Surface Plasmon Polariton Assisted Optical Switching in Noble Metal Nanoparticle Systems: A Sub-Band Gap Approach

In a proposed book chapter surface plasmon polariton assisted optical switching in noble metal nanoparticle systems is discussed in the sub-band gap formalism.Comment: 34 page, 13 figures, Submitted as Book chapter in The Annual Reviews in Plasmonics, edited by Professor Chris D. Geddes. Springer Scinec

Adjusting Phenotypes by Noise Control

Genetically identical cells can show phenotypic variability. This is often caused by stochastic events that originate from randomness in biochemical processes involving in gene expression and other extrinsic cellular processes. From an engineering perspective, there have been efforts focused on theory and experiments to control noise levels by perturbing and replacing gene network components. However, systematic methods for noise control are lacking mainly due to the intractable mathematical structure of noise propagation through reaction networks. Here, we provide a numerical analysis method by quantifying the parametric sensitivity of noise characteristics at the level of the linear noise approximation. Our analysis is readily applicable to various types of noise control and to different types of system; for example, we can orthogonally control the mean and noise levels and can control system dynamics such as noisy oscillations. As an illustration we applied our method to HIV and yeast gene expression systems and metabolic networks. The oscillatory signal control was applied to p53 oscillations from DNA damage. Furthermore, we showed that the efficiency of orthogonal control can be enhanced by applying extrinsic noise and feedback. Our noise control analysis can be applied to any stochastic model belonging to continuous time Markovian systems such as biological and chemical reaction systems, and even computer and social networks. We anticipate the proposed analysis to be a useful tool for designing and controlling synthetic gene networks

Phytoplankton-Specific Response to Enrichment of Phosphorus-Rich Surface Waters with Ammonium, Nitrate, and Urea

<div><p>Supply of anthropogenic nitrogen (N) to the biosphere has tripled since 1960; however, little is known of how <em>in situ</em> response to N fertilisation differs among phytoplankton, whether species response varies with the chemical form of N, or how interpretation of N effects is influenced by the method of analysis (microscopy, pigment biomarkers). To address these issues, we conducted two 21-day <em>in situ</em> mesocosm (3140 L) experiments to quantify the species- and genus-specific responses of phytoplankton to fertilisation of P-rich lake waters with ammonium (NH₄⁺), nitrate (NO₃⁻), and urea ([NH₂]₂CO). Phytoplankton abundance was estimated using both microscopic enumeration of cell densities and high performance liquid chromatographic (HPLC) analysis of algal pigments. We found that total algal biomass increased 200% and 350% following fertilisation with NO₃⁻ and chemically-reduced N (NH₄⁺, urea), respectively, although 144 individual taxa exhibited distinctive responses to N, including compound-specific stimulation (<em>Planktothrix agardhii</em> and NH₄⁺), increased biomass with chemically-reduced N alone (<em>Scenedesmus</em> spp., <em>Coelastrum astroideum</em>) and no response (<em>Aphanizomenon flos-aquae</em>, <em>Ceratium hirundinella</em>). Principle components analyses (PCA) captured 53.2–69.9% of variation in experimental assemblages irrespective of the degree of taxonomic resolution of analysis. PCA of species-level data revealed that congeneric taxa exhibited common responses to fertilisation regimes (e.g., <em>Microcystis aeruginosa</em>, <em>M</em>. <em>flos-aquae</em>, <em>M</em>. <em>botrys</em>), whereas genera within the same division had widely divergent responses to added N (e.g., <em>Anabaena</em>, <em>Planktothrix</em>, <em>Microcystis</em>). Least-squares regression analysis demonstrated that changes in phytoplankton biomass determined by microscopy were correlated significantly (<em>p<</em>0.005) with variations in HPLC-derived concentrations of biomarker pigments (<em>r</em>² = 0.13–0.64) from all major algal groups, although HPLC tended to underestimate the relative abundance of cyanobacteria. Together, these findings show that while fertilisation of P-rich lakes with N can increase algal biomass, there is substantial variation in responses of genera and divisions to specific chemical forms of added N.</p> </div