Jack began working to the exclusion of all else, even forgetting the dinner he had promised Phylicia. But Phylicia didn’t forget Jack, she helped him move to a cheaper apartment and continued to check in with him and even contributed some of her expertise to his research.
He worked for weeks programming and simulating his virus detection idea. When finished he put the resultant software, V-Detect, up on the web site.
Next, he started modifying his old IC software to build his delivery vehicle, d-cages. Research in a corner of science called foldamers (self-assembling molecular folding structures) was helpful with this step.
His approach proposed to use two spherical cages, one inside the other. The outer cage would be covered in virus detectors. Once attached to a virus the cage would exactly mimic the topology of the virus. The synthetic biology tool would then identify the virus-associated protein and create a program for the blocking molecules.
Inside the inner cage DNA snippets (held there so that they could be protected from the identification tools of the outer cage) would be assembled according to the program created by the synthetic biology tool until the blocking molecule was complete. When finished the blocking molecule would be released into the body.
Unlike integrated circuits, his d-cages would self-organize. He would have to add to the software so that the primary structure, the arrangement of atomic composition and chemical bonds needed for the desired result, could be predicted. Then he would add simulation of the self-assembly of the cage in different solvent baths and extract the resulting size parameters.
It was a few more weeks until he first put the software, D-Cages, up on the website provided by the school.
Next, he integrated his software with the ANI cloud expert provided by the university. This consisted mostly of running many design iterations and training the ANI until it could propose, set up and run its own designs. Surprisingly this took more time than anything else.
Finally, with the help of Phylicia, he put up his proposal for the DNA assembly of the blocking molecules. This part of the design was necessarily the sketchiest as Jack had never been able to test any of its ideas.
When finished Jack decided to promote his site. He posted announcements to all the biology magazines that had an online presence and an open blog. Finally, he made the announcement on a biocoder blog page, a page that a lot of the DIY biology community outside academia and some academics frequented.
He hoped that his open software approach would attract researchers with whom he could establish a relationship and maybe encourage them to pursue his complete program. The response was encouraging, especially from the biocoder community, which led to his next problem.
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