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.Comment: 23 pages, 7 figures, 1 tabl

Special issue: Dynamics of systems on the nanoscale (2018). Editorial

The structure, formation and dynamics of both animate and inanimate matter on the nanoscale are a highly interdisciplinary field of rapidly emerging research engaging a broad community encompassing experimentalists, theorists, and technologists. It is relevant for a large variety of molecular and nanosystems of different origin and composition and concerns numerous phenomena originating from physics, chemistry, biology, or materials science. This Topical Issue presents a collection of original research papers devoted to different aspects of structure and dynamics on the nanoscale. Some of the contributions discuss specific applications of the research results in several modern technologies and in next generation medicine. Most of the works of this topical issue were reported at the Fifth International Conference on Dynamics of Systems on the Nanoscale (DySoN) – the premier forum for the presentation of cutting-edge research in this field that was held in Potsdam, Germany in October of 2018

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.Comment: 24 pages, 10 figure

Dynamical screening of an endohedral atom

The present work is a generalisation of the dynamical screening factor presented in [1] to consider an atom located at an arbitrary position within the fullerene. A more elaborated investigation into the case where the atom is located at the centre is performed and compared with quantum mechanical calculations for dynamical screening factor of Ar@C$_{60}$ [2] and Mg@C$_{60}$ [3]. The $\pi$ and $\sigma$ plasmons of the fullerene are accounted for in a modified screening factor to improve correspondence with the quantum calculations. The spatial dependence of the screening factor was explored with Ar@C$_{60}$ and Ar@C$_{240}$ and found to depend significantly on the radial distance of the atom from the centre of the fullerene. A spatial averaging of the screening factor is presented.Comment: 18 pages, 7 figure

Finslerian 3-spinors and the generalized Duffin-Kemmer equation

The main facts of the geometry of Finslerian 3-spinors are formulated. The close connection between Finslerian 3-spinors and vectors of the 9-dimensional linear Finslerian space is established. The isometry group of this space is described. The procedure of dimensional reduction to 4-dimensional quantities is formulated. The generalized Duffin-Kemmer equation for a Finslerian 3-spinor wave function of a free particle in the momentum representation is obtained. From the viewpoint of a 4-dimensional observer, this 9-dimensional equation splits into the standard Dirac and Klein-Gordon equations.Comment: LaTeX2e, 11 pages, no figures, will be published in "Fundamental and Applied Mathematics

A multi-scale approach to the physics of ion beam cancer therapy

We propose a multi-scale approach to understanding physics related to the ion/proton-beam cancer therapy and calculation of the probability of the DNA damage as a result of irradiation of patients with energetic (up to 430 MeV/u) ions. This approach is inclusive with respect to different scales starting from the long scale defined by the ion stopping followed by a smaller scale defined by secondary electrons and radicals 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 the DNA and suggest a way of further elaboration of such calculations.Comment: submitted to RADAM2008 proceedings. 8 pages,5 Figures, class files for AIP include

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.Comment: 30 pages, 12 figures, 2 table

Evolution of electronic and ionic structure of Mg-clusters with the growth cluster size

The optimized structure and electronic properties of neutral and singly charged magnesium clusters have been investigated using ab initio theoretical methods based on density-functional theory and systematic post-Hartree-Fock many-body perturbation theory accounting for all electrons in the system. We have systematically calculated the optimized geometries of neutral and singly charged magnesium clusters consisting of up to 21 atoms, electronic shell closures, binding energies per atom, ionization potentials and the gap between the highest occupied and the lowest unoccupied molecular orbitals. We have investigated the transition to the hcp structure and metallic evolution of the magnesium clusters, as well as the stability of linear chains and rings of magnesium atoms. The results obtained are compared with the available experimental data and the results of other theoretical works.Comment: 30 pages, 10 figures, 3 table

Formalism for Multiphoton Plasmon Excitation in Jellium Clusters

We present a new formalism for the description of multiphoton plasmon excitation processes in jellium clusters. By using our method, we demonstrate that, in addition to dipole plasmon excitations, the multipole plasmons (quadrupole, octupole, etc) can be excited in a cluster by multiphoton absorption processes, which results in a significant difference between plasmon resonance profiles in the cross sections for multiphoton as compared to single-photon absorption. We calculate the cross sections for multiphoton absorption and analyse the balance between the surface and volume plasmon contributions to multipole plasmons.Comment: 29 pages, 1 figur

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.Comment: 47 pages, 16 figure