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Final Project Ideas

I am not very sure about what I want my final project to be. I am alsp not sure what's a reasonable project goal for a semester long project. But the top three projects/ideas that i find exciting

  1. BioFPGA - I did a bunch of VLSI design, advanced Micro-controller design classes, labs for Verilog etc in undergrad. I am interested in the idea that Professor Jacobson discussed in class although I am not sure how the system would be reprogrammable etc.
  1. I have been fascinated by some of the projects in the Molecular Programming Project at Caltech. I am particularly fascinated with molecular systems that learn like - Neural network computation with DNA strand etc. I am not sure what purpose it would serve but It would be fun to make a DNA robot that can carry out tasks like following a path, picking up molecules - delivering them etc.
  1. Another topic I find fun - Optogenetics and light activated proteins. (Not sure if I have any concrete ideas here yet! )

Updates -

1) Algorithmic self-assembly of electronic circuits with DNA tiles - 3) Super computers in a test tube - DNA tiles general purpose combinatorial optimization with neural cellular automata - Cutting stock problem/Combinatorial explosion (Basically you input a combinatorial search problem you want to compute with the tiles and then let the ml/cellular system

Algorithmic Self Assembly

I was reading about algorithmic self assembly of complex geometric structures by Erik Winfree's group at caltech -http://www.dna.caltech.edu/DNAresearch_publications.html. They use DNA tiles with sticky ends to achieve self assembly into complex nanoscale structures

https://vimeo.com/54214122

DNA tiles are also used to compute things like square roots

Ideas- Assembly growths for computing two things in parallel - Square root(2) + 4. Boolean logic in the growth. Maybe slightly relates to cellular automata system where you have to figure out cell level rules/tiles for simulating the growth for computing any complex algorithm. 3D cellular automata for 3D dna structures.

References

Xuncai Zhang, Yanfeng Wang, Zhihua Chen, Jin Xu, andGuangzhao Cui.Arithmetic computation using self-assembly of DNA tiles:subtraction and division.Progress in Natural Science, 19(3):377 – 388, 2009.

Logical computation using algorithmic self-assembly of DNA triple-crossover molecules Chengde Mao, Thomas H. LaBean, John H. Reif & Nadrian C. Seeman