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.

Classifying dynamical forcing mechanisms using a climatology of extratropical cyclones

A climatology of almost 700 extratropical cyclones is compiled by applying an automated feature tracking algorithm to a database of objectively identified cyclonic features. Cyclones are classified according to the relative contributions to the midlevel vertical motion of the forcing from upper and lower levels averaged over the cyclone intensification period (average U/L ratio) and also by the horizontal separation between their upper-level trough and low-level cyclone (tilt). The frequency distribution of the average U/L ratio of the cyclones contains two significant peaks and a long tail at high U/L ratio. Although discrete categories of cyclones have not been identified, the cyclones comprising the peaks and tail have characteristics that have been shown to be consistent with the type A, B, and C cyclones of the threefold classification scheme. Using the thresholds in average U/L ratio determined from the frequency distribution, type A, B, and C cyclones account for 30\%, 38\%, and 32\% of the total number of cyclones respectively. Cyclones with small average U/L ratio are more likely to be developing cyclones (attain a relative vorticity $\ge 1.2 \times 10^{-4} \mbox{s}^{-1}$) whereas cyclones with large average U/L ratio are more likely to be nondeveloping cyclones (60\% of type A cyclones develop whereas 31\% of type C cyclones develop). Type A cyclogenesis dominates in the development region East of the Rockies and over the gulf stream, type B cyclogenesis dominates in the region off the East coast of the USA, and type C cyclogenesis is more common over the oceans in regions of weaker low-level baroclinicity.

Mechanisms and dynamics of protein clustering on a solid surface

A methodology for discovering the mechanisms and dynamics of protein clustering on solid surfaces is presented. In situ atomic force microscopy images are quantitatively compared to Monte Carlo simulations using cluster statistics to differentiate various models. We study lysozyme adsorption on mica as a model system and find that all surface-supported clusters are mobile, not just the monomers, with diffusion constant inversely related to cluster size. The surface monomer diffusion constant is measured to be D1∼9×10-16  cm2 s-1, such a low value being difficult to measure using other techniques.

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.

Microscopic Mechanisms of Strain Hardening in Glassy Polymers

The mechanisms underlying the increase in stress for large mechanical strains of a polymer glass, quantified by the strain-hardening modulus, are still poorly understood. In the present paper we aim to elucidate this matter and present new mechanisms. Molecular-dynamics simulations of two polymers with very different strain-hardening moduli (polycarbonate and polystyrene) have been carried out. Nonaffine displacements occur because of steric hindrances and connectivity constraints. We argue that it is not necessary to introduce the concept of entanglements to understand strain hardening, but that hardening is rather coupled with the increase in the rate of nonaffine particle displacements. This rate increases faster for polycarbonate, which has the higher strain-hardening modulus. Also more nonaffine chain stretching is present for polycarbonate. It is shown that the inner distances of such a nonaffinely deformed chain can be well described by the inner distances of the worm-like chain, but with an effective stiffness length (equal to the Kuhn length for an infinite worm-like chain) that increases during deformation. It originates from the finite extensibility of the chain. In this way the increase in nonaffine particle displacement can be understood as resulting from an increase in the effective stiffness length of the perturbed chain during deformation, so that at larger strains a higher rate of plastic events in terms of nonaffine displacement is necessary, causing in turn the observed strain hardening in polymer glasses.

On the generation mechanisms of short-scale unbalanced modes in rotating two-layer flows with vertical shear

We report on the results of a laboratory investigation using a rotating two-layer annulus experiment, which exhibits both large-scale vortical modes and short-scale divergent modes. A sophisticated visualization method allows us to observe the flow at very high spatial and temporal resolution. The balanced long-wavelength modes appear only when the Froude number is supercritical (i.e. $F\,{>}\,F_\mathrm{critical}\,{\equiv}\, \upi^2/2$), and are therefore consistent with generation by a baroclinic instability. The unbalanced short-wavelength modes appear locally in every single baroclinically unstable flow, providing perhaps the first direct experimental evidence that all evolving vortical flows will tend to emit freely propagating inertia–gravity waves. The short-wavelength modes also appear in certain baroclinically stable flows. We infer the generation mechanisms of the short-scale waves, both for the baro-clinically unstable case in which they co-exist with a large-scale wave, and for the baroclinically stable case in which they exist alone. The two possible mechanisms considered are spontaneous adjustment of the large-scale flow, and Kelvin–Helmholtz shear instability. Short modes in the baroclinically stable regime are generated only when the Richardson number is subcritical (i.e. $\hbox{\it Ri}\,{<}\,\hbox{\it Ri}_\mathrm{critical}\,{\equiv}\, 1$), and are therefore consistent with generation by a Kelvin–Helmholtz instability. We calculate five indicators of short-wave generation in the baroclinically unstable regime, using data from a quasi-geostrophic numerical model of the annulus. There is excellent agreement between the spatial locations of short-wave emission observed in the laboratory, and regions in which the model Lighthill/Ford inertia–gravity wave source term is large. We infer that the short waves in the baroclinically unstable fluid are freely propagating inertia–gravity waves generated by spontaneous adjustment of the large-scale flow.

Modeling the mechanisms that control in-stream dissolved organic carbon dynamics in upland and forested catchments

[1] We present a new, process-based model of soil and stream water dissolved organic carbon (DOC): the Integrated Catchments Model for Carbon (INCA-C). INCA-C is the first model of DOC cycling to explicitly include effects of different land cover types, hydrological flow paths, in-soil carbon biogeochemistry, and surface water processes on in-stream DOC concentrations. It can be calibrated using only routinely available monitoring data. INCA-C simulates daily DOC concentrations over a period of years to decades. Sources, sinks, and transformation of solid and dissolved organic carbon in peat and forest soils, wetlands, and streams as well as organic carbon mineralization in stream waters are modeled. INCA-C is designed to be applied to natural and seminatural forested and peat-dominated catchments in boreal and temperate regions. Simulations at two forested catchments showed that seasonal and interannual patterns of DOC concentration could be modeled using climate-related parameters alone. A sensitivity analysis showed that model predictions were dependent on the mass of organic carbon in the soil and that in-soil process rates were dependent on soil moisture status. Sensitive rate coefficients in the model included those for organic carbon sorption and desorption and DOC mineralization in the soil. The model was also sensitive to the amount of litter fall. Our results show the importance of climate variability in controlling surface water DOC concentrations and suggest the need for further research on the mechanisms controlling production and consumption of DOC in soils.

Confronting social defence mechanisms: avoiding disorganization during crises

Crises cause social disturbances within their host organisation and the patterns of interpersonal ties that emerge are an important determinant of crisis management efficiency. In this article, social network analysis is used within a construction project context, to demonstrate that efficient crisis management depends upon the design and maintenance of an appropriate social fabric. However, crises have defence mechanisms that make management difficult by inducing forces that encourage people to pursue inappropriate social ties. Purposeful social intervention is therefore an essential part of the crisis management process to confront and avoid disorganisation.

Using idealized snow forcing to test teleconnections with the Indian summer monsoon in the Hadley Centre GCM

Anomalous heavy snow during winter or spring has long been regarded as a possible precursor of deficient Indian monsoon rainfall during the subsequent summer. However previous work in this field is inconclusive, in terms of the mechanism that communicates snow anomalies to the monsoon summer, and even the region from which snow has the most impact. In this study we explore these issues in coupled and atmosphere-only versions of the Hadley Centre model. A 1050-year control integration of the HadCM3 coupled model, which well represents the seasonal cycle of snow cover over the Eurasian continent, is analysed and shows evidence for weakened monsoons being preceded by strong snow forcing (in the absence of ENSO) over either the Himalaya/Tibetan Plateau or north/west Eurasia regions. However, empirical orthogonal function (EOF) analysis of springtime interannual variability in snow depth shows the leading mode to have opposite signs between these two regions, suggesting that competing mechanisms may be possible. To determine the dominant region, ensemble integrations are carried out using HadAM3, the atmospheric component of HadCM3, and a variety of anomalous snow forcing initial conditions obtained from the control integration of the coupled model. Forcings are applied during spring in separate experiments over the Himalaya/Tibetan Plateau and north/west Eurasia regions, in conjunction with climatological SSTs in order to avoid the direct effects of ENSO. With the aid of idealized forcing conditions in sensitivity tests, we demonstrate that forcing from the Himalaya region is dominant in this model via a Blanford-type mechanism involving reduced surface sensible heat and longwave fluxes, reduced heating of the troposphere over the Tibetan Plateau and consequently a reduced meridional tropospheric temperature gradient which weakens the monsoon during early summer. Snow albedo is shown to be key to the mechanism, explaining around 50% of the perturbation in sensible heating over the Tibetan Plateau, and accounting for the majority of cooling through the troposphere.

Mechanisms of midlatitude cross-tropopause transport using a potential vorticity budget approach

[ 1] A potential vorticity (PV) budget method has been used to attribute vertical transport across the near-tropopause ( 1 PVU surface) in extratropical weather systems to radiative, latent heating and cooling, and mixing processes. Sources and sinks of PV due to nonconservative processes are calculated online and advected as passive tracers. There is reasonable agreement between the spatial distribution of transport determined from the PV budget method and the transport across the 1 - 2 PVU zone from a passive tracer and trajectories, but different aspects of exchange can be diagnosed with each method. Stratosphere-to-troposphere transport occurred in the broad upper level PV anomalies and was attributed mainly to latent heating and cooling processes; troposphere-to-stratosphere transport occurred toward the tail of a PV filament and in a ridge region and was attributed mainly to radiative processes. The contribution of mixing processes to transport was comparatively small. Using the PV budget method, the domain integrated exchange across the 1 PVU surface was from stratosphere to troposphere, and the magnitude of 1 x 10(15) kg over a 2 day winter integration in a large North Atlantic domain is consistent with stratosphere-troposphere exchange calculations from other studies. This exchange arises from an approximate balance between the dominant stratosphere-to-troposphere transport due to latent heating and cooling processes and troposphere-to-stratosphere transport due to radiative processes. The direction of transport across the tropopause in a fold was found to be critically dependent on the PV surface considered to represent the tropopause.