Stretch-induced plasmonic anisotropy of self-assembled gold nanoparticle mats

Close-packed monolayers of 20 nm Au nanoparticles are self-assembled at hexane/water interfaces and transferred to elastic substrates. Stretching the resulting nanoparticle mats provides active and reversible tuning of their plasmonic properties, with a clear polarization dependance. Both uniaxial and biaxial strains induce strong blue shifts in the plasmonic resonances. This matches theoretical simulations and indicates that plasmonic coupling at nanometer scale distances is responsible for the observed spectral tuning. Such stretch-tunable metal nanoparticle mats can be exploited for the development of optical devices, such as flexible colour filters and molecular sensors. (C) 2012 American Institute of Physics. [doi:10.1063/1.3683535]

Hydrobiogeochemical Interactions along “Flow Tubes” Controls: Watershed Scale Contaminant Flow and Transformation at the Oak Ridge IFRC

Geochemical,spectrographic, microbiological and hydrogeologic studies at the ORIFRC site indicate that groundwater transport in structured media may behave as a system of parallel flow tubes. These tubes are preferred flowpaths that enable contaminant transport parallel to bedding planes (strike) over distances of 1000s of meters. A significant flux of groundwater is focused within an interval defined by the interface between the competent bedrock and overlying highly-weathered saprolite, commonly referred to as the"transition zone." Characteristics of this transition zone are dense fractures and the relative absence of weathering products (e.g. clays)results in a significantly higher permeability compared to both the overlying clay-saprolite and underlying bedrock. Several stratabound low seismic velocity zones located below the transition zone were identified during geophysics studies and were also determined to be fractured high permeability preferred contaminant transport pathways during subsequent drilling activities. XANES analysis of precipitates collected from these deeper flow zones indicate 95% or more of the U deposited is U(VI). Linear combination fitting of the EXAFS data shows that precipitates are ~51±5% U(VI)-carbonate-like phase (e.g., liebigite) and ~49±5% U(VI) associated with an iron oxide phase; inclusion of a third component in the fit suggests that up to 15% of the U(VI) may be associated with a phosphate phase or OH- phase (e.g.,schoepite). Although precipitates with similar U(VI)-carbonate and/or phosphate associations were identified in the transition zone pathways,there were also U(VI) complexes adsorbed to mineral surfaces that would tend to be more readily mobilized. Groundwater in the different flow tubes has been determined to consist of different water quality types that vary with the solid phase encountered (e.g., clays, carbonates, clastics) as contaminants migrate along the flow paths. This lateral and vertical variability in geochemistry, particularly pH, has a significant impact on microbiological community composition and activity. Ribosomal RNA gene analyses coupled with physiological and genomic analyses suggest that bacteria from the genus Rhodanobacter(a diverse population of denitrifiers that are moderately acid tolerant) have a high relative abundance in the acidic source zone at the ORIFRC site.Watershed-scale analysis across different flow paths/tubes revealed strong negative correlation between pH and the absolute and relative abundance of Rhodanobacter. Recent studies also confirmed that the ORIFRC site hosts a diverse fungal community, with significant differences observed between acidic (pH <5) and circumneutral (>5) wells. The lack of nitrous oxide reduction capability in fungi, and the detection of denitrification potential in slurry microcosms suggest that fungi may have aheretofore under appreciated role in biogeochemical transformations, with implications forsite remediation and greenhouse gas emissions. Further research is needed to determine if these organisms can influence U(VI) mobility either directly through immobilization or indirectly through the depletion of nitrate.In conclusion, additional studies are required to quantify the processes (e.g., solid phase reactions, recharge, diffusion, microbial interactions) that are occurring along the groundwater flow tubes identified at the ORIFRC so predictive models can be parameterized and used to assess long-term contaminant fate and transport and remedial options.

Simplifying the representation of complex free-energy landscapes using sketch-map

A new scheme, sketch-map, for obtaining a low-dimensional representation of the region of phase space explored during an enhanced dynamics simulation is proposed. We show evidence, from an examination of the distribution of pairwise distances between frames, that some features of the free-energy surface are inherently high-dimensional. This makes dimensionality reduction problematic because the data does not satisfy the assumptions made in conventional manifold learning algorithms We therefore propose that when dimensionality reduction is performed on trajectory data one should think of the resultant embedding as a quickly sketched set of directions rather than a road map. In other words, the embedding tells one about the connectivity between states but does not provide the vectors that correspond to the slow degrees of freedom. This realization informs the development of sketch-map, which endeavors to reproduce the proximity information from the high-dimensionality description in a space of lower dimensionality even when a faithful embedding is not possible.

Asprich Peptides Are Occluded in Calcite and Permanently Disorder Biomineral Crystals

Macromolecules are a minority but important component of the minerals formed by living organisms, or biominerals. The role these macromolecules play at the early stages of biomineral formation, as well as their long-term and long-range effects on the mature biomineral, is poorly understood. A 42-amino acid peptide, asp2, was derived from the Asprich family of proteins. In this study we present X-ray absorption near-edge structure spectroscopy and X-ray photoelectron emission microscopy data from the asp2 peptide, the calcite (CaCO3) crystals, and the peptide + crystal composites. The results clearly show that asp2 is occluded in fully formed biomineral crystals and slightly but permanently disorders the crystal structure at short- and long-range distances.

Primary assembly of soil communities: disentangling the effect of dispersal and local environment

It has long been recognised that dispersal abilities and environmental factors are important in shaping invertebrate communities, but their relative importance for primary soil community assembly has not yet been disentangled. By studying soil communities along chronosequences on four recently emerged nunataks (ice-free land in glacial areas) in Iceland, we replicated environmental conditions spatially at various geographical distances. This allowed us to determine the underlying factors of primary community assembly with the help of metacommunity theories that predict different levels of dispersal constraints and effects of the local environment. Comparing community assembly of the nunataks with that of non-isolated deglaciated areas indicated that isolation of a few kilometres did not affect the colonisation of the soil invertebrates. When accounting for effects of geographical distances, soil age and plant richness explained a significant part of the variance observed in the distribution of the oribatid mites and collembola communities, respectively. Furthermore, null model analyses revealed less co-occurrence than expected by chance and also convergence in the body size ratio of co-occurring oribatids, which is consistent with species sorting. Geographical distances influenced species composition, indicating that the community is also assembled by dispersal, e.g. mass effect. When all the results are linked together, they demonstrate that local environmental factors are important in structuring the soil community assembly, but are accompanied with effects of dispersal that may "override" the visible effect of the local environment.