Energy Budget Approach Research Articles

Adapting the dynamic energy budget (DEB) approach to include non-continuous growth (moulting) and provide better predictions of biological performance in crustaceans

Abstract Dynamic energy budget (DEB) theory offers a comprehensive framework for understanding the overall physiological performance (growth, development, respiration, reproduction, etc.) of an organism over the course of its life cycle. We present here a simplified DEB model for the swimming crab Liocarcinus depurator. To the best of our knowledge, this is the first to be presented for this species. Most applications of the standard DEB model assume continuous growth in all size metrics (length, wet mass, carbon content) of the modelled species. However, in crustaceans growth, measured as an increase of carapace length/width, occurs periodically via moult. To account for this, we have extended the model to track the continuous increase in carbon mass as well as the episodic increase in physical size. Model predictions were consistent with the patterns in the observed data, predicting both the moult increment and the intermoult period of an individual. In addition to presenting the model itself, we also make recommendations for further development, and evaluate the potential applications of such a model, both at the individual level (e.g. aquaculture) and as a potential tool for population level dynamics (e.g. fisheries stock assessment).

The role of evapotranspiration in streamflow modeling – An analysis using entropy

Informational entropy can be used to elucidate some important relationships between precipitation, evapotranspiration (ET), and discharge over a range of spatial and temporal scales. Entropy does not suffer from any a priori assumptions of linearity or distributional characteristics. In a study of the Southeastern United States, entropy and mutual information were used to identify relationships between hydrologic variables over spatial scales from a few hundred to several thousand km2 and temporal scales from days to months. Two distinct ET data sets were compared- one based on a highly parameterized energy budget approach and the other based on a complex iterative solution and a modified Penman method. It was found that there was a considerable difference in uncertainty between the two methods and that, although they each contained some amount of explanatory information regarding streamflow the more complex approach contained the most shared information. Further, it was found that streamflow entropy, or uncertainty, increased with drainage area, indicating that larger basins have more uncertainty to be reduced, in that more information can possibly be gained through the knowledge of other variables. However, the knowledge of ET reduces a greater proportion of uncertainty in smaller basins (<1500 km2), while larger basins have more unexplained variability.

Modeling tumor growth inhibition and toxicity outcome after administration of anticancer agents in xenograft mice: A Dynamic Energy Budget (DEB) approach

Host features, such as cell proliferation rates, caloric intake, metabolism and energetic conditions, significantly influence tumor growth; at the same time, tumor growth may have a dramatic impact on the host conditions. For example, in clinics, at certain stages of the tumor growth, cachexia (body weight reduction) may become so relevant to be considered as responsible for around 20% of cancer deaths. Unfortunately, anticancer therapies may also contribute to the development of cachexia due to reduced food intake (anorexia), commonly observed during the treatment periods. For this reason, cachexia is considered one of the major toxicity findings to be evaluated also in preclinical studies. However, although various pharmacokinetic-pharmacodynamic (PK-PD) tumor growth inhibition (TGI) models are currently available, the mathematical modeling of cachexia onset and TGI after an anticancer administration in preclinical experiments is still an open issue. To cope with this, a new PK-PD model, based on a set of tumor-host interaction rules taken from Dynamic Energy Budget (DEB) theory and a set of drug tumor inhibition equations taken from the well-known Simeoni TGI model, was developed. The model is able to describe the body weight reduction, splitting the cachexia directly induced by tumor and that caused by the drug treatment under study. It was tested in typical preclinical studies, essentially designed for efficacy evaluation and routinely performed as a part of the industrial drug development plans. For the first time, both the dynamics of tumor and host growth could be predicted in xenograft mice untreated or treated with different anticancer agents and following different schedules. The model code is freely available for downloading at http://repository.ddmore.eu (model number DDMODEL00000274).

Evaluating Micrometeorological Estimates of Groundwater Discharge from Great Basin Desert Playas.

Groundwater availability studies in the arid southwestern United States traditionally have assumed that groundwater discharge by evapotranspiration (ETg ) from desert playas is a significant component of the groundwater budget. However, desert playa ETg rates are poorly constrained by Bowen ratio energy budget (BREB) and eddy-covariance (EC) micrometeorological measurement approaches. Best attempts by previous studies to constrain ETg from desert playas have resulted in ETg rates that are within the measurement error of micrometeorological approaches. This study uses numerical models to further constrain desert playa ETg rates that are within the measurement error of BREB and EC approaches, and to evaluate the effect of hydraulic properties and salinity-based groundwater density contrasts on desert playa ETg rates. Numerical models simulated ETg rates from desert playas in Death Valley, California and Dixie Valley, Nevada. Results indicate that actual ETg rates from desert playas are significantly below the uncertainty thresholds of BREB- and EC-based micrometeorological measurements. Discharge from desert playas likely contributes less than 2% of total groundwater discharge from Dixie and Death Valleys, which suggests discharge from desert playas also is negligible in other basins. Simulation results also show that ETg from desert playas primarily is limited by differences in hydraulic properties between alluvial fan and playa sediments and, to a lesser extent, by salinity-based groundwater density contrasts.

Ecosystem engineering as an energy transfer process: a simple agent-based model

Ecosystem engineers are defined as organisms who modulate the availability of resources for themselves and other organisms by physically changing the environment. Ecosystem engineering is a well-recognised ecological interaction, but there is a limited number of general models due to the recent development of the field. Agent-based models are often used to study how organisms respond to changing environments and are suitable for modelling ecosystem engineering. To our knowledge, agent-based methodology has not yet been used to model ecosystem engineering. In this paper, we develop a simple agent-based population dynamics model of ecosystem engineering as an energy transfer process. We apply energy budget approach to conceptually explain how ecosystem engineers transfer energy to the environment and define various types of energy transfers relative to their effects on the engineers and other organisms. We simulate environments with various levels of resource abundance and compare the results of the model without ecosystem engineering agents to the model with ecosystem engineering agents. We find that in environments with higher levels of resources, the presence of ecosystem engineers increases the average carrying capacity and the strength of population fluctuations, while in environments with lower levels of resources, ecosystem engineering mitigates fluctuations, increases average carrying capacity and makes environments more resilient. Finally, we discuss about the further application of agent-based modelling for the theoretical and experimental development of the ecosystem engineering concept.

Modeling plant density and ponding water effects on flooded rice evapotranspiration and crop coefficients: critical discussion about the concepts used in current methods

The aim of the study is to propose new modeling approaches for daily estimations of crop coefficient K c for flooded rice (Oryza sativa L., ssp. indica) under various plant densities. Non-linear regression (NLR) and artificial neural networks (ANN) were used to predict K c based on leaf area index LAI, crop height, wind speed, water albedo, and ponding water depth. Two years of evapotranspiration ET c measurements from lysimeters located in a Mediterranean environment were used in this study. The NLR approach combines bootstrapping and Bayesian sensitivity analysis based on a semi-empirical formula. This approach provided significant information about the hidden role of the same predictor variables in the Levenberg-Marquardt ANN approach, which improved K c predictions. Relationships of production versus ET c were also built and verified by data obtained from Australia. The results of the study showed that the daily K c values, under extremely high plant densities (e.g., for LAI max > 10), can reach extremely high values (K c > 3) during the reproductive stage. Justifications given in the discussion question both the K c values given by FAO and the energy budget approaches, which assume that ET c cannot exceed a specific threshold defined by the net radiation. These approaches can no longer explain the continuous increase of global rice yields (currently are more than double in comparison to the 1960s) due to the improvement of cultivars and agriculture intensification. The study suggests that the safest method to verify predefined or modeled K c values is through preconstructed relationships of production versus ET c using field measurements.

Dynamic energy budget approach to evaluate antibiotic effects on biofilms

Quantifying the action of antibiotics on biofilms is essential to devise therapies against chronic infections. Biofilms are bacterial communities attached to moist surfaces, sheltered from external aggressions by a polymeric matrix. Coupling a dynamic energy budget based description of cell metabolism to surrounding concentration fields, we are able to approximate survival curves measured for different antibiotics. We reproduce numerically stratified distributions of cell types within the biofilm and introduce ways to incorporate different resistance mechanisms. Qualitative predictions follow that are in agreement with experimental observations, such as higher survival rates of cells close to the substratum when employing antibiotics targeting active cells or enhanced polymer production when antibiotics are administered. The current computational model enables validation and hypothesis testing when developing therapies.

The subtle origins of surface-warming hiatuses

Using an energy budget approach to understanding decadal temperature trends, this study highlights that observational uncertainty exceeds energy–flux deviations that affect such trends. Thus the origin of recent warming slowdown is unidentifiable.

Vertically resolved weak temperature gradient analysis of the Madden‐Julian Oscillation in SP‐CESM

AbstractThe collective effects of convection can influence large‐scale circulations that, in turn, act to organize convective activity. Such scale interactions may play an important role in moisture‐convection feedbacks thought to be important to both convective aggregation and the Madden‐Julian Oscillation, yet such interactions are not fully understood. New diagnostics based on tropical weak temperature gradient (WTG) theory have begun to make this problem more tractable, and are leveraged in this study to analyze the relationship between various apparent heating processes and large‐scale vertical moisture advection in SP‐CESM. WTG theory provides a framework for accurately diagnosing intraseasonal variations in large‐scale vertical motion from apparent heating, allowing large‐scale vertical moisture advection to be decomposed into contributions from microphysical processes, subgrid scale eddy fluxes, and radiative heating. This approach is consistent with the column moist static energy (MSE) budget approach, and has the added benefit of allowing the vertical advection term of the column MSE budget to be quantitatively partitioned into contributions from the aforementioned apparent heating processes. This decomposition is used to show that the MJO is an instability strongly supported by radiative feedbacks and damped by horizontal advection, consistent with the findings of previous studies. Periods of low, moderate, and high MJO amplitude are compared, and it is shown that changes in the vertical structure of apparent heating do not play a dominant role in limiting the amplitude of the MJO in SP‐CESM. Finally, a diagnostic approach to scale analysis of tropical dynamics is used to investigate how the governing dynamics of various phenomena differ throughout wavenumber‐frequency space. Findings support previous studies that suggest the governing dynamics of the MJO differ from those of strongly divergent convectively coupled equatorial waves.

Comparison of Arctic Sea Ice Thickness from Satellites, Aircraft, and PIOMAS Data

In this study, six Arctic sea ice thickness products are compared: the AVHRR Polar Pathfinder-extended (APP-x), ICESat, CryoSat-2, SMOS, NASA IceBridge aircraft flights, and the Pan-Arctic Ice Ocean Modeling and Assimilation System (PIOMAS). The satellite products are based on three different retrieval methods: an energy budget approach, measurements of ice freeboard, and the relationship between passive microwave brightness temperatures and thin ice thickness. Inter-comparisons are done for the periods of overlap from 2003 to 2013. Results show that ICESat sea ice is thicker than APP-x and PIOMAS overall, particularly along the north coast of Greenland and Canadian Archipelago. The relative differences of APP-x and PIOMAS with ICESat are −0.48 m and −0.31 m, respectively. APP-x underestimates thickness relative to CryoSat-2, with a mean difference of −0.19 m. The biases for APP-x, PIOMAS, and CryoSat-2 relative to IceBridge thicknesses are 0.18 m, 0.18 m, and 0.29 m. The mean difference between SMOS and CryoSat-2 for 0~1 m thick ice is 0.13 m in March and −0.24 m in October. All satellite-retrieved ice thickness products and PIOMAS overestimate the thickness of thin ice (1 m or less) compared to IceBridge for which SMOS has the smallest bias (0.26 m). The spatial correlation between the datasets indicates that APP-x and PIOMAS are the most similar, followed by APP-x and CryoSat-2.

Analysis and simulation of concentrating photovoltaic systems with a microchannel heat sink

A new cooling technique for low concentration photovoltaic (LCPV) system is presented using a microchannel heat sink. This study investigates the influence of operating conditions such as concentration ratio, cooling mass flow rate, wind speed, ambient temperature, and cooling liquid inlet temperature on the performance of the low concentration photovoltaic thermal system. A comprehensive thermal model is developed which includes a thermal model for the photovoltaic, coupled with a thermo-fluid model for the microchannel heat sink. The numerical results are validated using different sets of the available experimental and computational data. The variation of solar cell temperature and electrical and thermal efficiency with operating conditions is investigated using the energy budget approach to interpreting the influence of operating conditions. The predicted results indicate that the use of a microchannel heat sink is a very effective cooling technique. This is especially true for concentrated photovoltaic systems in which a significant reduction in solar cell temperature is attained, along with uniform temperature distribution. At a microchannel flow Reynolds number of 100, it is found that at a concentration ratio of 20, the local solar cell temperature varies between 33.5 and 35.6°C, while at a concentration ratio of 40 the local solar cell temperature ranges from 37 and 41°C. Furthermore, at a concentration ratio of 40, the electrical efficiency reaches 18.5%, and the thermal efficiency achieves the maximum of 62.5%, whereas the power loss in microchannel friction is estimated to be about 0.4% of the electrical power output. Finally, a comparison between the previous solar cell temperatures using different cooling systems and the current results using microchannel is conducted using the dimensional analysis approach to finding the common groups for the various cooling methodologies used. Comparisons indicate that using a microchannel cooling technique achieves the utmost possible reduction of solar cell temperature.

Modelling growth of northern krill (Meganyctiphanes norvegica) using an energy-budget approach

Northern krill (Meganyctiphanes norvegica) is an important species in the North Atlantic and the Mediterranean Sea, but very little life-history information is available under controlled (laboratory) conditions. Here, we use the DEBkiss model to piece together the available data into a quantitative energy budget. We use this model to analyse larval growth curves, and to reconstruct the feeding history for field populations from their (reconstructed) multi-year growth patterns. The resulting model parameters are also used to provide estimates for respiration, feeding and reproduction rates that are consistent with measured values. Many uncertainties remain, but this analysis demonstrates how simple and generic energy-budget models have the potential to integrate observations on different traits, to interpret growth as a function of food and temperature, and to compare different species in a meaningful manner.

Using daily air temperature thresholds to evaluate snow melting occurrence and amount on Alpine glaciers by &amp;lt;i&amp;gt;T&amp;lt;/i&amp;gt;-index models: the case study of the Forni Glacier (Italy)

Abstract. Glacier melt conditions (i.e., null surface temperature and positive energy budget) can be assessed by analyzing data acquired by a supraglacial automatic weather station (AWS), such as the station installed on the surface of Forni Glacier (Italian Alps). When an AWS is not present, the assessment of actual melt conditions and the evaluation of the melt amount is more difficult and simple methods based on T-index (or degree days) models are generally applied. These models require the choice of a correct temperature threshold. In fact, melt does not necessarily occur at daily air temperatures higher than 0 °C. In this paper, we applied both energy budget and T-index approaches with the aim of solving this issue. We start by distinguishing between the occurrence of snowmelt and the reduction in snow depth due to actual ablation (from snow depth data recorded by a sonic ranger). Then we find the daily average temperature thresholds (by analyzing temperature data acquired by an AWS on Forni Glacier) which, on the one hand, best capture the occurrence of significant snowmelt conditions and, on the other, make it possible, using the T-index, to quantify the actual snow ablation amount. Finally we investigated the applicability of the mean tropospheric lapse rate to reproduce air temperature conditions at the glacier surface starting from data acquired by weather stations located outside the glacier area. We found that the mean tropospheric lapse rate allows for a good and reliable reconstruction of glacier air temperatures and that the choice of an appropriate temperature threshold in T-index models is a very important issue. From our study, the application of the +0.5 °C temperature threshold allows for a consistent quantification of snow ablation while, instead, for detecting the beginning of the snow melting processes a suitable threshold has proven to be at least −4.6 °C.

A coupled biogeochemical-Dynamic Energy Budget model as a tool for managing fish production ponds

The sustainability of semi-intensive aquaculture relies on management practices that simultaneously improve production efficiency and minimize the environmental impacts of this activity. The purpose of the present work was to develop a mathematical model that reproduced the dynamics of a semi-intensive fish earth pond, to simulate different management scenarios for optimizing fish production. The modeling approach consisted of coupling a biogeochemical model that simulated the dynamics of the elements that are more likely to affect fish production and cause undesirable environmental impacts (nitrogen, phosphorus and oxygen) to a fish growth model based on the Dynamic Energy Budget approach. The biogeochemical sub-model successfully simulated most water column and sediment variables. A good model fit was also found between predicted and observed white seabream (Diplodus sargus) growth data over a production cycle. In order to optimize fish production, different management scenarios were analysed with the model (e.g. increase stocking densities, decrease/increase water exchange rates, decrease/increase feeding rates, decrease phosphorus content in fish feeds, increase food assimilation efficiency and decrease pellets sinking velocity) to test their effects on the pond environment as well as on fish yields and effluent nutrient discharges. Scenarios were quantitatively evaluated and compared using the Analytical Hierarchical Process (AHP) methodology. The best management options that allow the maximization of fish production while maintaining a good pond environment and minimum impacts on the adjacent coastal system were to double standard stocking densities and to improve food assimilation efficiency.

Geometric calculation of view factors for stream surface radiation modelling in the presence of riparian forest

Many efforts to model stream temperature by using an energy budget approach have not accounted for view factors in modelling stream surface radiative exchanges, used informal approaches for computing them, or relied on calibration, which is not applicable for prediction at unmonitored sites or for predicting the effects of changes in riparian vegetation. In this paper, equations are derived for calculating view factors on the basis of geometric considerations for streams with and without riparian forest. The solutions can accommodate vegetation overhanging the stream surface. Example calculations illustrate the substantial variability of view factors across the stream width, which has implications for the estimation of view factors from point-scale radiation measurements over the stream surface, and the important influence of overhanging vegetation on view factors for narrow streams. View factors computed from the geometric model agreed well with view factors computed from hemispherical photography for streams ranging from 1 to almost 50 m wide, indicating that the model appears to be reasonably robust to deviations from the simplified geometry assumed by the model. In addition to their use in modelling stream surface energy exchanges, the solutions could also be adapted for application to energy balance and microclimate modelling in linear forest openings, such as seismic lines used in oil and gas exploration. Copyright © 2013 John Wiley & Sons, Ltd.

Energetics and carbon budgets of dominant calanoid copepods in the northern Benguela upwelling system

Respiration rates of 16 calanoid copepod species from the northern Benguela upwelling system were measured on board RRS Discovery in September/October 2010 to determine their energy requirements and assess their significance in the carbon cycle. Individual respiration rates were standardised to a mean copepod body mass and a temperature regime typical of the northern Benguela Current. These adjusted respiration rates revealed two different activity levels (active and resting) in copepodids C5 of Calanoides carinatus and females of Rhincalanus nasutus, which reduced their metabolism during dormancy by 82% and 62%, respectively. An allometric function (Imax) and an energy budget approach were performed to calculate ingestion rates. Imax generally overestimated the ingestion rates derived from the energy budget approach by >75%. We suggest that the energy budget approach is the more reliable approximation with a total calanoid copepod (mainly females) consumption of 78mg Cm−2d−1 in neritic regions and 21mg Cm−2d−1 in oceanic regions. The two primarily herbivorous copepods C. carinatus (neritic) and Nannocalanus minor (oceanic) contributed 83% and 5%, respectively, to total consumption by calanoid copepods. Locally, C. carinatus can remove up to 90% of the diatom biomass daily. In contrast, the maximum daily removal of dinoflagellate biomass by N. minor was 9%. These estimates imply that C. carinatus is an important primary consumers in the neritic province of the northern Benguela system, while N. minor has little grazing impact on phytoplankton populations further offshore. Data on energy requirements and total consumption rates of dominant calanoid copepods of this study are essential for the development of realistic carbon budgets and food-web models for the northern Benguela upwelling system.

Dynamic energy budget approach to modeling mechanisms of CdSe quantum dot toxicity

A mechanistic model of bacterial growth based on dynamic energy budget (DEB) theory is utilized to investigate mechanisms of toxicity of CdSe quantum dots (QDs). The model of QD toxicity is developed by extending a previously published DEB model of cadmium ion toxicity to include a separate model of QD toxic action. The extension allows for testing whether toxicity from QD exposure can be explained fully by dissolved cadmium exposure only, or if the separate effects of QDs need to be taken into account as well. Two major classes of QD toxicity mechanisms are considered: acclimation expressed through initial retardation of growth, and three separate metabolic effects that can be a result of QDs either reversibly or irreversibly associating with the cell. The model is consistent with the data, and is able to distinguish toxic effects due to QD nano-particles from the effects due to cadmium ions. Results suggest that, in contrast to ionic exposure where required acclimation remains constant as exposure increases, increase of the energy required for acclimation with exposure is the primary toxic effect of QDs. Reactive oxygen species measurements help conclude that increase in energetic cost of maintenance processes such as cellular repair and maintenance of cross-membrane gradients is the most important of the three metabolic effects of QD toxicity.

Modelling the growth of white seabream (Diplodus sargus) and gilthead seabream (Sparus aurata) in semi-intensive earth production ponds using the Dynamic Energy Budget approach

Fish growth models may help understanding the influence of environmental, physiological and husbandry factors on fish production, providing crucial information to maximize the growth rates of cultivated species. The main objectives of this work were to: i) develop and implement an Individual Based Model using a Dynamic Energy Budget (IBM-DEB) approach to simulate the growth of two commercially important Sparidae species in semi-intensive earth ponds, the white seabream which is considered as a potential candidate for Mediterranean aquaculture and the gilthead seabream that has been cultivated since the early 80s; ii) evaluate which model parameters are more likely to affect fish performance, and iii) investigate which parameters might account for growth differences between the cultivated species. The model may be run in two modes: the “state variable” mode, in which an average fish is simulated with a particular parameter set and the “Individual Based Model” (IBM) mode that simulates a population of n fishes, each with its specific parameter set assigned randomly. The IBM mode has the advantage of allowing a quick model calibration and an evaluation of the parameter sets that produce the best fit between predicted and observed fish growth. Results revealed that the model reproduces reasonably well the growth of the two seabreams. Fish performance was mainly affected by parameters related to feed ingestion/assimilation and reserves utilization, suggesting that special attention should be taken in the estimation of these parameters when applying the model to other species. Comparing the DEB parameters set of the two sparids it seems that the white seabream's low growth rates are a result of higher maintenance costs and a lower feed assimilation efficiency. Hence, the development of new feed formulations may be crucial for the success of white seabream production in semi-intensive earth ponds.

Evaluation of pan coefficient equations in a semi-arid Mediterranean environment using the ASCE-standardized Penman-Monteith method

Reference crop evapotranspiration (ETo) is essential for irrigation, water resources management and environmental assessment. The indirect estimation of ETo is based a) on energy budget approach using meteorological data and b) pan evaporation measurements (Epan) multiplied by pan coefficients (kp) adapted to the surrounding environmental conditions. Significant interest is shown for the kp equations, which have to be tested before their use. The purpose of this study is to evaluate six different kp equations, such as those of Cuenca, Allen and Puitt, Snyder, Pereira et al., Orang, Raghuwanshi and Wallender for the summer growing season (April to October) of Thessaloniki plain in Greece, which is characterized by a semi-arid Mediterranean environment. The evaluation of the kp equations is performed by two years Epan measurements, using as reference the daily ETo values estimated by the ASCE-standardized Penman-Monteith equation (ASCE-PM) in hourly time step. The results of this study showed that Cuenca’s equation provided more accurate daily estimations. Additional analysis is performed in other methods such as those of FAO-56 and Hargreaves based on the calculation time step (hourly or daily) and their correspondence to the ASCE-PM.

Simulating Australian Urban Climate in a Mesoscale Atmospheric Numerical Model

We develop an urban canopy scheme coupled to a mesoscale atmospheric numerical model and evaluate the simulated climate of an Australian city. The urban canopy scheme is based on the Town Energy Budget approach, but is modified to efficiently represent the predominately suburban component of Australian cities in regional climate simulations. Energy conservation is improved by adding a simple model of air-conditioning to prevent the urban parametrization acting as an energy sink during the Australian summer. In-canyon vegetation for suburban areas is represented by a big-leaf model, but with a largely reduced set of prognostic variables compared to previous approaches. Although we have used a recirculation/venting based parametrization of in-canyon turbulent heat fluxes that employs two canyon wall energy budgets, we avoid using a fixed canyon orientation by averaging the canyon fluxes after integrating over 180° of possible canyon orientations. The urban canopy scheme is evaluated by simulating the climate for Melbourne, Australia after coupling it to The Air Pollution Model. The combined system was found to predict a realistic climatology of air temperatures and winds when compared with observations from Environmental Protection Authority monitoring stations. The model also produced a plausible partitioning of the urban energy budget when compared to urban flux-tower studies. Overall, the urban canyon parametrization appears to have reasonable potential for studying present and predicting changes in future Australian urban climates in regional climate simulations.