From a855951e53faa3cade936bd5891a84b1911c7abd Mon Sep 17 00:00:00 2001
From: Zhefu Li <zf-li23@mails.tsinghua.edu.cn>
Date: Tue, 24 Sep 2024 03:01:16 +0000
Subject: [PATCH] Update model.html
---
wiki/pages/model.html | 164 +++++++++++++++++++++---------------------
1 file changed, 80 insertions(+), 84 deletions(-)
diff --git a/wiki/pages/model.html b/wiki/pages/model.html
index 6daf672c..3f33ab38 100644
--- a/wiki/pages/model.html
+++ b/wiki/pages/model.html
@@ -7,9 +7,7 @@
<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>
@@ -325,87 +323,85 @@
<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
- ```
+% 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>
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