Optofluidic Distributed Feedback Dye Lasers

We review our recent work on poly(dimethylsiloxane) (PDMS)-based optofluidic dye lasers using a guided wave distributed feedback (DFB) cavity. We show experimental results of single-mode operation, an integrated laser array, multiple color dye lasing, mechanical and fluidic tuning, and monolithic integration with microfluidic circuits. Potential applications and future directions are discussed

Nature of well-defined conductance of amine anchored molecular junctions

Amine terminated molecules show well behaved conductance in the scanning tunneling microscope break-junction experimental measurements. We performed density functional theory based electron transport calculations to explain the nature of this phenomenon. We find that amines can be adsorbed only on apex Au atom, while thiolate group can be attached equally well to undercoordinated and clean Au surfaces. Our calculations show that only one adsorption geo metry is sterically and energetically possible for amine anchored junction whereas three different adsorption geometries with very distinct transport pro perties are almost equally probable for thiolate anchored junction. We calculated the conductance as a function of the junction stretching when the molecules are pulled by the scanning tunneling microscope tip from the Au electrode. Our calculations show that the stretching of the thiolate anchored junction during its formation is accompanied by significant electrode geometry distortio n. The amine anchored junctions exhibit very different behavior -- the electrode remains intact when the scan ning tunneling microscope tip stretches the junction

Empirical Bayes estimation of posterior probabilities of enrichment

To interpret differentially expressed genes or other discovered features, researchers conduct hypothesis tests to determine which biological categories such as those of the Gene Ontology (GO) are enriched in the sense of having differential representation among the discovered features. We study application of better estimators of the local false discovery rate (LFDR), a probability that the biological category has equivalent representation among the preselected features. We identified three promising estimators of the LFDR for detecting differential representation: a semiparametric estimator (SPE), a normalized maximum likelihood estimator (NMLE), and a maximum likelihood estimator (MLE). We found that the MLE performs at least as well as the SPE for on the order of 100 of GO categories even when the ideal number of components in its underlying mixture model is unknown. However, the MLE is unreliable when the number of GO categories is small compared to the number of PMM components. Thus, if the number of categories is on the order of 10, the SPE is a more reliable LFDR estimator. The NMLE depends not only on the data but also on a specified value of the prior probability of differential representation. It is therefore an appropriate LFDR estimator only when the number of GO categories is too small for application of the other methods. For enrichment detection, we recommend estimating the LFDR by the MLE given at least a medium number (~100) of GO categories, by the SPE given a small number of GO categories (~10), and by the NMLE given a very small number (~1) of GO categories.Comment: exhaustive revision of Zhenyu Yang and David R. Bickel, "Minimum Description Length Measures of Evidence for Enrichment" (December 2010). COBRA Preprint Series. Article 76. http://biostats.bepress.com/cobra/ps/art7