Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Sensitivity analysis methodologies for analysing emergence using agent-based models
    Broeke, Guus ten - \ 2017
    Wageningen University. Promotor(en): J. Molenaar, co-promotor(en): G.A.K. van Voorn; A. Ligtenberg. - Wageningen : Wageningen University - ISBN 9789463436991 - 211
    mathematics - computational mathematics - mathematical models - dynamic modeling - sensitivity analysis - adaptation - methodology - simulation - wiskunde - computerwiskunde - wiskundige modellen - dynamisch modelleren - gevoeligheidsanalyse - adaptatie - methodologie - simulatie

    Many human and natural systems are highly complex, because they consist of many interacting parts. Such systems are known as complex adaptive systems (CAS). Understanding CAS is possible only by studying the interactions between constituent parts, rather than focussing only on the properties of the parts in isolation. Often, the possibilities for systematically studying these interactions in real-life systems are limited. Simulation models can then be an important tool for testing what properties may emerge, given various assumptions on the interactions in the system. Agent-based models (ABMs) are particularly useful for studying CAS, because ABMs explicitly model interactions between autonomous agents and their environment.

    Currently, the utility of ABMs is limited by a lack of available methodologies for analysing their results. The main tool for analysing CAS models is sensitivity analysis. Yet, standard methods of sensitivity analysis are not well-suited to deal with the complexity of ABMs. Thus, there is a need for sensitivity analysis methodologies that are specifically developed for analysing ABMs. The objective of this thesis is to contribute such methodologies. Specifically, we propose methodologies for (1) detecting tipping points, (2) analysing the effects of agent adaptation, and (3) analysing resilience of ABMs.

    Chapter 2 introduces traditional methods of sensitivity analysis. These methods are demonstrated by applying them to rank the most influential parameters of an ODE model of predator-prey interaction. Furthermore, the role of sensitivity analysis in model validation is discussed.

    In Chapter 3 we investigate the use of sensitivity analysis for detecting tipping points. Whereas bifurcation analysis methods are available for detecting tipping points in ODE models, these methods are not applicable to ABMs. Therefore, we use an ODE model to verify the results from sensitivity analysis against those of bifurcation analysis. We conclude that one-factor-at-a-time sensitivity analysis (OFAT) is a helpful method for detecting tipping points. However, OFAT is a local method that considers only changes in individual parameters. It is therefore recommended to supplement OFAT with a global method to investigate interaction effects. For this purpose, we recommend all-but-one-at-a-time sensitivity analysis (ABOS) as a graphical sensitivity analysis method that takes into account parameter interactions and can help with the detection of tipping points.

    In Chapter 4 we introduce a basic ABM model of agents competing in a spatial environment for a renewable resource. This basic model will be extended in the subsequent chapters, and will serve as a testing case for various sensitivity analysis methods. In Chapter 4, it is used to assess the utility of existing sensitivity analysis methods for ABMs. The results show that traditional methods of sensitivity are not sufficient to analyse the ABM, due to the presence of tipping points and other strong non-linearities in the model output. In contrast, OFAT is found to be helpful for detecting tipping points, as was suggested in Chapter 3. Based on these outcomes, OFAT is recommended as a starting point for sensitivity analysis of ABMs, preferably supplemented by a global method to investigate interaction effects.

    In Chapter 5 we extend the ABM of Chapter 4 by adding agent adaptation in the form of a mechanism of natural selection. On short time-scales, the model behaviour appears to be similar to the non-adaptive model version. On longer time-scales, the agent adaptation causes the state of the model to gradually change as agents continue to adapt to their surroundings. We propose a sensitivity analysis method to measure the effects of this adaptation. This method is based on a quantification of the difference between probability density functions of model version with and without adaptation. Using this method, we show that this adaptation increases the resilience of the system by giving it the flexibility needed to respond to pressures.

    In Chapter 6 we further extend the test-case by giving agents the option to harvest either cooperatively or individually. Cooperation increases the potential yields, but introduces the risk of defection of the interaction partner. It is shown that ecological factors, which are usually not considered in models on cooperation, strongly affect the level of cooperation in the system. For example, low levels of cooperation lead to a decreased population size, and causes the formation of small groups of agents with a higher level of cooperation. As a result, cooperation persists even without any mechanisms to promote it. Nevertheless, the inclusion of such mechanisms in the form of indirect reciprocity does further increase the level of cooperation. Furthermore, we show that the resulting high levels of cooperation, depending on the circumstances, can increase the resilience of the agent population against shocks.

    To conclude, in this thesis several methodologies have been proposed to help with ABM analysis. Specifically, OFAT and ABOS are recommended for detecting tipping points in ABMs, and in Chapter 5 a protocol is introduced for quantifying the effects of adaptation. By suggesting these methodologies, this thesis aims to contribute to the utility of ABMs, especially for studying CAS.

    Plant cortical microtubule dynamics and cell division plane orientation
    Chakrabortty, Bandan - \ 2017
    Wageningen University. Promotor(en): B.J.G. Scheres; B.M. Mulder. - Wageningen : Wageningen University - ISBN 9789463431828 - 124
    microtubules - plant cell biology - cell division - plant development - molecular biology - morphogenesis - simulation - microtubuli - plantencelbiologie - celdeling - plantenontwikkeling - moleculaire biologie - morfogenese - simulatie

    This thesis work aimed at a better understanding of the molecular basis of oriented cell division in plant cell. As, the efficiency of plant morphogenesis depends on oriented cell division, this work should contribute towards a fundamental understanding of the molecular basis of efficient plant morphogenesis. We describe a modelling framework that allows us to simulate microtubule dynamics on the surface of arbitrary shapes. We further explored the generic role of microtubule regulatory effects such as shape anisotropy, edge-catastrophe and enhanced microtubule stabilization on the orientation of the microtubule array. Through a combined approach of experimental observations of cell division patterns and simulation of microtubule dynamics, we describe a possible molecular basis of oriented cell division during Arabidopsis early embryogenesis. We also infer the necessity of incorporating anisotropic growth/stress response of microtubules towards understanding division plane orientation in the growing epidermal root cells of Arabidopsis.

    Using probabilistic graphical models to reconstruct biological networks and linkage maps
    Wang, Huange - \ 2017
    Wageningen University. Promotor(en): F.A. Eeuwijk, co-promotor(en): J. Jansen. - Wageningen : Wageningen University - ISBN 9789463431538 - 150
    probabilistic models - models - networks - linkage - mathematics - statistics - quantitative trait loci - phenotypes - simulation - waarschijnlijkheidsmodellen - modellen - netwerken - koppeling - wiskunde - statistiek - loci voor kwantitatief kenmerk - fenotypen - simulatie

    Probabilistic graphical models (PGMs) offer a conceptual architecture where biological and mathematical objects can be expressed with a common, intuitive formalism. This facilitates the joint development of statistical and computational tools for quantitative analysis of biological data. Over the last few decades, procedures based on well-understood principles for constructing PGMs from observational and experimental data have been studied extensively, and they thus form a model-based methodology for analysis and discovery. In this thesis, we further explore the potential of this methodology in systems biology and quantitative genetics, and illustrate the capabilities of our proposed approaches by several applications to both real and simulated omics data.

    In quantitative genetics, we partition phenotypic variation into heritable, genetic, and non-heritable, environmental, parts. In molecular genetics, we identify chromosomal regions that drive genetic variation: quantitative trait loci (QTLs). In systems genetics, we would like to answer the question of whether relations between multiple phenotypic traits can be organized within wholly or partially directed network structures. Directed edges in those networks can be interpreted as causal relationships, causality meaning that the consequences of interventions are predictable: phenotypic interventions in upstream traits, i.e. traits occurring early in causal chains, will produce changes in downstream traits. The effect of a QTL allele can be considered to represent a genetic intervention on the phenotypic network. Various methods have been proposed for statistical reconstruction of causal phenotypic networks exploiting previously identified QTLs. In chapter 2, we present a novel heuristic search algorithm, namely the QTL+phenotype supervised orientation (QPSO) algorithm, to infer causal relationships between phenotypic traits. Our algorithm shows good performance in the common, but so far uncovered case, where some traits come without QTLs. Therefore, our algorithm is especially attractive for applications involving expensive phenotypes, like metabolites, where relatively few genotypes can be measured and population size is limited.

    Standard QTL mapping typically models phenotypic variations observable in nature in relation to genetic variation in gene expression, regardless of multiple intermediate-level biological variations. In chapter 3, we present an approach integrating Gaussian graphical modeling (GGM) and causal inference for simultaneous modeling of multilevel biological responses to DNA variations. More specifically, for ripe tomato fruits, the dependencies of 24 sensory traits on 29 metabolites and the dependencies of all the sensory and metabolic traits further on 21 QTLs were investigated by three GGM approaches including: (i) lasso-based neighborhood selection in combination with a stability approach to regularization selection, (ii) the PC-skeleton algorithm and (iii) the Lasso in combination with stability selection, and then followed by the QPSO algorithm. The inferred dependency network which, though not essentially representing biological pathways, suggests how the effects of allele substitutions propagate through multilevel phenotypes. Such simultaneous study of the underlying genetic architecture and multifactorial interactions is expected to enhance the prediction and manipulation of complex traits. And it is applicable to a range of population structures, including offspring populations from crosses between inbred parents and outbred parents, association panels and natural populations.

    In chapter 4, we report a novel method for linkage map construction using probabilistic graphical models. It has been shown that linkage map construction can be hampered by the presence of genotyping errors and chromosomal rearrangements such as inversions and translocations. Our proposed method is proven, both theoretically and practically, to be effective in filtering out markers that contain genotyping errors. In particular, it carries out marker filtering and ordering simultaneously, and is therefore superior to the standard post-hoc filtering using nearest-neighbour stress. Furthermore, we demonstrate empirically that the proposed method offers a promising solution to genetic map construction in the case of a reciprocal translocation.

    In the domain of PGMs, Bayesian networks (BNs) have proven, both theoretically and practically, to be a promising tool for the reconstruction of causal networks. In particular, the PC algorithm and the Metropolis-Hastings algorithm, which are representatives of mainstream methods to BN structure learning, are reported to have been successfully applied to the field of biology. In view of the fact that most biological systems exist in the form of random network or scale-free network, in chapter 5 we compare the performance of the two algorithms in constructing both random and scale-free BNs. Our simulation study shows that for either type of BN, the PC algorithm is superior to the M-H algorithm in terms of timeliness; the M-H algorithm is preferable to the PC algorithm when the completeness of reconstruction is emphasized; but when the fidelity of reconstruction is taken into account, the better one of the two algorithms varies from case to case. Moreover, whichever algorithm is adopted, larger sample sizes generally permit more accurate reconstructions, especially in regard to the completeness of the resulting networks.

    Finally, chapter 6 presents a further elaboration and discussion of the key concepts and results involved in this thesis.

    Logistics network design & control : managing product quality in a blooming sector
    Keizer, M. de - \ 2015
    Wageningen University. Promotor(en): Jack van der Vorst, co-promotor(en): Jacqueline Bloemhof-Ruwaard; Rene Haijema. - Wageningen : Wageningen University - ISBN 9789462576025 - 239
    logistiek - netwerkanalyse - sierteelt - kwaliteitszorg - kwaliteit - productie - tuinbouw - verse producten - voedselproducten - simulatiemodellen - simulatie - logistics - network analysis - ornamental horticulture - quality management - quality - production - horticulture - fresh products - food products - simulation models - simulation
    A model based method for evaluation of crop operation scenarios in greenhouses
    Ooster, A. van 't - \ 2015
    Wageningen University. Promotor(en): Eldert van Henten, co-promotor(en): Jan Bontsema; Silke Hemming. - Wageningen : Wageningen University - ISBN 9789462573024 - 169
    kastechniek - glastuinbouw - simulatie - discrete simulatie - simulatiemodellen - arbeid (werk) - rozen - greenhouse technology - greenhouse horticulture - simulation - discrete simulation - simulation models - labour - roses

    Abstract

    This research initiated a model-based method to analyse labour in crop production systems and to quantify effects of system changes in order to contribute to effective greenhouse crop cultivation systems with efficient use of human labour and technology. This method was gradually given shape in the discrete event simulation model GWorkS, acronym for Greenhouse Work Simulation. Model based evaluation of labour in crop operations is relatively new in greenhouse horticulture and could allow for quantitative evaluation of existing greenhouse crop production systems, analysis of improvements, and identification of bottlenecks in crop operations. The modelling objective was a flexible and generic approach to quantify effects of production system changes. Cut-rose was selected as a case-study representative for many cut-flowers and fruit vegetables.

    The first focus was a queueing network model of the actions of a worker harvesting roses in a mobile cultivation system. Data and observations from a state-of-art mobile rose production system were used to validate and test the harvesting model. Model experiments addressed target values of operational parameters for best system performance. The model exposed effects of internal parameters not visible in acquired data. This was illustrated for operator and gutter speed as a function of crop yield. The structure and setup of the GWorkS model was generic where possible and system specific where inevitable.

    The generic concept was tested by transferring GWorkS to harvesting a greenhouse section in a static growing system for cut-roses and extending it with navigation in the greenhouse, product handling, and multiple operator activity (up to 3 workers). Also for rose harvesting in a static growing system, the model reproduced harvesting accurately. A seven workday validation for an average skilled harvester showed a relative root mean squared error (RRMSE) under 5% for both labour time and harvest rate. A validation for 96 days with various harvesters showed a higher RRMSE, 15.2% and 13.6% for labour time and harvest rate respectively. This increase was mainly caused by the absence of model parameters for individual harvesters. Work scenarios were simulated to examine effects of skill, equipment, and harvest management. For rose yields of 0.5 and 3 harvested roses per m2, harvest rate was 346 and 615 stems h-1 for average skilled harvesters, 207 and 339 stems h-1 for new harvesters and 407 and 767 stems h-1 for highly skilled harvesters. Economic effects of trolley choice are small, 0-2 € per 1000 stems and two harvest cycles per day was only feasible if yield quality effects compensate for extra costs of 0.2-1.1 eurocents per stem.

    In a sensitivity analysis and uncertainty analysis, parameters with strong influence on labour performance in harvesting roses in a static system were identified as well as effects of parameter uncertainty on key performance indicators. Differential sensitivity was analysed, and results were tested for linearity and superposability and verified using the robust Monte Carlo method. The model was not extremely sensitive for any of the 22 tested input parameters. Individual sensitivities changed with crop yield. Labour performance was most affected by greenhouse section dimensions, single rose cut time, and yield. Throughput was most affected by cut time of a single rose, yield, number of harvest cycles, greenhouse length and operator transport velocity. In uncertainty analysis the coefficient of variation for the most important outputs labour time and throughput is around 5%. The main sources of model uncertainty were in parallel execution of actions and trolley speed. The uncertainty effect of these parameters in labour time, throughput and utilisation of the operator is acceptably small with CV less than 5%. The combination of differential sensitivity analysis and Monte Carlo analysis gave full insight in both individual and total sensitivity of key performance indicators.

    To realise the objective of model based improvement of the operation of horticultural production systems in resources constrained system, the GWorkS-model was extended for simultaneous crop operations by multiple workers analysis. This objective was narrowed down to ranking eight scenarios with worker skill as a central theme including a labour management scenario applied in practise. The crop operations harvest, disbudding and bending were considered, which represent over 90% of crop-bound labour time. New sub-models on disbudding and bending were verified using measured data. The integrated scenario study on harvest, disbudding and bending showed differences between scenarios of up to 5 s per harvested rose in simulated labour time and up to 7.1 € m-2 per year in labour costs. The simulated practice of the grower and the scenario with minimum costs indicated possible savings of 4 € m-2 per year, which equals 15% of labour cost for harvest, disbudding and bending. Multi-factorial assessment of scenarios pointed out that working with low skilled, low paid workers is not effective. Specialised workers were most time effective with -17.5% compared to the reference, but overall a permanent team of skilled generalists ranked best. Reduced diversity in crop operations per day improved labour organisational outputs but ranked almost indifferent. The reference scenario was outranked by 5 scenarios.

    Discrete event simulation, as applied in the GWorkS-model, described greenhouse crop operations mechanistically correct and predicts labour use accurately. This model-based method was developed and validated by means of data sets originating from commercial growers. The model provided clear answers to research questions related to operations management and labour organisation using the full complexity of crop operations and a multi-factorial criterion. To the best of our knowledge, the GWorkS-model is the first model that is able to simulate multiple crop operations with constraints on available staff and resources. The model potentially supports analysis and evaluation of design concepts for system innovation.

    Assessment of uncertainties in simulated European precipitation
    Haren, R. van - \ 2015
    Wageningen University. Promotor(en): Wilco Hazeleger, co-promotor(en): G.J. van Oldenborgh. - Wageningen : Wageningen University - ISBN 9789462572324 - 132
    neerslag - simulatie - hydrologie - klimaatverandering - modellen - europa - precipitation - simulation - hydrology - climatic change - models - europe

    The research presented in this thesis is aimed to understanding the changes and the simulation of precipitation in Europe. A correct representation of simulated (trends in) European precipitation is important to have confidence in projections of future changes therein. These projections are relevant for different hydrological applications. Among others, simulated changes of summer drying are often accompanied by an enhanced increase in air temperatures [Zampieri et al., 2009]. This can be expected to have large impacts on society and ecosystems, affecting, for example, water resources, agriculture and fire risk [Rowell, 2009]. Projections of changes in extreme precipitation are critical for estimates of future discharge extremes of large river basins, and changes in frequency of major flooding events [e.g. Kew et al., 2010].

    The subjects that are studied in this thesis are divided in three parts: (1) evaluation of 20th century European precipitation trends; (2) effect of general circulation model (GCM) spatial resolution on simulated western European winter precipitation in the current climate; and (3) effect of GCM spatial resolution on simulated future summer drying in central and southern Europe.

    In the first part of the thesis (chapters 2 and 3) an investigation of (extreme) precipitation trends in multi-model ensembles including both global and regional climate models is performed. The results show that these models fail to reproduce the observed trends over (parts of) the past century. In many regions the model spread does not cover the trend in the observations: the models significantly underestimate the observed trend. A misrepresentation of large scale atmospheric circulation changes in climate models is found to be responsible for the underestimation of winter precipitation trends in Europe over the past century. Additionally, the underestimation of trends in winter precipitation extremes in the Rhine basin is directly related to this as well. In summer a misrepresentation of sea surface temperature (SST) trends is responsible for the underestimation of summer precipitation trends along the coastal regions of western Europe.

    The second part (chapter 4) investigates the effect of GCM spatial resolution on modeled precipitation over Europe using an atmosphere-only GCM at two resolutions (EC-Earth, ~25 km and ~112 km horizontal resolution). The results show that the high resolution model gives a more accurate representation of northern and central European winter precipitation. The medium resolution model has a larger positive bias in precipitation in most of the northern half of Europe. Storm tracks are better simulated in the high resolution model, providing for a more accurate horizontal moisture transport and precipitation. A decomposition of the precipitation difference between the medium- and high resolution model in a part related and a part unrelated to a difference in the distribution of vertical atmospheric velocity confirms that the reduced precipitation in the high resolution model is likely the result of a reduced moisture transport at this resolution: the precipitation difference in this area in unrelated to a difference in the distribution of vertical atmospheric velocity. In areas with orography the change in vertical velocity distribution is more important.

    Using the same atmosphere-only model, the third part (chapter 5) of this thesis investigates the influence of GCM spatial resolution on the simulated future summer drying of central Europe. High resolution models have a more realistic representation of circulation in the current climate and could provide more confidence on future projections of circulation forced drying. The results show that the high resolution model is characterized by a stronger drying in spring and summer, mainly forced by circulation changes. The initial spring drying intensifies the summer drying by a positive soil moisture feedback. The results are confirmed by finding analogs of the difference between the high and medium-resolution model circulation in the natural variability in another ensemble of climate model simulations. In current climate, these show the same precipitation difference pattern resulting from the summer circulation difference. In future climate the spring circulation plays a key role as well. It is concluded that the reduction of circulation biases due to increased resolution gives higher confidence in the strong drying trend projected for central Europe by the high-resolution version of the model.

    Improving obstacle awareness for robotic harvesting of sweet-pepper
    Bac, C.W. - \ 2015
    Wageningen University. Promotor(en): Eldert van Henten, co-promotor(en): Jochen Hemming. - Wageningen : Wageningen University - ISBN 9789462571808 - 186
    robots - oogsten - paprika's - obstructie - detectie - spectraalanalyse - beeldverwerking - simulatie - kassen - robots - harvesting - sweet peppers - obstruction - detection - spectral analysis - image processing - simulation - greenhouses

    Abstract

    Obstacles are densely spaced in a sweet-pepper crop and they limit the free workspace for a robot that can detach the fruit from the plant. Previous harvesting robots mostly attempted to detach a fruit without using any information of obstacles, thereby reducing the harvest success and damaging the fruit and plant. The hypothesis evaluated in this research is that a robot capable of distinguishing between hard and soft obstacles, and capable of employing this knowledge, improves harvest success and decreases plant damages during harvesting. In line with this hypothesis, the main objective was to develop a sweet-pepper harvesting robot capable of distinguishing between hard and soft obstacles, and of employing this knowledge.

    As a start, the thesis describes the crop environment of a harvesting robot, reviews all harvesting robots developed for high-value crops, and defines challenges for future development. Based on insights from this review, we explored the ability to distinguish five plant parts. A multi-spectral imaging set-up and artificial lighting were developed and pixels were classified using a decision tree classifier and a feature selection algorithm. Classification performance was found insufficient and therefore post-processing methods were employed to enhance performance and detect plant parts on a blob basis. Still, performance was found insufficient and a focussed study was conducted on stem localization. The imaging set-up and algorithm developed for stem localization were used to provide real stem locations for motion planning simulations. To address the motion planning problem, we developed a new method of selecting the grasp pose of the end-effector. The new method and the stem localization algorithm were both integrated in the harvesting robot, and we tested their contribution to performance. This research is the first to report a performance evaluation of a sweet-pepper harvesting robot tested under greenhouse conditions. The robot was able to harvest sweet-peppers in a commercial greenhouse, but at limited success rates: harvest success was 6% when the Fin Ray end-effector was mounted, and 2% when the Lip-type end-effector was mounted. After simplifying the crop, by removal of fruit clusters and occluding leaves, harvest success was 26% (Fin Ray) and 33% (Lip-Type). Hence, these properties of the crop partly caused the low performance. The cycle time per fruit was commonly 94 s, i.e. a factor of 16 too long compared with an economically feasible time of 6 s. Several recommendations were made to bridge the gap in performance. Additionally, the robot’s novel functionality of stem-dependant determination of the grasp pose was evaluated to respond to the hypothesis.

    Testing the effect of enabling stem-dependent determination of the grasp pose revealed that, in a simplified crop, grasp success increased from 41% to 61% for the Lip-type end-effector, and stem damage decreased from 19% to 13% for the Fin Ray end-effector. Although these effects seem large, they were not statistically significant and therefore resulted in rejection of the hypothesis. To re-evaluate significance of the effects, more samples should be tested in future work.

    In conclusion, this PhD research improves the obstacle awareness for robotic harvesting of sweet-pepper by the robot’s capability of perceiving and employing hard obstacles (plant stems), whereas previous harvesting robots either lumped all obstacles in one obstacle class, or did not perceive obstacles. This capability may serve as useful generic functionality for future robots.

    Simulating the expansion of large-sized farms in rural Netherlands: A land exchange model
    Alam, S.J. ; Bakker, M.M. ; Karali, E. ; Dijk, J. van; Rounsevell, M.D.A. - \ 2014
    Lecture Notes in Computer Science 8235 (2014)LNAI. - ISSN 0302-9743 - p. 115 - 128.
    ruilverkaveling - grote landbouwbedrijven - plattelandsplanning - landgebruik - landbouw - natuurbescherming - simulatie - achterhoek - gelderland - land consolidation - large farms - rural planning - land use - agriculture - nature conservation - simulation - achterhoek - gelderland
    This paper introduces a data-driven agent-based simulation model of rural land exchange in the Netherlands. The model development process is part of an ongoing research program aiming at understanding the effects of climate change and socioeconomic drivers on agriculture land use and nature conservation. The first model version reported in this paper, is being developed for the Baakse Beek region in the Netherlands and is empirically grounded. The general framework described in this paper will be applied to another case study area in the Netherlands in the second phase of our research program and compare the projected land use patterns in the two case studies region.
    Innovations in hands-on simulations for competence development : authenticity and ownership of learning and their effects on student learning in secondary and higher vocational education
    Khaled, A.E. - \ 2014
    Wageningen University. Promotor(en): Martin Mulder, co-promotor(en): Harm Biemans; Judith Gulikers. - Wageningen : Wageningen University - ISBN 9789462570825 - 178
    vaardigheidsonderwijs - middelbaar beroepsonderwijs - beroepsopleiding (hoger) - vakbekwaamheid - loopbaantraining - agrarisch onderwijs - beroepsopleiding - simulatie - leerplan - leren - competency based education - intermediate vocational training - professional education - professional competence - career education - agricultural education - vocational training - simulation - curriculum - learning
    Hands-on simulaties, ofwel praktijksimulaties, worden zeer regelmatig ingezet in het (groene) middelbaar en hoger beroepsonderwijs, vooral voor het toepassen van procedurele en technische vaardigheden. Wat is de toegevoegde waarde van hands-on simulaties, ofwel praktijksimulaties, in een innovatief beroepsgericht curriculum dat zich naast vakmanschap ook op competenties zoals probleemoplossen, innovatief denken en flexibel werken richt? Het proefschrift laat zien dat praktijksimulaties competentieontwikkeling kunnen stimuleren. Voor meer competentieontwikkeling is het niet voldoende om de simulaties authentieker te maken (realiteitsgehalte verhogen) en studenten meer zelfsturing en zelfregulatie te geven. Praktijksimulaties moeten bij de studentpercepties te betrokken worden en studenten gedurende het gehele curriculum te leren zelfsturende en zelfregulerende strategieën in te zetten.
    Exploring the Impact of Land Cover and Topography on Rainfall Maxima in the Netherlands
    Maat, H.W. ter; Moors, E.J. ; Hutjes, R.W.A. ; Holtslag, A.A.M. ; Dolman, A.J. - \ 2013
    Journal of Hydrometeorology 14 (2013)2. - ISSN 1525-755X - p. 524 - 542.
    landgebruik - bossen - neerslag - bodemwater - simulatie - modellen - veluwe - land use - forests - precipitation - soil water - simulation - models - veluwe - climate-change - convective boundary - soil-moisture - surface - model - evaporation - prediction - diffusion - exchange
    The relative contribution of topography and land use on precipitation is analyzed in this paper for a forested area in the Netherlands. This area has an average yearly precipitation sum that can be 75–100 mm higher than the rest of the country. To analyze this contribution, different configurations of land use and topography are fed into a mesoscale model. The authors use the Regional Atmospheric Modeling System (RAMS) coupled with a land surface scheme simulating water vapor, heat, and momentum fluxes [Soil–Water–Atmosphere Plant System–Carbon (SWAPS-C)]. The model simulations are executed for two periods that cover varying large-scale synoptic conditions of summer and winter periods. The output of the experiments leads to the conclusion that the precipitation maximum at the Veluwe is forced by topography and land use. The effect of the forested area on the processes that influence precipitation is smaller in summertime conditions when the precipitation has a convective character. In frontal conditions, the forest has a more pronounced effect on local precipitation through the convergence of moisture. The effect of topography on monthly domain-averaged precipitation around the Veluwe is a 17% increase in the winter and a 10% increase in the summer, which is quite remarkable for topography with a maximum elevation of just above 100 m and moderate steepness. From this study, it appears that the version of RAMS using Mellor–Yamada turbulence parameterization simulates precipitation better in wintertime, but the configuration with the medium-range forecast (MRF) turbulence parameterization improves the simulation of precipitation in convective circumstances.
    Effect van ULO en DCS bewaarcondities en Smartfresh TM op de vruchtkwaliteit van Elstar in de keten en in een ketensimulatie
    Schoorl, F.W. - \ 2013
    Randwijk : Praktijkonderzoek Plant en Omgeving, Bloembollen, Boomkwekerij & Fruit - 17
    appels - voedselkwaliteit - gasbewaring - voedselketens - systemen na de oogst - simulatie - technieken - monitoring - vergelijkend onderzoek - apples - food quality - controlled atmosphere storage - food chains - postharvest systems - simulation - techniques - monitoring - comparative research
    Elstar altijd Raak is een initiatief om de kwaliteit van Elstar aan het eind van de keten te verbeteren en daarmee teleurstellingen bij de consument zoveel mogelijk te voorkomen. Een consistent hogere produkt kwaliteit is nodig om de positie van Elstar te borgen. In de hier beschreven test is gekeken naar de kwaliteitsontwikkeling van verschillende monsters die een praktijkketen hebben doorlopen en monsters die in een gesimuleerde keten hebben gestaan.
    Onderzoek naar de affecten van de aanleg van damwanden en grondverdichting op tandwalvissen in het Dolfinarium Harderwijk
    Haan, D. de - \ 2013
    IJmuiden : IMARES (Report / IMARES Wageningen UR C020/13) - 62
    dammen - uitrusting - zeezoogdieren - dierentuindieren - simulatie - diergedrag - dierenwelzijn - geluiden - veluwe - walvissen - oscillatie - dams - equipment - marine mammals - zoo animals - simulation - animal behaviour - animal welfare - sounds - veluwe - whales - oscillation
    Voor het vaststellen van de effecten van de aanleg van damwandinstallaties en grondverdichting als onderdelen van het grootschalig bouwplan Waterfront Harderwijk van de gemeente Harderwijk werden op vijf verschillende locaties van het bouwplan installaties gesimuleerd en de geluidseffecten daarvan in vier verschillende bassins op het terrein van het dolfinarium simultaan gemeten. Het onderzoek naar de effecten van het trilgeluid was beperkt tot de bassins waar bruinvissen en tuimelaars werden gehouden. Omdat er tijdens de proeven sterke reacties van haaien en roggen in het roggenbasin werden waargenomen, zijn in dit rapport enkele mitigerende maatregelen voor deze diersoorten opgenomen.
    One size fits all? : optimization of rainbow trout breeding program under diverse preferences and genotype-by-environment interaction
    Sae-Lim, P. - \ 2013
    Wageningen University. Promotor(en): Johan van Arendonk, co-promotor(en): Hans Komen; A. Kause. - S.l. : s.n. - ISBN 9789461734648 - 200
    regenboogforel - dierveredeling - veredelingsprogramma's - genotype-milieu interactie - optimalisatie - kenmerken - genetische winst - selectief fokken - simulatie - visteelt - aquacultuur - rainbow trout - animal breeding - breeding programmes - genotype environment interaction - optimization - traits - genetic gain - selective breeding - simulation - fish culture - aquaculture

    Global fish breeders distribute improved animal material to several continents to be farmed under diverse environments, and for very different market conditions. When establishing a global breeding program, there is a need to assess whether or not a single breeding objective satisfies the markets across different countries. It may be challenging to develop a single fish stock that performs well across all environments due to genotype-by-environment interaction (GxE). GxE is a phenomenon describing the possibility that different genotypes have a different sensitivity to changes in an environment. The objective of this thesis was to develop an optimized global breeding program for rainbow trout (Oncorhynchus mykiss) in terms of a balanced breeding goal that satisfies preferences of trout producers and maximized genetic gains across environments in the presence of GxE in production traits. Analytic hierarchy process (AHP) was used to estimate preferences, which can be aggregated to consensus preference values using weighted goal programming (WGP). The analysis revealed that the 6 most important traits were thermal growth coefficient (TGC), survival (Surv), feed conversion ratio (FCR), condition factor (CF), fillet percentage (FIL%), and late maturation (LMat). Individual trait preferences are different for farmers having different farming environments and producing different end-products. Calculating consensus preference values resulted in consensus desired genetic gains. To satisfy most farmers, consensus desired genetic gains can be taken into account in a global breeding strategy. Strong genotype re-ranking was found for all growth traits across environments. Based on simulation, re-location of breeding program led to highest total genetic gain for body weight at harvest. Alternatively, including sib performance into selection index increased genetic gain in all environments. Finally, environment-specific program can be used, but this is costly. There is a possibility of a conflict between 2 profits: from a breeding company and fish farmers and an optimum solution for that conflict can be found by using macroeconomics and cost-benefit analysis.

    Aerosol processes relevant for the Netherlands
    Brugh, J.M.J. Aan de - \ 2013
    Wageningen University. Promotor(en): Maarten Krol, co-promotor(en): M. Schaap. - S.l. : s.n. - ISBN 9789461734211 - 172
    aërosolen - atmosfeer - simulatie - luchtverontreiniging - klimaat - simulatiemodellen - modellen - europa - nederland - aerosols - atmosphere - simulation - air pollution - climate - simulation models - models - europe - netherlands

    Particulate matter (or aerosols) are particles suspended in the atmosphere. Aerosols are believed to be the most important pollutant associated with increased human mortality and morbidity. Therefore, it is important to investigate the relationship between sources of aerosols (such as industry) and the concentration of harmful aerosols at ground level. Furthermore, aerosols influence the climate system by scattering and absorbing solar radiation and by influencing cloud properties. The total climate effect of aerosols is poorly understood compared to the climate effect of greenhouse gases. Therefore, climate studies also benefit from a better understanding of aerosols.

    The goal of this thesis is to investigate the spatial distribution of aerosols over Europe with focus on the Netherlands. The aerosol life cycle and effects are calculated with numerical simulations. Performing numerical simulations of aerosols is very challenging, because, in contrast to gas molecules, each individual aerosol differs in size, composition and microphysical properties. Without simplifications, a model has to track each individual particle, which would take far too much computational time, even for modern supercomputers. The challenge is to design simplifications in such a way that the life cycle of aerosols and the effects of aerosols on human health and climate are still properly represented.

    Many model studies are supported by measurements. Both the measurements and the models can have different purposes. Using the correct combination of different models and observations is key for studies on aerosols. A different combination of models and observations is required to accomplish the different sub goals of this thesis. These sub goals are:

    Investigation of the aerosol life cycle over Europe Improvement of the understanding of gas-aerosol phase transition of ammonium nitrate and aerosol optics Improvement of representation of aerosols and their effects in models

    The life cycle of aerosols in Europe is investigated in chapter 3. The full life cycle of aerosols has been implemented in a global transport model. It is concluded that Europe is a net source of anthropogenic (man-made) aerosols and a net sink of natural aerosols. The most important sink of anthropogenic aerosols is removal by clouds and rain, while natural aerosols are removed predominantly by dry deposition processes. By comparing model results with observations, it is concluded that the largest uncertainties are caused by the parameterisation of wet removal processes and by missing emissions.

    In the Netherlands, emissions of nitrogen oxides and ammonia are high because of the high population density and intensive agriculture. After oxidation of nitrogen oxides to nitric acid, ammonium nitrate aerosols can be formed. This aerosol is special, because it can evaporate under warm and dry conditions and condense back to the aerosol phase under cold and moist conditions. Like the case of clouds, the phase equilibrium changes with altitude as the atmospheric temperature decreases with altitude. The phase of ammonium nitrate is poorly detected by many measurement instruments, because the gas-aerosol partitioning can change inside the instrument. Partly due to the scarcity of reliable measurements, the phase transition of ammonium nitrate is poorly implemented in large-scale models.

    Because ammonium nitrate aerosol and its phase transition is important for the aerosol budget of the Netherlands, this process has further been investigated in case studies. The goal of case studies is to gain detailed insight in the aerosol processes and, ultimately, to develop better parameterisations for large-scale models. These case-studies are performed with more detailed small-scale models. In these models, not the full aerosol life cycle is simulated but only the processes that are being investigated. A large advantage, however, is that these models have a higher resolution both in the spatial and the temporal domain. As a result, the important processes can be resolved more precisely.

    Chapter 4 presents a case study where the interaction between ammonium nitrate phase transition and mixing in the lower atmosphere (boundary layer) is investigated for a warm day in spring. During an intensive measurement campaign near the Cabauw tower in the Netherlands, measurements of ammonium nitrate have been performed. Importantly, the gas and the aerosol phases have been separated with a special instrument so that both concentrations are measured without errors due to phase transition inside the instrument. It is shown that the observed partitioning between gas and aerosol ammonium nitrate deviates significantly from the thermodynamic equilibrium. The hypothesised explanation for this mismatch is that aerosol-rich air from higher altitudes (where the aerosol phase is preferred due to lower temperatures) is transported to the surface, increasing the aerosol-phase fraction of ammonium nitrate at the surface. This implies that the thermodynamic equilibrium is not instantaneously restored at the surface. A simulation of ammonium nitrate partitioning in the boundary layer has been performed with a simplified column model. The match between model results and observations improved drastically when applying a delay timescale up to two hours for the gas-aerosol equilibrium.

    The interaction between turbulence and ammonium nitrate partitioning is further investigated in a more detailed model study (chapter 5). In this model, turbulent motions are explicitly resolved. As highlighted above, downward motions are associated with higher aerosol concentrations, because the phase equilibrium of ammonium nitrate is shifted towards the aerosol phase at higher altitudes. Therefore, turbulent motions induce a fluctuating concentration of aerosol ammonium nitrate with updrafts containing lower aerosol ammonium nitrate concentrations and subsidence motions containing enhanced aerosol ammonium nitrate concentrations. It is discussed that these fluctuations in observations may provide information about the speed of gas-aerosol partitioning, which is very difficult to measure directly.

    Throughout chapters 3 to 5, several ideas for model improvements have been posed. These ideas originate both from knowledge gained in the studies and from further challenges that are discovered. One such improvement for models is a computationally efficient and adequate representation of the optical properties of aerosols. Implementation of aerosol optics has been quite challenging, because the physics of aerosol optics is very complicated. Chapter 6 presents a package that allows easy implementation of aerosol optics in atmospheric models that represent aerosols.

    Aerosol modelling is a very challenging task and can be developed much further. In this thesis, important steps have been taken to improve knowledge about aerosols. Future research should proceed by unravelling remaining aerosol mysteries, such as those presented in the final chapter (7) of this thesis.

    Het Nieuwe Telen Tomaat 2010
    Gelder, A. de; Warmenhoven, M.G. ; Grootscholten, M. - \ 2012
    Bleiswijk : Wageningen UR Glastuinbouw (Rapporten GTB 1178) - 30
    teelt onder bescherming - glastuinbouw - tomaten - energiegebruik - reductie - teeltsystemen - botrytis - schimmelziekten - simulatie - proeven - gewaskwaliteit - protected cultivation - greenhouse horticulture - tomatoes - energy consumption - reduction - cropping systems - botrytis - fungal diseases - simulation - trials - crop quality
    In 2010 is het tweede experiment voor Het Nieuwe Telen met tomaat uitgevoerd. Daarin is met 23 m 3 aardgas per m 2 kas 68 kg grove trostomaat “Komeett” geproduceerd. Het extra heldere folie waarmee de teelt startte is vanwege condens problemen vervangen door AC-Folie. Het CO 2 gebruik was hoog maar onzeker is of dit goed is geregistreerd. De botrytis druk en infectie waren goed beheersbaar. Ook bij het nieuwe telen tomaat moet het uitgangspunt zijn geen botrytis infectie. De temperatuur in relatie tot de stralingssom per dag werd goed gerealiseerd. In deze proef was de relatie tussen straling en temperatuur 17.5 o C + 1.5 o C per 1000 joule/cm 2 .dag. Het gerealiseerde energie gebruik was met KASPRO goed na te rekenen. De simulatie klopte zeer goed met de gemeten waarden per week. Er waren geen problemen met de vruchtkwaliteit.
    Modellering ruimtelijke lichtverdeling in gewassen: Opbouw en toepassing van een 3D model voor kas en gewas
    Visser, P.H.B. de; Buck-Sorlin, G.H. - \ 2011
    Wageningen : Wageningen UR Glastuinbouw (Rapporten GTB 1104) - 60
    kasgewassen - modellen - 3d analyse - lampen - licht - lichtverdeling - energiegebruik - belichting - simulatie - greenhouse crops - models - 3d analysis - lamps - light - light distribution - energy consumption - illumination - simulation
    Een 3D model voor lichtverdeling in kasgewassen is ontwikkeld om de meest efficiënte plaatsing van lampen (SONT, LED) te berekenen om hiermee op groeilicht en energie te kunnen besparen. Het onderzoek, in het kader van het programma Kas als Energiebron en gefinancierd door Productschap Tuinbouw en Ministerie van ELI, behelsde de bouw en test van het model, dat rekening houdt met lampposities en -eigenschappen, bladstanden en rijstructuur. De lichtabsorptie en gewasfotosynthese voor een ingevoerd lichtplan wordt gesimuleerd. In het rapport zijn een reeks kansrijke belichtingsscenario’s doorgerekend voor een representatieve gewasstructuur voor tomaat en roos. Het resultaat bleek sterk afhankelijk van padbreedte en aantal bladeren, maar minder van bladvorm en bladhoek. De belichting wordt efficiënter bij gerichtere plantbelichting door aanpassing van de lampreflector, gebruik van tussenbelichting en schermreflectie. Het lichtverlies naar vloer en kasdek worden hiermee gereduceerd. Voor vragen uit de sector is het 3D model nu op verzoek inzetbaar.
    FISHRENT; Bio-economic simulation and optimisation model
    Salz, P. ; Buisman, F.C. ; Soma, K. ; Frost, H. ; Accadia, P. ; Prellezo, R. - \ 2011
    The Hague : LEI, part of Wageningen UR (Report / LEI : Onderzoeksveld Natuurlijke hulpbronnen ) - ISBN 9789086155149 - 74
    visserij - economie - biologie - economische modellen - simulatie - dynamische modellen - visbestand - landbouwbeleid - europese unie - fisheries - economics - biology - economic models - simulation - dynamic models - fishery resources - agricultural policy - european union
    Key findings: The FISHRENT model is a major step forward in bio-economic model-ling, combining features that have not been fully integrated in earlier models: 1- Incorporation of any number of species (or stock) and/or fleets 2- Integration of simulation and optimisation over a period of 25 years 3- Integration of effort and TAC-driven management policies 4- Three independent relations for stock growth, production and investments. The feedbacks within the model allow for a dynamic simulation. The main application of the model is scenario analysis of policy options. Complementary findings: The model formulates a complete set of mathematical relations, but it also con-tains a number of important assumptions, which remain to be tested empirically. Therefore the model presents a challenging agenda for empirical research, which should lead to further qualitative and quantitative improvements of the in-dividual mathematical equations and parameter values. Method: This model was developed during the EU-funded project 'Remuneration of spawning stock biomass'. Its aim was to generate consistent sets of scenarios for an assessment of potential resource rents in different EU fisheries. The model comprises six modules, each focussing on a different aspect of the functioning of the fisheries system: biology (stocks), economy (costs, earnings and profits), policy (TACs, effort and access fees), behaviour (investments), prices (fish and fuel) and an interface linking the modules together. Input, calculation and output are clearly separated. The model produces a standard set of graphics, which provide a quick insight into the results of any model run. All output of the model runs can be exported to database software for further analysis. The model has been built in Excel, which makes it accessible for most us-ers. It has been used in new applications and even translated to other software. The model is continually further developed.
    Optimale verlichting van melkveestallen. Deelproject Simulaties
    Swinkels, G.L.A.M. - \ 2010
    Wageningen : Wageningen UR Glastuinbouw - 30
    melkveehouderij - stallen - huisvesting van koeien - licht - emissie - verlichting - simulatiemodellen - simulatie - stalinrichting - dairy farming - stalls - cow housing - light - emission - lighting - simulation models - simulation - animal housing design
    In dit rapport wordt de reductie van de lichtuitstoot van melkveestallen bepaald in relatie tot de positie van de lichtbronnen, de mate van gevelafscherming en het type afscherming en worden praktische handvatten opgeleverd om de lichtuitstoot te minimaliseren.
    Klimaatbestendigheid van de EHS 1 : simulatieruns met de modellen SMART2-SUMO2 voor stikstof scenario's
    Wamelink, G.W.W. ; Wieggers, H.J.J. ; Mol-Dijkstra, J.P. ; Voogd, J.C.H. ; Kros, J. ; Schouwenberg, E.P.A.G. - \ 2009
    Wageningen : Alterra (Alterra-rapport 1918) - 32
    bodemchemie - stikstof - simulatiemodellen - modellen - simulatie - uitspoelen - vegetatie - ecologische hoofdstructuur - scenario-analyse - soil chemistry - nitrogen - simulation models - models - simulation - leaching - vegetation - ecological network - scenario analysis
    In de eerste fase van het project zijn de klimaatbestendige modellen SMART2-SUMO2 gedraaid voor 4 verschillende stikstofscenario's. De verschillen tussen de gebruikte scenario's zijn niet groot, maximaal 10% verschil in depositie. Voor bodem pH worden nauwelijks verschillen gesimuleerd. De verschillen in stikstofbeschikbaarheid zijn wel redelijk groot. Deze verschillen komen ook tot uiting in de hoeveelheid stikstof die uitspoelt, maar niet in de biomassa van de aanwezige vegetatie. De vegetatie blijkt voor alle sites in de EHS de maximale hoeveelheid stikstof op te nemen, de rest spoelt uit.
    C3 and C4 photosynthesis models: an overview from the perspective of crop modelling
    Yin, X. ; Struik, P.C. - \ 2009
    NJAS Wageningen Journal of Life Sciences 57 (2009)1. - ISSN 1573-5214 - p. 27 - 38.
    fotosynthese - energiemetabolisme - modellen - elektronenoverdracht - simulatie - gewasgroeimodellen - photosynthesis - energy metabolism - models - electron transfer - simulation - crop growth models - temperature response functions - gas-exchange measurements - zea-mays l - mesophyll conductance - internal conductance - stomatal conductance - carbon-dioxide - elevated co2 - electron-transport - in-vivo
    Nearly three decades ago Farquhar, von Caemmerer and Berry published a biochemical model for C3 photosynthetic rates (the FvCB model). The model predicts net photosynthesis (A) as the minimum of the Rubisco-limited rate of CO2 assimilation (Ac) and the electron transport-limited rate of CO2 assimilation (Aj). Given its simplicity and the growing availability of the required enzyme kinetic constants, the FvCB model has been used for a wide range of studies, from analysing underlying C3 leaf biochemistry to predicting photosynthetic fluxes of ecosystems in response to global warming. However, surprisingly, this model has seen limited use in existing crop growth models. Here we highlight the elegance, simplicity, and robustness of this model. In the light of some uncertainties with photosynthetic electron transport pathways, a recently extended FvCB model to calculate Aj is summarized. Applying the FvCB-type model in crop growth models for predicting leaf photosynthesis requires a stomatal conductance (gs) model to be incorporated, so that intercellular CO2 concentration (Ci) can be estimated. In recent years great emphasis has been put on the significant drawdown of Rubisco carboxylation-site CO2 concentration (Cc) relative to Ci. To account for this drawdown, mesophyll conductance (gm) for CO2 transfer can be added. We present an analytical algorithm that incorporates a gs model and uses gm as a temperature-dependent parameter for calculating A under various environmental scenarios. Finally we discuss a C4-equivalent version of the FvCB model. In addition to the algorithms already elaborated for C3 photosynthesis, most important algorithms for C4 photosynthesis are those that capture the CO2 concentrating mechanism and the extra ATP requirement by the C4 cycle. Although the current estimation of the C4 enzyme kinetic constants is less certain, applying FvCB-type models to both C3 and C4 crops is recommended to accurately predict the response of crop photosynthesis to multiple, interactive environmental variables
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