Computational mechanics analysis of the hidden conformational dynamics within a molecular trajectory

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Modelling a biochemical reaction with computational fluid dynamics

Earlier investigations (Cartland Glover et al., 2004) into the use of computational fluid dynamics (CFD) for the modelling of gas-liquid and gas-liquid-solid flow allowed a simple biochemical reaction model to be implemented. A single plane mesh was used to represent the transport and reaction of molasses, the mould Aspergillus niger and citric acid in a bubble column with a height to diameter aspect ratio of 20:1. Two specific growth rates were used to examine the impact that biomass growth had on the local solids concentration and the effect this had on the local hydrodynamics of the bubble column.

Computational methods for traditional Chinese medicine:a survey

Traditional Chinese Medicine (TCM) has been actively researched through various approaches, including computational techniques. A review on basic elements of TCM is provided to illuminate various challenges and progresses in its study using computational methods. Information on various TCM formulations, in particular resources on databases of TCM formulations and their integration to Western medicine, are analyzed in several facets, such as TCM classifications, types of databases, and mining tools. Aspects of computational TCM diagnosis, namely inspection, auscultation, pulse analysis as well as TCM expert systems are reviewed in term of their benefits and drawbacks. Various approaches on exploring relationships among TCM components and finding genes/proteins relating to TCM symptom complex are also studied. This survey provides a summary on the advance of computational approaches for TCM and will be useful for future knowledge discovery in this area. © 2007 Elsevier Ireland Ltd. All rights reserved.

Intonation contour realisation for Standard Yorùbá text-to-speech synthesis:a fuzzy computational approach

This paper presents a novel intonation modelling approach and demonstrates its applicability using the Standard Yorùbá language. Our approach is motivated by the theory that abstract and realised forms of intonation and other dimensions of prosody should be modelled within a modular and unified framework. In our model, this framework is implemented using the Relational Tree (R-Tree) technique. The R-Tree is a sophisticated data structure for representing a multi-dimensional waveform in the form of a tree. Our R-Tree for an utterance is generated in two steps. First, the abstract structure of the waveform, called the Skeletal Tree (S-Tree), is generated using tone phonological rules for the target language. Second, the numerical values of the perceptually significant peaks and valleys on the S-Tree are computed using a fuzzy logic based model. The resulting points are then joined by applying interpolation techniques. The actual intonation contour is synthesised by Pitch Synchronous Overlap Technique (PSOLA) using the Praat software. We performed both quantitative and qualitative evaluations of our model. The preliminary results suggest that, although the model does not predict the numerical speech data as accurately as contemporary data-driven approaches, it produces synthetic speech with comparable intelligibility and naturalness. Furthermore, our model is easy to implement, interpret and adapt to other tone languages.

Impact of co-adsorbed oxygen on crotonaldehyde adsorption over gold nanoclusters:a computational study

Crotonaldehyde (2-butenal) adsorption over gold sub-nanometer particles, and the influence of co-adsorbed oxygen, has been systematically investigated by computational methods. Using density functional theory, the adsorption energetics of crotonaldehyde on bare and oxidised gold clusters (Au , d = 0.8 nm) were determined as a function of oxygen coverage and coordination geometry. At low oxygen coverage, sites are available for which crotonaldehyde adsorption is enhanced relative to bare Au clusters by 10 kJ mol. At higher oxygen coverage, crotonaldehyde is forced to adsorb in close proximity to oxygen weakening adsorption by up to 60 kJ mol relative to bare Au. Bonding geometries, density of states plots and Bader analysis, are used to elucidate crotonaldehyde bonding to gold nanoparticles in terms of partial electron transfer from Au to crotonaldehyde, and note that donation to gold from crotonaldehyde also becomes significant following metal oxidation. At high oxygen coverage we find that all molecular adsorption sites have a neighbouring, destabilising, oxygen adatom so that despite enhanced donation, crotonaldehyde adsorption is always weakened by steric interactions. For a larger cluster (Au, d = 1.1 nm) crotonaldehyde adsorption is destabilized in this way even at a low oxygen coverage. These findings provide a quantitative framework to underpin the experimentally observed influence of oxygen on the selective oxidation of crotyl alcohol to crotonaldehyde over gold and gold-palladium alloys. © 2014 the Partner Organisations.