Metal-Ion Catalysis In the Tetrahymena Ribozyme Reaction

LL catalytic RNAs (ribozymes) require or are stimulated by divalent metal ions, but it has been difficult to separate the contribution of these metal ions to formation of the RNA tertiary structure1 from a more direct role in catalysis. The Tetrahymena ribozyme catalyses cleavage of exogenous RNA2,3 or DNA4,5 substrates with an absolute requirement for Mg2+ or Mn2+ (ref. 6). A DNA substrate, in which the bridging 3' oxygen atom at the cleavage site is replaced by sulphur, is cleaved by the ribozyme about 1,000 times more slowly than the corresponding unmodified DNA substrate when Mg2+ is present as the only divalent metal ion. But addition of Mn2+ or Zn2+ to the reaction relieves this negative effect, with the 3' S–P bond being cleaved nearly as fast as the 3' O–P bond. Considering that Mn2+ and Zn2+ coordinate sulphur more strongly than Mg2+ does7,8, these results indicate that the metal ion contributes directly to catalysis by coordination to the 3' oxygen atom in the transition state, presumably stabilizing the developing negative charge on the leaving group. We conclude that the Tetrahymena ribozyme is a metalloenzyme, with mechanistic similarities to several protein enzymes9–12.

Complex fiber bundle model for optimization of heterogeneous materials

We propose a complex fiber bundle model for the optimization of heterogeneous materials, which consists of many simple bundles. We also present an exact and compact recursion relation for the failure probability of a simple fiber bundle model with local load sharing, which is more efficient than the ones reported previously. Using a ''renormalization method'' and the recursion relation developed for the simple bundle, we calculate the failure probabilities of the complex fiber bundle. When the total number of fibers is given, we find that there exists an optimum way to organize the complex bundle, in which one gets a stronger bundle than in other ways.

Blue bottle light: lecture demonstrations of homogeneous and heterogeneous photo-induced electron transfer reactions

The classic, non-photochemical blue bottle experiment involves the reaction of methylene blue (MB) with deprotonated glucose, to form a bleached form of the dye, leuco-methylene blue (LMB), and subsequent colour recovery by shaking with air. This reaction is a popular demonstrator of key principles in kinetics and reaction mechanisms. Here it is modified so as to highlight features of homogenous and heterogeneous photoinduced electron transfer (PET) (Pure Appl. Chem., 2007, 79, 293-465) reactions, i.e. blue bottle light experiments. The homogeneous blue bottle light experiment uses methylene blue, MB, as the photo-sensitizer and triethanolamine as the sacrificial electron donor. Visible light irradiation of this system leads to its rapid bleaching, followed by the ready restoration of its original colour upon shaking away from the light source. The heterogeneous blue bottle light experiment uses titania as the photo-sensitizer, MB as a redox indicator and glucose as the sacrificial electron donor. UVA light irradiation of this system leads to the rapid bleaching of the MB and the gradual restoration of its original colour with shaking and standing. The latter 'dark' step can be made facile and more demonstrator-friendly by using platinised titania particles. These two photochemical versions of the blue bottle experiment are used to explore the factors which underpin homogeneous and heterogeneous PET reactions and provide useful demonstrations of homogeneous and heterogeneous photochemistry.

OXYGEN CATALYSIS BY ANHYDROUS RUTHENIUM(IV) OXIDE

The results of a kinetic study of the oxidation of water to oxygen by Ce(IV) ions in different acid media, mediated by anhydrous ruthenium(IV) oxide are described. In an acid medium which is predominantly HClO4 the kinetics are diffusion controlled and first order with respect to both [Ce(IV)] and [RuO2] and exhibit an activation energy of 19 kJ mol-1. In 0.5 mol dm-3 H2SO4 the kinetics are much slower and complex, the rate decreasing with increasing [Ce(III)]. The kinetics of catalysis observed in all the different acid media studied are readily interpreted using an electrochemical model in which the catalyst particles are considered as acting as microelectrodes which mediate electron transfer between a Nernstian reduction reaction (Ce(IV) --> Ce(III)) and an irreversible oxidation reaction (H2O --> 2H+ + 1/2O2). This electrochemical model is used to analyse the complex kinetics observed in 0.5 mol dm-3 H2SO4 and extract mechanistic information concerning the nature of the rate determining step.

Targeting heterogeneous architectures via macro data flow

We propose a data flow based run time system as an efficient tool for supporting execution of parallel code on heterogeneous architectures hosting both multicore CPUs and GPUs. We discuss how the proposed run time system may be the target of both structured parallel applications developed using algorithmic skeletons/parallel design patterns and also more "domain specific" programming models. Experimental results demonstrating the feasibility of the approach are presented. © 2012 World Scientific Publishing Company.

Rapid Implementation and Optimisation of DSP Systems on SoPC Heterogeneous Platforms

The emergence of programmable logic devices as processing platforms for digital signal processing applications poses challenges concerning rapid implementation and high level optimization of algorithms on these platforms. This paper describes Abhainn, a rapid implementation methodology and toolsuite for translating an algorithmic expression of the system to a working implementation on a heterogeneous multiprocessor/field programmable gate array platform, or a standalone system on programmable chip solution. Two particular focuses for Abhainn are the automated but configurable realisation of inter-processor communuication fabrics, and the establishment of novel dedicated hardware component design methodologies allowing algorithm level transformation for system optimization. This paper outlines the approaches employed in both these particular instances.