the interaction of a projectile with all atoms of the crystalline environment. Numerical data on the spectral distribution, brilliance, number of photons and power of radiation emitted by 10 GeV electron and positron beams passing through diamond, silicon and germanium crystals are presented and analyzed. The case studies presented in the paper refer to the FACET-II beams available at the SLAC facility. It is shown that the SASP bending gives rise to the radiation enhancement in the GeV photon energy range where the peak brilliance of radiation can be as high as on the 10^{24} photons/s/mrad^2/mm^2/0.1BW. The parameters of radiation can be tuned by varying the amplitude and period of bending., Comment: 25 pages, 17 figures

The role of thermal effects in the focused electron beam induced deposition (FEBID) process of Me$_2$Au(tfac) is studied by means of irradiation-driven molecular dynamics simulations. The FEBID of Me$_2$Au(tfac), a commonly used precursor molecule for the fabrication of gold nanostructures, is simulated at different temperatures in the range of $300-450$ K. The deposit's structure, morphology, growth rate, and elemental composition at different temperatures are analyzed. The fragmentation cross section for Me$_2$Au(tfac) is evaluated on the basis of the cross sections for structurally similar molecules. Different fragmentation channels involving the dissociative ionization (DI) and dissociative electron attachment (DEA) mechanisms are considered. The conducted simulations of FEBID confirm experimental observations that deposits consist of small gold clusters embedded into a carbon-rich organic matrix. The simulation results indicate that accounting for both DEA- and DI-induced fragmentation of all the covalent bonds in Me$_2$Au(tfac) and increasing the amount of energy transferred to the system upon fragmentation increase the concentration of gold in the deposit. The simulations predict an increase in Au:C ratio in the deposit from 0.18 to 0.25 upon the temperature increase from 300 K to 450 K, being within the range of experimentally reported values., Comment: 14 pages, 8 figures

This paper provides an explanation of the key effects behind the deflection of ultra-relativistic electron beams by means of oriented quasi-mosaic Bent Crystals (qmBC). It is demonstrated that accounting for specific geometry of the qmBC and its orientation with respect to a collimated electron beam, its size and emittance is essential for an accurate quantitative description of experimental results on the beam deflection by such crystals. In an exemplary case study a detailed analysis of the recent experiment at the SLAC facility is presented. The methodology developed has enabled to understand the peculiarities in the measured distributions of the deflected electrons. This achievement constitutes an important progress in the efforts towards the practical realization of novel gamma-ray crystal-based light sources and puts new challenges for the theory and experiment in this research area., Comment: 6 pages, 4 figures plus Supplemental Material

Brilliance of novel gamma-ray Crystal-based Light Sources (CLS) that can be constructed through exposure of oriented crystals to beams of ultra-relativistic charged particles is calculated basing on the atomistic scale numerical modeling of the channeling process. In an exemplary case study, the brilliance of radiation emitted in a diamond-based Crystalline Undulator LS by a 10 GeV positron beam available at present at the SLAC facility is computed. Intesity of CU radiation in the photon energy range 10^0 - 10^1 MeV, which is inaccessible to conventional synchrotrons, undulators and XFELs, greatly exceeds that of laser-Compton scattering LSs and can be higher than predicted in the Gamma Factory proposal to CERN. Construction of novel CLSs is a challenging task which constitutes a highly interdisciplinary field entangling a broad range of correlated activities. CLSs provide a low-cost altenative to conventional LSs and have enomorous number of applications., Comment: 6 pages, 4 figures plus Supplementary Material with 2 figures

The growth of iron-containing nanostructures in the process of focused electron beam-induced deposition (FEBID) of Fe(CO)$_5$ is studied by means of atomistic irradiation-driven molecular dynamics (IDMD) simulations. The geometrical characteristics (lateral size, height and volume), morphology and metal content of the grown nanostructures are analyzed at different irradiation and precursor replenishment conditions corresponding to the electron-limited and precursor-limited regimes (ELR & PLR) of FEBID. A significant variation of the deposit's morphology and elemental composition is observed with increasing the electron current from 1 to 4 nA. At low beam current (1 nA) corresponding to the ELR and a low degree of Fe(CO)$_5$ fragmentation, the nanogranular structures are formed which consist of isolated iron clusters embedded into an organic matrix. In this regime, metal clusters do not coalesce with increasing electron fluence, resulting in relatively low metal content of the nanostructures. A higher beam current of 4 nA corresponding to the PLR facilitates the precursor fragmentation and the coalescence of metal clusters into a dendrite-like structure with the size corresponding to the primary electron beam. The IDMD simulations enable atomistic-level predictions on the nanoscopic characterization of the initial phase of nanostructure growth in the FEBID process. These predictions can be verified in high-resolution transmission electron microscopy experiments., Comment: 13 pages, 7 figures

Ion-induced DNA damage is an important effect underlying ion-beam cancer therapy. This paper introduces the methodology of modeling DNA damage induced by a shock wave caused by a projectile ion. Specifically, it is demonstrated how single- and double-strand breaks in a DNA molecule could be described by the reactive CHARMM (rCHARMM) force field implemented in the program MBN Explorer. The entire workflow of performing the shock wave simulations, including obtaining the crucial simulation parameters, is described in seven steps. Two exemplary analyses are provided for a case study simulation serving to (i) quantify the shock wave propagation and (ii) describe the dynamics of the formation of DNA breaks. The paper concludes by discussing the computational cost of the simulations and revealing the possible maximal computational time for different simulation setups., Comment: 11 pages, 6 figures. Originally submitted version of the manuscript

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. D

Computational multiscale modeling encompasses a wide range of end-products and a great number of technological applications. This paper provides an overview of the computational multiscale modeling approach based on the utilization of MBN Explorer and MBN Studio software packages, the universal and powerful tools for computational modeling in different areas of challenging research arising in connection with the development of novel and emerging technologies. Three illustrative case studies of multiscale modeling are reviewed in relation to (i) the development of novel sources of monochromatic high-energy radiation based on the crystalline undulators, (ii) controlled fabrication of nanostructures using the focused electron-beam induced deposition, and (iii) ion-beam cancer therapy. These examples illustrate the key algorithms and unique methodologies implemented in the software., Comment: 18 pages, 16 figures. Review paper to be published in Eur. Phys. J. D

This paper presents a detailed computational protocol for atomistic simulation of the formation and growth of metal-containing nanostructures during the Focused Electron Beam Induced Deposition (FEBID) process. The protocol is based upon the 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, irradiation regimes, etc. 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(PF$_3$)$_4$ - a widely studied precursor molecule - on a SiO$_2$ surface. The simulations reveal the processes driving the initial phase of nanostructure formation during FEBID, including nucleation of Pt atoms, 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 space resolved relative metal content, height and the growth rate of the deposits which represent valuable reference data for the experimental characterization of the nanostructures grown by FEBID., Comment: 19 pages, 12 figures

Functionalized metal nanoparticles (NPs) have been proposed as promising radiosensitizing agents for more efficient radiotherapy treatment using photons and ion beams. Radiosensitizing properties of NPs may depend on many different parameters (such as size, composition and density) of the metal core, organic coatings and the molecular environment. A systematic exploration of each of these parameters on the atomistic level remains a costly experimental task but it can be addressed by means of advanced computational modeling. This paper outlines a detailed computational procedure for the construction and atomistic-level characterization of radiosensitizing metal NPs in explicit molecular media. The procedure is general and extensible to many different combinations of the core, coating and environment. As an illustrative and experimentally relevant case study, we consider nanometre-sized gold NPs coated with thiol-poly(ethylene glycol)-amine molecules of different length and surface density and solvated in water at ambient conditions. Radial distribution of different atoms in the coatings as well as distribution and structural properties of water around the coated NPs are analyzed and linked to radiosensitizing properties of the NPs. It is revealed that the structure of the coating layer on the solvated NPs depends strongly on the surface density of ligands. At surface densities below $\sim$3 molecules/nm$^{2}$ the coating represents a mixture of different conformation states, whereas elongated "brush"-like structures are formed at higher densities of ligands. The water content in denser coatings is significantly lower at distances from 1 to 3 nm from the gold surface depending on the length of ligands. Such dense and thick coatings may suppress the production of hydroxyl radicals by low-energy electrons emitted from the metal NPs and thus diminish their radiosensitizing properties., Comment: 16 pages, 11 figures

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 figures

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., Comment: 10 pages, 7 figures

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., Comment: Main text: 9 pages, 4 figures; Supplementary information: 11 pages, 6 figures, 1 table

Structure and stability of 3 nm size Ag$_{887}$, Au$_{887}$ and Ti$_{787}$ clusters deposited on graphite under soft-landing conditions ($\sim 10^{-3}- 10^0$ eV per atom) are studied by means of molecular dynamics simulations. Parameters for the cluster-surface interaction are derived from complementary ab initio calculations. We found that the shape of clusters on the surface is governed by their elemental composition and depends also on the initial cluster structure and landing conditions. At deposition energies below 0.1 eV/atom, the Ag$_{887}$ cluster acquires an ellipsoidal shape, while Au$_{887}$ and Ti$_{787}$ clusters transform into oblate and prolate truncated spheroids, respectively, due to stronger adhesion to graphite. The clusters flatten over the surface and eventually disintegrate as the deposition energy increases. Simulation results reveal that Ag$_{887}$ and Au$_{887}$ fragment at about $0.75 - 1.0$ eV/atom whereas higher energy of about 3 eV/atom is required for the fragmentation of Ti$_{787}$. The contact angle, contact radius and height of the clusters as functions of deposition energy are determined from fitting the positions of cluster surface atoms with a surface equation. The dependence of these parameters on the internal energy of the clusters is also analyzed., Comment: 11 pages, 8 figures