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Systematic coarsegraining in nucleation theory Schweizer, M. ; Sagis, L.M.C.  \ 2015
Journal of Chemical Physics 143 (2015).  ISSN 00219606  18 p. vaporliquid nucleation  montecarlosimulation  translationrotation paradox  homogeneous nucleation  moleculardynamics  freeenergy  supersaturated vapor  semiphenomenological theory  inhomogeneousmedia  physical clusters
In this work, we show that the standard method to obtain nucleation ratepredictions with the aid of atomistic Monte Carlo simulations leads to nucleation rate predictions that deviate 3  5 orders of magnitude from the recent bruteforce molecular dynamics simulations [Diemand et al., J. Chem. Phys. 139, 074309 (2013)] conducted in the experimental accessible supersaturation regime for LennardJones 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 19326203  10 p. montecarlosimulation  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 densitybased carbon sequestration. We give recommendations to minimize errors in vegetation surveys and recommendations for further indepth research.


Chain length distribution and kinetic characteristics of an enzymatically produced polymer Mulders, K.J.M. ; Beeftink, H.H.  \ 2013
ePolymers 13 (2013)1.  ISSN 16187229  p. 261  272. montecarlosimulation  multiple attack mechanism  sequential reactions  actinfilaments  enzyme  model  transglycosylation  fragmentation  competition  reactors
Nonprocessive 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 n1 and elongation by monomer addition to length n. Polymerization reactions were assumed to be zero order in monomer concentration and to obey MichaelisMenten kinetics with respect to polymer concentrations. In addition, the amount of enzyme available for each individual reaction (n n+1) is assumed to be Nonprocessive 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 n1 and elongation by monomer addition to length n. Polymerization reactions were assumed to be zero order in monomer concentration and to obey MichaelisMenten 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 1storder 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 1storder 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 starbranched 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. blockcopolymer micelles  consistentfield theory  poly(methacrylic acid) brushes  moleculardynamics simulations  modified poly(ethylene oxide)  angle neutronscattering  montecarlosimulation  aqueoussolutions  polymer brushes  ionicstrength
Aqueous solutions of starlike polyelectrolytes (PEs) exhibit distinctive features that originate from the topological complexity of branched macromolecules. In a saltfree 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 stimuliinduced conformational transitions in starlike 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 alphaamylase Besselink, T. ; Baks, T. ; Janssen, A.E.M. ; Boom, R.M.  \ 2008
Biotechnology and Bioengineering 100 (2008)4.  ISSN 00063592  p. 684  697. montecarlosimulation  bacilluslicheniformis  enzymatichydrolysis  soluble starch  kineticmodel  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 twodimensional 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 welldefined 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 nonproductive 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 depolymerasebased systems

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