Parameter optimization for the Gaussian model of protein folding

Computational models of protein folding and ligand docking are large and complex. Few systematic methods have yet been developed to optimize the parameters in such models. We describe here an iterative parameter optimization strategy that is based on minimizing a structural error measure by descent in parameter space. At the start, we know the ‘correct’ native structure that we want the model to produce, and an initial set of parameters representing the relative strengths of interactions between the amino acids. The parameters are changed systematically until the model native structure converges as closely as possible to the correct native structure. As a test, we apply this parameter optimization method to the recently developed Gaussian model of protein folding: each amino acid is represented as a bead and all bonds, covalent and noncovalent, are represented by Hooke's law springs. We show that even though the Gaussian model has continuous degrees of freedom, parameters can be chosen to cause its ground state to be identical to that of Go-type lattice models, for which the global ground states are known. Parameters for a more realistic protein model can also be obtained to produce structures close to the real native structures in the protein database.     

Identification of Lysophosphatidylcholine–Chlorohydrin in Human Atherosclerotic Lesions

Lysophosphatidylcholine (LysoPtdCho) levels are elevated in sera in patients with atherosclerosis and in atherosclerotic tissue. Previous studies have shown that reactive chlorinating species attack plasmalogens in human coronary artery endothelial cells (HCAEC), forming lysoPtdCho and lysoPtdCho–chlorohydrin (lysoPtdCho–ClOH). The results herein demonstrate for the first time that lysoPtdCho–ClOH is elevated over 60-fold in human atherosclerotic lesions. In cultured HCAEC, 18:0 lysoPtdCho–ClOH led to a statistically significant increase in P-selectin cell-surface expression, but unlike 18:1 lysoPtdCho did not lead to cyclooxygenase-2 protein expression. These data show that 18:0 lysoPtdCho–ClOH is elevated in atherosclerotic tissue and may have unique pro-atherogenic properties compared to lysoPtdCho.     

Easily made and handled carbon nanocones for scanning tunneling microscopy and electroanalysis

Well-formed carbon nanocones at the ends of micrometer-diameter carbon fibers (CFs) were fashioned into functional tips for scanning tunneling microscopy (STM) and miniaturized voltammetric sensors. Sharpening of single graphite filaments was achieved by simple DC electrochemical etching in 0.1 N NaOH. Operated as STM tips, pointed CFs resolved in air the contour and surface morphology of a nanoscopic Au line pattern and imaged in vacuum a Si (1 1 1) surface with clear atomic resolution. Subjecting already etched CFs to tip-sparing insulation with electrodeposited paint produced conical carbon ultramicroelectrodes (UMEs) with effective radii down to about 900 nm. Comparative cyclic voltammetry trials in alkaline, neutral and acidic solutions showed that the conical carbon UME’s had a wider practical potential window for electroanalytic applications than, for instance, Pt disk UMEs. The CF-based conical sensors described here are exceptionally easy to make with simple laboratory equipment and perform well in STM topography imaging and voltammetry. The inherent simplicity of sensor production widens the field of potential users, and offers clear advantages over existing types of UMEs, in particular those based on carbon nanotubes, which are especially hard to handle in an optical microscope setting.     

Nonenzymatic glucose sensing based on deposited palladium nanoparticles on epoxy-silver electrodes

A new approach for nonenzymatic glucose sensing, based on a simple modification of epoxy-silver surfaces deposited on the tip of commercial copper electric wires, is presented. Palladium was galvanically displaced on the surface of the epoxy-silver surface in order to obtain metal nanoparticles that act as catalyst for the direct oxidation of glucose. Scanning electron microscopy revealed the formation of the metal nanoparticles. X-ray photoelectron spectroscopy confirmed the metallic nature of the formed nanostructures on the surface. Electrochemical characterization and calibration of the palladium-modified epoxy-silver electrode is reported, obtaining a linear range of 1–20 mM for the detection of glucose with low interference of ascorbic acid and uric acid. A simple 3-step coulometry was used as the detection technique. The developed sensing material is believed to be a great candidate for integration in small devices for clinical essays, due to the simplicity and cost effectiveness of the presented approach, compared to the state-of-the-art devices reported recently in the literature. Simplicity in the coulometry determinations makes these Pd-modified epoxy-silver sensors a good candidate for easy glucose determinations.     

Direct synthesis of carbon nanofibers on the surface of copper powder

A novel approach to synthesize carbon nanofibers (CNFs) directly on the surface of metal μm-sized particles to evenly disperse the carbon nanomaterials in a composite material was proposed. As a metal matrix, 5–10 μm copper particles were utilized. As a carbon source, C₂H₂, CH₄ and CO were examined. The best conditions were found to be in C₂H₂ (30 cm³/min) and H₂ (260 cm³/min) atmosphere at the temperature of 750 °C. The composites based on copper and CNFs prepared by vacuum hot pressing showed the increase in hardness from 35 to 60 kg/mm² almost retaining pure copper electrical properties.     

The perfluoropolymer upper bound

Perfluoropolymers have fundamentally distinct thermodynamic partitioning properties compared to those of their hydrocarbon counterparts. However, current upper bound theory assumes hydrocarbon solubility behavior for all polymers. Herein, the fundamental presupposition of invariance in solubility behavior to upper bound performance is critically assessed for perfluoropolymers and hydrocarbon polymers. By modifying solubility relationships, theoretical perfluoropolymer upper bounds are established, showing a positive shift of the upper bound front as a result of beneficial solubility selectivities for certain gas pairs, including N₂/CH₄, He/H₂, He/N₂, He/CH₄, and He/CO₂. Within the framework of the solution–diffusion model, an analysis is presented to compare two independent approaches often pursued in efforts to surpass the polymer upper bound: (a) achieving solubility selectivity via perfluoropolymers and (b) improving diffusion selectivity via rigid hydrocarbon polymers. This analysis demonstrates the significant benefit that can be achieved by considering both the chemical composition and morphology of solid-state macromolecules when designing membrane materials.     

Dietary intakes of six intense sweeteners by Irish adults

This research investigated the intakes of six intense sweeteners: acesulfame-K (E950), aspartame (E951), cyclamate (E952), saccharin (E954), sucralose (E955), and steviol glycosides (E960) in the diets of Irish adults, using data from the National Adult Nutrition Survey. A food label survey that included products currently available on the Irish market supplemented the analysis. Sweetener intakes were investigated using three different exposure scenarios; beginning with a crude assessment which assumed that all foods permitted to contain the additives of interest always did contain them, and at their maximum permitted level (Tier 1). Refined assessments estimated intakes of the six sweeteners using food consumption data up to brand level with additive occurrence data from a survey of products currently available on the Irish market (Tier 2) and sweetener concentration data (Tier 3). Results of all exposure assessment scenarios demonstrate that intakes of each of the sweeteners of interest by the total population were below the relevant ADI level (mg kg^?1 bodyweight^?1), even by high consumers (P99). The three sweeteners consumed in highest amounts were acesulfame-k, aspartame, and sucralose. The main sources of these sweeteners in the diet were ‘cider and perry’, ‘energy reduced and no added sugar (ER and NAS) carbonated flavoured drinks’, ‘table-top sweeteners’, ‘dairy products’, ‘solid food supplements’, and ‘sauces’. Intakes of the six intense sweeteners are currently not a concern among Irish adults. However, exposure to these chemicals should be monitored on a regular basis due to evolving market and consumption patterns.     

Sustainable Oxidative Cleavage of Vegetable Oils into Diacids by Organo-Modified Molybdenum Oxide Heterogeneous Catalysts

Exploiting vegetable oils to produce industrially valuable diacids via an eco‐friendly process requires an efficient and recyclable catalyst. In this work, a novel catalytic system based on organo‐modified molybdenum trioxide was synthesized by a green hydrothermal method in one simple step, using Mo powder as precursor, hydrogen peroxide, and amphiphilic surfactants cetyltrimethylammonium bromide (CTAB) and tetramethylammonium bromide (TMAB) as capping agents. The synthesized materials were first characterized by different techniques including XRD, SEM, TGA, and FT‐IR. Interestingly, various morphologies were obtained depending on the nature of the surfactants and synthetic conditions. The synthesized catalysts were employed in oxidative cleavage of oleic acid, the most abundant unsaturated fatty acid, to produce azelaic and pelargonic acids with a benign oxidant, H₂O₂. Excellent catalytic activities resulting in full conversion of initial oleic acid were obtained, particularly for CTAB‐capped molybdenum oxide (CTAB/Mo molar ratio of 1:3) that gave 83 and 68% yields of production of azelaic and pelargonic acids, respectively. These are the highest yields that have been obtained for this reaction by heterogeneous catalysts up to now. Moreover, the CTAB‐capped catalyst could be conveniently separated from the reaction mixture by simple centrifugation and reused without significant loss of activity up to at least four cycles.     

Avalanching flow of cohesive powders

The flow dynamics of cohesive powders is investigated in rotating cylinders with an L : R ratio of 3 : 1 using experiments and DEM simulations. Flow onset and steady-state behavior are compared for free-flowing (cohesionless) dry glass beads, wet glass beads, and “dry” cohesive powders (lactose, microcrystalline cellulose). The avalanching dynamics of powders is substantially different from those observed for free-flowing or wet-cohesive glass beads. Dry cohesive powders exhibit history-dependent flow dynamics, significant dilation, aperiodic avalanche frequencies, and variable avalanche size. These behaviors also provide a route for effective characterization of cohesive forces under dilated conditions characteristic of unconfined flows.