arXiv subjects

Andrey V. Solov'yov

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

At least 73 records · Page 4Linked to original sources

arXiv2016

Reconciling simulated melting and ground-state properties of metals with a modified embedded-atom method potential

We propose a modification of the embedded-atom method-type potential aiming at reconciling simulated melting and ground-state properties of metals by means of classical molecular dynamics. Considering titanium, magnesium, gold, and platinum as case studies, we demonstrate that simulations performed with the modified force field yield quantitatively correctly both the melting temperature of the metals and their ground-state properties. It is shown that the accounting for the long-range interatomic interactions noticeably affect the melting point assessment. The introduced modification weakens the interaction at interatomic distances exceeding the equilibrium one by a characteristic vibration amplitude defined by the Lindemann criterion, thus allowing for the correct simulation of melting, while keeping its behavior in the vicinity of the ground state minimum. The modification of the many-body potential has a general nature and can be applicable to metals with different characteristics of the electron structure as well as for many different molecular and solid state systems experiencing phase transitions.

cond-mat.mes-hall↗

arXiv2015

Studying chemical reactions in biological systems with MBN Explorer: implementation of molecular mechanics with dynamical topology

The concept of molecular mechanics force field has been widely accepted nowadays for studying various processes in biomolecular systems. In this paper, we suggest a modification for the standard CHARMM force field that permits simulations of systems with dynamically changing molecular topologies. The implementation of the modified force field was carried out in the popular program MBN Explorer, and, to support the development, we provide several illustrative case studies where dynamical topology is necessary. In particular, it is shown that the modified molecular mechanics force field can be applied for studying processes where rupture of chemical bonds plays an essential role, e.g., in irradiation- or collision-induced damage, and also in transformation and fragmentation processes involving biomolecular systems.

physics.chem-ph↗

arXiv2015

Transport of secondary electrons and reactive species in ion tracks

The transport of reactive species brought about by ions traversing tissue-like medium is analysed analytically. Secondary electrons ejected by ions are capable of ionizing other molecules; the transport of these generations of electrons is studied using the random walk approximation until these electrons remain ballistic. Then, the distribution of solvated electrons produced as a result of interaction of low-energy electrons with water molecules is obtained. The radial distribution of energy loss by ions and secondary electrons to the medium yields the initial radial dose distribution, which can be used as initial conditions for the predicted shock waves. The formation, diffusion, and chemical evolution of hydroxyl radicals in liquid water are studied as well.

physics.bio-ph↗

arXiv2015

Comparative analysis of the secondary electron yield from carbon nanoparticles and pure water medium

The production of secondary electrons generated by carbon nanoparticles and pure water medium irradiated by fast protons is studied by means of model approaches and Monte Carlo simulations. It is demonstrated that due to a prominent collective response to an external field, the nanoparticles embedded in the medium enhance the yield of low-energy electrons. The maximal enhancement is observed for electrons in the energy range where plasmons, which are excited in the nanoparticles, play the dominant role. Electron yield from a solid carbon nanoparticle composed of fullerite, a crystalline form of C60 fullerene, is demonstrated to be several times higher than that from liquid water. Decay of plasmon excitations in carbon-based nanosystems thus represents a mechanism of increase of the low-energy electron yield, similar to the case of sensitizing metal nanoparticles. This observation gives a hint for investigation of novel types of sensitizers to be composed of metallic and organic parts.

physics.atm-clus↗

arXiv2014

Electron production by sensitizing gold nanoparticles irradiated by fast ions

The yield of electrons generated by gold nanoparticles due to irradiation by fast charged projectiles is estimated. The results of calculations are compared to those obtained for pure water medium. It is demonstrated that a significant increase in the number of emitted electrons arises from collective electron excitations in the nanoparticle. The dominating enhancement mechanisms are related to the formation of (i) plasmons excited in a whole nanoparticle, and (ii) atomic giant resonances due to excitation of d electrons in individual atoms. Decay of the collective electron excitations in a nanoparticle embedded in a biological medium thus represents an important mechanism of the low-energy electron production. Parameters of the utilized model approach are justified through the calculation of the photoabsorption spectra of several gold nanoparticles, performed by means of time-dependent density-functional theory.

physics.atm-clus↗

arXiv2014

Revealing the Mechanism of Low-Energy Electron Yield Enhancement from Sensitizing Nanoparticles

We provide a physical explanation for enhancement of the low-energy electron production by sensitizing nanoparticles due to irradiation by fast ions. It is demonstrated that a significant increase in the number of emitted electrons arises from the collective electron excitations in the nanoparticle. We predict a new mechanism of the yield enhancement due to the plasmon excitations and quantitatively estimate its contribution to the electron production. Revealing the nanoscale mechanism of the electron yield enhancement, we provide an efficient tool for evaluating the yield of emitted electron from various sensitizers. It is shown that the number of low-energy electrons generated by the gold and platinum nanoparticles of a given size exceeds that produced by the equivalent volume of water and by other metallic (e.g., gadolinium) nanoparticles by an order of magnitude. This observation emphasizes the sensitization effect of the noble metal nanoparticles and endorses their application in novel technologies of cancer therapy with ionizing radiation.

physics.atm-clus↗

arXiv2014

Molecular dynamics study of the stability of a carbon nanotube atop a catalytic nanoparticle

The stability of a single-walled carbon nanotube placed on top of a catalytic nickel nanoparticle is investigated by means of molecular dynamics simulations. As a case study, we consider the $(12,0)$ nanotube consisting of 720 carbon atoms and the icosahedral Ni$_{309}$ cluster. An explicit set of constant-temperature simulations is performed in order to cover a broad temperature range from 400 to 1200 K, at which a successful growth of carbon nanotubes has been achieved experimentally by means of chemical vapor deposition. The stability of the system depending on parameters of the involved interatomic interactions is analyzed. It is demonstrated that different scenarios of the nanotube dynamics atop the nanoparticle are possible depending on the parameters of the Ni-C potential. When the interaction is weak the nanotube is stable and resembles its highly symmetric structure, while an increase of the interaction energy leads to the abrupt collapse of the nanotube in the initial stage of simulation. In order to validate the parameters of the Ni-C interaction utilized in the simulations, DFT calculations of the potential energy surface for carbon-nickel compounds are performed. The calculated dissociation energy of the Ni-C bond is in good agreement with the values, which correspond to the case of a stable and not deformed nanotube simulated within the MD approach.

physics.chem-ph↗

arXiv2013

Multiscale approach to the physics of radiation damage with ions

The multiscale approach to the assessment of biodamage resulting upon irradiation of biological media with ions is reviewed, explained and compared to other approaches. The processes of ion propagation in the medium concurrent with ionization and excitation of molecules, transport of secondary products, dynamics of the medium, and biological damage take place on a number of different temporal, spatial and energy scales. The multiscale approach, a physical phenomenon-based analysis of the scenario that leads to radiation damage, has been designed to consider all relevant effects on a variety of scales and develop an approach to the quantitative assessment of biological damage as a result of irradiation with ions. This paper explains the scenario of radiation damage with ions, overviews its major parts, and applies the multiscale approach to different experimental conditions. On the basis of this experience, the recipe for application of the multiscale approach is formulated. The recipe leads to the calculation of relative biological effectiveness.

physics.bio-ph↗

arXiv2013

Interplay of the volume and surface plasmons in the electron energy loss spectra of C$_{60}$

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.

physics.atm-clus↗

arXiv2013

Quantum and classical features of the photoionization spectrum of C$_{60}$

By considering photoionization of the C$_{60}$ fullerene, we elucidate the contributions of various classical and quantum physics phenomena appearing in this process. By comparing the results, based on the {\it ab initio} and model approaches, we map the well-resolved features of the photoabsoprtion spectrum to single-particle and collective excitations which have the different physical nature. It is demonstrated that the peculiarities arising in the photoionization spectrum of C$_{60}$ atop the dominating plasmon excitations have the quantum origin. In particular, we demonstrate that a series of individual peaks can be assigned either to the optically allowed discrete transitions or to ionization of particular molecular orbitals of the system. The analysis performed gives a detailed information on the nature of numerous features in the photoabsorption spectrum of C$_{60}$.

physics.atm-clus↗

arXiv2013

Simulation of Ultra-Relativistic Electrons and Positrons Channeling in Crystals with MBN Explorer

A newly developed code, implemented as a part of the \MBNExplorer package \cite{MBN_ExplorerPaper,MBN_ExplorerSite} to simulate trajectories of an ultra-relativistic projectile in a crystalline medium, is presented. The motion of a projectile is treated classically by integrating the relativistic equations of motion with account for the interaction between the projectile and crystal atoms. The probabilistic element is introduced by a random choice of transverse coordinates and velocities of the projectile at the crystal entrance as well as by accounting for the random positions of the atoms due to thermal vibrations. The simulated trajectories are used for numerical analysis of the emitted radiation. Initial approbation and verification of the code have been carried out by simulating the trajectories and calculating the radiation emitted by $\E=6.7$ GeV and $\E=855$ MeV electrons and positrons in oriented Si(110) crystal and in amorphous silicon. The calculated spectra are compared with the experimental data and with predictions of the Bethe-Heitler theory for the amorphous environment.

physics.acc-ph↗

arXiv2012

Kinetics of liquid-solid phase transition in large nickel clusters

In this paper we have explored computationally the solidification process of large nickel clusters. This process has the characteristic features of the first order phase transition occurring in a finite system. The focus of our research is placed on the elucidation of correlated dynamics of a large ensemble of particles in the course of the nanoscale liquid-solid phase transition through the computation and analysis of the results of molecular dynamics (MD) simulations with the corresponding theoretical model. This problem is of significant interest and importance, because the controlled dynamics of systems on the nanoscale is one of the central topics in the development of modern nanotechnologies. MD simulations in large molecular systems are rather computer power demanding. Therefore, in order to advance with MD simulations we have used modern computational methods based on the graphics processing units (GPU). The advantages of the use of GPUs for MD simulations in comparison with the CPUs are demonstrated and benchmarked. The reported speedup reaches factors greater than 400. This work opens a path towards exploration with the use of MD of a larger number of scientific problems inaccessible earlier with the CPU based computational technology.

physics.comp-ph↗

arXiv2012

Formalism of collective electron excitations in fullerenes

We present a detailed formalism for the description of collective electron excitations in fullerenes in the process of the electron inelastic scattering. Considering the system as a spherical shell of a finite width, we show that the differential cross section is defined by three plasmon excitations, namely two coupled modes of the surface plasmon and the volume plasmon. The interplay of the three plasmons appears due to the electron diffraction of the fullerene shell. Plasmon modes of different angular momenta provide dominating contributions to the differential cross section depending on the transferred momentum.

physics.atm-clus↗

arXiv2012

Calculation of complex DNA damage induced by ions

This paper is devoted to the analysis of the complex damage of DNA irradiated by ions. The analysis and assessment of complex damage is important because cells in which it occurs are less likely to survive because the DNA repair mechanisms may not be sufficiently effective. We studied the flux of secondary electrons through the surface of nucleosomes and calculated the radial dose and the distribution of clustered damage around the ion's track. The calculated radial dose distribution is compared to simulations. The radial distribution of the complex damage is found to be different from that of the dose. Comparison with experiments may solve the question of what is more lethal for the cell, damage complexity or absorbed energy. We suggest a way to calculate the probability of cell death based on the complexity of the damage. This work is done within the framework of the phenomenon-based multiscale approach to radiation damage by ions.

physics.bio-ph↗

arXiv2012

Double strand breaks in DNA resulting from double-electron-emission events

A mechanism of double strand breaking (DSB) in DNA due to the action of two electrons is considered. These are the electrons produced in the vicinity of DNA molecules due to ionization of water molecules with a consecutive emission of two electrons, making such a mechanism possible. This effect qualitatively solves a puzzle of large yields of DSBs following irradiation of DNA molecules. The transport of secondary electrons, including the additional electrons, is studied in relation to the assessment of radiation damage due to incident ions. This work is a stage in the inclusion of Auger mechanism and like effects into the multiscale approach to ion-beam cancer therapy.

physics.bio-ph↗

arXiv2011

Role of exchange interaction in self-consistent calculations of endohedral fullerenes

Results of the self-consistent calculation of electronic structure of endohedral fullerene Ar@C$_{60}$ within the Hartree-Fock and the local density approximations are presented. Hartree-Fock approximation is used for the self-consistent description for the first time. It is shown that the accurate account of the exchange interaction between all electrons of the compound leads to the significant modification of the atomic valent shell which causes the noticeable charge redistribution inside the endohedral compound.

physics.atm-clus↗

arXiv2011

Fragmentation pathways of nanofractal structures on surface

We present a detailed systematical theoretical analysis of the post-growth processes occurring in nanofractals grown on surface. For this study we developed a method which accounts for the internal dynamics of particles in a fractal. We demonstrate that particle diffusion and detachment controls the shape of the emerging stable islands on surface. We consider different scenarios of fractal post-growth relaxation and analyze the time evolution of the island's morphology. The results of our calculations are compared with available experimental observations, and experiments in which the post-growth relaxation of deposited nanostructures can be probed are suggested.

physics.atm-clus↗

arXiv2010

Vacancy decay in endohedral atoms: the role of non-central position of the atom

We demonstrate that the Auger decay rate in an endohedral atom is very sensitive to the atom's location in the fullerene cage. Two additional decay channels appear in an endohedral system: (a) the channel due to the change in the electric field at the atom caused by dynamic polarization of the fullerene electron shell by the Coulomb field of the vacancy, (b) the channel within which the released energy is transferred to the fullerene electron via the Coulomb interaction. % The relative magnitudes of the correction terms are dependent not only on the position of the doped atom but also on the transition energy $\om$. Additional enhancement of the decay rate appears for transitions whose energies are in the vicinity of the fullerene surface plasmons energies of high multipolarity. % It is demonstrated that in many cases the additional channels can dominate over the direct Auger decay resulting in pronounced broadening of the atomic emission lines. % The case study, carried out for Sc$^{2+}$@C$_{80}^{6-}$, shows that narrow autoionizing resonances in an isolated Sc$^{2+}$ within the range $\om = 30... 45$ eV are dramatically broadened if the ion is located strongly off-the-center. % Using the developed model we carry out quantitative analysis of the photoionization spectrum for the endohedral complex Sc$_3$N@C$_{80}$ and demonstrate that the additional channels are partly responsible for the strong modification of the photoionization spectrum profile detected experimentally by Müller et al. (J. Phys.: Conf. Ser. 88, 012038 (2008)).

physics.atm-clus↗