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

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

Computational reconstruction and analysis of structural models of avian cryptochrome 4

A recent study by Xu et al. (Nature,2021, 594, 535−540) provided strongevidence that cryptochrome 4 (Cry4) is a key protein to endow migratory birds with the magneticcompass sense. The investigation compared the magneticfield response of Cry4 from migratoryand nonmigratory bird species and suggested that a difference in magnetic sensitivity could exist.Thisfinding prompted an in-depth investigation into Cry4 protein differences on the structuraland dynamic levels. In the present study, the pigeon Cry4 (ClCry4) crystal structure was used toreconstruct the missing avian Cry4 protein structures via homology modeling for carefullyselected bird species. The reconstructed Cry4 structure from European robin, Eurasian blackcap,zebrafinch, chicken, and pigeon were subsequently simulated dynamically and analyzed. Thestudied avian Cry4 structures showflexibility in analogous regions pointing to similar activationmechanisms and/or signaling interaction partners. It can be concluded that the experimentallyrecorded difference in the magneticfield sensitivity of Cry4 from different birds is unlikely to bedue to solely intrinsic dynamics of the proteins but requires additional factors that have not yet been identified

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.Comment: 27 pages, 13 figure

Double strand breaks in DNA resulting from double-electron-emission events

A mechanism of double strand breaking (DSB) in DNA due to the action of two electrons is considered. These are the electrons produced in the vicinity of DNA molecules due to ionization of water molecules with a consecutive emission of two electrons, making such a mechanism possible. This effect qualitatively solves a puzzle of large yields of DSBs following irradiation of DNA molecules. The transport of secondary electrons, including the additional electrons, is studied in relation to the assessment of radiation damage due to incident ions. This work is a stage in the inclusion of Auger mechanism and like effects into the multiscale approach to ion-beam cancer therapy.Comment: 4 pages, 3 figure

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

Roadmap on dynamics of molecules and clusters in the gas phase

This roadmap article highlights recent advances, challenges and future prospects in studies of the dynamics of molecules and clusters in the gas phase. It comprises nineteen contributions by scientists with leading expertise in complementary experimental and theoretical techniques to probe the dynamics on timescales spanning twenty order of magnitudes, from attoseconds to minutes and beyond, and for systems ranging in complexity from the smallest (diatomic) molecules to clusters and nanoparticles. Combining some of these techniques opens up new avenues to unravel hitherto unexplored reaction pathways and mechanisms, and to establish their significance in, e.g. radiotherapy and radiation damage on the nanoscale, astrophysics, astrochemistry and atmospheric science

Phase transitions in polypeptides: analysis of energy fluctuations

The helix↔random coil transition in alanine, valine, and leucine polypeptides consisting of 30 amino acids is studied in vacuo using the Langevin molecular dynamics approach. The influence of side chain radicals on internal energy and heat capacity of the polypeptides is discussed. The heat capacity of these polypeptides is calculated as a function of temperature using two different methods, namely, as the derivative of the energy with respect to temperature, and on the basis of energy fluctuations in the system. The convergence of the fluctuations based approach is analyzed as a function of simulation time. This study provides a comparison of methods for the description of structural transitions in polypeptides