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
University. Promotor(en): Jaap Molenaar, co-promotor(en): George van Voorn; Arend 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
University. Promotor(en): Ben Scheres; Bela 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
University. Promotor(en): Fred van Eeuwijk, co-promotor(en): Hans 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.

Agent-Based Modeling: A Powerful Tool for Tourism Researchers
Nicholls, Sarah ; Amelung, B. ; Student, Jillian - \ 2017
Journal of Travel Research 56 (2017)3. - ISSN 0047-2875 - p. 3 - 15.
agent-based modeling - complexity - simulation - systems - tourism
Agent-based modeling (ABM) is a way of representing complex systems of autonomous agents or actors, and of simulating the multiple potential outcomes of these agents’ behaviors and interactions in the form of a range of alternatives or futures. Despite the complexity of the tourism system, and the power and flexibility of ABM to overcome the assumptions such as homogeneity, linearity, equilibrium, and rationality typical of traditional modeling techniques, ABM has received little attention from tourism researchers and practitioners. The purpose of this paper is to introduce ABM to a wider tourism audience. Specifically, the appropriateness of tourism as a phenomenon to be subjected to ABM is established; the power and benefits of ABM as an alternative scientific mechanism are illuminated; the few existing applications of ABM in the tourism arena are summarized; and, a range of potential applications in the areas of tourism planning, development, marketing and management is proposed.
LiGAPS-Beef
Linden, A. van der; Ven, G.W.J. van de; Oosting, S.J. ; Ittersum, M.K. van; Boer, I.J.M. de - \ 2016
models - simulation - beef - cattle
LiGAPS-Beef is a mechanistic model to assess potential and feed-limited beef production in different beef production systems across the world. The model is one of the first using concepts of production ecology to simulate livestock production. LiGAPS-Beef consists of a thermoregulation sub-model, a feed intake and digestion sub-model, and an energy and protein utilization sub-model. Energy and protein flows are included. Livestock production can be assessed for individual animals and herds. LiGAPS-Beef simulates cattle growth based on defining growth factors (genotype or breed and climate) and limiting growth factors (feed quality and feed quantity). The model can be used to assess yield gaps in beef production systems, and to explore improvement options for yield gap mitigation.
Towards a tipping point? Exploring the capacity to self-regulate Antarctic tourism using agent-based modelling
Student, J.R. ; Amelung, B. ; Lamers, M.A.J. - \ 2016
Journal of Sustainable Tourism 24 (2016)3. - ISSN 0966-9582 - p. 412 - 429.
IAATO - agent-based modelling (ABM) - self-regulation - Antarctic tourism - simulation - scenario analysis
Antarctica attracts tourists who want to explore its unique nature and landscapes. Antarctic tourism has rapidly grown since 1991 and is currently picking up again after the recent global economic downturn. Tourism activities are subject to the rules of the Antarctic Treaty System (ATS) and the decisions made by the Antarctic Treaty Consultative Parties (ATCPs), but within this context, the industry has considerable freedom to self-organise. The industry is self-regulated by a voluntary member-based
group, the International Association of Antarctica Tour Operators (IAATO). Researchers and policy-makers express concern about IAATO’s ability to deal with further tourism development and the environmental consequences. This study applies a new approach to understand what affects self-regulation, consisting of a literature review and agent-based modelling (ABM). The review identifies four challenges for self-regulation: operator commitment, tourism growth, operator diversification, and
accidents. The ABM simulations help conceptualise the complex concepts and theories surrounding self-regulation. Self-regulation is measured by the capacity of the simulated self-regulatory system to maintain a majority membership at the end of 20 years. The model suggests that a number of the challenges are nonlinear and have tipping points. This approach provides insights that industry officials and policy-makers can use to proactively regulate Antarctic tourism.
Logistics network design & control : managing product quality in a blooming sector
Keizer, M. de - \ 2015
University. Promotor(en): Jack van der Vorst, co-promotor(en): Jacqueline Bloemhof-Ruwaard; Rene Haijema. - Wageningen : Wageningen University - ISBN 9789462576025 - 239 p.
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
Modelling the Influence of Groundwater Abstractions on the Water Level of Lake Naivasha, Kenya Under Data-Scare Conditions
Hogeboom, R.H.J. ; Oel, P.R. van; Krol, M. ; Booij, M.J. - \ 2015
Water Resources Management 29 (2015)12. - ISSN 0920-4741 - p. 4447 - 4463.
rift-valley - flow model - catchment - management - simulation - aquifer
This study presents the state-of-the-art understanding of the data-scarce and hydrogeologically complex groundwater system of Lake Naivasha, Kenya, with the particular aim of exploring the influence groundwater abstractions have on Lake Naivasha’s water level. We developed multiple alternative but plausible parameterizations for a MODFLOW groundwater model, based on literature, existing models and available data, while trying not to over-complicate the model. In doing so, we illustrate a possible strategy of going about data-scarce regions in modelling in general. Processes encountered in the calibrated parameterizations show groundwater flows laterally from the escarpments to the valley floor and axially from the lake along the Rift, with a larger portion flowing out southward than northward. Extraction of groundwater interrupts the flow from the northwestern highlands to the lake, leading to a lake stage reduction of 0.7–7.5 cm due to abstractions at our target farm (Flower Business Park) or an implied 7–75 cm due to total groundwater abstractions in the area. Although this study demonstrates our understanding of Naivasha’s groundwater system remains fragile and the current model cannot be embedded in operational water management yet, it (i) reflects the contemporary understanding of the local groundwater system, (ii) illustrates how to go about modelling in data-scarce environments and (iii) provides a means to assess focal areas for future data collection and model improvements.
Low-resolution modeling of dense drainage networks in confining layers
Pauw, P.S. ; Zee, S.E.A.T.M. van der; Leijnse, A. ; Delsman, J.R. ; Louw, P.G.B. de; Lange, W.J. de; Oude Essink, G.H.P. - \ 2015
Groundwater 53 (2015)5. - ISSN 0017-467X - p. 771 - 781.
grondwaterstroming - watervoerende lagen - modellen - klimaatverandering - groundwater flow - aquifers - models - climatic change - aquifer - simulation - intrusion - seepage - florida - system - field - flow
Groundwater-surface water (GW-SW) interaction in numerical groundwater flow models is generally simulated using a Cauchy boundary condition, which relates the flow between the surface water and the groundwater to the product of the head difference between the node and the surface water level, and a coefficient, often referred to as the “conductance.” Previous studies have shown that in models with a low grid resolution, the resistance to GW-SW interaction below the surface water bed should often be accounted for in the parameterization of the conductance, in addition to the resistance across the surface water bed. Three conductance expressions that take this resistance into account were investigated: two that were presented by Mehl and Hill (2010) and the one that was presented by De Lange (1999). Their accuracy in low-resolution models regarding salt and water fluxes to a dense drainage network in a confined aquifer system was determined. For a wide range of hydrogeological conditions, the influence of (1) variable groundwater density; (2) vertical grid discretization; and (3) simulation of both ditches and tile drains in a single model cell was investigated. The results indicate that the conductance expression of De Lange (1999) should be used in similar hydrogeological conditions as considered in this paper, as it is better taking into account the resistance to flow below the surface water bed. For the cases that were considered, the influence of variable groundwater density and vertical grid discretization on the accuracy of the conductance expression of De Lange (1999) is small.
Quantifying the source-sink balance and carbohydrate content in three tomato cultivars
Li, T. ; Heuvelink, E. ; Marcelis, L.F.M. - \ 2015
Frontiers in Plant Science 6 (2015). - ISSN 1664-462X
dry-matter production - leaf photosynthesis - plant-growth - leaves - strength - yield - metabolism - simulation - storage - light
Supplementary lighting is frequently applied in the winter season for crop production in greenhouses. The effect of supplementary lighting on plant growth depends on the balance between assimilate production in source leaves and the overall capacity of the plants to use assimilates. This study aims at quantifying the source-sink balance and carbohydrate content of three tomato cultivars differing in fruit size, and to investigate to what extent the source/sink ratio correlates with the potential fruit size. Cultivars Komeet (large size), Capricia (medium size), and Sunstream (small size, cherry tomato) were grown from 16 August to 21 November, at similar crop management as in commercial practice. Supplementary lighting (High Pressure Sodium lamps, photosynthetic active radiation at 1 m below lamps was 162 mu mol photons m(-2) s(-1); maximum 10 h per day depending on solar irradiance level) was applied from 19 September onward. Source strength was estimated from total plant growth rate using periodic destructive plant harvests in combination with the crop growth model TOMSIM. Sink strength was estimated from potential fruit growth rate which was determined from non-destructively measuring the fruit growth rate at non-limiting assimilate supply, growing only one fruit on each truss. Carbohydrate content in leaves and stems were periodically determined. During the early growth stage, Komeet' and Capricia' showed sink limitation and 'Sunstream' was close to sink limitation. During this stage reproductive organs had hardly formed or were still small and natural irradiance was high (early September) compared to winter months. Subsequently, during the fully fruiting stage all three cultivars were strongly source-limited as indicated by the low source/sink ratio (average source/sink ratio from 50 days after planting onward was 0.17, 0.22, and 0.33 for 'Komeet, 'Capricia,' and 'Sunstream,' respectively). This was further confirmed by the fact that pruning half of the fruits hardly influenced net leaf photosynthesis rates. Carbohydrate content in leaves and stems increased linearly with the source/sink ratio. We conclude that during the early growth stage under high irradiance, tomato plants are sink-limited and that the level of sink limitation differs between cultivars but it is not correlated with their potential fruit size. During the fully fruiting stage tomato plants are source-limited and the extent of source limitation of a cultivar is positively correlated with its potential fruit size.
Reducing ventilation requirements in semi-closed greenhouses increases water use efficiency
Katsoulas, N. ; Sapounas, A. ; Zwart, H.F. de; Dieleman, J.A. ; Stanghellini, C. - \ 2015
Agricultural Water Management 156 (2015). - ISSN 0378-3774 - p. 90 - 99.
closed greenhouses - climate conditions - plant-compounds - tomato yield - crop - evapotranspiration - irrigation - simulation - quality - leaf
We explore an under-appreciated side effect of semi-closed greenhouses: the ability to recover transpired water, thereby increasing water use efficiency. Semi-closed greenhouses are fit with cooling equipment, to limit natural ventilation requirements for temperature and humidity control. We assess the effect of cooling system capacity on ventilation needs of semi-closed greenhouses under different climate conditions and provide a general framework to evaluate potential water savings using the semi-closed greenhouse concept in different regions. We simulate greenhouse climate and crop yields for various cooling system capacities in Central Europe (The Netherlands) and Mediterranean (Greece and Algeria) by implementing a "cooling module" into an existing greenhouse model (KASPRO) and validating it using concurrent experimental data. Increasing the capacity of the cooling system has a double effect on water use efficiency (WUE): increase of fruit yield due to improved microclimate and lower water use, due to collection and reuse of vapour condensed in the heat exchanger and, to a lesser extent, lower crop transpiration. Thus WUE is strongly associated to the capacity of the cooling system. Finally, we show that there is a unique relationship between water use efficiency and the coupling of greenhouse environment to the outside air (an indicator of ventilation requirements), for all regions studied.
A model based method for evaluation of crop operation scenarios in greenhouses
Ooster, A. van 't - \ 2015
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.

Opportunities to improve the areal oil productivity of microalgae
Breuer, G. ; Lamers, P.P. ; Janssen, M.G.J. ; Wijffels, R.H. ; Martens, D.E. - \ 2015
Bioresource Technology 186 (2015). - ISSN 0960-8524 - p. 294 - 302.
triacylglycerol tag accumulation - nitrogen starvation - scenedesmus-obliquus - starchless mutants - photosynthesis - light - photobioreactors - temperature - metabolism - simulation
Microalgae are often considered as a promising alternative source of vegetable oils. These oils can be used for food and biofuel applications. Productivities that are projected for large-scale microalgal oil production are, however, often poorly supported by scientific evidence and based on too optimistic assumptions. To facilitate the inclusion of the microalgal physiology in these projections, existing knowledge and novel scientific insights were condensed into a mechanistic model that describes photosynthesis and carbon partitioning during nitrogen starvation. The model is validated using experimental data from both wild-type and a starchless mutant of Scenedesmus obliquus. The model is subsequently used to quantify how reactor design, process design, and strain improvement can improve the oil productivity from 2.1 to up to 10.9 g m-2 day-1. These projected productivities are used to reflect on commonly assumed oil productivities and it is concluded that the microalgal oil productivity is often overestimated several folds.
Environmental potentials of policy instruments to mitigate nutrient emissions in Chinese livestock production
Zheng, C. ; Liu, Y. ; Bluemling, B. ; Mol, A.P.J. ; Chen, J. - \ 2015
Science of the Total Environment 502 (2015). - ISSN 0048-9697 - p. 149 - 156.
spatial models - phosphorus - innovation - implementation - modernization - agriculture - simulation - diffusion
To minimize negative environmental impact of livestock production, policy-makers face a challenge to design and implement more effective policy instruments for livestock farmers at different scales. This research builds an assessment framework on the basis of an agent-based model, named ANEM, to explore nutrient mitigation potentials of five policy instruments, using pig production in Zhongjiang county, southwest China, as the empirical filling. The effects of different policy scenarios are simulated and compared using four indicators and differentiating between small, medium and large scale pig farms. Technology standards, biogas subsidies and information provisioning prove to be the most effective policies, while pollution fees and manure markets fail to environmentally improve manure management in pig livestock farming. Medium-scale farms are the more relevant scale category for a more environmentally sound development of Chinese livestock production. A number of policy recommendations are formulated as conclusion, as well as some limitations and prospects of the simulations are discussed.
Assessment of uncertainties in simulated European precipitation
Haren, R. van - \ 2015
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.

Surfactant-polymer interactions: molecular architecture does matter
Banerjee, S. ; Cazeneuve, C. ; Baghdadli, N. ; Ringeissen, S. ; Leermakers, F.A.M. ; Luengo, G.S. - \ 2015
Soft Matter 11 (2015). - ISSN 1744-683X - p. 2504 - 2511.
block copolymer adsorption - nonionic surfactants - statistical thermodynamics - chain molecules - phase-behavior - simulation - interface - association - mixtures - water
Polymer–surfactant mixtures are found in many industrial formulations, and hence there is a significant interest in understanding, at a molecular level, how the self-assembly of surfactant is affected by oppositely-charged polyelectrolytes (PEs). We use self-consistent field modeling and show that the modes of interaction of PEs strongly depend on the architecture of the PE on the segmental level. Hydrophilic cationic PEs with their charge proximal to the linear backbone are expected to bind electrostatically to the outsides of the coronas of the spherical micelles of anionic surfactants, such as sodium laureth sulphate (SLES). As a result, the surfactant aggregation number increases, but at the same time the colloidal stability deteriorates, due to bridging of the PEs between micelles. PEs with their charge somewhat displaced from the backbone by way of short hydrophobic spacers, are expected to be present inside a micelle at the core–corona boundary. In this case the aggregation number decreases, yet the colloidal stability is retained. Hence, SLES tends to remove hydrophilic PEs from an aqueous solution, whereas it solubilizes more hydrophobic ones. The binding isotherm shows that the uptake of PEs remains typically below charge compensation and in this case the spherical micelle topology remains the preferred state.
Improving obstacle awareness for robotic harvesting of sweet-pepper
Bac, C.W. - \ 2015
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 - 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.

The Challenge of Forecasting the Onset and Development of Radiation Fog Using Mesoscale Atmospheric Models
Steeneveld, G.J. ; Ronda, R.J. ; Holtslag, A.A.M. - \ 2015
Boundary-Layer Meteorology 154 (2015)2. - ISSN 0006-8314 - p. 265 - 289.
boundary-layer - climate models - prediction - resolution - weather - system - parameterization - detrainment - sensitivity - simulation
The numerical weather prediction of radiation fog is challenging, as many models typically show large biases for the timing of the onset and dispersal of the fog, as well as for its depth and liquid water content. To understand the role of physical processes, i.e. turbulence, radiation, land-surface coupling, and microphysics, we evaluate the HARMONIE and Weather Research and Forecasting (WRF) mesoscale models for two contrasting warm fog episodes at the relatively flat terrain around the Cabauw tower facility in the Netherlands. One case involves a radiation fog that arose in calm anticyclonic conditions, and the second is a radiation fog that developed just after a cold front passage. The WRF model represents the radiation fog well, while the HARMONIE model forecasts a stratus lowering fog layer in the first case and hardly any fog in the second case. Permutations of parametrization schemes for boundary-layer mixing, radiation and microphysics, each for two levels of complexity, have been evaluated within the WRF model. It appears that the boundary-layer formulation is critical for forecasting the fog onset, while for fog dispersal the choice of the microphysical scheme is a key element, where a double-moment scheme outperforms any of the single-moment schemes. Finally, the WRF model results appear to be relatively insensitive to horizontal grid spacing, but nesting deteriorates the modelled fog formation. Increasing the domain size leads to a more scattered character of the simulated fog. Model results with one-way or two-way nesting show approximately comparable results.
Structural signatures of dynamic heterogeneities in monolayers of colloidal ellipsoids
Zheng, Z.Y. ; Ni, R. ; Wang, F. ; Dijkstra, M. ; Wang, Y.R. ; Han, Y.L. - \ 2014
Nature Communications 5 (2014). - ISSN 2041-1723
glass-forming liquids - supercooled liquids - orientational order - jamming transition - hard ellipsoids - crystallization - frustration - relaxation - simulation - insights
When a liquid is supercooled towards the glass transition, its dynamics drastically slows down, whereas its static structure remains relatively unchanged. Finding a structural signature of the dynamic slowing down is a major challenge, yet it is often too subtle to be uncovered. Here we discover the structural signatures for both translational and rotational dynamics in monolayers of colloidal ellipsoids by video microscopy experiments and computer simulations. The correlation lengths of the dynamic slowest-moving clusters, the static glassy clusters, the static local structural entropy and the dynamic heterogeneity follow the same power-law divergence, suggesting that the kinetic slowing down is caused by a decrease in the structural entropy and an increase in the size of the glassy cluster. Ellipsoids with different aspect ratios exhibit single-or double-step glass transitions with distinct dynamic heterogeneities. These findings demonstrate that the particle shape anisotropy has important effects on the structure and dynamics of the glass.
Multiscale analysis of structure development in expanded starch snacks
Sman, R.G.M. van der; Broeze, J. - \ 2014
Journal of Physics-Condensed Matter 26 (2014)46. - ISSN 0953-8984
mass-transfer - food materials - bubble-growth - porous-media - systems - polymer - phase - model - simulation - extrusion
In this paper we perform a multiscale analysis of the food structuring process of the expansion of starchy snack foods like keropok, which obtains a solid foam structure. In particular, we want to investigate the validity of the hypothesis of Kokini and coworkers, that expansion is optimal at the moisture content, where the glass transition and the boiling line intersect. In our analysis we make use of several tools, (1) time scale analysis from the field of physical transport phenomena, (2) the scale separation map (SSM) developed within a multiscale simulation framework of complex automata, (3) the supplemented state diagram (SSD), depicting phase transition and glass transition lines, and (4) a multiscale simulation model for the bubble expansion. Results of the time scale analysis are plotted in the SSD, and give insight into the dominant physical processes involved in expansion. Furthermore, the results of the time scale analysis are used to construct the SSM, which has aided us in the construction of the multiscale simulation model. Simulation results are plotted in the SSD. This clearly shows that the hypothesis of Kokini is qualitatively true, but has to be refined. Our results show that bubble expansion is optimal for moisture content, where the boiling line for gas pressure of 4 bars intersects the isoviscosity line of the critical viscosity 10(6) Pa.s, which runs parallel to the glass transition line.
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