Mesoscale simulations of organized convection: importance of convective equilibrium

The validity of convective parametrization breaks down at the resolution of mesoscale models, and the success of parametrized versus explicit treatments of convection is likely to depend on the large-scale environment. In this paper we examine the hypothesis that a key feature determining the sensitivity to the environment is whether the forcing of convection is sufficiently homogeneous and slowly varying that the convection can be considered to be in equilibrium. Two case studies of mesoscale convective systems over the UK, one where equilibrium conditions are expected and one where equilibrium is unlikely, are simulated using a mesoscale forecasting model. The time evolution of area-average convective available potential energy and the time evolution and magnitude of the timescale of convective adjustment are consistent with the hypothesis of equilibrium for case 1 and non-equilibrium for case 2. For each case, three experiments are performed with different partitionings between parametrized and explicit convection: fully parametrized convection, fully explicit convection and a simulation with significant amounts of both. In the equilibrium case, bulk properties of the convection such as area-integrated rain rates are insensitive to the treatment of convection. However, the detailed structure of the precipitation field changes; the simulation with parametrized convection behaves well and produces a smooth field that follows the forcing region, and the simulation with explicit convection has a small number of localized intense regions of precipitation that track with the mid-levelflow. For the non-equilibrium case, bulk properties of the convection such as area-integrated rain rates are sensitive to the treatment of convection. The simulation with explicit convection behaves similarly to the equilibrium case with a few localized precipitation regions. In contrast, the cumulus parametrization fails dramatically and develops intense propagating bows of precipitation that were not observed. The simulations with both parametrized and explicit convection follow the pattern seen in the other experiments, with a transition over the duration of the run from parametrized to explicit precipitation. The impact of convection on the large-scaleflow, as measured by upper-level wind and potential-vorticity perturbations, is very sensitive to the partitioning of convection for both cases. © Royal Meteorological Society, 2006. Contributions by P. A. Clark and M. E. B. Gray are Crown Copyright.

The expected imprint of flux rope geometry on suprathermal electrons in magnetic clouds

Magnetic clouds are a subset of interplanetary coronal mass ejections characterized by a smooth rotation in the magnetic field direction, which is interpreted as a signature of a magnetic flux rope. Suprathermal electron observations indicate that one or both ends of a magnetic cloud typically remain connected to the Sun as it moves out through the heliosphere. With distance from the axis of the flux rope, out toward its edge, the magnetic field winds more tightly about the axis and electrons must traverse longer magnetic field lines to reach the same heliocentric distance. This increased time of flight allows greater pitch-angle scattering to occur, meaning suprathermal electron pitch-angle distributions should be systematically broader at the edges of the flux rope than at the axis. We model this effect with an analytical magnetic flux rope model and a numerical scheme for suprathermal electron pitch-angle scattering and find that the signature of a magnetic flux rope should be observable with the typical pitch-angle resolution of suprathermal electron data provided ACE's SWEPAM instrument. Evidence of this signature in the observations, however, is weak, possibly because reconnection of magnetic fields within the flux rope acts to intermix flux tubes.

Fourier transform infrared spectra of H2CS and D2CS

Infrared spectra of thoformaldehyde, H2CS and D2CS, were observed in the gas phase at a resolution of better than 0.1 cm−1 from 4000 to 400 cm−1 using a Nicolet FTIR system. Vibrational band origins and rotational constants were determined for ν2, ν3, ν4, and ν6 of H2CS and for ν1, ν2, ν3, ν4, and ν6 of D2CS. The ν3, ν4, and ν6 bands of H2CS were analyzed as a set of three Coriolis interacting bands, and three Coriolis constants were determined; similarly the ν4 and ν6 bands of D2CS were analyzed as a pair of interacting bands and one Coriolis constant was determined. A general harmonic force field was determined, without constraints, to fit the vibrational wavenumbers, Coriolis constants, and centrifugal distortion constants. A zero-point (rz) structure was determined from the ground-state rotational constants, and the equilibrium (re) bond lengths were estimated.

The infrared vibration-rotation spectrum of trans and cis nitrous acid

Infrared spectra of the trans and the cis isomers of nitrous acid, both HONO and DONO, have been observed in the gas phase using a Fourier transform interferometer with a resolution of about 0.05 cm−1 from 4000 to 500 cm−1. Rotational analyses are reported on eleven of the fundamentals and some overtones.

The ν2, 2ν2, 3ν2, ν4 and ν2+ν4 bands of 15NH3

The ir absorption of gaseous 15NH3 between 510 and 3040 cm−1 was recorded with a resolution of 0.06 cm−1. The ν2, 2ν2, 3ν2, ν4, and ν2 + ν4 bands were measured and analyzed on the basis of the vibration-rotation Hamiltonian developed by V. Špirko, J. M. R. Stone, and D. Papoušek (J. Mol. Spectrosc. 60, 159–178 (1976)). A set of effective molecular parameters for the ν2 = 1, 2, 3 states was derived, which reproduced the transition frequencies within the accuracy of the experimental measurements. For ν4 and ν2 + ν4 bands the standard deviation of the calculated spectrum is about four times larger than the measurements accuracy: a similar result was found for ν4 in 14NH3 by Š. Urban et al. (J. Mol. Spectrosc. 79, 455–495 (1980)). This result suggests that the present treatment takes into account only the most significant part of the rovibration interaction in the doubly degenerate vibrational states of ammonia.

Vibration-rotation spectra and the harmonic force field of HOCl

Vibration-rotation spectra of HOCl have been measured at a resolution of 0.05 cm−1 to determine vibration rotation constants, and 35–37 Cl isotope shifts in the vibration frequencies. The spectrum of DOCl has also been recorded, and a preliminary analysis for the band origins has been made. The vibrational frequency data and centrifugal distortion constants have been used to determine the harmonic force field in a least-squares refinement; the force field obtained also gives a good fit to data on the vibrational contributions to the inertial defect. The equilibrium rotational constants of HOCl have been obtained, and an equilibrium structure has been estimated.

Second order Coriolis resonance in the v2, v5 Raman bands of CH3F

The vibration-rotation Raman spectrum of the ν2 and ν5 fundamentals of CH3F is reported, from 1320 to 1640 cm−1, with a resolution of about 0.3 cm−1. The Coriolis resonance between the two bands leads to many perturbation-allowed transitions. Where the resonance is still sufficiently weak that the quantum number K′ retains its meaning, perturbation-allowed transitions are observed for all values of ΔK from +4 to −4; in regions of strong resonance, however, we can only say that the observed transitions obey the selection rule Δ(k−l) = 0 or ±3. The spectrum has been analyzed by band contour simulation using a computer program based on exact diagonalization of the Hamiltonian within the ν2, ν5 vibrational levels, and improved vibration-rotation constants for these bands are reported. The relative magnitudes and relative sings of polarizability derivatives involved in these vibrations are also reported.

The infra-red spectra of silyl fluoride and silyl fluoride-d3

Infra-red spectra have been recorded for silyl fluoride and silyl fluoride-d3 at a resolution of circa 0·3 cm-1. Rotational structure has been observed for parallel fundamentals in both molecules, and for all perpendicular fundamentals. In both SiH3F and SiD3F the A1 and E species deformation modes interact strongly via a Coriolis perturbation; this has been analysed, and the band origin of v5 for SiH3F is reassigned. A hybrid-orbital force field based on the experimental data is also reported.

The infrared spectrum of silicon difluoride

The infrared spectrum of the stretching fundamentals of SiF2 has been obtained at a resolution of ≈ 0.1 cm−1 using a FTIR spectrometer. The spectrum has been analysed using computer simulation based on a coupled hamiltonian for v1 and v3, giving v1 = 855.01 cm−1 and v3 = 870.40 cm−1. The relative magnitude and sign of the vibrational transition moments has been determined from the ξC13 Coriolis coupling.

Vibrational Renner-Teller effects in the infrared spectrum of carbonsuboxide

The infrared spectrum of carbon suboxide has been recorded with a resolution of 0•01cm-1 from 400 to 700 cm-1. The region from 530 to 570 cm-1 shows intense absorption due to the v6(Πu) band system, of which the fundamental band only has been assigned and analysed, giving v6=540•221 cm-1. The region 590 to 660 cm-1 shows weaker absorption due to the v5(Πg) band system appearing in combination with odd quanta of the v7(Πu) fundamental at 18 cm-1. The v5 + v7 band and several hot bands have been assigned and analysed, and the effective v7 bending potential in the v5 state has been deduced. This potential shows a splitting as the large amplitude bending coordinate q7 is displaced due to interaction between v5 and v7 analogous to the Renner-Teller effect in electronic spectroscopy. This splitting is about 4 cm-1 for the classical turning points in q7 and the mean q7 bending potential is closely similar to that in the ground state.

The infrared spectrum, equilibrium structure and harmonic and anharmonic force field of thioborine, HBS

Infrared spectra of the two stretching fundamentals of both HBS and DBS have been observed, using a continuous flow system through a multiple reflection long path cell at a pressure around 1 Torr and a Nicolet Fourier Transform spectrometer with a resolution of about 0•1 cm-1. The v3 BS stretching fundamental of DBS, near 1140 cm-1, is observed in strong Fermi resonance with the overtone of the bend 2v2. The bending fundamental v2 has not been observed and must be a very weak band. The analysis of the results in conjunction with earlier work gives the equilibrium structure (re(BH) = 1•1698(12) , re(BS) = 1•5978(3) ) and the harmonic and anharmonic force field.

Simultaneous analysis of v1, v4, 2v2, v2+v5, and 2v5 bands of 12CH3F

The Fourier-transform spectrum of CH3F from 2800 to 3100 cm−1, obtained by Guelachvili in Orsay at a resolution of about 0.003 cm−1, was analyzed. The effective Hamiltonian used contained all symmetry allowed interactions up to second order in the Amat-Nielsen classification, together with selected third-order terms, amongst the set of nine vibrational basis functions represented by the states ν1(A1), ν4(E), 2ν2(A1), ν2 + ν5(E), 2ν50(A1), and 2ν5±2(E). A number of strong Fermi and Coriolis resonances are involved. The vibrational Hamiltonian matrix was not factorized beyond the requirements of symmetry. A total of 59 molecular parameters were refined in a simultaneous least-squares analysis to over 1500 upper-state energy levels for J ≤ 20 with a standard deviation of 0.013 cm−1. Although the standard deviation remains an order of magnitude greater than the precision of the measurements, this work breaks new ground in the simultaneous analysis of interacting symmetric top vibrational levels, in terms of the number of interacting vibrational states and the number of parameters in the Hamiltonian.

The infrared spectrum of the ν2 and ν3 bands of H16OF, H18OF, and D16OF

Fourier transform IR spectra in the ν2 and ν3 regions between 800 and 1500 cm−1 have been measured of H16OF with a resolution of 0.007 cm−1 and of H18OF and DOF with a resolution of 0.040 cm−1. Ground state constants have been improved for H16OF and have been obtained for the first time for H18OF. Parameters of the v2 = 1 and v3 = 1 excited states have been determined from rovibrational analyses of ca. 1000 ν2/ν3 lines which were fitted with σ 0.36, 4.5, and 7.6 × 10−3 cm−1 for H16OF, H18OF, and D16OF, respectively. Band centers of ν2/ν3 are 1353.40466(5)/889.07974(6), 1350.3976(5)/862.2967(7), and 1002.0083(9)/891.0014(15) cm−1, respectively, for the three isotopic species. While ν2 and ν3 are sufficiently separated in HOF to be treated independently, a Coriolis resonance is evident in DOF, the interaction constant ξ23c = 0.19073(16) cm−1 being in agreement with the prediction from the harmonic force field.

The taxonomic status of pest species of Coptotermes in Southeast Asia: Resolving the paradox in the pest status of the termites, Coptotermes gestroi, C-havilandi and C-travians (Isoptera : Rhinotermitidae)

The taxonomic status of Coptotermes gestroi (Wasmann), C. havilandi Holmgren, C. travians (Haviland) and C. borneensis Oshima (Isoptera: Rhinotermitidae) is revised. The apparent discrepancy between the reported importance of C. havitandi in countries to which it has been introduced and the region from which it originated is shown to be due to misidentification and taxonomic confusion between C. travians, C. havilandi and C. gestroi. Based on an examination of specimens from Southeast Asia, two species are recognized, namely C. gestroi and C. travians. Coptotermes havilandi, described from imagos, is shown to be the same species as C. gestro described earlier from the soldier caste, and is designated a junior synonym. Coptotermes gestroi occurs from Assam through Burma and Thailand to Malaysia and the Indonesian archipelago, and has been introduced into other geographic regions, including parts of North and South America and the Caribbean. It is frequently found damaging wood in buildings, and is often intercepted outside its range in cargo onboard ships and sailing vessels, which is a likely mechanism for its spread to new geographical areas. Coptotermes gestroi has been misidentified in much literature as C. travians. Conversely, C. travians has been misidentified in recent literature in Peninsular Malaysia as C. havilandi and was redescribed from Borneo as C. borneensis, which is here designated a junior synonym of C. travians. It has a known distribution from Peninsular Malaysia to Borneo, and has not been found infesting wood in buildings. It is envisaged that the resolution of this taxonomic problem will enable the deployment of common pest management strategies for C. gestro the primary pest species of Coptotermes originating from Southeast Asia.

Crystal structure of a monomeric form of SARS-CoV endonuclease nsp15 suggests a role for hexamerization as an allosteric switch

Mature nonstructural protein-15 (nsp15) from the severe acute respiratory syndrome coronavirus (SARS-CoV) contains a novel uridylate-specific Mn2+-dependent endoribonuclease (NendoU). Structure studies of the full-length form of the obligate hexameric enzyme from two CoVs, SARS-CoV and murine hepatitis virus, and its monomeric homologue, XendoU from Xenopus laevis, combined with mutagenesis studies have implicated several residues in enzymatic activity and the N-terminal domain as the major determinant of hexamerization. However, the tight link between hexamerization and enzyme activity in NendoUs has remained an enigma. Here, we report the structure of a trimmed, monomeric form of SARS-CoV nsp15 (residues 28 to 335) determined to a resolution of 2.9 A. The catalytic loop (residues 234 to 249) with its two reactive histidines (His 234 and His 249) is dramatically flipped by approximately 120 degrees into the active site cleft. Furthermore, the catalytic nucleophile Lys 289 points in a diametrically opposite direction, a consequence of an outward displacement of the supporting loop (residues 276 to 295). In the full-length hexameric forms, these two loops are packed against each other and are stabilized by intimate intersubunit interactions. Our results support the hypothesis that absence of an adjacent monomer due to deletion of the hexamerization domain is the most likely cause for disruption of the active site, offering a structural basis for why only the hexameric form of this enzyme is active.