Merge branch 'main' of https://gitlab.igem.org/2023/hopkins into main

wiki/pages/model.html

@@ -55,14 +55,14 @@ figcaption {
     <h4 style = "color:rgb(255, 255, 255)">Model of our engineered sequence is consistent with prior measurements of a disulfide bond</h4>
     <p>
       While the AlphaFold <a href="#ref1"><sup>[1]</sup></a> predictions are low confidence of the H-fibroin structure as a whole, the use of energy minimization and molecular 
-      dynamics <a href="#ref2"><sup>[2]</sup></a>,<a href="#ref3"><sup>[4]</sup></a>,<a href="#ref4"><sup>[7]</sup></a> builds confidence in the quality of this output. Most importantly, our model suggests that key residue-specific interactions 
+      dynamics <a href="#ref2"><sup>[2]</sup></a>,<a href="#ref3"><sup>[3]</sup></a>,<a href="#ref4"><sup>[4]</sup></a> builds confidence in the quality of this output. Most importantly, our model suggests that key residue-specific interactions 
       between L- and H-fibroin are preserved in our engineered sequences, relative to their native counterparts. A strong cysteine-cysteine disulfide 
       interaction between h- and L-fibroin is predicted to be preserved—for instance, the model suggests that the cysteine ~20 residues from the end 
       of our engineered H-fibroin and the cysteine between residues 150 and 200 of the L-fibroin are consistent with their expected relative positions 
       and that they maintain the strong cysteine-cysteine disulfide interaction observed in existing caddisfly silk proteins.<a href="#ref5"><sup>[5]</sup></a>
     </p>
     <p>
-      In prior biochemical experiments on homologous l- and H-fibroin subunits in the silkworm Bombyx mori, performed by Tanaka et al., Cys-172 of 
+      In prior biochemical experiments on homologous l- and H-fibroin subunits in the silkworm <m>Bombyx mori</m>, performed by Tanaka et al., Cys-172 of 
       L-chain and Cys-c20 of H-chain had been experimentally validated as the residues to form a disulfide bond in that species. These measurements and 
       validations guided our identification of similar interactions proposed by our model—between cysteine residues in the same regions. 
     </p>
@@ -142,7 +142,7 @@ figcaption {
         <li>Periodic Boundary Conditions: XYZ</li>
         <li>Simulation temperature: 400K. 400K was used to simulate a higher energy system to allow for faster protein structure changes</li>
       </ul>
-      <li>Production simulation with NVT ensemble</li>
+      <li>Production simulation with NVT ensemble:</li>
       <ul class="sub-arrow-list">
         <li>Timestep: 20 femtoseconds</li>
         <li>Simulation Steps: 10^6 (20 nanosecond total)</li>