A hybrid nanotube, high-performance, dynamically reconfigurable architecture, NATURE, is provided, and a design optimization flow method and system, NanoMap. A run-time reconfigurable architecture is provided by associating a non-volatile universal memory to each logic element to enable cycle-by-cycle reconfiguration and logic folding, while remaining CMOS compatible. Through logic folding, significant logic density improvement and flexibility in performing area-delay tradeoffs are possible. NanoMap incorporates temporal logic folding during the logic mapping, temporal clustering and placement steps. NanoMap provides for automatic selection of a best folding level, and uses force-direct scheduling to balance resources across folding stages. Mapping can thereby target various optimization objectives and user constraints. A high-density, high-speed carbon nanotube RAM can be implemented as the universal memory, allowing on-chip multi-context configuration storage, enabling fine-grain temporal logic folding, and providing a significant increase in relative logic density.