Modeling ultra-high frequency radiation emission in PIC codes

From the mysterious?ray bursts, which can be studied through the spatiotemporal structure of the radiation we receive, to the creation of sources of x-rays capable of probing nanoscale structures, radiation emission by relativistic charges is a key research field in plasma physics.The processes behind radiation emission in plasmas result from strongly non-linear many body interactions which involve relativistic effects, so they are best modeled through Particle-In-Cell (PIC) simulations. However, capturing this radiation directly in PIC simulations is very challenging due to the large disparity between the temporal and spatial scales associated with such phenomena. Current algorithms only describe radiation processes in the Fourier space (e.g.JRAD [1]), missing the spatiotemporal features of the emitted radiation, which is crucial to many fields, such as super-resolution microscopy [2] and astrophysics [3].info:eu-repo/semantics/publishedVersio

RaDiO: An efficient spatiotemporal radiation diagnostic for particle-in-cell codes

This work describes a novel radiation algorithm designed to capture the three-dimensional, space-time resolved electromagnetic field structure emitted by large ensembles of charged particles. The algorithm retains the full set of degrees of freedom that characterize electromagnetic waves by employing the Liénard-Wiechert fields to retrieve radiation emission. Emitted electric and magnetic fields are deposited in a virtual detector using a temporal interpolation scheme. This feature is essential to accurately predict field amplitudes and preserve the continuous character of radiation emission, even though particle dynamics is known only in a discrete set of temporal steps. Our algorithm retains and accurately captures, by design, full spatial and temporal coherence effects. We demonstrate that our numerical approach recovers well known theoretical radiated spectra in standard scenarios of radiation emission. We show that the algorithm is computationally efficient by computing the full spatiotemporal radiation features of High Harmonic Generation through a plasma mirror in a Particle-In-Cell (PIC) simulation.info:eu-repo/semantics/publishedVersio

A simple, low-cost conductive composite material for 3D printing of electronic sensors

3D printing technology can produce complex objects directly from computer aided digital designs. The technology has traditionally been used by large companies to produce fit and form concept prototypes (‘rapid prototyping’) before production. In recent years however there has been a move to adopt the technology as full-scale manufacturing solution. The advent of low-cost, desktop 3D printers such as the RepRap and Fab@Home has meant a wider user base are now able to have access to desktop manufacturing platforms enabling them to produce highly customised products for personal use and sale. This uptake in usage has been coupled with a demand for printing technology and materials able to print functional elements such as electronic sensors. Here we present formulation of a simple conductive thermoplastic composite we term ‘carbomorph’ and demonstrate how it can be used in an unmodified low-cost 3D printer to print electronic sensors able to sense mechanical flexing and capacitance changes. We show how this capability can be used to produce custom sensing devices and user interface devices along with printed objects with embedded sensing capability. This advance in low-cost 3D printing with offer a new paradigm in the 3D printing field with printed sensors and electronics embedded inside 3D printed objects in a single build process without requiring complex or expensive materials incorporating additives such as carbon nanotubes

Accurate and Wide-Field-of-View MEMS-Based Sun Sensor for Industrial Applications

This paper describes the design, fabrication, sim- ulation, and experimental results of an improved miniaturized two-axis sun sensor for industrial applications, created by adapt- ing a technology used previously in satellite applications. The sensor for each axis is composed of six photodiodes integrated in a crystalline-silicon substrate and a layer of cover glass, which is used to protect the silicon and to hold the windows. The high precision is obtained by the subdivision of the field of view, which is ± 60 ◦ , with a resolution of 0.1 ◦ . Each region is controlled by an independent high-precision solar sensor. The sensor can be used for sun-tracking applications in a photovoltaic system, heliostat concentration plants, and lighting applications.Gobierno de España. AYA2009- 07188-E, ACI2010-1094, AIC-B-2011-0702 (Sensosol project)Junta de Andalucía (España) P08-TIC-03590 (Satsol project

Structure of the poly-C9 component of the complement membrane attack complex

The membrane attack complex (MAC)/perforin-like protein complement component 9 (C9) is the major component of the MAC, a multi-protein complex that forms pores in the membrane of target pathogens. In contrast to homologous proteins such as perforin and the cholesterol-dependent cytolysins (CDCs), all of which require the membrane for oligomerisation, C9 assembles directly onto the nascent MAC from solution. However, the molecular mechanism of MAC assembly remains to be understood. Here we present the 8 Å cryo-EM structure of a soluble form of the poly-C9 component of the MAC. These data reveal a 22-fold symmetrical arrangement of C9 molecules that yield an 88-strand pore-forming β-barrel. The N-terminal thrombospondin-1 (TSP1) domain forms an unexpectedly extensive part of the oligomerisation interface, thus likely facilitating solution-based assembly. These TSP1 interactions may also explain how additional C9 subunits can be recruited to the growing MAC subsequent to membrane insertion

Comparison of Airway Intubation Devices When Using a Biohazard Suit: A Feasibility Study

OBJECTIVES: We set out to compare emergency medicine residents\u27 intubating times and success rates for direct laryngoscopy (DL), GlideScope-assisted intubation (GS), and the Supraglottic Airway Laryngopharyngeal Tube (SALT) airway with and without biohazard gear. METHODS: Each resident passed through 2 sets of 3 testing stations (DL, GS, SALT) in succession, intubating Laerdal mannequin heads with the 3 modalities after randomization to start with or without biohazard gear. RESULTS: Thirty-seven residents participated, and 27 were male (73%); 14 (37.8%) had prior experience intubating in biohazard suits. There was a statistically significant difference in those who had prior intubation experience between DL (37, 100%), GS (32, 86.5%), and SALT (12, 32.4%) (P \u3c .001) and in median time to intubation (48 seconds, no suit; 57 seconds, with suits) (P = .03). There was no statistically significant difference between the overall times to intubate for the 3 devices. First-pass success was highest for DL (91.2%, no suit; 83.7%, suit) followed by GS (89%, no suit; 78.3%, suit) and SALT (51%, no suit; 67.6%, suit). CONCLUSION: A minority of participants had prior experience intubating in biohazard suits. Use of biohazard suits extends time to successful intubation. There was no difference in time to intubation for the 3 devices, but first-pass success was highest for DL (with or without biohazard gear)

Conformational changes during pore formation by the perforin-related protein pleurotolysin

Membrane attack complex/perforin-like (MACPF) proteins comprise the largest superfamily of pore-forming proteins, playing crucial roles in immunity and pathogenesis. Soluble monomers assemble into large transmembrane pores via conformational transitions that remain to be structurally and mechanistically characterised. Here we present an 11 Å resolution cryo-electron microscopy (cryo-EM) structure of the two-part, fungal toxin Pleurotolysin (Ply), together with crystal structures of both components (the lipid binding PlyA protein and the pore-forming MACPF component PlyB). These data reveal a 13-fold pore 80 Å in diameter and 100 Å in height, with each subunit comprised of a PlyB molecule atop a membrane bound dimer of PlyA. The resolution of the EM map, together with biophysical and computational experiments, allowed confident assignment of subdomains in a MACPF pore assembly. The major conformational changes in PlyB are a ~70° opening of the bent and distorted central β-sheet of the MACPF domain, accompanied by extrusion and refolding of two α-helical regions into transmembrane β-hairpins (TMH1 and TMH2). We determined the structures of three different disulphide bond-trapped prepore intermediates. Analysis of these data by molecular modelling and flexible fitting allows us to generate a potential trajectory of β-sheet unbending. The results suggest that MACPF conformational change is triggered through disruption of the interface between a conserved helix-turn-helix motif and the top of TMH2. Following their release we propose that the transmembrane regions assemble into β-hairpins via top down zippering of backbone hydrogen bonds to form the membrane-inserted β-barrel. The intermediate structures of the MACPF domain during refolding into the β-barrel pore establish a structural paradigm for the transition from soluble monomer to pore, which may be conserved across the whole superfamily. The TMH2 region is critical for the release of both TMH clusters, suggesting why this region is targeted by endogenous inhibitors of MACPF function

rs5888 Variant of SCARB1 Gene Is a Possible Susceptibility Factor for Age-Related Macular Degeneration

Major genetic factors for age-related macular degeneration (AMD) have recently been identified as susceptibility risk factors, including variants in the CFH gene and the ARMS2 LOC387715/HTRA1locus. Our purpose was to perform a case-control study in two populations among individuals who did not carry risk variants for CFHY402H and LOC387715 A69S (ARMS2), called “study” individuals, in order to identify new genetic risk factors. Based on a candidate gene approach, we analyzed SNP rs5888 of the SCARB1 gene, coding for SRBI, which is involved in the lipid and lutein pathways. This study was conducted in a French series of 1241 AMD patients and 297 controls, and in a North American series of 1257 patients with advanced AMD and 1732 controls. Among these individuals, we identified 61 French patients, 77 French controls, 85 North American patients and 338 North American controls who did not carry the CFH nor ARMS2 polymorphisms. An association between AMD and the SCARB1 gene was seen among the study subjects. The genotypic distribution of the rs5888 polymorphism was significantly different between cases and controls in the French population (p<0.006). Heterozygosity at the rs5888 SNP increased risk of AMD compared to the CC genotypes in the French study population (odds ratio (OR) = 3.5, CI95%: 1.4–8.9, p<0.01) and after pooling the 2 populations (OR = 2.9, 95% CI: 1.6–5.3, p<0.002). Subgroup analysis in exudative forms of AMD revealed a pooled OR of 3.6 for individuals heterozygous for rs5888 (95% CI: 1.7–7.6, p<0.0015). These results suggest the possible contribution of SCARB1, a new genetic factor in AMD, and implicate a role for cholesterol and antioxidant micronutrient (lutein and vitamin E) metabolism in AMD

Crystal, Solution and In silico Structural Studies of Dihydrodipicolinate Synthase from the Common Grapevine

Dihydrodipicolinate synthase (DHDPS) catalyzes the rate limiting step in lysine biosynthesis in bacteria and plants. The structure of DHDPS has been determined from several bacterial species and shown in most cases to form a homotetramer or dimer of dimers. However, only one plant DHDPS structure has been determined to date from the wild tobacco species, Nicotiana sylvestris (Blickling et al. (1997) J. Mol. Biol. 274, 608–621). Whilst N. sylvestris DHDPS also forms a homotetramer, the plant enzyme adopts a ‘back-to-back’ dimer of dimers compared to the ‘head-to-head’ architecture observed for bacterial DHDPS tetramers. This raises the question of whether the alternative quaternary architecture observed for N. sylvestris DHDPS is common to all plant DHDPS enzymes. Here, we describe the structure of DHDPS from the grapevine plant, Vitis vinifera, and show using analytical ultracentrifugation, small-angle X-ray scattering and X-ray crystallography that V. vinifera DHDPS forms a ‘back-to-back’ homotetramer, consistent with N. sylvestris DHDPS. This study is the first to demonstrate using both crystal and solution state measurements that DHDPS from the grapevine plant adopts an alternative tetrameric architecture to the bacterial form, which is important for optimizing protein dynamics as suggested by molecular dynamics simulations reported in this study

Crystallographic and Molecular Dynamics Analysis of Loop Motions Unmasking the Peptidoglycan-Binding Site in Stator Protein MotB of Flagellar Motor

Background: The C-terminal domain of MotB (MotB-C) shows high sequence similarity to outer membrane protein A and related peptidoglycan (PG)-binding proteins. It is believed to anchor the power-generating MotA/MotB stator unit of the bacterial flagellar motor to the peptidoglycan layer of the cell wall. We previously reported the first crystal structure of this domain and made a puzzling observation that all conserved residues that are thought to be essential for PG recognition are buried and inaccessible in the crystal structure. In this study, we tested a hypothesis that peptidoglycan binding is preceded by, or accompanied by, some structural reorganization that exposes the key conserved residues. Methodology/Principal Findings: We determined the structure of a new crystalline form (Form B) of Helicobacter pylori MotB-C. Comparisons with the existing Form A revealed conformational variations in the petal-like loops around the carbohydrate binding site near one end of the b-sheet. These variations are thought to reflect natural flexibility at this site required for insertion into the peptidoglycan mesh. In order to understand the nature of this flexibility we have performed molecular dynamics simulations of the MotB-C dimer. The results are consistent with the crystallographic data and provide evidence that the three loops move in a concerted fashion, exposing conserved MotB residues that have previously been implicated in binding of the peptide moiety of peptidoglycan. Conclusion/Significance: Our structural analysis provides a new insight into the mechanism by which MotB inserts into th