Modelling Bivalves in estuaries and coastal areas

Kooijman, S.A.L.M. [Promotor]Meer, J. [Promotor]van der Neves, R. [Promotor]Sousa, T. [Copromotor

Mechanistic models to explore combined effects of toxic chemicals and natural stressing factors: case study on springtails

Kooijman, S.A.L.M. [Promotor]Laskowski, R. [Promotor]Jager, D.T. [Copromotor

Hiding State in CλaSH Hardware Descriptions

Synchronous hardware can be modelled as a mapping from input and state to output and a new state, such mappings are referred to as transition functions. It is natural to use a functional language to implement transition functions. The CaSH compiler is capable of translating transition functions to VHDL. Modelling hardware using multiple components is convenient. Components in CaSH can be considered as instantiations of functions. To avoid packing and unpacking state when composing components, functions are lifted to arrows. By using arrows the chance of making errors will decrease as it is not required to manually (un)pack the state. Furthermore, the Haskell do-syntax for arrows increases the readability of hardware designs. This is demonstrated using a realistic example of a circuit which consists of multiple components

Food Quality in Producer-Grazer Models: A Generalized Analysis

Stoichiometric constraints play a role in the dynamics of natural populations, but are not explicitly considered in most mathematical models. Recent theoretical works suggest that these constraints can have a significant impact and should not be neglected. However, it is not yet resolved how stoichiometry should be integrated in population dynamical models, as different modeling approaches are found to yield qualitatively different results. Here we investigate a unifying framework that reveals the differences and commonalities between previously proposed models for producer-grazer systems. Our analysis reveals that stoichiometric constraints affect the dynamics mainly by increasing the intraspecific competition between producers and by introducing a variable biomass conversion efficiency. The intraspecific competition has a strongly stabilizing effect on the system, whereas the variable conversion efficiency resulting from a variable food quality is the main determinant for the nature of the instability once destabilization occurs. Only if the food quality is high an oscillatory instability, as in the classical paradox of enrichment, can occur. While the generalized model reveals that the generic insights remain valid in a large class of models, we show that other details such as the specific sequence of bifurcations encountered in enrichment scenarios can depend sensitively on assumptions made in modeling stoichiometric constraints.Comment: Online appendixes include

Dynamic Energy Budget (DEB) parameters for ensis directus

In this report a Dynamic Energy Budget (DEB) model for razor clams (Ensis directus) is presented. A DEB model is a generic model describing growth and development of individual organisms as a function of environmental conditions. The DEB model for Ensis directus is based on the standard DEB model. The species specific primary DEB parameters are estimated with the Add_my_pet procedure, using literature data and the results of laboratory experiments with Ensis directus. The performance of the model is demonstrated by theoretical model experiments with varying environmental conditions. In following projects, the model will be used to predict and quantify the effects of sand mining on the shellfish community in the Dutch coastal zone. For this purpose the functional response of the model should be adapted so that the combined effect of changing phytoplankton and suspended sediment concentration on the uptake rate can be simulated