List of Departments
Topmost Scientific Results
- Department of Astrophysics and Elementary Particles
- Department of High-Density Energy Physics
- Department of Theory of Quantum Processes in Nanosystems
- Department of Mathematical Methods in Theoretical Physics
- Department of Theory of Nonlinear Processes in Condensed Matter
- Department of Synergetics
- Department of Theory of Nuclei and Quantum Field Theory
- Department of Theoretical and Computational Biophysics
- Department of Computer Maintenance
Department of Theoretical and Computational Biophysics
- Molecular dynamics simulations of five systems with DNA, water molecules and alkali metal cations (Li⁺, Na⁺, K⁺, Rb⁺, Cs⁺) were performed. Based on the obtained trajectories, the vibrational spectra of the elements of the studied systems were calculated using two independent approaches based on the autocorrelation functions of the velocities and the autocorrelation functions of the dipole moments. Analysis of the infrared spectra of DNA in solutions with different salts showed that the studied ions have little effect on the vibrational dynamics of the atomic groups of DNA. The exception is Li⁺ ions, the effect of which is observed in the spectral range where the vibrations of the double helix backbone lie.Using the calculated spectra of the density of vibrational states of cations localized in different regions of DNA, the influence of the nature of hydration of ions on their vibrational dynamics was revealed. Additionally, the spectra of the density of vibrational states of water molecules of the hydrated shells of the studied ions were calculated and it was shown that in the obtained spectra an isobestic point is observed, which arises due to steric restrictions caused by the DNA surface and, also, by ions.
T.L. Bubon, S.M. Perepelytsya
- The paper analyzes the problems of the observer and measurement in quantum mechanics, outlined by P. Dirac and J. Bell, based on a critical rethinking of classical and modern approaches. A new analytical model of a measurement experiment is proposed, which allows a new interpretation of the role of measurement, and its main consequences are discussed.
Ye.S. Kryachko
- A model of DNA macromolecule deformation is presented that takes into account both external and internal deformation components and their interrelationship. The external components describe the twisting and stretching of the double helix, while the internal components are characterized by the relative displacement of structural elements within the base pairs of the double helix. The model assumes an interaction between the twisting, stretching, and internal component deformations. As a result, a counterintuitive behavior is revealed: under the action of a stretching force, the DNA double helix can undergo an increase in torsion. This anomalous behavior persists until a certain critical force is reached, after which the molecule exhibits more normal behavior, unwinding in response to further stretching. The results emphasize the crucial role of the interaction between the inner and outer components in the mechanics of the double helix under the influence of an applied force in the piconewton range. The model agrees well with experimental data, confirming its reliability.
P.P. Kanevska, S.N. Volkov
- The structure of DNA solutions with the addition of LiCl salt was studied based on measurements of their electrical conductivity in a wide temperature range. It was found that the presence of DNA significantly reduces the electrical conductivity of LiCl solutions and determines the presence of three characteristic concentration regions. In the first concentration region (0-0.3 M), the electrical conductivity of solutions containing DNA increases more slowly compared to the electrical conductivity of the corresponding LiCl solutions without DNA. In the second region (0.3-0.9 M), both systems are characterized by almost the same rate of increase in electrical conductivity. In the third region (above 0.9 M), the electrical conductivity of DNA solutions again increases significantly more slowly than in pure salt solutions. The revealed regularities are qualitatively explained within the framework of the developed model, which links the observed effects with the ordering of ions induced by the DNA macromolecule, which limits their mobility and reduces the contribution to the processes of electric charge transfer. The obtained results indicate the promising use of such systems in DNA-based technologies, in particular in the development of electrolytic electrochemical current sources.
S.M. Perepelytsya
- Quantum-chemical analysis of Ag+ complexes with DNA nitrogenous bases was performed, including the binding of Ag+ to the N1 atom of thymine, the N1 and N7 atoms of guanine, and the N3 atom of 5-bromocytosine. The results reveal clear patterns that determine the stability of these systems: the coordination behavior of Ag+ strongly depends on the type of nucleotide base and the position of the donor atom. Electroneutral Ag+ complexes with the N3 atom of thymine and the N1 atom of guanine demonstrated the highest thermodynamic stability. In contrast, positively charged Ag+ complexes with the N1 atom of adenine turned out to be the least stable, which explains the experimentally observed "jumping out" of adenine from the double helix in metallized Ag-DNA. A comparison of the computational approaches used in this work shows that the B3LYP functional in combination with the SMD solvation model provides the most suitable description of Ag+-nucleotide base complexes, as it systematically yields lower formation energies than B3LYP/PCM and predicts Ag-N bond lengths more consistently than M062X. The results provide a solid theoretical basis for interpreting the structural features of metallized Ag-DNA as a promising nanoscale electronic material.
E.S. Osokin, S.M. Perepelytsya
- A review is prepared on ion-DNA interactions as a key factor in shaping the structural and functional properties of DNA. The role of ions in controlling hydration, stability, and compaction of the macromolecule is shown, and their importance for applications in DNA nanotechnology, biosensors, genetic material delivery, and nanoelectronics is summarized. The growing role of computer modeling in predicting the properties and designing DNA-based nanomaterials is emphasized.
S. Perepelytsya, D. Piatnytskyi, T. Bubon
- The Manning model is extended to the case of a two-dimensional array of parallel charged molecules of a polyelectrolyte of the DNA type. The free energy of the system and the number of condensed ions are determined and it is shown that at certain intermolecular distances the ions acquire a collective character and do not belong to the ionic atmosphere of a separate molecule, which is fundamentally important for understanding the behavior of the ionic atmosphere of DNA in the condensed state.
B.S. Reshotka, S.M. Perepelytsya
- The problem of morphological classification of galaxies from the Galaxy Zoo DECaLS dataset is considered using classical machine learning methods. It is shown that most classical classifiers achieve the highest performance in combination with LLE, achieving accuracy comparable to that of simple neural networks. Moreover, in the case of shape classification, the 3D representation remains interpretable, in contrast to the often observed loss of interpretability after nonlinear transformations. We also examined k-means clustering in reduced dimensionality to assess whether the data exhibit a natural tendency toward a certain number of clusters. While the Davis-Boulden estimate indicates a slight preference for four clusters, which is closely related to the classifications made by human astronomers, other measures do not support a clear clustering structure.
V.B. Tymchyshyn
- A machine learning method is proposed that introduces the XiEff representation, a neural field-based parameterization of the effective susceptibility. Moving to the Lippmann-Schwinger equation for near-field optics, an optimization strategy is proposed to reconstruct the effective susceptibility distribution directly from NFI data. The optimized XiEff representation provides an interpretable and explanatory model of the particle shape. Evaluations on a synthetically generated NFI dataset demonstrate the effectiveness of the method, allowing for high IoU levels even for complex geometries. Furthermore, the approach demonstrates desirable robustness to measurement noise, which is a crucial property for practical applications.
V.B. Tymchyshyn