Density-functional theory study of gramicidin A ion channel geometry and electronic properties

Understanding the mechanisms underlying ion channel function from the atomic-scale requires accurate ab initio modelling as well as careful experiments. Here, we present a density functional theory (DFT) study of the ion channel gramicidin A (gA), whose inner pore conducts only monovalent cations and whose conductance has been shown to depend on the side chains of the amino acids in the channel. We investigate the ground state geometry and electronic properties of the channel in vacuum, focusing on their dependence on the side chains of the amino acids. We find that the side chains affect the ground state geometry, while the electrostatic potential of the pore is independent of the side chains. This study is also in preparation for a full, linear scaling DFT study of gA in a lipid bilayer with surrounding water. We demonstrate that linear scaling DFT methods can accurately model the system with reasonable computational cost. Linear scaling DFT allows ab initio calculations with 10 000–100 000 atoms and beyond, and will be an important new tool for biomolecular simulations.     

The effect of interparticle forces on fluidization regimes in the magnetized fluidized beds

This paper investigated the influence of interparticle forces on the quality of fluidization in a magnetically stabilized fluidized bed (MSFB), where we can “artificially” create interparticle forces (F_attr) of any magnitude by applying an external magnetic field to ferromagnetic particles. A theoretical model was proposed which predicts the transition point from a homogeneous to a heterogeneous fluidization as a function of the magnitude of the interparticle force and other physical characteristics of both particles and fluids that are usually observed in fluidizationρ _p, ρ_f,μ, d_p, ε). The concept of the elastic wave velocity, U_e, and the continuity wave velocity, U_ε, was introduced. In particular, the interparticle force manipulated by an externally applied magnetic field was taken into account in addition to a general consideration of a conventional fluidized bed. Bubbles form in a bed when the continuity wave velocity becomes faster than the elastic wave velocity. The simulation demonstrated the proposed model could predict the transition point of fluidization regime with reasonable accuracy.     

Surface properties of Lactobacillus and Leuconostoc isolates from homemade cheeses showing auto-aggregation ability

Ten lactobacilli and one leuconostoc showing auto-aggregation ability were isolated from artisanal cheeses. Furthermore, non-aggregation strains were isolated from the same cheese sample, if existed. The analysis of factor(s) possibly involved in auto-aggregation was performed. The pretreatment of cells with proteinase K resulted in the disappearance of auto-aggregation ability. Moreover, cells also lost aggregation ability after three-times, successive washing in distilled water. Testing the ability of strain Lactobacillus paracasei subsp. paracasei BGSJ2-8 and its aggregation-deficient derivative BGSJ2-81 to co-aggregate with Listeria innocua ATCC33090, Escherichia coli ATCC25922 or Salmonella typhimurium TR251 showed that strain BGSJ2-8 co-aggregated with these strains, but derivative BGSJ2-81 was not. However, the treatment of L. paracasei subsp. paracasei BGSJ2-8 with proteinase K prior to co-aggregation tests resulted in losing co-aggregation ability. Surface properties of selected strains were analyzed by MATS (microbial adhesion to solvents) method. It was noticed that the strains with auto-aggregation ability were highly hydrophobic in comparison with aggregation-deficient ones. Comparative analyses of the surface features of strain L. paracasei subsp. paracasei BGSJ2-8 and its derivative BGSJ2-81 revealed notable difference.     

Characterisation of oat bran products with and without supercritical carbon dioxide extraction

Morphology, starch structures and thermal and pasting properties of oat bran concentrate (OBC) and Nutrim‐OB (NOB), a jet‐cooked oat bran product, with or without supercritical carbon dioxide extraction (SCD) were studied. Oil composition was analysed. OBC had three thermal transitions, starch gelatinisation and two amylose–lipid complex transitions. NOB only had amorphous amylose–lipid transition. SCD significantly decreased gelatinisation temperatures of OBC. Pasting properties, showed NOB had significantly higher peak viscosity and breakdown, with significantly lower final viscosity, setback and pasting temperature compared with OBC. SCD increased peak viscosity for NOB and final viscosity for OBC. Thermogravimetric analysis showed NOB had higher water‐holding capacity (WHC) than OBC, while SCD decreased WHC. Amylopectin molecular weight was 3.4 × 10⁸ for OBC and was significantly lower for NOB (1.4 × 10⁸). Predominant fatty acids were oleic (41%), linoleic (38%) and palmitic (16%). Study showed NOB had different properties from OBC thereby expanding industrial applications.     

Electrocatalytic activation of Ni electrode for hydrogen production by electrodeposition of Co and V species

Hydrogen is considered to be the most promising candidate as a future energy carrier. One of the most used technologies for the electrolytic hydrogen production is alkaline water electrolysis. Electrode materials used in alkaline water electrolysis are mainly made from Ni or Ni-based alloys due to their desirable mechanical and chemical stability in hot and alkaline solution. Considerable research effort has been conducted on enhancement of electrocatalytic activity of Ni electrodes.     

Solvents in organic synthesis: Replacement and multi-step reaction systems

The solvent selection methodology developed earlier by Gani et al. [Gani, R., Jiménez-González, C., & Constable, D. J. C. (2005). Method for selection of solvents for promotion of organic reactions. Computers and Chemical Engineering, 29, 1661–1676] has been extended to handle multi-step reaction systems as well as solvent substitution for specific reaction steps for existing processing systems. The problems were formulated based on the methodology guidelines, and solved using ICAS software tool [ICAS Documentation. (2003). Internal report. CAPEC, Department of Chemical Engineering, Technical University of Denmark]. Highly promising results were obtained, either in accordance with results previously published in the literature, or with industrial process data. This shows that the methodology has potential for application to complex reaction schemes as well as on the problems of solvent replacement.     

Isoconversional Kinetic Analysis of Isothermal Selective Ethanol Adsorption on Zeolite Type NaZSM‐5

The kinetic parameters of the selective isothermal adsorption of ethanol from an aqueous solution onto a hydrophobic zeolite type NaZSM‐5 were determined using a series of the so‐called standard methods (the initial rate, the saturation rate and the maximum rate methods). The kinetic model of ethanol adsorption was determined by the “model fitting” method. The dependence of the kinetic parameters on the degree of adsorption and the presence of a compensation effect were determined by the isoconversional method. The complex changes of the activation energy and pre‐exponential factor with the degree of adsorption were explained by the model of the activation energy distribution of elemental adsorption processes.