Jarosław Rybicki

Tailoring Graphene to Achieve Negative Poisson's Ratio Properties

Graphene can be made auxetic through the introduction of vacancy defects. This results in the thinnest negative Poissons ratio material at ambient conditions known so far, an effect achieved via a nanoscale de-wrinkling mechanism that mimics the behavior at the macroscale exhibited by a crumpled sheet of paper when stretched.

Theoretical study of polymerization mechanism of p-xylylene based polymers.

The mechanism of polymerization of p-xylylene and its derivatives is analyzed at the theoretical level. The polymerization reaction takes place in vacuo without any catalyst. The first step is a pyrolytic decomposition of starting material for polymerization, p-cyclophane, a cyclic dimer of p-xylylene, into biradical linear dimer and finally into two quinonoid monomeric molecules of p-xylylene. The quinonoid monomer is diamagnetic; i.e., it has a singlet ground state. The monomers after pyrolysis, when the temperature is lowered, do not re-form cyclic dimers but instead polymerize into long chain molecules. The initiation of polymerization requires dimerization of two monomers leading to formation of a genuine noncoupled biradical dimer. The chain molecules grow through the propagation reaction only one unit at a time, by the attachment of a monomer to a radical chain end. In this work the pyrolysis reaction, the initiation reaction and the first propagation steps of parylene polymerization (up to pentamer) are studied in details using different quantum chemical methods: AM1 and PM6 semiempirical methods and density functional theory (DFT) approach using B3LYP functional with two basis sets of different size (SVP and TZVP).

Tools, Methods and Services Enhancing the Usage of the Kepler-based Scientific Workflow Framework

Abstract Scientific workflow systems are designed to compose and execute either a series of computational or data manipulation steps, or workflows in a scientific application. They are usually a part of a larger eScience environment. The usage of workflow systems, however very beneficial, is mostly not irrelevant for scientists. There are many requirements for additional functionalities around scientific workflows systems that need to be taken into account, like the ability of sharing workflows, provision of the user-friendly GUI tools for automation of some tasks or submission to distributed computing infrastructures, etc. In this paper we present tools developed in response to the requirements of three different scientific communities. These tools simplify and empower their work with the Kepler scientific workflow system. The usage of such tools and services is presented on Nanotechnology, Astronomy and Fusion scenarios examples.

A highly-efficient technique for evaluating bond-orientational order parameters

We propose a novel, highly-efficient approach for the evaluation of bond-orientational order parameters (BOPs). Our approach exploits the properties of spherical harmonics and Wigner 3jj-symbols to reduce the number of terms in the expressions for BOPs, and employs simultaneous interpolation of normalised associated Legendre polynomials and trigonometric functions to dramatically reduce the total number of arithmetic operations. Using realistic test cases, we show how the above, combined with a CPU-cache-friendly data structure, leads to a 10 to 50-fold performance increase over approaches currently in use, depending on the size of the interpolation grids and the machine used. As the proposed approach is an approximation, we demonstrate that the errors it introduces are well-behaved, controllable and essentially negligible for practical grid sizes. We benchmark our approach against other structure identification methods (centro-symmetry parameter (CSP), common neighbour analysis (CNA), common neighbourhood parameter (CNP) and Voronoi analysis), generally regarded as much faster than BOPs, and demonstrate that our formulation is able to outperform them for all studied systems.

Photoacoustic response of a common starfish tissue

A sample of common starfish (Asterias Rubens) tissue has been prepared in the shape of a film to study its photoacoustic (PA) response. A broad absorption band in the PA spectrum is detected in the visible region (a peak at about 570 nm), while the ultraviolet region is distinguished by the absorption bands originating from π → π* and π → n charge transfer transitions. The visible PA spectrum strongly depends on decomposition of sample in the open air. The PA spectrum measured by us is very similar to those obtained earlier for the other living organisms, e.g. Trunculariopis Trunculus and Sea Urchin. The absorption band near 570 nm is similar to that found for spermidine, which is of importance in the information transfer to DNA. The results obtained in this work confirm experimentally that geologically very old organisms have been absorbing especially intensely in that part of solar spectrum for which the water is transparent.

Central-force decomposition of spline-based modified embedded atom method potential

Central-force decompositions are fundamental to the calculation of stress fields in atomic systems by means of Hardy stress. We derive expressions for a central-force decomposition of the spline-based modified embedded atom method (s-MEAM) potential. The expressions are subsequently simplified to a form that can be readily used in molecular-dynamics simulations, enabling the calculation of the spatial distribution of stress in systems treated with this novel class of empirical potentials. We briefly discuss the properties of the obtained decomposition and highlight further computational techniques that can be expected to benefit from the results of this work. To demonstrate the practicability of the derived expressions, we apply them to calculate stress fields due to an edge dislocation in bcc Mo, comparing their predictions to those of linear elasticity theory.

Photoacoustic spectra of green and red leaves of ficus Benjamina plant

Tissue samples of a ficus Benjamina plant are prepared in the shape of thick film for photoacoustic spectroscopy studies. Two absorption bands in the elec- tromagnetic photoacoustic (PA) spectrum are detected in the visible range. They are peaked at about 398 and 670 nm for a green leaf, and 544 and 570 nm for a red leaf. The absorption bands detected in the ultraviolet range are attributed to π  π* and π  n charge transfer transitions. The visible PA spectra strongly depend on the processes responsible for colouring of leaves. The absorption band at 670 nm could be related to photosynthesis. The absorption band observed at 398 nm for the green leaf disappears for the red one, though a different band located at 544 nm appears. The absorption spectra measured in this work are closely similar to those obtained earlier for the other living organisms. The absorption band near 544 nm is close to that found for spermidine, which is important in the information transfer to DNA. The results obtained in this work confirm experimentally that the red leaves absorb particularly strongly in that spectral region of solar radiation, which is intensely ra- diated in autumn.