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<!--
Google IO 2012/2013 HTML5 Slide Template
Authors: Eric Bidelman <[email protected]>
Luke Mahé <[email protected]>
URL: https://code.google.com/p/io-2012-slides
-->
<!DOCTYPE html>
<html>
<head>
<title></title>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="chrome=1">
<!--<meta name="viewport" content="width=device-width, initial-scale=1.0, minimum-scale=1.0">-->
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<meta name="apple-mobile-web-app-capable" content="yes">
<link rel="stylesheet" media="all" href="theme/css/default.css">
<link rel="stylesheet" media="only screen and (max-device-width: 480px)" href="theme/css/phone.css">
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<script data-main="js/slides" src="js/require-1.0.8.min.js"></script>
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<style>
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font: 10px sans-serif;
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<body style="opacity: 0">
<script src="http://d3js.org/d3.v2.min.js?2.9.6"></script>
<slides class="layout-widescreen">
<slide class="title-slide segue nobackground">
<aside class="gdbar"><img src="images/log.png"></aside>
<!-- The content of this hgroup is replaced programmatically through the slide_config.json. -->
<hgroup class="auto-fadein">
<h1 data-config-title><!-- populated from slide_config.json --></h1>
<h2 data-config-subtitle><!-- populated from slide_config.json --></h2>
<p data-config-presenter><!-- populated from slide_config.json --></p>
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</slide>
<slide>
<h1 class="black">Agenda</h1><br>
<article class="smaller">
<div style="float:left">
<ul>
<li>Introduction</li>
<li>Why Molecular Dynamics?</li>
<li>MD Basic Process</li>
<li>Classical Mechnics</li>
<li>Interaction Model</li>
<li>Force Field</li>
<li>Integration Algorithm</li>
<li>Boundary Condition</li>
<li>Quantum Mechanics</li>
<li>Simulation</li>
<li>Summary</li>
</ul>
</div>
<div style="float:right" class=iris> </div>
<footer class="source">"All of today's DNA, strung through all the cells of the earth, is simply an extension and elaboration of [the] first molecule. - Lewis Thomos.</footer>
</article>
</slide>
<slide>
<h1 class="black">Introduction</h1><br>
<article class="smaller">
<div>
<div style="float:left" width="300px">
<h1>Molecular Dynamics (MD)</h1> <br>
<ul>
<li> Simulation Technique</li>
<li> Dynamic motion of a group of particles (e.g. atoms) </li>
<li> Solving the Newton's equation.</li>
<img style="float:center" width="300px" heigth="200px" src="iris_pics/Newtons.png"><br>
</ul>
</div><br><br><br>
<div style="float:right" width="300px">
<img style="float:right; margin-right:80px" width="300px" heigth="200px" src="iris_pics/MD_animation.gif"><br>
</div>
<footer class="source">Source: http://www.cs.berkeley.edu/~bvs/cs267_hw2/animation.gif</footer>
</article>
</slide>
<slide>
<h1 class="black">Why Molecular Dynamics?</h1>
<article class="smaller">
<div>
<div style="float:left" width="300px"><br>
<ul><li>An example of SH2 which is a protein domain involved in protein-protein interactions.</li><br>
<video style="float:center;margin-left: 200px" autoplay loop muted width="600px" heigth="500px" src="iris_pics/Visualizing the Induced Binding of SH2-Phosphopeptide (Supporting Video 1)-V0Z52u8h2es.mp4">
</ul>
</div>
<footer class="source">Source: https://www.youtube.com/watch?v=V0Z52u8h2es</footer>
</article>
</slide>
<slide>
<h1 class="black">MD Basic Process</h1>
<article class="smaller">
<div>
<div style="float:left" width="300px"><br>
<ul><br><br>
<!-- <li>An example of SH2 which is a protein domain involved in protein-protein interactions.</li><br> -->
<img style="float:center;margin-left: 100px" width="800px" heigth="800px" src="iris_pics/BasicProcess.png"><br>
<br>
</ul>
</div>
<footer class="source">Source: https://nanohub.org/resources/7573/download/Martini_L1_Introduction.pdf</footer>
</article>
</slide>
<slide>
<h1 class="black">MD Basic Process</h1>
<article class="smaller">
<div>
<div style="float:left" width="300px"><br>
<ul><br><br>
<!-- <li>An example of SH2 which is a protein domain involved in protein-protein interactions.</li><br> -->
<img style="float:center;margin-left: 100px" width="800px" heigth="800px" src="iris_pics/BasicProcess2.png"><br>
</ul>
</div>
<footer class="source">Source: https://nanohub.org/resources/7573/download/Martini_L1_Introduction.pdf</footer>
</article>
</slide>
<slide>
<h1 class="black">Molecular Modeling</h1>
<article class="smaller">
<div>
<div style="float:left" width="300px"><br>
<ul><li>.</li><br>
<img style="float:left" width="950px" heigth="900px" src="iris_pics/modelling.png">
</ul>
</div>
<footer class="source">Source: https://www.youtube.com/watch?v=V0Z52u8h2es</footer>
</article>
</slide>
<slide>
<h1 class="black">Classical Mechanics</h1>
<article>
<div>
<div style="float:left" width="300px"><br>
<ul><li>Force</li><br>
<img style="float:center;margin-left: 100px" width="200px" heigth="200px" src="iris_pics/F.png"><br>
</ul>
</div>
<footer class="source">Source: http://xray.bmc.uu.se/gerard/embo2001/modval/01.html</footer>
</article>
</slide>
<slide>
<h1 class="black">Classical Mechanics</h1>
<article>
<div>
<div style="float:left" width="300px"><br>
<ul><li>Force ￫ Acceleration</li><br>
<img style="float:center;margin-left: 100px" width="200px" heigth="200px" src="iris_pics/F.png"><br>
<img style="float:center;margin-left: 100px" width="180px" heigth="180px" src="iris_pics/a.png">
</ul>
</div>
<footer class="source">Source: http://xray.bmc.uu.se/gerard/embo2001/modval/01.html</footer>
</article>
</slide>
<slide>
<h1 class="black">Classical Mechanics</h1>
<article>
<div>
<div style="float:left" width="300px"><br>
<ul><li>Force ￫ Acceleration ￫ Velocity</li><br>
<img style="float:center;margin-left: 100px" width="200px" heigth="200px" src="iris_pics/F.png"><br>
<img style="float:center;margin-left: 100px" width="180px" heigth="180px" src="iris_pics/a.png"><br>
<img style="float:center;margin-left: 100px" width="180px" heigth="180px" src="iris_pics/v.png">
</ul>
</div>
<footer class="source">Source: http://xray.bmc.uu.se/gerard/embo2001/modval/01.html</footer>
</article>
</slide>
<slide>
<h1 class="black">Classical Mechanics</h1>
<article>
<div>
<div style="float:left" width="300px"><br>
<ul><li>Force ￫ Acceleration ￫ Velocity ￫ Position</li><br>
<img style="float:center;margin-left: 100px" width="200px" heigth="200px" src="iris_pics/F.png"><br>
<img style="float:center;margin-left: 100px" width="180px" heigth="180px" src="iris_pics/a.png"><br>
<img style="float:center;margin-left: 100px" width="180px" heigth="180px" src="iris_pics/v.png"><br>
</ul>
</div>
<div style="float:right" width="300px"><br><br><br><br><br>
<img style="float:right;margin-right: 150px" width="300px" height="300px" src="iris_pics/position.png">
</div>
<footer class="source">Source: http://xray.bmc.uu.se/gerard/embo2001/modval/01.html</footer>
</article>
</slide>
<slide>
<h1 class="black">Interaction Model</h1>
<article class="smaller">
<div>
<div style="float:left" width="300px"><br>
<ul><li>Interaction force is the spacial derivative of the <b>Potential Energy</b>.</li></ul><br><br>
<img style="float:center;margin-left: 80px" width="850px" heigth="850px" src="iris_pics/Model.png">
</div>
</article>
<footer class="source">Source: http://en.wikipedia.org/wiki/Force_field_(chemistry)#mediaviewer/File:MM_PEF.png</footer>
</slide>
<slide>
<h1 class="black">Interaction Model</h1>
<article class="smaller">
<div>
<div style="float:left" width="300px"><br>
<ul><li>Interaction force is the spacial derivative of the <b>Potential Energy</b>.</li></ul><br><br>
<img style="float:center;margin-left: 80px" width="850px" heigth="850px" src="iris_pics/Model2.png">
</div>
</article>
<footer class="source">Source: http://en.wikipedia.org/wiki/Force_field_(chemistry)#mediaviewer/File:MM_PEF.png</footer>
</slide>
<slide>
<h1 class="black">Force Field</h1>
<article class="smaller">
<div>
<br>
<ul><li>The form and parameters of mathematical functions used to describe the <b>Potential Energy</b> of a system of particles (typically molecules and atoms)</li></ul>
<div style="float:left" width="100%">
<img style="float:center;margin-left: 80px" width="400px" heigth="400px" src="iris_pics/Energy.gif">
</div>
<div style="right">
<img style="float:right;margin-right: 100px" width="250px" heigth="200px" src="iris_pics/length.jpg">
<img style="float:right;margin-right: 100px" width="250px" heigth="200px" src="iris_pics/Angle.png">
</div>
</div>
</article>
<footer class="source">Source: http://en.wikipedia.org/wiki/Force_field_(chemistry)#mediaviewer/File:MM_PEF.png</footer>
</slide>
<slide>
<h1 class="black">Force Field</h1>
<article class="smaller">
<div>
<br>
<ul><li>The form and parameters of mathematical functions used to describe the <b>Potential Energy</b> of a system of particles (typically molecules and atoms)</li></ul>
<div style="float:left" width="100%">
<img style="float:center;margin-left: 80px" width="400px" heigth="400px" src="iris_pics/Energy.gif">
</div>
<div style="right"><br><br><br>
<img style="float:right;margin-right: 120px" width="300px" heigth="300px" src="iris_pics/Torsion.png">
</div>
</div>
</article>
<footer class="source">Source: http://en.wikipedia.org/wiki/Force_field_(chemistry)#mediaviewer/File:MM_PEF.png</footer>
</slide>
<slide>
<h1 class="black">Force Field</h1>
<article class="smaller">
<div>
<div style="float:left" width="100%"><br>
<ul><li>The form and parameters of mathematical functions used to describe the <b>Potential Energy</b> of a system of particles (typically molecules and atoms)</li></ul><br><br>
<img style="float:left;margin-left: 100px" width="300px" heigth="300px" src="iris_pics/nonBond.png">
<img style="float:center" width="250px" heigth="250px" src="iris_pics/Nonbond.jpg"><br>
<!-- <img style="float:right;margin-right: 100px" width="210px" heigth="210px" src="iris_pics/Coulomb_Law.png"> -->
</div>
</article>
<footer class="source">Source: http://en.wikipedia.org/wiki/Force_field_(chemistry)#mediaviewer/File:MM_PEF.png</footer>
</slide>
<slide>
<h1 class="black">Force Field</h1>
<article class="smaller">
<div>
<div style="float:left" width="100%"><br>
<ul><li>The form and parameters of mathematical functions used to describe the <b>Potential Energy</b> of a system of particles (typically molecules and atoms)</li></ul><br><br>
<img style="float:left;margin-left: 100px" width="300px" heigth="300px" src="iris_pics/nonBond.png">
<img style="float:center" width="250px" heigth="250px" src="iris_pics/Nonbond.jpg"><br>
<img style="float:right;margin-right: 100px" width="210px" heigth="210px" src="iris_pics/Coulomb_Law.png">
</div>
</article>
<footer class="source">Source: http://en.wikipedia.org/wiki/Force_field_(chemistry)#mediaviewer/File:MM_PEF.png</footer>
</slide>
<!-- <slide>
<h1 class="black">Effect of Cutoff</h1>
<article class="smaller"><br>
<div style="float:left" width="300px">
<ul><li>Three cutoff scheme : </li></ul>
<ul><ul>
<li>Strict / Druncation</li>
<li>Shift</li>e
<li>SWitch</li></ul></ul>
<img style="float:left;margin-left: 200px" width="700px" heigth="700px" src="iris_pics/cutoff.png">
</div><br>
</article>
<footer class="source">Source: http://en.wikipedia.org/wiki/Force_field_(chemistry)#mediaviewer/File:MM_PEF.png</footer>
</slide> -->
<slide>
<h1 class="black">Optimization Techniques</h1>
<article class="smaller"><br><br>
<div style="float:center" width="300px"><br>
<img style="float:left;margin-left: 150px" width="500px" heigth="500px" src="iris_pics/OptimizationAlg.png">
<ul><li>Steepest Descent </li></ul>
</div>
</article>
<footer class="source">Source: http://en.wikipedia.org/wiki/Force_field_(chemistry)#mediaviewer/File:MM_PEF.png</footer>
</slide>
<slide>
<h1 class="black">MD Basic Process</h1>
<article class="smaller">
<div>
<div style="float:left" width="300px"><br>
<ul><br><br>
<!-- <li>An example of SH2 which is a protein domain involved in protein-protein interactions.</li><br> -->
<img style="float:center;margin-left: 100px" width="800px" heigth="800px" src="iris_pics/BasicProcess.png"><br>
</ul>
</div>
<footer class="source">Source: https://nanohub.org/resources/7573/download/Martini_L1_Introduction.pdf</footer>
</article>
</slide>
<slide>
<h1 class="black">MD Basic Process</h1>
<article class="smaller">
<div>
<div style="float:left" width="300px"><br>
<ul><br><br>
<!-- <li>An example of SH2 which is a protein domain involved in protein-protein interactions.</li><br> -->
<img style="float:center;margin-left: 100px" width="800px" heigth="800px" src="iris_pics/BasicProcess3.png"><br>
</ul>
</div>
<footer class="source">Source: https://nanohub.org/resources/7573/download/Martini_L1_Introduction.pdf</footer>
</article>
</slide>
<slide>
<h1 class="black">Integration Algorithm</h1>
<article class="smaller">
<div>
<div style="float:left" width="300px">
<ul>
<ul><li>There is no analytical solution to the equations of motion which must be solved numerically</li></ul><br>
<img style="float:center;margin-left: 150px" width="700px" heigth="700px" src="iris_pics/Algorithm1.png"><br>
</ul>
</div>
<footer class="source">Source: http://reaktiveplasmen.rub.de/files/lehre/md/01-1.pdf</footer>
</article>
</slide>
<slide>
<h1 class="black">Integration Algorithm</h1>
<article class="smaller">
<div>
<div style="float:left" width="300px">
<ul>
<ul><li>There is no analytical solution to the equations of motion which must be solved numerically</li></ul><br>
<img style="float:center;margin-left: 150px" width="700px" heigth="700px" src="iris_pics/Algorithm2.png"><br>
</ul>
</div>
<footer class="source">Source: http://reaktiveplasmen.rub.de/files/lehre/md/01-1.pdf</footer>
</article>
</slide>
<slide>
<hgroup>
<h1 class="black">Boundary Condition</h1>
</hgroup>
<article class="smaller">
<li><b>No boundaries</b></li><br>
<ul><ul>
<li>Free boundaries condition</li>
<li>Ex: Droplet of liquid, protein in vacuum;</li>
</ul></ul>
</article>
</slide>
<slide>
<hgroup>
<h1 class="black">Boundary Condition</h1>
</hgroup>
<article class="smaller">
<li>No boundaries</li><br>
<li><b>Fixed boundaries</b></li><br>
<ul><ul>
<li>Rigid boundaries condition</li>
<li>In principle we need a ‘sacrificial region’ between the part of the system under study and a fixed boundary</li>
<img style="float:center;margin-left: 200px" width="500px" heigth="500px" src="iris_pics/FixedBoundary.png">
</ul></ul>
</article>
<footer class="source">Source: https://nanohub.org/resources/7577/download/Martini_L5_BoundaryConditions.pdf </footer>
</slide>
<slide>
<hgroup>
<h1 class="black">Boundary Condition</h1>
</hgroup>
<article class="smaller">
<li>No boundaries</li><br>
<li>Fixed boundaries</li><br>
<li><b>Periodic boundaries</b></li><br>
<img style="float:right; margin-right:100px" width="300px" heigth="300px" src="iris_pics/Periodic.jpg">
<ul><ul><ul>
<li>The most widely used</li>
<li>Simulated interactions of "bulk" material</li>
<li>Out one side, in the other</li></ul></ul></ul>
</article>
<footer class="source">Source: http://isaacs.sourceforge.net/phys/pbc.html </footer>
</slide>
<slide>
<hgroup>
<h1 class="black">Quantum mechanics</h1>
</hgroup>
<article class="smaller">
<ul><ul>
<li>Solve the limitation of Classical Mechanics</li>
<li>Offers the principally most accurate description of intra- and intermolecular interactions. </li></ul>
</article>
<!-- <hgroup>
<h1 class="black">Classical mechanics vs. Quantum mechanics</h1>
</hgroup> -->
</slide>
<slide>
<hgroup>
<h1 class="black">Quantum mechanics</h1>
</hgroup>
<article class="smaller">
<ul><ul>
<li>Solve the limitation of Classical Mechanics</li>
<li>Offers the principally most accurate description of intra- and intermolecular interactions. </li></ul>
</article><br>
<hgroup>
<h1 class="black">Classical mechanics vs. Quantum mechanics</h1><br><br>
<article class="flexbox vcenter">
<TABLE border="5px" style="width:75%" cellpadding="4px" cellspacing="3px">
<TR>
<TH><b>Classical Mechanics</b></TH>
<TH><b>Quantum Mechanics</b></TH>
</TR>
<TR>
<TD>Atom as sphere (point charge & mass)</TD>
<TD>Electrons</TD>
</TR>
<TR>
<TD>Newton's Law</TD>
<TD>Uncertainty Principle & Probability</TD>
</TR>
<TR>
<TD>Less computational complexity</TD>
<TD>High computational complexity</TD>
</TR>
</TABLE>
</article>
</hgroup>
</slide>
<slide>
<h1 class="black">Simulation Example</h1>
<article class="smaller">
<div>
<div style="float:left" width="300px"><br>
<ul><li>Water Channels in Cell Membranes</li>
<video style="float: center;margin-left: 100px" autoplay loop muted width="800px" heigth="800px" src="iris_pics/Water Channels in Cell Membranes-GSi5-y6NHjY.mp4">
</ul>
</div>
<footer class="source">Source: https://www.youtube.com/watch?v=V0Z52u8h2es</footer>
</article>
</slide>
<slide>
<hgroup>
<h1 class="black">Molecular Dynamic Software</h1>
</hgroup>
<article class="flexbox vcenter">
<ul>
<li><b>CHARMM</b></li>
<li>Amber</li>
<li>GROMOS</li>
<li>Gromacs</li>
<li>NAMD</li>
</ul>
<!-- <TABLE border="5px" style="width:75%" cellpadding="4px" cellspacing="3px">
<TR>
<TH><b>Package name</b></TH>
<TH><b>Supprot Force-field</b></TH>
</TR>
<TR>
<TD>CHARMM</TD>
<TD>CHARMM (E / I; AA / UA), Amber</TD>
</TR>
<TR>
<TD>Amber</TD>
<TD>Amber (E / I ; AA)</TD>
</TR>
<TR>
<TD>GROMOS</TD>
<TD>Gromos (E / vacuum ; UA)</TD>
</TR>
<TR>
<TD>Gromacs</TD>
<TD>Amber, Gromos, OPLS - (all E)</TD>
</TR>
<TR>
<TD>NAMD</TD>
<TD>CHARMM, Amber, Gromos, ...</TD>
</TR>
</TABLE> -->
</article>
<hgroup>
</hgroup>
</slide>
<slide>
<hgroup>
<h1 class="black">Summary</h1>
</hgroup>
<article class="smaller">
<div style="float:left">
<ul><ul><ul><ul>
<li>Why molecular dynamic simulation?</li>
<li>Why classical mechanics?</li>
<li>How molecule modelled?</li>
<li>What's more to know?</li>
</ul></ul></ul></ul>
</div>
<div style="float:right" class=iris> </div>
</article>
</slide>
<slide class="thank-you-slide segue nobackground">
<aside class="gdbar right"><img src="images/log.png"></aside>
<article class="flexbox vleft auto-fadein">
<h2><Thank You!></h2>
<p>Questions?</p>
</article>
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