arXiv subjects

Andrey V. Solov'yov

Publications and source records attributed to Andrey V. Solov'yov.

At least 37 records · Page 2Linked to original sources

arXiv2023

Multiple scattering of 855 MeV electrons in amorphous and crystalline silicon: simulations versus experiment

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.

physics.comp-ph↗

arXiv2023

All-atom relativistic molecular dynamics simulations of channeling and radiation processes in oriented crystals

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.

physics.acc-ph↗

arXiv2022

Role of the molecular environment in quenching the irradiation-driven fragmentation of Fe(CO)$_5$: a reactive molecular dynamics study

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.

physics.chem-ph↗

arXiv2022

Atomistic modelling of the channeling process with radiation reaction force included

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.

physics.acc-ph↗

arXiv2022

Atomistic modelling and characterizaion of light sources based on small-amplitude short-period periodically bent crystals

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.

physics.acc-ph↗

arXiv2022

Atomistic modeling of thermal effects in focused electron beam induced deposition of Me$_2$Au(tfac)

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.

cond-mat.mtrl-sci↗

arXiv2022

Extremely brilliant crystal-based light sources

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.

physics.acc-ph↗

arXiv2022

Molecular dynamics characterisation of radiosensitising coated gold nanoparticles in aqueous environment

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.

physics.atm-clus↗

arXiv2022

Atomistic simulation of the FEBID-driven growth of iron-based nanostructures

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.

cond-mat.mtrl-sci↗

arXiv2022

Ultra-relativistic electron beams deflection by quasi-mosaic crystals

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.

physics.acc-ph↗

arXiv2021

Irradiation driven molecular dynamics simulation of the FEBID process for Pt(PF$_3$)$_4$

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.

physics.chem-ph↗

arXiv2021

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.

physics.bio-ph↗

arXiv2021

Modeling the effect of ion-induced shock waves and DNA breakage with the reactive CHARMM force field

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.

physics.bio-ph↗

arXiv2021

Advances in multiscale modeling for novel and emerging technologies

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.

physics.comp-ph↗

arXiv2021

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.

physics.chem-ph↗

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

Crystal-based intensive gamma-ray light sources

We discuss design and practical realization of novel gamma-ray Crystal-based Light Sources (CLS) that can be constructed through exposure of oriented crystals (linear, bent, periodically bent) to beams of ultrarelativistic charged particles. In an exemplary case study, we estimate brilliance of radiation emitted in a Crystalline Undulator (CU) LS by available positron beams. Intensity 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. Brilliance of CU-LSs can be boosted by up to 8 orders of magnitude through the process of superradiance by a pre-bunched beam. 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 alternative to conventional LSs and have enormous number of applications.

physics.acc-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↗