Assembled Structures of Perfluorosulfonic Acid Ionomers Investigated by Anisotropic Modeling and Simulations

Nafion, a classic of perfluorosulfonic acid ionomers, has broad applications in proton conduction, attributed from the unique structures. However, a satisfactory structure model from theoretical calculation and simulation that can match with the well-known experimental observations is still absent. We performed GPU-accelerated molecular dynamics simulations to investigate the assembled structures of Nafion at different water contents based on an anisotropic coarse-grained model equipped with Gay–Berne potential. Accurate parameters for the coarse-grained model are collected by matching energy profiles based on density functional theory calculations. The results show that the hydrophilic phase in Nafion assemblies undergoes a crossover from isolated spherical clusters to interconnected cluster/channel networks with the increase of water content. We found the crystalline domains in polymer matrix and they are suppressed at elevated water content. These microphase-separated structures achieve quantitative agreement with existing experimental observations, including morphologies from electron microscopy and intensity profiles from scattering experiments. This work suggests that accurate consideration of the anisotropy is a key to reveal the formation of unique assembled structures of perfluorosulfonic acid ionomers at different water contents

Conformation and Dynamics of Individual Star in Shear Flow and Comparison with Linear and Ring Polymers

How polymers with different architectures respond to shear stress is a key issue to develop a fundamental understanding of their dynamical behaviors. We investigate the conformation, orientation, dynamics, and rheology of individual star polymers in a simple shear flow by multiparticle collision dynamics integrated with molecular dynamics simulations. Our studies reveal that star polymers present a linear transformation from tumbling to tank-treading-like motions as the number of arms increases. In the transformation region, the flow-induced deformation, orientation, frequency of motions, and rheological properties show universal scaling relationships against the reduced Weissenberg number, independent of the number and the length of arms. Further, we make a comprehensive comparison on the flow-induced behaviors between linear, ring, and star polymers. The results indicate that distinct from linear polymers, star and ring polymers present weaker deformation, orientation change, and shear thinning, either contributed by a dense center or without ends

Conformation and Dynamics of Individual Star in Shear Flow and Comparison with Linear and Ring Polymers

How polymers with different architectures respond to shear stress is a key issue to develop a fundamental understanding of their dynamical behaviors. We investigate the conformation, orientation, dynamics, and rheology of individual star polymers in a simple shear flow by multiparticle collision dynamics integrated with molecular dynamics simulations. Our studies reveal that star polymers present a linear transformation from tumbling to tank-treading-like motions as the number of arms increases. In the transformation region, the flow-induced deformation, orientation, frequency of motions, and rheological properties show universal scaling relationships against the reduced Weissenberg number, independent of the number and the length of arms. Further, we make a comprehensive comparison on the flow-induced behaviors between linear, ring, and star polymers. The results indicate that distinct from linear polymers, star and ring polymers present weaker deformation, orientation change, and shear thinning, either contributed by a dense center or without ends

Conformation and Dynamics of Individual Star in Shear Flow and Comparison with Linear and Ring Polymers

How polymers with different architectures respond to shear stress is a key issue to develop a fundamental understanding of their dynamical behaviors. We investigate the conformation, orientation, dynamics, and rheology of individual star polymers in a simple shear flow by multiparticle collision dynamics integrated with molecular dynamics simulations. Our studies reveal that star polymers present a linear transformation from tumbling to tank-treading-like motions as the number of arms increases. In the transformation region, the flow-induced deformation, orientation, frequency of motions, and rheological properties show universal scaling relationships against the reduced Weissenberg number, independent of the number and the length of arms. Further, we make a comprehensive comparison on the flow-induced behaviors between linear, ring, and star polymers. The results indicate that distinct from linear polymers, star and ring polymers present weaker deformation, orientation change, and shear thinning, either contributed by a dense center or without ends

Conformation and Dynamics of Individual Star in Shear Flow and Comparison with Linear and Ring Polymers

How polymers with different architectures respond to shear stress is a key issue to develop a fundamental understanding of their dynamical behaviors. We investigate the conformation, orientation, dynamics, and rheology of individual star polymers in a simple shear flow by multiparticle collision dynamics integrated with molecular dynamics simulations. Our studies reveal that star polymers present a linear transformation from tumbling to tank-treading-like motions as the number of arms increases. In the transformation region, the flow-induced deformation, orientation, frequency of motions, and rheological properties show universal scaling relationships against the reduced Weissenberg number, independent of the number and the length of arms. Further, we make a comprehensive comparison on the flow-induced behaviors between linear, ring, and star polymers. The results indicate that distinct from linear polymers, star and ring polymers present weaker deformation, orientation change, and shear thinning, either contributed by a dense center or without ends

The average end-to-end distance (<i>R</i>_<i>f</i>) of backbone for MCLCP and SCLCP.

<p>The average end-to-end distance (<i>R</i>_<i>f</i>) of backbone for MCLCP and SCLCP.</p

Structural and SAXS profiles comparison among initial (green), target (blue) and simulation (red) structures for ubiquitin and cytochrome C using experimental target SAXS profiles.

<p>The calculated SAXS profiles are the average of all 1,250 conformations in the last 5 ns of hybrid MD-MC simulations.</p

Sampling efficiency as a function of R₂/R₁ and R₁.

<p>The number of trajectories, the mean of R₂, R₁ and SE are calculated based on 180 trajectories in the backward MD and MD-MC simulations at 370K. Here, R₂ is the sampling range in simulations, R₁ is RMSD between the initial structure and the target structure, SE is the sampling efficiency of a simulation trajectory and the calculated values by Reva’s model are listed in following brackets.</p

Sampling performance of the MD-MC method in five representative trajectories.

<p>The time evolution of RMSD_T for MD-MC (solid line) and MD (dash line), the time evolution of χ_T, as well as 3D structures and SAXS profiles of the initial (I), the target (T) and closest (C) structures for trajectories of Poly-Asn, Poly-Phe, Poly-Pro, Poly-Ala and Poly-Ser are presented.</p

Sampling Enrichment toward Target Structures Using Hybrid Molecular Dynamics-Monte Carlo Simulations

<div><p>Sampling enrichment toward a target state, an analogue of the improvement of sampling efficiency (SE), is critical in both the refinement of protein structures and the generation of near-native structure ensembles for the exploration of structure-function relationships. We developed a hybrid molecular dynamics (MD)-Monte Carlo (MC) approach to enrich the sampling toward the target structures. In this approach, the higher SE is achieved by perturbing the conventional MD simulations with a MC structure-acceptance judgment, which is based on the coincidence degree of small angle x-ray scattering (SAXS) intensity profiles between the simulation structures and the target structure. We found that the hybrid simulations could significantly improve SE by making the top-ranked models much closer to the target structures both in the secondary and tertiary structures. Specifically, for the 20 mono-residue peptides, when the initial structures had the root-mean-squared deviation (RMSD) from the target structure smaller than 7 Å, the hybrid MD-MC simulations afforded, on average, 0.83 Å and 1.73 Å in RMSD closer to the target than the parallel MD simulations at 310K and 370K, respectively. Meanwhile, the average SE values are also increased by 13.2% and 15.7%. The enrichment of sampling becomes more significant when the target states are gradually detectable in the MD-MC simulations in comparison with the parallel MD simulations, and provide >200% improvement in SE. We also performed a test of the hybrid MD-MC approach in the real protein system, the results showed that the SE for 3 out of 5 real proteins are improved. Overall, this work presents an efficient way of utilizing solution SAXS to improve protein structure prediction and refinement, as well as the generation of near native structures for function annotation.</p></div