On the nudging terms at open boundaries in regional ocean models

For open boundary conditions (OBCs) in regional models, a nudging term added to radiative and/or advective conditions during the wave or flow propagation outward from the model domain of interest is widely used, to prevent the predicted boundary values from evolving to become quite different from the external data, especially for a long-term integration. However, nudging time scales are basically unknown, leading to many empirical selections. In this paper, a method for objectively estimating nudging time scales during outward propagation is proposed, by using internal model dynamics near the boundary. We tested this method and other several commonly used OBCs for cases of both an idealized model domain and a realistic configuration, and model results demonstrated that the proposed method improves the model solutions. Many similarities are found between the nudging and mixing time scales, in magnitude, spatial and temporal variations, since the nudging mainly replaces the effect of the mixing terms in this study. However, the mixing time scale is not an intrinsic property of the nudging term because in other studies the nudging term might replace terms other than the mixing terms and, thus, should reflect other characteristic time scales.

High temperature thermal stability investigations of ammonium sulphide passivated InGaAs and interface formation with Al2O3 studied by synchrotron radiation based photoemission

High resolution synchrotron radiation core level photoemission measurements have been used to undertake a comparative study ofthe high temperature thermal stability ofthe ammonium sulphide passivated InGaAs surface and the same surface following the atomic layer deposition (ALD) of an ultrathin (∼1 nm) Al2O3 layer. The solution based ex situ sulphur passivation was found to be effective at removing a significant amount of the native oxides and protecting the surface against re-oxidation upon air exposure. The residual interfacial oxides which form between sulphur passivated InGaAs and the ultrathin Al2O3 layer can be substantially removed at high temperature (up to 700 ◦C) without impacting on the InGaAs stoichiometry while significant loss of indium was recorded at this temperature on the uncovered sulphur passivated InGaAs surface.

High-temperature stability study of 1 nm Al2O3 deposited on InAs surfaces investigated by synchrotron radiation based photoemission spectroscopy

High-resolution soft x-ray photoemission spectroscopy (SXPS) has been used to study the high-temperature thermal stability of ultra-thin atomic layer deposited (ALD) Al2O3 layers (~1 nm) on sulfur passivated and native oxide covered InAs surfaces. While the arsenic oxides were removed from both interfaces following a 600 °C anneal, a residual indium oxide signal remained. No significant differences were observed between the sulfur passivated and native oxide surfaces other than the thickness of the interfacial oxide layer while the Al2O3 stoichiometry remained unaffected by the anneals. The energy band offsets were determined for the Al2O3 on the sulfur passivated InAs surface using both valence band edge and shallow core-level photoemission measurements.

The potential for the use of agent-based models in ecotoxicology

This chapter introduces ABMs, their construction, and the pros and cons of their use. Although relatively new, agent-basedmodels (ABMs) have great potential for use in ecotoxicological research – their primary advantage being the realistic simulations that can be constructed and particularly their explicit handling of space and time in simulations. Examples are provided of their use in ecotoxicology primarily exemplified by different implementations of the ALMaSS system. These examples presented demonstrate how multiple stressors, landscape structure, details regarding toxicology, animal behavior, and socioeconomic effects can and should be taken into account when constructing simulations for risk assessment. Like ecological systems, in ABMs the behavior at the system level is not simply the mean of the component responses, but the sum of the often nonlinear interactions between components in the system; hence this modeling approach opens the door to implementing and testing much more realistic and holistic ecotoxicological models than are currently used.

Temperature-responsive water-soluble copolymers based on 2-hydroxyethyl acrylate and butyl acrylate

Amphiphilic copolymers have been synthesised by free radical copolymerisation of 2-hydroxyethyl acrylate with butyl acrylate, the reactivity ratios of which indicate practically equal reactivity. The copolymers containing less than 30 mol-% of BA were soluble in water and exhibited a LCST in aqueous solutions. It was found that the interaction between these copolymers and poly(acrylic acid) in aqueous solutions resulted in the formation of interpolymer complexes stabilised by hydrogen bonds and hydrophobic interactions. This interaction was significantly affected by solution I pH and led to modification of the temperature-responsive behaviour of the copolymers.

Novel temperature-responsive water-soluble copolymers based on 2-hydroxyethylacrylate and vinyl butyl ether and their interactions with poly(carboxylic acids)

Novel water-soluble amphiphilic copolymers have been synthesized by free radical copolymerization of 2-hydroxyethylacrylate with vinyl butyl ether. In water these copolymers exhibit lower critical solution temperature, which depends on the content of hydrophobic vinyl butyl ether units. The interaction between these copolymers and poly(acrylic acid) or poly(methacrylic acid) in aqueous solutions results in formation of interpolymer complexes stabilized by hydrogen bonds and hydrophobic interactions. An increase in hydrophobicity of the copolymers leads to the enhancement of their complex formation ability with respect to poly(acrylic acid) and poly(methacrylic acid). Poly(methacrylic acid) forms stronger complexes with the copolymers when compared with poly(acrylic acid). The complexes exhibit dual sensitivity to pH- and temperature and this property may be easily adjusted regulating the strength of interaction. (c) 2005 Wiley Periodicals, Inc.

Classifying general nonlinear force laws in cell-based models via the continuum limit

though discrete cell-based frameworks are now commonly used to simulate a whole range of biological phenomena, it is typically not obvious how the numerous different types of model are related to one another, nor which one is most appropriate in a given context. Here we demonstrate how individual cell movement on the discrete scale modeled using nonlinear force laws can be described by nonlinear diffusion coefficients on the continuum scale. A general relationship between nonlinear force laws and their respective diffusion coefficients is derived in one spatial dimension and, subsequently, a range of particular examples is considered. For each case excellent agreement is observed between numerical solutions of the discrete and corresponding continuum models. Three case studies are considered in which we demonstrate how the derived nonlinear diffusion coefficients can be used to (a) relate different discrete models of cell behavior; (b) derive discrete, intercell force laws from previously posed diffusion coefficients, and (c) describe aggregative behavior in discrete simulations.

Representing the acquisition and use of energy by individuals in agent-based models of animal populations

Summary 1. Agent-based models (ABMs) are widely used to predict how populations respond to changing environments. As the availability of food varies in space and time, individuals should have their own energy budgets, but there is no consensus as to how these should be modelled. Here, we use knowledge of physiological ecology to identify major issues confronting the modeller and to make recommendations about how energy budgets for use in ABMs should be constructed. 2. Our proposal is that modelled animals forage as necessary to supply their energy needs for maintenance, growth and reproduction. If there is sufficient energy intake, an animal allocates the energy obtained in the order: maintenance, growth, reproduction, energy storage, until its energy stores reach an optimal level. If there is a shortfall, the priorities for maintenance and growth/reproduction remain the same until reserves fall to a critical threshold below which all are allocated to maintenance. Rates of ingestion and allocation depend on body mass and temperature. We make suggestions for how each of these processes should be modelled mathematically. 3. Mortality rates vary with body mass and temperature according to known relationships, and these can be used to obtain estimates of background mortality rate. 4. If parameter values cannot be obtained directly, then values may provisionally be obtained by parameter borrowing, pattern-oriented modelling, artificial evolution or from allometric equations. 5. The development of ABMs incorporating individual energy budgets is essential for realistic modelling of populations affected by food availability. Such ABMs are already being used to guide conservation planning of nature reserves and shell fisheries, to assess environmental impacts of building proposals including wind farms and highways and to assess the effects on nontarget organisms of chemicals for the control of agricultural pests. Keywords: bioenergetics; energy budget; individual-based models; population dynamics.

Population based models of cortical drug response: insights from anaesthesia

A great explanatory gap lies between the molecular pharmacology of psychoactive agents and the neurophysiological changes they induce, as recorded by neuroimaging modalities. Causally relating the cellular actions of psychoactive compounds to their influence on population activity is experimentally challenging. Recent developments in the dynamical modelling of neural tissue have attempted to span this explanatory gap between microscopic targets and their macroscopic neurophysiological effects via a range of biologically plausible dynamical models of cortical tissue. Such theoretical models allow exploration of neural dynamics, in particular their modification by drug action. The ability to theoretically bridge scales is due to a biologically plausible averaging of cortical tissue properties. In the resulting macroscopic neural field, individual neurons need not be explicitly represented (as in neural networks). The following paper aims to provide a non-technical introduction to the mean field population modelling of drug action and its recent successes in modelling anaesthesia.

Calibration and evaluation of individual-based models using Approximate Bayesian Computation

This paper investigates the feasibility of using approximate Bayesian computation (ABC) to calibrate and evaluate complex individual-based models (IBMs). As ABC evolves, various versions are emerging, but here we only explore the most accessible version, rejection-ABC. Rejection-ABC involves running models a large number of times, with parameters drawn randomly from their prior distributions, and then retaining the simulations closest to the observations. Although well-established in some fields, whether ABC will work with ecological IBMs is still uncertain. Rejection-ABC was applied to an existing 14-parameter earthworm energy budget IBM for which the available data consist of body mass growth and cocoon production in four experiments. ABC was able to narrow the posterior distributions of seven parameters, estimating credible intervals for each. ABC’s accepted values produced slightly better fits than literature values do. The accuracy of the analysis was assessed using cross-validation and coverage, currently the best available tests. Of the seven unnarrowed parameters, ABC revealed that three were correlated with other parameters, while the remaining four were found to be not estimable given the data available. It is often desirable to compare models to see whether all component modules are necessary. Here we used ABC model selection to compare the full model with a simplified version which removed the earthworm’s movement and much of the energy budget. We are able to show that inclusion of the energy budget is necessary for a good fit to the data. We show how our methodology can inform future modelling cycles, and briefly discuss how more advanced versions of ABC may be applicable to IBMs. We conclude that ABC has the potential to represent uncertainty in model structure, parameters and predictions, and to embed the often complex process of optimizing an IBM’s structure and parameters within an established statistical framework, thereby making the process more transparent and objective.

Predicting how many animals will be where: how to build, calibrate and evaluate individual-based models

Individual-based models (IBMs) can simulate the actions of individual animals as they interact with one another and the landscape in which they live. When used in spatially-explicit landscapes IBMs can show how populations change over time in response to management actions. For instance, IBMs are being used to design strategies of conservation and of the exploitation of fisheries, and for assessing the effects on populations of major construction projects and of novel agricultural chemicals. In such real world contexts, it becomes especially important to build IBMs in a principled fashion, and to approach calibration and evaluation systematically. We argue that insights from physiological and behavioural ecology offer a recipe for building realistic models, and that Approximate Bayesian Computation (ABC) is a promising technique for the calibration and evaluation of IBMs. IBMs are constructed primarily from knowledge about individuals. In ecological applications the relevant knowledge is found in physiological and behavioural ecology, and we approach these from an evolutionary perspective by taking into account how physiological and behavioural processes contribute to life histories, and how those life histories evolve. Evolutionary life history theory shows that, other things being equal, organisms should grow to sexual maturity as fast as possible, and then reproduce as fast as possible, while minimising per capita death rate. Physiological and behavioural ecology are largely built on these principles together with the laws of conservation of matter and energy. To complete construction of an IBM information is also needed on the effects of competitors, conspecifics and food scarcity; the maximum rates of ingestion, growth and reproduction, and life-history parameters. Using this knowledge about physiological and behavioural processes provides a principled way to build IBMs, but model parameters vary between species and are often difficult to measure. A common solution is to manually compare model outputs with observations from real landscapes and so to obtain parameters which produce acceptable fits of model to data. However, this procedure can be convoluted and lead to over-calibrated and thus inflexible models. Many formal statistical techniques are unsuitable for use with IBMs, but we argue that ABC offers a potential way forward. It can be used to calibrate and compare complex stochastic models and to assess the uncertainty in their predictions. We describe methods used to implement ABC in an accessible way and illustrate them with examples and discussion of recent studies. Although much progress has been made, theoretical issues remain, and some of these are outlined and discussed.

Soil water evaporation under densities of coverage with vegetable residue

O presente estudo foi realizado no Instituto Agronômico do Paraná (IAPAR), em Londrina, Estado do Paraná (latitude de 23º18'S, longitude de 51º09'W e altitude média de 585 m). O clima local, segundo a classificação do Köppen, é do tipo Cfa, ou seja, subtropical úmido, com chuvas em todas as estações, podendo ocorrer secas no período de inverno. Determinou-se a evaporação (E) da água do solo sob diferentes densidades de cobertura com resíduo da cultura de trigo. Os tratamentos foram instalados em lisímetros de pesagem de 2,66 m² e 1,3 m de profundidade, que permitem determinar E por diferença de massa com precisão equivalente a 0,1 mm em intervalos de uma hora. Os tratamentos consistiram em 0; 2,5; 5 e 10 t ha-1 de resíduos da cultura do trigo, colocadas de forma homogênea em cada lisímetro. No primeiro ciclo (22/09 a 20/10/2008), a redução de E em relação ao solo descoberto foi de 4; 15 e 24%, enquanto no segundo ciclo (01/12 a 30/12/2008), a redução foi de 15; 22 e 25%, respectivamente, para os tratamentos 2,5; 5 e 10 t ha-1.