Dataset Information

Coarse-Grained Modelling and Temperature Effect on the Morphology of PS-b-PI Copolymer.

ABSTRACT: Spontaneous spatial organization behavior and the aggregate morphology of polystyrene-block-polyisoprene (PS-b-PI) copolymer were investigated. Molecular dynamic (MD) and mesoscopic simulations using the dynamic of mean field density functional theory (DDF) were adopted to investigate the morphology changes exhibited by this block copolymer (BCP). In the mesoscopic simulations, several atoms in repeating units were grouped together into a bead representing styrene or isoprene segments as a coarse-grained model. Inter-bead interactions and essential parameters for mesoscopic models were optimized from MD simulations. Study indicated that morphology alternations can be induced in this system at annealing temperature of 393, 493, and 533 K. From our simulations, lamellar, bicontinuous, and hexagonally packed cylindrical equilibrium morphologies were achieved. Our simulated morphologies agree well with the reported experimental evidence at the selected temperature. The process of aggregate formation and morphology evolution were concretely clarified.

SUBMITTER: Chiangraeng N

PROVIDER: S-EPMC6630459 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature

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Coarse-Grained Modelling and Temperature Effect on the Morphology of PS-<i>b</i>-PI Copolymer.

Chiangraeng Natthiti N Lee Vannajan Sanghiran VS Nimmanpipug Piyarat P

Polymers 20190606 6

Spontaneous spatial organization behavior and the aggregate morphology of polystyrene-block-polyisoprene (PS-b-PI) copolymer were investigated. Molecular dynamic (MD) and mesoscopic simulations using the dynamic of mean field density functional theory (DDF) were adopted to investigate the morphology changes exhibited by this block copolymer (BCP). In the mesoscopic simulations, several atoms in repeating units were grouped together into a bead representing styrene or isoprene segments as a coars ...[more]

PMID: 31174400

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Project description:Coarse-grained (CG) methods for sampling protein conformational space have the potential to increase computational efficiency by reducing the degrees of freedom. The gain in computational efficiency of CG methods often comes at the expense of non-protein like local conformational features. This could cause problems when transitioning to full atom models in a hierarchical framework. Here, a CG potential energy function was validated by applying it to the problem of loop prediction. A novel method to sample the conformational space of backbone atoms was benchmarked using a standard test set consisting of 351 distinct loops. This method used a sequence-independent CG potential energy function representing the protein using [Formula: see text]-carbon positions only and sampling conformations with a Monte Carlo simulated annealing based protocol. Backbone atoms were added using a method previously described and then gradient minimised in the Rosetta force field. Despite the CG potential energy function being sequence-independent, the method performed similarly to methods that explicitly use either fragments of known protein backbones with similar sequences or residue-specific [Formula: see text]/[Formula: see text]-maps to restrict the search space. The method was also able to predict with sub-Angstrom accuracy two out of seven loops from recently solved crystal structures of proteins with low sequence and structure similarity to previously deposited structures in the PDB. The ability to sample realistic loop conformations directly from a potential energy function enables the incorporation of additional geometric restraints and the use of more advanced sampling methods in a way that is not possible to do easily with fragment replacement methods and also enable multi-scale simulations for protein design and protein structure prediction. These restraints could be derived from experimental data or could be design restraints in the case of computational protein design. C++ source code is available for download from http://www.sbg.bio.ic.ac.uk/phyre2/PD2/.

Dataset Information

Coarse-Grained Modelling and Temperature Effect on the Morphology of PS-b-PI Copolymer.

Publications

Coarse-Grained Modelling and Temperature Effect on the Morphology of PS-<i>b</i>-PI Copolymer.

Similar Datasets

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