CG-BigSMILES: Line Notation for Coarse-Grained Models of Polymers

The stochastic nature of polymers poses a challenge for developing machine-readable molecular representations, especially for coarse-grained computational models of materials. BigSMILES, a line notation that represents stochastic graphs, addresses this issue for atomistically resolved structures. Here, BigSMILES is extended to accommodate nonatomic particles, enabling it to represent coarse-grained models of polymers in a manner directly analogous to atomic structures. A new syntax, called coarse-grained BigSMILES (CG-BigSMILES), combines a layer-based annotation with linking to force field files to capture both chemical structures and interacting potentials, providing a complete description of coarse-grained models. The syntax allows optional definition of the mapping between the molecular structure and the coarse-grained “beads”, for both polymers and small molecules, in single- and multicomponent systems. CG-BigSMILES serves as a robust representation that allows researchers to unambiguously index coarse-grained systems in a manner analogous to that of atomistically resolved ones, enabling both types of systems to be integrated in single data structures and associated databases.

Duke Scholars

Author Michael Rubinstein Thomas Lord Department of Mechanical Engineering and Materia ...