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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    Core-shell particles at fluid interfaces : performance as interfacial stabilizers
    Buchcic, C. - \ 2016
    Wageningen University. Promotor(en): Martien Cohen Stuart, co-promotor(en): R.H. Tromp; Marcel Meinders. - Wageningen : Wageningen University - ISBN 9789462578968 - 140
    stabilization - stabilizers - particles - colloidal properties - adsorption - interface - fluids - stabilisatie - stabiliseermiddelen - deeltjes - colloïdale eigenschappen - adsorptie - grensvlak - vloeistoffen (fluids)

    There is a growing interest in the use of particles as stabilizers for foams and emulsions. Applying hard particles for stabilization of fluid interface is referred to as Pickering stabilization. By using hard particles instead of surfactants and polymers, fluid interfaces can be effectively stabilized against Ostwald ripening and coalescence. A drawback of the use of hard particles as interfacial stabilizers is that they often experience a pronounced energy barrier for interfacial adsorption and that hard particles are very specific with regard to the type of fluid interface they can adsorb to. Soft particles, on the other hand, are known as good stabilizers against coalescence and they spontaneously adsorb to a variety of different fluid interfaces.

    The aim of this thesis was to investigate core-shell particles comprising a hard core and soft shell with regard to their interfacial behaviour and their ability to act as sole stabilizers for foams and emulsions. We hypothesised that the presence of the soft shell allows for easier interfacial adsorption of core-shell particles compared to the hard core particles only. To test this hypothesis, we prepared core-shell particles comprising a solid polystyrene (PS) core and a soft poly-N-isopropylacrylamide (PNIPAM) shell. To ascertain the effect of shell thickness, we prepared a range of core-shell particles with different shell thicknesses, containing identical core particles. We found that core-shell particles are intrinsically surface active and can generate high surface pressures at the air-water interface and oil-water interfaces, whereas core particles seemed to experience a large energy barrier for interfacial adsorption and did not lower the surface tension. We also confirmed by microscopy that core-shell particles are actually adsorbing to the fluid interface and form densely packed interfacial layers. Further, we found that a certain critical thickness of the soft shell is necessary in order to ensure facile interfacial adsorption. If the PNIPAM shell on top of the core particles is well above 100nm thick, particle adsorption at the air-water interface was found to be diffusion limited.

    By gentle hand-shaking we were able to produce dispersion of air bubbles and emulsion droplets solely stabilized by core-shell particles. The resulting bubbles still underwent Ostwald ripening, albeit slowly. For oil-in-water emulsions of hexane and toluene, both of which have a relatively high solubility in the continuous phase, we found that core-shell particles can stop Ostwald ripening. The resulting emulsion droplets adopted pronounced non-spherical shapes, indicating a high elasticity of the interface. The high stability and the remarkable non-spherical shape of the emulsion droplets stabilized by core-shell particles were features we also observed for fluid dispersion stabilized by hard particles. This shows that in terms of emulsion stability core-shell particles behave similar to hard particles as interfacial stabilizer.

    As to why the differences between the stability of bubble and oil dispersions arise could not be finally answered. Yet, microscopic analysis of the interfacial configuration of core-shell particles at the air-water interface reveals some peculiar insights which may suggest that core-shell particles adsorb in a polymer-like fashion with the soft PNIPAM shells adsorbing to the air-water interface only, while the hard PS cores reside in the continuous phase.

    In summary, we showed that core-shell particles with a hard core and a soft shell can indeed combine the advantageous properties of hard and soft particles. The soft shell enables spontaneous adsorption to a variety of fluid interfaces. Despite their spontaneous adsorption, core-shell particles strongly anchor and do not spontaneously desorb from the fluid interface again. Further, the hard core provides enough rigidity to the core-shell particles to allow the establishment of a stress bearing interfacial particle network. This network eventually stops Ostwald ripening in oil-in-water emulsions. Our results therefore show that in the case of oil-water interfaces, core-shell particles can perform better than solely hard particles as interfacial stabilizers.

    Stability Properties of Surfactant-Free Thin Films at Different Ionic Strengths: Measurements and Modeling
    Lech, F.J. ; Wierenga, P.A. ; Gruppen, H. ; Meinders, M.B.J. - \ 2015
    Langmuir 31 (2015)9. - ISSN 0743-7463 - p. 2777 - 2782.
    sodium dodecyl-sulfate - subsequent criticism - hydrophobic forces - standing foams - liquid-films - interface - electrolyte - coalescence - proteins - drainage
    Foam lamellae are the smallest structural elements in foam. Such lamellae can experimentally be studied by analysis of thin liquid films in glass cells. These thin liquid films usually have to be stabilized against rupture by surface active substances, such as proteins or low molecular weight surfactants. However, horizontal thin liquid films of pure water with a radius of 100 µm also show remarkable stability when created in closed Sheludko cells. To understand thin film stability of surfactant-free films, the drainage behavior and rupture times of films of water and NaCl solutions were determined. The drainage was modeled with an extended Derjaguin–Landau–Verwey–Overbeek (DLVO) model, which combines DLVO and hydrophobic contributions. Good correspondence between experiment and theory is observed, when hydrophobic interactions are included, with fitted values for surface potential (¿0,water) of -60 ± 5 mV, hydrophobic strength (Bhb,water) of 0.22 ± 0.02 mJ/m2, and a range of the hydrophobic interaction (¿hb, water) of 15 ± 1 nm in thin liquid films. In addition, Vrij’s rupture criterion was successfully applied to model the stability regions and rupture times of the films. The films of pure water are stable over long time scales (hours) and drain to a final thickness >40 nm if the concentration of electrolytes is low (resistivity 18.2 MQ). With increasing amounts of ions (NaCl) the thin films drain to
    Surfactant-polymer interactions: molecular architecture does matter
    Banerjee, S. ; Cazeneuve, C. ; Baghdadli, N. ; Ringeissen, S. ; Leermakers, F.A.M. ; Luengo, G.S. - \ 2015
    Soft Matter 11 (2015). - ISSN 1744-683X - p. 2504 - 2511.
    block copolymer adsorption - nonionic surfactants - statistical thermodynamics - chain molecules - phase-behavior - simulation - interface - association - mixtures - water
    Polymer–surfactant mixtures are found in many industrial formulations, and hence there is a significant interest in understanding, at a molecular level, how the self-assembly of surfactant is affected by oppositely-charged polyelectrolytes (PEs). We use self-consistent field modeling and show that the modes of interaction of PEs strongly depend on the architecture of the PE on the segmental level. Hydrophilic cationic PEs with their charge proximal to the linear backbone are expected to bind electrostatically to the outsides of the coronas of the spherical micelles of anionic surfactants, such as sodium laureth sulphate (SLES). As a result, the surfactant aggregation number increases, but at the same time the colloidal stability deteriorates, due to bridging of the PEs between micelles. PEs with their charge somewhat displaced from the backbone by way of short hydrophobic spacers, are expected to be present inside a micelle at the core–corona boundary. In this case the aggregation number decreases, yet the colloidal stability is retained. Hence, SLES tends to remove hydrophilic PEs from an aqueous solution, whereas it solubilizes more hydrophobic ones. The binding isotherm shows that the uptake of PEs remains typically below charge compensation and in this case the spherical micelle topology remains the preferred state.
    The coproduction of knowledge and policy in coastal governance: Integrating mussel fisheries and nature restoration
    Molen, F. van der; Puente Rodriguez, D. ; Swart, J.A.A. ; Windt, H.J. v.d. - \ 2015
    Ocean & Coastal Management 106 (2015). - ISSN 0964-5691 - p. 49 - 60.
    dutch-wadden sea - local ecological knowledge - marine protected areas - adaptive governance - zone management - interface - science - conservation - framework - dynamics
    One of the challenges of coastal governance is to connect a variety of knowledge systems. The purpose of this paper is to show how a coastal governance practice can emerge and stabilize, such that actors with disparate knowledge systems collaborate towards the shared goal of sustainable resource use. We analyze this stabilization in terms of the coproduction of knowledge and policy. This paper is empirically informed by a case study on the transition towards a sustainable mussel fishery in the Dutch Wadden Sea. Our study illuminates the difficulties of underpinning a coastal governance practice with scientific research, since the relevance, quality, and results of research are interpreted differently from the perspectives of resource users and conservationists. Furthermore, our analysis shows that such a governance practice can stabilize through a combination of rule negotiation, legal, societal, and political pressure, along with collaborative knowledge creation. Based on our analysis, we identify several aspects of collaborative knowledge creation that enable the formation of a shared knowledge base for governance in a context of controversy. These include the shared ownership of research, knowledge creation as an integral part of governance, a focus on data and basic facts, and the close involvement of trusted experts. The findings of this study suggest that a controversial setting strongly structures knowledge creation, while at the same time knowledge creation enables coastal governance as a way of dealing with conflicts.
    An operational, multi-scale, multi-model system for consensus-based, integrated water management and policy analysis: The Netherlands Hydrological Instrument
    Lange, W.J. de; Prinsen, G.F. ; Hoogewoud, J.C. ; Veldhuizen, A.A. ; Verkaik, J. ; Essink, G.H.P.O. ; Walsum, P.E.V. van; Delsman, J.R. ; Hunink, J.C. ; Massop, H.T.L. ; Kroon, T. - \ 2014
    Environmental Modelling & Software 59 (2014). - ISSN 1364-8152 - p. 98 - 108.
    distributed modeling system - flow - simulation - interface - europeen - openmi - she
    Water management in the Netherlands applies to a dense network of surface waters for discharge, storage and distribution, serving highly valuable land-use. National and regional water authorities develop long-term plans for sustainable water use and safety under changing climate conditions. The decisions about investments on adaptive measures are based on analysis supported by the Netherlands Hydrological Instrument NHI based on the best available data and state-of-the-art technology and developed through collaboration between national research institutes. The NHI consists of various physical models at appropriate temporal and spatial scales for all parts of the water system. Intelligent connectors provide transfer between different scales and fast computation, by coupling model codes at a deep level in software. A workflow and version management system guarantees consistency in the data, software, computations and results. The NHI is freely available to hydrologists via an open web interface that enables exchange of all data and tools. (C) 2014 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY license (
    Growth of bubbles on a solid surface in response to a pressure reduction
    Li, J. ; Chen, H. ; Zhou, W. ; Wu, B. ; Stoyanov, S.D. ; Pelan, E.G. - \ 2014
    Langmuir 30 (2014)15. - ISSN 0743-7463 - p. 4223 - 4228.
    contact angles - drop size - dynamics - water - nanobubbles - cavitation - interface - line
    A diffusion-controlled method is presented to study the growth of bubbles on a solid surface. The bubbles are nucleated spontaneously on a hydrophobic smooth surface in response to a sudden pressure reduction and then grow with an expanding contact line. The evolution of the bubbles in the early stage is found to grow with a constant bubble radius and a decreasing contact angle, while the bubbles continue their growth with a constant contact angle and an increasing bubble radius after the contact angle reaches its equilibrium value. A total variation of about 60° of the contact angle is observed during the growth of the bubbles with the size scale of 10–100 µm in radius. The growing process is described by the diffusion theory with the validation of the growth constant.
    Nonequilibrium thermodynamics of nucleation
    Schweizer, M. ; Sagis, L.M.C. - \ 2014
    Journal of Chemical Physics 141 (2014). - ISSN 0021-9606 - 13 p.
    homogeneous nucleation - inhomogeneous-media - general formalism - complex fluids - systems - clusters - dynamics - temperature - interface - equations
    We present a novel approach to nucleation processes based on the GENERIC framework (general equation for the nonequilibrium reversible-irreversible coupling). Solely based on the GENERIC structure of time-evolution equations and thermodynamic consistency arguments of exchange processes between a metastable phase and a nucleating phase, we derive the fundamental dynamics for this phenomenon, based on continuous Fokker-Planck equations. We are readily able to treat non-isothermal nucleation even when the nucleating cores cannot be attributed intensive thermodynamic properties. In addition, we capture the dynamics of the time-dependent metastable phase being continuously expelled from the nucleating phase, and keep rigorous track of the volume corrections to the dynamics. Within our framework the definition of a thermodynamic nuclei temperature is manifest. For the special case of nucleation of a gas phase towards its vapor-liquid coexistence, we illustrate that our approach is capable of reproducing recent literature results obtained by more microscopic considerations for the suppression of the nucleation rate due to nonisothermal effects.
    Improved emulsion stability by succinylation of patatin is caused by partial unfolding rather than charge effects
    Delahaije, R.J.B.M. ; Wierenga, P.A. ; Giuseppin, M.L.F. ; Gruppen, H. - \ 2014
    Journal of Colloid and Interface Science 430 (2014). - ISSN 0021-9797 - p. 69 - 77.
    in-water emulsions - protein-exposed hydrophobicity - beta-lactoglobulin - drop size - adsorption - flocculation - interface - stabilization - ph - dependence
    This study investigates the influence of succinylation on the molecular properties (i.e. charge, structure and hydrophobicity) and the flocculation behavior of patatin-stabilized oil-in-water emulsions. Patatin was succinylated to five degrees (0% (R0) to 57% (R2.5)). Succinylation not only resulted in a change of the protein charge but also in (partial) unfolding of the secondary structure, and consequently in an increased initial adsorption rate of the protein to the oil–water interface. The stability against salt-induced flocculation showed two distinct regimes, instead of a gradual shift in stability as expected by the DLVO theory. While flocculation was observed at ionic strengths > 30 mM for the emulsions stabilized by the variants with the lowest degrees of modification (R0–R1), the other variants (R1.5–R2.5) were stable against flocculation ¿ 200 mM. This was related to the increased initial adsorption rate, and the consequent transition from a protein-poor to a protein-rich regime. This was confirmed by the addition of excess protein to the emulsions stabilized by R0–R1 which resulted in stability against salt-induced flocculation. Therefore, succinylation of patatin indirectly results in stability against salt-induced flocculation, by increasing the initial adsorption rate of the protein to the oil–water interface, leading to a shift to the protein-rich regime.
    Coagulation by simple multivalent counterions
    Lyklema, J. - \ 2014
    Colloids and Surfaces. A: Physicochemical and Engineering Aspects 460 (2014). - ISSN 0927-7757 - p. 468 - 472.
    electrical double-layer - charge inversion - ions - interface - stability
    The origin of the strong screening power of multivalent counterions in electric double layers is reconsidered. Even for simple multivalent ions like La3+ and Th4+ more than one mechanism may be held responsible. The most critical alternatives are adsorption by specific non-electrostatic forces and enrichment by ion correlations. Many multivalent ions tend to hydrolyse in water, thereby producing highly absorbable hydrolysis products. This leads to a pH dependence of overcharging by specific adsorption, but as ion correlations are virtually independent of pH, this influence helps to discriminate between the two mechanisms. Some critical literature illustrations show that the number of publications that prove the effect of ion correlations unambiguously is very limited.
    Colloids at liquid interfaces: dynamics and organization
    Ershov, D.S. - \ 2014
    Wageningen 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.

    Measurementality’ in biodiversity governance: knowledge, transparency, and the Intergovernmental Science–Policy Platform on Biodiversity and Ecosystem Services (IPBES)
    Turnhout, E. ; Neves, K. ; Lijster, E.B. de - \ 2014
    Environment and Planning A 46 (2014)3. - ISSN 0308-518X - p. 581 - 597.
    environmental governance - interface - politics - accountability - conservation - information
    Current policies and practices in biodiversity conservation have been increasingly influenced by neoliberal approaches since the 1990s. The authors focus on the principle of transparency as a self-proclaimed basis of neoliberal environmental governance, and on the role of standardized science-based measurements which it purportedly affords. The authors introduce the term ‘measurementality’ to signify the governance logic that emerges when transparency comes to stand next to effectiveness and efficiency as neoliberal principles and to highlight the connections that are forged between economic, managerial, and technocratic discourses. The example of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) is used to discuss the role of measurementality in global biodiversity governance. The analysis suggests that IPBES aims to coordinate the science–policy interface in order to optimize the generation of user-friendly knowledge of those elements of biodiversity that are considered politically and economically relevant: at the current economic juncture, these being in essence ecosystem services. Based on these findings, the authors proceed by critically reflecting on the ways in which the measurementality logic of IPBES may not only result in an impoverishment of the biodiversity research agenda, but also in an impoverished understanding of biodiversity itself. To conclude, the authors argue that measurementality is part and parcel of the neoliberal paradigm in which science produces the raw materials for subsequent control and exchange and that, as a result, the intersection of science, discourse, policy, and economics within these governance systems requires sustained critical scrutiny.
    Responding to coastal problems: Interactive knowledge development in a US nature restoration project
    Seijger, C. ; Tatenhove, J.P.M. van; Dewulf, G. ; Otter, H.S. - \ 2014
    Ocean & Coastal Management 89 (2014). - ISSN 0964-5691 - p. 29 - 38.
    climate-change - policy - governance - science - management - systems - information - interface - lessons - delta
    Coastal decision-making is impacted by global climate change and region-specific changes related to population growth, economic activities and the natural environment. This results in complex and interdependent problems. Addressing these problems requires the involvement of decision-makers, researchers and other societal actors in knowledge production. However, such means of knowledge production are poorly understood when it comes to coastal regions. Using a conceptual framework that makes a distinction between project arrangements and knowledge arrangements, this paper analyses interactive knowledge development in a nature restoration project on the US West Coast. The project adopted a collaborative approach, and involved diverse organisations in developing knowledge for reaching its restoration solutions. The case study analysis results in seven causal mechanisms. The mechanisms are divided into two groups. One group discusses processes that affect interactive knowledge development, such as the need for public support. The other group explains how interactive knowledge development functions, for example through facilitation and the creation of safe environments for researchers and regulators. Through identifying these mechanisms, this paper contributes to an improved understanding of interactive knowledge development in coastal regions.
    Joint development of insight into colloid stability and surface conduction
    Lyklema, J. - \ 2014
    Colloids and Surfaces. A: Physicochemical and Engineering Aspects 440 (2014). - ISSN 0927-7757 - p. 161 - 169.
    electrical double-layer - silver-iodide - streaming potentials - particles - electrolytes - electrochemistry - interface - emulsions - capacity - mercury
    This paper presents a historical overview of the parallels between the developments of colloid stability and surface conductivity. Starting from the situation during the Second World War, the interaction between the developments of these two branches of science appeared mutually beneficial. In particular, the properties of the non-diffuse parts of the double layers drew much attention. Implementations in the direction of future developments are given.
    Evaluating OpenMI as a model integration platform across disciplines
    Knapen, M.J.R. ; Janssen, S.J.C. ; Roosenschoon, O.R. ; Verweij, P.J.F.M. ; Winter, W.P. de; Uiterwijk, M. ; Wien, J.J.F. - \ 2013
    Environmental Modelling & Software 39 (2013). - ISSN 1364-8152 - p. 274 - 282.
    simulation - communication - management - frameworks - interface - systems - science
    For decision makers in the domains of agriculture and environment, for instance in government agencies, farmers, environmental NGOs and farmers' unions, it is beneficial to evaluate ex-post or to asses ex-ante the impacts of their choices. To research these interdisciplinary relationships, models developed by different scientific disciplines and often operating at different scales can be integrated into model chains that cover processes across disciplines. In order to assemble models into an operational model chain conceptual, semantic and technical levels of integration have to be taken into account. The main focus of this paper is on technical integration to ensure repeatability and reproducibility of model chain runs and to optimize use of computer hardware for model simulations. Technical integration itself can be achieved by different approaches (i.e. manual, scripting, building or using a proprietary framework, using an open framework based on standards). From the many available modelling frameworks (e.g. OMS, TIME, KEPLER, FRAMES, MODCOM, OpenMI) the emphasis will be on OpenMI, the Open Modelling Interface and its use and usefulness as a readily available, generally accepted and open standards based framework. OpenMI is an open source software standard for dynamically linking models at runtime, which can potentially be used in many domains, but is currently mainly applied in the water and environmental domains. This paper describes and evaluates the use of OpenMI in several multi-disciplinary large projects that worked on integrated models. These projects operated in the disciplines of agriculture, land use, nitrogen cycling, forestry, hydrology and economics. To this end two workshops were organized to acquire feedback from both software developers and modellers that contributed to the aforementioned projects on the use of OpenMI. Perceived advantages and disadvantages of OpenMI differed between modellers and software engineers, although both identified the lack of standard functionality as a major disadvantage and the prescription of a way of working through OpenMI as a standard as a major advantage. In conclusion, OpenMI can be used as a standard for technical model integration across disciplines, and it is not limited to one particular discipline. (C) 2012 Elsevier Ltd. All rights reserved.
    On the collapse transition of a polymer brush: the case of lateral mobility
    Leermakers, F.A.M. ; Egorov, S.A. - \ 2013
    Soft Matter 9 (2013)12. - ISSN 1744-683X - p. 3341 - 3348.
    terminally attached chains - consistent field-theory - poor solvents - molecular-dynamics - tethered polymers - model - adsorption - interface - surfaces - layers
    We consider a polymer brush composed of end-grafted polymer chains. Classical theory advocates that a worsening of the solvent quality results in a smooth decrease of the brush height from a swollen to a dense brush. We report that a homogeneous brush under poor solvent conditions can have a negative surface pressure, indicating an instability in favour of lateral segregation. Also by using a two-gradient version of the self-consistent field (SCF) theory we show that, in contradiction to the classical result, but in line with the negative pressure, the collapse transition for laterally mobile chains has a first-order character, exemplified by the presence of a compact brush that coexists with a dilute gas of end-grafted chains. The dense brush assumes a pancake shape wherein the chains balance the stretching entropy against surface energies. The height of the pancake scales sub-linearly with the chain length because the local grafting density decreases with increasing chain length. In analogy with wetting studies we discuss how the spreading parameter has an influence on the pancake structure. Accordingly, the height increases with worsening of the solvent quality and decreases with increased affinity for the substrate. The two-phase state is expected in many practical situations
    Bending rigidities of surfactant bilayers using self-consistent field theory
    Leermakers, F.A.M. - \ 2013
    Journal of Chemical Physics 138 (2013). - ISSN 0021-9606 - 11 p.
    interacting chain molecules - lipid-bilayers - curvature elasticity - statistical-theory - adsorption - membranes - size - thermodynamics - interface - relevance
    Self-consistent field (SCF) theory is used to find bending moduli of surfactant and lipid bilayers. Recently, we successfully applied low-memory search methods to solve the SCF equations. Using these we are now able to directly evaluate the Gaussian bending modulus for molecularly detailed models of bilayers by evaluating the excess Helmholtz energy of tensionless bilayers in a (part of the) Im3m cubic phase. The result prompted us to reconsider the protocol that has been used thus far to find the mean bending modulus k c and Gaussian bending modulus k¯. With respect to previous predictions, the value of k c is reduced by a factor of two and the Gaussian bending modulus is less negative and much closer to zero. In line with experimental data we now find that k¯can also become positive. In this paper we use the non-ionic surfactants series of the type C n E m for illustration.
    Structure and dynamics of polyelectrolyte complex coacervates studied by scattering of neutrons, X-rays, and light
    Spruijt, E. ; Leermakers, F.A.M. ; Fokkink, R.G. ; Schweins, R. ; Well, A.A. van; Cohen Stuart, M.A. ; Gucht, J. van der - \ 2013
    Macromolecules 46 (2013)11. - ISSN 0024-9297 - p. 4596 - 4605.
    gelatin/polyelectrolyte complexes - angle scattering - reversible gels - micelles - polymer - protein - macromolecules - chloride) - interface - hydrogels
    We investigate the microscopic structure and density fluctuations of complex coacervates of flexible polyelectrolytes using scattering of neutrons, X-rays, and light. Poly(acrylic acid) and poly(N,N-dimethylaminoethyl methacrylate) offer a well-defined model system that allows for selective labeling and systematic variation of the strength of the attractive electrostatic interactions. Two neutron scattering experiments have been carried out: (i) we use deuterated polymeric tracers in a complex coacervate with an overall neutron scattering length density that is matched to that of the solvent, to probe the conformation of single polymer chains in the complex coacervates, and (ii) we measure complex coacervates in which all polymer chains of one type are deuterated, to probe their overall structure. The single chain static structure factors reveal that both polycations and polyanions have an ideal Gaussian chain conformation in the complex coacervates. At the same time, the overall structure is similar to that of a semidilute polymer solution, with polycations and polyanions strongly overlapping to form a network with a mesh size that is much smaller than the radius of gyration of the polymers. The mesh size decreases with decreasing salt concentration, following a scaling that is in good agreement with predictions from the corresponding salt–polymer phase diagram. These findings are confirmed by complementary X-ray scattering experiments. Finally, in all scattering experiments with light, X-rays, and neutrons, and for all polymer chain lengths and salt concentrations, we find a remarkable low-q excess scattering, following a power law with a slope close to -2. This points to the presence of equilibrium, large-scale density fluctuations in the complex coacervates. Dynamic light scattering experiments reveal two complementary diffusive modes in the complex coacervates, corresponding to fluctuations of the polymer mesh and diffusion of domains of varying density, respectively
    User-friendly solutions for microarray quality control and pre-processing on
    Eijssen, L.M. ; Jaillard, M. ; Adriaens, M.E. ; Gaj, S. ; Groot, P.J. de; Müller, M.R. ; Evelo, C.T. - \ 2013
    Nucleic acids research 41 (2013)W1. - ISSN 0305-1048 - p. W71 - W76.
    affymetrix-genechip data - expression analysis - probe level - bioconductor - interface - database - package - biology - biomart - update
    Quality control (QC) is crucial for any scientific method producing data. Applying adequate QC introduces new challenges in the genomics field where large amounts of data are produced with complex technologies. For DNA microarrays, specific algorithms for QC and pre-processing including normalization have been developed by the scientific community, especially for expression chips of the Affymetrix platform. Many of these have been implemented in the statistical scripting language R and are available from the Bioconductor repository. However, application is hampered by lack of integrative tools that can be used by users of any experience level. To fill this gap, we developed a freely available tool for QC and pre-processing of Affymetrix gene expression results, extending, integrating and harmonizing functionality of Bioconductor packages. The tool can be easily accessed through a wizard-like web portal at or downloaded for local use in R. The portal provides extensive documentation, including user guides, interpretation help with real output illustrations and detailed technical documentation. It assists newcomers to the field in performing state-of-the-art QC and pre-processing while offering data analysts an integral open-source package. Providing the scientific community with this easily accessible tool will allow improving data quality and reuse and adoption of standards.
    A review of science-policy interactions in the Dutch Wadden Sea - The cockle fishery and gas exploitation controversies
    Floor, J.R. ; Koppen, C.S.A. van; Lindeboom, H.J. - \ 2013
    Journal of Sea Research 82 (2013). - ISSN 1385-1101 - p. 165 - 175.
    decision-making - perspective - interface - ecology
    The potential ecological effects of cockle fisheries and gas exploitation in the Dutch Wadden Sea and their implications for policy and management have been the topic of vigorous societal debates. Ecological science has played crucial but controversial roles in these debates. Several social science studies have been dedicated to analysing these roles and making recommendations for the improvement of science–policy interactions. In reviewing these studies, this article aims to draw lessons for (ecological) scientists and policy makers on how to understand and guide the interactions of science and policy in Wadden Sea management. Studies addressing science–policy interactions in the Dutch Wadden Sea can be grouped into three main perspectives, emphasizing the social and economic dynamics of resource management, the role of nature views and discourses in controversies, and the influence of science dynamics in policy and management debates. The review demonstrates that ecological knowledge and ecological scientists have played important roles in the controversies on cockle fisheries and gas exploitation. However, scientific knowledge was not always the most important factor in the decision-making process, and scientific insights were not always used as expected by the scientists. How scientific knowledge is used and interpreted by stakeholders was dependent on their interests, their nature views and on the dominant policy discourses. Ecological knowledge and scientists themselves became part of the policy debates, e.g. in discussions on uncertainty and reliability. The position of scientists in policy debates was strongly influenced by the policy setting and by changes in this setting, e.g. by the operation of mediators or by new interpretations of legal rules. A lesson to be drawn for scientists is that they should reflect on the sort of position – e.g. independent outsider, or engaged stakeholder – they take in a debate. They should also be aware that this position cannot be chosen at will: it is strongly influenced by the policy context. For government and other stakeholders, an important lesson is that by shaping adequate policy settings they can contribute to more productive and effective interactions with science and scientists.
    Integrating three lake models into a Phytoplankton Prediction System for Lake Taihu (Taihu PPS) with Python
    Huang, J.C. ; Gao, J.F. ; Hormann, G. ; Mooij, W.M. - \ 2012
    Journal of Hydroinformatics 14 (2012)2. - ISSN 1464-7141 - p. 523 - 534.
    water-quality - framework - interface - ecosystem - issues - tools - china
    In the past decade, much work has been done on integrating different lake models using general frameworks to overcome model incompatibilities. However, a framework may not be flexible enough to support applications in different fields. To overcome this problem, we used Python to integrate three lake models into a Phytoplankton Prediction System for Lake Taihu (Taihu PPS). The system predicts the short-term (1-4 days) distribution of phytoplankton biomass in this large eutrophic lake in China. The object-oriented scripting language Python is used as the so-called 'glue language' (a programming language used for connecting software components). The distinguishing features of Python include rich extension libraries for spatial and temporal modelling, modular software architecture, free licensing and a high performance resulting in short execution time. These features facilitate efficient integration of the three models into Taihu PPS. Advanced tools (e. g. tools for statistics, 3D visualization and model calibration) could be developed in the future with the aid of the continuously updated Python libraries. Taihu PPS simulated phytoplankton biomass well and has already been applied to support decision making.
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