libMesh : a C++ library for parallel adaptive mesh refinement/coarsening simulations

In this paper we describe the libMesh (http://libmesh.sourceforge.net) framework for parallel adaptive finite element applications. libMesh is an open-source software library that has been developed to facilitate serial and parallel simulation of multiscale, multiphysics applications using adaptive mesh refinement and coarsening strategies. The main software development is being carried out in the CFDLab (http://cfdlab.ae.utexas.edu) at the University of Texas, but as with other open-source software projects; contributions are being made elsewhere in the US and abroad. The main goals of this article are: (1) to provide a basic reference source that describes libMesh and the underlying philosophy and software design approach; (2) to give sufficient detail and references on the adaptive mesh refinement and coarsening (AMR/C) scheme for applications analysts and developers; and (3) to describe the parallel implementation and data structures with supporting discussion of domain decomposition, message passing, and details related to dynamic repartitioning for parallel AMR/C. Other aspects related to C++ programming paradigms, reusability for diverse applications, adaptive modeling, physics-independent error indicators, and similar concepts are briefly discussed. Finally, results from some applications using the library are presented and areas of future research are discussed.     

Selenium content of feeds and effect of dietary selenium on hair and blood serum.

A selenium depletion diet (.025 ppm selenium) was fed to two male Holstein calves for its effect on concentrations of selenium in serum. By 90 days, selenium in serum was depressed from .022 ppm to .013 ppm, and one of two calves had died of "possible white muscle disease." Repletion was rapid in that a diet containing .200 ppm selenium increased selenium in serum to .028 ppm within 2 wk. Dietary .280 ppm selenium increased it to .051 ppm in 1 wk. Eleven cows and eleven calves showed averages of .030 ppm in serum (range of .013 to .051 ppm) fed a diet of corn silage (.039 ppm) and supplement (.090 ppm). A sampling of feedstuffs showed a wide range of selenium among feedstuffs (.023 for corn cobs to 2.663 ppm for dried egg albumin) and a wide range within one type feedstuff (shelled corn, .017 to .219 ppm).     

Stability of Static Power Inverters and Synchronous Reluctance Multimotor Systems

Ten to 100 kVA multimotor variable frequency inverter systems are generally unstable over part of their frequency range. Experimental results from dozens of tests made with single and multimotors, and with several inverters varying in capacity and output impedance, are presented. Aberrations in output shaft angular velocity is the measured variable. Both gain and phase measurements are made while controlled excitation signals are applied to the inverter system. Practical stability criteria for synchronous motors are presented. A system model is presented in block diagram form. Correlation of theory with previously published synchronous reluctance motor analyses is achieved.     

RNA polymerase II transcription complex assembly in nuclear extracts

Variation in superovulatory responses in cattle may be related to the stage of follicular growth at the time of gonadotropin treatment. Waves of follicle growth are regulated by both follicle-stimulating hormone (FSH) and oestradiol. The objective of experiment 1 was to determine the dynamics of follicle wave emergence and the relationship with FSH and oestradiol concentrations, after treatment of heifers with oestradiol benzoate (ODB) in the presence of an intravaginal progesterone-releasing device (CIDR-B). Experiment 2 examined the superovulatory response, embryo yield and quality following treatment with porcine follicle-stimulating hormone (pFSH) at different times relative to ODB injection. In experiment 1, 28 beef heifers were treated with a CIDR for 9 days and allocated at random to one of four groups to receive either: (I) CIDR only, or 5 mg ODB given as a single intramuscular injection at (II) day 0 (d0); (III) day 1.5 (d1.5); or (IV) day 3 (d3) post CIDR insertion. Ovaries were examined using daily ultrasound and blood samples were collected twice daily for 11 days. In experiment 2, 96 heifers were treated with a CIDR and 5 mg ODB as in experiment 1, and were allocated using a 4 x 3 factorial design plan to a superovulation programme using three doses (400 IU; 600 IU; 800 IU) of pFSH. FSH was given for 4 days at 12-h intervals beginning 6.5 days after CIDR insertion. Heifers received prostaglandin analogue 12 h before CIDR removal and were inseminated (AI) at 48 and 60 h post CIDR withdrawal and embryos were recovered 7 days after AI. In experiment 1, the interval from CIDR insertion to follicle wave emergence (FWE) was longer (P < 0.05) in heifers treated with ODB at d1.5 (5.4 +/- 0.4 days) and d3 (5.1 +/- 0.6 days) compared to heifers treated with CIDR only (2.4 +/- 0.4 days). On the basis of time to proposed injection of pFSH heifers would have had follicle emergence 4.4, 2.3, 1.5 and 1.4 days prior to pFSH for groups I, II, III and IV, respectively. In experiment 2, heifers treated with ODB at d1.5 had a higher (P < 0.05) superovulatory response (18.2 +/- 1.7) than heifers treated at d3 (12.8 +/- 1.7), but superovulatory response in both groups did not differ (P > 0.05) from heifers treated at d0 (14.4 +/- 2.0) or with CIDR only (15.0 +/- 1.8). There were fewer (P < 0.05) freezable-grade embryos recovered from heifers treated with ODB at d0 (1.5 +/- 0.7) and d3 (2.1 +/- 0.5) compared to heifers treated at d1.5 (3.0 +/- 0.6) or in heifers treated with CIDR only (3.4 +/- 0.7). Increasing the dose of pFSH caused a linear increase in the superovulatory response (11.7 +/- 1.0, 15.8 +/- 1.4 and 18.0 +/- 1.9) and in the number of embryos recovered (5.8 +/- 0.9, 7.0 +/- 0.8 and 9.1 +/- 1.0) for 400 IU, 600 IU and 800 IU, respectively. In conclusion, heifers treated with ODB had wide variation in time to follicle wave emergence and there was not a consistent beneficial effect of pretreatment with ODB on embryo yield and quality following superovulation.     

Cross-Sectional Study of Macrodefects in MBE Dual-Band HgCdTe on CdZnTe

HgCdTe dual-band mid-wave infrared/long-wave infrared focal-plane arrays on CdZnTe are a key component in advanced electrooptic sensor applications. Molecular beam epitaxy (MBE) has been used successfully for growth of dual-band layers on larger CdZnTe substrates. However, the macrodefect density, which is known to reduce the pixel operability and its run-to-run variation, is larger when compared with layers grown on Si substrate. This paper reports the macrodefect density versus size signature of a well-optimized MBE dual-band growth and a cross-sectional study of a macrodefect that represents the most prevalent class using focused ion beam, scanning transmission electron microscopy, and energy-dispersive x-ray spectroscopy. The results show that the macrodefect originates from a void, which in turn is associated with a pit on the CdZnTe substrate.     

Large-Format HgCdTe Dual-Band Long-Wavelength Infrared Focal-Plane Arrays

Raytheon Vision Systems (RVS) continues to further its capability to deliver state-of-the-art high-performance, large-format, HgCdTe focal-plane arrays (FPAs) for dual-band long-wavelength infrared (L/LWIR) detection. Specific improvements have recently been implemented at RVS in molecular-beam epitaxy (MBE) growth and wafer fabrication and are reported in this paper. The aim of the improvements is to establish producible processes for 512 × 512 30-μm-unit-cell L/LWIR FPAs, which has resulted in: the growth of triple-layer heterojunction (TLHJ) HgCdTe back-to-back photodiode detector designs on 6 cm × 6 cm CdZnTe substrates with 300-K Fourier-transform infrared (FTIR) cutoff wavelength uniformity of ±0.1 μm across the entire wafer; demonstration of detector dark-current performance for the longer-wavelength detector band approaching that of single-color liquid-phase epitaxy (LPE) LWIR detectors; and uniform, high-operability, 512 × 512 30-μm-unit-cell FPA performance in both LWIR bands.     

HgCdTe Growth on 6 cm × 6 cm CdZnTe Substrates for Large-Format Dual-Band Infrared Focal-Plane Arrays

This paper describes molecular-beam epitaxy growth of mid-wavelength infrared (MWIR) and long-wavelength infrared (LWIR) dual-band device structures on large-area (6 cm × 6 cm) CdZnTe substrates. Wafer-level composition and defect mapping techniques were used to investigate the limiting mechanisms in improving the cutoff wavelength (λ _c) uniformity and reducing the defect density. Structural quality of epitaxial layers was monitored using etch pit density (EPD) measurements at various depths in the epitaxial layers. Finally, 640 × 480, 20-μm-pixel-pitch dual-band focal-plane arrays (FPAs) were fabricated to demonstrate the overall maturity of growth and fabrication processes of epitaxial layers. The MWIR/LWIR dual-band layers, at optimized growth conditions, show a λ _c variation of ±0.15 μm across a 6 cm × 6 cm CdZnTe substrate, a uniform low macrodefect density with an average of 1000 cm⁻², and an average EPD of 1.5 × 10⁵ cm⁻². FPAs fabricated using these layers show band 1 (MWIR) noise equivalent temperature difference (NETD) operability of 99.94% and band 2 (LWIR) NETD operability of 99.2%, which are among the highest reported to date.     

Impact of Tellurium Precipitates in CdZnTe Substrates on MBE HgCdTe Deposition

State-of-the-art (112)B CdZnTe substrates were examined for near-surface tellurium precipitate-related defects. The Te precipitate density was observed to be fairly uniform throughout the bulk of the wafer, including the near-surface region. After a molecular beam epitaxy (MBE) preparation etch, exposed Te precipitates, small pits, and bumps on the (112)B surface of the CdZnTe wafer were observed. From near-infrared and dark field microscopy, the bumps and small pits on the CdZnTe surface are associated with strings of Te precipitates. Raised bumps are Te precipitates near the surface of the (112)B CdZnTe where the MBE preparation etch has not yet exposed the Te precipitate(s). An exposed Te precipitate sticking above the etched CdZnTe surface plane occurs when the MBE preparation etch rapidly undercuts a Te precipitate. Shallow surface pits are formed when the Te precipitate is completely undercut from the surrounding (112)B surface plane. The Te precipitate that was previously located at the center of the pit is liberated by the MBE preparation etch process.     

Effectiveness of cationically modified cellulose polymers for dewatering algae

A method to flocculate algal cultures of Chlamydomonas reinhardtii using four different industrially produced polymers is presented. Starting with a 1 wt% stock polymer solution, flocculation times less than 60 min were observed for 0.1 to 0.6 g polymer per L of algae culture, while control samples took greater than 1400 min to flocculate. Cell counts showed that 99% of the cells were flocculated using the polymers compared to 73% for the control. Finally, the flocculation process was successful at both 5 and 40 mL batch sizes for one polymer; therefore, the method is efficient, effective and may be scalable.