Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
lecturemolecularprogramming [2019/10/25 16:48]
Nicolas Schabanel [Past Lectures summary]
lecturemolecularprogramming [2023/11/14 15:33] (current)
Nicolas Schabanel [Tentative schedule]
Line 5: Line 5:
  
 ====== Molecular programming:​ Theory & wet-lab experiments ====== ====== Molecular programming:​ Theory & wet-lab experiments ======
 +
 +For 2023-24, lectures will take place on **Tuesdays** at **15:​45-17:​45** and **Fridays** at **13:​30-15:​30.**
 +
 +<color red>​**First lecture on Tuesday September 19th, 2023 at 15:​45-17:​45**</​color>​
  
 ==== Presentation ==== ==== Presentation ====
Line 17: Line 21:
   * Wetlab experiments:​ making a DNA origami from scratch, making a DNA strand displacement circuit from scratch   * Wetlab experiments:​ making a DNA origami from scratch, making a DNA strand displacement circuit from scratch
  
-==== Schedule ​==== +==== Grading ​==== 
-  * **Thursdays morning (Room B1ENS de Lyon Monod 4th floor)**  +  * The final grade will be the sum of HOMEWORK and EXAM both over 10 points \\ FINAL_GRADE = HOMEWORK + EXAM 
-    8:45-10:45: Lecture +  ​HOMEWORK will be the sum of the grades for a set of 5 tiny exercices to solve from one week to the next 
-    * //<color gray> ​(15 min break)</​color>//​ +  ​EXAM = MINI-PROJECT + WRITTEN_EXAM where MINI-PROJECT is graded over 4pts et WRITTEN_EXAM is over 6pts 
-    11:00-12:00Exercises session +  * MINI-PROJECT will be a mini-project to realize using ENSnano by groups of 3-5 people over about a month 
-  * Dates: **<color gray>​17/​10,</​color>​ 24/10, 7/11, 14/11, 21/11, 28/11** (wetlab ​experiments)**5/12, 12/12** (wetlab experiments)**19/129/1** +  * WRITTEN_EXAM will be a 1h30/​2h-written exam at the end of the lecture 
-  * //No prior experience on experiments required// +This grading system ensures that you will work and train regularly for the final exam and get the best grade possible. 
-  ​+ 
 +==== Tentative schedule ==== 
 +<color purple>​**Lectures start on Tuesday Sep 192023 at 15:45**</​color>​ 
 + 
 +  ​<color gray>Tue 09.19 15:45 Lecture 1/16 Introduction to molecular programming</​color>​ [ [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​enseignement/​M2IF/​2023/​lecture1-intro.pdf|slides]] | [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​enseignement/​M2IF/​2023/​HW1.pdf| HW1]] | [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​enseignement/​M2IF/​2023/​HW1-SOL.pdf|Solutions]] ] \\ 
 +  * <color gray>Fri 09.22 13:30 Lecture ​2/16 - aTAM: Tile assembly systems </​color>​\\ 
 +  <color gray>Tue 09.26 15:45 Lecture 3/16 - Universality in aTAM </color> [ [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​enseignement/​M2IF/​2023/​lecture2-universality.pdf|slides]] ] \\ 
 +  * <color gray>Fri 09.29 13:30 Lecture 4/16 - How do we make DNA origami </​color>​ [ [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​enseignement/​M2IF/​2023/​lecture4-origami.pdf|slides]] ] \\ 
 +  * <color gray>Tue 10.03 15:45 Lecture 5/16 - Experimental realization of a universal computer with DNA nanotubes ​</​color> ​[ [[http://perso.ens-lyon.fr/​nicolas.schabanel/​enseignement/​M2IF/​2023/​lecture3-110.pdf|slides]] ] \\ 
 +  <color gray>Fri 10.06 13:30 Lecture 6/16 Intrinsic universality in aTAM </​color>​ [ [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​enseignement/​M2IF/​2023/​lecture5-intrinsic.pdf|slides]] | [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​enseignement/​M2IF/​2023/​HW2.pdf| HW2]] | [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​enseignement/​M2IF/​2023/​HW2-SOL.pdf|Solutions]] ] \\ 
 +  * <color gray>Tue 10.10 15:45 Lecture 7/16 - Oritatami </​color> ​ [ [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​enseignement/​M2IF/​2023/​lecture6-oritatami.pdf|slides]] | [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​enseignement/​M2IF/​2023/​HW3.pdf| HW3]] | [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​enseignement/​M2IF/​2023/​HW3-SOL.pdf|Solutions]] ] \\ 
 +  ​<color gray>Fri 10.13 13:30 Lecture 8/16 - Oritatami simulates Turedo</​color>​\\ 
 +  ​* <color gray>Tue 10.17 15:45 Lecture 9/16 - Universality in Turedos [ [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​enseignement/​M2IF/​2023/​lecture7-turedos.pdf|slides]] | [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​enseignement/​M2IF/​2023/​lecture7-turedos-article.pdf|article]]]</​color>​\\ 
 +  * <color gray>​Fri ​10.20 13:30 Lecture 10/16 - Strand displacements and DNA Boolean circuits [ [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​enseignement/​M2IF/​2023/​lecture8-strand-displacement.pdf|slides]] ] </​color>​\\ 
 +  * <color gray>Tue 10.24 15:45 Lecture 11/16 - PEN toolbox [ [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​enseignement/​M2IF/​2023/​lecture9-pentoolbox.pdf|slides]] | [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​enseignement/​M2IF/​2023/​lecture9-pentoolbox.mp4|Yannick Rondelez'​s talk video]] | [[https://​blogs.ed.ac.uk/​dnananotechwebinars/​|DNA in action webinar]] ] </​color>​\\ 
 +  * <color red>​Fri ​10.27 13:30 Lecture 12/16: Mini-project presentation<​/color> [ [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​enseignement/​M2IF/​2023/​HW4.pdf|HW4]] ​ | [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​enseignement/​M2IF/​2023/​HW4-SOL.pdf|Solutions]] | [[https://​www.youtube.com/​watch?​v=1wBYPjkGRdo|pistol shrimp in action]] ]\\ 
 +  * <color gray>//​Vacation 10.30-11.03//</​color>​ \\ 
 +  * <color gray>​Tue ​11.07 :!: 10:15 (exceptionally) :!: Lecture 13/16</​color>​\\ 
 +  * <color gray>​Fri ​11.10 13:30 Lecture 14/16 - Final written exam</​color>​\\ 
 +  ​* **Tue 11.14 15:45 Lecture 15/16 - Lab experiments ​1/2: mixing and cooking <color red>RDV DANS LE HALL D'​ENTREE COTE ENSEIGNEMENT à 15:​45</​color>​ (Salle TP Bio + LBMC)**\\ 
 +  * **Fri 11.17 13:30 Lecture 16/16 - Lab experiments 2/2: AFM imaging (salle 027 & AFM au sous-sol en face du foyer) ​**  
 + 
 +==== Mini-projects ​(Due on Fri Oct 27==== 
 + 
 +<color purple>:​!:​ We are asked to address one of the three questions bellow in **groups of 3-5 persons.** **A short report will be returned** (at most 4 pages including illustrations). **A short presentation will be given by each group on Friday Oct 27**. We will discuss the proposed solutions together during that session. At the end of the session, **we will vote for the best P01-design** to be ordered, assembled and imaged at the end of the lecture.</​color>​ 
 + 
 +  * **[P01] Trapezoid with alpha-stacking:​** Add complementary protuberances and recessions on the ensnano file [[http://perso.ens-lyon.fr/nicolas.schabanel/enseignement/​M2IF/​2023/​trapezoid/​trapezoid.ens|trapezoid.ens]] (the xover positions are not optimized). How to make sure that the pieces get together upright (and make a circle) and not upside down (which would assemble a line)? 
 +  ​* **[P02] Parametrized shape:** Propose a framework that allows a parametrized definition of a multi-component flat 2D shape and propose an algorithm that solves the constraints (assuming a scaffold length) and positions the corresponding helices in ENSnano (beware that the scaffold must be routed within every helices). What kind of shapes can your algorithm solve? Show an execution of your algorithm on a small representative example. (no implementation asked) 
 +  * **[P03] Adapting helices parameters:​** you are given a shape that is supposed to assemble into a lattice (as for the P01-trapezoid),​ some helices are identified as "​identical"​ as they are supposed to click one into the other. Propose a data structure and an algorithm that adjust the helices parameters (roll, rise, helicity) so that each pair of helices marked as identical matches. What kind of constraints can your algorithm solve? Show an execution of your algorithm on a small representative example. (no implementation asked) ​   
 +==== Internship proposals ==== 
 +  * :!: **__2024 M2 Internship proposal:__ [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​stage/​2021_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/​]]
Line 32: Line 66:
   * [[https://​dna.hamilton.ie/​woods/​]]   * [[https://​dna.hamilton.ie/​woods/​]]
  
-==== Past Lectures ​summary ====+==== Previous edition (2019) 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]] ]** 
 +      - 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** **Lecture 2 (2019.10.24):​ Universality in assembly Model (I): Theory and experiment**
Line 58: Line 156:
     * Definition     * Definition
     * Minimizing the assembly time     * Minimizing the assembly time
-  * **Exercise sessions [ [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​enseignement/​M2IF/​2019-2020/​HW1.pdf|HW1]] ​ ]** +  * **Exercise sessions [ [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​enseignement/​M2IF/​2019-2020/​HW1.pdf|HW1]] ]** 
-    - Guess the assembly 1 +   ​
-    - Guess the assembly 2 +
-    - :!: A binary counter  +
-    - Assembly time = O(rank of the produced shape) +
-    - Staged self-assembly +