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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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.
Adsorption of charged and neutral polymer chains on silica surfaces: The role of electrostatics, volume exclusion, and hydrogen bonding
Spruijt, E. ; Biesheuvel, P.M. ; Vos, W.M. de - \ 2015
Physical Review. E, Statistical nonlinear, and soft matter physics 91 (2015). - ISSN 2470-0045 - 11 p.
polyelectrolyte adsorption - double-layer - free-energy - poly(vinylpyrrolidone) - relaxation - desorption - stability - kinetics - colloids - density
We develop an off-lattice (continuum) model to describe the adsorption of neutral polymer chains and polyelectrolytes to surfaces. Our continuum description allows taking excluded volume interactions between polymer chains and ions directly into account. To implement those interactions, we use a modified hard-sphere equation of state, adapted for mixtures of connected beads. Our model is applicable to neutral, charged, and ionizable surfaces and polymer chains alike and accounts for polarizability effects of the adsorbed layer and chemical interactions between polymer chains and the surface. We compare our model predictions to data of a classical system for polymer adsorption: neutral poly(N-vinylpyrrolidone) (PVP) on silica surfaces. The model shows that PVP adsorption on silica is driven by surface hydrogen bonding with an effective maximum binding energy of about 1.3kBT per PVP segment at low pH. As the pH increases, the Si-OH groups become increasingly dissociated, leading to a lower capacity for H bonding and simultaneous counterion accumulation and volume exclusion close to the surface. Together these effects result in a characteristic adsorption isotherm, with the adsorbed amount dropping sharply at a critical pH. Using this model for adsorption data on silica surfaces cleaned by either a piranha solution or an O2 plasma, we find that the former have a significantly higher density of silanol groups.
Accurate pKa Calculation of the Conjugate Acids of Alkanolamines, Alkaloids and Nucleotide Bases by Quantum Chemical Methods
Gangarapu, S. ; Marcelis, A.T.M. ; Zuilhof, H. - \ 2013
ChemPhysChem 14 (2013)5. - ISSN 1439-4235 - p. 990 - 995.
density-functional theory - co2 capture technology - gas-phase basicities - pk(a) values - continuum model - free-energy - amines - molecules - prediction - proton
The pKa of the conjugate acids of alkanolamines, neurotransmitters, alkaloid drugs and nucleotide bases are calculated with density functional methods (B3LYP, M08-HX and M11-L) and ab initio methods (SCS-MP2, G3). Implicit solvent effects are included with a conductor-like polarizable continuum model (CPCM) and universal solvation models (SMD, SM8). G3, SCS-MP2 and M11-L methods coupled with SMD and SM8 solvation models perform well for alkanolamines with mean unsigned errors below 0.20 pKa units, in all cases. Extending this method to the pKa calculation of 35 nitrogen-containing compounds spanning 12 pKa units showed an excellent correlation between experimental and computational pKa values of these 35 amines with the computationally low-cost SM8/M11-L density functional approach.
Self-consistent field theory of protein adsorption in a non-Gaussian polyelectrolyte brush
Biesheuvel, P.M. ; Leermakers, F.A.M. ; Stuart, M.A.C. - \ 2006
Physical Review. E, Statistical nonlinear, and soft matter physics 73 (2006)1. - ISSN 1539-3755 - 9 p.
including charge regulation - electrical double-layer - grafted polymer brush - finite extensibility - free-energy - model - sedimentation - equilibrium - interfaces - equation
To describe adsorption of globular protein molecules in a polyelectrolyte brush we use the strong-stretching approximation of the Edwards self-consistent field equation, combined with corrections for a non-Gaussian brush. To describe chemical potentials in this mixture of (globular) species of widely varying sizes (ions, brush polyelectrolyte segments, globular protein molecules), we use the Boublik-Mansoori-Carnahan-Starling-Leland equation of state derived for polydisperse mixtures of spherical particles. The polyelectrolyte chain is described in this approach as a string of beads with the beads of a size related to the chain diameter. We use the one-dimensional Poisson equation to describe the electrostatic field and include the ionizable character of both the brush polyions and the protein molecules. This model explains the experimental observation of high amounts of protein adsorption in a polyacid brush for pH values above the isoelectric point of the protein as being due to charge reversal of the protein molecules upon entry in the brush. We find a distinct minimum in protein concentration near the edge of the brush. With increasing pH this barrier to protein transfer becomes larger, but much less so when we increase the ionic strength, a difference that might relate to an experimentally observed difference in the protein release rate in these two cases. A free energy analysis shows that the release of small ions from the brush and the increase of brush ionization are the two driving forces for protein adsorption in a like-charged brush
Ligand and Charge Distribution (LCD) model for the description of fulvic acid adsorption to goethite
Weng, L.P. ; Riemsdijk, W.H. van; Koopal, L.K. ; Hiemstra, T. - \ 2006
Journal of Colloid and Interface Science 302 (2006)2. - ISSN 0021-9797 - p. 442 - 457.
natural organic-matter - nica-donnan model - metal-ion binding - electrical double-layer - interacting chain molecules - surface structural approach - oxide-water interface - humic substances - variable-charge - free-energy
The LCD model (Ligand and Charge Distribution) has recently been proposed to describe the adsorption of humic substances to oxides, in which the CD-MUSIC model and the NICA model for ion binding to respectively oxides and humic substances are integrated. In this paper, the LCD model is improved by applying the ADAPT model (ADsorption and AdaPTation) to calculate the equilibrium distribution of the humic substances based on the change of the average chemical state of the particles. The improved LCD model is applied to calculate the adsorption of fulvic acid (Strichen) to goethite, in which it is assumed that the carboxylic type of groups of fulvic acid can form innersphere complexes with the surface sites. The charge of the carboxylic groups in the innersphere complexes is distributed between the 0- and d-plane, whereas the charge of the other carboxylic and phenolic groups is located in the d-plane. The average distribution of the carboxylic and phenolic groups among their various chemical states (carboxylic groups: innersphere complex, protonated and deprotonated; phenolic groups: protonated and deprotonated) depends on pH, ionic strength and loading, and are the outcome of the model. The calculation shows that the LCD model can describe sufficiently the effects of pH, ionic strength and loading on the adsorption of fulvic acid, using one adjustable parameter (log over(K, ¿)S, 1). The model calculations indicate that the chemical complexation between fulvic acid and goethite is the main driving force of the adsorption, while the electrostatic repulsion between the particles and the surface is the major limiting factor for further adsorption
Calcium-induced tertiary structure modifications of endo-B-1,3-glucanase form Pyrococcus furiosus in 7.9 M guanidinium chloride
Chiaraluce, R. ; Gianese, G. ; Angelaccio, S. ; Florio, R. ; Lieshout, J.F.T. van; Oost, J. van der; Consalvi, V. - \ 2005
Biochemical Journal 386 (2005)3. - ISSN 0264-6021 - p. 515 - 524.
transform infrared-spectroscopy - protein secondary structure - 3-dimensional structures - ftir spectroscopy - free-energy - recognition - database - endo-beta-1,3-glucanase - intermediate - alignments
The family 16 endo-b-1,3 glucanase from the extremophilic archaeon Pyrococcus furiosus is a laminarinase, which in 7.9 M GdmCl (guanidinium chloride) maintains a significant amount of tertiary structure without any change of secondary structure. The addition of calcium to the enzyme in 7.9 M GdmCl causes significant changes to the near-UV CD and fluorescence spectra, suggesting a notable increase in the tertiary structure which leads to a state comparable, but not identical, to the native state. The capability to interact with calcium in 7.9 M GdmCl with a consistent recovery of native tertiary structure is a unique property of this extremely stable endo-b-1,3 glucanase. The effect of calcium on the thermodynamic parameters relative to the GdmCl-induced equilibrium unfolding has been analysed by CD and fluorescence spectroscopy. The interaction of calcium with the native form of the enzyme is studied by Fourier-transform infrared spectroscopy in the absorption region of carboxylate groups and by titration in the presence of a chromophoric chelator. A homology-based model of the enzyme is generated and used to predict the putative binding site(s) for calcium and the structural interactions potentially responsible for the unusual stability of this protein, in comparison with other family 16 glycoside hydrolases
Theory for concentration and solvency effects in size-exclusion chromatography of polymers
Fleer, G.J. ; Skvortsov, A.M. - \ 2005
Macromolecules 38 (2005)6. - ISSN 0024-9297 - p. 2492 - 2505.
osmotic-pressure chromatography - gaussian-chain theory - finely porous-glass - theta solvent - concentration-dependence - free-energy - semiflexible macromolecules - confined macromolecules - depletion interaction - nonadsorbing polymer
A simple analytical equation for the distribution coefficient K in size-exclusion chromatography (SEC) as a function of molar mass, concentration, and solvent quality is presented. The theory is based upon a modified Casassa equation, using a recently proposed mean-field relation for the depletion thickness ¿, which for better than ¿ conditions reads 1/¿2 = 1/¿02 + 1/¿2. Here ¿0 is the well-known (chain-length-dependent) depletion thickness at infinite dilution, and ¿ is the (concentration- and solvency-dependent) correlation length in the solution. Numerical lattice calculations for mean-field chains in slitlike pores of width D as a function of concentration are in quantitative agreement with our analytical equation, both for good solvents and in a ¿ solvent. Comparison of our mean-field theory with Monte Carlo data for the concentration dependence of K for self-avoiding chains shows qualitatively the same trends; moreover, our model can also be adjusted to obtain nearly quantitative agreement. The modified Casassa equation works excellently in the wide-pore regime (where K = 1 - 2¿/D) and gives an upper bound for the narrow-pore regime. In fact, the simple form K = 1 - 2¿ID for 2¿/D <1 and K = 0 for 2¿/D > 1 gives a first estimate of concentration effects even in the narrow-pore regime. A more detailed analysis of interacting depletion layers in narrow pores shows that a different length scale ¿i (the "interaction distance") enters, which in semidilute solutions is somewhat higher than ¿, leading to a smaller K than that obtained with the wide-pore length scale ¿. Predictions for the effects of chain length, solvency, and chain stiffness on the basis of our analytical equation are in accordance with Monte Carlo simulations.
Evidence for charge regulation in the sedimentation of charged colloids
Biesheuvel, P.M. - \ 2004
Journal of Physics-Condensed Matter 16 (2004)49. - ISSN 0953-8984 - p. L499 - L504.
free-energy - profiles - equilibrium
Recent experimental data for the centrifugal sedimentation-diffusion profile of charged colloidal silica (ø ~ 44 nm) in ethanol is analysed based on local charge neutrality and by either assuming a fixed particle charge or incorporating charge regulation. Especially at a high Debye length (>30 nm) the two models deviate at higher particle volume fractions ø (>0.1 vol%) with the data much better reproduced when charge regulation is included.
Molecular basis for redox-Bohr and cooperative effects in cytochrome c3 from Desulfovibrio desulfuricans ATCC 27774: crystallographic and modelling studies of oxidised and reduced high-resolution structures at pH 7.6
Bento, I. ; Matias, P.M. ; Baptista, A.M. ; Costa, P.N. da; Dongen, W.M.A.M. van; Saraiva, L.M. ; Schneider, T.R. ; Soares, C.M. ; Carrondo, M.A. - \ 2004
Proteins : Structure, Function, and Bioinformatics 54 (2004)1. - ISSN 0887-3585 - p. 135 - 152.
vulgaris miyazaki-f - photosynthetic reaction centers - free-energy - electrostatic calculations - tetraheme cytochrome - angstrom resolution - dielectric-constants - crystal-structure - rhodopseudomonas-viridis - ionizable residues
The tetraheme cytochrome c, is a small metalloprotein with ca. 13,000 Da found in sulfate-reducing bacteria, which is believed to act as a partner of hydrogenase. The three-dimensional structure of the oxidized and reduced forms of cytochrome c(3) from Desulfovibrio desulfuricans ATCC 27774 at pH 7.6 were determined using high-resolution X-ray crystallography and were compared with the previously determined oxidized form at pH 4.0. Theoretical calculations were performed with both structures, using continuum electrostatic calculations and Monte Carlo sampling of protonation and redox states, in order to understand the molecular basis of the redox-Bohr and cooperativity effects related to the coupled transfer of electrons and protons. We were able to identify groups that showed redox-linked conformational changes. In particular, Glu61, His76, and propionate D of heme II showed important contributions to the redox-cooperativity, whereas His76, propionate A of heme I, and propionate D of heme IV were the key residues for the redox-Bohr effect. Upon reduction, an important movement of the backbone region surrounding hemes I and II was also identified, that, together with a few redox-linked conformational changes in side-chain residues, results in a significant decrease in the solvent accessibility of hemes I and II. (C) 2003 Wiley-Liss, Inc.
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