Nanopolysaccharide Builder: A User-Friendly Tool for Atomistic Models of Polysaccharide-Based Nanostructures

Area of Science:

• Materials Science
• Biotechnology
• Computational Chemistry

Background:

• Polysaccharides like cellulose, chitin, and chitosan are fundamental biopolymers with diverse applications.
• Understanding their nanostructure is crucial for developing advanced materials and biotechnologies.
• Existing tools may lack the flexibility to model complex polysaccharide architectures.

Purpose of the Study:

• To introduce Nanopolysaccharide Builder (NPB), a novel software for constructing polysaccharide nanostructures.
• To provide a user-friendly platform for generating cellulose, chitin, and chitosan-based nanostructures with customizable properties.
• To facilitate the creation of large-scale bundles mimicking biological systems for advanced research.

Main Methods:

• Development of a graphical user interface (GUI) for intuitive operation.
• Implementation of algorithms to generate polysaccharide allomorphs and bundles from experimental data or user parameters.
• Ensuring compatibility with major molecular dynamics (MD) engines through standard output formats (PDB, PSF, PARM).

Main Results:

• Successful generation of cellulose and chitin allomorphs with tunable biochemical topologies.
• Construction of large polysaccharide bundles replicating natural nanostructures (e.g., plant cell walls, arthropod cuticles).
• Output of atomic coordinates and connectivity files compatible with leading MD simulation software.

Conclusions:

• NPB offers a powerful and accessible tool for atomic-scale modeling of polysaccharide nanostructures.
• The software supports research in areas such as sustainable chemistry, biomass utilization, and biological material science.
• NPB is expected to accelerate AI-guided research in understanding polysaccharide evolution in various biological contexts.