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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Application of high performance computing for comparison of two highly branched lysine molecules of different topology
Neelov, Igor M. ; Shavykin, Oleg V. ; Ilyash, Maxim Y. ; Bezrodnyi, Valeriy V. ; Mikhtaniuk, Sofia E. ; Marchenko, Anna A. ; Fatullaev, Emil I. ; Darinskii, Anatolii A. ; Leermakers, Frans A.M. - \ 2018
Supercomputing Frontiers and Innovations 5 (2018)3. - ISSN 2409-6008 - p. 60 - 64.
Dendrimer - Dendritic brush - High performance computing - Poly-L-lysine

High performance computations were performed for comparison of size and other properties of big heavily charged biocompatible molecules of complex topology in water. Lysine dendrimer and short dendritic brush of the same molecular weight were studied by molecular dynamics simulation method and GROMACS software package. The size and structural properties of these two systems were compared. It was shown that dendritic brush has smaller size and more dense core than the dendrimer. Radial density profile for both molecules is not monotonous and has minimum near core of molecules. This minimum is wider and deeper for dendrimer than for dendritic brush. Thus dendrimer has larger region of low density than dendritic brush and is more suitable for use for encapsulation and delivery of hydrophobic drugs.

Effect of an asymmetry of branching on structural characteristics of dendrimers revealed by Brownian dynamics simulations
Shavykin, O.V. ; Mikhailov, I.V. ; Darinskii, A.A. ; Neelov, I.M. ; Leermakers, F.A.M. - \ 2018
Polymer 146 (2018). - ISSN 0032-3861 - p. 256 - 266.
Asymmetry of branching - Brownian dynamic simulation - Coarse-grained model - Dendrimers

Dendrimers in dilute solution with asymmetry of branching were simulated by the Brownian dynamics method. In this simulation a coarse-grained dendrimer model and athermal solvent conditions were implemented, extending previous work to a wider range of branch asymmetries at fixed average spacer lengths and high generation numbers close to the theoretical limit. We considered both global and local structural characteristics of dendrimers. The global ones, such as the average distance of ends from the center, the radius of gyration, the hydrodynamic radius and the dendrimer shape anisotropy, are practically insensitive to the asymmetry of branching. The effect of the spacer asymmetry is revealed mainly in the local structure of dendrimers. In particular the radial density profile changes its shape from a convex to a concave one with an increase of the asymmetry. As compared to symmetrical case, the distribution of terminal monomer units in asymmetrical dendrimers shifts towards the dendrimers periphery. The terminal monomers in an asymmetrical dendrimer are on average in a denser environment compared to their symmetrical analogs. The shorter spacers are less stretched and more turned back to the core than the longer ones located at the same topological distance from the dendrimer periphery. The simulations also demonstrated that the asymmetry of branching leads to a smaller radial overlap of dendron fragments inside the dendrimer as compared to the symmetrical case. However, the total overlap was found to be independent of the asymmetry of branching.

Self-Assembly of Lysine-Based Dendritic Surfactants Modeled by the Self-Consistent Field Approach
Shavykin, O.V. ; Leermakers, F.A.M. ; Neelov, I.M. ; Darinskii, A.A. - \ 2018
Langmuir 34 (2018)4. - ISSN 0743-7463 - p. 1613 - 1626.
Implementing a united atom model, we apply self-consistent field theory to study structure and thermodynamic properties of spherical micelles composed of surfactants that combine an alkyl tail with a charged lysine-based dendritic headgroup. Following experiments, the focus was on dendron surfactants with varying tail length and dendron generations G0, G1, G2. The heads are subject to acetylation modification which reduces the charge and hydrophilicity. We establish a reasonable parameter set which results in semiquantitative agreement with the available experiments. The critical micellization concentration, aggregation number, and micelle size are discussed. The strongly charged dendronic surfactants micelles are stable for generation numbers G0 and G1, for progressively higher ionic strengths. Associates of G2 surfactants are very small and can only be found at extreme surfactant concentration and salt strengths. Micelles of corresponding weaker charged acetylated variants exist up to G2, tolerate significantly lower salt concentrations, but lose the spherical micelle topology for G0 at high ionic strengths.
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