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Electrostatic Interactions in Coarse-Grained Simulations: Implementations and Applications
Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
2013 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Electrostatic interactions between charged species play a prominent role in determining structures and states of physical system, leading to important technological and biological applications. In coarse-grained simulations, accurate description of electrostatic interactions is crucial in addressing physical phenomena at larger spatial and longer temporal scales.

In this thesis, we implement ENUF method, an abbreviation for Ewald summation based on non-uniform fast Fourier transform technique, into dissipative particle dynamics (DPD) scheme. With determined suitable parameters, the computational complexity of ENUF-DPD method is approximately described as O(N logN). The ENUF-DPD method is further validated by investigating dependence of polyelectrolyte conformations on charge fraction of polyelectrolyte and counterion valency of added salts, and studying of specific binding structures of dendrimers on amphiphilic membranes.

In coarse-grained simulations, electrostatic interactions are either explicitly calculated with suitable methods, or implicitly included in effective potentials. The effect of treatment fashion of electrostatic interactions on phase behavior of [BMIM][PF6] ionic liquid (IL) is systematically investigated. Our systematic analyses show that electrostatic interactions should be incorporated explicitly in development of effective potentials, as well as in coarse-grained simulations to improve reliability of simulation results.

Detailed image of microscopic structures and orientations of [BMIM][PF6] at graphene and vacuum interfaces are investigated by using atomistic simulations. Imidazolium rings and alkyl side chains of [BMIM] lie preferentially flat on graphene surface. At IL-vacuum interface, ionic groups pack closely together to form polar domains, leaving alkyl side chains populated at interface and imparting hydrophobic character. With the increase of IL filmthickness, orientations of [BMIM] change gradually from dominant flat distributions along graphene surface to orientations where imidazolium rings are either parallel or perpendicular to IL-vacuum interface with tilted angles. The interfacial spatial ionic structural heterogeneity formed by ionic groups also contributes to heterogeneous dynamics in interfacial regions.

Place, publisher, year, edition, pages
Stockholm: Department of Materials and Environmental Chemistry (MMK), Stockholm University , 2013. , 82 p.
Keyword [en]
dissipative particle dynamics, electrostatic interaction, ionic liquid, coarse-grained model
National Category
Physical Chemistry
Research subject
Physical Chemistry
Identifiers
URN: urn:nbn:se:su:diva-92707ISBN: 978-91-7447-727-6 (print)OAI: oai:DiVA.org:su-92707DiVA: diva2:641063
Public defence
2013-09-27, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 09:30 (English)
Opponent
Supervisors
Available from: 2013-09-05 Created: 2013-08-15 Last updated: 2013-08-15Bibliographically approved
List of papers
1. Implementation of non-uniform FFT based Ewald summation in dissipative particle dynamics method
Open this publication in new window or tab >>Implementation of non-uniform FFT based Ewald summation in dissipative particle dynamics method
2013 (English)In: Journal of Computational Physics, ISSN 0021-9991, E-ISSN 1090-2716, Vol. 235, 666-682 p.Article in journal (Refereed) Published
Abstract [en]

The ENUF method, i.e., Ewald summation based on the non-uniform FFT technique (NFFT), is implemented in dissipative particle dynamics (DPD) simulation scheme to fast and accurately calculate the electrostatic interactions at mesoscopic level. In a simple model electrolyte system, the suitable ENUF–DPD parameters, including the convergence parameter α, the NFFT approximation parameter p, and the cut-offs for real and reciprocal space contributions, are carefully determined. With these optimized parameters, the ENUF–DPD method shows excellent efficiency and scales as O(NlogN)O(NlogN). The ENUF–DPD method is further validated by investigating the effects of charge fraction of polyelectrolyte, ionic strength and counterion valency of added salts on polyelectrolyte conformations. The simulations in this paper, together with a separately published work of dendrimer–membrane complexes, show that the ENUF–DPD method is very robust and can be used to study charged complex systems at mesoscopic level.

Keyword
Ewald summation method, Dissipative particle dynamics, Fast Fourier transform technique, Polyelectrolyte conformation, Dendrimer–membrane complexes
National Category
Physical Chemistry
Research subject
Physical Chemistry
Identifiers
urn:nbn:se:su:diva-92703 (URN)10.1016/j.jcp.2012.09.023 (DOI)000314153900035 ()
Available from: 2013-08-15 Created: 2013-08-15 Last updated: 2017-12-06Bibliographically approved
2. Specific binding structures of dendrimers on lipid bilayer membranes
Open this publication in new window or tab >>Specific binding structures of dendrimers on lipid bilayer membranes
2012 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 14, no 23, 8348-8359 p.Article in journal (Refereed) Published
Abstract [en]

Dissipative particle dynamics simulations are used to study the specific binding structures of polyamidoamine (PAMAM) dendrimers on amphiphilic membranes and the permeation mechanisms. Mutually consistent coarse-grained (CG) models both for PAMAM dendrimers and for dimyristoylphosphatidylcholine (DMPC) lipid molecules are constructed. The PAMAM CG model describes correctly the conformational behavior of the dendrimers, and the DMPC CG model can properly give the surface tension of the amphiphilic membrane. A series of systematic simulations is performed to investigate the binding structures of the dendrimers on membranes with varied length of the hydrophobic tails of amphiphiles. The permeability of dendrimers across membranes is enhanced upon increasing the dendrimer size (generation). The length of the hydrophobic tails of amphiphiles in turn affects the dendrimer conformation, as well as the binding structure of the dendrimer-membrane complexes. The negative curvature of the membrane formed in the dendrimer-membrane complexes is related to dendrimer concentration. Higher dendrimer concentration together with increased dendrimer generation is observed to enhance the permeability of dendrimers across the amphiphilic membranes.

National Category
Chemical Sciences
Identifiers
urn:nbn:se:su:diva-79725 (URN)10.1039/c2cp40700k (DOI)000304353600013 ()
Note

AuthorCount:3;

Available from: 2012-09-12 Created: 2012-09-11 Last updated: 2017-12-07Bibliographically approved
3. Multiscale coarse-grained simulations of ionic liquids: comparison of three approaches to derive effectivepotentials
Open this publication in new window or tab >>Multiscale coarse-grained simulations of ionic liquids: comparison of three approaches to derive effectivepotentials
2013 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 15, no 20, 7701-7712 p.Article in journal (Refereed) Published
Abstract [en]

A coarse-grained model, with three sets of effective pair potentials for 1-butyl-3-methylimidazolium hexafluorophosphate ([Bmim][PF6]) ionic liquid, is introduced and used to study the structural and dynamical properties over extended length and time scales. Three sets of effective pair potentials between coarse-grained beads are obtained using the Newton Inversion and the Iterative Boltzmann Inversion methods, respectively, with different treatment of electrostatic interactions. The coarse-grained simulation results are compared systematically with corresponding atomistic simulation results on several thermodynamical and structural quantities together with charge density distributions. In addition, the scattering and dynamical properties are also calculated and compared to both atomistic simulation results and experimental measurements. While all three sets of the effective potentials provide perfect agreement with the atomistic simulation for radial distribution functions, our analysis shows that in coarse-grained simulations, the long-range electrostatic interactions between ionic groups are important and should be treated explicitly to improve the reliability of other simulation results. With explicit incorporation of electrostatic interactions derived from the Newton Inversion, the coarse-grained potentials provide the most consistent description of thermodynamical, scattering and dynamical properties including their temperature dependence as compared to atomistic simulations. We conclude also that the current atomistic force field should be further improved to meet specific requirements for studying the dynamical properties of the [Bmim][PF6] system over a large temperature range.

Keyword
ionic liquid, coarse-graining
National Category
Physical Chemistry
Research subject
Physical Chemistry
Identifiers
urn:nbn:se:su:diva-92705 (URN)10.1039/C3CP44108C (DOI)000318306100036 ()
Available from: 2013-08-15 Created: 2013-08-15 Last updated: 2017-12-06Bibliographically approved
4. Influence of ionic liquid film thickness on ion pair distributionsand orientations at graphene and vacuum interfaces
Open this publication in new window or tab >>Influence of ionic liquid film thickness on ion pair distributionsand orientations at graphene and vacuum interfaces
2013 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 15, no 32, 13559-13569 p.Article in journal (Refereed) Published
Abstract [en]

Microscopic structures, orientational preferences together with mass, number and electron density distributions of 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]) ionic liquid (IL) have been studied on a neutral hydrophobic graphene surface, and at the IL–vacuum interface using atomistic Molecular Dynamics simulations. At the IL–graphene interface, distinct mass, number and electron density distributions are observed oscillating into the bulk region with several compact structural layers. The imidazolium ring of [BMIM] cations lies preferentially flat on the graphene surface, with its methyl and butyl side chains elongated along the graphene surface. At the IL–vacuum interface, however, the distributions of [BMIM][PF6] ion pairs are strongly influenced by the thickness of IL film. With the increase of IL film thickness, the orientations of [BMIM] cations at the IL–vacuum interface change gradually from dominant flat distributions along the graphene surface to orientations where the imidazolium rings are either parallel or perpendicular to the IL–vacuum interface with tilted angles. The outmost layers are populated with alkyl groups and imparted with distinct hydrophobic character. The calculated radial distribution functions suggest that ionic structures of [BMIM][PF6] ion pairs in IL–graphene and IL–vacuum interfacial regions are significantly different from each other and also from that in bulk regions.

Keyword
graphene, ionic liquid
National Category
Physical Chemistry
Research subject
Physical Chemistry
Identifiers
urn:nbn:se:su:diva-92706 (URN)10.1039/C3CP51226F (DOI)000322401600033 ()
Available from: 2013-08-15 Created: 2013-08-15 Last updated: 2017-12-06Bibliographically approved

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