Understanding Demographic and Behavioral Mechanisms that Guide Responses of Neotropical Migratory Birds to Urbanization: a Simulation Approach

Although studies often report that densities of many forest birds are negatively related to urbanization, the mechanisms guiding this pattern are poorly understood. Our objective was to use a population simulation to examine the relative influence of six demographic and behavioral processes on patterns of avian abundance in urbanizing landscapes. We constructed an individual-based population simulation model representing the annual cycle of a Neotropical migratory songbird. Each simulation was performed under two landscape scenarios. The first scenario had similar proportions of high- and low-quality habitat across the urban to rural gradient. Under the first scenario, avian density was negatively related to urbanization only when rural habitats were perceived to be of higher quality than they actually were. The second landscape scenario had declining proportions of high-quality habitat as urbanization increased. Under the second scenario, each mechanism generated a negative relationship between density and urbanization. The strongest effect on density resulted when birds preferentially selected habitats in landscapes from which they fledged or were constrained from dispersing. The next strongest patterns occurred when birds directly evaluated habitat quality and accurately selected the highest-quality available territories. When birds selected habitats based on the presence of conspecifics, the density–urbanization relationship was only one-third the strength of other habitat selection mechanisms and only occurred under certain levels of population survival. Although differences in adult or nest survival in the face of random habitat selection still elicited reduced densities in urban landscapes, the relationships between urbanization and density were weaker than those produced by the conspecific attraction mechanism. Results from our study identify key predictions and areas for future research, including assessing habitat quality in urban and rural areas in order to determine if habitats in urban areas are underutilized.

Simulation of monsoon disturbances in the LMD GCM

The monsoon depressions that form over India during the summer are analyzed using simulations from the Laboratoire de Meteorologie Dynamique general circulation model. This type of synoptic system often occurs with a frequency of one to two per month and can produce a strong Indian rainfall. Two kinds of analyses are conducted in this study. The first one is a subjective analysis based on the evolution of the precipitation rate and the pattern of the sea level pressure. The second one is an objective analysis performed using the TRACK program, which identifies and tracks the minima in the sea level pressure anomaly held and computes the statistics for the distribution of systems. The analysis of a 9-yr control run, which simulates strong precipitation rates over the foothills of the Himalayas and over southern India but weak rates over central India, shows that the number of disturbances is coo low and that they almost never occur during August, when break conditions prevail. The generated disturbances more often move north, toward the foothills of the Himalayas. Another analysis is performed to study the effect of the Tibetan Plateau elevation on these disturbances with a 9-yr run carried out with a Tibetan Plateau at 50% of its current height. It is shown that this later integration simulates more frequent monsoon disturbances, which move rather northwestward, in agreement with the current observations. The comparison between the two runs shows that the June-July-August rainfall difference is in large part due to changes in the occurrence of the monsoon disturbances.

Simulation of the diurnal cycle in a climate model and its evaluation using data from Meteosat 7

The representation of the diurnal cycle in the Hadley Centre climate model is evaluated using simulations of the infrared radiances observed by Meteosat 7. In both the window and water vapour channels, the standard version of the model with 19 levels produces a good simulation of the geographical distributions of the mean radiances and of the amplitude of the diurnal cycle. Increasing the vertical resolution to 30 levels leads to further improvements in the mean fields. The timing of the maximum and minimum radiances reveals significant model errors, however, which are sensitive to the frequency with which the radiation scheme is called. In most regions, these errors are consistent with well documented errors in the timing of convective precipitation, which peaks before noon in the model, in contrast to the observed peak in the late afternoon or evening. When the radiation scheme is called every model time step (half an hour), as opposed to every three hours in the standard version, the timing of the minimum radiance is improved for convective regions over central Africa, due to the creation of upper-level layer-cloud by detrainment from the convection scheme, which persists well after the convection itself has dissipated. However, this produces a decoupling between the timing of the diurnal cycles of precipitation and window channel radiance. The possibility is raised that a similar decoupling may occur in reality and the implications of this for the retrieval of the diurnal cycle of precipitation from infrared radiances are discussed.

Numerical simulation of baroclinic waves with a parameterized boundary layer

A dry three-dimensional baroclinic life cycle model is used to investigate the role of turbulent fluxes of heat and momentum within the boundary layer on mid-latitude cyclones. Simulations are performed of life cycles for two basic states, both with and without turbulent fluxes. The different basic states produce cyclones with contrasting frontal and mesoscale-flow structures. The analysis focuses on the generation of potential-vorticity (PV) in the boundary layer and its subsequent transport into the free troposphere. The dynamic mechanism through which friction mitigates a barotropic vortex is that of Ekman pumping. This has often been assumed to be also the dominant mechanism for baroclinic developments. The PV framework highlights an additional, baroclinic mechanism. Positive PV is generated baroclinically due to friction to the north-east of a surface low and is transported out of the boundary layer by a cyclonic conveyor belt flow. The result is an anomaly of increased static stability in the lower troposphere which restricts the growth of the baroclinic wave. The reduced coupling between lower and upper levels can be sufficient to change the character of the upper-level evolution of the mature wave. The basic features of the baroclinic damping mechanism are robust for different frontal structures, with and without turbulent heat fluxes, and for the range of surface roughness found over the oceans.

Improved simulation of water vapour and clear-sky radiation using 24 hour forecasts from ERA40

Monthly mean water vapour and clear-sky radiation extracted from the European Centre for Medium Range Weather Forecasts 40-year reanalysis (ERA40) forecasts are assessed using satellite observations and additional reanalysis data. There is a marked improvement in the interannual variability of column-integrated water vapour (CWV) over the oceans when using the 24-hour forecasts compared with the standard 6-hour forecasts products. The spatial distribution of CWV are well simulated by the 6-hour forecasts; using the 24-hour forecasts does not degrade this simulation substantially and in many cases improves on the quality. There is also an improved simulation of clear-sky radiation from the 24-hour forecasts compared with the 6-hour forecasts based on comparison with satellite observations and empirical estimates. Further work is required to assess the quality of water vapour simulation by reanalyses over land regions. Over the oceans, it is recommended that 24-hour forecasts of CWV and clear-sky radiation are used in preference to the standard 6-hour forecast products from ERA40

Evaluation of the Met Office global forecast model using Geostationary Earth Radiation Budget (GERB) data

Simulations of the top-of-atmosphere radiative-energy budget from the Met Office global numerical weather-prediction model are evaluated using new data from the Geostationary Earth Radiation Budget (GERB) instrument on board the Meteosat-8 satellite. Systematic discrepancies between the model simulations and GERB measurements greater than 20 Wm-2 in outgoing long-wave radiation (OLR) and greater than 60 Wm-2 in reflected short-wave radiation (RSR) are identified over the period April-September 2006 using 12 UTC data. Convective cloud over equatorial Africa is spatially less organized and less reflective than in the GERB data. This bias depends strongly on convective-cloud cover, which is highly sensitive to changes in the model convective parametrization. Underestimates in model OLR over the Gulf of Guinea coincide with unrealistic southerly cloud outflow from convective centres to the north. Large overestimates in model RSR over the subtropical ocean, greater than 50 Wm-2 at 12 UTC, are explained by unrealistic radiative properties of low-level cloud relating to overestimation of cloud liquid water compared with independent satellite measurements. The results of this analysis contribute to the development and improvement of parametrizations in the global forecast model.

Linear viscoelasticity from molecular dynamics simulation of entangled polymers

The linear viscoelastic (LVE) spectrum is one of the primary fingerprints of polymer solutions and melts, carrying information about most relaxation processes in the system. Many single chain theories and models start with predicting the LVE spectrum to validate their assumptions. However, until now, no reliable linear stress relaxation data were available from simulations of multichain systems. In this work, we propose a new efficient way to calculate a wide variety of correlation functions and mean-square displacements during simulations without significant additional CPU cost. Using this method, we calculate stress−stress autocorrelation functions for a simple bead−spring model of polymer melt for a wide range of chain lengths, densities, temperatures, and chain stiffnesses. The obtained stress−stress autocorrelation functions were compared with the single chain slip−spring model in order to obtain entanglement related parameters, such as the plateau modulus or the molecular weight between entanglements. Then, the dependence of the plateau modulus on the packing length is discussed. We have also identified three different contributions to the stress relaxation:  bond length relaxation, colloidal and polymeric. Their dependence on the density and the temperature is demonstrated for short unentangled systems without inertia.

An observing system simulation experiment for climate monitoring with GNSS radio occulation data: setup and testbed study

The long-term stability, high accuracy, all-weather capability, high vertical resolution, and global coverage of Global Navigation Satellite System (GNSS) radio occultation (RO) suggests it as a promising tool for global monitoring of atmospheric temperature change. With the aim to investigate and quantify how well a GNSS RO observing system is able to detect climate trends, we are currently performing an (climate) observing system simulation experiment over the 25-year period 2001 to 2025, which involves quasi-realistic modeling of the neutral atmosphere and the ionosphere. We carried out two climate simulations with the general circulation model MAECHAM5 (Middle Atmosphere European Centre/Hamburg Model Version 5) of the MPI-M Hamburg, covering the period 2001–2025: One control run with natural variability only and one run also including anthropogenic forcings due to greenhouse gases, sulfate aerosols, and tropospheric ozone. On the basis of this, we perform quasi-realistic simulations of RO observables for a small GNSS receiver constellation (six satellites), state-of-the-art data processing for atmospheric profiles retrieval, and a statistical analysis of temperature trends in both the “observed” climatology and the “true” climatology. Here we describe the setup of the experiment and results from a test bed study conducted to obtain a basic set of realistic estimates of observational errors (instrument- and retrieval processing-related errors) and sampling errors (due to spatial-temporal undersampling). The test bed results, obtained for a typical summer season and compared to the climatic 2001–2025 trends from the MAECHAM5 simulation including anthropogenic forcing, were found encouraging for performing the full 25-year experiment. They indicated that observational and sampling errors (both contributing about 0.2 K) are consistent with recent estimates of these errors from real RO data and that they should be sufficiently small for monitoring expected temperature trends in the global atmosphere over the next 10 to 20 years in most regions of the upper troposphere and lower stratosphere (UTLS). Inspection of the MAECHAM5 trends in different RO-accessible atmospheric parameters (microwave refractivity and pressure/geopotential height in addition to temperature) indicates complementary climate change sensitivity in different regions of the UTLS so that optimized climate monitoring shall combine information from all climatic key variables retrievable from GNSS RO data.

Analysis of convectively-generated gravity waves in mesoscale model simulations and wind profiler observations

The characteristics of convectively-generated gravity waves during an episode of deep convection near the coast of Wales are examined in both high resolution mesoscale simulations [with the (UK) Met Oce Unified Model] and in observations from a Mesosphere-Stratosphere-Troposphere (MST) wind profiling Doppler radar. Deep convection reached the tropopause and generated vertically propagating, high frequency waves in the lower stratosphere that produced vertical velocity perturbations O(1 m/s). Wavelet analysis is applied in order to determine the characteristic periods and wavelengths of the waves. In both the simulations and observations, the wavelet spectra contain several distinct preferred scales indicated by multiple spectral peaks. The peaks are most pronounced in the horizontal spectra at several wavelengths less than 50 km. Although these peaks are most clear and of largest amplitude in the highest resolution simulations (with 1 km horizontal grid length), they are also evident in coarser simulations (with 4 km horizontal grid length). Peaks also exist in the vertical and temporal spectra (between approximately 2.5 and 4.5 km, and 10 to 30 minutes, respectively) with good agreement between simulation and observation. Two-dimensional (wavenumber-frequency) spectra demonstrate that each of the selected horizontal scales contains peaks at each of preferred temporal scales revealed by the one- dimensional spectra alone.

New insights on growth mechanisms of protein clusters at surfaces: an AFM and simulation study

Despite its relevance to a wide range of technological and fundamental areas, a quantitative understanding of protein surface clustering dynamics is often lacking. In inorganic crystal growth, surface clustering of adatoms is well described by diffusion-aggregation models. In such models, the statistical properties of the aggregate arrays often reveal the molecular scale aggregation processes. We investigate the potential of these theories to reveal hitherto hidden facets of protein clustering by carrying out concomitant observations of lysozyme adsorption onto mica surfaces, using atomic force microscopy. and Monte Carlo simulations of cluster nucleation and growth. We find that lysozyme clusters diffuse across the substrate at a rate that varies inversely with size. This result suggests which molecular scale mechanisms are responsible for the mobility of the proteins on the substrate. In addition the surface diffusion coefficient of the monomer can also be extracted from the comparison between experiments and simulations. While concentrating on a model system of lysozyme-on-mica, this 'proof of concept' study successfully demonstrates the potential of our approach to understand and influence more biomedically applicable protein-substrate couples.

Simulation of the Earth's radiation budget by the European Centre for Medium-Range Weather Forecasts 40-year reanalysis (ERA40)

The radiation budget simulated by the European Centre for Medium-Range Weather Forecasts (ECMWF) 40-year reanalysis (ERA40) is evaluated for the period 1979–2001 using independent satellite data and additional model data. This provides information on the quality of the radiation products and indirect evaluation of other aspects of the climate produced by ERA40. The climatology of clear-sky outgoing longwave radiation (OLR) is well captured by ERA40. Underestimations of about 10 W m−2 in clear-sky OLR over tropical convective regions by ERA40 compared to satellite data are substantially reduced when the satellite sampling is taken into account. The climatology of column-integrated water vapor is well simulated by ERA40 compared to satellite data over the ocean, indicating that the simulation of downward clear-sky longwave fluxes at the surface is likely to be good. Clear-sky absorbed solar radiation (ASR) and clear-sky OLR are overestimated by ERA40 over north Africa and high-latitude land regions. The observed interannual changes in low-latitude means are not well reproduced. Using ERA40 to analyze trends and climate feedbacks globally is therefore not recommended. The all-sky radiation budget is poorly simulated by ERA40. OLR is overestimated by around 10 W m−2 over much of the globe. ASR is underestimated by around 30 W m−2 over tropical ocean regions. Away from marine stratocumulus regions, where cloud fraction is underestimated by ERA40, the poor radiation simulation by ERA40 appears to be related to inaccurate radiative properties of cloud rather than inaccurate cloud distributions.