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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      We will mail you new results for this query: keywords==Simulation
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    SSM-iCrop2 : A simple model for diverse crop species over large areas
    Soltani, A. ; Alimagham, S.M. ; Nehbandani, A. ; Torabi, B. ; Zeinali, E. ; Dadrasi, A. ; Zand, E. ; Ghassemi, S. ; Pourshirazi, S. ; Alasti, O. ; Hosseini, R.S. ; Zahed, M. ; Arabameri, R. ; Mohammadzadeh, Z. ; Rahban, S. ; Kamari, H. ; Fayazi, H. ; Mohammadi, S. ; Keramat, S. ; Vadez, V. ; Ittersum, M.K. van; Sinclair, T.R. - \ 2020
    Agricultural Systems 182 (2020). - ISSN 0308-521X
    Climate change - Crop model - Food security - Orchards - Perennial forages - Simulation

    Crop models are essential in undertaking large scale estimation of crop production of diverse crop species, especially in assessing food availability and climate change impacts. In this study, an existing model (SSM, Simple Simulation Models) was adapted to simulate a large number of plant species including orchard species and perennial forages. Simplification of some methods employed in the original model was necessary to deal with limited data availability for some of the plant species to be simulated. The model requires limited, readily available input information. The simulations account for plant phenology, leaf area development and senescence, dry matter accumulation, yield formation, and soil water balance in a daily time step. Parameterization of the model for new crops/cultivars is easy and straight-forward. The resultant model (SSM-iCrop2) was parameterized and tested for more than 30 crop species of Iran using numerous field experiments. Tests showed the model was robust in the predictions of crop yield and water use. Root mean square of error as percentage of observed mean for yield was 18% for grain field crops, 14% for non-grain crops 14% for vegetables and 28% for fruit trees.

    The potential of serious games to solve water problems : Editorial to the special issue on game-based approaches to sustainable water governance
    Medema, Wietske ; Mayer, Igor ; Adamowski, Jan ; Wals, Arjen E.J. ; Chew, Chengzi - \ 2019
    Water 11 (2019)12. - ISSN 2073-4441
    Game-based learning - Integrated water resource management (IWRM) - Natural resource management - Serious game - Simulation - Social learning - Stakeholder collaboration - Sustainability - Water governance

    In this editorial, the authors (and guest editors) introduce the Special Issue titled Understanding Game-based Approaches for Improving SustainableWater Governance: The Potential of Serious Games to SolveWater Problems. The authors take another look at the twelve contributions, starting from the subtitle question: what is the potential? The authors summarize the insights and give directions for future research.

    Algorithm for a particle-based growth model for plant tissues
    Opheusden, Joost H.J. van; Molenaar, Jaap - \ 2018
    Royal Society Open Science 5 (2018)11. - ISSN 2054-5703
    Morphology - Simulation - Structure

    We have developed an algorithm for a particle-based model for the growth of plant tissues in three dimensions in which each cell is represented by a single particle, and connecting cell walls are represented as permanent bonds between particles. A sample of plant tissue is represented by a fixed network of bonded particles. If, and only if a cell divides, this network is updated locally. The update algorithm is implemented in a model where cell growth and division gives rise to forces between the cells, which are relaxed in steepest descent minimization. The same forces generate a pressure inside the cells, which moderates growth. The local nature of the algorithm makes it efficient computationally, so the model can deal with a large number of cells. We used the model to study the growth of plant tissues for a variety of model parameters, to show the viability of the algorithm.

    Unravelling variation in feeding, social interaction and growth patterns among pigs using an agent-based model
    Boumans, Iris J.M.M. ; Boer, Imke J.M. de; Hofstede, Gert Jan ; Bokkers, Eddie A.M. - \ 2018
    Physiology and Behavior 191 (2018). - ISSN 0031-9384 - p. 100 - 115.
    Animal welfare - Feeding behaviour - Group dynamics - Growing pigs - Productivity - Simulation
    Domesticated pigs, Sus scrofa, vary considerably in feeding, social interaction and growth patterns. This variation originates partly from genetic variation that affects physiological factors and partly from behavioural strategies (avoid or approach) in competitive food resource situations. Currently, it is unknown how variation in physiological factors and in behavioural strategies among animals contributes to variation in feeding, social interaction and growth patterns in animals. The aim of this study was to unravel causation of variation in these patterns among pigs. We used an agent-based model to explore the effects of physiological factors and behavioural strategies in pigs on variation in feeding, social interaction and growth patterns. Model results show that variation in feeding, social interaction and growth patterns are caused partly by chance, such as time effects and coincidence of conflicts. Furthermore, results show that seemingly contradictory empirical findings in literature can be explained by variation in pig characteristics (i.e. growth potential, positive feedback, dominance, and coping style). Growth potential mainly affected feeding and growth patterns, whereas positive feedback, dominance and coping style affected feeding patterns, social interaction patterns, as well as growth patterns. Variation in behavioural strategies among pigs can reduce aggression at group level, but also make some pigs more susceptible to social constraints inhibiting them from feeding when they want to, especially low-ranking pigs and pigs with a passive coping style. Variation in feeding patterns, such as feeding rate or meal frequency, can indicate social constraints. Feeding patterns, however, can say something different about social constraints at group versus individual level. A combination of feeding patterns, such as a decreased feed intake, an increased feeding rate, and an increased meal frequency might, therefore, be needed to measure social constraints at individual level.
    Effective sampling strategy to detect food and feed contamination : Herbs and spices case
    Bouzembrak, Yamine ; Fels, Ine van der - \ 2018
    Food Control 83 (2018). - ISSN 0956-7135 - p. 28 - 37.
    Cost-effectiveness - Heterogeneous contamination - Sampling protocol - Simulation

    Sampling plans for food safety hazards are aimed to be used to determine whether a lot of food is contaminated (with microbiological or chemical hazards) or not. One of the components of sampling plans is the sampling strategy. The aim of this study was to compare the performance of three different sampling strategies, being simple random sampling (SRS), stratified random sampling (STRS), and systematic sampling (SS), with each other for their probability of detecting a heterogeneously distributed contamination in a lot of herbs or spices (i.e., a dry food product). To this end, a simulation model was developed, and applied to different scenarios for contamination level and numbers of samples collected. In addition, as a case study, the sampling plan of a company processing herbs and spices was evaluated using the simulation model. Results showed that the effectiveness of the sampling plan is influenced by the sampling strategy. With expected low contamination levels the SS strategy performs better than the two other strategies. At higher expected contaminated levels, the STRS strategy is preferred.

    Modeling Biomass Logistics
    Annevelink, Bert ; Anttila, Perttu ; Väätäinen, Kari ; Gabrielle, Benoît ; García-Galindo, Daniel ; Leduc, Sylvain ; Staritsky, Igor - \ 2017
    In: Modeling and Optimization of Biomass Supply Chains Elsevier - ISBN 9780128123034 - p. 79 - 103.
    Biomass supply chain - Design tools - Logistical component - Logistical concept - Optimization - Simulation

    This chapter will presents the current status and the main challenges of biomass logistics. Logistical aspects of the biomass supply chain will be delineated. It further provides a thorough description of different methodologies to design biomass value chains combined with relevant logistical assessment criteria. This includes also descriptions for how to integrate the various logistical components in modeling logistical tools that are currently available to implement the described methodologies. The chapter finishes with a set of case studies based on local data and made with these logistical tools.

    Can increased leaf photosynthesis be converted into higher crop mass production? A simulation study for rice using the crop model GECROS
    Yin, Xinyou ; Struik, Paul C. - \ 2017
    Journal of Experimental Botany 68 (2017)9. - ISSN 0022-0957 - p. 2345 - 2360.
    Crop modelling - Crop productivity - GECROS - Genetic transformation - Photosynthesis - Radiation use efficiency - Simulation - Water use efficiency - Yield potential

    Various genetic engineering routes to enhance C3 leaf photosynthesis have been proposed to improve crop productivity. However, their potential contribution to crop productivity needs to be assessed under realistic field conditions. Using 31 year weather data, we ran the crop model GECROS for rice in tropical, subtropical, and temperate environments, to evaluate the following routes: (1) improving mesophyll conductance (gm); (2) improving Rubisco specificity (Sc/o); (3) improving both gm and Sc/o; (4) introducing C4 biochemistry; (5) introducing C4 Kranz anatomy that effectively minimizes CO2 leakage; (6) engineering the complete C4 mechanism; (7) engineering cyanobacterial bicarbonate transporters; (8) engineering a more elaborate cyanobacterial CO2-concentrating mechanism (CCM) with the carboxysome in the chloroplast; and (9) a mechanism that combines the low ATP cost of the cyanobacterial CCM and the high photosynthetic capacity per unit leaf nitrogen. All routes improved crop mass production, but benefits from Routes 1, 2, and 7 were ≤10%. Benefits were higher in the presence than in the absence of drought, and under the present climate than for the climate predicted for 2050. Simulated crop mass differences resulted not only from the increased canopy photosynthesis competence but also from changes in traits such as light interception and crop senescence. The route combinations gave larger effects than the sum of the effects of the single routes, but only Route 9 could bring an advantage of ≥50% under any environmental conditions. To supercharge crop productivity, exploring a combination of routes in improving the CCM, photosynthetic capacity, and quantum efficiency is required.

    Folding of proteins with a flavodoxin-like architecture
    Houwman, Joseline A. ; Mierlo, Carlo P.M. van - \ 2017
    FEBS Journal 284 (2017)19. - ISSN 1742-464X - p. 3145 - 3167.
    Apoflavodoxin - CheY - Cotranslational folding - Frustration - Molten globule - NtrC - Off-pathway intermediate - Ribosome-nascent chain complex - Simulation - Spo0F
    The flavodoxin-like fold is a protein architecture that can be traced back to the universal ancestor of the three kingdoms of life. Many proteins share this α-β parallel topology and hence it is highly relevant to illuminate how they fold. Here, we review experiments and simulations concerning the folding of flavodoxins and CheY-like proteins, which share the flavodoxin-like fold. These polypeptides tend to temporarily misfold during unassisted folding to their functionally active forms. This susceptibility to frustration is caused by the more rapid formation of an α-helix compared to a β-sheet, particularly when a parallel β-sheet is involved. As a result, flavodoxin-like proteins form intermediates that are off-pathway to native protein and several of these species are molten globules (MGs). Experiments suggest that the off-pathway species are of helical nature and that flavodoxin-like proteins have a nonconserved transition state that determines the rate of productive folding. Folding of flavodoxin from Azotobacter vinelandii has been investigated extensively, enabling a schematic construction of its folding energy landscape. It is the only flavodoxin-like protein of which cotranslational folding has been probed. New insights that emphasize differences between in vivo and in vitro folding energy landscapes are emerging: the ribosome modulates MG formation in nascent apoflavodoxin and forces this polypeptide toward the native state.
    Flow through a filter plate backed by a packed bed of spheres
    Sman, R.G.M. van der - \ 2017
    Chemical Engineering Science 158 (2017). - ISSN 0009-2509 - p. 154 - 163.
    Filtration - Fluid flow - Orifice - Simulation

    In this paper we perform direct numerical simulation (DNS) on the problem of fluid flow through a filter plate backed by a packed bed of spheres, resembling a cake layer on top of a membrane. For both the complete problem, and its single components (the filter plate and a bed of spheres of finite height) we have observed three flow regimes, depending on the Reynolds number. In each regime the flow resistance is showing a different scaling with the Reynolds number. In the Stokes flow regime the total flow resistance can be decomposed in linear independent components. The interior flows inside the filter holes and inside the packed bed follow the same correlations as hold for the single component. However, at the transition zone between filter plate and packed bed, there is a diverging flow in the first row of the packed bed, whose contribution in the flow resistance scales with the fractional hole to the power −1.5. Similar scaling exponent has been found earlier for the viscous-inertial regime with Reynolds numbers larger than 10, which has been modelled using the porous medium approach. Our findings suggest that also in the Stokes flow and the weakly flow regime the problem can also be solved with the same porous medium approach using the Navier-Stokes equation having Darcy–Brinkman terms incorporated. This investigation provides a good basis for developing more accurate analytical models for the flow resistance of membrane filters with a cake layer on top.

    Assessing the inequality of lifetime healthcare expenditures : a nearest neighbour resampling approach
    Wong, Albert ; Boshuizen, Hendriek ; Polder, Johan ; Ferreira, José António - \ 2017
    Journal of the Royal Statistical Society. Series A, Statistics in Society 180 (2017)1. - ISSN 0964-1998 - p. 141 - 180.
    Healthcare expenditures - Healthcare systems - Inequality - Inequity - Life cycles - Nearest neighbour resampling - Non-parametric methods - Simulation

    The rise in healthcare expenditures has raised doubts about the sustainability of health systems and instigated a discussion on their design. Policy making in this field requires a proper understanding of how healthcare expenditures evolve throughout an individual's lifetime, and of how they vary between individuals. Given the lack of data on healthcare expenditures during an individual's lifetime, we developed a new nearest neighbour resampling approach to construct realistic individual life cycles of healthcare expenditures based on cross-sectional data from the Netherlands. This approach provides insight into lifetime healthcare expenditures. Our main finding is that the inequality in lifetime healthcare expenditures is much smaller than the inequality as derived from cross-sectional healthcare expenditures.

    Simulating Crop Growth and Development Using Functional-Structural Plant Modeling
    Evers, J.B. - \ 2016
    In: Canopy Photosynthesis / Hikosaka, Kouki, Niinemets, Ulo, Anten, Niels P.R., Dordrecht : Springer (Advances in Photosynthesis and Respiration ) - ISBN 9789401772907 - p. 219 - 236.
    Plant architecture - Simulation - Leaf photosynthesis - Sink strength - Crop performance
    Crop canopies are composed of individual plants. Yet, in the analysis of crop
    characteristics such as canopy photosynthesis, growth and performance, plants are normally not considered as individual entities with their own developmental pattern and plastic responses to their environment. Therefore, in research questions that implicitly or explicitly contain aspects of individual plant development, modelling tools that scale up processes at the level of the plant to the level of the canopy can be used. In this chapter, the functional-structural plant (FSP) modelling approach will be introduced. FSP modelling provides the possibilities to simulate individual plants in a stand setting, and their architecture
    in 3D over time. It can take into account light interception and scattering at the level of the leaf as a function of leaf size, angle and optical properties, and use this information to determine photosynthesis, photomorphogenesis, and overall plant growth and development. Therefore, FSP modelling can be used to translate individual plant behaviour to whole canopy performance while taking into account phenotypic variation between individuals and plastic responses to local conditions, as well as the consequences of active manipulation of plant architecture such as pruning or herbivory.
    This chapter will treat the underlying principles of FSP modelling as well as the
    calibration and validation of such models. It will subsequently describe how the interaction between light and a canopy composed of individual plants with their own architecture can be simulated, and how the feedback of photosynthesis, carbon allocation and growth as well as photomorphogenetic processes on light capture can be included.
    A systematic approach to preventing chilled-food waste at the retail outlet
    Tromp, Seth Oscar ; Haijema, René ; Rijgersberg, Hajo ; Vorst, Jack G.A.J. van der - \ 2016
    International Journal of Production Economics 182 (2016). - ISSN 0925-5273 - p. 508 - 518.
    Food waste - Quality decay - Retail outlet - Shelf life - Simulation - Use-by date

    The objective of this paper is to develop a systematic overview of interventions for preventing chilled-food waste at retail outlets, and to assess the impact of these interventions for a particular case of fresh-cut iceberg lettuce at a Dutch retail outlet. The structure of the simulation model as presented in this paper is generic, hence suitable for other retailers and other chilled-food products as well. The generated systematic overview focusses on interventions that do not require a system change. A distinction is made into technical, logistical and marketing interventions. Model simulations show the effectiveness of these interventions. It is concluded that a number of ‘waste drivers’ exists, such as a low and varying consumer demand, high selection behaviour, the order lead time, a fixed order unit, and a short use-by date. The retailer can fine-tune the replenishment level of his order policy and the way of rounding to the given order unit, but by doing so he is at best able to exchange waste for out-of-stock or the other way around. The systematic overview of interventions is valuable input to future research on defining and estimating the effectiveness of combining interventions, and interventions that do require a system change.

    Determination of single cell lag times of Cronobacter spp. strains exposed to different stress conditions : Impact on detection
    Margot, H. ; Zwietering, M.H. ; Joosten, H. ; Stephan, R. - \ 2016
    International Journal of Food Microbiology 236 (2016). - ISSN 0168-1605 - p. 161 - 166.
    Bacterial inactivation - Enrichment - Powdered infant formula - Sampling plan - Simulation - Strain variability

    The variability of stress resistance and lag time of single cells can have a big impact on their growth and therefore on the probability of their detection in food. In this study, six strains of Cronobacter spp. were subjected to heat, acid and desiccation stress and single cell lag times were determined using optical density measurements. The duration of lag time was highest after acid stress and did not correlate to stress resistance. The effect that the inactivation caused by stress and an extended lag time had on the projected cfu level reached after enrichment was simulated in different scenarios. For most strains, an enrichment time of 18 h was sufficient for stressed cells to reach the suggested minimum level of cell inoculum for the Cronobacter screening broth detection. Particular strains may require longer recovery periods. Further, probability calculations showed that the number of samples taken from a batch may have an important effect on detection probability, especially at low contamination rates. Therefore, in addition to increasing the recovery period, increasing the number of samples is a suitable strategy to improve detection.

    Testing improvements in the chocolate traceability system : Impact on product recalls and production efficiency
    Saltini, Rolando ; Akkerman, Renzo - \ 2012
    Food Control 23 (2012)1. - ISSN 0956-7135 - p. 221 - 226.
    Chocolate - Food safety - Recall - Simulation - Supply chain - Traceability

    The primary aim of food traceability is to increase food safety, but traceability systems can also bring other benefits to production systems and supply chains. In the literature these benefits are extensively discussed, but studies that quantify them are scarce. In this paper we propose two hypothetical improvements of the traceability system within the chocolate production system and supply chain and we illustrate the resulting benefits by using a case study. Based on the case study, we quantify the influence of these improvements on production efficiency and recall size in case of a safety crisis by developing a simulation tool. These results are aimed to illustrate and quantify the additional benefits of traceability information, and could help food industries in deciding whether and how to improve their traceability systems.

    Balancing environmental and economic performance in the food processing industry
    Akkerman, Renzo ; Donk, Dirk Pieter Van - \ 2010
    International Journal of Entrepreneurship and Innovation Management 11 (2010)3. - ISSN 1368-275X - p. 330 - 340.
    Decision support - Economic performance - Environmental performance - Food industry - Operations management - Process design - Product design - Scenario analysis - Simulation - Sustainability

    Changing customer requirements, unpredictable disturbances combined with expensive production facilities, are major problems for food processing companies to achieve synergy between the economic and environmental performance. There is notably a lack of tools to support decisions to explore effects on performance related to new product introductions, changes in production equipment, changes in planning concepts and their cross sections. We argue that interdisciplinary research that uses operations research techniques, operations management insights, food process technology and product design helps in exploring the effect of uncertainty in demand and production. As a result, process design can be more robust: both economic and environmental. This position paper explores the problem and the main elements of the proposed scenario-based simulation approach.

    Influence of capacity- and time-constrained intermediate storage in two-stage food production systems
    Akkerman, Renzo ; Donk, Dirk Pieter Van; Gaalman, Gerard - \ 2007
    International Journal of Production Research 45 (2007)13. - ISSN 0020-7543 - p. 2955 - 2973.
    Capacity constraints - Food processing - Simulation - Storage tanks - Time constraints

    In food processing, two-stage production systems with a batch processor in the first stage and packaging lines in the second stage are common and mostly separated by capacity- and time-constrained intermediate storage. This combination of constraints is common in practice, but the literature hardly pays any attention to this. In this paper, we show how various capacity and time constraints influence the performance of a specific two-stage system. We study the effects of several basic scheduling and sequencing rules in the presence of these constraints in order to learn the characteristics of systems like this. Contrary to the common sense in operations management, the LPT rule is able to maximize the total production volume per day. Furthermore, we show that adding one tank has considerable effects. Finally, we conclude that the optimal setup frequency for batches in the first stage is dictated by the storage time constraint.

    Relationships between climate change and rice development and its yield formation : A simulation study
    Liu, Taoju ; Yin, Xinyou ; Qi, Changhan ; Tang, Jianjun ; Chen, Meiqiu - \ 2005
    Chinese Journal of applied Ecology 16 (2005)3. - ISSN 1001-9332 - p. 486 - 490.
    Climate change - Rice development and its yield formation - Simulation

    With the application of mechanistic model (RICAM 1.3, RIce growth Calendar Model), this paper simulated the rice development and its yield formation under different climatic conditions at multi-locations of Asia. A three-stage Beta model (3s-Beta) was developed to predict the flowering stage of rice and to describe its three successive phases of photo-thermal response, i. e., basic vegetative phase, photoperiod-sensitive phase, and post photoperiod-sensitive phase. The 1980-1989 multi-location data of Morioka (Japan, 39°43′N), Nanchang (China, 28°36′N) and Los Banos (Philippines, 14°11′N) were used to verify the suitability of the model in studying ecosystem change. Comparisons of simulated results with observed data showed that this model could generally predict the eco-physiological processes of rice, and performed very well over a wide range of environments.

    Reallocation of beds to reduce waiting time for cardiac surgery
    Akkerman, Renzo ; Knip, Marrig - \ 2004
    Health Care Management Science 7 (2004)2. - ISSN 1386-9620 - p. 119 - 126.
    Cardiac surgery - Length of stay - Markov chain - Simulation - Waiting time

    Waiting times for cardiac surgery is a significant problem in the medical world. The fact that patients' length of stay varies considerably makes effective hospital operation a difficult job. This paper analyzes patients' length of stay in hospital wards following cardiac surgery. Three scenarios for hospital management are presented and evaluated using Markov chain theory and simulation experiments. The aim of our analyses is to examine unused bed capacity in hospital wards. This makes it possible to attain a more efficient allocation of hospital beds. The results presented in this paper provide useful insight into relationships between patients' length of stay, bed availability, and hospital waiting lists.

    A Compartmental Model of an External Urethral Sphincter Motoneuron of Onuf's Nucleus
    Heldoorn, M. ; Marani, E. ; Leeuwen, J.L. Van; Vanderschoot, J. - \ 2003
    Archives of Physiology and Biochemistry 111 (2003)3. - ISSN 1381-3455 - p. 193 - 201.
    Bistable behavior - Compartmental model - Genesis - Ionic conductances - Onuf's nucleus - Plateau potentials - Simulation

    This article discusses a model of the electrical behavior of an external urethral sphincter motoneuron, based on morphological parameters like soma size, dendritic diameters and spatial dendritic configuration, and several electrical parameters. Because experimental data about the exact ion conductance mix of external urethral sphincter neurons is scarce, the gaps in knowledge about external urethral sphincter motoneurons were filled in with known data of α-motoneurons. The constructed compartmental model of motoneurons of Onuf's nucleus contains six voltage-dependent ionic conductances: a fast sodium and potassium conductance and an anomalous rectifier in the soma; a fast delayed rectifier type potassium conductance and a fast sodium conductance in the initial axon segment; an L-type calcium channel in the dendritic compartments. This paper considers the simulation of external urethral sphincter motoneuron responses to current injections that evoke bistable behavior. Simulations show self-sustained discharge following a depolarizing pulse through the microelectrode; the firing was subsequently terminated by a short hyperpolarizing pulse. This behavior is highly functional for neurons that have to exhibit prolonged activation during sphincter closure. In addition to these 'on' and 'off' responses, we also observed a particular firing behavior in response to long-lasting triangular current pulses. When the depolarizing current was slowly increased and then decreased (triangular pulse) the firing frequency was higher during the descending phase than during the initial ascending phase.

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