NanoModeler

NanoModeler models and parametrizes monolayer-protected metal nanoparticles at coarse-grained resolution to enable coarse-grained molecular dynamics simulations and the engineering of functional nanoparticles.

Key Features:

• Coarse-Grained Resolution: Operates at a coarse-grained level to enable coarse-grained molecular dynamics (MD) simulations while reducing computational complexity.
• NanoModeler CG variant: Implements the coarse-grained extension for construction and parametrization of monolayer-protected metal NPs.
• Core Shapes and Monolayer Morphologies: Supports eight distinct core shapes and eight monolayer morphologies and can represent systems with up to 800,000 coarse-grained beads.
• Force Field Compatibility: Generates topologies compatible with the Martini force field and can extend parameters to other force fields by parsing custom input.
• Automated Construction and Parametrization: Automates the construction and parametrization of functionalized and monolayer-protected nanoparticles, including functionalized gold NPs and other metals.

Scientific Applications:

• Structural validation: Reproduces experimental structural characteristics of alkylthiolated nanoparticles to validate theoretical models against empirical data.
• Surface phase behavior: Rationalizes brush-to-mushroom phase transitions observed in PEGylated anionic nanoparticles to inform design of surface properties.
• Domain applications: Supports studies in biotechnology, materials science, and energy conversion involving interactions of monolayer-protected NPs with different matrices.

Methodology:

Constructs and parametrizes monolayer-protected metal nanoparticles at coarse-grained resolution, generates Martini-compatible topologies, parses custom input to extend parameters to other force fields, and automates preparation of functionalized gold NPs and other metals.