Microscopic and Macroscopic Surface Dynamics of Highly Anisotropic Crystals

Zadanie pt. Digitalizacja i udostępnienie w Cyfrowym Repozytorium Uniwersytetu Łódzkiego kolekcji czasopism naukowych wydawanych przez Uniwersytet Łódzki nr 885/P-DUN/2014 zostało dofinansowane ze środków MNiSW w ramach działalności upowszechniającej naukę

Stability, Bifurcation and Transitions of the Nonlinear Molecular Chain In Electric Field

The rotational dynamics of molecular adsorbed chain in longitudinal electric field is studied theoretically. The nonlinear dynamic equations are obtained with accounting of quadrupolar interactions between molecules. A new dimensionless parameter (relation of electric and intermolecular interactions) is introduced in the system of the dynamical equations. It is shown that topology of the energy relief on the angle space is transformed in dependence on the electric intensity. The rotational reordering in electric field is complex phenomenon that have several stages. One of the intermediate states is an indifferent equilibrium net (orientation melting). The stable state is found in strong electric fields

explorase: Multivariate Exploratory Analysis and Visualization for Systems Biology

The datasets being produced by high-throughput biological experiments, such as microarrays, have forced biologists to turn to sophisticated statistical analysis and visualization tools in order to understand their data. We address the particular need for an open-source exploratory data analysis tool that applies numerical methods in coordination with interactive graphics to the analysis of experimental data. The software package, known as explorase, provides a graphical user interface (GUI) on top of the R platform for statistical computing and the GGobi software for multivariate interactive graphics. The GUI is designed for use by biologists, many of whom are unfamiliar with the R language. It displays metadata about experimental design and biological entities in tables that are sortable and filterable. There are menu shortcuts to the analysis methods implemented in R, including graphical interfaces to linear modeling tools. The GUI is linked to data plots in GGobi through a brush tool that simultaneously colors rows in the entity information table and points in the GGobi plots.

Twin Boundary in hcp Crystals: Quantum and Thermal Behavior

The 180° twin boundary (TB) (stacking fault) is investigated in the hexagonal close-packed (hcp) light materials. It is shown that atomic symmetry inside the twin boundary is lower than in hcp phase due to interatomic interaction between neighbors. In the case of quantum or thermal behavior, for the isosurfaces, an initial spherical form (in hcp phase) transforms into ellipsoid (in the boundary). We introduce the isosurface deformation parameter. The self-consistent description is developed to estimate the parameters of the thermodynamic potential, and the models of hard spheres and ellipsoids are used. It is shown that the quantum or thermal behavior of the boundary atoms causes the following effects: (i) the increase of degree of overlap of the atomic wave functions or trajectories within the twin boundaries, (ii) the increase of diffusion inside the twin boundaries, and (iii) the decrease of energy and broadening of the quantum boundary in comparison with the classical case

Phonon spectrum and vibrational characteristics of linear nanostructures in solid matrices

The atomic dynamics of linear chains embedded in a crystalline matrix or adsorbed on its surface is studied. A linear chain formed by substitutional impurities in a surface layer and at the same time offsetting from this layer was analyzed particularly. This system models the actively studied experimentally structures in which gas molecules are adsorbed on the walls of the bundles of carbon nanotubes located in certain medium. It is shown that the quasi-1D features are typical for the chains in which the interatomic interaction is higher than the interaction between the atoms of the chain and the atoms of the crystal matrix. On the local phonon density of atoms of the chain, the transition to quasi-one-dimensional behavior has the form of the kink. In other words, it is the first (lowest-frequency) van Hove singularity, which in 3D structures (the system under consideration is generally three-dimensional) corresponds to the transition from closed to open constant-frequency (quasi-plane) surfaces. The local phonon densities of atoms in the chain have one-dimensional character at frequencies higher than the frequency of the van Hove singularity. The rms-amplitude of embedded chains atoms vibrations is calculated and the behavior of the atomic vibrations contribution in the low-temperature heat capacity of the system is analyzed.Comment: 14 pages, 7 figure