Synthesis and structure of mycolactone E isolated from frog mycobacterium

The structure of mycolactone E, isolated from the frog pathogen Mycobacterium liflandii, was established via organic synthesis. Within the mycolactone family of metabolites, a structural variation has been seen only at the unsaturated fatty acid moiety thus far, and mycolactone E follows this observation. Interestingly, the absolute configuration of its unsaturated fatty acid matches that of the mycolactones from human mycobacteria, rather than the structurally more closely related mycolactone F from fish mycobacteria.     

Drude polarizable force field for aliphatic ketones and aldehydes,and their associated acyclic carbohydrates

The majority of computer simulations exploring biomolecular function employ Class I additive force fields (FF), which do not treat polarization explicitly. Accordingly, much effort has been made into developing models that go beyond the additive approximation. Development and optimization of the Drude polarizable FF has yielded parameters for selected lipids, proteins, DNA and a limited number of carbohydrates. The work presented here details parametrization of aliphatic aldehydes and ketones (viz. acetaldehyde, propionaldehyde, butaryaldehyde, isobutaryaldehyde, acetone, and butanone) as well as their associated acyclic sugars (d-allose and d-psicose). LJ parameters are optimized targeting experimental heats of vaporization and molecular volumes, while the electrostatic parameters are optimized targeting QM water interactions, dipole moments, and molecular polarizabilities. Bonded parameters are targeted to both QM and crystal survey values, with the models for ketones and aldehydes shown to be in good agreement with QM and experimental target data. The reported heats of vaporization and molecular volumes represent a compromise between the studied model compounds. Simulations of the model compounds show an increase in the magnitude and the fluctuations of the dipole moments in moving from gas phase to condensed phases, which is a phenomenon that the additive FF is intrinsically unable to reproduce. The result is a polarizable model for aliphatic ketones and aldehydes including the acyclic sugars d-allose and d-psicose, thereby extending the available biomolecules in the Drude polarizable FF.     

Post-modern valence bond theory for strongly correlated electron spins

We give a pedagogical overview of our recently introduced electronic-structure method, Coupled Cluster Valence Bond (CCVB). We show that CCVB can be viewed as an approximation to the accurate, yet very expensive, Spin Coupled Valence Bond model (SCVB). Both of these models are intended for use on strongly correlated molecular systems, especially when the strong correlations are due to electron spin coupling. Using familiar ideas from electronic-structure theory, we provide definitions for these strong-correlation concepts. We show that CCVB and SCVB generally produce similar results, with more substantial discrepancies occurring for systems displaying electronic resonance. We conclude that CCVB is a useful, inexpensive alternative to SCVB.     

Parameter identifiability in application of soft particle electrokinetic theory to determine polymer and polyelectrolyte coating thicknesses on colloids

Soft particle electrokinetic models have been used to determine adsorbed nonionic polymer and polyelectrolyte layer properties on nanoparticles or colloids by fitting electrophoretic mobility data. Ohshima first established the formalism for these models and provided analytical approximations ( Ohshima, H. Adv. Colloid Interface Sci.1995, 62, 189 ). More recently, exact numerical solutions have been developed, which account for polarization and relaxation effects and require fewer assumptions on the particle and soft layer properties. This paper characterizes statistical uncertainty in the polyelectrolyte layer charge density, layer thickness, and permeability (Brinkman screening length) obtained from fitting data to either the analytical or numerical electrokinetic models. Various combinations of particle core and polymer layer properties are investigated to determine the range of systems for which this analysis can provide a solution with reasonably small uncertainty bounds, particularly for layer thickness. Identifiability of layer thickness in the analytical model ranges from poor confidence for cases with thick, highly charged coatings, to good confidence for cases with thin, low-charged coatings. Identifiability is similar for the numerical model, except that sensitivity is improved at very high charge and permeability, where polarization and relaxation effects are significant. For some poorly identifiable cases, parameter reduction can reduce collinearity to improve identifiability. Analysis of experimental data yielded results consistent with expectations from the simulated theoretical cases. Identifiability of layer charge density and permeability is also evaluated. Guidelines are suggested for evaluation of statistical confidence in polymer and polyelectrolyte layer parameters determined by application of the soft particle electrokinetic theory.     

Dynamical diversity induced by individual responsive immunization

A voluntary vaccination allows for a healthy individual to choose vaccination according to the individual’s local information. Hence, vaccination has the potential to provide a complex negative feedback (non-infection decreases propensity for vaccination, hence increasing infection and vice versa). In this paper, we investigate a kind of SIS epidemic model with a deterministic and voluntary vaccination scheme in scale-free networks. We first study a threshold model with no historical information. By using the comparative method we confirm that under some conditions there exist two critical values of infection rates to determine three kinds of epidemic dynamical behaviors: the epidemic spread, the asymptotical decay and the exponential decay. Furthermore, a mean-field approximation model can predict the maximal infection level but cannot predict the existence of two critical infection rates. In numerical simulations, we observe a maximum in epidemic duration as a function of the model parameter. A similar phenomenon has been found in the model with historical information. Finally, we study a degree-weighted model with a nonnegative exponent α$\alpha$ where α=0$\alpha =0$ corresponds to the threshold model. We find that at the steady state the infection density increases with α$\alpha$, while the variation of the vaccination fraction is less straightforward.     

Modelling the effect of heterogeneous vaccination on metapopulation epidemic dynamics

Vaccination as an epidemic control strategy has a significant effect on epidemic spreading. In this paper, we propose a novel epidemic spreading model on metapopulation networks to study the impact of heterogeneous vaccination on epidemic dynamics, where nodes represent geographical areas and links connecting nodes correspond to human mobility between areas. Using a mean-field approach, we derive the theoretical spreading threshold revealing a non-trivial dependence on the heterogeneity of vaccination. Extensive Monte Carlo simulations validate the theoretical threshold and also show the complex temporal epidemic behaviours above the threshold.