Graphene-based perfect optical absorbers harnessing guided mode resonances

We numerically and experimentally investigate graphene-based optical absorbers that exploit guided mode resonances (GMRs) achieving perfect absorption over a bandwidth of few nanometers (over the visible and near-infrared ranges) with a 40-fold increase of the monolayer graphene absorption. We analyze the influence of the geometrical parameters on the absorption rate and the angular response for oblique incidence. Finally, we experimentally verify the theoretical predictions in a one-dimensional, dielectric grating and placing it near either a metallic or a dielectric mirror

Graphene-based absorber exploiting guided mode resonances in one-dimensional gratings

A one-dimensional dielectric grating, based on a simple geometry, is proposed and investigated to enhance light absorption in a monolayer graphene exploiting guided mode resonances. Numerical findings reveal that the optimized configuration is able to absorb up to 60% of the impinging light at normal incidence for both TE and TM polarizations resulting in a theoretical enhancement factor of about 26 with respect to the monolayer graphene absorption (about 2.3%). Experimental results confirm this behaviour showing CVD graphene absorbance peaks up to about 40% over narrow bands of few nanometers. The simple and flexible design paves the way for the realization of innovative, scalable and easy-to-fabricate graphene-based optical absorbers

Kronos: a workflow assembler for genome analytics and informatics.

BackgroundThe field of next-generation sequencing informatics has matured to a point where algorithmic advances in sequence alignment and individual feature detection methods have stabilized. Practical and robust implementation of complex analytical workflows (where such tools are structured into "best practices" for automated analysis of next-generation sequencing datasets) still requires significant programming investment and expertise.ResultsWe present Kronos, a software platform for facilitating the development and execution of modular, auditable, and distributable bioinformatics workflows. Kronos obviates the need for explicit coding of workflows by compiling a text configuration file into executable Python applications. Making analysis modules would still require programming. The framework of each workflow includes a run manager to execute the encoded workflows locally (or on a cluster or cloud), parallelize tasks, and log all runtime events. The resulting workflows are highly modular and configurable by construction, facilitating flexible and extensible meta-applications that can be modified easily through configuration file editing. The workflows are fully encoded for ease of distribution and can be instantiated on external systems, a step toward reproducible research and comparative analyses. We introduce a framework for building Kronos components that function as shareable, modular nodes in Kronos workflows.ConclusionsThe Kronos platform provides a standard framework for developers to implement custom tools, reuse existing tools, and contribute to the community at large. Kronos is shipped with both Docker and Amazon Web Services Machine Images. It is free, open source, and available through the Python Package Index and at https://github.com/jtaghiyar/kronos

In vitro Evaluation of the Cytotoxicity of Different Root Canal Filling Materials

Objective: Aim of the present study was to evaluate the cytotoxicity of Real Seal 1 compared to other commercially available endodontic filling materials: Real Seal (SybronEndo, Orange, CA, USA) and Thermafil (Tulsa Dental, Tulsa, OK, USA). Material and Methods: Periodontal ligament cells from healthy patients were cultured. The eluate of Real Seal 1TM (RS1), Real Seal (RS) and Thermafil (TF) samples was used for the cells viability tests, both diluted (50%) or undiluted (100%). Incubation of the specimens was performed in culture medium for 24 h, 48 h and 72 h at 37 °C under sterile conditions. The cellular mortality was evaluated by MTT test. Results were statistically analysed and the statistical significance was set at p< 0.05. Results: None of the studied materials showed toxic effects during the period of observation (0 -72 h) when compared to the control group. Only RS induced a very modest increase in cell mortality (about 3% at both concentrations used, during the first 24 hours), when increasing the incubation time, however, only the lower concentration continued to show modest toxicity. Conclusions: Results of the present study showed that all tested materials did not exhibit cytotoxic effects when compared to the control group. © Gambarini et al

On-surface synthesis of a dicationic diazahexabenzocoronene derivative on the Au(111) surface

The atomically precise control over the size, shape and structure of nanographenes (NGs) or the introduction of heteroatom dopants into their sp2-carbon lattice confer them valuable electronic, optical and magnetic properties. Herein, we report on the design and synthesis of a hexabenzocoronene derivative embedded with graphitic nitrogen in its honeycomb lattice, achieved via on-surface assisted cyclodehydrogenation on the Au(111) surface. Combined scanning tunnelling microscopy/spectroscopy and non-contact atomic force microscopy investigations unveil the chemical and electronic structures of the obtained dicationic NG. Kelvin probe force microscopy measurements reveal a considerable variation of the local contact potential difference toward lower values with respect to the gold surface, indicative of its positive net charge. Altogether, we introduce the concept of cationic nitrogen doping of NGs on surfaces, opening new avenues for the design of novel carbon nanostructure

Optical Properties of Ordered Plasmonic Nanostructures in Linear and Nonlinear Regimes

ABSTRACT In this paper we review our recent advances in subwavelength plasmonic structures in linear and nonlinear regimes. We show several examples of subwavelength plasmonic devices in different configurations and schemes. We emphasize how these devices can be exploited for many applications, such as sensing, spectroscopy, photovoltaics and optical communications. Finally we will illustrate some challenges that are still open and need to be fulfilled. Keywords: plasmonics, plasmonic resonance, scattering, field enhancement, thin film, nonlinear harmonic generation. INTRODUCTION The propagation of Surface Plasmon Polaritons (SPPs) has gained great interest in the last decades since it has been demonstrated that their excitation on metal gratings or metal nanostructures can be usefully exploited to solve several problems relative to many applications, such as Raman spectroscopy, sensing, data storage, light emission and amplification as well as absorption enhancement for energy harvesting purpose

Genome-Wide Discovery of Somatic Regulatory Variants in Diffuse Large B-Cell Lymphoma

Diffuse large B-cell lymphoma (DLBCL) is an aggressive cancer originating from mature B-cells. Prognosis is strongly associated with molecular subgroup, although the driver mutations that distinguish the two main subgroups remain poorly defined. Through an integrative analysis of whole genomes, exomes, and transcriptomes, we have uncovered genes and non-coding loci that are commonly mutated in DLBCL. Our analysis has identified novel cis-regulatory sites, and implicates recurrent mutations in the 3′ UTR of NFKBIZ as a novel mechanism of oncogene deregulation and NF-κB pathway activation in the activated B-cell (ABC) subgroup. Small amplifications associated with over-expression of FCGR2B (the Fcγ receptor protein IIB), primarily in the germinal centre B-cell (GCB) subgroup, correlate with poor patient outcomes suggestive of a novel oncogene. These results expand the list of subgroup driver mutations that may facilitate implementation of improved diagnostic assays and could offer new avenues for the development of targeted therapeutics.&nbsp

Clustered brachiopod Hox genes are not expressed collinearly and are associated with lophotrochozoan novelties

Temporal collinearity is often considered the main force preserving Hox gene clusters in animal genomes. Studies that combine genomic and gene expression data are scarce, however, particularly in invertebrates like the Lophotrochozoa. As a result, the temporal collinearity hypothesis is currently built on poorly supported foundations. Here we characterize the complement, cluster, and expression of Hox genes in two brachiopod species, Terebratalia transversa and Novocrania anomala. T. transversa has a split cluster with 10 genes (lab, pb, Hox3, Dfd, Scr, Lox5, Antp, Lox4, Post2, and Post1), whereas N. anomala has 9 genes (apparently missing Post1). Our in situ hybridization, real-time quantitative PCR, and stage-specific transcriptomic analyses show that brachiopod Hox genes are neither strictly temporally nor spatially collinear; only pb (in T. transversa), Hox3 (in both brachiopods), and Dfd (in both brachiopods) show staggered mesodermal expression. Thus, our findings support the idea that temporal collinearity might contribute to keeping Hox genes clustered. Remarkably, expression of the Hox genes in both brachiopod species demonstrates cooption of Hox genes in the chaetae and shell fields, two major lophotrochozoan morphological novelties. The shared and specific expression of Hox genes, together with Arx, Zic, and Notch pathway components in chaetae and shell fields in brachiopods, mollusks, and annelids provide molecular evidence supporting the conservation of the molecular basis for these lophotrochozoan hallmarks

Genome-Wide Identification of Transcription Start Sites, Promoters and Transcription Factor Binding Sites in E. coli

Despite almost 40 years of molecular genetics research in Escherichia coli a major fraction of its Transcription Start Sites (TSSs) are still unknown, limiting therefore our understanding of the regulatory circuits that control gene expression in this model organism. RegulonDB (http://regulondb.ccg.unam.mx/) is aimed at integrating the genetic regulatory network of E. coli K12 as an entirely bioinformatic project up till now. In this work, we extended its aims by generating experimental data at a genome scale on TSSs, promoters and regulatory regions. We implemented a modified 5′ RACE protocol and an unbiased High Throughput Pyrosequencing Strategy (HTPS) that allowed us to map more than 1700 TSSs with high precision. From this collection, about 230 corresponded to previously reported TSSs, which helped us to benchmark both our methodologies and the accuracy of the previous mapping experiments. The other ca 1500 TSSs mapped belong to about 1000 different genes, many of them with no assigned function. We identified promoter sequences and type of σ factors that control the expression of about 80% of these genes. As expected, the housekeeping σ70 was the most common type of promoter, followed by σ38. The majority of the putative TSSs were located between 20 to 40 nucleotides from the translational start site. Putative regulatory binding sites for transcription factors were detected upstream of many TSSs. For a few transcripts, riboswitches and small RNAs were found. Several genes also had additional TSSs within the coding region. Unexpectedly, the HTPS experiments revealed extensive antisense transcription, probably for regulatory functions. The new information in RegulonDB, now with more than 2400 experimentally determined TSSs, strengthens the accuracy of promoter prediction, operon structure, and regulatory networks and provides valuable new information that will facilitate the understanding from a global perspective the complex and intricate regulatory network that operates in E. coli

Generating antiaromaticity in polycyclic conjugated hydrocarbons by thermally selective skeletal rearrangements at interfaces

Antiaromatic polycyclic conjugated hydrocarbons (PCHs) are attractive research targets because of their interesting structural, electronic and magnetic properties. Unlike aromatic compounds, the synthesis of antiaromatic PCHs is challenging because of their high reactivity and lack of stability, which stems from the small energy gap between their highest occupied and lowest unoccupied molecular orbitals. Here we describe a strategy for the introduction of antiaromatic units in PCHs via thermally selective intra- and intermolecular ring-rearrangement reactions of dibromomethylene-functionalized molecular precursors upon sublimation on a hot Au(111) metal surface, not available in solution chemistry. The synthetic value of these reactions is proven by the integration of pentalene segments into acene-based precursors, which undergo intramolecular ring rearrangement, and the formation of π-conjugated ladder polymers, linked through cyclobutadiene connections, due to ring-rearrangement and homocoupling reactions of indenofluorene-based precursors. The reaction products are investigated by scanning tunnelling microscopy and non-contact atomic force microscopy, and mechanistic insights are unveiled by computational studies. [Figure not available: see fulltext.] © 2023, The Author(s), under exclusive licence to Springer Nature Limited.This project has received funding from Comunidad de Madrid (projects QUIMTRONIC-CM (Y2018/NMT-4783) and NanoMagCost (P2018/NMT-4321)), an ERC Consolidator Grant (ELECNANO, 766555), ERC (SyG TOMATTO ERC-2020-951224) and Ministerio de Ciencia, Innovacion y Universidades (projects SpOrQuMat (PGC2018-098613-B-C21), CTQ2017-83531-R, PID2019-108532GB-I00, PID2020-114653RB-I00 and CTQ2016-81911-REDT). We acknowledge the support from the ‘(MAD2D-CM)-UCM’ and the ‘(MAD2D-CM)-IMDEA-Nanociencia’ projects funded by Comunidad de Madrid, by the Recovery, Transformation and Resilience Plan, and by NextGenerationEU from the European Union. IMDEA Nanociencia is appreciative of support from the ‘Severo Ochoa’ Programme for Centers of Excellence in R&D (MINECO, grant nos. SEV-2016-0686 and CEX2020-001039-S). Q.C., D.S.-P. and P.J. acknowledge funding support from the CzechNanoLab Research Infrastructure supported by MEYS CR (LM2023051) and GACR project no. 20-13692X. Computational resources were provided by the e-INFRA CZ project (ID 90140), supported by the Ministry of Education, Youth and Sports of the Czech Republic. A.S.-G. acknowledges funding from the ‘Ministerio de Universidades’ for the ‘Plan de Recuperación, Transformación y Resiliencia’ under Margarita Salas grant agreement CA1/RSUE/2021-00369. J.I.U. acknowledges the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement no. 886314. We acknowledge B. Cirera for fruitful discussions.The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request. The Fireball software package is available 458 at: https://github.com/fireball-QMD and PP-SPM software package can be downloaded at: https://github.com/Probe-Particle/ppafm#probe-particle-model.Peer reviewe