Gap Air Research Articles

426 Modeling a Flood-Freeze Situation of a Cranberry Bog using Finite Element Analysis

It is commonplace in Wisconsin for cranberry growers to flood their beds to form thick ice during winter to protect the uprights from dangerously low winter air temperatures. However, the specifics of ice thickness and zone temperature within and below the ice vs. surface air temperature have not been studied. We have developed several models using finite element analysis, a process by which a complex system is divided into finite segments and analyzed individually. All pieces are then recombined into the complete system so a comprehensive picture of the activity of the freezing cranberry bed may be visualized. It was determined that cold surface air temperatures of -25 °C and thin ice of 15 cm, soil and gap air temperatures do not drop lower then -5 °C, which is congruent with data collected from the field. Models on sand beds and peat beds did not show enough difference to be of concern. Temperatures within the ice, where the uprights would be encased, reached -15 °C under the cold air regime, which has been proven to be well within the survival range of the dormant buds.

The energetics of small internal loops in RNA

The energetics of small internal loops are important for prediction of RNA secondary and tertiary structure, selection of drug target sites, and understanding RNA structure-function relationships. Hydrogen bonding, base stacking, electrostatic interactions, backbone distortion, and base-pair size compatibility all contribute to the energetics of small internal loops. Thus, the sequence dependence of these energetics are idiosyncratic. Current approximations for predicting the free energies of internal loops consider size, asymmetry, closing base pairs, and the potential to form GA, GG, or UU pairs. The database of known three-dimensional structures allows for comparison with the models used for predicting stability from sequence.

Structure of the 3'-hairpin of the TYMV pseudoknot: preformation in RNA folding.

The solution structure of an RNA-hairpin present in the pseudoknot, which is found at the 3'-terminus of turnip yellow mosaic virus genomic RNA, has been solved by nuclear magnetic resonance spectroscopy. The loop, which contains the sequence 5'-GGGUCA-3', was found to be highly structured and, contrary to expectations, does not attain its stability through GA or GC base pair formation but by triple interactions between the tilted adenosine and the minor groove sides of the first two guanosines. Interestingly, a very similar conformation was found for the cognate pseudoknot, implying that the 3'-hairpin is preformed for folding into a pseudoknotted structure. These findings suggest a mechanism of 'predetermined-fit' as a principle in RNA folding.

15N NMR of RNA Fragments Containing Specifically Labeled Tandem GA Pairs

15N and 13C NMR have been used to study three specifically labeled RNA fragments that include two tandem GU wobble pairs of different thermal stability and a tetraloop GU pair. The data are also compared to earlier 15N NMR work on an isolated, intrahelical GU pair. The results provide qualitative information on the relative contributions by stacking and hydrogen bonding to chemical shift changes at specific sites in a variety of GU pairs. Chemical shifts for the unpaired guanine amino groups in the isolated and both tandem wobble pairs are all significantly upfield of corresponding paired GC aminos. The guanine amino of the tetraloop is further downfield, as expected for a base paired hydrogen bond donor. Thus, 15N NMR can be diagnostic for the presence of base−base pairing in RNA. Chemical shifts of the guanine N1 in all four GU pairs show significant shielding effects, particularly those of the more stable tandem GU pair. Similar shielding is also seen in the 13C data for the C2 atom of the GU wobble pa...

Estimation of the Amount of Water Removed by Gap and Atomization Air Streams During Pelletization in a Rotary Processor

ABSTRACTThe purpose of this study was to estimate the amount of water removed by the gap and atomization air streams during pelletization by the wet granulation technique in a rotary processor and to test the hypothesis that the influence of the water addition rate on the pellet size (1,7) mainly originates from differences in the amount of water removed by these air streams. Estimations from flow, temperature, and relative humidity measurements of the air streams, and estimations from moisture content measurements, indicated that approximately 3.6 g of waterImin was removed during spheronization. The estimations from the air streams' characteristics obtained for the water loss during the water addition phase (2.6 g/min) reflected the water removal during the later stages and did not reflect the overall rate of water removal during the total water addition phase as estimated from moisture content measurements (2.0 g/min). This was attributed to the fact that estimations from the air streams' characteristics could not take into account the early stages of the water addition phase. In these early stages, the amount of water removed was very limited. Using the foregoing estimations, differences in amount of water removed by the air streams could be compensated by adding more water when the water addition rate was decreased. This resulted in similar pellet sizes (geometric mean diameter of 800–850 μm) using different water addition rates. Thus, the hypothesis that the major influence of the water addition rate on the pellet size mainly originates from differences in the amount of water removed by the gap and atomization air streams was confirmed.

Reconstructed-structure-dependent surface reaction in metal-organic molecular beam epitaxy of GaAs

The initial stage of the surface reaction during metalorganic molecular beam epitaxy (MOMBE) is discussed as a function of relaxed or reconstructed GaAs surface structure on the basis of the scattering of continuous and pulsed trimethylgallium (TMG) beams from structure-controlled GaAs(100), (110) and (111)B surfaces. The results of TMG scattering are interpreted within the framework of the precursor-mediated adsorption mechanism, where TMG molecules are trapped in the precursor states in the initial stage of the scattering. In the case of the scattering from highly stabilized GaAs surfaces, we find that TMG molecules are desorbed after a long surface residence time without decomposition, while, in the case of the scattering from less stabilized surfaces, the trapped TMG molecules are efficiently chemisorbed with dissociation. The surface structure dependence of the precursor state suggests that the precursor states are attributed to the charge distribution in the relaxed or reconstructed surface. This is supported by the result that the surface residence time on the GaAs(100)-(2 × 4) surface decreases when metallic Ga is deposited onto the surface, resulting in the decrease in the number of AsGa pairs generating electric field.

Relation between the Metastability and the Configuration of Iron-Acceptor Pairs in Silicon

To determine the energy differences between the first and second nearest-neighbor iron (Fe)-acceptor pairs in silicon, the generation and annihilation processes of these pairs were investigated by means of electron spin resonance (ESR). Isochronal annealing of the Fe-doped specimen revealed that the concentrations of iron-group III acceptor pairs attained maxima at about 100° C, and then decreased with increasing temperature. An isothermal annealing experiment showed that the concentrations of these pairs increased monotonically with annealing and approached constant values after a long duration of annealing. The temperature dependence of the ratio of the concentrations of these two atomic configurations at equilibrium showed that the pair with trigonal symmetry was stable and that with orthorhombic symmetry was metastable in the cases of Fe–Al and Fe–Ga pairs, in contrast, the pair with trigonal symmetry was metastable and that with orthorhombic symmetry was stable in the case of Fe–In pairs. The energy differences in the two configurations of these pairs were 0.07 eV, 0.03 eV and 0.09 eV for Fe–Al, Fe–Ga and Fe–In pairs, respectively.

Partial Structural Functions of Liquid Bi30Ga70Alloy Estimated from the Anomalous X-Ray Scattering Measurement in Asymmetrical Reflection Geometry with Synchrotron Radiation

An apparatus for controlling the glancing angle of incident beam from a synchrotron source has been newly built for structural studies of high temperature liquids by the anomalous X-ray scattering (AXS) method in the reflection mode. The usefulness and capability of this apparatus were demonstrated by obtaining the individual partial structural functions of the liquid Bi 30 Ga 70 alloy using the energies close to the Ga K and Bi L III absorption edges. The data processing for estimating three partials includes the intensity data obtained at the energy of 15.0 keV, which is far from both edges and the reverse Monte Carlo (RMC) simulation technique. The resultant partial structural function for Ga–Ga pairs was found to be rather similar to that of pure Ga. On the other hand, partial structural function for Bi–Bi pairs differs from the pure Bi case and the coexistence of more than two species is rather well-recognized in the Bi 30 Ga 70 liquid alloy.

The structure of an essential splicing element: stem loop IIa from yeast U2 snRNA.

Eukaryotic genes are usually transcribed as precursor mRNAs which are then spliced, removing introns to produce functional mRNAs. Splicing is performed by the spliceosome and provides an important level of post-translational control of gene expression. Stem loop IIa from U2 small nuclear (sn)RNA is required for the efficient association of the U2 small nuclear ribonuclear protein (snRNP) with the nascent spliceosome in yeast. Genetic analysis suggests that stem loop IIa is involved in RNA-protein interactions early in splicing, and it may also interact with other RNA sequences in U2. The sequence of loop IIa is well conserved, consistent with the idea that this loop is important for function. We have solved the structure of U2A, a 20-base analogue of stem loop IIa from Saccharomyces cerevisiae, using NMR and restrained molecular dynamics. In the process, we have demonstrated the efficacy of a new structure calculation protocol, torsion angle molecular dynamics. The structure that has emerged, which is consistent with the in vivo chemical protection data available for stem loop IIa in the context of intact U2 snRNA, contains a sheared GA pair followed by a U-turn in the loop. The U-turn conformation, which resembles the U-turns in tRNA anticodon loops, makes this stretch of U2 snRNA an obvious target for interactions with proteins and/or other RNA sequences. The phenotypes of many stem loop IIa mutants can be rationalized assuming that the U-turn conformation in the loop must be preserved for efficient splicing. This observation, combined with the phylogenetic conservation of its sequence, suggests that the conformation of the loop of stem loop IIa is essential for its function in pre-mRNA splicing.

High-energy electron emission from ion-bombarded surfaces of Ga, Ge, In and Sn

Intense, continuous distributions of kinetic emitted electrons, often with energies extending to greater than 100 eV, have been observed for Ga, Ge, In and Sn surfaces bombarded with keV Ar + ions. These broad distributions, which clearly are not associated with Auger excitation, can be understood in terms of a one-electron collisional-excitation model involving orbital interaction, promotion, and direct-to-continuum deexcitation. Possible pathways for electron promotion have been obtained for the above elements from detailed calculations of correlation diagrams which have been used to predict successfully the probability of collisional excitation and deep-level promotion. Element-specific differences observed in the kinetic emission spectra between the two pairs of elements, the Ga and Ge pair and the In and Sn pair (associated with collisional level-coupling and promotion processes), also have been interpreted from these correlation diagrams. We conclude that the high-energy, kinetic electron emission as well as the specific differences observed between the Ga and Ge pair and the In and Sn pair are consistent with this one-electron promotion/deexcitation model.

Ag films on [formula omitted]: from clean surfaces to atomic Ga structures

We prepare 150 nm thick epitaxial Ag buffer layers on Fe-precovered GaAs(001) at 380 K. Post-annealing at 570 K improves the morphology of the films, as observed by scanning tunneling microscopy (STM), without changing the chemical composition at the surface. The main type of defects are screw dislocations. Nevertheless we achieve a mean terrace width of 36 nm. At temperatures above 620 K, Ga atoms diffuse through the Ag buffer layer to the surface and form an overlayer. Depth profiles and quantitative analysis of X-ray photoemission data yield surface coverages of up to 0.3 ML and Ga concentrations within the Ag bulk of a few at%. The GaAs substrate acts as a source of Ga atoms even at temperatures much lower than the GaAs vacuum decomposition temperature of 890 K. STM images show that in some areas the overlayer consists of Ga tetramers. Their size and orientation are determined by the separation vector between next-nearest neighbour atoms of the Ag(001) substrate. In other areas the tetramers line up to form parallel rows of Ga pairs. This row structure is reflected in the low-energy electron diffraction (LEED) patterns as a (4√2 × √2)R45° superstructure. Based on STM and LEED data we propose a structure model with two Ga atoms per surface unit cell. Finally we predict a long-range interaction between rows and a relaxation of the GaGa separation within the rows.

An experimental study on three dimensional heat transfer characteristics of simulated electronic chips

Naphthalene sublimation technique is employed to investigate three dimensional heat transfer characteristics of the simulated electronic chips. Experiments are performed for a single chip and chip arrays. In case of a single chip, local heat transfer coefficients on four surfaces of the chip are measured for various gap sizes and air velocities. Dramatic change of local heat transfer is seen on each surface of the chip, and gap size between chip and base plate is found to affect heat transfer significantly. In case of chip arrays, heat transfer characteristics from two-dimensional array of rectangular modules and three-dimensional array of hexahedral modules are investigated. Chip location, gap between chip and base plate and streamwise chip without gap. Fully developed behavior is found from the third row, but it slightly depends on flow conditions. Local and average heat transfer coefficients of three-dimensional modules are a little bit greater than those of two-dimensional modules. The differences in magnitude decrease as the longitudinal chip spacing decreases.

Concerted integration of linear retroviral DNA by the avian sarcoma virus integrase in vitro: dependence on both long terminal repeat termini.

We have reconstituted integration reactions in vitro with specially designed donor DNAs, a supercoiled plasmid acceptor, purified bacterium-derived Rous sarcoma virus integrase (IN), and a host cell DNA-bending protein, HMG1. The duplex donor DNAs are approximately 300 deoxynucleotides in length and contain only 15 bp of the RSV U3 and U5 termini at the respective ends. The donor has blunt U3 and U5 termini which end with the sequence 5'CATT. Joining of the donor DNA to the acceptor DNA is detected by using a simple biochemical assay. Integration was found to be dependent on both U3 and U5 termini; mutations in either result in a significant decrease in the level of integration in vitro. Restriction digestion of the products is consistent with most integrants representing a concerted integration in which both long terminal repeat termini come from the same donor molecule. The U5 and U3 sequences in the substrate flank a supF tRNA gene, permitting biological selection of integrants. Many integrants have been sequenced, and have all of the hallmarks of authentic viral integration, including the removal of a terminal TT dinucleotide from each donor DNA end, and duplication of acceptor sequences at the integration site without introducing deletions into the acceptor. Target site selection in the acceptor plasmid was random except that the orientation of integrants selected was apparently influenced by supF transcription. Mutations which substituted the conserved CA dinucleotide with a GA pair led to a decreased rate of integration. In 2 of 14 mutant integrants sequenced, deoxynucleotides were deleted from either the U5 or U3 terminus. In one instance, an internal CA dinucleotide was used, which resulted in a 10-bp U5 donor deletion. In the other, an internal GA dinucleotide was used, which produced a 5-bp U3 donor deletion. Both of these integrants provide further evidence that concerted integration in this reconstituted system requires interactions between IN and the U3 and U5 termini from the same donor molecule.

Optical filters from photonic band gap air bridges

Surrounding waveguides by air reduces radiation losses so the air bridge geometry can produce optical filters with sharp transmission resonances and very wide stop bands.

Bistability of Si Ga−Si Ga pairs in MBE(001) δ-doped GaAs

Bistability of Si Ga−Si Ga pairs in MBE(001) δ-doped GaAs

The Role of Moisture and Gap Air Pressure in the Formation of Spherical Granules by Rotary Processing

Spheroids are usually produced by a multi-step extrusion-spheronization process. The single-step production of spheroids may be carried out in a rotoprocessor. The use of feed materials in powder form requires an adaptation of the spheronizer machinery. This study investigates the formation and growth of spheroids and the changes in the spheroid moisture content in a single-step agglomeration-spheronization method. There was a rapid increase in size and formfactor values when spheroids started to form and grow from the powder mix. Although there was a continual and considerable loss of moisture with time, this did not have an appreciable effect on spheroid size and shape after the spheroid formation stage as the spheroid structure had already been determined. Spheroid size increased with higher liquid spray rates. The use of higher gap air pressures resulted in a greater rate of moisture loss and the production of smaller spheroids.

Gallium vacancy related defects in silicon doped GaAs grown at low temperatures

Point defects and complexes in silicon doped GaAs grown at low temperatures were investigated. Large differences between the donor and carrier concentrations imply that the crystals contain high concentrations of compensating defects. The detection of Si Ga V Ga pairs confirms the expectation that they are gallium vacancies and their concentration appears to be controlled by the Fermi level or silicon concentration. The lattice expansion of the low temperature GaAs is related to the concentration of As Ga antisite related defects which do not appear to affect significantly the electrical properties of the material. The annealing behaviour may be explained by the nucleation of Si clustering by V Ga related defects.

Step-Controlled Epitaxial Growth of 4H-SiC and Doping of Ga as a Blue Luminescent Center

Homoepitaxial growth of 4H-SiC could be achieved at 1500°C on off-oriented 4H-SiC{0001} substrates by means of a vapor phase epitaxial method. Grown layers showed specular smooth surfaces on both (0001)Si and (0001̄)C faces. Doping of Ga during crystal growth was carried out and photoluminescence of grown layers was studied. Bluish-violet photoluminescence due to donor(N)-acceptor(Ga) pair recombination and recombination of a free electron with a hole at a Ga acceptor was observed. The emission attributed to the latter recombination process became dominant at high temperatures above 100 K. The luminescence of Ga-doped 4H-SiC was not quenched up to temperatures as high as 150 K, whereas the luminescence intensity of Al-doped 6H-SiC and 4H-SiC started to decrease at 70 and 85 K, respectively.

Base pairing geometry in GA mismatches depends entirely on the neighboring sequence

We have synthesized nine self-complementary DNA oligomers containing different flanking sequences adjacent to a pair of contiguous GA mismatches, and have used high resolution nuclear magnetic resonance (n.m.r.) to investigate the GpA phosphodiester backbone conformation and mismatch pairing schemes in these duplexes. We found dramatic effects of the flanking base pair on the hydrogen bonding and backbone conformation, which appear to be coupled. Thus the G anti-A anti base pairing scheme in a N A GA T N sequence switches to a more stable sheared GA base pairing scheme in a N C GA G N or N T GA A N context, while no duplex is formed (or only GA bulges occur) when N A GA T N is changed to N N GA C N . Furthermore, the more stable sheared GA pairing in N Py GA Pu N sequences is associated with a B II rather than B I backbone conformation for the phosphodiester between the adjacent mismatched GA pairs. The overall stability of these adjacent GA mismatches as measured by imino proton n.m.r. studies is Py-GA-Pu > A-GA-T > G-GA-C.

Ga vacancy-assisted diffusion of Si in GaAs

A model for Si diffusion into GaAs based on the formation of Si+Ga-V−Ga pairs is developed. The model follows the formalism developed by M. E. Greiner and J. F. Gibbons [Appl. Phys. Lett. 44, 750 (1984)]. Using recently derived values for the Ga vacancy diffusivity, it is shown that the pair diffusion coefficient is approximately equal to three-quarters its value. The results of the model are demonstrated to be in good agreement with the Si diffusion data.