Parisian Master of Research in Computer Science
Master Parisien de Recherche en Informatique (MPRI)

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cours:c-2-11-1 [2019/10/11 08:22]
schabanel [Approximation Algorithms& Molecular Algorithms(2019/2020, 8x3h, 3 ECTS)Wednesdays 8:45-11:45 Room SG1014]
cours:c-2-11-1 [2019/10/21 15:48] (current)
schabanel [Approximation Algorithms& Molecular Algorithms(2019/2020, 8x3h, 3 ECTS)Wednesdays 8:45-11:45 Room SG1014]
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 ** <color gray>Molecular programming</color> ** ** <color gray>Molecular programming</color> **
   * <color gray>Lecture 5: Wed 9 OCT //Molecular algorithms 1/4//</color>   * <color gray>Lecture 5: Wed 9 OCT //Molecular algorithms 1/4//</color>
-  * Lecture 6: Wed 16 OCT //Molecular algorithms 2/4//+  * <color gray>Lecture 6: Wed 16 OCT //Molecular algorithms 2/4//</color>
   * Lecture 7: Wed 23 OCT //Molecular algorithms 3/4//   * Lecture 7: Wed 23 OCT //Molecular algorithms 3/4//
   * <color gray>// No lecture on Wed 30 OCT //</color>   * <color gray>// No lecture on Wed 30 OCT //</color>
   * Lecture 8: Wed 6 NOV //Molecular algorithms 4/4//   * Lecture 8: Wed 6 NOV //Molecular algorithms 4/4//
 ** <color gray>Final exam</color> ** ** <color gray>Final exam</color> **
-  * <color gray>// No lecture on Wed 13 OCT //</color> +  * <color gray>// No lecture on Wed 13 and 20 OCT //</color> 
-  * <color purple>**Final Exam: Wed 20 or 27 NOV**</color>+  * <color red>**Final Exam: Wed 27 NOV 8:45-11:45**</color>
  
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 ==== Course Summary 2019-20: Molecular programming  (Lectures 5-8) ==== ==== Course Summary 2019-20: Molecular programming  (Lectures 5-8) ====
  
-**Lecture 5: Introduction to DNA programming & Tile Assembly Systems [ [[http://perso.ens-lyon.fr/nicolas.schabanel/enseignement/MPRI/2019-2020/Lecture1.pdf|Slides]] ]**+**Lecture 6 (2019.10.16): 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 nantubes 
 +    * Atomic Force Microscopy (AFM) 
 +    * Marking 0s and 1s using biotin-ptreptavidin 
 +    * kTAM cinetic assembly model 
 +    * Error correction using proof-reading tiles 
 +    * DNA nanotube circuit model  
 +  * **Exercise sessions [ [[http://perso.ens-lyon.fr/nicolas.schabanel/enseignement/MPRI/2019-2020/HW2.pdf|HW2]] ]** 
 +    - Staged self-assembly (from HW1) 
 +    - Exponential random variables and kTAM implementation 
 +    - :!: Tileset for simulating cellular automata  //**return your solution by Wed Oct 23 before 11:45**// 
 +    - Probabilistic simulation of Turing Machine at T°=1 in 2D 
 + 
 +**Lecture 5 (2019.10.09): Introduction to DNA programming & Tile Assembly Systems [ [[http://perso.ens-lyon.fr/nicolas.schabanel/enseignement/MPRI/2019-2020/Lecture1.pdf|Slides]] ]**
   * Introduction to DNA programming & overview of the field   * Introduction to DNA programming & overview of the field
   * Abstract tile assembly systems:   * Abstract tile assembly systems:
     * Definition     * Definition
     * Minimizing the assembly time     * Minimizing the assembly time
-  * **Exercise sessions [ [[http://perso.ens-lyon.fr/nicolas.schabanel/enseignement/MPRI/2019-2020/HW1.pdf|HW1]] ]**+  * **Exercise sessions [ [[http://perso.ens-lyon.fr/nicolas.schabanel/enseignement/MPRI/2019-2020/HW1.pdf|HW1]] | [[http://perso.ens-lyon.fr/nicolas.schabanel/enseignement/MPRI/2019-2020/HW1-SOL.pdf|Solutions]] ]**
     - Guess the assembly 1     - Guess the assembly 1
     - Guess the assembly 2     - Guess the assembly 2
-    - :!: A binary counter //**return your solution by Wed Oct 16 before 11:45**//+    - :!: A binary counter
     - Staged self-assembly     - Staged self-assembly
     - Assembly time = O(rank of the produced shape)     - Assembly time = O(rank of the produced shape)
 
Universités partenaires Université Paris-Diderot
Université Paris-Saclay
ENS Cachan École polytechnique Télécom ParisTech
ENS
Établissements associés Université Pierre-et-Marie-Curie CNRS INRIA CEA