Update model.html

wiki/pages/model.html

@@ -66,7 +66,8 @@
             <li><a href="#description">General Description of Modeling</a></li>
             <li><a href="#topic1">Compartment Model for Muscone Inhalation</a></li>
             <li><a href="#topic2">Topic2</a></li>
-            <li><a href="#topic3">Topic3</a></li>
+            <li><a href="#topic3">Ordinary Differential Equation of the signal transduction of the yeast MAPK
+                    pathway</a></li>
             <li><a href="#topic4">Topic4</a></li>
         </ul>
     </div>
@@ -323,85 +324,85 @@
                 <button id="Button1" onclick="toggleCodeSnippet()">Expand the code</button>
 
                 <div id="codeSnippet" class="code-snippet">
-% 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>
                 <script>
                     function toggleCodeSnippet() {
@@ -454,24 +455,21 @@ end
     <div class="row mt-4">
         <div class="col-lg-12">
             <h2 id="topic3">
-                <h2>Topic3</h2>
-                <hr>
-                <p>Admission to Tsinghua for both undergraduate and graduate schools is extremely competitive.
-                    Undergraduate admissions for domestic students is decided through the gaokao, the Chinese national
-                    college entrance exam, which allows students to list Tsinghua University among their preferred
-                    college choices. While selectivity varies by province, the sheer number of high school students
-                    applying for college each year has resulted in overall acceptance rates far lower than 0.1% of all
-                    test takers. Admission to Tsinghua's graduate schools is also very competitive. Only about 16% of
-                    MBA applicants are admitted each year.</p>
-                <p>Department of Mathematical Sciences
-                    The Department of Mathematical Sciences (DMS) was established in 1927.
-                    In 1952, Tsinghua DMS was merged with the Peking University Department of Mathematical Sciences.
-                    Then in 1979 it was renamed "Department of Applied Mathematics", and renamed again in 1999 to its
-                    current title.
-                    Tsinghua DMS has three institutes at present, the institute of Pure Mathematics which has 27 faculty
-                    members, the Institute of Applied Mathematics and Probability and Statistics which has 27 faculty
-                    members, and the Institute of Computational Mathematics and Operations Research which has 20 faculty
-                    members. There are currently about 400 undergraduate students and 200 graduate students.</p>
+                <h2>Ordinary Differential Equation of the signal transduction of the yeast MAPK pathway</h2>
+
+                <h3>Model Description</h3>
+                <p>In our project, we express the musk ketone receptor (GPCR) on the yeast cell membrane. After a
+                    certain concentration of musk ketone diffuses into the intestine and binds to the receptor, it
+                    activates the receptor, which in turn activates the G protein. The G protein dissociates into α and
+                    βγ subunits, with the βγ subunit releasing and activating Ste20 and the scaffold protein Ste5. Ste5
+                    can undergo oligomerization and other behaviors, recruiting Ste11, Ste7, and Fus3 near the plasma
+                    membrane. The cascade reaction is initiated by Ste20, and the signal is transmitted along the
+                    Ste11-Ste7-Fus3 cascade. Fus3 activates the transcription factor pFUS1, and the downstream gene is
+                    LahA, which expresses lactate dehydrogenase LDH, catalyzing the conversion of pyruvate to lactate.
+                    This model simulates the changes in the concentrations and phosphorylation states of molecules in
+                    the signaling transduction pathway by writing out chemical reactions and converting them into
+                    ordinary differential equations, in order to obtain the quantitative relationship between musk
+                    ketone activation and lactate secretion. The model includes the following main processes:</p>
         </div>
     </div>