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

Modeling of nanoparticle coatings for medical applications

Abstract Gold nanoparticles (AuNPs) have been shown to possess properties beneficial for the treatment of cancerous tumors by acting as radiosensitizers for both photon and ion radiation. Blood circulation time is usually increased by coating the AuNPs with poly(ethylene glycol) (PEG) ligands. The effectiveness of the PEG coating, however, depends on both the ligand surface density and length of the PEG molecules, making it important to understand the structure of the coating. In this paper the thickness, ligand surface density, and density of the PEG coating is studied with classical molecular dynamics using the software package MBN Explorer. AuNPs consisting of 135 atoms (approximately 1.4 nm diameter) in a water medium have been studied with the number of PEG ligands varying between 32 and 60. We find that the thickness of the coating is only weakly dependent on the surface ligand density and that the degree of water penetration is increased when there is a smaller number of attached ligands

Molecular Dynamics Simulations of Bio-Nano Systems with MBN Explorer

AbstractWe present results of molecular dynamics simulations performed using a multi-purpose computer code MBN Explorer. In particular we consider the process of laser induced acoustic desorption of lysine amino acids from the surface of a nickel foil. We analyze the rate of lysine desorption from the nickel foil at different foil accelerations and suggest a simple theoretical model to describe the observed results. We note that despite the universality, the computational efficiency of MBN Explorer is comparable (and in some cases even higher) than the computational efficiency of other software packages, making MBN Explorer a possible alternative to the available codes

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

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

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

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

Influence of the litter features on pedogenesis in forests of the middle Dniprо flood-lands

Узагальнено сучасний стан лісових біогеоценозів заплави середньої течії Дніпра на прикладі Дніпровсько-Орільського природного заповідника. Наведено дані про якісні зміни рівня трофності ґрунтів у ході сукцесій лісової рослинності заплави Дніпра. Узагальнено сучасний стан лісових біогеоценозів заплави середньої течії Дніпра на прикладі Дніпровсько-Орільського природного заповідника. Наведено дані про якісні зміни рівня трофності ґрунтів у ході сукцесій лісової рослинності заплави ДніпраThe modern status of forest ecosystems of the middleDnieperflood-lands is characterized by the example of Dniprovsko-Orelsky nature reserve. The data of qualitative changes of the soil fertility in the course of wood vegetation’s succession in theDnieperflood-lands are presented

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.Comment: 18 pag,5 fig, submitted to PR

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.Comment: 5 figures, Proceedings of the 5th Conference on Elementary Processes in Atomic Systems (CEPAS 2011), submitted to Nuclear Instruments and Methods in Physics Research Section