Effect of defects on thermal denaturation of DNA Oligomers

The effect of defects on the melting profile of short heterogeneous DNA chains are calculated using the Peyrard-Bishop Hamiltonian. The on-site potential on a defect site is represented by a potential which has only the short-range repulsion and the flat part without well of the Morse potential. The stacking energy between the two neigbouring pairs involving a defect site is also modified. The results are found to be in good agreement with the experiments.Comment: 11 pages including 5 postscript figure; To be appear in Phys. Rev.

Pd/Au based catalyst immobilization in polymeric nanofibrous membranes via electrospinning for the selective oxidation of 5-hydroxymethylfurfural

Innovative nanofibrous membranes based on Pd/Au catalysts immobilized via electrospinning onto different polymers were engineered and tested in the selective oxidation of 5- (hydroxymethyl)furfural in an aqueous phase. The type of polymer and the method used to insert the active phases in the membrane were demonstrated to have a significant effect on catalytic performance. The hydrophilicity and the glass transition temperature of the polymeric component are key factors for producing active and selective materials. Nylon-based membranes loaded with unsupported metal nanoparticles were demonstrated to be more efficient than polyacrylonitrilebased membranes, displaying good stability and leading to high yield in 2,5-furandicarboxylic acid. These results underline the promising potential of large-scale applications of electrospinning for the preparation of catalytic nanofibrous membranes to be used in processes for the conversion of renewable molecules

DNA hybridization to mismatched templates: a chip study

High-density oligonucleotide arrays are among the most rapidly expanding technologies in biology today. In the {\sl GeneChip} system, the reconstruction of the target concentration depends upon the differential signal generated from hybridizing the target RNA to two nearly identical templates: a perfect match (PM) and a single mismatch (MM) probe. It has been observed that a large fraction of MM probes repeatably bind targets better than the PMs, against the usual expectation from sequence-specific hybridization; this is difficult to interpret in terms of the underlying physics. We examine this problem via a statistical analysis of a large set of microarray experiments. We classify the probes according to their signal to noise ($S/N$) ratio, defined as the eccentricity of a (PM, MM) pair's `trajectory' across many experiments. Of those probes having large $S/N$ ($>3$) only a fraction behave consistently with the commonly assumed hybridization model. Our results imply that the physics of DNA hybridization in microarrays is more complex than expected, and they suggest new ways of constructing estimators for the target RNA concentration.Comment: 3 figures 1 tabl

Solving the riddle of the bright mismatches: hybridization in oligonucleotide arrays

HDONA technology is predicated on two ideas. First, the differential between high-affinity (perfect match, PM) and lower-affinity (mismatch, MM) probes is used to minimize cross-hybridization. Second, several short probes along the transcript are combined, introducing redundancy. Both ideas have shown problems in practice: MMs are often brighter than PMs, and it is hard to combine the pairs because their brightness often spans decades. Previous analysis suggested these problems were sequence-related; publication of the probe sequences has permitted us an in-depth study of this issue. Our results suggest that fluorescently labeling the nucleotides interferes with mRNA binding, causing a catch-22 since, to be detected, the target mRNA must both glow and stick to its probe: without labels it cannot be seen even if bound, while with too many it won't bind. We show that this conflict causes much of the complexity of HDONA raw data, suggesting that an accurate physical understanding of hybridization by incorporating sequence information is necessary to perfect microarray analysis.Comment: 4 figure

Effects of isopropanol on collagen fibrils in new parchment

Background: Isopropanol is widely used by conservators to relax the creases and folds of parchment artefacts. At present, little is known of the possible side effects of the chemical on parchments main structural component- collagen. This study uses X-ray Diffraction to investigate the effects of a range of isopropanol concentrations on the dimensions of the nanostructure of the collagen component of new parchment. Results: It is found in this study that the packing features of the collagen molecules within the collagen fibril are altered by exposure to isopropanol. The results suggest that this chemical treatment can induce a loss of structural water from the collagen within parchment and thus a rearrangement of intermolecular bonding. This study also finds that the effects of isopropanol treatment are permanent to parchment artefacts and cannot be reversed with rehydration using deionised water. Conclusions: This study has shown that isopropanol induces permanent changes to the packing features of collagen within parchment artefacts and has provided scientific evidence that its use to remove creases and folds on parchment artefacts will cause structural change that may contribute to long-term deterioration of parchment artefacts. This work provides valuable information that informs conservation practitioners regarding the use of isopropanol on parchment artefacts

H2 production by methane steam reforming over Rh/Al2O3 catalyst packed in Cu foams: A strategy for the kinetic investigation in concentrated conditions

The concept of Rh/Al2O3 catalyst pellets packed in highly conductive copper foams has been successfully tested in methane steam reforming showing the beneficial effects of thermal conductivity on the obtainment of gradient-less radial temperature profiles. In this work, the same concept is proposed as a strategy for the lab-scale kinetic investigation under concentrated conditions at ambient pressure; thanks to the homogeneous heating of the catalyst mass across the reactor section and the measurement of axial temperature profiles, well-controlled temperature conditions are obtained, and the experimental investigation can be extended to usually unfeasible conditions of high reactant concentrations, overcoming the typical challenges for the kinetic study. Here, steam reforming experiments were performed with CH4 and H2O feed molar fractions in the ranges of 10−20 % and 40–90 %, respectively. The co-feed of CO and H2 was also investigated. A kinetic scheme was developed that substantially confirmed the main results of previous kinetic investigations in annular micro-reactor, performed under diluted conditions; in particular, the first order dependence of the rate of steam reforming on methane partial pressure, the independence from H2O partial pressure, and the important inhibiting effect of CO were confirmed. The independence of the reaction rate from the H2 co-feed was here demonstrated for the first time. The new experimental campaign allowed to identify more clearly the kinetic dependencies of the water gas shift reaction, positively influenced by H2O partial pressure but scarcely affected by CO partial pressure, which could be also explained based on the inhibiting effect of surface CO coverage. Parameter estimates were obtained by model fit over a wide temperature range (400−850 °C), conveying robustness to the proposed kinetic scheme for future reactor design applications

Conversion of CO 2 to Valuable Chemicals: Organic Carbonate as Green Candidates for the Replacement of Noxious Reactants

Due to their chemical versatility and harmless nature, organic carbonates (OCs) have been indicated as proper raw materials for the replacement of noxious and waste-producing reactants. In particular, from the development of chlorine-free processes for the synthesis of OCs, the design of industrial processes based on the conversion of the latter has become a crucial topic for both academia and industry. The industrialization of chemical processes that involve the use of CO 2 as starting material for the synthesis of OC finally made OCs the sustainable counterpart of halogenated compounds in alkylation and carboxylation reactions

5-Hydroxymethyl-2-Furfural Oxidation Over Au/CexZr1-xO2 Catalysts

A series of gold catalysts supported on pure CeO, ZrO, and two different Ce-Zr mixed oxides have been prepared and tested in the 5-hydroxymethyl-2-furfural oxidation reaction. All catalysts show high catalytic activity (100% conversion) and important selectivity (27–41%) to the desired product i.e., 2,5-furandicarboxylic acid at low base concentration. Products selectivity changes with the support nature as expected, however, the observed trend cannot be related neither to gold particle size, nor to catalyst reducibility and oxygen mobility. An important relation between the FDCA selectivity and the support textural properties is observed, conducing to the general requirement for optimal pore size for this reaction

Gas-Phase Catalytic Transfer Hydrogenation of Methyl Levulinate with Ethanol over ZrO2

This paper reports about the gas-phase reduction of methyl levulinate to valerolactone (GVL) via catalytic transfer hydrogenation using ethanol as the H-donor. In particular, high-surface-area, tetragonal zirconia has proven to be a suitable catalyst for the reaction. Under optimized conditions, the reaction is selective toward the formation of GVL (yield 70%). However, both the deposition of heavy oligomeric compounds over the catalytic surface and the progressive conversion from Lewis to Brønsted acidity, due to the reaction with the water formed in situ, led to a progressive change in the chemo-selectivity, promoting side reactions, e.g. the alcoholysis of angelica lactones to ethyl levulinate. However, the in situ regeneration of the catalyst performed by feeding air at 400 °C for 2 h permitted an almost total recovery of the initial catalytic behavior, proving that the deactivation is reversible. The reaction has been tested also using a true bioethanol, derived from agricultural waste

Continuous Flow Synthesis of Bimetallic AuPd Catalysts for the Selective Oxidation of 5-Hydroxymethylfurfural to 2,5-Furandicarboxylic Acid

The production of 2,5-furandicarboxylic acid (FDCA) from the selective oxidation of 5-hydroxymethylfurfural (HMF) is a critical step in the production of biopolymers from biomass-derived materials. In this study, we report the catalytic performance of monometallic Au and Pd, and bimetallic AuPd nanoparticles with different Au : Pd molar ratios synthesised under continuous flow conditions using a millifluidic set-up and subsequently deposited onto titanium dioxide as the chosen support. This synthetic technique provided a better control over mean particle size and metal alloy composition, that resulted in higher FDCA yield when the catalysts were compared to similar batch-synthesised materials. A 99% FDCA yield was obtained with the millifluidic-prepared AuPd/TiO2 catalyst (Au : Pd molar composition of 75 : 25) after being calcined and reduced at 200 \ub0C. The heat treatment caused a partial removal of the protective ligand (polyvinyl alcohol) encapsulating the nanoparticles and so induced stronger metal-support interactions. The catalyst reusability was also tested, and showed limited particle sintering after five reaction cycles