Mean climate and transience in the tropics of the UGAMP GCM - sensitivity to convective parametrization

The sensitivity of the UK Universities Global Atmospheric Modelling Programme (UGAMP) General Circulation Model (UGCM) to two very different approaches to convective parametrization is described. Comparison is made between a Kuo scheme, which is constrained by large-scale moisture convergence, and a convective-adjustment scheme, which relaxes to observed thermodynamic states. Results from 360-day integrations with perpetual January conditions are used to describe the model's tropical time-mean climate and its variability. Both convection schemes give reasonable simulations of the time-mean climate, but the representation of the main modes of tropical variability is markedly different. The Kuo scheme has much weaker variance, confined to synoptic frequencies near 4 days, and a poor simulation of intraseasonal variability. In contrast, the convective-adjustment scheme has much more transient activity at all time-scales. The various aspects of the two schemes which might explain this difference are discussed. The particular closure on moisture convergence used in this version of the Kuo scheme is identified as being inappropriate.

How many facets are needed to represent the surface energy balance of an urban area?

We investigate the question of how many facets are needed to represent the energy balance of an urban area by developing simplified 3-, 2- and 1-facet versions of a 4-facet energy balance model of two-dimensional streets and buildings. The 3-facet model simplifies the 4-facet model by averaging over the canyon orientation, which results in similar net shortwave and longwave balances for both wall facets, but maintains the asymmetry in the heat fluxes within the street canyon. For the 2-facet model, on the assumption that the wall and road temperatures are equal, the road and wall facets can be combined mathematically into a single street-canyon facet with effective values of the heat transfer coefficient, albedo, emissivity and thermodynamic properties, without further approximation. The 1-facet model requires the additional assumption that the roof temperature is also equal to the road and wall temperatures. Idealised simulations show that the geometry and material properties of the walls and road lead to a large heat capacity of the combined street canyon, whereas the roof behaves like a flat surface with low heat capacity. This means that the magnitude of the diurnal temperature variation of the street-canyon facets are broadly similar and much smaller than the diurnal temperature variation of the roof facets. Consequently, the approximation that the street-canyon facets have similar temperatures is sound, and the road and walls can be combined into a single facet. The roof behaves very differently and a separate roof facet is required. Consequently, the 2-facet model performs similarly to the 4-facet model, while the 1-facet model does not. The models are compared with previously published observations collected in Mexico City. Although the 3- and 2-facet models perform better than the 1-facet model, the present models are unable to represent the phase of the sensible heat flux. This result is consistent with previous model comparisons, and we argue that this feature of the data cannot be produced by a single column model. We conclude that a 2-facet model is necessary, and for numerical weather prediction sufficient, to model an urban surface, and that this conclusion is robust and therefore applicable to more general geometries.

Water vapor variability in the tropics and its links to dynamics and precipitation

The distribution and variability of water vapor and its links with radiative cooling and latent heating via precipitation are crucial to understanding feedbacks and processes operating within the climate system. Column-integrated water vapor (CWV) and additional variables from the European Centre for Medium-Range Weather Forecasts (ECMWF) 40-year reanalysis (ERA40) are utilized to quantify the spatial and temporal variability in tropical water vapor over the period 1979–2001. The moisture variability is partitioned between dynamical and thermodynamic influences and compared with variations in precipitation provided by the Climate Prediction Center Merged Analysis of Precipitation (CMAP) and the Global Precipitation Climatology Project (GPCP). The spatial distribution of CWV is strongly determined by thermodynamic constraints. Spatial variability in CWV is dominated by changes in the large-scale dynamics, in particular associated with the El Niño–Southern Oscillation (ENSO). Trends in CWV are also dominated by dynamics rather than thermodynamics over the period considered. However, increases in CWV associated with changes in temperature are significant over the equatorial east Pacific when analyzing interannual variability and over the north and northwest Pacific when analyzing trends. Significant positive trends in CWV tend to predominate over the oceans while negative trends in CWV are found over equatorial Africa and Brazil. Links between changes in CWV and vertical motion fields are identified over these regions and also the equatorial Atlantic. However, trends in precipitation are generally incoherent and show little association with the CWV trends. This may in part reflect the inadequacies of the precipitation data sets and reanalysis products when analyzing decadal variability. Though the dynamic component of CWV is a major factor in determining precipitation variability in the tropics, in some regions/seasons the thermodynamic component cancels its effect on precipitation variability.

Modelling monsoons: understanding and predicting current and future behaviour

The global monsoon system is so varied and complex that understanding and predicting its diverse behaviour remains a challenge that will occupy modellers for many years to come. Despite the difficult task ahead, an improved monsoon modelling capability has been realized through the inclusion of more detailed physics of the climate system and higher resolution in our numerical models. Perhaps the most crucial improvement to date has been the development of coupled ocean-atmosphere models. From subseasonal to interdecadal time scales, only through the inclusion of air-sea interaction can the proper phasing and teleconnections of convection be attained with respect to sea surface temperature variations. Even then, the response to slow variations in remote forcings (e.g., El Niño—Southern Oscillation) does not result in a robust solution, as there are a host of competing modes of variability that must be represented, including those that appear to be chaotic. Understanding the links between monsoons and land surface processes is not as mature as that explored regarding air-sea interactions. A land surface forcing signal appears to dominate the onset of wet season rainfall over the North American monsoon region, though the relative role of ocean versus land forcing remains a topic of investigation in all the monsoon systems. Also, improved forecasts have been made during periods in which additional sounding observations are available for data assimilation. Thus, there is untapped predictability that can only be attained through the development of a more comprehensive observing system for all monsoon regions. Additionally, improved parameterizations - for example, of convection, cloud, radiation, and boundary layer schemes as well as land surface processes - are essential to realize the full potential of monsoon predictability. A more comprehensive assessment is needed of the impact of black carbon aerosols, which may modulate that of other anthropogenic greenhouse gases. Dynamical considerations require ever increased horizontal resolution (probably to 0.5 degree or higher) in order to resolve many monsoon features including, but not limited to, the Mei-Yu/Baiu sudden onset and withdrawal, low-level jet orientation and variability, and orographic forced rainfall. Under anthropogenic climate change many competing factors complicate making robust projections of monsoon changes. Absent aerosol effects, increased land-sea temperature contrast suggests strengthened monsoon circulation due to climate change. However, increased aerosol emissions will reflect more solar radiation back to space, which may temper or even reduce the strength of monsoon circulations compared to the present day. Precipitation may behave independently from the circulation under warming conditions in which an increased atmospheric moisture loading, based purely on thermodynamic considerations, could result in increased monsoon rainfall under climate change. The challenge to improve model parameterizations and include more complex processes and feedbacks pushes computing resources to their limit, thus requiring continuous upgrades of computational infrastructure to ensure progress in understanding and predicting current and future behaviour of monsoons.

A comparative method to evaluate and validate stochastic parametrizations

There is a growing interest in using stochastic parametrizations in numerical weather and climate prediction models. Previously, Palmer (2001) outlined the issues that give rise to the need for a stochastic parametrization and the forms such a parametrization could take. In this article a method is presented that uses a comparison between a standard-resolution version and a high-resolution version of the same model to gain information relevant for a stochastic parametrization in that model. A correction term that could be used in a stochastic parametrization is derived from the thermodynamic equations of both models. The origin of the components of this term is discussed. It is found that the component related to unresolved wave-wave interactions is important and can act to compensate for large parametrized tendencies. The correction term is not proportional to the parametrized tendency. Finally, it is explained how the correction term could be used to give information about the shape of the random distribution to be used in a stochastic parametrization. Copyright © 2009 Royal Meteorological Society

The cumulus-capped boundary layer. I: Modelling transports in the cloud layer

Scalar-flux budgets have been obtained from large-eddy simulations (LESs) of the cumulus-capped boundary layer. Parametrizations of the terms in the budgets are discussed, and two parametrizations for the transport term in the cloud layer are proposed. It is shown that these lead to two models for scalar transports by shallow cumulus convection. One is equivalent to the subsidence detrainment form of convective tendencies obtained from mass-flux parametrizations of cumulus convection. The second is a flux-gradient relationship that is similar in form to the non-local parametrizations of turbulent transports in the dry-convective boundary layer. Using the fluxes of liquid-water potential temperature and total water content from the LES, it is shown that both models are reasonable diagnostic relations between fluxes and the vertical gradients of the mean fields. The LESs used in this study are for steady-state convection and it is possible to treat the fluxes of conserved thermodynamic variables as independent, and ignore the effects of condensation. It is argued that a parametrization of cumulus transports in a model of the cumulus-capped boundary layer should also include an explicit representation of condensation. A simple parametrization of the liquid-water flux in terms of conserved variables is also derived.

Evaluation of the sea ice simulation in a new coupled atmosphere-ocean climate model (HadGEM1)

[ 1] A rapid increase in the variety, quality, and quantity of observations in polar regions is leading to a significant improvement in the understanding of sea ice dynamic and thermodynamic processes and their representation in global climate models. We assess the simulation of sea ice in the new Hadley Centre Global Environmental Model (HadGEM1) against the latest available observations. The HadGEM1 sea ice component uses elastic-viscous-plastic dynamics, multiple ice thickness categories, and zero-layer thermodynamics. The model evaluation is focused on the mean state of the key variables of ice concentration, thickness, velocity, and albedo. The model shows good agreement with observational data sets. The variability of the ice forced by the North Atlantic Oscillation is also found to agree with observations.

Redefinition of the kilogram, ampere, kelvin and mole: a proposed approach to implementing CIPM recommendation 1 (CI-2005)

The International System of Units (SI) is founded on seven base units, the metre, kilogram, second, ampere, kelvin, mole and candela corresponding to the seven base quantities of length, mass, time, electric current, thermodynamic temperature, amount of substance and luminous intensity. At its 94th meeting in October 2005, the International Committee for Weights and Measures (CIPM) adopted a recommendation on preparative steps towards redefining the kilogram, ampere, kelvin and mole so that these units are linked to exactly known values of fundamental constants. We propose here that these four base units should be given new definitions linking them to exactly defined values of the Planck constant h, elementary charge e, Boltzmann constant k and Avogadro constant NA, respectively. This would mean that six of the seven base units of the SI would be defined in terms of true invariants of nature. In addition, not only would these four fundamental constants have exactly defined values but also the uncertainties of many of the other fundamental constants of physics would be either eliminated or appreciably reduced. In this paper we present the background and discuss the merits of these proposed changes, and we also present possible wordings for the four new definitions. We also suggest a novel way to define the entire SI explicitly using such definitions without making any distinction between base units and derived units. We list a number of key points that should be addressed when the new definitions are adopted by the General Conference on Weights and Measures (CGPM), possibly by the 24th CGPM in 2011, and we discuss the implications of these changes for other aspects of metrology.

Correlations between microphysical properties of large-scale semi-transparent cirrus and the state of the atmosphere

By making use of TOVS Path-B satellite retrievals and ECMWF reanalyses, correlations between bulk microphysical properties of large-scale semi-transparent cirrus (visible optical thickness between 0.7 and 3.8) and thermodynamic and dynamic properties of the surrounding atmosphere have been studied on a global scale. These clouds constitute about half of all high clouds. The global averages (from 60°N to 60°S) of mean ice crystal diameter, De, and ice water path (IWP) of these clouds are 55 μm and 30 g m−2, respectively. IWP of these cirrus is slightly increasing with cloud-top temperature, whereas De of cold cirrus does not depend on this parameter. Correlations between De and IWp of large-scale cirrus seem to be different in the midlatitudes and in the tropics. However, we observe in general stronger correlations between De and IWP and atmospheric humidity and winds deduced from the ECMWF reanalyses: De and IWP increase both with increasing atmospheric water vapour. There is also a good distinction between different dynamical situations: In humid situations, IWP is on average about 10 gm−2 larger in regions with strong large-scale vertical updraft only that in regions with strong large-scale horizontal winds only, whereas the mean De of cold large-scale cirrus decreases by about 10 μm if both strong large-scale updraft and horizontal winds are present.

ASYM20: a program for force constant and normal coordinate calculations, with a critical review of the theory involved

The theory of harmonic force constant refinement calculations is reviewed, and a general-purpose program for force constant and normal coordinate calculations is described. The program, called ASYM20. is available through Quantum Chemistry Program Exchange. It will work on molecules of any symmetry containing up to 20 atoms and will produce results on a series of isotopomers as desired. The vibrational secular equations are solved in either nonredundant valence internal coordinates or symmetry coordinates. As well as calculating the (harmonic) vibrational wavenumbers and normal coordinates, the program will calculate centrifugal distortion constants, Coriolis zeta constants, harmonic contributions to the α′s. root-mean-square amplitudes of vibration, and other quantities related to gas electron-diffraction studies and thermodynamic properties. The program will work in either a predict mode, in which it calculates results from an input force field, or in a refine mode, in which it refines an input force field by least squares to fit observed data on the quantities mentioned above. Predicate values of the force constants may be included in the data set for a least-squares refinement. The program is written in FORTRAN for use on a PC or a mainframe computer. Operation is mainly controlled by steering indices in the input data file, but some interactive control is also implemented.

Resolving the energy paradox of chaperone/usher-mediated fibre assembly

Periplasmic chaperone/usher machineries are used for assembly of filamentous adhesion organelles of Gram-negative pathogens in a process that has been suggested to be driven by folding energy. Structures of mutant chaperone-subunit complexes revealed a final folding transition (condensation of the subunit hydrophobic core) on the release of organelle subunit from the chaperone-subunit pre-assembly complex and incorporation into the final fibre structure. However, in view of the large interface between chaperone and subunit in the pre-assembly complex and the reported stability of this complex, it is difficult to understand how final folding could release sufficient energy to drive assembly. In the present paper, we show the X-ray structure for a native chaperone-fibre complex that, together with thermodynamic data, shows that the final folding step is indeed an essential component of the assembly process. We show that completion of the hydrophobic core and incorporation into the fibre results in an exceptionally stable module, whereas the chaperone-subunit preassembly complex is greatly destabilized by the high-energy conformation of the bound subunit. This difference in stabilities creates a free energy potential that drives fibre formation.

Copper complexes of new benzodioxotetraaza macrocycles with potential applications in nuclear medicine

Two novel benzodioxotetraaza macrocycles [2,9-dioxo-1,4,7,10-tetraazabicyclo[10.4.0]1,11-hexadeca-1(11),13,15-triene (H(2)L1) and 2,10-dioxo-1,4,8,11-tetraazabicyclo[11.4.0]1,12-heptadeca-1(12),14,16-triene (H(2)L2)] were synthesized by a [1 + 1] crablike cyclization. The protonation constants of both ligands were determined by H-1 NMR titration and by potentiometry at 25.0 degrees C in 0.10 M ionic strength in KNO3. The latter method was also used to ascertain the stability constants of their copper(II) complexes. These studies showed that the CuL1 complex has a much lower thermodynamic stability than the CuL2, and the H(2)L2 displays an excellent affinity for copper(II), due to the good fit of copper(II) into its cavity. The copper complexes of the novel ligands were characterized by electronic spectroscopy in solution and by crystal X-ray diffraction. These studies indicated that the copper center in the CuL1 complex adopts a square-pyramidal geometry with the four nitrogen atoms of the macrocycle forming the equatorial plane and a water molecule at axial position, and the copper in the CuL2 complex is square-planar. Several labeling conditions were tested, and only H(2)L2 could be labeled with Cu-67 efficiently (> 98%) in mild conditions (39 degrees C, 15 min) to provide a slightly hydrophilic radioligand (log D = -0.19 +/- 0.03 at pH 7.4). The in vitro stability was studied in the presence of different buffers or with an excess of diethylenetriamine-pentaethanoic acid. Very high stability was shown under these conditions for over 5 days. The incubation of the radiocopper complex in human serum showed 6% protein binding.

LDA or GGA? A combined experimental inelastic neutron scattering and ab initio lattice dynamics study of alkali metal hydrides

In a previous work, we carried out inelastic neutron scattering (INS) spectroscopy experiments and preliminary first principles calculations on alkali metal hydrides. The complete series of alkali metal hydrides, LiH, NaH, KH, RbH and CsH was measured in the high-resolution TOSCA INS spectrometer at ISIS. Here, we present the results of ab initio electronic structure calculations of the properties of the alkali metal hydrides using both the local density approximation (LDA) and the generalized gradient approximation (GGA), using the Perdew–Burke–Ernzerhof (PBE) parameterization. Properties calculated were lattice parameters, bulk moduli, dielectric constants, effective charges, electronic densities and inelastic neutron scattering (INS) spectra. We took advantage of the currently available computer power to use full lattice dynamics theory to calculate thermodynamic properties for these materials. For the alkali metal hydrides (LiH, NaH, KH, RbH and CsH) using lattice dynamics, we found that the INS spectra calculated using LDA agreed better with the experimental data than the spectra calculated using GGA. Both zero-point effects and thermal contributions to free energies had an important effect on INS and several thermodynamic properties.

First 5f-element complexes with the tetradentate BTBP ligand. Synthesis and crystal structure of uranyl(VI) compounds with CyMe4BTBP

Treatment of [UO2(OTf)(2)] or [UO2I2(thf)(3)] with 1 equiv. of CyMe4BTBP in anhydrous acetonitrile led to the formation of [UO2(CyMe4BTBP)(OTf)(2)] (1) and [UO2(CyMe4BTBP)I-2] (2) which crystallized as the cationic forms [UO2(CyMe4BTBP)(py)][OTf](2) (3) and [UO2I(CyMe4BTBP)][I] (4) in pyridine and acetonitrile, respectively. These compounds are unique examples of structurally characterized actinide complexes with a BTBP molecule; this ligand adopts a planar conformation in the equatorial plane of the {UO2}(2+) ion. In pyridine, 1 is dissociated into [UO2(OTf)(2)(PY)(3)] and free CyMe4BTBP and the thermodynamic parameters (K, Delta H, Delta S) of this equilibrium have been determined by H-1 NMR spectroscopy. The ethoxide derivative [UO2(OEt)(CyMe4BTBP)][OTf] (5) crystallized from a solution of I in a mixture of ethanol and acetone under air, and the dinuclear mu-oxo complex [{UO2(CyMe4BTBP)}(2)(mu-O)][I](2) (6) was obtained from [UO2I(thf)(2.7)] and CyMe4BTBP. The crystal structures of 6 and of the analogous derivatives [{UO2(py)(4)}(2)(mu-O)][I](2)(7) and [{UO2(TPTZ)(py)}(2)(mu-O)][I-3](2)(8) exhibit a flexible [{UO2}-O-{UO2}](2+) moiety.

A pressure-jump time-resolved x-ray diffraction study of cubic-cubic transition kinetics in monoolein

In the past two decades, the geometric pathways involved in the transformations between inverse bicontinuous cubic phases in amphiphilic systems have been extensively theoretically modeled. However, little experimental data exists on the cubic-cubic transformation in pure lipid systems. We have used pressure-jump time-resolved X-ray diffraction to investigate the transition between the gyroid Q(II)(G) and double-diamond Q(II)(D) phases in mixtures of 1-monoolein in 30 wt% water. We find for this system that the cubic-cubic transition occurs without any detectable intermediate structures. In addition, we have determined the kinetics of the transition, in both the forward and reverse directions, as a function of pressure-jump amplitude, temperature, and water content. A recently developed model allows (at least in principle) the calculation of the activation energy for lipid phase transitions from such data. The analysis is applicable only if kinetic reproducibility is achieved, at least within one sample, and achievement of such kinetic reproducibility is shown here, by carrying out prolonged pressure-cycling. The rate of transformation shows clear and consistent trends with pressure-jump amplitude, temperature, and water content, all of which are shown to be in agreement with the effect of the shift in the position of the cubic-cubic phase boundary following a change in the thermodynamic parameters.