Simon Vanmaercke - Academia.edu (original) (raw)

Papers by Simon Vanmaercke

SUMMARY Based on a particle-based model used to describe initial, passive cell-spreading, a model... more SUMMARY Based on a particle-based model used to describe initial, passive cell-spreading, a model for endothelial cell active spreading and migration has been developed. To describe the interaction of this cell-model with a homogeneous viscoelastic solid substrate, the latter has been implemented using the non-inertial smoothed-particle hydrodynamics method. The combination of these models is validated using traction force microscopy on individual cells in addition to geometrical measures such as contact area and eccentricity. This mechanistic validated model allows for a detailed computational investigation of cell-matrix interaction in both 2D and 3D environments.

Simulations are becoming increasingly important for the optimization of various processes. Biolog... more Simulations are becoming increasingly important for the optimization of various processes. Biological variation, however, adds an extra challenge for agricultural applications. As the interactions between the crop stems and machine parts are quite complex, bulk models are often inadequate to properly describe the crop-machine interaction. Discrete element modeling (DEM) has been proposed as a better way to model the behavior of particulate systems (Tijskens et al., 2003). While DEM has already been successfully applied for modeling grain and fertilizer streams (Van Liedekerke et al, 2009), its use for simulating the flow and compression of stems has been limited, because bendable straw particles were not available in DEM softwares until very recently (Lenaerts et al, 2014). While the linear elastic models applied by Lenaerts et al. (2014) could describe the reversible bending of straw in a realistic way for small deformations, they are inadequate for describing the bending and compr...

AIP Conference Proceedings, 2017

Freshly harvested horticultural produce require a proper temperature management to maintain their... more Freshly harvested horticultural produce require a proper temperature management to maintain their high economic value. Towards this end, low temperature storage is of crucial importance to maintain a high product quality. Optimizing both the package design of packed produce and the different steps in the postharvest cold chain can be achieved by numerical modelling of the relevant transport phenomena. This work presents a novel methodology to accurately model both the random filling of produce in a package and the subsequent cooling process. First, a cultivar-specific database of more than 100 realistic CAD models of apple and pear fruit is built with a validated geometrical 3D shape model generator. To have an accurate representation of a realistic picking season, the model generator also takes into account the biological variability of the produce shape. Next, a discrete element model (DEM) randomly chooses surface meshed bodies from the database to simulate the gravitational filling process of produce in a box or bin, using actual mechanical properties of the fruit. A computational fluid dynamics (CFD) model is then developed with the final stacking arrangement of the produce to study the cooling efficiency of packages under several conditions and configurations. Here, a typical precooling operation is simulated to demonstrate the large differences between using actual 3D shapes of the fruit and an equivalent spheres approach that simplifies the problem drastically. From this study, it is concluded that using a simplified representation of the actual fruit shape may lead to a severe overestimation of the cooling behaviour.status: publishe

Simulations are becoming increasingly important for the optimization of various processes. Howeve... more Simulations are becoming increasingly important for the optimization of various processes. However, in the case of biomass handling the natural variability of the biological material adds an extra challenge. As the processing of crop stems is governed by the discrete interactions between the particles and the machine parts, bulk models are inadequate to properly describe the crop-machine interaction for low and moderate particle densities. Discrete element modeling (DEM) has been proposed as a better way to model the behavior of particulate systems (Tijskens et al., 2003). While DEM has already been successfully applied for modeling grain and fertilizer streams (Van Liedekerke et al, 2009). Recently, its usefulness for simulating the flow and compression of flexible stems has also been demonstrated (Lenaerts et al., 2014). However, while the linear elastic and Hertzian contact models can describe the reversible bending and compression of crop stems in a realistic way for small defor...

The Discrete Element Method is growing increasingly capable of modelling assemblies of complex sh... more The Discrete Element Method is growing increasingly capable of modelling assemblies of complex shapes and materials. Arbitrary particle shapes can be represented using two major approaches. One is to combine spheres into composite structures that approximate the shape of a desired object. Alternatively, one can make use of more complex primitive shapes (e.g. ellipsoids, cylinders, triangles etc.) that are better suited to represent the given shape. Successful examples of advances in the latter technique are the modelling of bendable straw as a combination of cylinders [1] and the realisation of a generalized contact model for arbitrary polyhedra [2]. An additional challenge in the representation of complex shapes arises in the modelling of bendable objects with a large surface-to-thickness ratio. Again, these flexible flat objects can be modelled as a collection of spheres or as assemblies of tubes, elliptical cylinders, or similarly derived base objects. However, the large surface-...

migration. Altogether, data suggest that our coupled cell-ECM model can capture important feature... more migration. Altogether, data suggest that our coupled cell-ECM model can capture important features of single cell migration and cell-matrix interaction. By validation with and feedback to experiments, this model can therefore aid in unravelling the mechanisms behind cell-matrix interaction.

Cooling of freshly harvested produce is crucial for maintaining a high product quality for a prol... more Cooling of freshly harvested produce is crucial for maintaining a high product quality for a prolonged storage period and to reduce postharvest losses. Modelling the cooling process of packed horticultural produce provides a means for improving package designs and cooling operations. In this work, a methodology to more accurately model the cooling process of randomly stacked produce in packages is presented. First, a validated geometrical 3D shape model generator of apple fruit is used to create realistic CAD models. The generator also considers the biological variability of the produce shape to create a database of more than 100 representative fruits of each cultivar. A discrete element model (DEM) then randomly selects surface meshed bodies from the database to simulate the gravitational packing of produce in a designated box or bin. The resulting stacking pattern of the produce is used to generate a computational fluid dynamics (CFD) model. The CFD model solves the airflow, heat ...

Computer Methods in Applied Mechanics and Engineering, 2017

We propose viscoelastic smoothed particle hydrodynamics (SPH) with extended boundary conditions a... more We propose viscoelastic smoothed particle hydrodynamics (SPH) with extended boundary conditions as a new method to model the extracellular matrix (ECM) in contact with a migrating cell. By drop out of the inertial terms in the SPH equations of motion, the new SPH formulation allows to solve problems in a low Reynolds environment with a timestep independent of the particle spacing,

Postharvest Biology and Technology, 2017

A non-destructive methodology was developed to automatically detect and quantify bruise volumes i... more A non-destructive methodology was developed to automatically detect and quantify bruise volumes in the equatorial region of apples, using X-ray CT images. Grey level threshold values were calculated to segment bruises in 'Jonagold', 'Joly Red' and 'Kanzi' apple fruit using the multi-level Otsu's threshold method. Comparisons were made between the CT-based bruise volume estimates and bruise volume estimates that were based on destructive measurements in combination with simple geometric assumptions. Visualisation of the bruises in both 2 and 3D showed that bruises, resulting from a pendulum impact with a spherical impactor, can be highly irregularly shaped which implies that the bruise volume estimations based on simple geometric assumptions cannot deliver accurate results.

Postharvest Biology and Technology, 2016

A contact force model was developed to model the visco-elastoplastic (VEP) behaviour of apples. T... more A contact force model was developed to model the visco-elastoplastic (VEP) behaviour of apples. The model is based on the elastoplastic Thornton model and has been written in a pressure-based formulation to extend the application of the model to Discrete Element Method (DEM) simulations with arbitrary rounded shapes. The parameters of the new developed VEP contact force model were determined by fitting the experimental data acquired from Jonagold, Joly Red and Kanzi apples impacted by a pendulum. With only one parameter set per cultivar and for a large impact range (impact velocity range: 0.3-1.5 m/s), the VEP-model (R 2 = 0.90 AE 0.13) provides a better description of the forcedeformation profiles than the viscoelastic Kono and Kuwabara (KK) model (R 2 = 0.71 AE 0.20). The equivalent Young's modulus (E *) was also determined under quasi-static conditions, which resulted in measured E *-values for Jonagold, Joly Red and Kanzi apples of respectively 4.24 AE 0.96 MPa, 5.09 AE 1.27 MPa and 7.82 AE 0.41 MPa. The novel VEP-model has the potential to help predict and understand bruise damage in apples as well as other horticultural products. 2016 Elsevier B.V. All rights reserved.

Computers and Electronics in Agriculture, 2016

A requirement for optimizing crop processing machinery using DEM simulations is the application o... more A requirement for optimizing crop processing machinery using DEM simulations is the application of virtual stems that behave realistically during deformation. In this study, data based bending models were developed for virtual segmented crop stems. These models combine realistic bending behaviour with a minimal number of model parameters. Also the effects of plastic deformation and damage were incorporated in the model. The bending model

Computer Methods in Applied Mechanics and Engineering, 2015

Many real-life applications of the Discrete Element Method (DEM) require a particle description w... more Many real-life applications of the Discrete Element Method (DEM) require a particle description which accounts for irregular and arbitrary shapes. In this work, a novel method is presented for calculating contact force interactions between polyhedral particles. A contact between two polyhedra is decomposed as a set of contacts between individual polygonal facets. For each polygon-polygon contact, an individual contact force is obtained by integrating a linear pressure over the area of its intersection. Both convex as well as partially concave polyhedra can be accurately represented. The proposed algorithm is validated by comparing to previously published experimental and computational gravitational particle depositions of identical cubes. Finally, the model is demonstrated in simulations of gravitational packing of various other polyhedral shapes.

International Journal of Heat and Mass Transfer, 2015

It is widely recognized that the control of the activity of dissolved oxygen is essential for the... more It is widely recognized that the control of the activity of dissolved oxygen is essential for the use of lead-bismuth eutectic (LBE) as primary coolant for nuclear systems. A lead oxide mass exchanger (PbO MX) comprised of a packed bed of lead oxide spheres is a promising solution to regulate the dissolved oxygen activity in the LBE. In order to design and operate a PbO MX properly, the dissolution kinetics of PbO in flowing LBE should be determined. A high-fidelity Computational Fluid Dynamic (CFD) model of solid-to-liquid mass transfer has been developed to determine the mass transfer coefficient of a PbO MX in flowing LBE. We validated the developed CFD model against experimental data obtained from the LBE test loop CRAFT, at SCKCEN. The model is in good agreement with the experimental data. The effect of the channel to particle diameter ratio (R) on the mass transfer coefficient was evaluated by using the validated model. A mass transfer correlation for PbO MX was obtained, in terms of the Sherwood number, by fitting the simulation results for the general case of a random packed bed with a porosity of about 0.4.

International Journal of Mechanical Sciences, 2015

Computer simulations are becoming increasingly important for the optimisation of various processe... more Computer simulations are becoming increasingly important for the optimisation of various processes since they can significantly reduce the development time and costs. The discrete element method (DEM) offers a powerful tool for simulating the interactions of large numbers of particles. The method has proven its usefulness for many applications where granular and spherical particles are handled. Very recently DEM, was used to simulate the interactions of tubular particles. While the existing linear elastic models could describe the reversible bending and denting of these particles in a realistic way for small deformations, they are inadequate for describing the bending and compression behaviour at higher forces. In this region, buckling phenomena become important. Therefore, new phenomenological models, inspired by the collapse of steel tubes due to ovalisation of the cross section and the formation of plastic hinges, have been implemented for metal and synthetic plastic tubes. Using these models virtual, bendable tubes were created in the DEMeterþ þ software. The DEM parameters were calibrated for copper and PVC tubes based on combined bending and denting tests conducted using an Universal Testing System. The simulations were in good agreement with the measurements (R 2 4 0:91). This realistic DEM model of bending can, in future research, be used to simulate the processing of large numbers of tubular particles (e.g. the processing of crop stems).

Biosystems Engineering, 2015

In order to optimise the processing of stem crops, insight into the deformation behaviour of the ... more In order to optimise the processing of stem crops, insight into the deformation behaviour of the crop and the interaction between crop and machine is essential. Most research in the area of mechanical and physical properties of crop stems is focused on characterising the agricultural products to the point

Computational Particle Mechanics, 2015

Advancing front packing algorithms have proven to be very efficient in 2D for obtaining high dens... more Advancing front packing algorithms have proven to be very efficient in 2D for obtaining high density sets of particles, especially disks. However, the extension of these algorithms to 3D is not a trivial task. In the present paper, an advancing front algorithm for obtaining highly dense sphere packings is presented. It is simpler than other advancing front packing methods in 3D and can also be used with other types of particles. Comparison with respect to other packing methods have been carried out and a significant improvement in the volume fraction (VF) has been observed. Moreover, the quality of packings was evaluated with indicators other than VF. As additional advantage, the number of generated particles with the algorithm is linear with respect to time.

SUMMARY Based on a particle-based model used to describe initial, passive cell-spreading, a model... more SUMMARY Based on a particle-based model used to describe initial, passive cell-spreading, a model for endothelial cell active spreading and migration has been developed. To describe the interaction of this cell-model with a homogeneous viscoelastic solid substrate, the latter has been implemented using the non-inertial smoothed-particle hydrodynamics method. The combination of these models is validated using traction force microscopy on individual cells in addition to geometrical measures such as contact area and eccentricity. This mechanistic validated model allows for a detailed computational investigation of cell-matrix interaction in both 2D and 3D environments.

Simulations are becoming increasingly important for the optimization of various processes. Biolog... more Simulations are becoming increasingly important for the optimization of various processes. Biological variation, however, adds an extra challenge for agricultural applications. As the interactions between the crop stems and machine parts are quite complex, bulk models are often inadequate to properly describe the crop-machine interaction. Discrete element modeling (DEM) has been proposed as a better way to model the behavior of particulate systems (Tijskens et al., 2003). While DEM has already been successfully applied for modeling grain and fertilizer streams (Van Liedekerke et al, 2009), its use for simulating the flow and compression of stems has been limited, because bendable straw particles were not available in DEM softwares until very recently (Lenaerts et al, 2014). While the linear elastic models applied by Lenaerts et al. (2014) could describe the reversible bending of straw in a realistic way for small deformations, they are inadequate for describing the bending and compr...

AIP Conference Proceedings, 2017

Freshly harvested horticultural produce require a proper temperature management to maintain their... more Freshly harvested horticultural produce require a proper temperature management to maintain their high economic value. Towards this end, low temperature storage is of crucial importance to maintain a high product quality. Optimizing both the package design of packed produce and the different steps in the postharvest cold chain can be achieved by numerical modelling of the relevant transport phenomena. This work presents a novel methodology to accurately model both the random filling of produce in a package and the subsequent cooling process. First, a cultivar-specific database of more than 100 realistic CAD models of apple and pear fruit is built with a validated geometrical 3D shape model generator. To have an accurate representation of a realistic picking season, the model generator also takes into account the biological variability of the produce shape. Next, a discrete element model (DEM) randomly chooses surface meshed bodies from the database to simulate the gravitational filling process of produce in a box or bin, using actual mechanical properties of the fruit. A computational fluid dynamics (CFD) model is then developed with the final stacking arrangement of the produce to study the cooling efficiency of packages under several conditions and configurations. Here, a typical precooling operation is simulated to demonstrate the large differences between using actual 3D shapes of the fruit and an equivalent spheres approach that simplifies the problem drastically. From this study, it is concluded that using a simplified representation of the actual fruit shape may lead to a severe overestimation of the cooling behaviour.status: publishe

Simulations are becoming increasingly important for the optimization of various processes. Howeve... more Simulations are becoming increasingly important for the optimization of various processes. However, in the case of biomass handling the natural variability of the biological material adds an extra challenge. As the processing of crop stems is governed by the discrete interactions between the particles and the machine parts, bulk models are inadequate to properly describe the crop-machine interaction for low and moderate particle densities. Discrete element modeling (DEM) has been proposed as a better way to model the behavior of particulate systems (Tijskens et al., 2003). While DEM has already been successfully applied for modeling grain and fertilizer streams (Van Liedekerke et al, 2009). Recently, its usefulness for simulating the flow and compression of flexible stems has also been demonstrated (Lenaerts et al., 2014). However, while the linear elastic and Hertzian contact models can describe the reversible bending and compression of crop stems in a realistic way for small defor...

The Discrete Element Method is growing increasingly capable of modelling assemblies of complex sh... more The Discrete Element Method is growing increasingly capable of modelling assemblies of complex shapes and materials. Arbitrary particle shapes can be represented using two major approaches. One is to combine spheres into composite structures that approximate the shape of a desired object. Alternatively, one can make use of more complex primitive shapes (e.g. ellipsoids, cylinders, triangles etc.) that are better suited to represent the given shape. Successful examples of advances in the latter technique are the modelling of bendable straw as a combination of cylinders [1] and the realisation of a generalized contact model for arbitrary polyhedra [2]. An additional challenge in the representation of complex shapes arises in the modelling of bendable objects with a large surface-to-thickness ratio. Again, these flexible flat objects can be modelled as a collection of spheres or as assemblies of tubes, elliptical cylinders, or similarly derived base objects. However, the large surface-...

migration. Altogether, data suggest that our coupled cell-ECM model can capture important feature... more migration. Altogether, data suggest that our coupled cell-ECM model can capture important features of single cell migration and cell-matrix interaction. By validation with and feedback to experiments, this model can therefore aid in unravelling the mechanisms behind cell-matrix interaction.

Cooling of freshly harvested produce is crucial for maintaining a high product quality for a prol... more Cooling of freshly harvested produce is crucial for maintaining a high product quality for a prolonged storage period and to reduce postharvest losses. Modelling the cooling process of packed horticultural produce provides a means for improving package designs and cooling operations. In this work, a methodology to more accurately model the cooling process of randomly stacked produce in packages is presented. First, a validated geometrical 3D shape model generator of apple fruit is used to create realistic CAD models. The generator also considers the biological variability of the produce shape to create a database of more than 100 representative fruits of each cultivar. A discrete element model (DEM) then randomly selects surface meshed bodies from the database to simulate the gravitational packing of produce in a designated box or bin. The resulting stacking pattern of the produce is used to generate a computational fluid dynamics (CFD) model. The CFD model solves the airflow, heat ...

Computer Methods in Applied Mechanics and Engineering, 2017

We propose viscoelastic smoothed particle hydrodynamics (SPH) with extended boundary conditions a... more We propose viscoelastic smoothed particle hydrodynamics (SPH) with extended boundary conditions as a new method to model the extracellular matrix (ECM) in contact with a migrating cell. By drop out of the inertial terms in the SPH equations of motion, the new SPH formulation allows to solve problems in a low Reynolds environment with a timestep independent of the particle spacing,

Postharvest Biology and Technology, 2017

A non-destructive methodology was developed to automatically detect and quantify bruise volumes i... more A non-destructive methodology was developed to automatically detect and quantify bruise volumes in the equatorial region of apples, using X-ray CT images. Grey level threshold values were calculated to segment bruises in 'Jonagold', 'Joly Red' and 'Kanzi' apple fruit using the multi-level Otsu's threshold method. Comparisons were made between the CT-based bruise volume estimates and bruise volume estimates that were based on destructive measurements in combination with simple geometric assumptions. Visualisation of the bruises in both 2 and 3D showed that bruises, resulting from a pendulum impact with a spherical impactor, can be highly irregularly shaped which implies that the bruise volume estimations based on simple geometric assumptions cannot deliver accurate results.

Postharvest Biology and Technology, 2016

A contact force model was developed to model the visco-elastoplastic (VEP) behaviour of apples. T... more A contact force model was developed to model the visco-elastoplastic (VEP) behaviour of apples. The model is based on the elastoplastic Thornton model and has been written in a pressure-based formulation to extend the application of the model to Discrete Element Method (DEM) simulations with arbitrary rounded shapes. The parameters of the new developed VEP contact force model were determined by fitting the experimental data acquired from Jonagold, Joly Red and Kanzi apples impacted by a pendulum. With only one parameter set per cultivar and for a large impact range (impact velocity range: 0.3-1.5 m/s), the VEP-model (R 2 = 0.90 AE 0.13) provides a better description of the forcedeformation profiles than the viscoelastic Kono and Kuwabara (KK) model (R 2 = 0.71 AE 0.20). The equivalent Young's modulus (E *) was also determined under quasi-static conditions, which resulted in measured E *-values for Jonagold, Joly Red and Kanzi apples of respectively 4.24 AE 0.96 MPa, 5.09 AE 1.27 MPa and 7.82 AE 0.41 MPa. The novel VEP-model has the potential to help predict and understand bruise damage in apples as well as other horticultural products. 2016 Elsevier B.V. All rights reserved.

Computers and Electronics in Agriculture, 2016

A requirement for optimizing crop processing machinery using DEM simulations is the application o... more A requirement for optimizing crop processing machinery using DEM simulations is the application of virtual stems that behave realistically during deformation. In this study, data based bending models were developed for virtual segmented crop stems. These models combine realistic bending behaviour with a minimal number of model parameters. Also the effects of plastic deformation and damage were incorporated in the model. The bending model

Computer Methods in Applied Mechanics and Engineering, 2015

Many real-life applications of the Discrete Element Method (DEM) require a particle description w... more Many real-life applications of the Discrete Element Method (DEM) require a particle description which accounts for irregular and arbitrary shapes. In this work, a novel method is presented for calculating contact force interactions between polyhedral particles. A contact between two polyhedra is decomposed as a set of contacts between individual polygonal facets. For each polygon-polygon contact, an individual contact force is obtained by integrating a linear pressure over the area of its intersection. Both convex as well as partially concave polyhedra can be accurately represented. The proposed algorithm is validated by comparing to previously published experimental and computational gravitational particle depositions of identical cubes. Finally, the model is demonstrated in simulations of gravitational packing of various other polyhedral shapes.

International Journal of Heat and Mass Transfer, 2015

It is widely recognized that the control of the activity of dissolved oxygen is essential for the... more It is widely recognized that the control of the activity of dissolved oxygen is essential for the use of lead-bismuth eutectic (LBE) as primary coolant for nuclear systems. A lead oxide mass exchanger (PbO MX) comprised of a packed bed of lead oxide spheres is a promising solution to regulate the dissolved oxygen activity in the LBE. In order to design and operate a PbO MX properly, the dissolution kinetics of PbO in flowing LBE should be determined. A high-fidelity Computational Fluid Dynamic (CFD) model of solid-to-liquid mass transfer has been developed to determine the mass transfer coefficient of a PbO MX in flowing LBE. We validated the developed CFD model against experimental data obtained from the LBE test loop CRAFT, at SCKCEN. The model is in good agreement with the experimental data. The effect of the channel to particle diameter ratio (R) on the mass transfer coefficient was evaluated by using the validated model. A mass transfer correlation for PbO MX was obtained, in terms of the Sherwood number, by fitting the simulation results for the general case of a random packed bed with a porosity of about 0.4.

International Journal of Mechanical Sciences, 2015

Computer simulations are becoming increasingly important for the optimisation of various processe... more Computer simulations are becoming increasingly important for the optimisation of various processes since they can significantly reduce the development time and costs. The discrete element method (DEM) offers a powerful tool for simulating the interactions of large numbers of particles. The method has proven its usefulness for many applications where granular and spherical particles are handled. Very recently DEM, was used to simulate the interactions of tubular particles. While the existing linear elastic models could describe the reversible bending and denting of these particles in a realistic way for small deformations, they are inadequate for describing the bending and compression behaviour at higher forces. In this region, buckling phenomena become important. Therefore, new phenomenological models, inspired by the collapse of steel tubes due to ovalisation of the cross section and the formation of plastic hinges, have been implemented for metal and synthetic plastic tubes. Using these models virtual, bendable tubes were created in the DEMeterþ þ software. The DEM parameters were calibrated for copper and PVC tubes based on combined bending and denting tests conducted using an Universal Testing System. The simulations were in good agreement with the measurements (R 2 4 0:91). This realistic DEM model of bending can, in future research, be used to simulate the processing of large numbers of tubular particles (e.g. the processing of crop stems).

Biosystems Engineering, 2015

In order to optimise the processing of stem crops, insight into the deformation behaviour of the ... more In order to optimise the processing of stem crops, insight into the deformation behaviour of the crop and the interaction between crop and machine is essential. Most research in the area of mechanical and physical properties of crop stems is focused on characterising the agricultural products to the point

Computational Particle Mechanics, 2015

Advancing front packing algorithms have proven to be very efficient in 2D for obtaining high dens... more Advancing front packing algorithms have proven to be very efficient in 2D for obtaining high density sets of particles, especially disks. However, the extension of these algorithms to 3D is not a trivial task. In the present paper, an advancing front algorithm for obtaining highly dense sphere packings is presented. It is simpler than other advancing front packing methods in 3D and can also be used with other types of particles. Comparison with respect to other packing methods have been carried out and a significant improvement in the volume fraction (VF) has been observed. Moreover, the quality of packings was evaluated with indicators other than VF. As additional advantage, the number of generated particles with the algorithm is linear with respect to time.