How might one design a nano-machine?
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Trinh Xuan Hoang is currently a postdoc at Penn State University. He is also a researcher at Institute of Physics, Vietnamese Academy of Science and Technology. Dmitry.
Significant advances in laboratory techniques in tailoring and processing materials at the atomic level have resulted in nanotechnology becoming an increasingly mature field. One of the exciting goals of nanotechnology is the design of powerful nano-machines, i.e. functional entities at the nano-scale that work like macro-world machines. A simple nano-machine would be an entity that is able to switch between two distinct conformations under some kind of external perturbation. In fact, molecular switching of various kinds has been the subject of many recent studies.
In our recent paper, my collaborators and I have asked what the basic principles are underlying the design of a nano-machine that is capable of molecular switching. Our starting point is based on the lessons learned from proteins and liquid crystals. Proteins are amazing molecules that are machineries of life. They perform many functions in our organisms (catalysis, transportation of oxygen, participation in the immune system etc. are just a few examples). Proteins are chain molecules built from 20 kinds of amino acids and have well-defined three-dimensional structures. Proteins can undergo a change in conformation upon binding to a substrate.
Liquid crystals are very useful materials for technological applications. The liquid crystal phase opens up between the crystal phase and the liquid phase, and is very sensitive to external perturbations. This very interesting phase of matter arises primarily from the anisotropy of the constituent molecules.
Back to our design problem, assume that we have a set of spheres and a set of rules for the interaction between them. Like in a “lego” system, there are numbers of ways one can build a machine from the spheres. Our goal is to build a machine that can exist in two well-defined geometries and is able to switch between them. Our design is armed with the insights from the behaviour of proteins and liquid crystals. First, like for proteins, we want our machine to be a chain molecule. This can be easily done by tethering the spheres in a linear chain. We consider also side spheres attached to the main chain in a specified direction, mimicking the side chains in proteins. Second, like for liquid crystals, the molecule should have an inherent anisotropy associated with its building blocks. This arises spontaneously in a chain molecule and can be accentuated by making the consecutive spheres overlap. The entity formed by two overlapping spheres has overt uniaxial symmetry instead of the spherical symmetry of each sphere. For simplicity, we use only two kinds of spheres, one for the main chain and the other for the side spheres (see Fig. below).
Fig. 1: Sketch of a chain molecule. The main chain is modeled as a chain of (blue) spheres. The nearest neighbor spheres along the main chain are allowed to overlap with each other thereby overtly introducing uniaxial anisotropy. 
and 
are the tangent and normal vectors assigned to each sphere, 
, except those at the ends of the chain.
Side-spheres (shown in pink) are attached to the main chain in the negative normal direction. The side-spheres are not allowed to overlap with either the main chain spheres or with each other.
By tuning the sphere radii and the range of attraction between the main chain spheres we showed that a machine built of just 30 spheres has an interesting phase diagram with robust ground state conformations such as the single helix and the twin helix. The single helix and twin helix phases exist between the random coil phase and the compact globule phase. Our Monte Carlo simulations showed that this machine/molecule is able to switch between the single helix and the twin helix conformation by thermal fluctuations (see movie).
The main lesson from our paper is that it behaves a designer of nifty machines to consider which phase of matter it occupies. The power of a machine derives from the choice of the appropriate phase. Taking a lesson from nature, we outline how we can exploit the same phase that has been used so successfully by living matter.
Further details and references can be found in our paper:
Jayanth R. Banavar, Marek Cieplak, Trinh X. Hoang, Amos Maritan. First-principles design of nano-machines. PNAS 106, 9601 (2009); arXiv:0904.4037
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