arXiv subjects

Andrey V. Solov'yov

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

87 records · Page 5Linked to original sources

arXiv2009

Spectra of secondary electrons generated in water by energetic ions

The energy distributions of secondary electrons produced by energetic carbon ions (in the energy range used, e.g., in hadron therapy), incident on liquid water, are discussed. For low-energy ions, a new parameterization of the singly-differential ionization cross sections is introduced, based on tuning the position of the Bragg peak. The resulting parameterization allows a fast calculation of the energy spectra of secondary electrons at different depths along the ion's trajectory, especially near the Bragg peak. At the same time, this parameterization provides penetration depths for a broad range of initial-ion energies within the therapeutically-accepted error. For high-energy ions, the energy distribution is obtained with a use of the dielectric response function approach. Different models are compared and discussed.

physics.bio-ph↗

arXiv2009

Synthesis of a fullerene-based one-dimensional nanopolymer through topochemical transformation of the parent nanowire

Large-scale practical applications of fullerene (C60) in nanodevices could be significantly facilitated if the commercially-available micrometer-scale raw C60 powder were further processed into a one-dimensional (1D) nanowire-related polymer displaying covalent bonding as molecular interlinks and resembling traditional important conjugated polymers. However, there has been little study thus far in this area despite the abundant literature on fullerene. Here we report the synthesis and characterization of such a C60-based nanowire polymer, (-C60TMB-)n, where TMB=1,2,4-trimethylbenzene, which displays a well-defined crystalline structure, exceptionally large length-to-width ratio and excellent thermal stability. The material is prepared by first growing the corresponding nanowire through a solution phase of C60 followed by a topochemical polymerization reaction in the solid state. Gas chromatography, mass spectrometry and 13C nuclear magnetic resonance evidence is provided for the nature of the covalent bonding mode adopted by the polymeric chains. Theoretical analysis based on detailed calculations of the reaction energetics and structural analysis provides an in-depth understanding of the polymerization pathway. The nanopolymer promises important applications in biological fields and in the development of optical, electrical, and magnetic nanodevices.

physics.chem-ph↗

arXiv2009

Many-body theory for angular resolved photoelectron spectra of metal clusters

Angular resolved photoelectron spectra of metal clusters have been experimentally measured for the first time only recently. These measurements have been performed systematically for sodium clusters in a broad range of cluster sizes. This work attracted a lot of attention and was reported practically at all major international cluster conferences because it revealed a very non-trivial behavior of the angular anisotropy parameter with respect to photon energy and provided a method for probing the angular momentum character of the valence orbitals of free nanoclusters. Initial attempts to explain these observations within single particle approximations fail completely. In this Letter we present a consistent many-body theory for the description of angular resolved photoelectron spectra of metal clusters. Jellium model formalism is employed. Our calculations demonstrate the dominant role of the many-body effects in the formation of angular distributions of photoelectrons emitted from sodium clusters and are in a good agreement with experimental data reported in. The concrete comparison of theory and experiment has been performed for the photoionization of $Na_7^{-}$ and $Na_{19}^{-}$ anions being characterized by the entirely closed shells of delocalized electrons.

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↗

arXiv2008

Physics of ion beam cancer therapy: a multi-scale approach

We propose a multi-scale approach to understand the physics related to ion-beam cancer therapy. It allows the calculation of the probability of DNA damage as a result of irradiation of tissues with energetic ions, up to 430 MeV/u. This approach covers different scales, starting from the large scale, defined by the ion stopping, followed by a smaller scale, defined by secondary electrons and radicals, and ending with the shortest scale, defined by interactions of secondaries with the DNA. We present calculations of the probabilities of single and double strand breaks of DNA, suggest a way to further expand such calculations, and also make some estimates for glial cells exposed to radiation.

physics.bio-ph↗

arXiv2008

Impurity effects on the melting of Ni clusters

We demonstrate that the addition of a single carbon impurity leads to significant changes in the thermodynamic properties of Ni clusters consisting of more than a hundred atoms. The magnitude of the change induced is dependent upon the parameters of the Ni-C interaction. Hence, thermodynamic properties of Ni clusters can be effectively tuned by the addition of an impurity of a particular type. We also show that the presence of a carbon impurity considerably changes the mobility and diffusion of atoms in the Ni cluster at temperatures close to its melting point. The calculated diffusion coefficients of the carbon impurity in the Ni cluster can be used for a reliable estimate of the growth rate of carbon nanotubes.

physics.atm-clus↗

arXiv2007

A Rational Method for Probing Macromolecules Dissociation: The Antibody-Hapten System

The unbinding process of a protein-ligand complex of major biological interest was investigated by means of a computational approach at atomistic classical mechanical level. An energy minimisation-based technique was used to determine the dissociation paths of the system by probing only a relevant set of generalized coordinates. The complex problem was reduced to a low-dimensional scanning along a selected distance between the protein and the ligand. Orientational coordinates of the escaping fragment (the ligand) were also assessed in order to further characterise the unbinding. Solvent effects were accounted for by means of the Poisson--Boltzmann continuum model. The corresponding dissociation time was derived from the calculated barrier height, in compliance with the experimentally reported Arrhenius-like behaviour. The computed results are in good agreement with the available experimental data.

physics.bio-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

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↗

arXiv2005

Ab initio study of alanine polypeptide chains twisting

We have investigated the potential energy surfaces for alanine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles Phi and Psi, which are widely used for the characterization of the polypeptide chains. These particular degrees of freedom are essential for the characterization of proteins folding process. Calculations have been carried out within ab initio theoretical framework based on the density functional theory and accounting for all the electrons in the system. We have determined stable conformations and calculated the energy barriers for transitions between them. Using a thermodynamic approach, we have estimated the times of characteristic transitions between these conformations. The results of our calculations have been compared with those obtained by other theoretical methods and with the available experimental data extracted from the Protein Data Base. This comparison demonstrates a reasonable correspondence of the most prominent minima on the calculated potential energy surfaces to the experimentally measured angles Phi and Psi for alanine chains appearing in native proteins. We have also investigated the influence of the secondary structure of polypeptide chains on the formation of the potential energy landscape. This analysis has been performed for the sheet and the helix conformations of chains of six amino acids.

physics.bio-ph↗

arXiv2005

Conformational changes in glycine tri- and hexapeptide

We have investigated the potential energy surfaces for glycine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles phi and psi, which are widely used for the characterization of the polypeptide chains. These particular degrees of freedom are essential for the characterization of proteins folding process. Calculations have been carried out within ab initio theoretical framework based on the density functional theory and accounting for all the electrons in the system. We have determined stable conformations and calculated the energy barriers for transitions between them. Using a thermodynamic approach, we have estimated the times of the characteristic transitions between these conformations. The results of our calculations have been compared with those obtained by other theoretical methods and with the available experimental data extracted from the Protein Data Base. This comparison demonstrates a reasonable correspondence of the most prominent minima on the calculated potential energy surfaces to the experimentally measured angles phi and psi for the glycine chains appearing in native proteins. We have also investigated the influence of the secondary structure of polypeptide chains on the formation of the potential energy landscape. This analysis has been performed for the sheet and the helix conformations of chains of six amino acids.

physics.bio-ph↗

arXiv2004

Conformational properties of neutral and charged alanine and glycine chains

We have investigated the potential energy surface for neutral and charged alanine and glycine chains consisting of up to 6 amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles phi and psi. Our calculations are performed within it ab initio theoretical framework based on the density functional theory and also within semi-empirical model approaches. We have demonstrated that the excessive positive charge of the system influences strongly its geometrical and conformational properties. With increasing of the excessive charge amino acid chains become unstable and decay into two or more fragments. We have analysed how the secondary structure of polypeptide chains influences the formation of the potential energy landscapes. We have calculated the energy barriers for transitions between different molecular conformations and determined the ones being energetically the most favourable.

physics.atm-clus↗

arXiv2004

Fission of charged alanine dipeptides

In this work we have performed for the first time a systematic analysis of the dissociation and fission pathways of neutral, singly and doubly charged alanine dipeptide ions with the aim to identify the fission mechanism and the most probable fragmentation channels of these type of molecules. We demonstrate the importance of rearrangement of the molecule structure during the fission process. This rearrangement may include transition to another isomer or a quasi-molecular state before actual separation of the daughter fragments begins.

physics.atm-clus↗

arXiv2001

Structure and properties of small sodium clusters

We have investigated structure and properties of small metal clusters using all-electron ab initio theoretical methods based on the Hartree-Fock approximation and density functional theory, perturbation theory and compared results of our calculations with the available experimental data and the results of other theoretical works. We have systematically calculated the optimized geometries of neutral and singly charged sodium clusters having up to 20 atoms, their multipole moments (dipole and quadrupole), static polarizabilities, binding energies per atom, ionization potentials and frequencies of normal vibration modes. Our calculations demonstrate the great role of many-electron correlations in the formation of electronic and ionic structure of small metal clusters and form a good basis for further detailed study of their dynamic properties, as well as structure and properties of other atomic cluster systems.

physics.atm-clus↗