We will overview the various approaches to the uprising field of Molecular programming where one uses algorithms to design real molecules that processes information algorithmically. We will explore in details the various theoretical models, their complexity and expressiveness, learn how to program them and survey their experimental realizations, in particular how to design algorithmically these molecules for real. We will have you take part to real wet-lab experiments where we will design molecules executing a (simple) program for us and observe the nanoscopic result of their execution (usually only about few 100nm large) thru atomic force microscope (DNA origami) and fluorescence microscopy (DNA circuit). Wet-lab experiments will be conducted in collaboration with the biology & physics departments.
Outline
- DNA as information processing material
- Tile assembly model : Theory & experiments
- Strand displacement circuits: Theory & experiments
- Oritatami, a computational model for co-transcriptional folding: Theory & experiments
- Wetlab experiments: making a DNA origami from scratch, making a DNA strand displacement circuit from scratch
Grading
- The final grade will be the sum of HOMEWORK and EXAM both over 10 points
FINAL_GRADE = HOMEWORK + EXAM - HOMEWORK will be the sum of the grades for a set of 5 tiny exercices to solve from one week to the next
- EXAM = MINI-PROJECT + WRITTEN_EXAM where MINI-PROJECT is graded over 4pts et WRITTEN_EXAM is over 6pts
- MINI-PROJECT will be a mini-project to realize using ENSnano by groups of 3-5 people over about a month
- WRITTEN_EXAM will be a 1h30/2h-written exam at the end of the lecture
This grading system ensures that you will work and train regularly for the final exam and get the best grade possible.
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