Simulation of Guided Wave Propagation in Isotropic and Composite Structures using LISA

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/97117/1/AIAA2012-1387.pd

Modelling Clock Synchronization in the Chess gMAC WSN Protocol

We present a detailled timed automata model of the clock synchronization algorithm that is currently being used in a wireless sensor network (WSN) that has been developed by the Dutch company Chess. Using the Uppaal model checker, we establish that in certain cases a static, fully synchronized network may eventually become unsynchronized if the current algorithm is used, even in a setting with infinitesimal clock drifts

Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)

As RNA-binding proteins (RBPs) play essential roles in cellular physiology by interacting with target RNA molecules, binding site identification by UV crosslinking and immunoprecipitation (CLIP) of ribonucleoprotein complexes is critical to understanding RBP function. However, current CLIP protocols are technically demanding and yield low-complexity libraries with high experimental failure rates. We have developed an enhanced CLIP (eCLIP) protocol that decreases requisite amplification by ~1,000-fold, decreasing discarded PCR duplicate reads by ~60% while maintaining single-nucleotide binding resolution. By simplifying the generation of paired IgG and size-matched input controls, eCLIP improves specificity in the discovery of authentic binding sites. We generated 102 eCLIP experiments for 73 diverse RBPs in HepG2 and K562 cells (available at https://www.encodeproject.org), demonstrating that eCLIP enables large-scale and robust profiling, with amplification and sample requirements similar to those of ChIP-seq. eCLIP enables integrative analysis of diverse RBPs to reveal factor-specific profiles, common artifacts for CLIP and RNA-centric perspectives on RBP activity

Plasmonic tunnel junctions for single-molecule redox chemistry

Nanoparticles attached just above a flat metallic surface can trap optical fields in the nanoscale gap. This enables local spectroscopy of a few molecules within each coupled plasmonic hotspot, with near thousand-fold enhancement of the incident fields. As a result of non-radiative relaxation pathways, the plasmons in such sub-nanometre cavities generate hot charge carriers, which can catalyse chemical reactions or induce redox processes in molecules located within the plasmonic hotspots. Here, surface-enhanced Raman spectroscopy allows us to track these hot-electron-induced chemical reduction processes in a series of different aromatic molecules. We demonstrate that by increasing the tunnelling barrier height and the dephasing strength, a transition from coherent to hopping electron transport occurs, enabling observation of redox processes in real time at the single-molecule level.We acknowledge financial support from EPSRC grants EP/G060649/1, EP/I012060/1, EP/L027151/1, ERC grant LINASS 320503. F.B. acknowledges support from the Winton Programme for the Physics of Sustainability. S.J.B. thanks the European Commission for a Marie Curie Fellowship (NANOSPHERE, 658360). M.K. thanks the European Commission for a Marie Curie Fellowship (SPARCLEs, 7020005). P.N. acknowledges support from the Harvard University Center for the Environment (HUCE). R.C. acknowledges support from the Dr Manmohan Singh scholarship from St John’s College. C.C. acknowledges support from the UK National Physical Laboratories. R.S. acknowledges computational resources provided by the Center for Computational Innovations (CCI) at Rensselaer Polytechnic Institute

Distinct and shared functions of ALS-associated proteins TDP-43, FUS and TAF15 revealed by multisystem analyses

The RNA-binding protein (RBP) TAF15 is implicated in amyotrophic lateral sclerosis (ALS). To compare TAF15 function to that of two ALS-associated RBPs, FUS and TDP-43, we integrate CLIP-seq and RNA Bind-N-Seq technologies, and show that TAF15 binds to ∼4,900 RNAs enriched for GGUA motifs in adult mouse brains. TAF15 and FUS exhibit similar binding patterns in introns, are enriched in 3′ untranslated regions and alter genes distinct from TDP-43. However, unlike FUS and TDP-43, TAF15 has a minimal role in alternative splicing. In human neural progenitors, TAF15 and FUS affect turnover of their RNA targets. In human stem cell-derived motor neurons, the RNA profile associated with concomitant loss of both TAF15 and FUS resembles that observed in the presence of the ALS-associated mutation FUS R521G, but contrasts with late-stage sporadic ALS patients. Taken together, our findings reveal convergent and divergent roles for FUS, TAF15 and TDP-43 in RNA metabolism.National Institutes of Health (U.S.) (Grant HG007005

Optimal Design of a Trickle Bed Reactor for Light Fuel Oxidative Desulfurization based on Experiments and Modelling

YesIn this work, the performance of oxidative desulfurization (ODS) of dibenzothiophene (DBT) in light gas oil (LGO) is evaluated with a homemade manganese oxide (MnO2/γ-Al2O3) catalyst. The catalyst is prepared by Incipient Wetness Impregnation (IWI) method with air under moderate operating conditions. The effect of different reaction parameters such as reaction temperature, liquid hour space velocity and initial concentration of DBT are also investigated experimentally. Developing a detailed and a validated trickle bed reactor (TBR) process model that can be employed for design and optimization of the ODS process, it is important to develop kinetic models for the relevant reactions with high accuracy. Best kinetic model for the ODS process taking into account hydrodynamic factors (mainly, catalyst effectiveness factor, catalyst wetting efficiency and internal diffusion) and the physical properties affecting the oxidation process is developed utilizing data from pilot plant experiments. An optimization technique based upon the minimization of the sum of the squared error between the experimental and predicted composition of oxidation process is used to determine the best parameters of the kinetic models. The predicted product conversion showed very good agreement with the experimental data for a wide range of the operating condition with absolute average errors less than 5%