N=1 Special Geometry, Mixed Hodge Variations and Toric Geometry

We study the superpotential of a certain class of N=1 supersymmetric type II compactifications with fluxes and D-branes. We show that it has an important two-dimensional meaning in terms of a chiral ring of the topologically twisted theory on the world-sheet. In the open-closed string B-model, this chiral ring is isomorphic to a certain relative cohomology group V, which is the appropriate mathematical concept to deal with both the open and closed string sectors. The family of mixed Hodge structures on V then implies for the superpotential to have a certain geometric structure. This structure represents a holomorphic, N=1 supersymmetric generalization of the well-known N=2 special geometry. It defines an integrable connection on the topological family of open-closed B-models, and a set of special coordinates on the space \cal M of vev's in N=1 chiral multiplets. We show that it can be given a very concrete and simple realization for linear sigma models, which leads to a powerful and systematic method for computing the exact non-perturbative N=1 superpotentials for a broad class of toric D-brane geometries.Comment: 40p, harvmac-

Holomorphic N=1 Special Geometry of Open--Closed Type II Strings

We outline a general geometric structure that underlies the N=1 superpotentials of a certain class of flux and brane configurations in type II string compactifications on Calabi-Yau threefolds. This ``holomorphic N=1 special geometry'' is in many respects comparable to, and in a sense an extension of, the familiar special geometry in N=2 supersymmetric type II string compactifications. It puts the computation of the instanton-corrected superpotential W of the four-dimensional N=1 string effective action on a very similar footing as the familiar computation of the N=2 prepotential F via mirror symmetry. In this note we present some of the main ideas and results, while more details as well as some explicit computations will appear in a companion paperComment: 18 pages, harvmac (b), no figure

Optical glucose sensor for single use microfluidic reactors

Glucose measurements are of tremendous interest in biotechnology. Electrochemical and optical methods to measure glucose have been intensively investigated in the last 30 years, in particular for medical diagnostics. A widely used principle is to measure the consumption of oxygen during the oxidation process of glucose facilitated by the enzyme glucose oxidase. The determination of glucose is based on a correlation between the oxygen consumption and the glucose concentration. In our contribution, we demonstrate the integration of a flow-through glucose sensor into microfluidic devices for cell culturing. The sensor consists of three layers: an oxygen sensitive layer, an enzymatic glucose-oxidase layer for glucose induced oxygen consumption and a diffusion layer. The oxygen sensitive layer contains polystyrene particles stained with meso-tetra(4-fluorophenyl)tetrabenzoporphyrin (PtTPTBPF4) embedded in a swellable hydrogel. The second layer contains aggregates of the enzyme glucose oxidase embedded in the same hydrogel. The last and final layer is a plain hydrogel diffusion barrier. By increasing the layer height of the diffusion layer, the dynamic range of the sensor can be tuned. Please click Additional Files below to see the full abstract

Mirror Symmetry and Landau Ginzburg Calabi-Yau Superpotentials in F-theory Compactifications

We study Landau Ginzburg (LG) theories mirror to 2D N=2 gauged linear sigma models on toric Calabi-Yau manifolds. We derive and solve new constraint equations for Landau Ginzburg elliptic Calabi-Yau superpotentials, depending on the physical data of dual linear sigma models. In Calabi-Yau threefolds case, we consider two examples. First, we give the mirror symmetry of the canonical line bundle over the Hirzebruch surfaces $\bf F_n$. Second, we find a special geometry with the affine so(8) Lie algebra toric data extending the geometry of elliptically fibered K3. This geometry leads to a pure N=1 six dimensional SO(8) gauge model from the F-theory compactification. For Calabi-Yau fourfolds, we give a new algebraic realization for ADE hypersurfaces.Comment: 27 pages, latex. To appear in Journal of Physics A: Mathematical and Genera

Integration and Application of Optical Chemical Sensors in Microbioreactors

The quantification of key variables such as oxygen, pH, carbon dioxide, glucose, and temperature provides essential information for biological and biotechnological applications and their development. Microfluidic devices offer an opportunity to accelerate research and development in these areas due to their small scale, and the fine control over the microenvironment, provided that these key variables can be measured. Optical sensors are well-suited for this task. They offer non-invasive and non-destructive monitoring of the mentioned variables, and the establishment of time-course profiles without the need for sampling from the microfluidic devices. They can also be implemented in larger systems, facilitating cross-scale comparison of analytical data. This tutorial review presents an overview of the optical sensors and their technology, with a view to support current and potential new users in microfluidics and biotechnology in the implementation of such sensors. It introduces the benefits and challenges of sensor integration, including, for example, their application for microbioreactors. Sensor formats, integration methods, device bonding options, and monitoring options are explained. Luminescent sensors for oxygen, pH, carbon dioxide, glucose and temperature are showcased alongside other optical detection methods, such as Raman and surface plasmon resonance. Areas where further development is needed are highlighted with the intent to guide future development efforts towards analytes for which reliable, stable, or easily integrated detection methods are not yet available

Thermosphere Dynamics Workshop, volume 2

Atmospheric observations reported on include recent measurements of thermospherical composition, gas temperatures, auroral emissions, ion-neutral collisional coupling, electric fields, and plasma convection. Theoretical studies reported on include model calculations of thermospherical general circulation, thermospheric tides, thermospheric tidal coupling to the lower atmosphere, interactions between thermospheic chemistry and dynamics and thermosphere-ionosphere coupling processes. The abstracts provide details given in each talk but the figures represent the fundamental information exchanged within the worksho

Exciton-magnon transitions in the frustrated chromium antiferromagnets CuCrO2, alpha-CaCr2O4, CdCr2O4, and ZnCr2O4

We report on optical transmission spectroscopy of the Cr-based frustrated triangular antiferromagnets CuCrO2 and alpha-CaCr2O4, and the spinels CdCr2O4 and ZnCr2O4 in the near-infrared to visible-light frequency range. We explore the possibility to search for spin correlations far above the magnetic ordering temperature and for anomalies in the magnon lifetime in the magnetically ordered state by probing exciton-magnon sidebands of the spin-forbidden crystal-field transitions of the Cr3+ ions (spin S = 3/2). In CuCrO2 and alpha-CaCr2O4 the appearance of fine structures below T_N is assigned to magnon sidebands by comparison with neutron scattering results. The temperature dependence of the line width of the most intense sidebands in both compounds can be described by an Arrhenius law. For CuCrO2 the sideband associated with the 4A2 -> 2T2 transition can be observed even above T_N. Its line width does not show a kink at the magnetic ordering temperature and can alternatively be described by a Z2 vortex scenario proposed previously for similar materials. The exciton-magnon features in alpha-CaCr2O4 are more complex due to the orthorhombic distortion. While for CdCr2O4 magnon sidebands are identified below T_N and one sideband excitation is found to persist across the magnetic ordering transition, only a weak fine structure related to magnetic ordering has been observed in ZnCr2O4.Comment: 14 pages, 10 figures, all comments are welcome and appreciated, accepted for publication in PR

Untangling the Conceptual Isssues Raised in Reydon and Scholz’s Critique of Organizational Ecology and Darwinian Populations

Reydon and Scholz raise doubts about the Darwinian status of organizational ecology by arguing that Darwinian principles are not applicable to organizational populations. Although their critique of organizational ecology’s typological essentialism is correct, they go on to reject the Darwinian status of organizational populations. This paper claims that the distinction between replicators and interactors, raised in modern philosophy of biology but not discussed by Reydon and Scholz, points the way forward for organizational ecologists. It is possible to conceptualise evolving Darwinian populations providing the inheritance mechanism is appropriately specified. By this approach, adaptation and selection are no longer dichotomised, and the evolutionary significance of knowledge transmission is highlightedPeer reviewe

System-wide Perturbation Analysis with Nearly Complete Coverage of the Yeast Proteome by Single-shot Ultra HPLC Runs on a Bench Top Orbitrap

Yeast remains an important model for systems biology and for evaluating proteomics strategies. In-depth shotgun proteomics studies have reached nearly comprehensive coverage, and rapid, targeted approaches have been developed for this organism. Recently, we demonstrated that single LC-MS/MS analysis using long columns and gradients coupled to a linear ion trap Orbitrap instrument had an unexpectedly large dynamic range of protein identification (Thakur, S. S., Geiger, T., Chatterjee, B., Bandilla, P., Frohlich, F., Cox, J., and Mann, M. (2011) Deep and highly sensitive proteome coverage by LC-MS/MS without prefractionation. Mol. Cell Proteomics 10, 10.1074/mcp.M110.003699). Here we couple an ultra high pressure liquid chromatography system to a novel bench top Orbitrap mass spectrometer (Q Exactive) with the goal of nearly complete, rapid, and robust analysis of the yeast proteome. Single runs of filter-aided sample preparation (FASP)-prepared and LysC-digested yeast cell lysates identified an average of 3923 proteins. Combined analysis of six single runs improved these values to more than 4000 identified proteins/run, close to the total number of proteins expressed under standard conditions, with median sequence coverage of 23%. Because of the absence of fractionation steps, only minuscule amounts of sample are required. Thus the yeast model proteome can now largely be covered within a few hours of measurement time and at high sensitivity. Median coverage of proteins in Kyoto Encyclopedia of Genes and Genomes pathways with at least 10 members was 88%, and pathways not covered were not expected to be active under the conditions used. To study perturbations of the yeast proteome, we developed an external, heavy lysine-labeled SILAC yeast standard representing different proteome states. This spike-in standard was employed to measure the heat shock response of the yeast proteome. Bioinformatic analysis of the heat shock response revealed that translation-related functions were down-regulated prominently, including nucleolar processes. Conversely, stress-related pathways were up-regulated. The proteomic technology described here is straightforward, rapid, and robust, potentially enabling widespread use in the yeast and other biological research communities