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Multiscale simulations of soft matter: systematic structure-based coarse-graining approach
Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
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 [en]
Multiscale modeling, Monte Carlo, Molecular dynamics, ion solution, lipid bilayer, coarse-graining
National Category
Physical Chemistry
Research subject
Physical Chemistry
Identifiers
URN: urn:nbn:se:su:diva-94756ISBN: 978-91-7447-755-9 (print)OAI: oai:DiVA.org:su-94756DiVA: diva2:655409
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
List of papers
1. Systematic coarse-graining of molecular models by the Newton inversion method
Open this publication in new window or tab >>Systematic coarse-graining of molecular models by the Newton inversion method
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.

National Category
Physical Chemistry
Research subject
Physical Chemistry
Identifiers
urn:nbn:se:su:diva-43228 (URN)10.1039/B901511F (DOI)000271017100003 ()
Available from: 2010-11-26 Created: 2010-10-04 Last updated: 2017-12-12Bibliographically approved
2. Effective solvent mediated potentials of Na+ and Cl ions in aqueous solution: temperature dependence
Open this publication in new window or tab >>Effective solvent mediated potentials of Na+ and Cl ions in aqueous solution: temperature dependence
2011 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, no 13, 5722-5727 p.Article in journal (Refereed) Published
Abstract [en]

The effective solvent-mediated potentials for Na+ and Cl ions in aqueous solution were calculated in a wide range of temperatures from 0 to 100 °C. The potentials have been determined using the inverse Monte Carlo approach, from the ion–ion radial distribution functions computed in 50 ns molecular dynamics simulations of ions and explicit water molecules. We further separated the effective potentials into a short-range part and an electrostatic long-range part represented by a coulombic potential with some dielectric permittivity. We adjusted the value of the dielectric permittivity to provide the fastest possible decay of the short-range potentials at larger distances. The obtained temperature dependence of the dielectric permittivity follows well the experimental data. We show also that the largest part of the temperature dependence of the effective potentials can be attributed to the temperature-dependent dielectric permittivity.

Keyword
ion solution, Monte Carlo
National Category
Physical Chemistry
Research subject
Physical Chemistry
Identifiers
urn:nbn:se:su:diva-67063 (URN)10.1039/C0CP02397C (DOI)
Projects
VR 2621-2010-5005
Funder
Swedish Research Council
Available from: 2011-12-28 Created: 2011-12-23 Last updated: 2017-12-08Bibliographically approved
3. MagiC: Software Package for Multiscale Modeling
Open this publication in new window or tab >>MagiC: Software Package for Multiscale Modeling
2013 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 9, no 3, 1512-1520 p.Article in journal (Refereed) Published
Abstract [en]

We present software package MagiC, which is designed to perform systematic structure-based coarse graining of molecular models. The effective pairwise potentials between coarse-grained sites of low-resolution molecular models are constructed to reproduce structural distribution functions obtained from the modeling of the system in a high resolution (atomistic) description. The software supports coarse-grained tabulated intramolecular bond and angle interactions, as well as tabulated nonbonded interactions between different site types in the coarse-grained system, with the treatment of long-range electrostatic forces by the Ewald summation. Two methods of effective potential refinement are implemented: iterative Boltzmann inversion and inverse Monte Carlo, the latter accounting for cross-correlations between pair interactions. MagiC uses its own Metropolis Monte Carlo sampling engine, allowing parallel simulation of many copies of the system with subsequent averaging of the properties, which provides fast convergence of the method with nearly linear scaling at parallel execution.

National Category
Physical Chemistry
Research subject
Physical Chemistry
Identifiers
urn:nbn:se:su:diva-89548 (URN)10.1021/ct301019v (DOI)000316168700023 ()
Funder
Swedish Research Council, 70525601
Note

AuthorCount:2;

Available from: 2013-05-02 Created: 2013-04-29 Last updated: 2017-12-06Bibliographically approved
4. Systematic implicit solvent coarse graining of DMPC lipids
Open this publication in new window or tab >>Systematic implicit solvent coarse graining of DMPC lipids
(English)Article in journal (Refereed) Submitted
Abstract [en]

A 10-site coarse-grained implicit solvent model of DMPC phospholipid is developed with effective solvent-mediated potentials derived using the inverse Monte Carlo method. The potentials providing for the coarse-grained model the same site-site RDFs, bond and angle distributions as those computed in atomistic simulations were computed for four different lipid-water molar ratios.It was shown that there is a significant concentration dependence for both effective potentials and properties of lipid bilayers simulated using these potentials. Thus, effective potentials computed at low lipid concentration favour to more condensed and ordered structure of the bilayer with lower average area per lipid, while potentials obtained at higher lipid concentrations provide more fluid-like structure. Introduction of bending angle interaction into coarse-grained model makes effective potentials somewhat less concentration-dependent. The best agreement with the reference data and experiment was achieved using the set of potentials derived from atomistic simulations at 1:30 lipid:water molar ratio providing full hydration of DMPC lipids in bilayer. Despite theoretical limitations of the structure-based approach expressed in state point dependence of the effective potentials, all the resulting potentials provide a stable bilayer structure with correct partitioning of different lipid groups across the bilayer as well as acceptable values of the average lipid area and compressibility. Another important property demonstrated by the model is liquid/gel phase transition observed at lowering the temperature. In addition to bilayer simulations, the model has proven its robustness in modeling of self-aggregation of lipids from randomly dispersed solution to ordered bilayer structures, bicells and vesicles.

National Category
Physical Chemistry
Research subject
Physical Chemistry
Identifiers
urn:nbn:se:su:diva-94762 (URN)
Available from: 2013-10-11 Created: 2013-10-11 Last updated: 2013-10-13Bibliographically approved

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