arXiv subjects

Ilia A. Solov'yov

Publications and source records attributed to Ilia A. Solov'yov.

At least 19 recordsLinked to original sources

arXiv2025

Stochastic dynamics simulation of the focused electron beam induced deposition process

This work reports on the development of a new approach to the multiscale computational modelling of the focused electron beam-induced deposition (FEBID), realised using the advanced software packages: MBN Explorer and MBN Studio. Our approach is based on stochastic dynamics (SD), which describes the probabilistic evolution of complex systems. The parameters for the new SD-based FEBID model were determined using molecular dynamics (MD) simulations. A new methodology was developed for this purpose and is described in detail. This methodology can be applied to many other case studies of the dynamics of complex systems. Our work focuses on the FEBID process involving W(CO)$_6$ precursor molecules deposited on a hydroxylated SiO$_2$-H substrate. Simulations and a detailed analysis of a growing W-rich nanostructure were performed. This new approach was shown to provide essential atomistic insights into the complex FEBID process, including the elemental composition and morphology of the deposit at each stage of growth. The derived results were then compared with experimental observations and validated. The multiscale methods developed in this study can be further upgraded and applied to important technological developments, such as 3D nanoprinting.

physics.comp-ph↗

arXiv2023

Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment

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.

physics.chem-ph↗

arXiv2022

Local elastic properties of polystyrene nanocomposites increase significantly due to non-affine deformations

We investigate the local elastic properties of polystyrene doped with SiO2 nanoparticles by analyzing the local density fluctuations. The density fluctuations were established from coarse-grained molecular dynamics simulations performed with the MARTINI force field. A significant increase in polystyrene stiffness was revealed within a characteristic range of 1.4 nm from the nanoparticle, while polystyrene density saturates to the bulk value at significantly shorter distances. The enhancement of the local elastic properties of the polymer was attributed to the effect of non-affine deformations at the length scale below 1 nm, which was further confirmed through the random matrix model with variable strength of disorder.

cond-mat.dis-nn↗

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

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↗

arXiv2019

Modeling elastic properties of polystyrene through coarse-grained molecular dynamics simulations

This paper presents an extended coarse-grained investigation of the elastic properties of polystyrene. In particular, we employ the well-known MARTINI force field and its modifications to perform extended molecular dynamics simulations at the $μ$s timescale, which take slow relaxation processes of polystyrene into account, such that the simulations permit analyzing the bulk modulus, the shear modulus, and the Poisson ratio. We show that through the iterative modification of MARTINI force field parameters it turns out to be possible to affect the shear modulus and the bulk modulus of the system, making them closer to those values reported in the experiment.

physics.comp-ph↗

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↗

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↗

arXiv2011

Mechanism of magnetic field effect in cryptochrome

Creatures as varied as mammals, fish, insects, reptiles, and migratory birds have an intriguing `sixth' sense that allows them to distinguish north from south by using the Earth's intrinsic magnetic field. Yet despite decades of study, the physical basis of this magnetic sense remains elusive. A likely mechanism is furnished by magnetically sensitive radical pair reactions occurring in the retina, the light-sensitive part of the eyes. A photoreceptor, cryptochrome, has been suggested to endow birds with magnetoreceptive abilities as the protein has been shown to exhibit the biophysical properties required for an animal magnetoreceptor to operate properly. Here, we propose a concrete light-driven reaction cycle in cryptochrome that lets a magnetic field influence the signaling state of the photoreceptor. The reaction cycle ties together transient absorption and electron-spin-resonance observations with known facts on avian magnetoreception. Our analysis establishes the feasibility of cryptochrome to act as a geomagnetic compass in birds, gives insight into structural and dynamic design features required for optimal detection of the geomagnetic field direction, and suggests further theoretical and experimental studies.

physics.bio-ph↗

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↗

arXiv2009

Uncovering a Solvent-Controlled Preferential Growth of Buckminsterfullerene (C60) Nanowires

The fullerene (C60) nanowires, which possess a highly unusual morphology featured by a prism-like central core and three nanobelt-like wings joined along the growth direction to give an overall Y-shaped cross section, have been studied. The experimental observation coupled with theoretical calculation have enabled us to elucidate both the role of the fullerene and of the solvent in the crystallization process, thus opening up an opportunity for the in-depth understanding of the crystal growth mechanism. More generally, the method developed in this work could be extended into understanding the growth of other inorganic nanowires that have both host and guest molecules involved in their crystal lattices.

physics.chem-ph↗

arXiv2007

Alpha helix-coil phase transition: analysis of ab initio theory predictions

In the present paper we present results of calculations obtained with the use of the theoretical method described in our preceding paper [1] and perform detail analysis of alpha helix-random coil transition in alanine polypeptides of different length. We have calculated the potential energy surfaces of polypeptides with respect to their twisting degrees of freedom and construct a parameter-free partition function of the polypeptide using the suggested method [1]. From the build up partition function we derive various thermodynamical characteristics for alanine polypeptides of different length as a function of temperature. Thus, we analyze the temperature dependence of the heat capacity, latent heat and helicity for alanine polypeptides consisting of 21, 30, 40, 50 and 100 amino acids. Alternatively, we have obtained same thermodynamical characteristics from the use of molecular dynamics simulations and compared them with the results of the new statistical mechanics approach. The comparison proves the validity of the statistical mechanic approach and establishes its accuracy.

physics.bio-ph↗

arXiv2007

Ab initio theory of helix-coil phase transition

In this paper we suggest a theoretical method based on the statistical mechanics for treating the alpha-helix-random coil transition in alanine polypeptides. We consider this process as a first-order phase transition and develop a theory which is free of model parameters and is based solely on fundamental physical principles. It describes essential thermodynamical properties of the system such as heat capacity, the phase transition temperature and others from the analysis of the polypeptide potential energy surface calculated as a function of two dihedral angles, responsible for the polypeptide twisting. The suggested theory is general and with some modification can be applied for the description of phase transitions in other complex molecular systems (e.g. proteins, DNA, nanotubes, atomic clusters, fullerenes).

physics.bio-ph↗

arXiv2007

Towards understanding of birds magnetoreceptor mechanism

In the present letter we suggest a new theoretical model for a quantitative description of the magnetoreception mechanism in birds. The considered mechanism involves two types of iron minerals (magnetite and maghemite) which were found in subcellular compartments within sensory dendrites of the upper beak of several bird species. The analysis of forces acting between the iron particles shows that the orientation of the external geomagnetic field can significantly change the probability of the mechanosensitive ion channels opening and closing. The performed theoretical analysis shows that the suggested magnetoreceptor system might be a sensitive biological magnetometer providing an essential part of the magnetic map for navigation.

physics.bio-ph↗

arXiv2007

Two center multipole expansion method: application to macromolecular systems

We propose a new theoretical method for the calculation of the interaction energy between macromolecular systems at large distances. The method provides a linear scaling of the computing time with the system size and is considered as an alternative to the well known fast multipole method. Its efficiency, accuracy and applicability to macromolecular systems is analyzed and discussed in detail.

physics.bio-ph↗