Determining the electronic structure and chemical potentials of molecules in solution

A simulation scheme is proposed for determining the excess chemical potential of a substance in solution. First, a Monte Carlo simulation is performed with classical models for solute and solvent molecules. A representative sample of these configurations is then used in a hybrid quantum/classical (QM/MM) calculation, where the solute is treated quantum-mechanically, and the average electronic structure is used to construct an improved classical model. This procedure is iterated to self-consistency in the classical model, which in practice is attained in one or two steps, depending on the quality of the initial guess. The excess free energy of the molecule within the QM/MM approach is determined relative to the classical model using thermodynamic perturbation theory with a cumulant expansion. The procedure provides a method of constructing classical point charge models appropriate for the solution and gives a measure of the importance of solvent fluctuations.

Solvation effects on equilibria: Triazoles and N-methyl piperidinol

We have performed calculations of the solvation effects on a number of equilibrium constants in water using a recently proposed hybrid quantum classical scheme in which the liquid environment is modelled using classical solvent molecules and the solute electronic structure is computed using modern quantum chemical methods. The liquid phase space is sampled from a fully classical simulation. We find that solvation effects on both triazole tautomeric equilibrium constants and piperidinol conformational equilibrium constants can be interpreted in terms of subtle differences in the local environment which can be seen in probability densities and radial distribution functions. Lower level calculations were performed for comparison and we conclude that the solvation thermodynamics can be predicted from a good classical model of solvent and solute molecules, but the implicit models that we tried are less successful.

DNA methyltransferase expression in the mouse germ line during periods of de novo methylation

DNA methyltransferase (DNMT) 3A and DNMT3B are both active de novo DNA methyltransferases required for development, whereas DNMT3L, which has no demonstrable methyltransferase activity, is required for methylation of imprinted genes in the oocyte. We show here that different mechanisms are used to restrict access by these proteins to their targets during germ cell development. Transcriptional control of the Dnmt3l promoter guarantees that message is low or absent except during periods of de novo activity. Use of an alternative promoter at the Dnmt3a locus produces the shorter Dnmt3a2 transcript in the germ line and postimplantation embryo only, whereas alternative splicing of the Dnmt3b transcript ensures that Dnmt3b1 is absent in the male prospermatogonia. Control of subcellular protein localization is a common theme for DNMT3A and DNMT3B, as proteins were seen in the nucleus only when methylation was occurring. These mechanisms converge to ensure that the only time that functional products from each locus are present in the germ cell nuclei is around embryonic day 17.5 in males and after birth in the growing oocytes in females.

WS02.7 Initial and chronic MRSA infection in cystic fibrosis

Objectives Chronic MRSA infection, which affects approximately 26% of CF patients in the USA, is associated with declining lung function and poor outcomes (Dasenbrook, 2010). Anaerobic niches have been described within the CF lung, potentially influencing the virulence of MRSA. This study aims to compare initial and chronic CF MRSA isolates, following aerobic and anaerobic culture. Methods Isolates, obtained from CF sputum at first isolation [“early” (n = 10)] or up to 5 years later, during chronic infection [“late” (n = 15)] were cultured in aerobic and anaerobic conditions. Differences in virulence were compared using the Galleria mellonella infection model. Biofilm formation of each isolate was assessed following staining with crystal violet. Production of Δ-haemolysin (Δ-hly), a surrogate marker for expression of the virulence regulator agr, was determined by haemolysis assay. Results MRSA grown in anaerobic conditions had significantly increased virulence in the G. mellonella model (p = 0.007), increased biofilm formation (p = 0.006) and increased Δ-hly production (p<0.0001). No significant difference between Δ-hly production or biofilm formation were observed between early and late isolates; however late isolates were found to be more virulent in the G. mellonella model (p = 0.0002). Conclusion These results suggest that an anaerobic environment, as found in the CF lung, may increase virulence of MRSA and aid in the establishment of chronic infection. Further clinical studies are required to determine how these phenotypic changes are associated with transition to chronic infection and patient outcome.

Abnormal Pedestrian Trajectory analysis based on arbitrary-length clustering

This papers examines the use of trajectory distance measures and clustering techniques to define normal
and abnormal trajectories in the context of pedestrian tracking in public spaces. In order to detect abnormal
trajectories, what is meant by a normal trajectory in a given scene is firstly defined. Then every trajectory
that deviates from this normality is classified as abnormal. By combining Dynamic Time Warping and a
modified K-Means algorithms for arbitrary-length data series, we have developed an algorithm for trajectory
clustering and abnormality detection. The final system performs with an overall accuracy of 83% and 75%
when tested in two different standard datasets.