Description of ANSTO’s confocal microprobe simulation program

The elemental composition of a sample can be determined by the analysis of its characteristic X-ray spectrum. Proton induced X-ray emission (PIXE) has been used for a number of decades for this purpose (e.g. Clayton et al. 1981). More recently techniques aimed at enhancing the spatial resolution in the samples have been investigated. One of these techniques is to restrict the field of view of the X-ray detector by the use of a polycapillary lens. In such a confocal set-up the sample is driven across the sensitive volume formed at the intersection of the proton beam and the area from which the lens collects radiation (Zitnik at al. 2009, Wolff et al. 2009). Here we detail early investigations of a set-up with a polycapilary lens attached to the detector and a FORTRAN program which calculates the yield from a homogeneous material. Once the working of the set-up and program have been investigated and validated for homogeneous sample, heterogeneous samples can be considered

Induced Magnetic Ordering by Proton Irradiation in Graphite

We provide evidence that proton irradiation of energy 2.25 MeV on highly-oriented pyrolytic graphite samples triggers ferro- or ferrimagnetism. Measurements performed with a superconducting quantum interferometer device (SQUID) and magnetic force microscopy (MFM) reveal that the magnetic ordering is stable at room temperature.Comment: 3 Figure

Determination of radiation hardness of silicon diodes

In this paper, we describe an experiment aimed to measure the physical observables, which can be used for the assessment of the radiation hardness of commercially available silicon photo diodes commonly used as nuclear detectors in particle accelerator laboratories. The experiment adopted the methodology developed during the International Atomic Energy Agency (IAEA) Coordinated Research Project (CRP No. F11016) “Utilization of Ion Accelerators for Studying and Modelling Ion Induced Radiation Defects in Semiconductors and Insulators”. This methodology is based on the selective irradiation of micrometer-sized regions with different fluences of MeV ions using an ion microbeam and on the measurement of the charge collection efficiency (CCE) degradation by Ion Beam Induced Charge (IBIC) microscopy performed in full depletion condition, using different probing ions. The IBIC results are analyzed through a theoretical approach based on the Shockley-Read-Hall model for the free carrier recombination in the presence of ion-induced deep traps. This interpretative model allows the evaluation of the material radiation hardness in terms of recombination parameters for both electrons and holes. The device under study in this experiment was a commercial p-i-n photodiode, which was initially characterized by i) standard electronic characterization techniques to determine its doping and ii) the Angle-Resolved IBIC to evaluate its effective entrance window. Nine regions of (100 × 100) µm2 were irradiated with 11.25 MeV He ions up to a maximum fluence of 3·1012 ions/cm2. The CCE degradation was measured by the IBIC technique using 11.25 MeV He and 1.4 MeV He as probing ions. The model presented here proved to be effective for fitting the experimental data. The fitting parameters correspond to the recombination coefficients, which are the key parameters for the characterization of the effects of radiation damage in semiconductors.</p

Cytological and transcript analyses reveal fat and lazy persister-like bacilli in tuberculous sputum

As nonreplicating tubercle bacilli are tolerant to the cidal action of antibiotics and resistant to multiple stresses, identification of this persister-like population of tubercle bacilli in sputum presents exciting and tractable new opportunities to investigate both responses to chemotherapy and the transmission of tuberculosis

High-throughput, quantitative analyses of genetic interactions in E. coli.

Large-scale genetic interaction studies provide the basis for defining gene function and pathway architecture. Recent advances in the ability to generate double mutants en masse in Saccharomyces cerevisiae have dramatically accelerated the acquisition of genetic interaction information and the biological inferences that follow. Here we describe a method based on F factor-driven conjugation, which allows for high-throughput generation of double mutants in Escherichia coli. This method, termed genetic interaction analysis technology for E. coli (GIANT-coli), permits us to systematically generate and array double-mutant cells on solid media in high-density arrays. We show that colony size provides a robust and quantitative output of cellular fitness and that GIANT-coli can recapitulate known synthetic interactions and identify previously unidentified negative (synthetic sickness or lethality) and positive (suppressive or epistatic) relationships. Finally, we describe a complementary strategy for genome-wide suppressor-mutant identification. Together, these methods permit rapid, large-scale genetic interaction studies in E. coli

3D-Hydrogen Analysis of Ferromagnetic Microstructures in Proton Irradiated Graphite

Recently, magnetic order in highly oriented pyrolytic graphite (HOPG) induced by proton broad- and microbeam irradiation was discovered. Theoretical models propose that hydrogen could play a major role in the magnetism mechanism. We analysed the hydrogen distribution of pristine as well as irradiated HOPG samples, which were implanted to micrometer-sized spots as well as extended areas with various doses of 2.25 MeV protons at the Leipzig microprobe LIPSION. For this we used the sensitive 3D hydrogen microscopy system at the Munich microprobe SNAKE. The background hydrogen level in pristine HOPG is determined to be less than 0.3 at-ppm. About 4.8e15 H-atoms/cm^2 are observed in the near-surface region (4 um depth resolution). The depth profiles of the implants show hydrogen located within a confined peak at the end of range, in agreement with SRIM Monte Carlo simulations, and no evidence of diffusion broadening along the c-axis. At sample with microspots, up to 40 at-% of the implanted hydrogen is not detected, providing support for lateral hydrogen diffusion.Comment: accepted for publication in Nucl. Instr. and Met

A high-fidelity quantum matter-link between ion-trap microchip modules

System scalability is fundamental for large-scale quantum computers (QCs) and is being pursued over a variety of hardware platforms. For QCs based on trapped ions, architectures such as the quantum charge-coupled device (QCCD) are used to scale the number of qubits on a single device. However, the number of ions that can be hosted on a single quantum computing module is limited by the size of the chip being used. Therefore, a modular approach is of critical importance and requires quantum connections between individual modules. Here, we present the demonstration of a quantum matter-link in which ion qubits are transferred between adjacent QC modules. Ion transport between adjacent modules is realised at a rate of 2424 s−1 and with an infidelity associated with ion loss during transport below 7 × 10−8. Furthermore, we show that the link does not measurably impact the phase coherence of the qubit. The quantum matter-link constitutes a practical mechanism for the interconnection of QCCD devices. Our work will facilitate the implementation of modular QCs capable of fault-tolerant utility-scale quantum computation

Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology

Modular and orthogonal genetic logic gates are essential for building robust biologically based digital devices to customize cell signalling in synthetic biology. Here we constructed an orthogonal AND gate in Escherichia coli using a novel hetero-regulation module from Pseudomonas syringae. The device comprises two co-activating genes hrpR and hrpS controlled by separate promoter inputs, and a σ54-dependent hrpL promoter driving the output. The hrpL promoter is activated only when both genes are expressed, generating digital-like AND integration behaviour. The AND gate is demonstrated to be modular by applying new regulated promoters to the inputs, and connecting the output to a NOT gate module to produce a combinatorial NAND gate. The circuits were assembled using a parts-based engineering approach of quantitative characterization, modelling, followed by construction and testing. The results show that new genetic logic devices can be engineered predictably from novel native orthogonal biological control elements using quantitatively in-context characterized parts

Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO).

Experimental data about gene functions curated from the primary literature have enormous value for research scientists in understanding biology. Using the Gene Ontology (GO), manual curation by experts has provided an important resource for studying gene function, especially within model organisms. Unprecedented expansion of the scientific literature and validation of the predicted proteins have increased both data value and the challenges of keeping pace. Capturing literature-based functional annotations is limited by the ability of biocurators to handle the massive and rapidly growing scientific literature. Within the community-oriented wiki framework for GO annotation called the Gene Ontology Normal Usage Tracking System (GONUTS), we describe an approach to expand biocuration through crowdsourcing with undergraduates. This multiplies the number of high-quality annotations in international databases, enriches our coverage of the literature on normal gene function, and pushes the field in new directions. From an intercollegiate competition judged by experienced biocurators, Community Assessment of Community Annotation with Ontologies (CACAO), we have contributed nearly 5,000 literature-based annotations. Many of those annotations are to organisms not currently well-represented within GO. Over a 10-year history, our community contributors have spurred changes to the ontology not traditionally covered by professional biocurators. The CACAO principle of relying on community members to participate in and shape the future of biocuration in GO is a powerful and scalable model used to promote the scientific enterprise. It also provides undergraduate students with a unique and enriching introduction to critical reading of primary literature and acquisition of marketable skills