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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Hydrodynamically Coupled Brownian Dynamics : A coarse-grain particle-based Brownian dynamics technique with hydrodynamic interactions for modeling self-developing flow of polymer solutions
Ahuja, V.R. ; Gucht, J. Van Der; Briels, W.J. - \ 2018
Journal of Chemical Physics 148 (2018)3. - ISSN 0021-9606
We present a novel coarse-grain particle-based simulation technique for modeling self-developing flow of dilute and semi-dilute polymer solutions. The central idea in this paper is the two-way coupling between a mesoscopic polymer model and a phenomenological fluid model. As our polymer model, we choose Responsive Particle Dynamics (RaPiD), a Brownian dynamics method, which formulates the so-called "conservative" and "transient" pair-potentials through which the polymers interact besides experiencing random forces in accordance with the fluctuation dissipation theorem. In addition to these interactions, our polymer blobs are also influenced by the background solvent velocity field, which we calculate by solving the Navier-Stokes equation discretized on a moving grid of fluid blobs using the Smoothed Particle Hydrodynamics (SPH) technique. While the polymers experience this frictional force opposing their motion relative to the background flow field, our fluid blobs also in turn are influenced by the motion of the polymers through an interaction term. This makes our technique a two-way coupling algorithm. We have constructed this interaction term in such a way that momentum is conserved locally, thereby preserving long range hydrodynamics. Furthermore, we have derived pairwise fluctuation terms for the velocities of the fluid blobs using the Fokker-Planck equation, which have been alternatively derived using the General Equation for the Non-Equilibrium Reversible-Irreversible Coupling (GENERIC) approach in Smoothed Dissipative Particle Dynamics (SDPD) literature. These velocity fluctuations for the fluid may be incorporated into the velocity updates for our fluid blobs to obtain a thermodynamically consistent distribution of velocities. In cases where these fluctuations are insignificant, however, these additional terms may well be dropped out as they are in a standard SPH simulation. We have applied our technique to study the rheology of two different concentrations of our model linear polymer solutions. The results show that the polymers and the fluid are coupled very well with each other, showing no lag between their velocities. Furthermore, our results show non-Newtonian shear thinning and the characteristic flattening of the Poiseuille flow profile typically observed for polymer solutions.
Enabling Practice-driven Innovation in the Animal Production Sector
Dijk, L. ; Buller, H. ; MacAllister, L.K. ; Baker, P. ; Mul, M.F. ; Neijenhuis, F. ; Plomp, M. ; Wichman, A. ; Yngvesson, J. ; Temple, D. ; Zak, J. ; Jozefova, J. ; Stokes, J. ; Weeks, C.A. ; Main, D.J.C. - \ 2017
- 12 p.
practice-driven - innovation - multi-actor networks - conditions - facilitation
Using the laying hen sector as a case study, the EU-H2020-funded Hennovation project has been testing mechanisms to enable practice-driven innovation through the establishment of innovation networks of farmers and within the laying-hen-processing industry that are facilitated to proactively search for, share and use new ideas to improve hen welfare, efficiency and sustainability. Networks are variably supported by scientists, veterinarians, advisors and others. Nineteen multi-actor networks have been mobilised on local and regional levels across the UK, Sweden, Netherlands, Spain and Czech-Republic.
Practice-driven innovation processes were network specific and evolved as the actors within the network came together to share common problems, experiment with possible solutions and learn. Their success was also affected by the institutional context, the structure of the poultry sector, current market forces and wider Agricultural Innovation Systems in each country. This paper explores the circumstances considered necessary by the facilitators to enable practice-driven innovation, providing examples of conditions affecting the innovation process. Further influences included conditions for innovation to happen (e.g. shared opportunity, motivation and knowledge), conditions to work effectively as a network (e.g. trust, collective purpose and contacts) and conditions for successful application in practice (e.g. capacity within the production system and market and legislative ability).
Network approach to stimulate and support practice-led onfarm innovations in the laying hen sector
Niekerk, T.G.C.M. van; Baker, P. ; Mul, M.F. ; Plomp, M. ; Stokes, J.R. ; Wichman, A. ; Zak, J. - \ 2017
Sensitivity of the landslide model LAPSUS_LS to vegetation and soil parameters
Rossi, L.M.W. ; Rapidel, B. ; Roupsard, O. ; Villatoro-sánchez, M. ; Mao, Z. ; Nespoulous, J. ; Perez, J. ; Prieto, I. ; Roumet, C. ; Metselaar, K. ; Schoorl, J.M. ; Claessens, L. ; Stokes, A. - \ 2017
Ecological Engineering 109 (2017)pt. B. - ISSN 0925-8574 - p. 249 - 255.
Bulk density - Cohesion - Modeling - Roots - Slope stability - Soil - Transmissivity
The influence of vegetation on slope stability is well understood at the slope level but scaling up to the catchment level is still a challenge, partially because of a lack of suitable data to validate models. We tested the physical landslide model, LAPSUS_LS, which models slope stability at the catchment scale. LAPSUS_LS combines a hydrological model with a Limit Equilibrium Method model, and calculates the factor of safety of individual cells based on their hydrological and geomorphological characteristics. We tested two types of vegetation on slope stability: (i) coffee monoculture (Coffea arabica) and (ii) a mixed plantation of coffee and deep rooting Erythrina (Erythrina poeppigiana) trees. Using soil and root data from Costa Rica, we performed simulations to test the response of LAPSUS_LS to root reinforcement, soil bulk density, transmissivity, internal friction angle and depth of shear plane. Furthermore, we modified the model to include biomass surcharge effect in the calculations. Results show that LAPSUS_LS was most sensitive to changes in additional cohesion from roots. When the depth of the shear plane was fixed at 1.0. m, slopes were not unstable. However, when the shear plane was fixed to 1.5. m, the mixed plantation of coffee and trees stabilized slopes, but the coffee monoculture was highly unstable, because root reinforcement was low at a depth of 1.5. m. Soil transmissivity had a limited impact on the results compared to bulk density and internal friction angle. Biomass surcharge did not have any significant effect on the simulations. In conclusion, LAPSUS_LS responded well to the soil and vegetation input data, and is a suitable candidate for modeling the stability of vegetated slopes at the catchment level.
Modeling soft interface dominated systems : A comparison of phase field and Gibbs dividing surface models
Lamorgese, A. ; Mauri, R. ; Sagis, L.M.C. - \ 2017
Physics Reports 675 (2017). - ISSN 0370-1573 - p. 1 - 54.
Coalescence - Conservation principles - Diffuse interface model - Droplet deformation and breakup - Gibbs dividing surface - Korteweg force - Order parameters - Phase separation - Soft multiphase materials - Surface excess properties - Surface rheology - Wetting
The two main continuum frameworks used for modeling the dynamics of soft multiphase systems are the Gibbs dividing surface model, and the diffuse interface model. In the former the interface is modeled as a two dimensional surface, and excess properties such as a surface density, or surface energy are associated with this sharp interface. Its motion and deformation, and the time evolution of the excess fields associated with it are calculated by a set of partial differential equations (the jump balances), which have to be solved together with the mass, momentum, and energy balances of the bulk phases. A wide range of phenomena have been modeled in this framework, such as the deformation of emulsion droplets in a flow field, the effects of interfacial rheology on multiphase flows, wave phenomena in stratified flows, bubbles rising in a quiescent liquid, phase separation in immiscible mixtures, wetting phenomena, and in-plane and cross-plane mass and heat transfer.In the diffuse interface model the interface is modeled as a three dimensional region of finite thickness, in which order parameters change continuously from their value in one bulk phase to their value in the adjoining bulk phase. The model starts from a free energy functional which contains nonlocal contributions, which to leading order are represented by a square gradient term of the order parameter. The spatial distribution of density or concentration within the interfacial region is then determined by free energy minimization. When a simple pairwise inter-particle potential is assumed, a natural extension of the van der Waals model of phase transitions is obtained. Assuming a simple constitutive relation for the diffusive material fluxes in very viscous binary mixtures, the Cahn-Hilliard theory of spinodal decomposition can be obtained. For systems where convective material fluxes cannot be neglected, a reversible body force, called Korteweg force, must be added to the Navier-Stokes equation, which is proportional to the chemical potential gradient. This force is non-zero only for systems not at equilibrium, and is responsible for the strong convection observed in phase separating mixtures, while it is absent in systems where chemical potentials are uniform. Like the Gibbs dividing surface model, the diffuse interface model has been applied to a wide range of phenomena, such as mixing and demixing in binary mixtures, buoyancy driven detachment of wall-bound droplets, droplet breakup and coalescence, Marangoni effects, and flow in nano- and microchannels.Here we discuss the derivation of the governing equations of these two frameworks, and compare their strengths and weaknesses. We also show how these two frameworks can be combined to solve multiphase problems more effectively.
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.

Bending moment dynamics during swimming of developing zebrafish larvae
Voesenek, C.J. ; Leeuwen, J.L. van - \ 2016
In: Sun, sea & science. - Society for Experimental Biology - p. 44 - 44.
Zebrafish larvae are able to swim immediately after hatching,
making effective escape manoeuvres at two days post fertilization
(dpf). From 2 to 5 dpf, larval zebrafish improve swimming
performance by increasing their tail-beat frequency and amplitude
(Van Leeuwen et al. (2015) J. R. Soc. Interface 12: 20150479). During
these first days of development, the larvae’s muscle system changes
rapidly, while it continues functioning to power swimming. This
requires them to use their muscles differently across development.
A first step towards understanding how the larvae achieve this
and how they change their performance, is by computing the
time-dependent internal bending moment distributions along
the body during swimming. This allows us to assess the changes
in local bending power as the fish grows. We developed a combined
experimental and computational approach for reconstructing timeresolved
bending moment distributions from high-speed videos of
free-swimming larvae (2-12 dpf). First, we reconstruct the threedimensional
position, orientation and body curvature from these
images. We feed these reconstructions into a computational fluiddynamics
solver in order to calculate the flow field and the fluid
forces along the fish’s body. Finally, we combine the motion of the
longitudinal body axis and the external fluid forces as input for an
optimization procedure to calculate the best fitting time-dependent
bending moment distribution. The dynamics of these bending
moments provide novel insight in the developmental mechanics of
swimming across the first stages of zebrafish.
A1.3 HOW TAIL-BEAT FREQUENCY AND
BODY CURVATURE AFFECT SWIMMING
PERFORMANCE IN LARVAL ZEBRAFISH
TUESDAY 5 JULY, 2016 14:30
GEN LI (CHIBA UNIVERSITY, JAPAN), ULRIKE K MÜLLER
(CALIFORNIA STATE UNIVERSITY FRESNO, UNITED STATES),
HAO LIU (CHIBA UNIVERSITY, JAPAN), JOHAN L VAN LEEUWEN
(WAGENINGEN UNIVERSITY, NETHERLANDS)
GENLI@CHIBA-U.JP
Small undulatory swimmers such as larval zebrafish operate in
the intermediate Reynolds regime and experience relatively high
drag during cyclic swimming. Experimental observations (J. R.
Soc. Interface 12: 20150479) demonstrated (a) that larval zebrafish
tend to increase both tail-beat frequency and amplitude with
swimming speed and (b) a negative power relationship between
Strouhal number and Reynolds number during cyclic swimming.
To elucidate the underlying mechanisms, we developed an
integrated 3D computational approach of hydrodynamics and
free-swimming body dynamics that couples the Navier-Stokes
(NS) equations to the equations of undulating body motion. A
numerical approach is required to analyze the highly non-linear
nature of the dynamics of large-amplitude undulatory swimming
in the intermediate Reynolds regime. Using the model, we explored
how tail-beat frequency and amplitude of lateral curvature along
the body affect swimming performance (in terms of speed, fluid
dynamic efficiency and cost of transport). The explored parameter
space extends beyond the experimentally observed frequencyamplitude
combinations in larval zebrafish.
Our computations predict that increasing both frequency and
amplitude to swim faster improves swimming performance, which
agrees with previous experimental observations. This suggests
that fish larvae adjust their body kinematics to optimize swimming
performance. In addition, a robust negative power relationship
between Re and St was predicted, again in line with experimental
observations, and irrespective of the employed combinations of
frequency and curvature amplitude. The coupling between Re and
St is not an effect of kinematic optimization, but results from fluid
dynamic constraints.
GFP as potential cellular viscosimeter
Visser, Antonie ; Westphal, A.H. ; Skakun, V.V. ; Borst, J.W. - \ 2016
Methods and Applications in Fluorescence 4 (2016)3. - ISSN 2050-6120
The molecular dimensions of proteins such as green fluorescent protein (GFP) are large as compared to the ones of solvents like water or glycerol. The microscopic viscosity, which determines the resistance to diffusion of, e.g. GFP, is then the same as that determined from the resistance of the solvent to flow, which is known as macroscopic viscosity. GFP in water/glycerol mixtures senses this macroscopic viscosity, because the translational and rotational diffusion coefficients are proportional to the reciprocal value of the viscosity as predicted by the Stokes–Einstein equations. To test this hypothesis, we have performed time-resolved fluorescence anisotropy (reporting on rotational diffusion) and fluorescence correlation spectroscopy (reporting on translational diffusion) experiments of GFP in water/glycerol mixtures. When the solvent also contains macromolecules of similar or larger dimensions as GFP, the microscopic and macroscopic viscosities can be markedly different and the Stokes–Einstein relations must be adapted. It was established from previous dynamic fluorescence spectroscopy observations of diffusing proteins with dextran polysaccharides as co-solvents (Lavalette et al 2006 Eur. Biophys. J. 35 517–22), that rotation and translation sense a different microscopic viscosity, in which the one arising from rotation is always less than that from translation. A microscopic viscosity parameter is defined that depends on scaling factors between GFP and its immediate environment. The direct consequence is discussed for two reported diffusion coefficients of GFP in living cells.
Coarse-grained simulations for flow of complex soft matter fluids in the bulk and in the presence of solid interfaces
Ahuja, V.R. ; Gucht, J. van der; Briels, W.J. - \ 2016
Journal of Chemical Physics 145 (2016)19. - ISSN 0021-9606

We present a coarse-grained particle-based simulation technique for modeling flow of complex soft matter fluids such as polymer solutions in the presence of solid interfaces. In our coarse-grained description of the system, we track the motion of polymer molecules using their centers-of-mass as our coarse-grain co-ordinates and also keep track of another set of variables that describe the background flow field. The coarse-grain motion is thus influenced not only by the interactions based on appropriate potentials used to model the particular polymer system of interest and the random kicks associated with thermal fluctuations, but also by the motion of the background fluid. In order to couple the motion of the coarse-grain co-ordinates with the background fluid motion, we use a Galilean invariant, first order Brownian dynamics algorithm developed by Padding and Briels [J. Chem. Phys. 141, 244108 (2014)], which on the one hand draws inspiration from smoothed particle hydrodynamics in a way that the motion of the background fluid is efficiently calculated based on a discretization of the Navier-Stokes equation at the positions of the coarse-grain coordinates where it is actually needed, but also differs from it because of the inclusion of thermal fluctuations by having momentum-conserving pairwise stochastic updates. In this paper, we make a few modifications to this algorithm and introduce a new parameter, viz., a friction coefficient associated with the background fluid, and analyze the relationship of the model parameters with the dynamic properties of the system. We also test this algorithm for flow in the presence of solid interfaces to show that appropriate boundary conditions can be imposed at solid-fluid interfaces by using artificial particles embedded in the solid walls which offer friction to the real fluid particles in the vicinity of the wall. We have tested our method using a model system of a star polymer solution at the overlap concentration.

Use of LAPSUS_LS model to investigate vegetation influence on catchment slope stability – A case of study in Llano Bonito, Costa Rica
Rossi, L.M.W. ; Rapidel, B. ; Roupsard, O. ; Villatoro, M. ; Roumet, C. ; Mao, Z. ; Metselaar, K. ; Schoorl, J.M. ; Claessens, L.F.G. ; Stokes, A. - \ 2016
Use of Lapsus-LS model to investigate vegetation influence on slope stability-a case of study in Llano Bonito, Costa Rica
Rossi, L.M.W. ; Rapidel, B. ; Roupsard, O. ; Villatoro, M. ; Mao, Z. ; Metselaar, K. ; Schoorl, J.M. ; Claessens, L.F.G. ; Stokes, A. - \ 2016
Receptor-Targeted Luminescent Silver Bionanoparticles
Bunschoten, Anton ; Chin, Patrick T.K. ; Buckle, Tessa ; Linden, Marte van der; Barendregt, Arjan ; Verheijen, Marcel A. ; Leeuwen, Fijs W.B. van - \ 2016
European Journal of Inorganic Chemistry 2016 (2016)18. - ISSN 1434-1948 - p. 3030 - 3035.
Bioinorganic chemistry - Drug delivery - Imaging agents - Medicinal chemistry - Nanoparticles - Silver

Luminescent Ag nanoclusters (Ag-NC) provide the next generation in bionanoparticles, wherein the luminescence (650 nm) and large Stokes shift of these inorganic nanoclusters are favorable for biological imaging. By combining these characteristics with those of human serum albumin (HSA; a protein capable of binding multiple endo- and exogenous compounds), the Ag nanoclusters can be shielded from the environment and functionalized with (receptor) targeting moieties. Encapsulation of the 1.5 nm Ag nanoclusters by HSA resulted in a threefold increase in luminescence intensity and a twofold increase of the luminescence lifetime (1.7 vs. 3.6 µs). To exemplify the potential of this targeted concept, we functionalized HSA-Ag nanoparticles with chemokine receptor 4 (CXCR4) targeting peptides [Ac-TZ14011(CO2H)]. The resulting Ac-TZ14011-HSA-Ag nanoparticles demonstrated specific binding to CXCR4-overexpressing tumor cells. Upon exposure to (ambient) light, particle-functionalized tumor cells were killed. Combined, these experiments illustrate that HSA-Ag nanoparticles may have a potential in biological imaging and possibly even in targeted theranostic applications.

Shape and stability in liquid threads and jets : a link to droplet formation
Heugten, W.G.N. van - \ 2015
University. Promotor(en): Cees van Rijn. - Wageningen : Wageningen University - ISBN 9789462575707 - 172
droplets - controlled droplet application - threads - viscosity - stability - fluid mechanics - druppels - draden - viscositeit - stabiliteit - vloeistofmechanica

This thesis explores relevant fluid dynamic processes for the formation of uniformly sized droplets in microfluidic systems. Growing droplets made from a bulk source have often liquid threads or jets in between to supply liquid to the droplet. Liquid threads and jets are however known to be instable and finding parameters determining their instability/stability will possibly promote a more controlled formation of uniformly sized droplets. Different droplet formation processes in microfluidic devices are explained, such as cross-flow, co-flow and flow focussing.

Dimensionless numbers (introduced in chapter 1) represent the ratio of relevant forces or pressures acting on the fluids and/or their interfaces. These forces and pressures originate from their related fluid dynamic parameters, such as viscosity, interfacial tension, mass density and velocity of the fluid within a specific fluidic confinement with a certain length scale. We show that the dimensionless Reynolds, Weber and Capillary numbers can be associated with the stability of liquid threads and/or jets and provide insight in droplet formation processes.

The phenomenon of spontaneous droplet formation at low flow rates of an inner fluid confined in a microfluidic channel is studied in chapter 2. A short overview of known processes of spontaneous droplet formation with micro-engineered microfluidic devices is presented. We have studied the process of auto breakup with rectangular and round glass capillaries, the latter provided with micro-corrugations and uniform sized droplets were obtained, but only if the outer fluid is able to enter the capillary during droplet formation.

The process of auto breakup is described by a new analytical model described in chapter 3. The model states that the instability of a liquid thread is induced by the decrease of a local liquid thread pressure inside the capillary near the growing droplet. Predicted droplet sizes have been experimentally verified accurately, and also the predicted breakup length inside a micro-corrugated capillary has been verified. The model states that viscous flow stabilises the liquid thread and that auto breakup happens as long as the capillary number is below a critical capillary number of 0.0625. Above 0.0625 droplets grow infinitely large. Auto breakup is however already hampered at Capillary numbers above 0.03, because between 0.03 and 0.0625 no well controlled droplet sizes could be obtained by auto breakup. This is explained by the observed formation of a partially collapsed inner liquid thread that remains open and supplies the growing droplet with inner fluid.

In chapter 4 the formation and stability of a liquid thread in free surface flow feeding a large growing droplet is demonstrated and discussed. The shape of the liquid thread is positively tapering (towards the droplet) and can be described accurately by a Navier-Stokes based ordinary differential equation (ODE) assuming steady state, axisymmetry and an averaged fluid velocity over the cross section of the liquid thread. The axial shape of a viscous liquid thread is concave and its radial dimension has initially a cubic dependence with respect to the axial dimension. A driving force to stabilise the liquid thread was identified, which is a pressure gradient Q = Q0/L – Q1. Q0 is the pressure drop over thread length L, and Q1 is interfacial based dissipation of energy of the outer fluid. The maximum length of the liquid thread is predicted to be reached when Q goes towards 0 as the ratio Q0/Q1.

Shape and stability of emanating liquid jets, which appear after impact of falling droplets from a deep liquid, is presented in chapter 5. During rise and fall of the jet due to gravity, the jet is additionally decelerated towards the liquid surface by a tensile retraction force from the surface tension force exerted on the jet surface by the liquid bath. The retracting force generates an inertial deceleration pressure inside the jet that is balanced by the local Laplace pressure, herewith defining its local curvature and therefore also the shape of the complete jet. A deceleration based Young-Laplace equation is introduced and the predicted shape is experimentally verified for different fluids. Furthermore, the size of droplets forming on the tip of the jet can also be explained by the found pressure balance between the local Laplace pressure and the inertial deceleration of the jet (including the forming droplet).

In general we found that the stability of a liquid thread or jet seems correlated with an applied pressure difference that is distributed between the begin and end of the thread or jet. Studying auto breakup (chapters 2 and 3) of a confined liquid thread it was found that only when the applied pressure is high enough the liquid thread is stable and infinitely large droplets are formed. For the free surface flow liquid thread (chapter 4) it was found that breakup happens when the applied pressure gradient over the length of the thread goes to zero. For the emanating jet (chapter 5) an inertial pressure difference between the base and tip of the jet comes into existence that opposes the squeezing Laplace pressure that wants to break up the liquid jet. Furthermore we found that the last stages of droplet breakup from a liquid thread or jet appeared to follow universal pinch-off, and also that micro-thread formation is observed between droplet and liquid thread or jet.

Simplifying modeling of nanoparticle aggregation-sedimentation behavior in environmental systems: A theoretical analysis
Quik, J.T.K. ; Meent, D. van de; Koelmans, A.A. - \ 2014
Water Research 62 (2014). - ISSN 0043-1354 - p. 193 - 201.
sedimentatie - bodemdeeltjes - waterkwaliteit - modellen - sedimentation - aggregates - water quality - models - engineered nanoparticles - carbon nanotubes - nanomaterials - exposure - heteroaggregation - coagulation - challenges - scenarios - kinetics - release
Parameters and simplified model approaches for describing the fate of engineered nanoparticles (ENPs) are crucial to advance the risk assessment of these materials. Sedimentation behavior of ENPs in natural waters has been shown to follow apparent first order behavior, a ‘black box’ phenomenon that is insufficiently understood and therefore of limited applicability. Here we use a detailed Smoluchowski-Stokes model that accounts for homo- and heteroaggregation and sedimentation of ENPs and natural colloids (NCs), to simulate and interpret experimental ENP aggregation-sedimentation data. The model adequately simulated the observed time and initial concentration dependence of CeO2 settling data, and also predicted the conditions for aggregation rate-limitations of overall removal. Heteroaggregation with natural colloids was identified as the dominating removal process. Finally, the empirical apparent first order model data were calibrated against the mechanistic Smoluchowski-Stokes model simulation data, showing excellent fits for a range of NC initial concentrations. Using first order removal rates thus can be considered a valid and informed approximation when modeling ENP fate in the aquatic environment
Colloids at liquid interfaces: dynamics and organization
Ershov, D.S. - \ 2014
University. Promotor(en): Jasper van der Gucht, co-promotor(en): Martien Cohen Stuart. - Wageningen : Wageningen University - ISBN 9789461738943 - 127
colloïden - oppervlaktechemie - grensvlak - oppervlakteverschijnselen - capillairen - vloeistoffen (liquids) - colloids - surface chemistry - interface - surface phenomena - capillaries - liquids

This thesis deals with spherical microparticles trapped at liquid interfaces. It focuses on two aspects of their behavior: firstly, the effect of the curvature of a liquid interface on interparticle interactions and their organization; secondly, the mobility of particles at visco-elastic interfaces.

In Chapter 2of this thesis we showed that it is possible to induce capillary interactions between spherical microparticles with homogeneous surface chemistry by tailoring the curvature of the liquid interface. If the interfacial curvature is anisotropic, the constraint of constant contact angle along the contact line can only be satisfied if the interface is deformed locally. These deformations create excess surface area, which changes when two particles approach each other. This leads to a change in the surface free energy, which manifests itself as a capillary interaction between the particles.

To study the effect of curvature on the interactions between particles, we created oil-water interfaces of different shape (ellipsoid, dumbbell, torus and squares) and added spherical negatively charged particles that adsorbed at these interfaces. On all these interfaces, we observed quadrupolar capillary interactions that organized the particles into square lattices. The order of this organization increased with increasing curvature anisotropy, indicating that capillary interactions are stronger as well. By contrast, on flat interfaces or on spherical droplets with homogeneous curvature, no attractive interaction was observed and only at very high surface coverage did the particles order in a hexagonal lattice, as a result of repulsive interactions.

In Chapter 3we studied the interface deformations around particles at curved interfaces and the resulting capillary interactions theoretically. We used the finite element method to solve the Young-Laplace equation for the shape of the interface around a particle and calculated the interaction potential between the particles numerically.

The main finding of these calculations is that for an anisotropically curved interface, with two different local principal curvatures, the particle deforms the interface in two ways simultaneously: concave deformation along one principal direction and convex – along the other, thus creating a deformation field with quadrupolar symmetry. Two particles with such deformations interact favorably only if the overlapping deformations are similar (concave-concave, convex-convex), which occurs when they approach each other along one of the two principal directions. Since the two local principal directions are always perpendicular, particles interacting along them will tend to arrange into a square pattern.

As a consequence of the quadrupolar deformation field, two particles approaching each other along a line forming 45 degrees with the principal axes will repel each other (which is confirmed by our observations), because in this case the deformation fields overlap with four different “petals” (2 pairs of concave-convex), and the excessive surface area doesn’t reduce upon approaching, but increases. A system of two particles oriented at an angle with respect to the principal axis is therefore subjected to a torque rotating the axis of the system so that it gets aligned with one of the two principal directions. The torque magnitude reaches its maximum when the system’s axis is at an angle of 45 degrees with respect to the principal direction and decreases to 0 when the axis is aligned with one of the principal directions.

The family of interaction potentials we obtained allows for calculating the minimum deviatoric curvature needed to initialize capillary interactions strong enough to compete with thermal energy, so that a stable organization can be expected. The calculated value was very close to the deviatoric curvature where ordering was observed experimentally in Chapter 2.

In Chapter 4we studied the mobility of 3 mm polystyrene particles in a monolayer of 1.5 mm core-shell microparticles deposited at flat air-water interfaces; all the particles present in the system were stabilized by negative charges.

In this exploratory chapter we made an attempt to characterize the mechanical properties of such monolayers by analyzing the mobility of the larger tracer particles in the monolayer. With increasing particle density of the monolayer, we observed that the mean-square displacement of the tracer particles was reduced, which can be interpreted as an increase of the viscosity of the monolayer. At very high densities the motion of the particles became subdiffusive and confined, pointing at elasticity of the monolayer. We also studied correlated movements between neighboring particles in an attempt to do two-point interfacial microrheology. A comparison between the one-point and two-point methods shows clear indications of heterogeneous dynamics of the tracer particles. Our results therefore call for a further development of two-point microrheology at interfaces.

In Chapter 5we used tracer particles to study the properties of thin cross-linked actin networks deposited at the surface of oil droplets. These networks are a model system for the intracellular actin cortex. We used the generalized Stokes-Einstein relation to extract the complex frequency-dependent shear modulus of such networks from the movement of the added tracer particles. We studied the effects of the length of actin filaments and the cross-linker concentration on the mechanical properties of these layers.

The advantage of this system is that actin networks are freely accessible from the water phase, and therefore can be subjected to in-situ addition of cross-linkers, enzymes or other chemicals of interest. Using this, we managed to show strong stiffening after addition of myosin motor proteins and ATP, which we ascribed to contraction of the actin-myosin network.

Microbiota diversity during neonatal colonization impacts gut physiology in a pig model
Lallès, J.P. ; Bizon, A. ; Taekema, A. ; Arnal, M.E. ; Stokes, C.R. ; Bailey, M. ; Smidt, H. ; Jansman, A.J.M. ; Koopmans, S.J. - \ 2013
Microbiota diversity during neonatal colonization impacts gut physiology in a pig model
Lallès, J.P. ; Bizon, A. ; Taekema, A. ; Arnal, M.E. ; Stokes, C.R. ; Bailey, M. ; Smidt, H. ; Jansman, A.J.M. ; Koopmans, S.J. - \ 2013
In: Book of Abstracts on Diet, Gut Microbiology and Human Health, 11-12 December 2013, Londen, UK. - Londen, UK : The Nutrition Society - p. 50 - 50.
Complete Sequence of pSAM7, an IncX4 Plasmid Carrying a Novel blaCTX-M-14b Transposition Unit Isolated from Escherichia coli and Enterobacter cloacae from Cattle
Stokes, M.O. ; Abuoun, M. ; Umur, S. ; Wu, G. ; Partridge, S.R. ; Mevius, D.J. ; Coldham, N.G. ; Fielder, M.D. - \ 2013
Antimicrobial Agents and Chemotherapy 57 (2013)9. - ISSN 0066-4804 - p. 4590 - 4594.
spectrum-beta-lactamases - klebsiella-pneumoniae - identification - gene - bacteria - strains - ctx-m-9 - humans - family
The same plasmid carrying blaCTX-M-14b was identified from an Escherichia coli isolate and an Enterobacter cloacae isolate collected from cattle in the United Kingdom by complete plasmid sequencing. This 35,341-bp plasmid, pSAM7, had an IncX4 backbone that is 99% identical to that of pJIE143 from a human isolate in Australia. PCR screening identified pSAM7-like plasmids in three other E. coli isolates of different multilocus sequence types isolated from cattle on different farms in the United Kingdom.
The occurrence of haplosporidian parasites, Haplosporidium nelsoni and Haplosporidium sp., in oysters in Ireland
Lynch, S.A. ; Villalba, A. ; Abollo, E. ; Engelsma, M.Y. ; Stokes, N. ; Culloty, S.C. - \ 2013
Journal of Invertebrate Pathology 112 (2013)3. - ISSN 0022-2011 - p. 208 - 212.
crassostrea-gigas - pacific oyster - ostrea-edulis - delaware bay - molecular phylogeny - bonamia-ostreae - eastern oyster - flat oyster - disease - msx
The phylum Haplosporidia is a group of obligate protozoan parasites that infect a number of freshwater and marine invertebrates. Haplosporidian parasites have caused significant mortalities in commercially important shellfish species worldwide. In this study, haplosporidia were detected in Pacific oysters Crassostrea gigas originating in Ireland and were subsequently identified independently in laboratories both in Ireland and in Spain as Haplosporidium nelsoni. In Ireland, H. nelsoni plasmodia were also observed in the heart tissue of a single Ostrea edulis. A range of techniques including heart smear screening, histology, standard polymerase chain reaction (PCR), direct sequencing and in situ hybridisation with an H. nelsoni specific DNA probe were carried out to confirm diagnosis. This is the first reporting of H. nelsoni in oysters in Ireland and this is the first reporting of the detection of this haplosporidian in O. edulis. In Ireland, another haplosporidian was also observed in a single O. edulis during heart smear screening. PCR and DNA sequencing were carried out and indicated the presence of a Haplosporidium sp., most likely Haplosporidium armoricanum. The low prevalence and intensity of infection of both haplosporidian species in Irish C. gigas and in particular O. edulis may indicate that their presence is inconsequential.
Analytical solution of electrohydrodynamic flow and transport in rectangular channels: inclusion of double layer effects
Joekar-Niasar, V. ; Schotting, R. ; Leijnse, A. - \ 2013
Computational Geosciences 17 (2013)3. - ISSN 1420-0597 - p. 497 - 513.
small zeta potentials - electroosmotic flow - electrokinetic flow - drug-delivery - ph - elctroosmosis - capillaries - remediation - dispersion - geometries
Upscaling electroosmosis in porous media is a challenge due to the complexity and scale-dependent nonlinearities of this coupled phenomenon. “Pore-network modeling” for upscaling electroosmosis from pore scale to Darcy scale can be considered as a promising approach. However, this method requires analytical solutions for flow and transport at pore scale. This study concentrates on the development of analytical solutions of flow and transport in a single rectangular channel under combined effects of electrohydrodynamic forces. These relations will be used in future works for pore-network modeling. The analytical solutions are valid for all regimes of overlapping electrical double layers and have the potential to be extended to nonlinear Boltzmann distribution. The innovative aspects of this study are (a) contribution of overlapping of electrical double layers to the Stokes flow as well as Nernst–Planck transport has been carefully included in the analytical solutions. (b) All important transport mechanisms including advection, diffusion, and electromigration have been included in the analytical solutions. (c) Fully algebraic relations developed in this study can be easily employed to upscale electroosmosis to Darcy scale using pore-network modeling.
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