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lecturemolecularprogramming [2019/07/08 10:41]
Nicolas Schabanel [Schedule]
lecturemolecularprogramming [2020/01/04 15:12] (current)
Nicolas Schabanel [Past Lectures summary]
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 ==== Schedule ==== ==== Schedule ====
-  * **Thursdays morning 8:45-10:15 (15min break) ​10:30-12:00** +  * **Thursdays morning ​(Room B1, ENS de Lyon Monod 4th floor)**  
-  * Dates: ​**17/10, 24/10, 7/11, 14/11, 21/11, 28/11 (experiments),​ 5/12, 12/12 (experiments), 19/12, 9/1**+    * 8:45-10:45: Lecture 
 +    * //<color gray> ​(15 min break)</​color>//​ 
 +    * 11:00-12:00: Exercises session 
 +  * Dates: ​<color gray>17/10, 24/10, 7/11 //(learn how to design DNA orgami)//, 14/11 //(vote for the origami to order for lab experiment)//​, 21/11, 28/11 (wetlab ​experiments),​ 5/12, 12/12, 19/12,</​color>​ **<color red>9/1 14:00-16:00 (Final exam)</​color>​**
   * //No prior experience on experiments required//   * //No prior experience on experiments required//
   ​   ​
 +==== Internship proposals ====
 +  * :!: **__2020 M2 Internship proposal:__ [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​stage/​2020_M2_Internship.pdf|DNA computing: Theory, Models and wet lab experiments]]**
 ==== Related resources ==== ==== Related resources ====
   * [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​]]   * [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​]]
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   * [[https://​dna.hamilton.ie/​woods/​]]   * [[https://​dna.hamilton.ie/​woods/​]]
  
 +==== Past Lectures summary ====
  
 +**Lecture 9 (2019.12.19 - Last): Oritatami Shapes & Strand displacement boolean circuits**
 +  * **Oritatami:​ building shapes** [ [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​enseignement/​M2IF/​2019-2020/​Lecture9A.pdf|Slides]] ]
 +    * The problem
 +    * Some impossible shapes
 +    * Scaling schemes
 +    * Algorithm for scales //​B//<​sub>//​n//​≥3</​sub>​
 +    * Filling a pseudo-hexagon
 +    * Bead type set for tight Oritatami systems
 +    * Algorithm for scales //​A//<​sub>//​n//​≥5</​sub>​
 +    * Algorithm for scale //​A//<​sub>​4</​sub>​
 +    * Algorithm for scale //​A//<​sub>​3</​sub>​
 +    * Time anomalies and how to fix them
 +
 +  * **Strand displacement boolean circuits** [ [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​enseignement/​M2IF/​2019-2020/​Lecture9B.pdf|Slides]] ]
 +    * DNA Strand displacement mechanism
 +    * Some basic of thermodynamics [ [[https://​www.irif.fr/​~nschaban/​M2IF/​Lecture9C.pdf|Slides]] ]
 +    * Reading with fluophore
 +    * Dealing with leaks
 +    * Double long domain [ [[https://​www.irif.fr/​~nschaban/​M2IF/​Lecture9D.pdf|Slides]] ]
 +
 +**Lecture 8 (2019.12.12):​ Oritatami: A computational model for co-transcriptional folding** [ [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​enseignement/​M2IF/​2019-2020/​Lecture8A.pdf|Slides A]] | [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​enseignement/​M2IF/​2019-2020/​Lecture8B.pdf|Slides B]] ]
 +  * RNA Origami experiments
 +  * Oritatami model
 +  * A binary counter
 +  * Proving the correctness of the folding
 +  * Tag system and Oritatami simulating Turing machine efficiently
 +  * An Oritatami system simulating any Cellular Automaton
 +  ​
 +  * **Exercise sessions [ [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​enseignement/​M2IF/​2019-2020/​HW4.pdf|HW4]] | [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​enseignement/​M2IF/​2019-2020/​HW4-SOL.pdf|Solutions]] ]**
 +      - Window movie lemma :!:
 +      - Oritatami
 +
 +**Lecture 7 (2019.12.05) **
 +  * L'an 01: [ [[http://​dl.free.fr/​jrOXDv8bP|mkv]] | //passwd: an01// ]
 +
 +**Lecture 6 (2019.11.28):​ Wetlab Experiments**
 +  * Making an Origami [ [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​enseignement/​MPRI/​2019-2020/​WL1.pdf|Instructions]] ]
 +
 +**Lecture 5 (2019.11.21):​ Intrinsic universality in tile assembly** [ [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​enseignement/​MPRI/​2019-2020/​Lecture3A.pdf|Slides]] ]
 +    * Intrinsic universality at T°2
 +    * The supercell, the probes
 +    * One (polygonal) tile is enough
 +
 +**Lecture 4 (2019.11.14):​ An experimental realisation of a universal computer (II)** [ [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​enseignement/​MPRI/​2019-2020/​Lecture2B.pdf|Slides]] ]
 +    * Examples of nanotube circuits
 +    * A 6-bits Turing universal nanotube circuit
 +    * Minimizing errors with proof-reading tiles
 +    * Counting the glues
 +    * Sequence design
 +    * Experiment results
 +
 +**Lecture 3 (2019.11.07):​ **
 +  * Useful stuff to install cadnano:
 +    * **Maya 2015**:
 +      * Linux: [[http://​dl.free.fr/​qySF9Q3Eh|http://​dl.free.fr/​qySF9Q3Eh]]
 +      * MacOS X: [[http://​dl.free.fr/​vLUy5QlY9|http://​dl.free.fr/​vLUy5QlY9]]
 +      * Windows: [[http://​dl.free.fr/​nzL3MS15h|(1) http://​dl.free.fr/​nzL3MS15h]] [[http://​dl.free.fr/​hHQDyYA9A|(2) http://​dl.free.fr/​hHQDyYA9A]]
 +    * **Cadnano 2.2** for Maya 2015 (All platforms): [[http://​dl.free.fr/​iBgfRXG07|http://​dl.free.fr/​iBgfRXG07]]
 +    * **Installation instructions**:​ [[https://​cadnano.org/​osx-installation.html|MacOS X]] [[https://​cadnano.org/​windows-installation.html|Windows]] [[https://​cadnano.org/​license.html#​download|Other]]
 +  * **standalone version for older MacOS X,** you can try to install the all-in-one package for cadnano 2.2: [[http://​dl.free.fr/​kN2MHDhPx|cadnano2.2.pkg.zip]] (try this first!)
 +  ​
 +  * **Exercise sessions [ [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​enseignement/​M2IF/​2019-2020/​HW3.pdf|HW3]] ]**
 +      - Making a DNA Origami
 +
 +**Lecture 2 (2019.10.24):​ Universality in assembly Model (I): Theory and experiment**
 +  * **Universality in assembly Model (I) [ [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​enseignement/​MPRI/​2019-2020/​Lecture2A.pdf|Slides]] ]**
 +    * Simulating a Turing machine at temperature T°=2 in aTAM
 +    * Optimal hardcoding of a binary string at T°=2 in aTAM
 +    * Simulating a Turing machine at temperature T°=1 in aTAM in 3D
 +  * **An experimental realisation of a universal computer (I) [ [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​enseignement/​MPRI/​2019-2020/​Lecture2B.pdf|Slides]] ]**
 +    * Single stranded tile nanotubes
 +    * Atomic Force Microscopy (AFM)
 +    * Marking 0s and 1s using biotin-streptavidin
 +    * kTAM kinetic assembly model
 +    * Error correction using proof-reading tiles
 +    * DNA nanotube circuit model 
 +  * **Exercise sessions [ [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​enseignement/​M2IF/​2019-2020/​HW2.pdf|HW2]] | [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​enseignement/​M2IF/​2019-2020/​HW2-SOL.pdf|Solutions]] ]**
 +    - Assembly time = O(rank of the produced shape) (from HW1)
 +    - Exponential random variables and kTAM implementation
 +    - Triangle tile assembly
 +    - :!: Tileset for simulating cellular automata **//(HW2: return your solution by email on or before Thursday Nov 7 at noon)//​** ​
 +    - Probabilistic simulation of Turing Machine at T°=1 in 2D
 +
 +**Lecture 1 (2019.10.17):​ Introduction to DNA programming & Tile Assembly Systems [ [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​enseignement/​M2IF/​2019-2020/​Lecture1.pdf|Slides]] ] **
 +  * Introduction to DNA programming & overview of the field
 +  * Abstract tile assembly model (aTAM):
 +    * Definition
 +    * Minimizing the assembly time
 +  * **Exercise sessions [ [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​enseignement/​M2IF/​2019-2020/​HW1.pdf|HW1]] |  [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​enseignement/​M2IF/​2019-2020/​HW1-SOL.pdf|Solutions]] ​ ]**
 +