Spontaneous aggregation and global polar ordering in squirmer suspensions

We have developed numerical simulations of three dimensional suspensions of active particles to characterize the capabilities of the hydrodynamic stresses induced by active swimmers to promote global order and emergent structures in active suspensions. We have considered squirmer suspensions embedded in a fluid modeled under a Lattice Boltzmann scheme. We have found that active stresses play a central role to decorrelate the collective motion of squirmers and that contractile squirmers develop significant aggregates.

Dissection of hormone-responsive plasma membrane to nucleus signaling of Bravis Radix : its role in vascular differentiation and root meristem growth

AbstractPlants continuously grow during their complete life span and understanding the mechanisms that qualitatively regulate their traits remains a challenging topic in biology. The hormone auxin has been identified as a crucial molecule for shaping plant growth, as it has a role in most developmental processes. In the root, the directional, so-called polar transport of auxin generates a peak of concentration that specifies and maintains the stem cell niche and a subsequent gradient of decreasing concentration that also regulates cell proliferation and differentiation. For these reasons, auxin is considered the main morphogen of the root, as it is fundamental for its organization and maintenance. Recently, in Arabidopsis thaliana, a natural variation screen allowed the discovery of BREVIS RADIX (BRX) gene as a limiting factor for auxin responsive gene expression and thus for root growth.In this study, we discovered that BRX is a direct target of auxin that positively feeds back on auxin signaling, as a transcriptional co-regulator, through interaction with the Auxin Response Factor (ARF) MONOPTEROS (MP), modulating the auxin gene response magnitude during the transition between division and differentiation in the root meristem. Moreover, we provide evidence that BRX is activated at the plasma membrane level as an associated protein before moving into the nucleus to modulate cellular growth.To investigate the discrepancy between the auxin concentration and the expression pattern of its downstream targets, we combined experimental and computational approaches. Expression profiles deviating from the auxin gradient could only be modeled after intersection of auxin activity with the observed differential endocytosis pattern and with positive auto- regulatory feedback through plasma- membrane-to-nucleus transfer of BRX. Because BRX is required for expression of certain auxin response factor targets, our data suggest a cell-type-specific endocytosis-dependent input into transcriptional auxin perception. This input sustains expression of a subset of auxin-responsive genes across the root meristem's division and transition zones and is essential for meristem growth. Thus, the endocytosis pattern provides specific positional information to modulate auxin response. RésuméLes plantes croissent continuellement tout au long de leur cycle de vie. Comprendre et expliquer les mécanismes impliqués dans ce phénomène reste à l'heure actuelle, un défi. L'hormone auxine a été identifiée comme une molécule essentielle à la régulation de la croissance des plantes, car impliquée dans la plupart des processus développementaux. Dans la racine, le transport polaire de l'auxine, par la génération d'un pic de concentration, spécifie et maintient la niche de cellules souches, et par la génération d'un gradient de concentration, contrôle la prolifération et la différentiation cellulaire. Puisque l'auxine est essentielle pour l'organisation et la maintenance du système racinaire, il est considéré comme son principal morphogène. Récemment, dans la plante modèle, Arabidopsis thalinana, un criblage des variations génétique a permis d'identifier le gène Brevis radix (BRX) comme facteur limitant l'expression des gènes de réponse à l'auxine et par là même, la croissance de la racine.Dans ce travail, nous avons découvert que BRX est une cible direct de l'auxine qui rétroactive positivement le signalement de l'hormone, agissant ainsi comme un régulateur transcriptionnel à travers l'interaction avec la protéine Monopteros (MP) de la famille des facteurs de réponse à l'auxine (Auxin Responsive Factor, ARF), et modulant ainsi la magnitude de la réponse des gènes reliés à l'auxine durant la division et la différentiation cellulaire dans le méristème de la racine. De plus, nous fournissons des preuves que BRX est activées au niveau de la membrane plasmique, tel une protéine associée se déplaçant à l'intérieur du noyau et modulant la croissance cellulaire.Pour mener à bien l'investigation des divergences entre la concentration de l'auxine et les schémas d'expression de ses propres gènes cibles, nous avons combiné les approches expérimentales et computationnelles. Les profiles d'expressions déviant du gradient d'auxine pourraient seulement être modéliser après intersection de l'activité de l'auxine avec les schémas différentiels d'endocytose observés et les boucles de rétroaction positives et autorégulatrices par le transfert de BRX de la membrane plasmique au noyau. Puisque BRX est requis pour l'expression de certains gènes cibles des facteurs de réponse à l'auxine, nos données suggèrent une contribution dépendante d'une endocytose spécifique au type de cellule dans la perception transcriptionnelle à l'auxine Cette contribution soutient l'expression d'un sous-set de gène de réponse à l'auxine dans la division du méristème racinaire et la zone de transition, et par conséquent, est essentielle pour la croissance méristematique. Ainsi, le schéma d'endocytose fournit des informations positionnelles spécifiques à la modulation de la réponse à l'auxine.

Light-mediated polarization of the PIN3 auxin transporter for the phototropic response in Arabidopsis.

Phototropism is an adaptation response, through which plants grow towards the light. It involves light perception and asymmetric distribution of the plant hormone auxin. Here we identify a crucial part of the mechanism for phototropism, revealing how light perception initiates auxin redistribution that leads to directional growth. We show that light polarizes the cellular localization of the auxin efflux carrier PIN3 in hypocotyl endodermis cells, resulting in changes in auxin distribution and differential growth. In the dark, high expression and activity of the PINOID (PID) kinase correlates with apolar targeting of PIN3 to all cell sides. Following illumination, light represses PINOID transcription and PIN3 is polarized specifically to the inner cell sides by GNOM ARF GTPase GEF (guanine nucleotide exchange factor)-dependent trafficking. Thus, differential trafficking at the shaded and illuminated hypocotyl side aligns PIN3 polarity with the light direction, and presumably redirects auxin flow towards the shaded side, where auxin promotes growth, causing hypocotyls to bend towards the light. Our results imply that PID phosphorylation-dependent recruitment of PIN proteins into distinct trafficking pathways is a mechanism to polarize auxin fluxes in response to different environmental and endogenous cues.

Energetics of climate models: net energy balance and meridional enthalpy transport

We analyze the publicly released outputs of the simulations performed by climate models (CMs) in preindustrial (PI) and Special Report on Emissions Scenarios A1B (SRESA1B) conditions. In the PI simulations, most CMs feature biases of the order of 1 W m −2 for the net global and the net atmospheric, oceanic, and land energy balances. This does not result from transient effects but depends on the imperfect closure of the energy cycle in the fluid components and on inconsistencies over land. Thus, the planetary emission temperature is underestimated, which may explain the CMs' cold bias. In the PI scenario, CMs agree on the meridional atmospheric enthalpy transport's peak location (around 40°N/S), while discrepancies of ∼20% exist on the intensity. Disagreements on the oceanic transport peaks' location and intensity amount to ∼10° and ∼50%, respectively. In the SRESA1B runs, the atmospheric transport's peak shifts poleward, and its intensity increases up to ∼10% in both hemispheres. In most CMs, the Northern Hemispheric oceanic transport decreases, and the peaks shift equatorward in both hemispheres. The Bjerknes compensation mechanism is active both on climatological and interannual time scales. The total meridional transport peaks around 35° in both hemispheres and scenarios, whereas disagreements on the intensity reach ∼20%. With increased CO 2 concentration, the total transport increases up to ∼10%, thus contributing to polar amplification of global warming. Advances are needed for achieving a self-consistent representation of climate as a nonequilibrium thermodynamical system. This is crucial for improving the CMs' skill in representing past and future climate changes.

Long-lived halocarbon trends and budgets from atmospheric chemistry modelling constrained with measurements in polar firn

The budgets of seven halogenated gases (CFC-11, CFC-12, CFC-113, CFC-114, CFC-115, CCl4 and SF6) are studied by comparing measurements in polar firn air from two Arctic and three Antarctic sites, and simulation results of two numerical models: a 2-D atmospheric chemistry model and a 1-D firn diffusion model. The first one is used to calculate atmospheric concentrations from emission trends based on industrial inventories; the calculated concentration trends are used by the second one to produce depth concentration profiles in the firn. The 2-D atmospheric model is validated in the boundary layer by comparison with atmospheric station measurements, and vertically for CFC-12 by comparison with balloon and FTIR measurements. Firn air measurements provide constraints on historical atmospheric concentrations over the last century. Age distributions in the firn are discussed using a Green function approach. Finally, our results are used as input to a radiative model in order to evaluate the radiative forcing of our target gases. Multi-species and multi-site firn air studies allow to better constrain atmospheric trends. The low concentrations of all studied gases at the bottom of the firn, and their consistency with our model results confirm that their natural sources are small. Our results indicate that the emissions, sinks and trends of CFC-11, CFC-12, CFC-113, CFC-115 and SF6 are well constrained, whereas it is not the case for CFC-114 and CCl4. Significant emission-dependent changes in the lifetimes of halocarbons destroyed in the stratosphere were obtained. Those result from the time needed for their transport from the surface where they are emitted to the stratosphere where they are destroyed. Efforts should be made to update and reduce the large uncertainties on CFC lifetimes.

In situ signatures of interchange reconnection between magnetic clouds and open magnetic fields: a mechanism for the erosion of polar coronal holes?

We outline a method to determine the direction of solar open flux transport that results from the opening of magnetic clouds (MCs) by interchange reconnection at the Sun based solely on in-situ observations. This method uses established findings about i) the locations and magnetic polarities of emerging MC footpoints, ii) the hemispheric dependence of the helicity of MCs, and iii) the occurrence of interchange reconnection at the Sun being signaled by uni-directional suprathermal electrons inside MCs. Combining those observational facts in a statistical analysis of MCs during solar cycle 23 (period 1995 – 2007), we show that the time of disappearance of the northern polar coronal hole (1998 – 1999), permeated by an outward-pointing magnetic field, is associated with a peak in the number of MCs originating from the northern hemisphere and connected to the Sun by outward-pointing magnetic field lines. A similar peak is observed in the number of MCs originating from the southern hemisphere and connected to the Sun by inward-pointing magnetic field lines. This pattern is interpreted as the result of interchange reconnection occurring between MCs and the open field lines of nearby polar coronal holes. This reconnection process closes down polar coronal hole open field lines and transports these open field lines equatorward, thus contributing to the global coronal magnetic field reversal process. These results will be further constrainable with the rising phase of solar cycle 24.

The changing atmospheric water cycle in polar regions in a warmer climate

We have examined the atmospheric water cycle of both Polar Regions, pole wards of 60°N and 60°S, using the ERA-Interim re-analysis and high-resolution simulations with the ECHAM5 model for both the present and future climate based on the IPCC, A1B scenario, representative of the last three decades of the 21st century. The annual precipitation in ERA-Interim amounts to ~17000 km3 and is more or less the same in the Arctic and the Antarctic, but it is composed differently. In the Arctic the annual evaporation is some 8000 km3 but some 3000 km3 less in the Antarctica where the net horizontal transport is correspondingly larger. The net water transport of the model is more intense than in ERA-Interim, in the Arctic the difference is 2.5% and in the Antarctic it is 6.2%. Precipitation and net horizontal transport in the Arctic has a maximum in August and September. Evaporation peaks in June and July. The seasonal cycle is similar in Antarctica with the highest precipitation in the austral autumn. The largest net transport occurs at the end of the major extra-tropical storm tracks in the Northern Hemisphere such as the eastern Pacific and eastern north Atlantic. The variability of the model is virtually identical to that of the re-analysis and there are no changes in variability between the present climate and the climate at the end of the 21st century when normalized with the higher level of moisture. The changes from year to year are substantial with the 20 and 30-year records being generally too short to identify robust trends in the hydrological cycle. In the A1B climate scenario the strength of the water cycle increases by some 25% in the Arctic and by 19% in the Antarctica, as measured by annual precipitation. The increase in the net horizontal transport is 29% and 22% respectively, and the increase in evaporation correspondingly less. The net transport follows closely the Clausius-Clapeyron relation. There is 2 a minor change in the annual cycle of the Arctic atmospheric water cycle with the maximum transport and precipitation occurring later in the year. There is a small imbalance of some 4-6% between the net transport and precipitation minus evaporation. We suggest that this is mainly due to the fact the transport is calculated from instantaneous 6-hourly data while precipitation and evaporation is accumulated over a 6 hour period. The residual difference is proportionally similar for all experiments and hardly varies from year to year.

The changing energy balance of the polar regions in a warmer climate

Energy fluxes for polar regions are examined for two 30-year periods, representing the end of the 20th and 21st centuries, using data from high resolution simulations with the ECHAM5 climate model. The net radiation to space for the present climate agrees well with data from the Clouds and the Earth’s Radiant Energy System (CERES) over the northern polar region but shows an underestimation in planetary albedo for the southern polar region. This suggests there are systematic errors in the atmospheric circulation or in the net surface energy fluxes in the southern polar region. The simulation of the future climate is based on the Intergovernmental Panel on Climate Change (IPCC) A1B scenario. The total energy transport is broadly the same for the two 30 year periods, but there is an increase in the moist energy transport of the order of 6 W m−2 and a corresponding reduction in the dry static energy. For the southern polar region the proportion of moist energy transport is larger and the dry static energy correspondingly smaller for both periods. The results suggest a possible mechanism for the warming of the Arctic that is discussed. Changes between the 20th and 21st centuries in the northern polar region show the net ocean surface radiation flux in summer increases ~18W m−2 (24%). For the southern polar region the response is different as there is a decrease in surface solar radiation. We suggest that this is caused by changes in cloudiness associated with the poleward migration of the storm tracks.

O_3-N_2O correlations from the Atmospheric Chemistry Experiment: revisiting a diagnostic of transport and chemistry in the stratosphere

Our knowledge of stratospheric O3-N2O correlations is extended, and their potential for model-measurement comparison assessed, using data from the Atmospheric Chemistry Experiment (ACE) satellite and the Canadian Middle Atmosphere Model (CMAM). ACE provides the first comprehensive data set for the investigation of interhemispheric, interseasonal, and height-resolved differences of the O_3-N_2O correlation structure. By subsampling the CMAM data, the representativeness of the ACE data is evaluated. In the middle stratosphere, where the correlations are not compact and therefore mainly reflect the data sampling, joint probability density functions provide a detailed picture of key aspects of transport and mixing, but also trace polar ozone loss. CMAM captures these important features, but exhibits a displacement of the tropical pipe into the Southern Hemisphere (SH). Below about 21 km, the ACE data generally confirm the compactness of the correlations, although chemical ozone loss tends to destroy the compactness during late winter/spring, especially in the SH. This allows a quantitative comparison of the correlation slopes in the lower and lowermost stratosphere (LMS), which exhibit distinct seasonal cycles that reveal the different balances between diabatic descent and horizontal mixing in these two regions in the Northern Hemisphere (NH), reconciling differences found in aircraft measurements, and the strong role of chemical ozone loss in the SH. The seasonal cycles are qualitatively well reproduced by CMAM, although their amplitude is too weak in the NH LMS. The correlation slopes allow a "chemical" definition of the LMS, which is found to vary substantially in vertical extent with season.

Comparison of polar ozone loss rates simulated by one-dimensional and three-dimensional models with Match observations in recent Antarctic and Arctic winters

Simulations of ozone loss rates using a three-dimensional chemical transport model and a box model during recent Antarctic and Arctic winters are compared with experimental loss rates. The study focused on the Antarctic winter 2003, during which the first Antarctic Match campaign was organized, and on Arctic winters 1999/2000, 2002/2003. The maximum ozone loss rates retrieved by the Match technique for the winters and levels studied reached 6 ppbv/sunlit hour and both types of simulations could generally reproduce the observations at 2-sigma error bar level. In some cases, for example, for the Arctic winter 2002/2003 at 475 K level, an excellent agreement within 1-sigma standard deviation level was obtained. An overestimation was also found with the box model simulation at some isentropic levels for the Antarctic winter and the Arctic winter 1999/2000, indicating an overestimation of chlorine activation in the model. Loss rates in the Antarctic show signs of saturation in September, which have to be considered in the comparison. Sensitivity tests were performed with the box model in order to assess the impact of kinetic parameters of the ClO-Cl2O2 catalytic cycle and total bromine content on the ozone loss rate. These tests resulted in a maximum change in ozone loss rates of 1.2 ppbv/sunlit hour, generally in high solar zenith angle conditions. In some cases, a better agreement was achieved with fastest photolysis of Cl2O2 and additional source of total inorganic bromine but at the expense of overestimation of smaller ozone loss rates derived later in the winter.

Forecast, measurement, and modeling of an unprecedented polar ozone filament event over Mauna Loa Observatory, Hawaii

In mid-March 2005 the northern lower stratospheric polar vortex experienced a severe stretching episode, bringing a large polar filament far south of Alaska toward Hawaii. This meridional intrusion of rare extent, coinciding with the polar vortex final warming and breakdown, was followed by a zonal stretching in the wake of the easterly propagating subtropical main flow. This caused polar air to remain over Hawaii for several days before diluting into the subtropics. After being successfully forecasted to pass over Hawaii by the high-resolution potential vorticity advection model Modèle Isentrope du transport Méso-échelle de l'Ozone Stratosphérique par Advection (MIMOSA), the filament was observed on isentropic surfaces between 415 K and 455 K (17–20 km) by the Jet Propulsion Laboratory stratospheric ozone lidar measurements at Mauna Loa Observatory, Hawaii, between 16 and 19 March 2005. It was materialized as a thin layer of enhanced ozone peaking at 1.6 ppmv in a region where the climatological values usually average 1.0 ppmv. These values were compared to those obtained by the three-dimensional Chemistry-Transport Model MIMOSA-CHIM. Agreement between lidar and model was excellent, particularly in the similar appearance of the ozone peak near 435 K (18.5 km) on 16 March, and the persistence of this layer at higher isentropic levels for the following three days. Passive ozone, also modeled by MIMOSA-CHIM, was at about 3–4 ppmv inside the filament while above Hawaii. A detailed history of the modeled chemistry inside the filament suggests that the air mass was still polar ozone–depleted when passing over Hawaii. The filament quickly separated from the main vortex after its Hawaiian overpass. It never reconnected and, in less than 10 days, dispersed entirely in the subtropics

Simultaneous lidar and EOS MLS measurements, and modeling, of a rare polar ozone filament event over Mauna Loa Observatory, Hawaii

In mid-March 2005, a rare lower stratospheric polar vortex filamentation event was observed simultaneously by the JPL lidar at Mauna Loa Observatory, Hawaii, and by the EOS MLS instrument onboard the Aura satellite. The event coincided with the beginning of the spring 2005 final warming. On 16 March, the filament was observed by lidar around 0600 UT between 415 K and 455 K, and by MLS six hours earlier. It was seen on both the lidar and MLS profiles as a layer of enhanced ozone, peaking at 1.7 ppmv in a region where the climatological values are usually around or below 1 ppmv. Ozone profiles measured by lidar and MLS were compared to profiles from the Chemical Transport Model MIMOSA-CHIM. The agreement between lidar, MLS, and the model is excellent considering the difference in the sampling techniques. MLS was also able to identify the filament at another location north of Hawaii.

Jet characterization in the upper troposphere/lower stratosphere (UTLS): applications to climatology and transport studies

A method of classifying the upper tropospheric/lower stratospheric (UTLS) jets has been developed that allows satellite and aircraft trace gas data and meteorological fields to be efficiently mapped in a jet coordinate view. A detailed characterization of multiple tropopauses accompanies the jet characterization. Jet climatologies show the well-known high altitude subtropical and lower altitude polar jets in the upper troposphere, as well as a pattern of concentric polar and subtropical jets in the Southern Hemisphere, and shifts of the primary jet to high latitudes associated with blocking ridges in Northern Hemisphere winter. The jet-coordinate view segregates air masses differently than the commonly-used equivalent latitude (EqL) coordinate throughout the lowermost stratosphere and in the upper troposphere. Mapping O3 data from the Aura Microwave Limb Sounder (MLS) satellite and the Winter Storms aircraft datasets in jet coordinates thus emphasizes different aspects of the circulation compared to an EqL-coordinate framework: the jet coordinate reorders the data geometrically, thus highlighting the strong PV, tropopause height and trace gas gradients across the subtropical jet, whereas EqL is a dynamical coordinate that may blur these spatial relationships but provides information on irreversible transport. The jet coordinate view identifies the concentration of stratospheric ozone well below the tropopause in the region poleward of and below the jet core, as well as other transport features associated with the upper tropospheric jets. Using the jet information in EqL coordinates allows us to study trace gas distributions in regions of weak versus strong jets, and demonstrates weaker transport barriers in regions with less jet influence. MLS and Atmospheric Chemistry Experiment-Fourier Transform Spectrometer trace gas fields for spring 2008 in jet coordinates show very strong, closely correlated, PV, tropopause height and trace gas gradients across the jet, and evidence of intrusions of stratospheric air below the tropopause below and poleward of the subtropical jet; these features are consistent between instruments and among multiple trace gases. Our characterization of the jets is facilitating studies that will improve our understanding of upper tropospheric trace gas evolution.

The ocean's role in polar climate change: asymmetric Arctic and Antarctic responses to greenhouse gas and ozone forcing

In recent decades, the Arctic has been warming and sea ice disappearing. By contrast, the Southern Ocean around Antarctica has been (mainly) cooling and sea-ice extent growing. We argue here that interhemispheric asymmetries in the mean ocean circulation, with sinking in the northern North Atlantic and upwelling around Antarctica, strongly influence the sea-surface temperature (SST) response to anthropogenic greenhouse gas (GHG) forcing, accelerating warming in the Arctic while delaying it in the Antarctic. Furthermore, while the amplitude of GHG forcing has been similar at the poles, significant ozone depletion only occurs over Antarctica. We suggest that the initial response of SST around Antarctica to ozone depletion is one of cooling and only later adds to the GHG-induced warming trend as upwelling of sub-surface warm water associated with stronger surface westerlies impacts surface properties. We organize our discussion around ‘climate response functions’ (CRFs), i.e. the response of the climate to ‘step’ changes in anthropogenic forcing in which GHG and/or ozone-hole forcing is abruptly turned on and the transient response of the climate revealed and studied. Convolutions of known or postulated GHG and ozone-hole forcing functions with their respective CRFs then yield the transient forced SST response (implied by linear response theory), providing a context for discussion of the differing warming/cooling trends in the Arctic and Antarctic. We speculate that the period through which we are now passing may be one in which the delayed warming of SST associated with GHG forcing around Antarctica is largely cancelled by the cooling effects associated with the ozone hole. By mid-century, however, ozone-hole effects may instead be adding to GHG warming around Antarctica but with diminished amplitude as the ozone hole heals. The Arctic, meanwhile, responding to GHG forcing but in a manner amplified by ocean heat transport, may continue to warm at an accelerating rate.

A comparison between ion characteristics observed by the POLAR and DMSP spacecraft in the high-latitude magnetosphere

We study here the injection and transport of ions in the convection-dominated region of the Earth’s magnetosphere. The total ion counts from the CAMMICE MICS instrument aboard the POLAR spacecraft are used to generate occurrence probability distributions of magnetospheric ion populations. MICS ion spectra are characterised by both the peak in the differential energy flux, and the average energy of ions striking the detector. The former permits a comparison with the Stubbs et al. (2001) survey of He2+ ions of solar wind origin within the magnetosphere. The latter can address the occurrences of various classifications of precipitating particle fluxes observed in the topside ionosphere by DMSP satellites (Newell and Meng, 1992). The peak energy occurrences are consistent with our earlier work, including the dawn-dusk asymmetry with enhanced occurrences on the dawn flank at low energies, switching to the dusk flank at higher energies. The differences in the ion energies observed in these two studies can be explained by drift orbit effects and acceleration processes at the magnetopause, and in the tail current sheet. Near noon at average ion energies of _1 keV, the cusp and open LLBL occur further poleward here than in the Newell and Meng survey, probably due to convectionrelated time-of-flight effects. An important new result is that the pre-noon bias previously observed in the LLBL is most likely due to the component of this population on closed field lines, formed largely by low energy ions drifting earthward from the tail. There is no evidence here of mass and momentum transfer from the solar wind to the LLBL by nonreconnection coupling. At higher energies (_2–20 keV), we observe ions mapping to the auroral oval and can distinguish between the boundary and central plasma sheets. We show that ions at these energies relate to a transition from dawnward to duskward dominated flow, this is evidence of how ion drift orbits in the tail influence the location and behaviour of the plasma populations in the magnetosphere.