Phonons in a Nanoparticle Mechanically Coupled to a Substrate

The discrete nature of the vibrational modes of an isolated nanometer-scale solid dramatically modifies its low-energy electron and phonon dynamics from that of a bulk crystal. However, nanocrystals are usually coupled--even if only weakly--to an environment consisting of other nanocrystals, a support matrix, or a solid substrate, and this environmental interaction will modify the vibrational properties at low frequencies. In this paper we investigate the modification of the vibrational modes of an insulating spherical nanoparticle caused by a weak {\it mechanical} coupling to a semi-infinite substrate. The phonons of the bulk substrate act as a bath of harmonic oscillators, and the coupling to this reservoir shifts and broadens the nanoparticle's modes. The vibrational density of states in the nanoparticle is obtained by solving the Dyson equation for the phonon propagator, and we show that environmental interaction is especially important at low frequencies. As a probe of the modified phonon spectrum, we consider nonradiative energy relaxation of a localized electronic impurity state in the nanoparticle, for which good agreement with experiment is found.Comment: 10 pages, Revte

Theory of Electron-Phonon Dynamics in Insulating Nanoparticles

We discuss the rich vibrational dynamics of nanometer-scale semiconducting and insulating crystals as probed by localized electronic impurity states, with an emphasis on nanoparticles that are only weakly coupled to their environment. Two principal regimes of electron-phonon dynamics are distinguished, and a brief survey of vibrational-mode broadening mechanisms is presented. Recent work on the effects of mechanical interaction with the environment is discussed.Comment: Revte

Optimum Magnetometer Transect Spacing to Locate Legacy Oil and Gas Wells: Preliminary Results

The purpose of this project was to examine the optimum transect spacing to locate legacy oil and gas wells using an Overhauser magnetometer. Widely known to be a potential environmental hazard, legacy oil and gas wells may act as a conduit for methane and/or deeper subsurface fluids (naturally occurring brines, injected waste fluids, or injected CO2) to the surface or shallow subsurface. Many plugged wells have all surface equipment removed leaving no visible trace at the surface and thus making the environmental assessment of these wells difficult. Using a magnetometer along a set of predefined transects, magnetic anomalies from the metal casing can be detected. In order to assess large numbers of wells, understanding the typical anomaly size is critical to maximize the transect spacing and therefore minimize magnetometer field work time. Here we briefly review the wide range of transect spacings reported in the literature and show the results of five wells with an initial survey grid at two meter spacing. Although there is significant variation in the anomaly size (X, Y, and Z), transect spacing of 20 m was sufficient to identify all buried wells using the method described herein. The anomalies associated with four of the wells ranged from approximately 1000-4000 nanoteslas (nT), while one well anomaly exhibited more than 10,000 nT above background

Effects of negative energy balance on liver gene and protein expression during the early postpartum period and its impacts on dairy cow fertility

End of project reportNegative energy balance (NEB) is a severe metabolic affecting high yielding dairy cows early post partum with both concurrent and latent negative effects on cow fertility as well as on milk production and cow health. The seasonal nature of Irish dairy production necessitates high cow fertility and a compact spring calving pattern in order to maximise grass utilisation. Poor dairy cow reproductive performance currently costs the Irish cattle industry in excess of €400 million annually. High milk yields have been associated with lower reproductive efficiency, and it has been suggested that this effect is probably mediated through its effects on the energy balance of the cow during lactation. The modern high genetic merit dairy cow prioritises nutrient supply towards milk production in early lactation and this demand takes precedence over the provision of optimal conditions for reproduction. In this study we used the bovine Affymetrix 23,000 gene microarray, which contains the most comprehensive set of bovine genes to be assembled and provides a means of investigating the modifying influences of energy balance on liver gene expression. Cows in severe negative energy balance (SNEB) in early lactation showed altered hepatic gene expression in metabolic processes as well as a down regulation of the insulin-like growth factor (IGF) system, where insulin like growth factor-1 (IGF-1), growth hormone receptor variant 1A (GHR1A) and insulin-like growth factor binding protein-acid labile subunit (IGFBP-ALS) were down regulated compared to the cows in the moderate negative energy balance MNEB group, consistent with a five-fold reduction in systemic concentrations of IGF1 in the SNEB group.Cows in SNEB showed elevated expression of key genes involved in the inflammatory response such as interleukin-8 (IL-8). There was a down regulation of genes involved in cellular growth in SNEB cows and moreover a negative regulator of cellular proliferation (HGFIN) was up regulated in SNEB cows, which is likely to compromise adaptation and recovery from NEB. The puma method of analysis revealed that 417 genes were differentially regulated by EB (P<0.05), of these genes 190 were up-regulated while 227 were down-regulated, with 405 genes having known biological functions. From Ingenuity Pathway Analysis (IPA), lipid catabolism was found to be the process most affected by differences in EB status

Inferring condition-specific transcription factor function from DNA binding and gene expression data

Numerous genomic and proteomic datasets are permitting the elucidation of transcriptional regulatory networks in the yeast Saccharomyces cerevisiae. However, predicting the condition dependence of regulatory network interactions has been challenging, because most protein–DNA interactions identified in vivo are from assays performed in one or a few cellular states. Here, we present a novel method to predict the condition-specific functions of S. cerevisiae transcription factors (TFs) by integrating 1327 microarray gene expression data sets and either comprehensive TF binding site data from protein binding microarrays (PBMs) or in silico motif data. Importantly, our method does not impose arbitrary thresholds for calling target regions ‘bound' or genes ‘differentially expressed', but rather allows all the information derived from a TF binding or gene expression experiment to be considered. We show that this method can identify environmental, physical, and genetic interactions, as well as distinct sets of genes that might be activated or repressed by a single TF under particular conditions. This approach can be used to suggest conditions for directed in vivo experimentation and to predict TF function

Convergent Evolution of Brain Morphology and Communication Modalities in Lizards

Animals communicate information within their environments via visual, chemical, auditory, and/or tactile modalities. The use of each modality is generally linked to particular brain regions, but it is not yet known whether the cellular morphology of neurons in these regions has evolved in association with the relative use of a modality. We investigated relationships between the behavioral use of communication modalities and neural morphologies in six lizard species. Two of these species (Anolis carolinensis and Leiocephalus carinatus) primarily use visual signals to communicate with conspecifics and detect potential prey, and two (Aspidoscelis gularis and Scincella lateralis) communicate and forage primarily using chemical signals. Two other species (Hemidactylus turcicus and Sceloporus olivaceus) use both visual and chemical signals. For each species, we performed behavioral observations and quantified rates of visual and chemical behaviors. We then cryosectioned brain tissues from 9-10 males of each species and measured the soma size and density of neurons in two brain regions associated with visual behaviors (the lateral geniculate nucleus and the nucleus rotundus) and one region associated with chemical behaviors (the nucleus sphericus). With analyses conducted in a phylogenetic context, we found that species that performed higher rates of visual displays had a denser lateral geniculate nucleus, and species that used a higher proportion of chemical displays had larger somas in the nucleus sphericus. These relationships suggest that neural morphologies in the brain have evolved convergently in species with similar communication behaviors