A Lagrangian model of air-mass photochemistry and mixing using a trajectory ensemble: the Cambridge Tropospheric Trajectory model of Chemistry And Transport (CiTTyCAT) version 4.2

A Lagrangian model of photochemistry and mixing is described (CiTTyCAT, stemming from the Cambridge Tropospheric Trajectory model of Chemistry And Transport), which is suitable for transport and chemistry studies throughout the troposphere. Over the last five years, the model has been developed in parallel at several different institutions and here those developments have been incorporated into one "community" model and documented for the first time. The key photochemical developments include a new scheme for biogenic volatile organic compounds and updated emissions schemes. The key physical development is to evolve composition following an ensemble of trajectories within neighbouring air-masses, including a simple scheme for mixing between them via an evolving "background profile", both within the boundary layer and free troposphere. The model runs along trajectories pre-calculated using winds and temperature from meteorological analyses. In addition, boundary layer height and precipitation rates, output from the analysis model, are interpolated to trajectory points and used as inputs to the mixing and wet deposition schemes. The model is most suitable in regimes when the effects of small-scale turbulent mixing are slow relative to advection by the resolved winds so that coherent air-masses form with distinct composition and strong gradients between them. Such air-masses can persist for many days while stretching, folding and thinning. Lagrangian models offer a useful framework for picking apart the processes of air-mass evolution over inter-continental distances, without being hindered by the numerical diffusion inherent to global Eulerian models. The model, including different box and trajectory modes, is described and some output for each of the modes is presented for evaluation. The model is available for download from a Subversion-controlled repository by contacting the corresponding authors.

Quantification of chemical and physical processes influencing ozone during long-range transport using a trajectory ensemble

During long-range transport, many distinct processes – including photochemistry, deposition, emissions and mixing – contribute to the transformation of air mass composition. Partitioning the effects of different processes can be useful when considering the sensitivity of chemical transformation to, for example, a changing environment or anthropogenic influence. However, transformation is not observed directly, since mixing ratios are measured, and models must be used to relate changes to processes. Here, four cases from the ITCT-Lagrangian 2004 experiment are studied. In each case, aircraft intercepted a distinct air mass several times during transport over the North Atlantic, providing a unique dataset and quantifying the net changes in composition from all processes. A new framework is presented to deconstruct the change in O3 mixing ratio (Δ O3) into its component processes, which were not measured directly, taking into account the uncertainty in measurements, initial air mass variability and its time evolution. The results show that the net chemical processing (Δ O3chem) over the whole simulation is greater than net physical processing (Δ O3phys) in all cases. This is in part explained by cancellation effects associated with mixing. In contrast, each case is in a regime of either net photochemical destruction (lower tropospheric transport) or production (an upper tropospheric biomass burning case). However, physical processes influence O3 indirectly through addition or removal of precursor gases, so that changes to physical parameters in a model can have a larger effect on Δ O3chem than Δ O3phys. Despite its smaller magnitude, the physical processing distinguishes the lower tropospheric export cases, since the net photochemical O3 change is −5 ppbv per day in all three cases. Processing is quantified using a Lagrangian photochemical model with a novel method for simulating mixing through an ensemble of trajectories and a background profile that evolves with them. The model is able to simulate the magnitude and variability of the observations (of O3, CO, NOy and some hydrocarbons) and is consistent with the time-average OH following air-masses inferred from hydrocarbon measurements alone (by Arnold et al., 2007). Therefore, it is a useful new method to simulate air mass evolution and variability, and its sensitivity to process parameters.

Infrared dynamics of decaying two-dimensional turbulence governed by the Charney-Hasegawa-Mima equation

The low wave number range of decaying turbulence governed by the Charney-Hasegawa-Mima (CHM) equation is examined theoretically and by direct numerical simulation. Here, the low wave number range is defined as values of the wave number k below the wave number kE corresponding to the peak of the energy spectrum, or alternatively the centroid wave number of the energy spectrum. The energy spectrum in the low wave number range in the infrared regime (k →0) is theoretically derived to be E(k) ∼k5, using a quasinormal Markovianized model of the CHM equation. This result is verified by direct numerical simulation of the CHM equation. The wave number triads (k,p,q) responsible for the formation of the low wave number spectrum are also examined. It is found that the energy flux Π(k) for k< kE can be entirely expressed by Π(-)(k), which is the total net input of energy to wave numbers k. Furthermore, the contribution of nonlocal triad interactions to the energy flux is found to be predominant in the range log (k/kE)<-0.5, where the nonlocal interactions are defined to be those triad interactions for which the ratio of the largest leg of the triad to the smallest leg is larger than four. ©2001 The Physical Society of Japan

The 22-Year Hale Cycle in cosmic ray flux: evidence for direct heliospheric modulation

The ability to predict times of greater galactic cosmic ray (GCR) fluxes is important for reducing the hazards caused by these particles to satellite communications, aviation, or astronauts. The 11-year solar-cycle variation in cosmic rays is highly correlated with the strength of the heliospheric magnetic field. Differences in GCR flux during alternate solar cycles yield a 22-year cycle, known as the Hale Cycle, which is thought to be due to different particle drift patterns when the northern solar pole has predominantly positive (denoted as qA>0 cycle) or negative (qA<0) polarities. This results in the onset of the peak cosmic-ray flux at Earth occurring earlier during qA>0 cycles than for qA<0 cycles, which in turn causes the peak to be more dome-shaped for qA>0 and more sharply peaked for qA<0. In this study, we demonstrate that properties of the large-scale heliospheric magnetic field are different during the declining phase of the qA<0 and qA>0 solar cycles, when the difference in GCR flux is most apparent. This suggests that particle drifts may not be the sole mechanism responsible for the Hale Cycle in GCR flux at Earth. However, we also demonstrate that these polarity-dependent heliospheric differences are evident during the space-age but are much less clear in earlier data: using geomagnetic reconstructions, we show that for the period of 1905 - 1965, alternate polarities do not give as significant a difference during the declining phase of the solar cycle. Thus we suggest that the 22-year cycle in cosmic-ray flux is at least partly the result of direct modulation by the heliospheric magnetic field and that this effect may be primarily limited to the grand solar maximum of the space-age.

X‑ray crystal structure of rac-[Ru(phen)2dppz]2+ with d(ATGCAT)2 shows enantiomer orientations and water ordering

We report an atomic resolution X-ray crystal structure containing both enantiomers of rac-[Ru(phen)2dppz]2+ with the d-(ATGCAT)2 DNA duplex (phen = phenanthroline; dppz = dipyridophenazine). The first example of any enantiomeric pair crystallized with a DNA duplex shows different orientations of the Λ and Δ binding sites, separated by a clearly defined structured water monolayer. Job plots show that the same species is present in solution. Each enantiomer is bound at a TG/CA step and shows intercalation from the minor groove. One water molecule is directly located on one phenazine N atom in the Δ-enantiomer only.

Is the Helmholtz equation really sign-indefinite?

The usual variational (or weak) formulations of the Helmholtz equation are sign-indefinite in the sense that the bilinear forms cannot be bounded below by a positive multiple of the appropriate norm squared. This is often for a good reason, since in bounded domains under certain boundary conditions the solution of the Helmholtz equation is not unique at wavenumbers that correspond to eigenvalues of the Laplacian, and thus the variational problem cannot be sign-definite. However, even in cases where the solution is unique for all wavenumbers, the standard variational formulations of the Helmholtz equation are still indefinite when the wavenumber is large. This indefiniteness has implications for both the analysis and the practical implementation of finite element methods. In this paper we introduce new sign-definite (also called coercive or elliptic) formulations of the Helmholtz equation posed in either the interior of a star-shaped domain with impedance boundary conditions, or the exterior of a star-shaped domain with Dirichlet boundary conditions. Like the standard variational formulations, these new formulations arise just by multiplying the Helmholtz equation by particular test functions and integrating by parts.

A synchrotron powder X-ray diffraction study of the skutterudite-related phases AB1.5Te1.5 (A=Co, Rh, Ir; B= Ge, Sn)

X-ray resonant scattering has been exploited to investigate the crystal structure of the AB1.5Te1.5 phases (A = Co, Rh, Ir; B = Ge, Sn). Analysis of the diffraction data reveals that CoGe1.5Te1.5 and ASn1.5Te1.5 adopt a rhombohedral skutterudite-related structure, containing diamond-shape B2Te2 rings, in which the B and Te atoms are ordered and trans to each other. Anion ordering is however incomplete, and with increasing the size of both cations and anions, the degree of anion ordering decreases. By contrast, the diffraction data of IrGe1.5Te1.5 are consistent with an almost statistical distribution of the anions over the available sites, although some ordered domains may be present. The thermoelectric properties of these materials are discussed in the light of these results.

Available potential energy density for a multicomponent Boussinesq fluid with arbitrary nonlinear equation of state

In this paper, the concept of available potential energy (APE) density is extended to a multicomponent Boussinesq fluid with a nonlinear equation of state. As shown by previous studies, the APE density is naturally interpreted as the work against buoyancy forces that a parcel needs to perform to move from a notional reference position at which its buoyancy vanishes to its actual position; because buoyancy can be defined relative to an arbitrary reference state, so can APE density. The concept of APE density is therefore best viewed as defining a class of locally defined energy quantities, each tied to a different reference state, rather than as a single energy variable. An important result, for which a new proof is given, is that the volume integrated APE density always exceeds Lorenz’s globally defined APE, except when the reference state coincides with Lorenz’s adiabatically re-arranged reference state of minimum potential energy. A parcel reference position is systematically defined as a level of neutral buoyancy (LNB): depending on the nature of the fluid and on how the reference state is defined, a parcel may have one, none, or multiple LNB within the fluid. Multiple LNB are only possible for a multicomponent fluid whose density depends on pressure. When no LNB exists within the fluid, a parcel reference position is assigned at the minimum or maximum geopotential height. The class of APE densities thus defined admits local and global balance equations, which all exhibit a conversion with kinetic energy, a production term by boundary buoyancy fluxes, and a dissipation term by internal diffusive effects. Different reference states alter the partition between APE production and dissipation, but neither affect the net conversion between kinetic energy and APE, nor the difference between APE production and dissipation. We argue that the possibility of constructing APE-like budgets based on reference states other than Lorenz’s reference state is more important than has been previously assumed, and we illustrate the feasibility of doing so in the context of an idealised and realistic oceanic example, using as reference states one with constant density and another one defined as the horizontal mean density field; in the latter case, the resulting APE density is found to be a reasonable approximation of the APE density constructed from Lorenz’s reference state, while being computationally cheaper.

An historical perspective on the development of the thermodynamic equation of seawater - 2010

Oceanography is concerned with understanding the mechanisms controlling the movement of seawater and its contents. A fundamental tool in this process is the characterization of the thermophysical properties of seawater as functions of measured temperature and electrical conductivity, the latter used as a proxy for the concentration of dissolved matter in seawater. For many years a collection of algorithms denoted the Equation of State 1980 (EOS-80) has been the internationally accepted standard for calculating such properties. However, modern measurement technology now allows routine observations of temperature and electrical conductivity to be made to at least one order of magnitude more accurately than the uncertainty in this standard. Recently, a new standard has been developed, the Thermodynamical Equation of Seawater 2010 (TEOS-10). This new standard is thermodynamically consistent, valid over a wider range of temperature and salinity, and includes a mechanism to account for composition variations in seawater. Here we review the scientific development of this standard, and describe the literature involved in its development, which includes many of the articles in this special issue.

Multiwavelength Observations of EXO 0748-676. I. Reprocessing of X-Ray Bursts

We present high time-resolution multiwavelength observations of X-ray bursts in the low-mass X-ray binary UY Vol. Strong reprocessed signals are present in the ultraviolet and optical, lagged and smeared with respect to the X-rays. The addition of far-ultraviolet coverage for one burst allows much tighter constraints on the temperature and geometry of the reprocessing region than previously possible. A blackbody reprocessing model for this burst suggests a rise in temperatures during the burst from 18,000 to 35,000 K and an emitting area comparable to that expected for the disk and/or irradiated companion star. The lags are consistent with those expected. The single-zone blackbody model cannot reproduce the ratio of optical to ultraviolet flux during the burst, however. The discrepancy seems too large to explain with deviations from a local blackbody spectrum and more likely indicates that a range of reprocessing temperatures are required. Comparable results are derived from other bursts, and in particular the lag and smearing both appear shorter when the companion star is on the near side of the disk as predicted. The burst observed by HST also yielded a spectrum of the reprocessed light. It is dominated by continuum, with a spectral shape consistent with the temperatures derived from lightcurve modeling. Taken as a whole, our observations confirm the standard paradigm of prompt reprocessing distributed across the disk and companion star, with the response dominated by a thermalized continuum rather than by emission lines.

Control and analysis of oriented thin films of lipid inverse bicontinuous cubic phases using grazing incidence small-angle X‑ray scattering

Lipid cubic phases are complex nanostructures that form naturally in a variety of biological systems, with applications including drug delivery and nanotemplating. Most X-ray scattering studies on lipid cubic phases have used unoriented polydomain samples as either bulk gels or suspensions of micrometer-sized cubosomes. We present a method of investigating cubic phases in a new form, as supported thin films that can be analyzed using grazing incidence small-angle X-ray scattering (GISAXS). We present GISAXS data on three lipid systems: phytantriol and two grades of monoolein (research and industrial). The use of thin films brings a number of advantages. First, the samples exhibit a high degree of uniaxial orientation about the substrate normal. Second, the new morphology allows precise control of the substrate mesophase geometry and lattice parameter using a controlled temperature and humidity environment, and we demonstrate the controllable formation of oriented diamond and gyroid inverse bicontinuous cubic along with lamellar phases. Finally, the thin film morphology allows the induction of reversible phase transitions between these mesophase structures by changes in humidity on subminute time scales, and we present timeresolved GISAXS data monitoring these transformations.

The influence of distractors on saccade­ target selection: saccade trajectory effects

It has long been known that the path (trajectory) taken by the eye to land on a target is rarely straight (Yarbus, 1967). Furthermore, the magnitude and direction of this natural tendency for curvature can be modulated by the presence of a competing distractor stimu­ lus presented along with the saccade target. The distractor­related modulation of saccade trajectories provides a subtle measure of the underlying competitive processes involved in saccade target selection. Here we review some of our own studies into the effects distract­ ors have on saccade trajectories, which can be regarded as a way of probing the competit­ ive balance between target and distractor salience.