http://www.nano-hive.org/index.shtml
Introduction
Nano-Hive is a modular simulator used for modeling the physical world at a nanometer scale. The intended purpose of the simulator is to act as a tool for the study, experimentation, and development of nanotech entities. Nano-Hive is a GPL/LGPL licensed open-source development - you can download and use it for free (see Licensing section for more details and restrictions.)
Nano-Hive can be run stand-alone, or easily integrated to support other applications such as CAD tools. See the Feature List and Software Architecture for a good understanding of what Nano-Hive is and what it has to offer.

odporucam pozriet hlavne tie mpegy tuto:
http://www.nano-hive.org/visualizations.shtml