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Mesoscale Simulations of Polymer Solution Self-Assembly: Selection of Model Parameters within an Implicit Solvent Approximation.

ABSTRACT: Coarse-grained modeling is an outcome of scientific endeavors to address the broad spectrum of time and length scales encountered in polymer systems. However, providing a faithful structural and dynamic characterization/description is challenging for several reasons, particularly in the selection of appropriate model parameters. By using a hybrid particle- and field-based approach with a generalized energy functional expressed in terms of density fields, we explore model parameter spaces over a broad range and map the relation between parameter values with experimentally measurable quantities, such as single-chain scaling exponent, chain density, and interfacial and surface tension. The obtained parameter map allows us to successfully reproduce experimentally observed polymer solution assembly over a wide range of concentrations and solvent qualities. The approach is further applied to simulate structure and shape evolution in emulsified block copolymer droplets where concentration and domain shape change continuously during the process.

SUBMITTER: Park J

PROVIDER: S-EPMC8003785 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature

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Mesoscale Simulations of Polymer Solution Self-Assembly: Selection of Model Parameters within an Implicit Solvent Approximation.

Park Juhae J Ramírez-Hernández Abelardo A Thapar Vikram V Hur Su-Mi SM

Polymers 20210319 6

Coarse-grained modeling is an outcome of scientific endeavors to address the broad spectrum of time and length scales encountered in polymer systems. However, providing a faithful structural and dynamic characterization/description is challenging for several reasons, particularly in the selection of appropriate model parameters. By using a hybrid particle- and field-based approach with a generalized energy functional expressed in terms of density fields, we explore model parameter spaces over a ...[more]

PMID: 33808863

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Project description:Adequate sampling of conformation space remains challenging in atomistic simulations, especially if the solvent is treated explicitly. Implicit-solvent simulations can speed up conformational sampling significantly. We compare the speed of conformational sampling between two commonly used methods of each class: the explicit-solvent particle mesh Ewald (PME) with TIP3P water model and a popular generalized Born (GB) implicit-solvent model, as implemented in the AMBER package. We systematically investigate small (dihedral angle flips in a protein), large (nucleosome tail collapse and DNA unwrapping), and mixed (folding of a miniprotein) conformational changes, with nominal simulation times ranging from nanoseconds to microseconds depending on system size. The speedups in conformational sampling for GB relative to PME simulations, are highly system- and problem-dependent. Where the simulation temperatures for PME and GB are the same, the corresponding speedups are approximately onefold (small conformational changes), between ∼1- and ∼100-fold (large changes), and approximately sevenfold (mixed case). The effects of temperature on speedup and free-energy landscapes, which may differ substantially between the solvent models, are discussed in detail for the case of miniprotein folding. In addition to speeding up conformational sampling, due to algorithmic differences, the implicit solvent model can be computationally faster for small systems or slower for large systems, depending on the number of solute and solvent atoms. For the conformational changes considered here, the combined speedups are approximately twofold, ∼1- to 60-fold, and ∼50-fold, respectively, in the low solvent viscosity regime afforded by the implicit solvent. For all the systems studied, 1) conformational sampling speedup increases as Langevin collision frequency (effective viscosity) decreases; and 2) conformational sampling speedup is mainly due to reduction in solvent viscosity rather than possible differences in free-energy landscapes between the solvent models.

Dataset Information

Mesoscale Simulations of Polymer Solution Self-Assembly: Selection of Model Parameters within an Implicit Solvent Approximation.

Publications

Mesoscale Simulations of Polymer Solution Self-Assembly: Selection of Model Parameters within an Implicit Solvent Approximation.

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