Nicolas Innocenti

Light absorption in conical silicon particles

The problem of the absorption of light by a nanoscale dielectric cone is discussed. A simplified solution based on the analytical Mie theory of scattering and absorption by cylindrical objects is proposed and supported by the experimental observation of sharply localized holes in conical silicon tips after high-fluence irradiation. This study reveals that light couples with tapered objects dominantly at specific locations, where the local radius corresponds to one of the resonant radii of a cylindrical object, as predicted by Mie theory.

SEK: sparsity exploiting k-mer-based estimation of bacterial community composition

MOTIVATION Estimation of bacterial community composition from a high-throughput sequenced sample is an important task in metagenomics applications. As the sample sequence data typically harbors reads of variable lengths and different levels of biological and technical noise, accurate statistical analysis of such data is challenging. Currently popular estimation methods are typically time-consuming in a desktop computing environment. RESULTS Using sparsity enforcing methods from the general sparse signal processing field (such as compressed sensing), we derive a solution to the community composition estimation problem by a simultaneous assignment of all sample reads to a pre-processed reference database. A general statistical model based on kernel density estimation techniques is introduced for the assignment task, and the model solution is obtained using convex optimization tools. Further, we design a greedy algorithm solution for a fast solution. Our approach offers a reasonably fast community composition estimation method, which is shown to be more robust to input data variation than a recently introduced related method. AVAILABILITY AND IMPLEMENTATION A platform-independent Matlab implementation of the method is freely available at http://www.ee.kth.se/ctsoftware; source code that does not require access to Matlab is currently being tested and will be made available later through the above Web site.

Landscape of RNA polyadenylation in E-coli

Abstract Polyadenylation is thought to be involved in the degradation and quality control of bacterial RNAs but relatively few examples have been investigated. We used a combination of 5΄-tagRACE and RNA-seq to analyze the total RNA content from a wild-type strain and from a poly(A)polymerase deleted mutant. A total of 178 transcripts were either up- or down-regulated in the mutant when compared to the wild-type strain. Poly(A)polymerase up-regulates the expression of all genes related to the FliA regulon and several previously unknown transcripts, including numerous transporters. Notable down-regulation of genes in the expression of antigen 43 and components of the type 1 fimbriae was detected. The major consequence of the absence of poly(A)polymerase was the accumulation of numerous sRNAs, antisense transcripts, REP sequences and RNA fragments resulting from the processing of entire transcripts. A new algorithm to analyze the position and composition of post-transcriptional modifications based on the sequence of unencoded 3΄-ends, was developed to identify polyadenylated molecules. Overall our results shed new light on the broad spectrum of action of polyadenylation on gene expression and demonstrate the importance of poly(A) dependent degradation to remove structured RNA fragments.

Optimal laser positioning for laser-assisted atom probe tomography

Laser-assisted atom probe tomography is a material analysis method based on field evaporating ions from a tip-shaped sample by a combination of a standing electric field and a short (pico- or femtosecond) laser pulse. The laser-pulse thereby acts as a starting signal for a time-of-flight mass analysis of the ions whereby the thermal energy deposited in the tip by the laser pulse temporarily enables the evaporation of ions from the surface of the tip. Here we will use simulations of the laser absorption on a silicon tip to find the optimal position of the laser spot in order to maximize the mass resolution achieved during the experiments. We will confirm our simulations by showing that the experimentally observed mass resolution indeed changes as predicted by the simulations.

Detection and quantitative estimation of spurious double stranded DNA formation during reverse transcription in bacteria using tagRNA-seq

Standard RNA-seq has a well know tendency to generate “ghost” antisense reads due to formation of spurious second strand cDNA in the sequencing process. We recently reported on a novel variant of RNA-seq coined “tagRNA-seq” introduced for the purpose of distinguishing primary from processed transcripts in bacteria. Incidentally, the additional information provided by the tags is also very suitable for detection of true anti-sense RNA transcripts and quantification of spurious antisense signals in a sample. We briefly explain how to perform such a detection and illustrate on previously published datasets.

External near-field resonance in coupled microcavities: mode enhancement and applications

Interference of the near optical field caused by evanescent waves leaking a coupled microcavity enhances the optical field between the cavity sections. This enhancement can be used for design of microcavity lasers with outside-cavity modes and for various sensors, for example, to precisely detect the direction of incident wavefront.

External field enhancement in coupled polymer microcavities - New options for integrated photonic components

Microcavities are key components for integrated optical devices and systems. Polymeric microcavities, as a particular type within the class, have been continually stimulating strong research interest owing to their potentials in bio- and nano-science applications (for example in “lab-on-a-chip” systems), and due to technological feasibility for cheap mass production, e.g. using nano-imprinting lithography technique [1,2]. Monolithic microcavities with gain material embedded in polymeric host matrix are also attractive for fabricating tunable lasers [3]. Unlike semiconductor photonic crystals, polymeric materials are applicable for operation in the visible range. In most cases, resonance optical field inside the cavity is the main object to manipulate and control performance of the microcavities.