Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Systematic coarse-graining of molecular models by the Newton inversion method
Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Physical Chemistry.
Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Physical Chemistry.
Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Physical Chemistry.
Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Physical Chemistry.
2010 (English)In: Faraday discussions (Online), ISSN 1359-6640, E-ISSN 1364-5498, Vol. 144, 43-56 p.Article in journal (Refereed) Published
Abstract [en]

Systematic construction of coarse-grained molecular models from detailed atomistic simulations, and even from ab initio simulations is discussed. Atomistic simulations are first performed to extract structural information about the system, which is then used to determine effective potentials for a coarse-grained model of the same system. The statistical-mechanical equations expressing the canonical properties in terms of potential parameters can be inverted and solved numerically according to the iterative Newton scheme. In our previous applications, known as the Inverse Monte Carlo, radial distribution functions were inverted to reconstruct pair potential, while in a more general approach the targets can be other canonical averages. We have considered several examples of coarse-graining; for the united atom water model we suggest an easy way to overcome the known problem of high pressure. Further, we have developed coarse-grained models for L- and D-prolines, dissolved here in an organic solvent (dimethylsulfoxide), keeping their enantiomeric properties from the corresponding all-atom proline model. Finally, we have revisited the previously developed coarse-grained lipid model based on an updated all-atomic force field. We use this model in large-scale meso-scale simulations demonstrating spontaneous formation of different structures, such as vesicles, micelles, and multi-lamellar structures, depending on thermodynamical conditions.

Place, publisher, year, edition, pages
2010. Vol. 144, 43-56 p.
National Category
Physical Chemistry
Research subject
Physical Chemistry
Identifiers
URN: urn:nbn:se:su:diva-43228DOI: 10.1039/B901511FISI: 000271017100003OAI: oai:DiVA.org:su-43228DiVA: diva2:354814
Available from: 2010-11-26 Created: 2010-10-04 Last updated: 2017-12-12Bibliographically approved
In thesis
1. Multiscale simulations of soft matter: systematic structure-based coarse-graining approach
Open this publication in new window or tab >>Multiscale simulations of soft matter: systematic structure-based coarse-graining approach
2013 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The soft matter field considers a wide class of objects such as liquids, polymers, gels, colloids, liquid crystals and biological macromolecules, which have complex internal structure and conformational flexibility leading to phenomena and properties having multiple spacial and time scales. Existing computer simulation methods are able to cover these scales, but with different resolutions, and ability to link them together performing a multiscale simulation is highly desirable.

The present work addresses systematic multiscaling approach for soft matter studies, using structure-based coarse-graining (CG) methods such as iterative Boltzmann inversion and inverse Monte Carlo. A new software package MagiC implementing these methods is introduced. The software developed for the purpose of effective CG potential derivation is applied for ionic water solution and for water solution of DMPC lipids. A thermodynamic transferability of the obtained potentials is studied.

The effective inter-ionic solvent mediated potentials derived for NaCl successfully reproduce structural properties obtained in explicit solvent simulation, which indicates the perspectives of using the structure-based coarse-graining for studies of ion-DNA and other polyelectrolytes systems. The potentials have temperature dependence, dominated mostly by the electrostatic long-range part which can be described by temperature dependent effective dielectric permittivity, leaving the short-range part of the potential thermodynamically transferable.

For CG simulations of lipids a 10-bead water-free model of dimyristoylphosphatidylcholine is introduced. Four atomistic reference systems, having different lipid/water ratio are used to derive the effective bead-bead potentials, which are used for subsequent coarse-grained simulations of lipid bilayer. A significant influence of lipid/water ratio in the reference system on the properties of the simulated bilayers is noted, however it can be softened by additional angle-bending interactions. At the same time the obtained bilayers have stable structure with correct density profiles. The model provides acceptable agreement between properties of coarse-grained and atomistic bilayer, liquid crystal - gel phase transition with temperature change, as well as realistic self-aggregation behavior, which results in formation of bilayer, bicell or vesicle from a dispersed lipid solution in a large-scale simulation.

Place, publisher, year, edition, pages
Stockholm: Department of Materials and Environmental Chemistry (MMK), Stockholm University, 2013. 62 p.
Keyword
Multiscale modeling, Monte Carlo, Molecular dynamics, ion solution, lipid bilayer, coarse-graining
National Category
Physical Chemistry
Research subject
Physical Chemistry
Identifiers
urn:nbn:se:su:diva-94756 (URN)978-91-7447-755-9 (ISBN)
Public defence
2013-11-14, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 10:00 (English)
Opponent
Supervisors
Note

At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Submitted. 

 

Available from: 2013-10-23 Created: 2013-10-11 Last updated: 2013-12-17Bibliographically approved

Open Access in DiVA

fulltext(1630 kB)912 downloads
File information
File name FULLTEXT01.pdfFile size 1630 kBChecksum SHA-512
2ad7cf8addefc388ec118a24ad512149070aac2d905870572756a0e1a4d00cb3c6e40c5ef5e59c11a4748bef20dd41b1a46b4193f72ee2d185ae5586b7008f87
Type fulltextMimetype application/pdf

Other links

Publisher's full text

Search in DiVA

By author/editor
Lyubartsev, AlexanderMirzoev, AlexanderChen, Li JunLaaksonen, Aatto
By organisation
Physical Chemistry
In the same journal
Faraday discussions (Online)
Physical Chemistry

Search outside of DiVA

GoogleGoogle Scholar
Total: 912 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

doi
urn-nbn

Altmetric score

doi
urn-nbn
Total: 747 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf