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# <img src="https://gitlab.tudelft.nl/aj-lab/teaching/raw/master/binder/images/logo.jpg" width="250"> Teaching environment of the [AJ lab](http://cryoem.tudelft.nl) at [TU Delft](http://tudelft.nl)
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## Physical Biology of the Cell 2 (NB2071)
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### Introduction
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This is the starting page for Practical 2 and Practical 6 of the course Physical Biology of the Cell 2.
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### Practical 2 – Biomolecular Interactions and Cooperative Binding
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Launch the virtual learning environment by clicking on the button below.
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[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/git/https%3A%2F%2Fgitlab.tudelft.nl%2Faj-lab%2Fteaching.git/master)
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Navigate to the `binder` folder and then start the file __`pboc2_practical02.ipynb`__ by clicking on it.
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This should open a Jupyter notebook containing your practical assignment.
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### You can find the solutions to this practical in the solutions folder when launching binder.
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### Practical 6 – Molecular Dynamics
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__In this is practical assignment you will learn:__
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* What are the basic concepts of molecular dynamics simulations.
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* How to build a simple molecular dynamics engine with a Verlet integrator.
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* How to run a molecular dynamics simulation with this engine and how to analyse it.
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* How molecular dynamics simulations can be used to model conformational transitions in proteins.
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Launch the virtual learning environment by clicking on the button below.
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[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/git/https%3A%2F%2Fgitlab.tudelft.nl%2Faj-lab%2Fteaching.git/master)
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Navigate to the `binder` folder and then start the file __`pboc2_practical06.ipynb`__ by clicking on it.
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This should open a Jupyter notebook containing your practical assignment.
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The Jupyter Notebook contains code fields such as the one below:
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<img src="https://gitlab.tudelft.nl/aj-lab/teaching/raw/master/binder/images/manual.jpg" width="800;">
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In order to execute these code fields you need to click on the field (which becomes highlighted as above). The order is important, so please work your way through the notebook from the beginning to the end. Also do read the accompanying text - it will explain everything necessary for you to succesfully work through the assignment
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### You can find the solutions to this practical in the solutions folder when launching binder.
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#### References
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This interactive practical uses the following dependencies:
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* [numpy](https://www.numpy.org/)
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* [nglview](http://nglviewer.org/nglview/latest/)
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* [mdanalysis](https://www.mdanalysis.org/)
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* [matplotlib](https://matplotlib.org/)
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The material on this page is distributed as Open Educational Resource (OER) under a [CC-BY-NC-SA](http://creativecommons.org/licenses/by-nc-sa/4.0/) licence.
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You may freely copy, reuse, adapt and distribute the material in any form compliant with this licence.
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<small>© Copyright 2019, Arjen J. Jakobi <a rel="license" href="http://creativecommons.org/licenses/by-nc-sa/4.0/"><b>CC-BY-NC-SA</b></a></small> |
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