Elaine Ann Moore

This chapter is about the optical properties of solids. These properties can arise from defects in the solid, from the electronic structure of the solid as a whole, or from the structure of the solid. Examples are used to illustrate the effects. Defects are involved in ruby lasers, phosphors for LEDs, and colour centers. Absorption and emission of radiation by electrons in bands are exemplified by GaAs lasers, LEDs, and photovoltaic (solar) cells. Carbon-based conducting polymers which can be used in LEDs and photovoltaic cells are described. As well as absorption and emission of radiation, the chapter also considers its refraction and how this affects calcite crystals and optical fibers. The properties of photonic crystals depend on the arrangement of two materials of different refractive index. The refractive index of metamaterials depends on their structure. Metamaterials with negative refractive indices find use as superlenses and cloaks of invisibility.

This chapter looks at nanostructures—materials with at least one dimension less than 100 nm. These include nanoparticles, nanoribbons, nanowires, nanotubes, nanowhiskers, and nanolayers. At this scale, properties may differ from those of the bulk material. The effects on electronic, optical, magnetic, and mechanical properties are discussed. Carbon nanostructures have been a particularly fruitful area of research. The structures, properties, and uses of graphene, carbon nanotubes, and buckminsterfullerene are described. The chapter also looks at graphite and its intercalation compounds. The uses of non-carbon nanostructures including quantum dots and metal nanoparticles are discussed. Nanoparticles can result from conventional solid-state syntheses, but in this chapter synthetic methods specifically aimed at producing nanostructures are introduced. These are divided into top-down and bottom-up methods.

It is generally recognized that insect odorant binding proteins (OBPs) mediate the solubilisation and transport of hydrophobic odorant molecules and contribute to the sensitivity of the insect olfactory system. However, the exact mechanism by which OBPs deliver odorants to olfactory receptors and their role, if any, as selectivity filters for specific odorants, are still a matter of debate. In the case of Anopheles gambiae, recent studies indicate that ligand discrimination is effected through the formation of heterodimers such as AgamOBP1 and AgamOBP4 (odorant binding proteins 1 and 4 from Anopheles gambiae). Furthermore, AgamOBPs have been reported to be promiscuous in binding more than one ligand simultaneously and repellents such as DEET (N,N-diethyl-3-toluamide) and 6-MH (6-methyl-5-hepten-2-one) interact directly with mosquito OBPs and/or compete for the binding of attractive odorants thus disrupting OBP heterodimerisation. In this paper, we propose mechanisms of action of DEET and 6-MH. We also predict that ligand binding can occur in several locations of AgamOBP1 with partial occupancies and propose structural features appropriate for repellent pharmacophores.

The effect of S-substitution on the O⁶ guanine site of a 13-mer DNA duplex containing a G:T mismatch is studied using molecular dynamics. The structure, dynamic evolution and hydration of the S-substituted duplex are compared with those of a normal duplex, a duplex with S-substitution on guanine, but no mismatch and a duplex with just a G:T mismatch. The S-substituted mismatch leads to cell death rather than repair. One suggestion is that the G:T mismatch recognition protein recognises the S-substituted mismatch (G^S:T) as G:T. This leads to a cycle of futile repair ending in DNA breakage and cell death. We find that some structural features of the helix are similar for the duplex with the G:T mismatch and that with the S-substituted mismatch, but differ from the normal duplex, notably the helical twist. These differences arise from the change in the hydrogen-bonding pattern of the base pair. However a marked feature of the S-substituted G:T mismatch duplex is a very large opening. This showed considerable variability. It is suggested that this enlarged opening would lend support to an alternative model of cell death in which the mismatch protein attaches to thioguanine and activates downstream damage-response pathways. Attack on the sulphur by reactive oxygen species, also leading to cell death, would also be aided by the large, variable opening.

This report covers papers published in 2012 dealing with the application of computational techniques to inorganic solids. It deals mainly with continuous solids that are ionic in nature; work on metals is excluded. Special attention is given to solids used in solid oxide fuel cells and batteries, solids with useful or potentially useful ferroelectric, electronic, magnetic and optical properties, applications of computation to solid state NMR and calculations of thermodynamic properties and phase changes. These last are often of interest to the life and earth sciences. Relevant advances in computational methods are also covered.