Photoluminescence Stokes shift and exciton fine structure in CdTe nanocrystals

The photoluminescence spectra of spherical CdTe nanocrystals with zincblende structure are studied by size-selective spectroscopic techniques. We observe a resonant Stokes shift of 15 meV when the excitation laser energy is tuned to the red side of the absorption band at 2.236 eV. The experimental data are analyzed within a symmetry-based tight-binding theory of the exciton spectrum, which is first shown to account for the size dependence of the fundamental gap reported previously in the literature. The theoretical Stokes shift presented as a function of the gap shows a good agreement with the experimental data, indicating that the measured Stokes shift indeed arises from the electron-hole exchange interaction.Comment: 8 pages, 4 figures, LaTe

PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses

PartitionFinder 2 is a program for automatically selecting best-fit partitioning schemes and models of evolution for phylogenetic analyses. PartitionFinder 2 is substantially faster and more efficient than version 1, and incorporates many new methods and features. These include the ability to analyze morphological datasets, new methods to analyze genome-scale datasets, new output formats to facilitate interoperability with downstream software, and many new models of molecular evolution. PartitionFinder 2 is freely available under an open source license and works on Windows, OSX, and Linux operating systems. It can be downloaded from www.robertlanfear.com/partitionfinder. The source code is available at https://github.com/brettc/partitionfinder.RML was supported by the Australian Research Council. AMW was supported by NSF DEB-1256993. This work was supported by the Macquarie University Genes to Geoscience center

Monte-Carlo simulations of the recombination dynamics in porous silicon

A simple lattice model describing the recombination dynamics in visible light emitting porous Silicon is presented. In the model, each occupied lattice site represents a Si crystal of nanometer size. The disordered structure of porous Silicon is modeled by modified random percolation networks in two and three dimensions. Both correlated (excitons) and uncorrelated electron-hole pairs have been studied. Radiative and non-radiative processes as well as hopping between nearest neighbor occupied sites are taken into account. By means of extensive Monte-Carlo simulations, we show that the recombination dynamics in porous Silicon is due to a dispersive diffusion of excitons in a disordered arrangement of interconnected Si quantum dots. The simulated luminescence decay for the excitons shows a stretched exponential lineshape while for uncorrelated electron-hole pairs a power law decay is suggested. Our results successfully account for the recombination dynamics recently observed in the experiments. The present model is a prototype for a larger class of models describing diffusion of particles in a complex disordered system.Comment: 33 pages, RevTeX, 19 figures available on request to [email protected]

Grounding knowledge and normative valuation in agent-based action and scientific commitment

Philosophical investigation in synthetic biology has focused on the knowledge-seeking questions pursued, the kind of engineering techniques used, and on the ethical impact of the products produced. However, little work has been done to investigate the processes by which these epistemological, metaphysical, and ethical forms of inquiry arise in the course of synthetic biology research. An attempt at this work relying on a particular area of synthetic biology will be the aim of this chapter. I focus on the reengineering of metabolic pathways through the manipulation and construction of small DNA-based devices and systems synthetic biology. Rather than focusing on the engineered products or ethical principles that result, I will investigate the processes by which these arise. As such, the attention will be directed to the activities of practitioners, their manipulation of tools, and the use they make of techniques to construct new metabolic devices. Using a science-in-practice approach, I investigate problems at the intersection of science, philosophy of science, and sociology of science. I consider how practitioners within this area of synthetic biology reconfigure biological understanding and ethical categories through active modelling and manipulation of known functional parts, biological pathways for use in the design of microbial machines to solve problems in medicine, technology, and the environment. We might describe this kind of problem-solving as relying on what Helen Longino referred to as “social cognition” or the type of scientific work done within what Hasok Chang calls “systems of practice”. My aim in this chapter will be to investigate the relationship that holds between systems of practice within metabolic engineering research and social cognition. I will attempt to show how knowledge and normative valuation are generated from this particular network of practitioners. In doing so, I suggest that the social nature of scientific inquiry is ineliminable to both knowledge acquisition and ethical evaluations

Betalain production is possible in anthocyanin-producing plant species given the presence of DOPA-dioxygenase and L-DOPA

<p>Abstract</p> <p>Background</p> <p>Carotenoids and anthocyanins are the predominant non-chlorophyll pigments in plants. However, certain families within the order Caryophyllales produce another class of pigments, the betalains, instead of anthocyanins. The occurrence of betalains and anthocyanins is mutually exclusive. Betalains are divided into two classes, the betaxanthins and betacyanins, which produce yellow to orange or violet colours, respectively. In this article we show betalain production in species that normally produce anthocyanins, through a combination of genetic modification and substrate feeding.</p> <p>Results</p> <p>The biolistic introduction of DNA constructs for transient overexpression of two different dihydroxyphenylalanine (DOPA) dioxygenases (DODs), and feeding of DOD substrate (L-DOPA), was sufficient to induce betalain production in cell cultures of <it>Solanum tuberosum </it>(potato) and petals of <it>Antirrhinum majus</it>. HPLC analysis showed both betaxanthins and betacyanins were produced. Multi-cell foci with yellow, orange and/or red colours occurred, with either a fungal DOD (from <it>Amanita muscaria</it>) or a plant DOD (from <it>Portulaca grandiflora</it>), and the yellow/orange foci showed green autofluorescence characteristic of betaxanthins. Stably transformed <it>Arabidopsis thaliana </it>(arabidopsis) lines containing <it>35S: AmDOD </it>produced yellow colouration in flowers and orange-red colouration in seedlings when fed L-DOPA. These tissues also showed green autofluorescence. HPLC analysis of the transgenic seedlings fed L-DOPA confirmed betaxanthin production.</p> <p>Conclusions</p> <p>The fact that the introduction of DOD along with a supply of its substrate (L-DOPA) was sufficient to induce betacyanin production reveals the presence of a background enzyme, possibly a tyrosinase, that can convert L-DOPA to <it>cyclo</it>-DOPA (or dopaxanthin to betacyanin) in at least some anthocyanin-producing plants. The plants also demonstrate that betalains can accumulate in anthocyanin-producing species. Thus, introduction of a DOD and an enzyme capable of converting tyrosine to L-DOPA should be sufficient to confer both betaxanthin and betacyanin production to anthocyanin-producing species. The requirement for few novel biosynthetic steps may have assisted in the evolution of the betalain biosynthetic pathway in the Caryophyllales, and facilitated multiple origins of the pathway in this order and in fungi. The stably transformed <it>35S: AmDOD </it>arabidopsis plants provide material to study, for the first time, the physiological effects of having both betalains and anthocyanins in the same plant tissues.</p

Proposal for a method to estimate nutrient shock effects in bacteria

Plating methods are still the golden standard in microbiology; however, some studies have shown that these techniques can underestimate the microbial concentrations and diversity. A nutrient shock is one of the mechanisms proposed to explain this phenomenon. In this study, a tentative method to assess nutrient shock effects was tested. Findings To estimate the extent of nutrient shock effects, two strains isolated from tap water (Sphingomonas capsulata and Methylobacterium sp.) and two culture collection strains (E. coli CECT 434 and Pseudomonas fluorescens ATCC 13525) were exposed both to low and high nutrient conditions for different times and then placed in low nutrient medium (R2A) and rich nutrient medium (TSA). The average improvement (A.I.) of recovery between R2A and TSA for the different times was calculated to more simply assess the difference obtained in culturability between each medium. As expected, A.I. was higher when cells were plated after the exposition to water than when they were recovered from high-nutrient medium showing the existence of a nutrient shock for the diverse bacteria used. S. capsulata was the species most affected by this phenomenon. This work provides a method to consistently determine the extent of nutrient shock effects on different microorganisms and hence quantify the ability of each species to deal with sudden increases in substrate concentration. <br/

Accessing bacterial dark matter for improved enzyme discovery and engineering

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Incentive Compatible Reimbursement Schemes for Physicians

We consider physicians with fixed capacity levels. If a physician’s capacity exceeds demand, she may have an incentive to overtreat, i.e., she may provide unnecessary treatments to use up idle capacity. By contrast, with excess demand she may undertreat, i.e., she may not provide necessary treatments since other activities are financially more attractive. We first show that simple fee-for-service reimbursement schemes do not provide proper incentives. If insurers use, however, fee-for-service schemes with quantity restrictions, they solve the fraudulent physician problem