The chemistry of ynol and thioynol ethers

Alkynyl ethers and alkynyl thioethers (‘ynol ethers’ and ‘thioynol ethers’) are appealing building-blocks in synthetic chemistry due to their ease of manipulation and predictable reactivity. Until recently however, their potential has remained underexploited due to difficulties in preparation and isolation. Although recent advances in synthetic chemistry have highlighted various applications for ynol ethers, the equivalent thioynol examples have been rather less exploited despite a unique and fascinating reactivity profile. Although superficially the chemistry of alkynyl ethers and their sulfide counterparts are similar, close examination of their chemistry reveals important differences which can be exploited by the synthetic chemist. This review will examine the preparation of both classes of compound and examine their reactivity to highlight their powerful synthetic applications. Particular focus will be made of thiynol ethers whose chemistry exhibits some fascinating differences compared to their oxygen counterparts and have immense untapped potential for synthetic chemistry

Structure and dielectric properties of polar fluids with extended dipoles: results from numerical simulations

The strengths and short-comings of the point-dipole model for polar fluids of spherical molecules are illustrated by considering the physically more relevant case of extended dipoles formed by two opposite charges $\pm q$ separated by a distance $d$ (dipole moment $\mu=q d$). Extensive Molecular Dynamics simulations on a high density dipolar fluid are used to analyse the dependence of the pair structure, dielectric constant \eps and dynamics as a function of the ratio $d/\sigma$ (\sig is the molecular diameter), for a fixed dipole moment $\mu$. The point dipole model is found to agree well with the extended dipole model up to d/\sig \simeq 0.3. Beyond that ratio, \eps shows a non-trivial variation with d/\sig. When d/\sig>0.6, a transition is observed towards a hexagonal columnar phase; the corresponding value of the dipole moment, \mu^2/\sig^3 k T=3, is found to be substantially lower than the value of the point dipole required to drive a similar transition.Comment: 10 pages, 11 figures; Paper submitted to Molecular Physic

The distribution and evolutionary history of the PRP8 intein

BACKGROUND: We recently described a mini-intein in the PRP8 gene of a strain of the basidiomycete Cryptococcus neoformans, an important fungal pathogen of humans. This was the second described intein in the nuclear genome of any eukaryote; the first nuclear encoded intein was found in the VMA gene of several saccharomycete yeasts. The evolution of eukaryote inteins is not well understood. In this report we describe additional PRP8 inteins (bringing the total of these to over 20). We compare and contrast the phylogenetic distribution and evolutionary history of the PRP8 intein and the saccharomycete VMA intein, in order to derive a broader understanding of eukaryote intein evolution. It has been suggested that eukaryote inteins undergo horizontal transfer and the present analysis explores this proposal. RESULTS: In total, 22 PRP8 inteins have been detected in species from three different orders of euascomycetes, including Aspergillus nidulans and Aspergillus fumigatus (Eurotiales), Paracoccidiodes brasiliensis, Uncinocarpus reesii and Histoplasma capsulatum (Onygales) and Botrytis cinerea (Helotiales). These inteins are all at the same site in the PRP8 sequence as the original Cryptococcus neoformans intein. Some of the PRP8 inteins contain apparently intact homing endonuclease domains and are thus potentially mobile, while some lack the region corresponding to the homing endonuclease and are thus mini-inteins. In contrast, no mini-inteins have been reported in the VMA gene of yeast. There are several examples of pairs of closely related species where one species carries the PRP8 intein while the intein is absent from the other species. Bio-informatic and phylogenetic analyses suggest that many of the ascomycete PRP8 homing endonucleases are active. This contrasts with the VMA homing endonucleases, most of which are inactive. CONCLUSION: PRP8 inteins are widespread in the euascomycetes (Pezizomycota) and apparently their homing endonucleases are active. There is no evidence for horizontal transfer within the euascomycetes. This suggests that the intein is of ancient origin and has been vertically transmitted amongst the euascomycetes. It is possible that horizontal transfer has occurred between the euascomycetes and members of the basidiomycete genus Cryptococcus

Numerical elimination and moduli space of vacua

We propose a new computational method to understand the vacuum moduli space of (supersymmetric) field theories. By combining numerical algebraic geometry (NAG) and elimination theory, we develop a powerful, efficient, and parallelizable algorithm toextract important information such as the dimension, branch structure, Hilbert series and subsequent operator counting, as well as variation according to coupling constants and mass parameters. We illustrate this method on a host of examples from gauge theory, string theory, and algebraic geometry

Spectral Classification; Old and Contemporary

Beginning with a historical account of the spectral classification, its refinement through additional criteria is presented. The line strengths and ratios used in two dimensional classifications of each spectral class are described. A parallel classification scheme for metal-poor stars and the standards used for classification are presented. The extension of spectral classification beyond M to L and T and spectroscopic classification criteria relevant to these classes are described. Contemporary methods of classifications based upon different automated approaches are introduced.Comment: To be published in "Principles and Perspectives in Cosmochemistry" Lecture Notes on Kodai School on Synthesis of Elements in Stars: Ed Aruna Goswami & Eswar Reddy, Springer Verlag, 2009, 17 pages, 10 figure

T2{}^2K2{}^2: The Twitter Top-K Keywords Benchmark

Information retrieval from textual data focuses on the construction of vocabularies that contain weighted term tuples. Such vocabularies can then be exploited by various text analysis algorithms to extract new knowledge, e.g., top-k keywords, top-k documents, etc. Top-k keywords are casually used for various purposes, are often computed on-the-fly, and thus must be efficiently computed. To compare competing weighting schemes and database implementations, benchmarking is customary. To the best of our knowledge, no benchmark currently addresses these problems. Hence, in this paper, we present a top-k keywords benchmark, T${}^2$K${}^2$, which features a real tweet dataset and queries with various complexities and selectivities. T${}^2$K${}^2$ helps evaluate weighting schemes and database implementations in terms of computing performance. To illustrate T${}^2$K${}^2$'s relevance and genericity, we successfully performed tests on the TF-IDF and Okapi BM25 weighting schemes, on one hand, and on different relational (Oracle, PostgreSQL) and document-oriented (MongoDB) database implementations, on the other hand

Numerical Algebraic Geometry: A New Perspective on String and Gauge Theories

The interplay rich between algebraic geometry and string and gauge theories has recently been immensely aided by advances in computational algebra. However, these symbolic (Gr\"{o}bner) methods are severely limited by algorithmic issues such as exponential space complexity and being highly sequential. In this paper, we introduce a novel paradigm of numerical algebraic geometry which in a plethora of situations overcomes these short-comings. Its so-called 'embarrassing parallelizability' allows us to solve many problems and extract physical information which elude the symbolic methods. We describe the method and then use it to solve various problems arising from physics which could not be otherwise solved.Comment: 36 page