All quality machines must begin with a design. While the question, "who designed the nanomachines that abound in nature?" is outside the scope of this brief treatise, it is clear from modern biochemistry (and other fields) that those machines are indeed made of discrete components such as protein. The design for those components is present in the DNA, as is well known by biotechnologists who make their living through the use of those templates. However, if we wish to design new components that fit together to make functional machines that can help us to cure illness, feed the hungry and colonize space, we need to create some new designs. This can be done with the help of molecular modeling software.
With our recent advancements in computer science we now have a powerful ability to perform otherwise tedious force field and quantum mechanical calculations. Such calculations allow us to determine conformational and electronic properties of single molecules. Furthermore, once the dimensions and electronic properties of several molecules are determined, they can be used as molecular components for designing supramolecular assemblies, otherwise known as nanomachines.
While the electronic properties of single molecules is governed by quantum mechanics instead of classical mechanics, molecules still fit together in ways similar to bricks, 2x4s, steel rods, manifolds, etc. Designing 3 dimensional objects and machines is an art that engineers have been honing for thousands of years before computers could tell us the HOMO and LUMO of a molecule. Now that they can, it is only a matter of time before the designs being made by nanotechnology enthusiasts can actually be built. Nanoscientists around the world are currently busy using combination CAD and Molecular Modeling software to design nanomachines.
