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lecturemolecularprogramming [2018/12/10 18:34] Nicolas Schabanel |
lecturemolecularprogramming [2020/11/12 18:21] Nicolas Schabanel [Molecular programming: Theory & wet-lab experiments] |
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- | {{ http://perso.ens-lyon.fr/nicolas.schabanel/enseignement/ENS/DNA-bandeau.png?800x0 }} | + | {{ http://perso.ens-lyon.fr/nicolas.schabanel/enseignement/ENS/DNA-bandeau.png?1000x0 }} |
//Research lecture (CR)// | //Research lecture (CR)// | ||
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====== Molecular programming: Theory & wet-lab experiments ====== | ====== Molecular programming: Theory & wet-lab experiments ====== | ||
+ | Lectures will be online until the end of the confinement, please go to: | ||
+ | |||
+ | **[[https://etudes.ens-lyon.fr/course/view.php?id=4557|Molecular programming at the Portail des études]]** | ||
+ | |||
+ | <color red>**First lecture on Monday November 16, 8:00-100:00 (gloups)**</color> | ||
+ | |||
+ | <color purple>Lectures will take place on **Mondays morning (8:00-10:00)** and **Thursdays morning (10:15-12:15)** online, until further notice.</color> | ||
==== Presentation ==== | ==== Presentation ==== | ||
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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, 12/12, 19/12,</color> **<color red>9/1 14:00-16:00 (Final exam)</color>** | ||
+ | * //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]] ]** | ||
+ |