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<!DOCTYPE html>
<html lang="en"><head>
<script src="slides_files/libs/clipboard/clipboard.min.js"></script>
<script src="slides_files/libs/quarto-html/tabby.min.js"></script>
<script src="slides_files/libs/quarto-html/popper.min.js"></script>
<script src="slides_files/libs/quarto-html/tippy.umd.min.js"></script>
<link href="slides_files/libs/quarto-html/tippy.css" rel="stylesheet">
<link href="slides_files/libs/quarto-html/light-border.css" rel="stylesheet">
<link href="slides_files/libs/quarto-html/quarto-html.min.css" rel="stylesheet" data-mode="light">
<link href="slides_files/libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" id="quarto-text-highlighting-styles"><meta charset="utf-8">
<meta name="generator" content="quarto-1.4.553">
<meta name="author" content="Yangyunchen Liu">
<title>MD Slides</title>
<meta name="apple-mobile-web-app-capable" content="yes">
<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent">
<meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no, minimal-ui">
<link rel="stylesheet" href="slides_files/libs/revealjs/dist/reset.css">
<link rel="stylesheet" href="slides_files/libs/revealjs/dist/reveal.css">
<style>
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
div.columns{display: flex; gap: min(4vw, 1.5em);}
div.column{flex: auto; overflow-x: auto;}
div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
ul.task-list{list-style: none;}
ul.task-list li input[type="checkbox"] {
width: 0.8em;
margin: 0 0.8em 0.2em -1em; /* quarto-specific, see https://github.com/quarto-dev/quarto-cli/issues/4556 */
vertical-align: middle;
}
/* CSS for syntax highlighting */
pre > code.sourceCode { white-space: pre; position: relative; }
pre > code.sourceCode > span { line-height: 1.25; }
pre > code.sourceCode > span:empty { height: 1.2em; }
.sourceCode { overflow: visible; }
code.sourceCode > span { color: inherit; text-decoration: inherit; }
div.sourceCode { margin: 1em 0; }
pre.sourceCode { margin: 0; }
@media screen {
div.sourceCode { overflow: auto; }
}
@media print {
pre > code.sourceCode { white-space: pre-wrap; }
pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
}
pre.numberSource code
{ counter-reset: source-line 0; }
pre.numberSource code > span
{ position: relative; left: -4em; counter-increment: source-line; }
pre.numberSource code > span > a:first-child::before
{ content: counter(source-line);
position: relative; left: -1em; text-align: right; vertical-align: baseline;
border: none; display: inline-block;
-webkit-touch-callout: none; -webkit-user-select: none;
-khtml-user-select: none; -moz-user-select: none;
-ms-user-select: none; user-select: none;
padding: 0 4px; width: 4em;
}
pre.numberSource { margin-left: 3em; padding-left: 4px; }
div.sourceCode
{ color: #383a42; }
@media screen {
pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
}
code span { color: #383a42; } /* Normal */
code span.al { color: #95da4c; background-color: #4d1f24; font-weight: bold; } /* Alert */
code span.an { color: #50a14f; } /* Annotation */
code span.at { color: #a626a4; } /* Attribute */
code span.bn { color: #986801; } /* BaseN */
code span.bu { color: #a626a4; } /* BuiltIn */
code span.cf { color: #a626a4; } /* ControlFlow */
code span.ch { color: #50a14f; } /* Char */
code span.cn { color: #986801; } /* Constant */
code span.co { color: #a0a1a7; font-style: italic; } /* Comment */
code span.cv { color: #e45649; font-style: italic; } /* CommentVar */
code span.do { color: #e45649; } /* Documentation */
code span.dt { color: #a626a4; } /* DataType */
code span.dv { color: #986801; } /* DecVal */
code span.er { color: #f44747; text-decoration: underline; } /* Error */
code span.ex { color: #4078f2; font-weight: bold; } /* Extension */
code span.fl { color: #986801; } /* Float */
code span.fu { color: #4078f2; } /* Function */
code span.im { color: #50a14f; } /* Import */
code span.in { color: #c45b00; } /* Information */
code span.kw { color: #a626a4; } /* Keyword */
code span.op { color: #a626a4; } /* Operator */
code span.ot { color: #27ae60; } /* Other */
code span.pp { color: #a626a4; } /* Preprocessor */
code span.re { color: #2980b9; background-color: #153042; } /* RegionMarker */
code span.sc { color: #0184bc; } /* SpecialChar */
code span.ss { color: #da4453; } /* SpecialString */
code span.st { color: #50a14f; } /* String */
code span.va { color: #e45649; } /* Variable */
code span.vs { color: #da4453; } /* VerbatimString */
code span.wa { color: #da4453; } /* Warning */
/* CSS for citations */
div.csl-bib-body { }
div.csl-entry {
clear: both;
margin-bottom: 0em;
}
.hanging-indent div.csl-entry {
margin-left:2em;
text-indent:-2em;
}
div.csl-left-margin {
min-width:2em;
float:left;
}
div.csl-right-inline {
margin-left:2em;
padding-left:1em;
}
div.csl-indent {
margin-left: 2em;
} </style>
<link rel="stylesheet" href="slides_files/libs/revealjs/dist/theme/quarto.css">
<link rel="stylesheet" href="theme/duke.css">
<link href="slides_files/libs/revealjs/plugin/quarto-line-highlight/line-highlight.css" rel="stylesheet">
<link href="slides_files/libs/revealjs/plugin/reveal-menu/menu.css" rel="stylesheet">
<link href="slides_files/libs/revealjs/plugin/reveal-menu/quarto-menu.css" rel="stylesheet">
<link href="slides_files/libs/revealjs/plugin/quarto-support/footer.css" rel="stylesheet">
<style type="text/css">
.callout {
margin-top: 1em;
margin-bottom: 1em;
border-radius: .25rem;
}
.callout.callout-style-simple {
padding: 0em 0.5em;
border-left: solid #acacac .3rem;
border-right: solid 1px silver;
border-top: solid 1px silver;
border-bottom: solid 1px silver;
display: flex;
}
.callout.callout-style-default {
border-left: solid #acacac .3rem;
border-right: solid 1px silver;
border-top: solid 1px silver;
border-bottom: solid 1px silver;
}
.callout .callout-body-container {
flex-grow: 1;
}
.callout.callout-style-simple .callout-body {
font-size: 1rem;
font-weight: 400;
}
.callout.callout-style-default .callout-body {
font-size: 0.9rem;
font-weight: 400;
}
.callout.callout-titled.callout-style-simple .callout-body {
margin-top: 0.2em;
}
.callout:not(.callout-titled) .callout-body {
display: flex;
}
.callout:not(.no-icon).callout-titled.callout-style-simple .callout-content {
padding-left: 1.6em;
}
.callout.callout-titled .callout-header {
padding-top: 0.2em;
margin-bottom: -0.2em;
}
.callout.callout-titled .callout-title p {
margin-top: 0.5em;
margin-bottom: 0.5em;
}
.callout.callout-titled.callout-style-simple .callout-content p {
margin-top: 0;
}
.callout.callout-titled.callout-style-default .callout-content p {
margin-top: 0.7em;
}
.callout.callout-style-simple div.callout-title {
border-bottom: none;
font-size: .9rem;
font-weight: 600;
opacity: 75%;
}
.callout.callout-style-default div.callout-title {
border-bottom: none;
font-weight: 600;
opacity: 85%;
font-size: 0.9rem;
padding-left: 0.5em;
padding-right: 0.5em;
}
.callout.callout-style-default div.callout-content {
padding-left: 0.5em;
padding-right: 0.5em;
}
.callout.callout-style-simple .callout-icon::before {
height: 1rem;
width: 1rem;
display: inline-block;
content: "";
background-repeat: no-repeat;
background-size: 1rem 1rem;
}
.callout.callout-style-default .callout-icon::before {
height: 0.9rem;
width: 0.9rem;
display: inline-block;
content: "";
background-repeat: no-repeat;
background-size: 0.9rem 0.9rem;
}
.callout-title {
display: flex
}
.callout-icon::before {
margin-top: 1rem;
padding-right: .5rem;
}
.callout.no-icon::before {
display: none !important;
}
.callout.callout-titled .callout-body > .callout-content > :last-child {
padding-bottom: 0.5rem;
margin-bottom: 0;
}
.callout.callout-titled .callout-icon::before {
margin-top: .5rem;
padding-right: .5rem;
}
.callout:not(.callout-titled) .callout-icon::before {
margin-top: 1rem;
padding-right: .5rem;
}
/* Callout Types */
div.callout-note {
border-left-color: #4582ec !important;
}
div.callout-note .callout-icon::before {
background-image: url('data:image/png;base64,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');
}
div.callout-note.callout-style-default .callout-title {
background-color: #dae6fb
}
div.callout-important {
border-left-color: #d9534f !important;
}
div.callout-important .callout-icon::before {
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<body class="quarto-light">
<div class="reveal">
<div class="slides">
<section id="title-slide" data-background-image="theme/logos/duke.png" data-background-position="50% 50%" data-background-size="15%" class="quarto-title-block center">
<h1 class="title">MD Slides</h1>
<div class="quarto-title-authors">
<div class="quarto-title-author">
<div class="quarto-title-author-name">
Yangyunchen Liu
</div>
<p class="quarto-title-affiliation">
Duke University
</p>
</div>
</div>
</section>
<section>
<section id="h1-header" class="title-slide slide level1 center">
<h1>H1 header</h1>
</section>
<section id="h2-header" class="slide level2">
<h2>H2 header</h2>
<h3 id="h3-header">H3 header</h3>
<h4 id="h4-header">H4 header</h4>
<h5 id="h5-header">H5 header</h5>
<h6 id="h6-header">H6 header</h6>
</section></section>
<section>
<section id="layout" class="title-slide slide level1 center">
<h1>Layout</h1>
</section>
<section id="columns" class="slide level2">
<h2>Columns</h2>
<div class="columns">
<div class="column" style="width:50%;">
<ul>
<li>Point 1</li>
<li>Point 2</li>
<li>d</li>
</ul>
</div><div class="column" style="width:50%;">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="./media/png.png"></p>
<figcaption>Some picture</figcaption>
</figure>
</div>
</div>
</div>
</section>
<section id="show-movie" class="slide level2">
<h2>Show movie</h2>
<div class="quarto-figure quarto-figure-center">
<figure>
<p><video data-src="./media/single_np4.mp4" controls=""><a href="./media/single_np4.mp4">Video</a></video></p>
<figcaption>my cell simulation</figcaption>
</figure>
</div>
</section></section>
<section>
<section id="syntax" class="title-slide slide level1 center">
<h1>Syntax</h1>
</section>
<section id="math-blocks" class="slide level2">
<h2>Math blocks</h2>
<p><span class="math display">\[\begin{equation}
\begin{aligned}
\dot{x} &= \sigma(y-x) \\
\dot{y} &= \rho x - y - xz \\
\dot{z} &= -\beta z + xy
\end{aligned}
\end{equation}\]</span></p>
</section>
<section id="code-blocks" class="slide level2">
<h2>Code blocks</h2>
<div class="sourceCode" id="cb1"><pre class="sourceCode numberSource r scrollable number-lines code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href=""></a><span class="co">#| fig-height: 8</span></span>
<span id="cb1-2"><a href=""></a><span class="co">#| fig-align: center</span></span>
<span id="cb1-3"><a href=""></a><span class="co">#| fig-cap: A random walk with noise</span></span>
<span id="cb1-4"><a href=""></a><span class="fu">library</span>(ggplot2)</span>
<span id="cb1-5"><a href=""></a><span class="fu">theme_set</span>(<span class="fu">theme_classic</span>(<span class="at">base_size =</span> <span class="dv">25</span>))</span>
<span id="cb1-6"><a href=""></a><span class="fu">library</span>(latex2exp)</span>
<span id="cb1-7"><a href=""></a><span class="fu">library</span>(patchwork)</span>
<span id="cb1-8"><a href=""></a><span class="fu">set.seed</span>(<span class="dv">42</span>)</span>
<span id="cb1-9"><a href=""></a>Y0 <span class="ot"><-</span> <span class="dv">10</span></span>
<span id="cb1-10"><a href=""></a>wt <span class="ot"><-</span> <span class="fu">rnorm</span>(<span class="dv">100</span>, <span class="at">sd =</span> <span class="dv">1</span>)</span>
<span id="cb1-11"><a href=""></a>vt <span class="ot"><-</span> <span class="fu">rnorm</span>(<span class="dv">100</span>, <span class="at">sd =</span> <span class="dv">3</span>)</span>
<span id="cb1-12"><a href=""></a>dat <span class="ot"><-</span> <span class="fu">data.frame</span>(</span>
<span id="cb1-13"><a href=""></a> <span class="at">t =</span> <span class="dv">1</span><span class="sc">:</span><span class="dv">100</span>,</span>
<span id="cb1-14"><a href=""></a> <span class="at">Y =</span> Y0 <span class="sc">+</span> <span class="fu">cumsum</span>(wt) <span class="sc">+</span> vt,</span>
<span id="cb1-15"><a href=""></a> <span class="at">vt =</span> vt,</span>
<span id="cb1-16"><a href=""></a> <span class="at">wt =</span> wt</span>
<span id="cb1-17"><a href=""></a>)</span>
<span id="cb1-18"><a href=""></a>p1 <span class="ot"><-</span> dat <span class="sc">|></span></span>
<span id="cb1-19"><a href=""></a> <span class="fu">ggplot</span>(<span class="fu">aes</span>(t,Y)) <span class="sc">+</span></span>
<span id="cb1-20"><a href=""></a> <span class="fu">geom_line</span>() <span class="sc">+</span></span>
<span id="cb1-21"><a href=""></a> <span class="fu">geom_line</span>(<span class="fu">aes</span>(<span class="at">y=</span>Y0<span class="sc">+</span><span class="fu">cumsum</span>(wt)), <span class="at">lty=</span><span class="dv">1</span>, <span class="at">color=</span><span class="st">'darkgreen'</span>) <span class="sc">+</span></span>
<span id="cb1-22"><a href=""></a> <span class="fu">labs</span>(<span class="at">y=</span><span class="fu">TeX</span>(<span class="st">'$Y_t$'</span>)) <span class="sc">+</span></span>
<span id="cb1-23"><a href=""></a> <span class="fu">theme</span>(<span class="at">axis.title.x.bottom =</span> <span class="fu">element_blank</span>())</span>
<span id="cb1-24"><a href=""></a>p2 <span class="ot"><-</span> dat <span class="sc">|></span></span>
<span id="cb1-25"><a href=""></a> <span class="fu">ggplot</span>(<span class="fu">aes</span>(t,vt)) <span class="sc">+</span></span>
<span id="cb1-26"><a href=""></a> <span class="fu">geom_point</span>(<span class="at">color=</span><span class="st">'red'</span>, <span class="at">size=</span>.<span class="dv">5</span>) <span class="sc">+</span></span>
<span id="cb1-27"><a href=""></a> <span class="fu">geom_linerange</span>(<span class="fu">aes</span>(<span class="at">ymin=</span><span class="dv">0</span>,<span class="at">ymax=</span>vt), <span class="at">color=</span><span class="st">'red'</span>) <span class="sc">+</span></span>
<span id="cb1-28"><a href=""></a> <span class="fu">geom_hline</span>(<span class="at">yintercept =</span> <span class="dv">0</span>, <span class="at">alpha=</span>.<span class="dv">5</span>) <span class="sc">+</span></span>
<span id="cb1-29"><a href=""></a> <span class="fu">labs</span>(<span class="at">y=</span><span class="fu">TeX</span>(<span class="st">'$v_t$'</span>)) <span class="sc">+</span></span>
<span id="cb1-30"><a href=""></a> <span class="fu">theme</span>(<span class="at">axis.title.x.bottom =</span> <span class="fu">element_blank</span>())</span>
<span id="cb1-31"><a href=""></a>p3 <span class="ot"><-</span> dat <span class="sc">|></span></span>
<span id="cb1-32"><a href=""></a> <span class="fu">ggplot</span>(<span class="fu">aes</span>(t,wt)) <span class="sc">+</span></span>
<span id="cb1-33"><a href=""></a> <span class="fu">geom_segment</span>(<span class="fu">aes</span>(<span class="at">x=</span>t,<span class="at">xend=</span>t,<span class="at">y=</span><span class="dv">0</span>,<span class="at">yend=</span>wt), <span class="at">color=</span><span class="st">'darkgreen'</span>,</span>
<span id="cb1-34"><a href=""></a> <span class="at">arrow =</span> <span class="fu">arrow</span>(<span class="at">length =</span> <span class="fu">unit</span>(<span class="fl">0.2</span>, <span class="st">"cm"</span>))) <span class="sc">+</span></span>
<span id="cb1-35"><a href=""></a> <span class="fu">geom_hline</span>(<span class="at">yintercept =</span> <span class="dv">0</span>, <span class="at">alpha=</span>.<span class="dv">5</span>) <span class="sc">+</span></span>
<span id="cb1-36"><a href=""></a> <span class="fu">labs</span>(<span class="at">y=</span><span class="fu">TeX</span>(<span class="st">'$w_t$'</span>))</span>
<span id="cb1-37"><a href=""></a>p1<span class="sc">/</span>p2<span class="sc">/</span>p3</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</section>
<section id="citation" class="slide level2">
<h2>Citation</h2>
<p>Here is a reference paper <span class="citation" data-cites="gardiner2015discrete">(<a href="#/reference" role="doc-biblioref" onclick="">Gardiner et al. 2015</a>)</span>, and another <span class="citation" data-cites="van2010particlebased">(<a href="#/reference" role="doc-biblioref" onclick="">Liedekerke et al. 2010</a>)</span></p>
</section>
<section id="reference" class="slide level2 smaller scrollable">
<h2>Reference</h2>
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<div id="ref-gardiner2015discrete" class="csl-entry" role="listitem">
Gardiner, Bruce S., Kelvin K. L. Wong, Grand R. Joldes, Addison J. Rich, Chin Wee Tan, Antony W. Burgess, and David W. Smith. 2015. <span>“Discrete Element Framework for Modelling Extracellular Matrix, Deformable Cells and Subcellular Components.”</span> <em>PLOS Computational Biology</em> 11 (October). <a href="https://doi.org/10.1371/journal.pcbi.1004544">https://doi.org/10.1371/journal.pcbi.1004544</a>.
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<div id="ref-van2010particlebased" class="csl-entry" role="listitem">
Liedekerke, P. Van, E. Tijskens, H. Ramon, P. Ghysels, G. Samaey, and D. Roose. 2010. <span>“Particle-Based Model to Simulate the Micromechanics of Biological Cells.”</span> <em>Physical Review E</em> 81 (June). <a href="https://doi.org/10.1103/physreve.81.061906">https://doi.org/10.1103/physreve.81.061906</a>.
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