Bound to Rise

Senior Project submitted to The Division of Languages and Literature of Bard College. Bound to Rise is a collection of short stories about people who discover themselves in the “fine drizzly rain” (or smirr, in Scottish lingo) of everyday life. They orient themselves and find some way forward, or they realize they have to. Thematically, it addresses a carnival (the carnivalesque), a demolition derby, multiple fires, photography, drinking, music, an eating disorder, and a birthday cake. It includes one original children’s story written in Russian and translated into English by the author

Toric self-dual Einstein metrics as quotients

We use the quaternion Kahler reduction technique to study old and new self-dual Einstein metrics of negative scalar curvature with at least a two-dimensional isometry group, and relate the quotient construction to the hyperbolic eigenfunction Ansatz. We focus in particular on the (semi-)quaternion Kahler quotients of (semi-)quaternion Kahler hyperboloids, analysing the completeness and topology, and relating them to the self-dual Einstein Hermitian metrics of Apostolov-Gauduchon and Bryant.Comment: 30 page

A note on monopole moduli spaces

We discuss the structure of the framed moduli space of Bogomolny monopoles for arbitrary symmetry breaking and extend the definition of its stratification to the case of arbitrary compact Lie groups. We show that each stratum is a union of submanifolds for which we conjecture that the natural $L^2$ metric is hyperKahler. The dimensions of the strata and of these submanifolds are calculated, and it is found that for the latter, the dimension is always a multiple of four.Comment: 17 pages, LaTe

Methods for selecting fixed-effect models for heterogeneous codon evolution, with comments on their application to gene and genome data

BACKGROUND: Models of codon evolution have proven useful for investigating the strength and direction of natural selection. In some cases, a priori biological knowledge has been used successfully to model heterogeneous evolutionary dynamics among codon sites. These are called fixed-effect models, and they require that all codon sites are assigned to one of several partitions which are permitted to have independent parameters for selection pressure, evolutionary rate, transition to transversion ratio or codon frequencies. For single gene analysis, partitions might be defined according to protein tertiary structure, and for multiple gene analysis partitions might be defined according to a gene's functional category. Given a set of related fixed-effect models, the task of selecting the model that best fits the data is not trivial. RESULTS: In this study, we implement a set of fixed-effect codon models which allow for different levels of heterogeneity among partitions in the substitution process. We describe strategies for selecting among these models by a backward elimination procedure, Akaike information criterion (AIC) or a corrected Akaike information criterion (AICc). We evaluate the performance of these model selection methods via a simulation study, and make several recommendations for real data analysis. Our simulation study indicates that the backward elimination procedure can provide a reliable method for model selection in this setting. We also demonstrate the utility of these models by application to a single-gene dataset partitioned according to tertiary structure (abalone sperm lysin), and a multi-gene dataset partitioned according to the functional category of the gene (flagellar-related proteins of Listeria). CONCLUSION: Fixed-effect models have advantages and disadvantages. Fixed-effect models are desirable when data partitions are known to exhibit significant heterogeneity or when a statistical test of such heterogeneity is desired. They have the disadvantage of requiring a priori knowledge for partitioning sites. We recommend: (i) selection of models by using backward elimination rather than AIC or AICc, (ii) use a stringent cut-off, e.g., p = 0.0001, and (iii) conduct sensitivity analysis of results. With thoughtful application, fixed-effect codon models should provide a useful tool for large scale multi-gene analyses

Photodynamic inactivation of Candida albicans with imidazoacridinones : influence of irradiance, photosensitizer uptake and reactive oxygen species generation

The increasing applicability of antifungal treatments, the limited range of available drug classes and the emergence of drug resistance in Candida spp. suggest the need for new treatment options. To explore the applicability of C. albicans photoinactivation, we examined nine structurally different imidazoacridinone derivatives as photosensitizing agents. The most effective derivatives showed a >10(4)-fold reduction of viable cell numbers. The fungicidal action of the three most active compounds was compared at different radiant powers (3.5 to 63 mW/cm2), and this analysis indicated that 7 mW/cm2 was the most efficient. The intracellular accumulation of these compounds in fungal cells correlated with the fungicidal activity of all 9 derivatives. The lack of effect of verapamil, an inhibitor targeting Candida ABC efflux pumps, suggests that these imidazoacridinones are not substrates for ABC transporters. Thus, unlike azoles, a major class of antifungals used against Candida, ABC transporter-mediated resistance is unlikely. Electron paramagnetic resonance (EPR)-spin trapping data suggested that the fungicidal light-induced action of these derivatives might depend on the production of superoxide anion. The highest generation rate of superoxide anion was observed for 1330H, 1610H, and 1611. Singlet oxygen production was also detected upon the irradiation of imidazoacridinone derivatives with UV laser light, with a low to moderate yield, depending on the type of compound. Thus, imidazoacridinone derivatives examined in the present study might act via mixed type I/type II photodynamic mechanism. The presented data indicate lack of direct correlation between the structures of studied imidazoacridinones, cell killing ability, and ROS production. However, we showed for the first time that for imidazoacridinones not only intracellular accumulation is necessary prerequisite of lethal photosensitization of C. albicans, but also localization within particular cellular structures. Our findings present IA derivatives as efficient antifungal photosensitizers with a potential to be used in local treatment of Candida infection

Inversion symmetric 3-monopoles and the Atiyah-Hitchin manifold

We consider 3-monopoles symmetric under inversion symmetry. We show that the moduli space of these monopoles is an Atiyah-Hitchin submanifold of the 3-monopole moduli space. This allows what is known about 2-monopole dynamics to be translated into results about the dynamics of 3-monopoles. Using a numerical ADHMN construction we compute the monopole energy density at various points on two interesting geodesics. The first is a geodesic over the two-dimensional rounded cone submanifold corresponding to right angle scattering and the second is a closed geodesic for three orbiting monopoles.Comment: latex, 22 pages, 2 figures. To appear in Nonlinearit

Simulations of the Micro-Bunching Instability for SOLEIL and KARA Using Two Different VFP Solver Codes

The longitudinal dynamics of a bunched electron beam is an important aspect in the study of existing and the development of new electron storage rings. The dynamics depend on different beam parameters as well as on the interaction of the beam with its surroundings. A well established method for calculating the resulting dynamics is to numerically solve the Vlasov-Fokker-Planck equation. Depending on the chosen parameters and the considered wakefields and impedances, different effects can be studied. One common application is the investigation of the longitudinal micro-wave and micro-bunching instabilities. The latter occurs for short electron bunches due to self-interaction with their own emitted coherent synchrotron radiation (CSR). In this contribution, two different VFP solvers are used to simulate the longitudinal dynamics with a focus on the micro-bunching instability at the Soleil synchrotron and the KIT storage ring KARA (Karlsruhe Research Accelerator)