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Brownian Dynamics Simulations of Macromolecules: Algorithm Development and Polymers under Confinement
Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
2012 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

In this thesis I have used computer simulations to study the structure and dynamics of grafted polymers during confinement. These systems are of importance for understanding e.g. colloidal stability and surface coatings. We have used Brownian dynamics simulations with the polymers modeled as discrete wormlike chains allowing for a variable persistence length as well as different non-bonded interactions. The size and shape of the chains are characterized by the radius of gyration and the degree of oblateness/prolateness, and the entanglement is followed by calculating the mean overcrossing number. Starting in the dilute regime with a single polymer mushroom we have investigated how the rate of compression and solvent quality effects the behaviour of a compressed chain. In the brush regime, we investigated how the surface coverage effects the behaviour during compression. For low coverages the chains have the possibilty to increase their lateral extension during confinement but in general, the chains have a low inter-entanglement, as they strive to keep their integrity during the confinement process.

To go from a polymer brush to the construction of a connected network, we have developed a method to construct a closed network without using periodic boundary conditions by building the network on a sphere in R4. In this way we avoid the restrictions of periodicity at the cell boundaries. We finally also show how to develop the idea of using spherical boundary conditions, by presenting a novel algorithm for simulating diffusion on a spherical surface. The method is more stable and allows for larger time steps, compared to commonly used methods in computer simulations.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis , 2012. , p. 58
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 937
National Category
Physical Chemistry
Identifiers
URN: urn:nbn:se:uu:diva-173435ISBN: 978-91-554-8377-7 (print)OAI: oai:DiVA.org:uu-173435DiVA, id: diva2:517608
Public defence
2012-06-04, Å2001, Ångströmlaboratoriet, Lägerhyddsvägen 1, Uppsala, 10:00 (English)
Opponent
Supervisors
Available from: 2012-05-14 Created: 2012-04-24 Last updated: 2014-12-30Bibliographically approved
List of papers
1. Off-equilibrium response of grafted polymer chains subject to a variable rate of compression
Open this publication in new window or tab >>Off-equilibrium response of grafted polymer chains subject to a variable rate of compression
2011 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 13, no 24, p. 11757-11765Article in journal (Refereed) Published
Abstract [en]

We present Brownian dynamics simulations of single grafted semiflexible chains (i.e., "polymer mushrooms'') with varying persistence lengths, intra-chain interactions, and subject to confinement. The results from different rates of compression are presented in the cases of an approaching infinite plane and a paraboloid tip. We discuss the different behaviour observed for grafted chains with strong and weak self-attraction (i.e., "hard'' and "soft'' polymer mushrooms). In both cases the effect on the size and shape is more pronounced for a slow compression rate, especially for "hard mushrooms''. We have also studied the relaxation of the chain while the compressing plane is maintained, and when it is removed suddenly. We find that the response depends strongly on the time allowed for relaxation in the compressed state. When using instead a paraboloid tip, the overall effects are similar yet less pronounced because the chain can dodge the confining object via an "escape transition.''

National Category
Natural Sciences Inorganic Chemistry
Research subject
Chemistry with specialization in Inorganic Chemistry
Identifiers
urn:nbn:se:uu:diva-155223 (URN)10.1039/c1cp20462a (DOI)000291395200037 ()
Available from: 2011-06-21 Created: 2011-06-20 Last updated: 2017-12-11Bibliographically approved
2. Brownian dynamics of a compressed polymer brush model: Off-equilibrium response as a function of surface coverage and compression rate
Open this publication in new window or tab >>Brownian dynamics of a compressed polymer brush model: Off-equilibrium response as a function of surface coverage and compression rate
2011 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 13, no 35, p. 16084-16094Article in journal (Refereed) Published
Abstract [en]

We study the compressive behaviour of a polymer-covered surface (i.e., a "polymer brush'') using Brownian dynamics simulations. The model consists of grafted chains with variable flexibility, variable intra-and inter-chain interactions, as well as different surface coverage. We discuss the polymer brush response to confinement by considering variable rates of compression under a hard plane. Our results show a small degree of inter-chain entanglement, regardless of whether the interaction is attractive or merely excluded volume. We observe that the molecular shape depends strongly on the surface coverage. Dense brushes exhibit a limited degree of lateral deformation under compression; instead, chains undergo a transition that produces a local patch with near-solid packing. This effect due to surface density can be undone partially by increasing the attractive nature of the chain interaction, by modulating the rate of compression, or by allowing "soft anchoring'', i.e., the possible Brownian drift of the grafting bead on the surface. We have also studied the polymer brush relaxation while maintaining the compressing plane, as well as after its sudden removal. We find evidence that also the relaxation depends on surface density; dense brushes appear to be configurationally frustrated at high compression and are unable to undergo swelling, regardless of the pressure applied.

National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-158668 (URN)10.1039/c1cp21433k (DOI)000294167700042 ()
Available from: 2011-09-13 Created: 2011-09-13 Last updated: 2017-12-08Bibliographically approved
3. Structure and compression dynamics of two mutually approaching polymer brushes
Open this publication in new window or tab >>Structure and compression dynamics of two mutually approaching polymer brushes
(English)Manuscript (preprint) (Other academic)
National Category
Natural Sciences Physical Chemistry
Identifiers
urn:nbn:se:uu:diva-173433 (URN)
Available from: 2012-04-24 Created: 2012-04-24 Last updated: 2012-08-01
4. Construction of a non-periodic closed network for computer simulations
Open this publication in new window or tab >>Construction of a non-periodic closed network for computer simulations
(English)Manuscript (preprint) (Other academic)
National Category
Physical Chemistry Mathematics
Identifiers
urn:nbn:se:uu:diva-173391 (URN)
Available from: 2012-04-23 Created: 2012-04-23 Last updated: 2012-08-01
5. Algorithm for generating a Brownian motion on a sphere
Open this publication in new window or tab >>Algorithm for generating a Brownian motion on a sphere
2010 (English)In: Journal of physics A: Mathematical and theoretical, ISSN 1751-8113, Vol. 43, no 50, p. 505001-Article in journal (Refereed) Published
Abstract [en]

We present a new algorithm for generation of a random walk on a two-dimensional sphere. The algorithm is obtained by viewing the 2-sphere as the equator in the 3-sphere surrounded by an infinitesimally thin band with boundary which reflects Brownian particles and then applying known effective methods for generating Brownian motion on the 3-sphere. To test the method, the diffusion coefficient was calculated in computer simulations using the new algorithm and, for comparison, also using a commonly used method in which the particle takes a Brownian step in the tangent plane to the 2-sphere and is then projected back to the spherical surface. The two methods are in good agreement for short time steps, while the method presented in this paper continues to give good results also for larger time steps, when the alternative method becomes unstable.

National Category
Mathematics Chemical Sciences
Identifiers
urn:nbn:se:uu:diva-134231 (URN)10.1088/1751-8113/43/50/505001 (DOI)000284879400003 ()
Available from: 2010-11-23 Created: 2010-11-23 Last updated: 2012-08-01Bibliographically approved

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