Work

MolPy: A Large Language Model-Friendly Toolkit for Reactive Topology Editing in Polymer Simulations

Year: 2026

Type: article

Abstract: Molecular modeling of synthetic polymers is today increasingly dependent on automation, high-throughput exploration, and the use of a diverse set of simulation tools. However, despite notable progress in molecular simulation methods, the practical infrastructure for constructing, modifying, and parametrizing polymer systems remains fragmented. Here, we launch a toolkit, MolPy, which aims to bridge this gap by providing an extensible and chemically intuitive platform for building polymer systems and orchestrating simulation workflows. The design philosophy emphasizes a clear separation of responsibilities, a stable and inspectable execution model, and a modular architecture that enables flexible extensions. In practice, the framework supports the introduction of new chemical building blocks and bonding schemes that automatically participate in construction, topology generation, and force-field assignment without requiring modification of existing modules. Interoperability with established simulation tools positions MolPy to support streamlined polymer modeling workflows that remain compatible with emerging large language model (LLM)-driven orchestration and other forms of automated pipeline construction.

Source: Journal of Chemical Information and Modeling

DOI: 10.1021/acs.jcim.6c01137

Authors: Jichen Li, Fabian Schwarz, Wentao Guo, Ge Sun, Daniel Brandell

Institutions: Uppsala University, California Institute of Technology, Courant Institute of Mathematical Sciences, New York University

Language: English

Topic: Advanced Physical and Chemical Molecular Interactions

Subfield: Physical and Theoretical Chemistry

Field: Chemistry

Domain: Physical Sciences

Open Access status: hybrid

Estimated APC paid: $4,500