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NanoCap is a generic application for the construction of low energy fullerene and capped nanotube structures. It provides an ideal tool to accompany the study of finite carbon molecules using computer simulation. The implementation involves a standalone application which includes a GUI and allows for dynamic visual inspection through 3D rendering. In addition, the NanoCap core libraries can be used in custom Python scripts that enabled the user to produce structures in bulk or to include the...

Smoldyn is a computer program for simulating reactions and diffusion at a mesoscopic size scale. This scale lies between the more traditional microscopic size scale, in which all or most atoms are considered.

The C Protein Folding Library is a minimalistic, high-performance modular library of C functions and data structures for computing folding simulations of proteins on a wide variety of computer hardware.