Fuzzy logic with biomolecules

 The uncertain and inexact nature of the chemical reactions used to implement DNA computations can be turned into an advantage for implementing robust soft computing systems. The key feature of DNA hybridization that makes it appropriate for fuzzy computing is the uncertainty and incompleteness in the formation of a double-stranded duplex from single-stranded oligonucleotides. To implement fuzzy computing, a set of encoding DNA molecules is given that reproduces a specific membership function in the energetics of the DNA duplex. In addition, a fuzzy inference system implemented with DNA hybridization on solid supports is discussed. The ultimate success of this idea as a general technique, however, is dependent on the actual geometry of the Gibbs free-energy landscapes in the space of all duplex formations. Elucidating this problem is undoubtedly of great importance for biomolecular implementation of soft-computing because it may, in particular, shed light on the true import of fuzzy models in biological processes fundamental to life.     

Oxygen reduction reaction on a Pt/carbon fuel cell catalyst in the presence of trace quantities of ammonium ions: An RRDE study

The effect of trace quantities of ammonia on oxygen reduction reaction (ORR) on carbon-supported platinum catalysts in perchloric acid solutions is assessed using rotating ring disk electrode (RRDE) technique. The study demonstrates that ammonia has detrimental effects on ORR. The most significant effect takes place in the potential region above 0.7 V vs RHE. The effect is explained by the electrochemical oxidation of ammonia, which blocks Pt active sites and increases the formation of H₂O₂. This leads to losses in the disk currents and increments in the ring currents. The apparent losses in ORR currents may occur in two ways, namely, through the blocking of the active sites for ORR as well as by generating a small anodic current, which is believed to have a lower contribution. In addition, a detrimental effect of sodium cations in the potential range below 0.75 V vs RHE was demonstrated. This effect is most likely due to the co-adsorption of sodium cations and perchlorate anions on the Pt surface.     

Independent testing and validation of prototype hydrogen sensors

In this article, the independent testing and validation of a packaged, electrochemical prototype hydrogen sensor at the National Renewable Energy Laboratory (NREL) is reported. Custom electronics were developed to be compatible with the data acquisition system at NREL. The specialized hydrogen sensor-testing laboratory at NREL used a variety of standardized test protocols to assess sensor performance. The system controlled and monitored humidity, pressure, and hydrogen gas concentration and introduced interference gases such as methane, carbon dioxide, carbon monoxide and ammonia.     

Arabinosylated phenolics obtained from SO2‐steam‐pretreated sugarcane bagasse

A pentose‐rich hydrolysate fraction obtained by extraction of steam‐pretreated sugarcane bagasse was analysed with regard to dissolved phenolics. The liquid obtained after steam pretreatment (2% SO₂ (w/w) at 190 °C for 5 min) was divided into two parts: one containing dissolved compounds originating from hemicellulose (with xylose as the dominating compound), and the other containing predominantly dissolved compounds originating from lignin. Using nuclear magnetic resonance, the main dissolved compounds originating from lignin were identified as the glycosylated aromatics, 5‐O‐(trans‐feruloyl)‐L‐Arabinofuranose and 5‐O‐(trans‐coumaroyl)‐L‐Arabinofuranose, together with p‐coumaric acid and small amounts of more common free phenolics such as p‐hydroxybenzaldehyde, p‐hydroxybenzoic acid and vanillin. The phenolic compounds were analysed and quantified using reversed‐phase high‐performance liquid chromatography. The findings show that SO₂ steam explosion opened up new degradation pathways during lignin degradation. Copyright © 2012 Society of Chemical Industry     

On codeword design in metric DNA spaces

Finding a large set of single DNA strands that do not crosshybridize to themselves and/or to their complements is an important problem in DNA computing, self-assembly, and DNA memories. We describe a theoretical framework to analyze this problem, gauge its computational difficulty, and provide nearly optimal solutions. In this framework, codeword design is reduced to finding large sets of strands maximaly separated in a DNA space and the size of such sets depends on the geometry of these metric spaces. We show that codeword design is NP-complete using any single reasonable measure that approximates the Gibbs energy, thus practically excluding the possibility of finding any procedure to find maximal sets efficiently. Second, we extend a technique known as shuffling to provide a construction that yields provably nearly-maximal codes. Third, we propose a filtering process that removes strands creating pairs with low Gibbs energies, as approximated by the nearest-neighbor model. These two steps produce large codes of thermodynamic high quality. The proposed framework can be used to gain an understanding of the Gibbs energy landscapes for DNA strands on which much of DNA computing and self-assembly are based.     

A narrow size distribution on a high shear mixer by applying a flux number approach

High shear granulation is a common technology for particle size enlargement, but generally the product properties are badly affected by the broad size distribution generated in the process. A recently published approach by Michaels et al. [J.N. Michaels, G. Wang, L. Farber, K.P. Hapgood, J.H. Chou, S. Heidel, and G.I. Tardos, 2006, One-dimensional scale-up of high-shear granulators, Paper 243c, World Congress Particle Technology 5, Orlando (FL)] employs low binder solution spray rates and long granulation times, whilst the solids are kept in roping flow, to avoid coarse formation. The present work applies this approach to a two-component binder system with a dry powder gum and water spray as activation agent. Similarities with fluidised bed granulation and coating processes are explored. The work shows that indeed narrow size distributions of fine granules can be achieved with ease. Dimensionless numbers for spray fluxes are useful to identify operating regimes and to steer optimisation efforts. Comparison of flux numbers for different systems shows that they are not useful (yet) for detailed product and process design. Further work on material-specific quantities controlling nucleation and growth, e.g. particle wetting, is recommended.