Kansa-RBF algorithms for elliptic problems in regular polygonal domains

We propose matrix decomposition algorithms for the efficient solution of the linear systems arising from Kansa radial basis function discretizations of elliptic boundary value problems in regular polygonal domains. These algorithms exploit the symmetry of the domains of the problems under consideration which lead to coefficient matrices possessing block circulant structures. In particular, we consider the Poisson equation, the inhomogeneous biharmonic equation, and the inhomogeneous Cauchy-Navier equations of elasticity. Numerical examples demonstrating the applicability of the proposed algorithms are presented.     

Ion flux through membrane channels--an enhanced algorithm for the Poisson-Nernst-Planck model

A novel algorithmic scheme for numerical solution of the 3D Poisson-Nernst-Planck model is proposed. The algorithmic improvements are universal and independent of the detailed physical model. They include three major steps: an adjustable gradient-based step value, an adjustable relaxation coefficient, and an optimized segmentation of the modeled space. The enhanced algorithm significantly accelerates the speed of computation and reduces the computational demands. The theoretical model was tested on a regular artificial channel and validated on a real protein channel-alpha-hemolysin, proving its efficiency.     

Wettability and topography of phospholipid DPPC multilayers deposited by spin-coating on glass, silicon, and mica slides

The surface free energy of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) layers deposited on glass, silicon, or mica by the spin-coating method was estimated. For this purpose, the advancing and receding contact angles of water, formamide, and diiodomethane were measured, and then two concepts of the interfacial interactions were applied. In the contact angle hysteresis approach, the apparent total surface free energy is calculated from the advancing and receding contact angles of the probe liquids, and in the Lifshitz-van der Waals/acid-base approach, the total surface free energy is calculated from previously determined components of the energy, that is, the apolar Lifshitz-van der Waals and the polar electron-donor and electron-acceptor, which are calculated from the advancing contact angles of the probe liquids alone. Comparison of the results obtained using these two approaches provided more information about changes in the hydrophobic/hydrophilic character of the DPPC layers and, simultaneously, a verification of the approaches. Moreover, the roughness and topography of the investigated layers were also examined by atomic force microscopy measurements. The hydrophilic character of the DPPC layers decreased if up to 0.5 mg of DPPC/mL was used to deposit on the substrates by the spin-coating method. Then it increased and leveled off if up to 2-2.5 mg of DPPC/mL was used. The changes in the energy were correlated with the changes in topography of the surfaces.     

Application of a renewable silver based mercury film electrode to the determination of Cr(VI) in soil samples

The design and experimental results of the application of a renewable mercury film silver based electrode to the determination of Cr(VI) in soil samples are presented. The main feature of this procedure is that it can be used in field measurements. The procedure is based on the extraction of total Cr(VI) exploiting the complexation property of diethylenetriaminepentaacetic acid (DTPA) followed by electrochemical reduction of Cr(VI) to Cr(III) with the formation of Cr(III)-H₂DTPA complex adsorbed on mercury film electrode. The voltammetric signal is caused by reduction of this complex. The validation of the proposed procedure was made by Cr(VI) determination in the certified reference material “Chromium VI in soil”. The protocol for Cr(VI) determination has also been applied to the analysis of Rendoll soil samples with satisfying precision.

     

Characterization of polyphosphoesters by fourier transform ion cyclotron resonance mass spectrometry

FT-ICR mass spectrometry, together with collision-induced dissociation and electron capture dissociation, has been used to characterize the polyphosphoester poly[1,4-bis(hydroxyethyl)terephthalate-alt-ethyloxyphosphate] and its degradation products. Three degradation pathways were elucidated: hydrolysis of the phosphate-[1,4-bis(hydroxyethyl)terephthalate] bonds; hydrolysis of the phosphate-ethoxy bonds; and hydrolysis of the ethyl-terephthalate bonds. The dominant degradation reactions were those that involved the phosphate groups. This work constitutes the first application of mass spectrometry to the characterization of polyphosphoesters and demonstrates the suitability of high mass accuracy FT-ICR mass spectrometry, with CID and ECD, for the structural analysis of polyphosphoesters and their degradation products.     

Topography and surface free energy of DPPC layers deposited on a glass, mica, or PMMA support

An investigation of energetic properties of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) layers deposited on glass, mica, and PMMA (poly(methyl methacrylate)) surfaces was carried out by means of contact angles measurements (advancing and receding) for three probe liquids (diiodomethane, water, and formamide). DPPC was deposited on the surfaces from water (on glass and mica) or methanol (on PMMA) solutions. The topography of the tested surfaces was determined with a help of scanning electron microscopy (SEM) and atomic force microscopy (AFM). Using the measured contact angles, the total apparent surface free energy and its components of the studied layers were determined from van Oss et al.'s (Lifshitz-van der Waals and acid-base components, LWAB) and contact angle hysteresis (CAH) approaches. It allowed us to learn about changes in the surface free energy of the layers (hydrophobicity/hydrophilicity) depending on their number and kind of support. It was found that the changes in the energy greatly depended on the surface properties of the substrate as well as the statistical number of monolayers of DPPC. However, principal changes took place for first three monolayers.     

Bisignate resonance Raman optical activity: a pseudo breakdown of the single electronic state model of RROA?

Raman optical activity (ROA) spectra were calculated for a set of conformers of astaxanthin, which is a non‐rigid molecule exhibiting strong resonance enhancement in the visible range. Single electronic state theory of the Resonance ROA (RROA) predicts the spectrum to be monosigned. For astaxanthin, it appeared that some of the conformers exhibit different sign of the bands than the other conformers. As a result, the conformer population averaged spectrum of astaxanthin can exhibit both signs of the bands, or be monosigned depending on which conformers are dominating, that reflects a departure from the single electronic state approximation. Moreover, use of different basis sets and/or density functional theory (DFT) functionals results in different conformer populations, thus yielding again either monosigned ROA spectrum or with bands of both signs. Consequences of these two findings for the astaxanthin RROA spectrum are discussed. Copyright © 2014 John Wiley & Sons, Ltd.     

The microenvironment effect on the generation of reactive oxygen species by Pd-bacteriopheophorbide

Generation of reactive oxygen species (ROS) is the hallmark of important biological processes and photodynamic therapy (PDT), where ROS production results from in situ illumination of certain dyes. Here we test the hypothesis that the yield, fate, and efficacy of the species evolved highly depend on the dye's environment. We show that Pd-bacteriopheophorbide (Pd-Bpheid), a useful reagent for vascular targeted PDT (VTP) of solid tumors, which has recently entered into phase II clinical trials under the code name WST09 (trade name TOOKAD), forms appreciable amounts of hydroxyl radicals, superoxide radicals, and probably hydrogen peroxide in aqueous medium but not in organic solvents where singlet oxygen almost exclusively forms. Evidence is provided by pico- and nanosecond time-resolved spectroscopies, ESR spectroscopy with spin-traps, time-resolved singlet oxygen phosphorescence, and chemical product analysis. The quantum yield for singlet oxygen formation falls from approximately 1 in organic solvents to approximately 0.5 in membrane-like systems (micelles or liposomes), where superoxide and hydroxyl radicals form at a minimal quantum yield of 0.1%. Analysis of photochemical products suggests that the formation of oxygen radicals involves both electron and proton transfer from (3)Pd-Bpheid at the membrane/water interface to a colliding oxygen molecule, consequently forming superoxide, then hydrogen peroxide, and finally hydroxyl radicals, with no need for metal catalysis. The ability of bacteriochlorophyll (Bchl) derivatives to form such radicals upon excitation at the near infrared (NIR) domain opens new avenues in PDT and research of redox regulation in animals and plants.     

Spatial tissue distribution of polyacetylenes in carrot root

The presented results show the usefulness of Raman spectroscopy in the investigation of polyacetylenes in carrot root. The components are measured directly in the plant tissue without any preliminary sample preparation. Compared with the strong polyacetylene signals the spectral impact of the surrounding biological matrix is weak, except for carotenoids, and therefore it does not contribute significantly to the obtained results. Three different Raman mapping techniques applied here have revealed essential information about the investigated compounds. Using point acquisition several spectra have been measured to demonstrate the complex composition of the polyacetylene fraction in carrot root. The molecular structures of falcarinol, falcarindiol and falcarindiol 3-acetate are similar but their Raman spectra exhibit differences demonstrated by the shift of their -C triple bond C- mode. Line mapping performed along the diameter of transversely cut carrot roots has been used to investigate the relative concentration of polyacetylenes and carotenoids. An area map provides detailed information regarding the distribution of both components. It has been found that high accumulation of polyacetylenes is located in the outer section of the root, namely the pericyclic parenchyma, and in the phloem part close to the secondary cambium. The highest concentration of carotenes is seen in the immediate vicinity to polyacetylene conglomerates.     

Mesoporous Carbons of Well-Organized Structure in the Removal of Dyes from Aqueous Solutions

Mesoporous carbons with differentiated properties were synthesized by using the method of impregnation of mesoporous well-organized silicas. The obtained carbonaceous materials and microporous activated carbon were investigated by applying different methods in order to determine their structural, surface and adsorption properties towards selected dyes from aqueous solutions. In order to verify applicability of adsorbents for removing dyes the equilibrium and kinetic experimental data were measured and analyzed by applying various equations and models. The structural and acid-base properties of the investigated carbons were evaluated by Small-Angle X-ray Scattering (SAXS) technique, adsorption/desorption of nitrogen, potentiometric titration, and Transmission Electron Microscopy (TEM). The results of these techniques are complementary, indicating the type of porosity and structural ordering, e.g., the pore sizes determined from the SAXS data are in good agreement with those obtained from nitrogen sorption data. The SAXS and TEM data confirm the regularity of mesoporous carbon structure. The adsorption experiment, especially kinetic measurements, reveals the utility of mesoporous carbons in dye removing, taking into account not only the adsorption uptake but also the adsorption rate.