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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    On the stability and finite-size effects of a columnar phase in single-component systems of hard-rod-like particles
    Dussi, Simone ; Chiappini, Massimiliano ; Dijkstra, Marjolein - \ 2018
    Molecular Physics 116 (2018)21-22. - ISSN 0026-8976 - p. 2792 - 2805.
    columnar phase - entropy - hard particles - Liquid crystals - Monte Carlo simulations

    Colloidal rod-like particles self-assemble into a variety of liquid crystal phases. In contrast to the formation of the nematic and smectic phases for which it is well understood that it can be driven by entropy, the stabilisation mechanism of a prolate columnar phase ((Formula presented.)), observed for example in fd-virus suspensions, is still unclear. Here, we investigate whether or not a (Formula presented.) phase can exist in a purely entropy-driven single-component system. We perform computer simulations of hard particles with different shapes: spherocylinders, top-shaped rods, cuboidal particles, and crooked rods. We show that the (Formula presented.) phases observed in previous simulation studies are mere artefacts due to either finite-size effects or simulation boxes that are incommensurate with the stable thermodynamic phase. In particular, we observe that the characteristic layering of the stable smectic or crystal phase disappears when the dimension of the simulation box along the direction of the layers is too small. Such a system-size effect depends both on particle shape and the competing phases, and appears to be more pronounced for less anisotropic particles.

    Multisource clustering of remote sensing images with Entropy-based Dempster-Shafer fusion
    Ranoeliarivao, S. ; Morsier, F. De; Tuia, D. ; Rakotoniaina, S. ; Borgeaud, M. ; Thiran, J.P. ; Rakotondraompiana, S. - \ 2013
    In: 2013 Proceedings of the 21st European Signal Processing Conference, EUSIPCO 2013. - European Signal Processing Conference, EUSIPCO (European Signal Processing Conference ) - ISBN 9780992862602
    Dempster-Shafer - entropy - fuzzy C-Means - multisource fusion - remote sensing - unsupervised

    In this paper, we propose a strategy for fusing clustering maps obtained with different remote sensing sources. Dempster-Shafer (DS) Theory is a powerful fusion method that allows to combine classifications from different sources and handles ignorance, imprecision and conflict between them. To do so, it attributes evidences (weights) to different hypothesis representing single or unions of classes. We introduce a fully unsupervised evidence assignment strategy exploiting the entropy among cluster memberships. Ambiguous pixels get stronger evidences for union of classes to better represent the uncertainty among them. On two multisource experiments, the proposed Entropy-based Dempster-Shafer (EDS) performs best along the different fusion methods with VHR images, when the single class accuracies from each source are complementary and one of the sources shows low overall accuracy.

    The clumping transition in niche competition: A robust critical phenomenon
    Fort, H. ; Scheffer, M. ; Nes, E.H. van - \ 2010
    Journal of Statistical Mechanics: Theory and Experiment 2010 (2010)5. - ISSN 1742-5468
    limiting similarity - body-size - entropy - space
    We show analytically and numerically that the appearance of lumps and gaps in the distribution of n competing species along a niche axis is a robust phenomenon whenever the finiteness of the niche space is taken into account. In this case, depending on whether the niche width of the species s is above or below a threshold sc, which for large n coincides with 2/n, there are two different regimes. For s > sc the lumpy pattern emerges directly from the dominant eigenvector of the competition matrix because its corresponding eigenvalue becomes negative. For s = sc the lumpy pattern disappears. Furthermore, this clumping transition exhibits critical slowing down as s is approached from above. We also find that the number of lumps of the species distribution versus s displays a stair-step structure. The positions of these steps are distributed according to a power law. It is thus straightforward to predict the number of groups that can be packed along a niche axis and this value is consistent with field measurements for a wide range of the model parameters
    Trendwatch combining expert opinion
    Hendrix, E.M.T. ; Kornelis, M. ; Pegge, S.M. ; Galen, M.A. van - \ 2006
    Wageningen : Agrotechnology & Food Sciences Group (Rapport / Agrotechnology & Food Sciences Group 622) - ISBN 9789085850113 - 31
    opinies - deskundigen - bayesiaanse theorie - modellen - entropie - tendensen - gegevensanalyse - gevalsanalyse - opinions - experts - bayesian theory - models - entropy - trends - data analysis - case studies
    In this study, focus is on a systematic way to detect future changes in trends that may effect the dynamics in the agro-food sector, and on the combination of opinions of experts. For the combination of expert opinions, the usefulness of multilevel models is investigated. Bayesian data analysis is used to obtain parameter estimates. The approach is illustrated by two case studies. The results are promising, but the procedures are just a first step into an appropriate combination of expert combination, which has to be completed on important issues, such as the identification of some well-known biases.
    Stochastic simulation of large grids using free and public domain software
    Bruin, S. de; Wit, A.J.W. de - \ 2005
    Computers and Geosciences 31 (2005)7. - ISSN 0098-3004 - p. 828 - 836.
    soil acidification - uncertainty - program - reservoir - entropy
    This paper proposes a tiled map procedure enabling sequential indicator simulation on grids consisting of several tens of millions of cells, without putting excessive memory requirements. Spatial continuity across map tiles is handled by conditioning adjacent tiles on their shared boundaries. Tiles across the area can be characterized by dissimilar models of spatial continuity (semi-variograms) thus relieving the requirement of a global stationarity decision. Additionally, the approach provides a simple mechanism for reseeding the pseudo random number generator. Implementation of the algorithm involved small modifications to a GSLIB program and Bash and awk scripting. The software was stable on several platforms, including 32-bit systems with a 4 Gb memory addressing limit. In an experiment we simulated 25 realizations of a 11,274×13,000 grid representing local uncertainty in the Dutch land cover at 25 m resolution. With the objective of mimicking the typical absence of well-distributed hard reference data, the simulations were only conditioned on local prior class probabilities and semi-variograms. Output was evaluated on the basis of reproduction of target levels of (1) cover type proportions, (2) overall class label accuracy and (3) spatially averaged local Shannon entropy. As expected, the realized statistics differed significantly from the target levels. However, the differences were consistent over the borders and the insides of map tiles. Thus, they did not result from the tiled map procedure but rather should be attributed to the used semi-conditional sequential indicator simulator. The current implementation can easily be adapted to accept other simulation algorithms
    Size regulation and stability of charged lipid vesicles
    Claessens, M.M.A.E. - \ 2003
    Wageningen University. Promotor(en): Martien Cohen Stuart, co-promotor(en): Frans Leermakers; Folkert Hoekstra. - Wageningen : S.n. - ISBN 9789058089274 - 140
    blaasjes - stabiliteit - entropie - osmotische druk - vesicles - stability - entropy - osmotic pressure
    A comparison of maximum entropy and maximum likelihood estimation
    Oude Lansink, A.G.J.M. - \ 1999
    Tijdschrift voor sociaalwetenschappelijk onderzoek van de landbouw 14 (1999)2. - ISSN 0921-481X - p. 64 - 73.
    akkerbouw - bedrijfsvergelijking in de landbouw - agrarische bedrijfsvoering - prijselasticiteit - entropie - schatting - maximale aannemelijkheid - arable farming - farm comparisons - farm management - price elasticities - entropy - estimation - maximum likelihood
    Gegevens betreffende het ondernemerschap op Nederlandse akkerbouwbedrijven zijn in 2 benaderingsmethodes verwerkt, welke onderling op voorspellende nauwkeurigheid en op prijs-elasticiteit zijn vergeleken
    Statistical thermodynamics of association colloids : the equilibrium structure of micelles, vesicles, and bilayer membranes
    Leermakers, F.A.M. - \ 1988
    Agricultural University. Promotor(en): J. Lyklema, co-promotor(en): J.M.H.M. Scheutjens. - S.l. : Leermakers - 149
    colloïden - dispersie - entropie - membranen - statistiek - thermodynamica - colloids - dispersion - entropy - membranes - statistics - thermodynamics - cum laude

    The aim of the present study was to unravel the general equilibrium physical properties of lipid bilayer membranes. We consider four major questions:
    1. What determines the morphology of the association colloids (micelles, membranes, vesicles) in general?
    2. Do the apolar tails of the lipids in the bilayer organise themselves more like matches in a box or rather like hot spaghetti in a pan?
    3. How does this membrane organisation depend on temperature?
    4. How do additives like surfactants or polymers interact with the bilayer?
    These four questions cover a wide range of topics currently subject to intensive research. Each one of them calls for a rigorous answer. We believed that it would be possible to design one single theory covering the whole field. The development of such a theory is undertaken in the present thesis.
    Recently, the statistical thermodynamics of homopolymers at interfaces has been worked out by Scheutjens and Fleer (SF). This theory is an extension of the Flory Huggins (FH) theory for polymers in solution in the sense that it allows for inhomogeneities in one dimension. In the other two dimensions a mean field, i.e., an average segment density, assumption is applied. One of the strong points of this theory is that, by using a Markov-type approximation, all possible conformations of the chains are considered with a minimum of computational effort. The SF theory can be extended to describe copolymers at interfaces.
    For well-chosen amphipolar molecules the theory is able to deal with local phase separation phenomena. Preliminary calculations on surfactant bilayers showed that the SF theory needed some modifications in order to be relevant to the four topics given above. The main reason for this is that for the very small surfactant molecules the Markov-type approximation is not very accurate. Five extensions of the theory are presented in this thesis:
    1. For the chain statistics the Markov-type approximation is extended to the so called rotational isomeric state scheme. This scheme prevents backfolding in chain sections of five consecutive segments. The improvement allowed us to adjust the stiffness of the chain as a function of temperature.
    2. The theory is generalised for arbitrary geometries. With this extension the polymorphism of association colloids could be studied.
    3. The theory is extended to account for branched chain molecules. This has been used to simulate lipid molecules with two apolar tails and one polar head group.
    4. In the SF theory the statistical weight of each conformation is found by Boltzmann statistics. The potential of each conformation depends on segment-segment interactions, hard core contact potentials, and the number of gauche bonds in the chain. A new weighting factor is introduced which accounts for the average orientation of the molecules. The statistical
    weight of a conformation is increased when its bond directions match with those of the surrounding molecules. With this molecular orientational field co-operative phenomena like crystallisation can be studied.
    5. Allowing for inhomogeneities in two dimensions enables us to study membrane-"protein" interactions.

    The properties of the theory with these new features are thoroughly examined in five chapters. A short summary of the results and main conclusions of each chapter is given below.

    Chapter 1 dealt with the morphology of association colloids. In this chapter we prove that the formation of micelles is a first order transition. However, the theoretical critical micelle concentration is not observed very sharply, because it is very low. We showed that, with Increasing concentration of bipolar molecules, the micelles first grow and eventually change their shapes. Lecithin-like molecules prefer lamellar aggregates over globular ones.

    In chapter 2 the rotational isomeric state scheme is presented and details of the statistics of branched chain molecules is given. We present an overview of the behaviour of the membranes as a function of the four energy parameters. There is no need to restrict the molecules to pre-assigned positions in the system. The membrane thickness adjusts itself. The equilibrium membrane is free of tension. Its excess free energy per surface area is very small. When fluctuations and long range Van der Waals attractions are neglected the excess free energy is essentially zero.

    Vesicle systems are studied in chapter 3. We show that the excess free energy of curvature per vesicle is constant for vesicles composed of one type of lipid, irrespective of the radius of the vesicle. This remains true for bi-lamellar and hence for multilamellar vesicles. We show that as a rule, the thicker a membrane is the more energy it costs to bend it. Adding surfactants to a system containing vesicle is disastrous for the vesicle structures. Increasing the surfactant/ lipid ratio causes the vesicles to brake up in micelles. When vesicles are formed by two compatible lipid molecules, the free energy of curvature varies linearly with their composition. If the two bipolar molecules do not mix, they partition themselves over the two membrane sides and the excess free energy of curvature shows, at constant vesicle radius, a minimum as a function of composition. For a given composition the vesicle adopts an optimal vesicle radius.

    The membrane structure predicted by the theory significantly improves when the orientational dependent molecular field is applied. We derive the partition function for this SCAF (Self-Consistent Anisotropic Field) theory in chapter 4. Among other things, the order parameter profiles now show the well known plateau along the lipid tails. In agreement with experiments, we find a first order phase transition which transforms the membrane from a high temperature liquid into a low temperature gel state. In the gel phase the lipid tails are virtually in a all trans conformation. Because of this, the density in the gel membrane is higher than in the liquid phase. For the model membrane we observed two possible gel phases. One gel phase was about twice as thick as the other. The thin, intercalated, gel membrane was found in the case that the membranes were isolated, i.e., when they did not interact with each other, while the other gel phase, obviously with non-intercalated membranes, was found in the concentrated regime.

    In the final chapter we studied two cases of the interaction of long copolymers ("proteins") with a model membrane. In the first example the molecule is in a trans membrane configuration. In the second example a group of four molecules is clustered together and forms a hydrophilic pore, through which polar molecules can pass the membrane. In this chapter we also study the boundary region between two areas of lipid molecules which do not mix (lateral phase separation). It is characteristic for membrane system, that the lipids in the membrane are very efficient in camouflaging the inhomogeneities in the boundary layers. No big differences in solvent profiles are observed along the boundary layers. This ability of the lipid molecules to compensate Irregularities explains why membranes are not easily disrupted.

    It is the first time that a statistical thermodynamical theory is presented that can deal with association phenomena without the requirement to fix the head groups to pre-assigned positions. We showed that this theory does give a very detailed insight into equilibrium membrane properties. The correspondence with experimental data is satisfactory. The theory can be easily extended to incorporate more details in the calculations and better quantitative agreement with experimental data Is well feasible.

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