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lecturemolecularprogramming [2018/12/10 18:30] Nicolas Schabanel |
lecturemolecularprogramming [2019/12/11 16:26] Nicolas Schabanel [Schedule] |
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+ | {{ http://perso.ens-lyon.fr/nicolas.schabanel/enseignement/ENS/DNA-bandeau.png?1000x0 }} | ||
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//Research lecture (CR)// | //Research lecture (CR)// | ||
- | {{ http://perso.ens-lyon.fr/nicolas.schabanel/enseignement/ENS/DNA-bandeau.png?800x0 }} | ||
====== Molecular programming: Theory & wet-lab experiments ====== | ====== Molecular programming: Theory & wet-lab experiments ====== | ||
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* 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 ==== | ||
+ | * **Thursdays morning (Room B1, ENS de Lyon Monod 4th floor)** | ||
+ | * 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,</color> **12/12, 19/12, 9/1** | ||
+ | * //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 7 (2019.12.05): ** | ||
+ | * L'an 01: [ [[http://dl.free.fr/jrOXDv8bP|mkv]] | //passwd: an01// ] | ||
+ | |||
+ | **Lecture 6 (2019.11.28): Experiments** | ||
+ | |||
+ | **Lecture 5 (2019.11.21): Intrinsic universality in tile assembly** | ||
+ | |||
+ | **Lecture 4 (2019.11.14): An experimental realisation of a universal computer (II)** | ||
+ | |||
+ | **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!) | ||
+ | |||
+ | **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]] ]** | ||
+ | - 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-PSOL.pdf|Partial solutions]] ]** | ||
+ | - Guess the assembly 1 | ||
+ | - Guess the assembly 2 | ||
+ | - :!: A binary counter | ||
+ | - Assembly time = O(rank of the produced shape) | ||
+ | - Staged self-assembly | ||