FISH mapping and molecular organization of the major repetitive sequences of tomato

This paper presents a bird's-eye view of the major repeats and chromatin types of tomato. Using fluorescence in-situ hybridization (FISH) with Cot-1, Cot-10 and Cot-100 DNA as probes we mapped repetitive sequences of different complexity on pachytene complements. Cot-100 was found to cover all heterochromatin regions, and could be used to identify repeat-rich clones in BAC filter hybridization. Next we established the chromosomal locations of the tandem and dispersed repeats with respect to euchromatin, nucleolar organizer regions (NORs), heterochromatin, and centromeres. The tomato genomic repeats TGRII and TGRIII appeared to be major components of the pericentromeres, whereas the newly discovered TGRIV repeat was found mainly in the structural centromeres. The highly methylated NOR of chromosome 2 is rich in [GACA](4), a microsatellite that also forms part of the pericentromeres, together with [GA](8), [GATA](4) and Ty1-copia. Based on the morphology of pachytene chromosomes and the distribution of repeats studied so far, we now propose six different chromatin classes for tomato: (1) euchromatin, (2) chromomeres, (3) distal heterochromatin and interstitial heterochromatic knobs, (4) pericentromere heterochromatin, (5) functional centromere heterochromatin and (6) nucleolar organizer regio

Measurement of a 2D fast-ion velocity distribution function by tomographic inversion of fast-ion D-alpha spectra

We present the first measurement of a local fast-ion 2D velocity distribution function f(v||, v⊥). To this end, we heated a plasma in ASDEX Upgrade by neutral beam injection and measured spectra of fast-ion Dα (FIDA) light from the plasma centre in three views simultaneously. The measured spectra agree very well with synthetic spectra calculated from a TRANSP/NUBEAM simulation. Based on the measured FIDA spectra alone, we infer f(v||, v⊥) by tomographic inversion. Salient features of our measurement of f(v||, v⊥) agree reasonably well with the simulation: the measured as well as the simulated f(v||, v⊥) are lopsided towards negative velocities parallel to the magnetic field, and they have similar shapes. Further, the peaks in the simulation of f(v||, v⊥) at full and half injection energies of the neutral beam also appear in the measurement at similar velocity-space locations. We expect that we can measure spectra in up to seven views simultaneously in the next ASDEX Upgrade campaign which would further improve measurements of f(v||, v⊥) by tomographic inversion

High-definition velocity-space tomography of fast-ion dynamics

Velocity-space tomography of the fast-ion distribution function in a fusion plasma is usually a photon-starved tomography method due to limited optical access and signal-to-noise ratio of fast-ion Dα (FIDA) spectroscopy as well as the strive for high-resolution images. In high-definition tomography, prior information makes up for this lack of data. We restrict the target velocity space through the measured absence of FIDA light, impose phase-space densities to be non-negative, and encode the known geometry of neutral beam injection (NBI) sources. We further use a numerical simulation as prior information to reconstruct where in velocity space the measurements and the simulation disagree. This alternative approach is demonstrated for four-view as well as for two-view FIDA measurements. The high-definition tomography tools allow us to study fast ions in sawtoothing plasmas and the formation of NBI peaks at full, half and one-third energy by time-resolved tomographic movies

An Effective-Medium Tight-Binding Model for Silicon

A new method for calculating the total energy of Si systems is presented. The method is based on the effective-medium theory concept of a reference system. Instead of calculating the energy of an atom in the system of interest a reference system is introduced where the local surroundings are similar. The energy of the reference system can be calculated selfconsistently once and for all while the energy difference to the reference system can be obtained approximately. We propose to calculate it using the tight-binding LMTO scheme with the Atomic-Sphere Approximation(ASA) for the potential, and by using the ASA with charge-conserving spheres we are able to treat open system without introducing empty spheres. All steps in the calculational method is {\em ab initio} in the sense that all quantities entering are calculated from first principles without any fitting to experiment. A complete and detailed description of the method is given together with test calculations of the energies of phonons, elastic constants, different structures, surfaces and surface reconstructions. We compare the results to calculations using an empirical tight-binding scheme.Comment: 26 pages (11 uuencoded Postscript figures appended), LaTeX, CAMP-090594-

Deuterium temperature, drift velocity, and density measurements in non-Maxwellian plasmas at ASDEX Upgrade

We measure the deuterium density, the parallel drift velocity, and parallel and perpendicular temperatures (T∥, T⊥) in non-Maxwellian plasmas at ASDEX Upgrade. This is done by taking moments of the ion velocity distribution function measured by tomographic inversion of five simultaneously acquired spectra of Dα-light. Alternatively, we fit the spectra using a bi-Maxwellian distribution function. The measured kinetic temperatures (T∥ = 9 keV, T⊥ = 11 keV) reveal the anisotropy of the plasma and are substantially higher than the measured boron temperature (7 keV). The Maxwellian deuterium temperature computed with TRANSP (6 keV) is not uniquely measurable due to the fast ions. Nevertheless, simulated kinetic temperatures accounting for fast ions based on TRANSP (T∥= 8.3 keV, T⊥ = 10.4 keV) are in excellent agreement with the measurements. Similarly, the Maxwellian deuterium drift velocity computed with TRANSP (300 km s-1) is not uniquely measurable, but the simulated kinetic drift velocity accounting for fast ions agrees with the measurements (400 km s-1) and is substantially larger than the measured boron drift velocity (270 km s-1). We further find that ion cyclotron resonance heating elevates T∥ and T⊥ each by 2 keV without evidence for preferential heating in the Dα spectra. Lastly, we derive an expression for the 1D projection of an arbitrarily drifting bi-Maxwellian onto a diagnostic line-of-sight

An Ultra-Low Background PMT for Liquid Xenon Detectors

Results are presented from radioactivity screening of two models of photomultiplier tubes designed for use in current and future liquid xenon experiments. The Hamamatsu 5.6 cm diameter R8778 PMT, used in the LUX dark matter experiment, has yielded a positive detection of four common radioactive isotopes: 238U, 232Th, 40K, and 60Co. Screening of LUX materials has rendered backgrounds from other detector materials subdominant to the R8778 contribution. A prototype Hamamatsu 7.6 cm diameter R11410 MOD PMT has also been screened, with benchmark isotope counts measured at <0.4 238U / <0.3 232Th / <8.3 40K / 2.0+-0.2 60Co mBq/PMT. This represents a large reduction, equal to a change of \times 1/24 238U / \times 1/9 232Th / \times 1/8 40K per PMT, between R8778 and R11410 MOD, concurrent with a doubling of the photocathode surface area (4.5 cm to 6.4 cm diameter). 60Co measurements are comparable between the PMTs, but can be significantly reduced in future R11410 MOD units through further material selection. Assuming PMT activity equal to the measured 90% upper limits, Monte Carlo estimates indicate that replacement of R8778 PMTs with R11410 MOD PMTs will change LUX PMT electron recoil background contributions by a factor of \times1/25 after further material selection for 60Co reduction, and nuclear recoil backgrounds by a factor of \times 1/36. The strong reduction in backgrounds below the measured R8778 levels makes the R11410 MOD a very competitive technology for use in large-scale liquid xenon detectors.Comment: v2 updated to include content after reviewer comments (Sep 2012

LUXSim: A Component-Centric Approach to Low-Background Simulations

Geant4 has been used throughout the nuclear and high-energy physics community to simulate energy depositions in various detectors and materials. These simulations have mostly been run with a source beam outside the detector. In the case of low-background physics, however, a primary concern is the effect on the detector from radioactivity inherent in the detector parts themselves. From this standpoint, there is no single source or beam, but rather a collection of sources with potentially complicated spatial extent. LUXSim is a simulation framework used by the LUX collaboration that takes a component-centric approach to event generation and recording. A new set of classes allows for multiple radioactive sources to be set within any number of components at run time, with the entire collection of sources handled within a single simulation run. Various levels of information can also be recorded from the individual components, with these record levels also being set at runtime. This flexibility in both source generation and information recording is possible without the need to recompile, reducing the complexity of code management and the proliferation of versions. Within the code itself, casting geometry objects within this new set of classes rather than as the default Geant4 classes automatically extends this flexibility to every individual component. No additional work is required on the part of the developer, reducing development time and increasing confidence in the results. We describe the guiding principles behind LUXSim, detail some of its unique classes and methods, and give examples of usage. * Corresponding author, [email protected]: 45 pages, 15 figure