Although minimalist models for patchy attractive particles have revealed powerful design rules for how particle valence directs colloidal assembly, less work has focused on comparably simple models of reversible, network-forming star polymers. Here, we use relative-entropy coarse-graining and simulation results from finer-resolution bead--spring star polymers to generate 5-bead models of dynamic, end-associating four-armed poly(ethylene glycol) macromers. Our results comparing structural correlations, network connectivity, and phase behavior of the coarse- and fine-grained models provide insight into how the accuracy and transferability of the coarse-grained models depend on the state point chosen for coarse-graining. The results also reveal intrinsic trade-offs between reducing degrees of freedom and expanding the range of effective interactions in coarse-graining that impact the total number of pairwise interactions in the resulting model, with implications for its computational efficiency.
Residue-level coarse-grained simulations provide a powerful route for modeling biomolecular condensates over length and time scales that are difficult to access with atomistic molecular dynamics. Coarse-grained models have been shown to reproduce many aspects of equilibrium phase behavior. However, it remains unclear t...
Soundhararajan Gopi, Han-Ling Qin, Robert B. Best et al.· bioRxiv· 1 citation
Establishing quantitative links between molecular-scale chain mechanics and the macroscopic response of polymer networks is critical for the design of high-performance soft materials. Here, we combine theoretical analysis with coarse-grained molecular dynamics simulations to investigate the mechanical behavior of two...
Hai-Bo Chen, Jia-Qi Li, Dong Yan et al.· Macromolecules· 0 citations
CGMas is presented, a multi-agent framework that automates topology construction, equilibration, mapping, potential derivation, and validation from a natural-language specification of the polymer and target resolution.
Coarse-grained (CG) molecular dynamics (MD) simulations offer an efficient route to explore long-time-scale dynamics of knots in proteins and polymers. Despite extensive studies of knots using both atomistic (AA-) and CG-MD simulations, systematic comparisons of how coarse-graining alters knot relaxation mechanisms, in...
S. Sarkar, Mark J. DelloStritto, Michael L. Klein· Journal of Physical Chemistr...· 0 citations
Soft materials linked by reversible covalent or supramolecular bonds form a diverse class of assemblies with promising applications from nanoscience to medicine. Experiments typically probe bulk phase behavior and rheology, but it remains difficult to measure how microscopic bonding kinetics and the mechanics of the co...
Tanner A. Wilcoxson, Tian-Hao Li, Tyla R. Holoman et al.· 0 citations
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