Merge remote-tracking branch 'refs/remotes/origin/main'

wiki/pages/model.html

@@ -535,7 +535,7 @@
         been released. The combination represents transcription factor released
         by both ligand-dependent and ligand-independent activation pathways. The
         ligand-independent pathway parameter is known to be nonzero (Morsut et
-        al., 2016; Roybal et al., 2016; Yang et al., 2020; ).
+        al., 2016; Roybal et al., 2016; Yang et al., 2020).
       </p>
       <p>
         Finally, we arrive at the three-state model, which we utilize in our
@@ -580,9 +580,9 @@
         src="https://static.igem.wiki/teams/4646/wiki/engineering/model-fig3.png"
       />
       <p>
-        <b>Figure 4:</b> Three-state system of used in computational work.
+        <b>Figure 4:</b> Three-state system of synNotch used in computational work.
         Simplified from the full cubic ternary complex model using biological
-        assumptions
+        assumptions.
       </p>
       <p>
         While ligand-independent activation has proven much more difficult to
@@ -612,7 +612,7 @@
           <td>Khait et al., 2016</td>
         </tr>
         <tr>
-          <td>\[k_act,{L,TF}\]</td>
+          <td>\[k_{act,L,TF}\]</td>
           <td>0.34</td>
           <td>\[s^{-1}\]</td>
           <td>Notch-Delta activation</td>
@@ -633,10 +633,10 @@
           <td>Sprinzak et al., 2010</td>
         </tr>
       </table>
-      <p><b>Table 3:</b> Parameter values used in the model simulations</p>
+      <p><b>Table 3:</b> Parameter values used in the model simulations.</p>
       <p>
         The final ODE system is shown below, as deduced from the schematic in
-        Figure 2 and the derivations above:
+        Figure 4 and the derivations above:
       </p>
       <p class="eq-wrapper">
         <!-- EQ 16 -->
@@ -649,6 +649,9 @@
         \[\frac {d[TF]}{dt} = k_{act,L,TF}[LSynTF] + k_{act,TF}[SynTF]
         \tag{18}\]
       </p>
+      <p>
+        Note that we take production to be zero, and we simply give <i>SynTF</i> a nonzero initial value to represent the total number of synNotch receptors expressed on the surface of the cell.
+      </p>
     </div>
     <div id="sens-anal">
       <h2>Sensitivity Analysis</h2>