This GNM method can be used by anyone wishing to better understand their structure. Additionally, it can be used to fine tune structures to their desired properties.
In the future, we would wish to provide an automated web service. Users would be able to upload the PDB file for their synthetic DNA structure to our website and get the fluctuation data immediately. They would be able to do this as many times as they wish, until they are satisfied with their structure properties. The web service should work for any synthetic DNA structure so long as a PDB file is provided.
Proposal: Transport Surface
One of the ideas we had was a surface with synthetic DNA structures that would provide a means to move liquids in the nano or pico liter ranges. The inspiration from this comes from both nature and our professor's paper: An engineered anisotropic nanoﬁlm with unidirectional wetting properties.  This paper regards movement of liquids on a micron-scale by using the anisotropic properties of the surface and the energy provided by a random vibration generator. Our idea mimics this but on a smaller scale:
The surface would consist of slanted DNA rods instead of slanted PPX rods. Since it is difficult to slant DNA, we decided to create a DNA box structure that has a slanted top similar to the image below:
The slanted surface would provide interaction for liquid droplets while the flat base provides a sturdy connection to the surface.
Once created, these slanted boxes would be assembled in an ordered fashion such that when the droplet travels past the peak of a box, it would not be able to move back. Self-assembly of these structures can be done by coordinating the DNA sequence of the base of the box to be complementary to a DNA surface. These DNA boxes would, of course, be spread evenly in a 3D plane (2D is depicted here for simplicity). Similar ideas are seen in the paper mentioned before. Here is a schematic of the surface:
While Malvadkar et al. required a vibrational force underneath their surface for the droplet to move, we think that the fluctuation of the DNA would be enough to move the droplet, especially on such a small scale. The requirement for the DNA slanted boxes is that the top of the box be more flexible than the bottom. This will allow the top of the box to fluctuation and push the water droplet along.
We created a structure in NanoEngineer-1 and then calcuated the fluctuations using the methods described in this project. We then imaged it with PyMOL for higher quality images.
Similar to the results seen in this project, warm colors depict high fluctuations while cool colors are for lower fluctuations. The image above shows that only the slanted part of the box has high fluctuation. We hypothesize that because of this unique property, a surface covered with these structure should be able to transport small volumes of liquid.