Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    We will mail you new results for this query: keywords==monte-carlo-simulation
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Systematic coarse-graining in nucleation theory
Schweizer, M. ; Sagis, L.M.C. - \ 2015
Journal of Chemical Physics 143 (2015). - ISSN 0021-9606 - 18 p.
vapor-liquid nucleation - monte-carlo-simulation - translation-rotation paradox - homogeneous nucleation - molecular-dynamics - free-energy - supersaturated vapor - semiphenomenological theory - inhomogeneous-media - physical clusters
In this work, we show that the standard method to obtain nucleation rate-predictions with the aid of atomistic Monte Carlo simulations leads to nucleation rate predictions that deviate 3 - 5 orders of magnitude from the recent brute-force molecular dynamics simulations [Diemand et al., J. Chem. Phys. 139, 074309 (2013)] conducted in the experimental accessible supersaturation regime for Lennard-Jones argon. We argue that this is due to the truncated state space the literature mostly relies on, where the number of atoms in a nucleus is considered the only relevant order parameter. We here formulate the nonequilibrium statistical mechanics of nucleation in an extended state space, where the internal energy and momentum of the nuclei are additionally incorporated. We show that the extended model explains the lack in agreement between the molecular dynamics simulations by Diemand et al. and the truncated state space. We demonstrate additional benefits of using the extended state space; in particular, the definition of a nucleus temperature arises very naturally and can be shown without further approximation to obey the fluctuation law of McGraw and LaViolette. In addition, we illustrate that our theory conveniently allows to extend existing theories to richer sets of order parameters.
An evaluation of plotless sampling using vegetation simulations and field data from a mangrove forest
Hijbeek, R. ; Koedam, N. ; Nabiul Islam Khan, M. - \ 2013
PLoS ONE 8 (2013)6. - ISSN 1932-6203 - 10 p.
monte-carlo-simulation - density estimators
In vegetation science and forest management, tree density is often used as a variable. To determine the value of this variable, reliable field methods are necessary. When vegetation is sparse or not easily accessible, the use of sample plots is not feasible in the field. Therefore, plotless methods, like the Point Centred Quarter Method, are often used as an alternative. In this study we investigate the accuracy of different plotless sampling methods. To this end, tree densities of a mangrove forest were determined and compared with estimates provided by several plotless methods. None of these methods proved accurate across all field sites with mean underestimations up to 97% and mean overestimations up to 53% in the field. Applying the methods to different vegetation patterns shows that when random spatial distributions were used the true density was included within the 95% confidence limits of all the plotless methods tested. It was also found that, besides aggregation and regularity, density trends often found in mangroves contribute to the unreliability. This outcome raises questions about the use of plotless sampling in forest monitoring and management, as well as for estimates of density-based carbon sequestration. We give recommendations to minimize errors in vegetation surveys and recommendations for further in-depth research.
Chain length distribution and kinetic characteristics of an enzymatically produced polymer
Mulders, K.J.M. ; Beeftink, H.H. - \ 2013
e-Polymers 13 (2013)1. - ISSN 1618-7229 - p. 261 - 272.
monte-carlo-simulation - multiple attack mechanism - sequential reactions - actin-filaments - enzyme - model - transglycosylation - fragmentation - competition - reactors
Non-processive enzymatic polymerization leads to a distribution of polymer chain lengths. A polymerization model was developed to investigate the relation between the extent of this distribution on one hand, and the polymerization start conditions and reaction kinetics on the other hand. The model describes changes in concentration of chains of length n as the result of two elongation reactions: elongation by monomer addition to length n-1 and elongation by monomer addition to length n. Polymerization reactions were assumed to be zero order in monomer concentration and to obey Michaelis-Menten kinetics with respect to polymer concentrations. In addition, the amount of enzyme available for each individual reaction (n n+1) is assumed to be Non-processive enzymatic polymerization leads to a distribution of polymer chain lengths. A polymerization model was developed to investigate the relation between the extent of this distribution on one hand, and the polymerization start conditions and reaction kinetics on the other hand. The model describes changes in concentration of chains of length n as the result of two elongation reactions: elongation by monomer addition to length n-1 and elongation by monomer addition to length n. Polymerization reactions were assumed to be zero order in monomer concentration and to obey Michaelis-Menten kinetics with respect to polymer concentrations. In addition, the amount of enzyme available for each individual reaction (n n+1) is assumed to be proportional to the concentration of polymer substrate of length n. The development of the shape of the chain length distribution was found to be independent of the value of the overall reaction rate constant; only the rate at which these shapes developed was influenced by the 1st-order rate constant. The value of the Michaelis parameter did affect the form of the chain length distribution curve since it affects the reaction order. An increase in reaction order was found to promote widening of the chain length distribution. Differences in kinetic parameters between the subsequent polymerization reactions, if any, were also found to have a large effect on the development of the chain length distribution. An increase in rate constants with chain length entailed a wider distribution; a more narrow distribution would require a decrease in rate constants with chain length.proportional to the concentration of polymer substrate of length n. The development of the shape of the chain length distribution was found to be independent of the value of the overall reaction rate constant; only the rate at which these shapes developed was influenced by the 1st-order rate constant. The value of the Michaelis parameter did affect the form of the chain length distribution curve since it affects the reaction order. An increase in reaction order was found to promote widening of the chain length distribution. Differences in kinetic parameters between the subsequent polymerization reactions, if any, were also found to have a large effect on the development of the chain length distribution. An increase in rate constants with chain length entailed a wider distribution; a more narrow distribution would require a decrease in rate constants with chain length.
Conformations and solution properties of star-branched polyelectrolytes
Borisov, O.V. ; Zhulina, E.B. ; Leermakers, F.A.M. ; Ballauff, M. ; Muller, A.H.E. - \ 2011
In: Self organized nanostructures of amphiphilic block copolymers I / Müller, A.H.E., Berlin : Springer (Advances in polymer science 241) - ISBN 9783642224850 - p. 1 - 55.
block-copolymer micelles - consistent-field theory - poly(methacrylic acid) brushes - molecular-dynamics simulations - modified poly(ethylene oxide) - angle neutron-scattering - monte-carlo-simulation - aqueous-solutions - polymer brushes - ionic-strength
Aqueous solutions of star-like polyelectrolytes (PEs) exhibit distinctive features that originate from the topological complexity of branched macromolecules. In a salt-free solution of branched PEs, mobile counterions preferentially localize in the intramolecular volume of branched macroions. Counterion localization manifests itself in a dramatic reduction of the osmotic coefficient in solutions of branched polyions as compared with those of linear PEs. The intramolecular osmotic pressure, created by entrapped counterions, imposes stretched conformations of branches and this leads to dramatic intramolecular conformational transitions upon variations in environmental conditions. In this chapter, we overview the theory of conformations and stimuli-induced conformational transitions in star-like PEs in aqueous solutions and compare these to the data from experiments and Monte Carlo and molecular dynamics simulations.
A stochastic model for predicting dextrose equivalent and saccharide composition during hydrolysis of starch by alpha-amylase
Besselink, T. ; Baks, T. ; Janssen, A.E.M. ; Boom, R.M. - \ 2008
Biotechnology and Bioengineering 100 (2008)4. - ISSN 0006-3592 - p. 684 - 697.
monte-carlo-simulation - bacillus-licheniformis - enzymatic-hydrolysis - soluble starch - kinetic-model - potato starch - amylopectin - amylolysis - enzymes - thermostability
A stochastic model was developed that was used to describe the formation and breakdown of all saccharides involved during -amylolytic starch hydrolysis in time. This model is based on the subsite maps found in literature for Bacillus amyloliquefaciens -amylase (BAA) and Bacillus licheniformis -amylase (BLA). Carbohydrate substrates were modeled in a relatively simple two-dimensional matrix. The predicted weight fractions of carbohydrates ranging from glucose to heptasaccharides and the predicted dextrose equivalent showed the same trend and order of magnitude as the corresponding experimental values. However, the absolute values were not the same. In case a well-defined substrate such as maltohexaose was used, comparable differences between the experimental and simulated data were observed indicating that the substrate model for starch does not cause these deviations. After changing the subsite map of BLA and the ratio between the time required for a productive and a non-productive attack for BAA, a better agreement between the model data and the experimental data was observed. Although the model input should be improved for more accurate predictions, the model can already be used to gain knowledge about the concentrations of all carbohydrates during hydrolysis with an -amylase. In addition, this model also seems to be applicable to other depolymerase-based systems
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