From 832ebee9bb0c9d03978ba136088cddbfc3ef2ecb Mon Sep 17 00:00:00 2001
From: Zhefu Li <zf-li23@mails.tsinghua.edu.cn>
Date: Tue, 24 Sep 2024 02:56:48 +0000
Subject: [PATCH] Update model.html
---
wiki/pages/model.html | 164 +++++++++++++++++++++---------------------
1 file changed, 84 insertions(+), 80 deletions(-)
diff --git a/wiki/pages/model.html b/wiki/pages/model.html
index 174b9486..6daf672c 100644
--- a/wiki/pages/model.html
+++ b/wiki/pages/model.html
@@ -7,7 +7,9 @@
<link rel="icon" type="image/png" href="https://static.igem.wiki/teams/5187/art/icon1.png" sizes="364x370">
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.5.1/styles/default.min.css">
<script src="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.5.1/highlight.min.js"></script>
- <script>hljs.highlightAll();</script>
+ <script>
+ hljs.highlightAll();
+ </script>
<title>Tsinghua - IGEM 2024</title>
<script type="text/javascript" async src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
<style>
@@ -323,85 +325,87 @@
<button id="Button1" onclick="toggleCodeSnippet()">Expand the code</button>
<div id="codeSnippet" class="code-snippet">
-```metlab
-% Define parameters
-Q_inhale = 100; % mg
-k_exhale = 10;
-k_perm = 0.005;
-k_adh = 0.001;
-k_diffMC = 0.01;
-k_diffLC = 0.05;
-k_dist = 0.001;
-k_excrete = 0.05;
-k_move = 0.02;
-
-% Define the time range
-tspan = [0 300]; % From 0 to 5 minutes
-initial_conditions = [0 0 0 0 0]; % The initial condition is 0
-
-% solve ODE
-[t, y] = ode45(@(t,y) odefun(t, y, Q_inhale, k_exhale, k_perm, k_adh, k_diffMC, k_diffLC, k_dist, k_excrete, k_move), tspan, initial_conditions);
-
-% calculate V_inhale
-V_inhale = Q_inhale / 5 * (heaviside(t) - heaviside(t-5));
-
-figure('Position', [100, 100, 1200, 1000]);
-
-% V_inhale(t)
-subplot(3,2,1)
-plot(t, V_inhale)
-title('V_{inhale}(t)')
-xlabel('Time (s)')
-ylabel('V_{inhale}')
-
-% Q_A(t)
-subplot(3,2,2)
-plot(t, y(:,1))
-title('Q_A(t)')
-xlabel('Time (s)')
-ylabel('Q_A')
-
-% Q_L(t)
-subplot(3,2,3)
-plot(t, y(:,2))
-title('Q_L(t)')
-xlabel('Time (s)')
-ylabel('Q_L')
-
-% Q_M(t)
-subplot(3,2,4)
-plot(t, y(:,3))
-title('Q_M(t)')
-xlabel('Time (s)')
-ylabel('Q_M')
-
-% Q_C(t)
-subplot(3,2,5)
-plot(t, y(:,4))
-title('Q_C(t)')
-xlabel('Time (s)')
-ylabel('Q_C')
-
-% Q_I(t)
-subplot(3,2,6)
-plot(t, y(:,5))
-title('Q_I(t)')
-xlabel('Time (s)')
-ylabel('Q_I')
-
-sgtitle('Simulation Results')
-
-% ODE
-function dydt = odefun(t, y, Q_inhale, k_exhale, k_perm, k_adh, k_diffMC, k_diffLC, k_dist, k_excrete, k_move)
- V_inhale = Q_inhale / 5 * (heaviside(t) - heaviside(t-5));
- dydt = zeros(5,1);
- dydt(1) = V_inhale - (k_exhale + k_perm) * y(1); % dQ_A/dt
- dydt(2) = k_perm * y(1) - k_diffLC * y(2); % dQ_L/dt
- dydt(3) = 0.0005 * k_adh * V_inhale - k_diffMC * y(3); % dQ_M/dt
- dydt(4) = k_diffMC * y(3) + k_diffLC * y(2) - k_dist * y(4) - k_excrete * y(4); % dQ_C/dt
- dydt(5) = k_dist * y(4) - k_move * y(5); % dQ_I/dt
-end
-```
+ ```metlab
+ % Define parameters
+ Q_inhale = 100; % mg
+ k_exhale = 10;
+ k_perm = 0.005;
+ k_adh = 0.001;
+ k_diffMC = 0.01;
+ k_diffLC = 0.05;
+ k_dist = 0.001;
+ k_excrete = 0.05;
+ k_move = 0.02;
+
+ % Define the time range
+ tspan = [0 300]; % From 0 to 5 minutes
+ initial_conditions = [0 0 0 0 0]; % The initial condition is 0
+
+ % solve ODE
+ [t, y] = ode45(@(t,y) odefun(t, y, Q_inhale, k_exhale, k_perm, k_adh, k_diffMC, k_diffLC, k_dist,
+ k_excrete, k_move), tspan, initial_conditions);
+
+ % calculate V_inhale
+ V_inhale = Q_inhale / 5 * (heaviside(t) - heaviside(t-5));
+
+ figure('Position', [100, 100, 1200, 1000]);
+
+ % V_inhale(t)
+ subplot(3,2,1)
+ plot(t, V_inhale)
+ title('V_{inhale}(t)')
+ xlabel('Time (s)')
+ ylabel('V_{inhale}')
+
+ % Q_A(t)
+ subplot(3,2,2)
+ plot(t, y(:,1))
+ title('Q_A(t)')
+ xlabel('Time (s)')
+ ylabel('Q_A')
+
+ % Q_L(t)
+ subplot(3,2,3)
+ plot(t, y(:,2))
+ title('Q_L(t)')
+ xlabel('Time (s)')
+ ylabel('Q_L')
+
+ % Q_M(t)
+ subplot(3,2,4)
+ plot(t, y(:,3))
+ title('Q_M(t)')
+ xlabel('Time (s)')
+ ylabel('Q_M')
+
+ % Q_C(t)
+ subplot(3,2,5)
+ plot(t, y(:,4))
+ title('Q_C(t)')
+ xlabel('Time (s)')
+ ylabel('Q_C')
+
+ % Q_I(t)
+ subplot(3,2,6)
+ plot(t, y(:,5))
+ title('Q_I(t)')
+ xlabel('Time (s)')
+ ylabel('Q_I')
+
+ sgtitle('Simulation Results')
+
+ % ODE
+ function dydt = odefun(t, y, Q_inhale, k_exhale, k_perm, k_adh, k_diffMC, k_diffLC, k_dist,
+ k_excrete, k_move)
+ V_inhale = Q_inhale / 5 * (heaviside(t) - heaviside(t-5));
+ dydt = zeros(5,1);
+ dydt(1) = V_inhale - (k_exhale + k_perm) * y(1); % dQ_A/dt
+ dydt(2) = k_perm * y(1) - k_diffLC * y(2); % dQ_L/dt
+ dydt(3) = 0.0005 * k_adh * V_inhale - k_diffMC * y(3); % dQ_M/dt
+ dydt(4) = k_diffMC * y(3) + k_diffLC * y(2) - k_dist * y(4) - k_excrete * y(4); % dQ_C/dt
+ dydt(5) = k_dist * y(4) - k_move * y(5); % dQ_I/dt
+ end
+ ```
</div>
<script>
function toggleCodeSnippet() {
--
GitLab