Wenduo Chen

Tumbling and tank-treading dynamics of individual ring polymers in shear flow

The dynamics of individual ring polymers in a shear flow is studied by a hybrid mesoscale simulation approach. New insight into the dynamics of ring polymers is provided: ring polymers exhibit both tumbling and tank-treading motions. A novel angle autocorrelation function is proposed to analyze the tank-treading motion that usually coexists with tumbling and may be applied to other highly deformable soft objects such as vesicles. The shear dependence of the average gyration tensor, the orientation angle, the tumbling and the tank-treading frequencies is determined quantitatively. The simulations also reveal that the existence of the tank-treading motion apparently increases the intrinsic viscosity of ring polymers under shear flow.

Diffusion behavior of polyelectrolytes in dilute solution：coupling effects of hydrodynamic and Coulomb interactions

The diffusion behavior of polyelectrolytes in dilute salt-free solution is studied through a hybrid mesoscale simulation technique that combines the molecular dynamics method and the multiparticle collision dynamics approach. To elucidate the effects of hydrodynamic interactions (HI), we compare results for hydrodynamic and random solvents. When HI are taken into account, we find that the chain diffusivity decreases initially and then increases gradually with the increasing strength of the Coulomb interaction. By contrast, when HI are switched off, the electrostatic-dependent diffusivity shows three distinct regions, and a plateau of approximately constant diffusivity manifests between two decreasing regions. The findings reveal that the dynamics of polyelectrolytes in dilute solution depend on the coupling effects of hydrodynamic and Coulomb interactions, and that these dynamics can be understood by considering the conformational changes of chains, the counterion condensation, and the dynamics of counterions.

GPU-Accelerated Molecular Dynamics Simulation to Study Liquid Crystal Phase Transition Using Coarse-Grained Gay-Berne Anisotropic Potential.

Gay-Berne (GB) potential is regarded as an accurate model in the simulation of anisotropic particles, especially for liquid crystal (LC) mesogens. However, its computational complexity leads to an extremely time-consuming process for large systems. Here, we developed a GPU-accelerated molecular dynamics (MD) simulation with coarse-grained GB potential implemented in GALAMOST package to investigate the LC phase transitions for mesogens in small molecules, main-chain or side-chain polymers. For identical mesogens in three different molecules, on cooling from fully isotropic melts, the small molecules form a single-domain smectic-B phase, while the main-chain LC polymers prefer a single-domain nematic phase as a result of connective restraints in neighboring mesogens. The phase transition of side-chain LC polymers undergoes a two-step process: nucleation of nematic islands and formation of multi-domain nematic texture. The particular behavior originates in the fact that the rotational orientation of the mesogenes is hindered by the polymer backbones. Both the global distribution and the local orientation of mesogens are critical for the phase transition of anisotropic particles. Furthermore, compared with the MD simulation in LAMMPS, our GPU-accelerated code is about 4 times faster than the GPU version of LAMMPS and at least 200 times faster than the CPU version of LAMMPS. This study clearly shows that GPU-accelerated MD simulation with GB potential in GALAMOST can efficiently handle systems with anisotropic particles and interactions, and accurately explore phase differences originated from molecular structures.

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

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.

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.