Update documentation

rwexler · Oct 21, 2024 · 620a453 · 620a453
1 parent e56709c
commit 620a453
Show file tree

Hide file tree

Showing 86 changed files with 1,700 additions and 17 deletions.
diff --git a/_images/00465eb12beb353030be1ac8540b9ce14e6fb8f5d83ac6a18541366607523fa7.png b/_images/00465eb12beb353030be1ac8540b9ce14e6fb8f5d83ac6a18541366607523fa7.png
diff --git a/_images/00b10de1d72b177fed8289e976dccc7e99e98d0e8a5cd3b13482fbbb6db275ef.png b/_images/00b10de1d72b177fed8289e976dccc7e99e98d0e8a5cd3b13482fbbb6db275ef.png
diff --git a/_images/028828704490f82179a02caf001f590f0b2e51daaa29f52caaed741b78357be1.png b/_images/028828704490f82179a02caf001f590f0b2e51daaa29f52caaed741b78357be1.png
diff --git a/_images/04d83d6ebe92bd46a4f743d91a4924118e9de0e9a22086d10dbfaa19e406ce38.png b/_images/04d83d6ebe92bd46a4f743d91a4924118e9de0e9a22086d10dbfaa19e406ce38.png
diff --git a/_images/0d3033142f92c6637d9dbe1aa0985a43d278f562dd2a2229337ee4aae2f2fb59.png b/_images/0d3033142f92c6637d9dbe1aa0985a43d278f562dd2a2229337ee4aae2f2fb59.png
diff --git a/_images/0e000fcb7e865ccab4425251bf2f2260fa67e48a0739fe2a51651f086c5b6cb4.png b/_images/0e000fcb7e865ccab4425251bf2f2260fa67e48a0739fe2a51651f086c5b6cb4.png
diff --git a/_images/0ea7b11c8aae0f255105a6e4236ba25f0a309bfe75496502e35e4d1d91047146.png b/_images/0ea7b11c8aae0f255105a6e4236ba25f0a309bfe75496502e35e4d1d91047146.png
diff --git a/_images/0f2aa8a21f50693552f3d4efc65c8e07ee386aa8d4898e3ee530c5610e5ac5b1.png b/_images/0f2aa8a21f50693552f3d4efc65c8e07ee386aa8d4898e3ee530c5610e5ac5b1.png
diff --git a/_images/106568605434a31c501b707d928325d21d367457e3a3b2b4b29c838f3132c611.png b/_images/106568605434a31c501b707d928325d21d367457e3a3b2b4b29c838f3132c611.png
diff --git a/_images/15f7437fe9fdc6039008b9360e6deaf64de58a291faf8efacb640706fb4aadb2.png b/_images/15f7437fe9fdc6039008b9360e6deaf64de58a291faf8efacb640706fb4aadb2.png
diff --git a/_images/17fd009f76f09851a11345d8e4ca001b963fc0ad777380f9dbcf8c1af0236a75.png b/_images/17fd009f76f09851a11345d8e4ca001b963fc0ad777380f9dbcf8c1af0236a75.png
diff --git a/_images/1b825e4039eb580a878edc21acdb6de01a1a8aafdfaa41ac517f4192b54bcdc5.png b/_images/1b825e4039eb580a878edc21acdb6de01a1a8aafdfaa41ac517f4192b54bcdc5.png
diff --git a/_images/240e50f1046b19e635a921a6256707b8ed795d364d106fe06585c07b6a96d239.png b/_images/240e50f1046b19e635a921a6256707b8ed795d364d106fe06585c07b6a96d239.png
diff --git a/_images/2428de71420290687a8d3b242d2d9f7cad9eae8b29a6af5c9a8bd080227cce5c.png b/_images/2428de71420290687a8d3b242d2d9f7cad9eae8b29a6af5c9a8bd080227cce5c.png
diff --git a/_images/2758cebfe16efc65a2ecf4a7793f0e1d5692495711d03ab1a54192c94d696657.png b/_images/2758cebfe16efc65a2ecf4a7793f0e1d5692495711d03ab1a54192c94d696657.png
diff --git a/_images/276b01b6503f7c53160ff87ea6ad03006d14512a27c1d61d14708ef156a886ee.png b/_images/276b01b6503f7c53160ff87ea6ad03006d14512a27c1d61d14708ef156a886ee.png
diff --git a/_images/28d717363377885114e47875e2427a0e6ed31f485a4e2b930efaafdfb305475a.png b/_images/28d717363377885114e47875e2427a0e6ed31f485a4e2b930efaafdfb305475a.png
diff --git a/_images/2a7c8ef3061368e297558ce2b609238f0d64de45bea6572638642bc505b4e697.png b/_images/2a7c8ef3061368e297558ce2b609238f0d64de45bea6572638642bc505b4e697.png
diff --git a/_images/2b799fd16b64fa2b0179b565c5a34a5006b32757cc4f3b505de7501593b5c627.png b/_images/2b799fd16b64fa2b0179b565c5a34a5006b32757cc4f3b505de7501593b5c627.png
diff --git a/_images/2f701bd378816ff6b5a62a246eb23715a2e850340770b9ea1e7356d1b5d588ce.png b/_images/2f701bd378816ff6b5a62a246eb23715a2e850340770b9ea1e7356d1b5d588ce.png
diff --git a/_images/3ac1560939aebf7b8e2c5edce21c147f21e37eceafb85d6c27a242255dcd93d0.png b/_images/3ac1560939aebf7b8e2c5edce21c147f21e37eceafb85d6c27a242255dcd93d0.png
diff --git a/_images/3b09b2a1cb903caf81f1590bdca16b6e1e56aeea81bf0a0a04c12553795cb1a0.png b/_images/3b09b2a1cb903caf81f1590bdca16b6e1e56aeea81bf0a0a04c12553795cb1a0.png
diff --git a/_images/3e299288905367ba649f8be24fbefb10f119a818505fbd25f6a22d6f2a959f21.png b/_images/3e299288905367ba649f8be24fbefb10f119a818505fbd25f6a22d6f2a959f21.png
diff --git a/_images/4128ea7ab76e8f1e95c369fd8423beac4cf2b2b6cf2f1060554f2cfca72c4581.png b/_images/4128ea7ab76e8f1e95c369fd8423beac4cf2b2b6cf2f1060554f2cfca72c4581.png
diff --git a/_images/430be7dd30bc502caffe5e7d50ef0664c4a0ff062977129386e29aa8b62aaaf8.png b/_images/430be7dd30bc502caffe5e7d50ef0664c4a0ff062977129386e29aa8b62aaaf8.png
diff --git a/_images/4355b54008bee1ca270315f8465003ed0fabdcff3900a5087d0001c9abe610d0.png b/_images/4355b54008bee1ca270315f8465003ed0fabdcff3900a5087d0001c9abe610d0.png
diff --git a/_images/44641152a82e23a6a2cbf1bbdf263b8f62ecc37a2afb320acb363a74c7f42965.png b/_images/44641152a82e23a6a2cbf1bbdf263b8f62ecc37a2afb320acb363a74c7f42965.png
diff --git a/_images/45dc5f42ce6e505377acd18eed838e885d30f2fb477e1fb9a735a16d7c8fdc49.png b/_images/45dc5f42ce6e505377acd18eed838e885d30f2fb477e1fb9a735a16d7c8fdc49.png
diff --git a/_images/4ab3137a51ee7763f85a56316bfc30eb0285e7c2d1f42b0353b182c486d9be64.png b/_images/4ab3137a51ee7763f85a56316bfc30eb0285e7c2d1f42b0353b182c486d9be64.png
diff --git a/_images/4e066855e57789767a1581d34df2c49a23ca52105ae2b093241ecd8fbafefbf2.png b/_images/4e066855e57789767a1581d34df2c49a23ca52105ae2b093241ecd8fbafefbf2.png
diff --git a/_images/4eec514f4457779f9fed4f16e97abd8d3274e3a31cedf43b399caae5b3ea9a33.png b/_images/4eec514f4457779f9fed4f16e97abd8d3274e3a31cedf43b399caae5b3ea9a33.png
diff --git a/_images/5fcc9e4c8980ab1eee85eca6d70a97d9b58985bbc61a0aa2d4baa12c3aa63564.png b/_images/5fcc9e4c8980ab1eee85eca6d70a97d9b58985bbc61a0aa2d4baa12c3aa63564.png
diff --git a/_images/61c8eafb0cadc04561b4bae5319dcece6610ff4cecd15d088c6f1877854aa83f.png b/_images/61c8eafb0cadc04561b4bae5319dcece6610ff4cecd15d088c6f1877854aa83f.png
diff --git a/_images/6dae2fbc71aa2a3c842d56e6ce790f0cd2d581873f4def69c2403afd6b8192aa.png b/_images/6dae2fbc71aa2a3c842d56e6ce790f0cd2d581873f4def69c2403afd6b8192aa.png
diff --git a/_images/6faa8bdd49a51ab659f168b11f994b9549bfa97f936caed82c083dc633ac5302.png b/_images/6faa8bdd49a51ab659f168b11f994b9549bfa97f936caed82c083dc633ac5302.png
diff --git a/_images/7c166ff0dbca11468fd6ad52cb03e9c169e25880f7f9b795645c929faf845058.png b/_images/7c166ff0dbca11468fd6ad52cb03e9c169e25880f7f9b795645c929faf845058.png
diff --git a/_images/818b4b605d1bcd9a826c9d954977715a181096b6172d43c02aea81f197fbf129.png b/_images/818b4b605d1bcd9a826c9d954977715a181096b6172d43c02aea81f197fbf129.png
diff --git a/_images/9076f245c00e1b5325aca0cd5415dbdda3da0e38f5a71b8ac72d6445fa4220d3.png b/_images/9076f245c00e1b5325aca0cd5415dbdda3da0e38f5a71b8ac72d6445fa4220d3.png
diff --git a/_images/91bc8b45bcdc8aefcfdc8f9f99ce3473f174736e02015876b1c47792af834b6a.png b/_images/91bc8b45bcdc8aefcfdc8f9f99ce3473f174736e02015876b1c47792af834b6a.png
diff --git a/_images/9cc30889c98cdae7f55e2efbd3727a81c13a64fa4f1e2a0f70df8f83c4104313.png b/_images/9cc30889c98cdae7f55e2efbd3727a81c13a64fa4f1e2a0f70df8f83c4104313.png
diff --git a/_images/9cdc01fda0a34b7edd02f9a03192ae4bb014fe17cc80697ea3593f75b6b82b2c.png b/_images/9cdc01fda0a34b7edd02f9a03192ae4bb014fe17cc80697ea3593f75b6b82b2c.png
diff --git a/_images/a2e7503a847b32e2c16aebbf9cc35bca40dd77474edb6deed7e99adc05fa4fba.png b/_images/a2e7503a847b32e2c16aebbf9cc35bca40dd77474edb6deed7e99adc05fa4fba.png
diff --git a/_images/a5ffdd948ab8f9628ae26b2d416ebd99b9454edb8a83ca765076fa903b0bfd95.png b/_images/a5ffdd948ab8f9628ae26b2d416ebd99b9454edb8a83ca765076fa903b0bfd95.png
diff --git a/_images/a8a4ee504b33cb37cf6539946e8828b8619d33380cf08f456748f7edb89fe9e9.png b/_images/a8a4ee504b33cb37cf6539946e8828b8619d33380cf08f456748f7edb89fe9e9.png
diff --git a/_images/aa405eb75cdf74db6400ca15ee6a81ee69b20f235174fce984863d24a671e2e9.png b/_images/aa405eb75cdf74db6400ca15ee6a81ee69b20f235174fce984863d24a671e2e9.png
diff --git a/_images/afdd3af4e706ec33c4d4f01c8d6b3042534fc3d0bdbd99698f1c6c4ba100e70c.png b/_images/afdd3af4e706ec33c4d4f01c8d6b3042534fc3d0bdbd99698f1c6c4ba100e70c.png
diff --git a/_images/b530ac1891c9505edaae9a67bcd1bde7fe0d61851ec392a8f2583b08fcabb058.png b/_images/b530ac1891c9505edaae9a67bcd1bde7fe0d61851ec392a8f2583b08fcabb058.png
diff --git a/_images/c4dc5574df800c4b6227309cdf584661c1014c9e30d475033bd4ad9a8d00a4f2.png b/_images/c4dc5574df800c4b6227309cdf584661c1014c9e30d475033bd4ad9a8d00a4f2.png
diff --git a/_images/cb0d757a2c99726e41e85c05ed5c2af50033314cc32c57c20ef75472b5661b6c.png b/_images/cb0d757a2c99726e41e85c05ed5c2af50033314cc32c57c20ef75472b5661b6c.png
diff --git a/_images/d1483bfedd25584c14f6e928844c91dd16a18b7bc4885752505e35d779f01468.png b/_images/d1483bfedd25584c14f6e928844c91dd16a18b7bc4885752505e35d779f01468.png
diff --git a/_images/d1d70c92c092863364887776c01deb5b4959446e9343ad46459e3b6899930bea.png b/_images/d1d70c92c092863364887776c01deb5b4959446e9343ad46459e3b6899930bea.png
diff --git a/_images/d25c670f252199383fb460069137b5900d52de5773e4ad511e269b2ba3eeabbe.png b/_images/d25c670f252199383fb460069137b5900d52de5773e4ad511e269b2ba3eeabbe.png
diff --git a/_images/d7dc4c4b76d023d456378afbe0014363b3782d52983df625e9d12e508d794613.png b/_images/d7dc4c4b76d023d456378afbe0014363b3782d52983df625e9d12e508d794613.png
diff --git a/_images/e186733bf85645c632406156980b67678be113998f8d0784684b0ffe05d2339a.png b/_images/e186733bf85645c632406156980b67678be113998f8d0784684b0ffe05d2339a.png
diff --git a/_images/e669d8ff6e3bc4195789d1f0c300d511a8416ebe12ce17ab7aa55135fba407e9.png b/_images/e669d8ff6e3bc4195789d1f0c300d511a8416ebe12ce17ab7aa55135fba407e9.png
diff --git a/_images/e827453d14641294f1c6f2f0d9152008265ebedd611aafc3182be8dc61eefcfc.png b/_images/e827453d14641294f1c6f2f0d9152008265ebedd611aafc3182be8dc61eefcfc.png
diff --git a/_images/e881d4497e65a8e6062164a87a1e656346cb5f4d325c991445e69dfac8261de4.png b/_images/e881d4497e65a8e6062164a87a1e656346cb5f4d325c991445e69dfac8261de4.png
diff --git a/_images/e9c58bbd8fbc712aeae02fd1298e88ac79aaef71bbba30eabafd56ff251574e2.png b/_images/e9c58bbd8fbc712aeae02fd1298e88ac79aaef71bbba30eabafd56ff251574e2.png
diff --git a/_images/ecea9377dbe8aea6d45df7a97088086168c008ef53ba12ae3a982a2a4ea02de3.png b/_images/ecea9377dbe8aea6d45df7a97088086168c008ef53ba12ae3a982a2a4ea02de3.png
diff --git a/_images/f175426f9563394e5a6358ab83b3b020fd426024f57eb89a465086133419abc9.png b/_images/f175426f9563394e5a6358ab83b3b020fd426024f57eb89a465086133419abc9.png
diff --git a/_images/fbf1927602ec660e9493d2f884b4c0e347b33bb7295f2651a084d23b6a3b44ab.png b/_images/fbf1927602ec660e9493d2f884b4c0e347b33bb7295f2651a084d23b6a3b44ab.png
diff --git a/_sources/lecture-18-adsorption.md b/_sources/lecture-18-adsorption.md
diff --git a/genindex.html b/genindex.html
@@ -197,6 +197,7 @@
 <li class="toctree-l1"><a class="reference internal" href="lecture-15-nanoparticles.html">Lecture 15: Nanoparticle Shape and Simulated Annealing</a></li>
 <li class="toctree-l1"><a class="reference internal" href="lecture-16-tech-details.html">Lecture 16: Technical Details: Boundary Conditions, Truncation of Interactions, <em>Etc.</em></a></li>
 <li class="toctree-l1"><a class="reference internal" href="lecture-17-lipids.html">Lecture 17: Lipid Interactions in Membranes and Monte Carlo Simulations</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-18-adsorption.html">Lecture 18: Introduction to Project 1: Monte Carlo Simulations of Adsorption on Surfaces</a></li>
 </ul>
 
     </div>

diff --git a/intro.html b/intro.html
@@ -201,6 +201,7 @@
 <li class="toctree-l1"><a class="reference internal" href="lecture-15-nanoparticles.html">Lecture 15: Nanoparticle Shape and Simulated Annealing</a></li>
 <li class="toctree-l1"><a class="reference internal" href="lecture-16-tech-details.html">Lecture 16: Technical Details: Boundary Conditions, Truncation of Interactions, <em>Etc.</em></a></li>
 <li class="toctree-l1"><a class="reference internal" href="lecture-17-lipids.html">Lecture 17: Lipid Interactions in Membranes and Monte Carlo Simulations</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-18-adsorption.html">Lecture 18: Introduction to Project 1: Monte Carlo Simulations of Adsorption on Surfaces</a></li>
 </ul>
 
     </div>
@@ -419,6 +420,7 @@ <h1>Welcome to Computational Problem Solving in the Chemical Sciences<a class="h
 <li class="toctree-l1"><a class="reference internal" href="lecture-15-nanoparticles.html">Lecture 15: Nanoparticle Shape and Simulated Annealing</a></li>
 <li class="toctree-l1"><a class="reference internal" href="lecture-16-tech-details.html">Lecture 16: Technical Details: Boundary Conditions, Truncation of Interactions, <em>Etc.</em></a></li>
 <li class="toctree-l1"><a class="reference internal" href="lecture-17-lipids.html">Lecture 17: Lipid Interactions in Membranes and Monte Carlo Simulations</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-18-adsorption.html">Lecture 18: Introduction to Project 1: Monte Carlo Simulations of Adsorption on Surfaces</a></li>
 </ul>
 </div>
 </section>

diff --git a/lecture-01-introduction.html b/lecture-01-introduction.html
@@ -196,6 +196,11 @@
 <li class="toctree-l1"><a class="reference internal" href="lecture-11-ensembles.html">Lecture 11: Ensembles and Ergodicity</a></li>
 <li class="toctree-l1"><a class="reference internal" href="lecture-12-monte-carlo.html">Lecture 12: The Monte Carlo Method</a></li>
 <li class="toctree-l1"><a class="reference internal" href="lecture-13-mc-integration.html">Lecture 13: Monte Carlo Integration</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-14-metropolis.html">Lecture 14: A Basic Monte Carlo Algorithm</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-15-nanoparticles.html">Lecture 15: Nanoparticle Shape and Simulated Annealing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-16-tech-details.html">Lecture 16: Technical Details: Boundary Conditions, Truncation of Interactions, <em>Etc.</em></a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-17-lipids.html">Lecture 17: Lipid Interactions in Membranes and Monte Carlo Simulations</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-18-adsorption.html">Lecture 18: Introduction to Project 1: Monte Carlo Simulations of Adsorption on Surfaces</a></li>
 </ul>
 
     </div>

diff --git a/lecture-02-packages.html b/lecture-02-packages.html
@@ -194,6 +194,11 @@
 <li class="toctree-l1"><a class="reference internal" href="lecture-11-ensembles.html">Lecture 11: Ensembles and Ergodicity</a></li>
 <li class="toctree-l1"><a class="reference internal" href="lecture-12-monte-carlo.html">Lecture 12: The Monte Carlo Method</a></li>
 <li class="toctree-l1"><a class="reference internal" href="lecture-13-mc-integration.html">Lecture 13: Monte Carlo Integration</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-14-metropolis.html">Lecture 14: A Basic Monte Carlo Algorithm</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-15-nanoparticles.html">Lecture 15: Nanoparticle Shape and Simulated Annealing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-16-tech-details.html">Lecture 16: Technical Details: Boundary Conditions, Truncation of Interactions, <em>Etc.</em></a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-17-lipids.html">Lecture 17: Lipid Interactions in Membranes and Monte Carlo Simulations</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-18-adsorption.html">Lecture 18: Introduction to Project 1: Monte Carlo Simulations of Adsorption on Surfaces</a></li>
 </ul>
 
     </div>
@@ -659,9 +664,9 @@ <h4>Generating Arrays with Specific Properties<a class="headerlink" href="#gener
 [[1. 1. 1.]
  [1. 1. 1.]
  [1. 1. 1.]]
-[[0.38020829 0.21567557 0.80942245]
- [0.64521477 0.95713798 0.25298782]
- [0.42812882 0.40446243 0.79382746]]
+[[0.54445861 0.74080792 0.94093989]
+ [0.00189169 0.07722415 0.51145732]
+ [0.18499263 0.06097679 0.19381219]]
 </pre></div>
 </div>
 </div>
@@ -742,7 +747,7 @@ <h4>Scatter Plots<a class="headerlink" href="#scatter-plots" title="Link to this
 </div>
 </div>
 <div class="cell_output docutils container">
-<img alt="_images/3813eb41bfc0b094fb0deeaf223a3589ba8299ceeb1f77815e9aef63ea3780bd.png" src="_images/3813eb41bfc0b094fb0deeaf223a3589ba8299ceeb1f77815e9aef63ea3780bd.png" />
+<img alt="_images/a5ffdd948ab8f9628ae26b2d416ebd99b9454edb8a83ca765076fa903b0bfd95.png" src="_images/a5ffdd948ab8f9628ae26b2d416ebd99b9454edb8a83ca765076fa903b0bfd95.png" />
 </div>
 </div>
 </section>
@@ -787,7 +792,7 @@ <h4>Histograms<a class="headerlink" href="#histograms" title="Link to this headi
 </div>
 </div>
 <div class="cell_output docutils container">
-<img alt="_images/26b6cd7c500fe8ffc2e502b476e09ebc4148f22520a235ae40ea139cd0caa0aa.png" src="_images/26b6cd7c500fe8ffc2e502b476e09ebc4148f22520a235ae40ea139cd0caa0aa.png" />
+<img alt="_images/afdd3af4e706ec33c4d4f01c8d6b3042534fc3d0bdbd99698f1c6c4ba100e70c.png" src="_images/afdd3af4e706ec33c4d4f01c8d6b3042534fc3d0bdbd99698f1c6c4ba100e70c.png" />
 </div>
 </div>
 </section>
@@ -870,11 +875,11 @@ <h3>4.2 Series: The 1D Data Structure<a class="headerlink" href="#series-the-1d-
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>0    2.804001
-1   -0.258769
-2    1.045537
-3    0.985343
-4   -0.646079
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>0   -0.231752
+1    0.281163
+2   -0.926110
+3   -0.623194
+4    0.588479
 dtype: float64
 </pre></div>
 </div>
@@ -906,11 +911,11 @@ <h3>4.3 DataFrame: The 2D Data Structure<a class="headerlink" href="#dataframe-t
 </div>
 <div class="cell_output docutils container">
 <div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>          A         B
-0 -0.661308  0.093195
-1  0.009564  0.094149
-2  0.444864  0.048416
-3 -0.797464  0.281626
-4 -0.059068  0.607767
+0  2.309414  0.694430
+1 -0.671326  0.515353
+2 -1.005650  0.102987
+3 -0.084647  0.952898
+4  0.639877  0.712845
 </pre></div>
 </div>
 </div>

diff --git a/lecture-03-control.html b/lecture-03-control.html
@@ -194,6 +194,11 @@
 <li class="toctree-l1"><a class="reference internal" href="lecture-11-ensembles.html">Lecture 11: Ensembles and Ergodicity</a></li>
 <li class="toctree-l1"><a class="reference internal" href="lecture-12-monte-carlo.html">Lecture 12: The Monte Carlo Method</a></li>
 <li class="toctree-l1"><a class="reference internal" href="lecture-13-mc-integration.html">Lecture 13: Monte Carlo Integration</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-14-metropolis.html">Lecture 14: A Basic Monte Carlo Algorithm</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-15-nanoparticles.html">Lecture 15: Nanoparticle Shape and Simulated Annealing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-16-tech-details.html">Lecture 16: Technical Details: Boundary Conditions, Truncation of Interactions, <em>Etc.</em></a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-17-lipids.html">Lecture 17: Lipid Interactions in Membranes and Monte Carlo Simulations</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-18-adsorption.html">Lecture 18: Introduction to Project 1: Monte Carlo Simulations of Adsorption on Surfaces</a></li>
 </ul>
 
     </div>

diff --git a/lecture-04-optimization.html b/lecture-04-optimization.html
@@ -196,6 +196,11 @@
 <li class="toctree-l1"><a class="reference internal" href="lecture-11-ensembles.html">Lecture 11: Ensembles and Ergodicity</a></li>
 <li class="toctree-l1"><a class="reference internal" href="lecture-12-monte-carlo.html">Lecture 12: The Monte Carlo Method</a></li>
 <li class="toctree-l1"><a class="reference internal" href="lecture-13-mc-integration.html">Lecture 13: Monte Carlo Integration</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-14-metropolis.html">Lecture 14: A Basic Monte Carlo Algorithm</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-15-nanoparticles.html">Lecture 15: Nanoparticle Shape and Simulated Annealing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-16-tech-details.html">Lecture 16: Technical Details: Boundary Conditions, Truncation of Interactions, <em>Etc.</em></a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-17-lipids.html">Lecture 17: Lipid Interactions in Membranes and Monte Carlo Simulations</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-18-adsorption.html">Lecture 18: Introduction to Project 1: Monte Carlo Simulations of Adsorption on Surfaces</a></li>
 </ul>
 
     </div>
@@ -742,7 +747,7 @@ <h3>Step 2: Minimizing the Equilibrium Equation<a class="headerlink" href="#step
 <div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>25%
 </pre></div>
 </div>
-<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/var/folders/n9/q030dl3x6qgfqffys4wc7d4c0000gn/T/ipykernel_75226/1733916972.py:1: OptimizeWarning: Initial guess is not within the specified bounds
+<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/var/folders/n9/q030dl3x6qgfqffys4wc7d4c0000gn/T/ipykernel_86439/1733916972.py:1: OptimizeWarning: Initial guess is not within the specified bounds
   result = minimize(
 </pre></div>
 </div>

diff --git a/lecture-05-integration.html b/lecture-05-integration.html
@@ -196,6 +196,11 @@
 <li class="toctree-l1"><a class="reference internal" href="lecture-11-ensembles.html">Lecture 11: Ensembles and Ergodicity</a></li>
 <li class="toctree-l1"><a class="reference internal" href="lecture-12-monte-carlo.html">Lecture 12: The Monte Carlo Method</a></li>
 <li class="toctree-l1"><a class="reference internal" href="lecture-13-mc-integration.html">Lecture 13: Monte Carlo Integration</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-14-metropolis.html">Lecture 14: A Basic Monte Carlo Algorithm</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-15-nanoparticles.html">Lecture 15: Nanoparticle Shape and Simulated Annealing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-16-tech-details.html">Lecture 16: Technical Details: Boundary Conditions, Truncation of Interactions, <em>Etc.</em></a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-17-lipids.html">Lecture 17: Lipid Interactions in Membranes and Monte Carlo Simulations</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-18-adsorption.html">Lecture 18: Introduction to Project 1: Monte Carlo Simulations of Adsorption on Surfaces</a></li>
 </ul>
 
     </div>

diff --git a/lecture-06-linalg.html b/lecture-06-linalg.html
@@ -196,6 +196,11 @@
 <li class="toctree-l1"><a class="reference internal" href="lecture-11-ensembles.html">Lecture 11: Ensembles and Ergodicity</a></li>
 <li class="toctree-l1"><a class="reference internal" href="lecture-12-monte-carlo.html">Lecture 12: The Monte Carlo Method</a></li>
 <li class="toctree-l1"><a class="reference internal" href="lecture-13-mc-integration.html">Lecture 13: Monte Carlo Integration</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-14-metropolis.html">Lecture 14: A Basic Monte Carlo Algorithm</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-15-nanoparticles.html">Lecture 15: Nanoparticle Shape and Simulated Annealing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-16-tech-details.html">Lecture 16: Technical Details: Boundary Conditions, Truncation of Interactions, <em>Etc.</em></a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-17-lipids.html">Lecture 17: Lipid Interactions in Membranes and Monte Carlo Simulations</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-18-adsorption.html">Lecture 18: Introduction to Project 1: Monte Carlo Simulations of Adsorption on Surfaces</a></li>
 </ul>
 
     </div>

diff --git a/lecture-07-regression.html b/lecture-07-regression.html
@@ -196,6 +196,11 @@
 <li class="toctree-l1"><a class="reference internal" href="lecture-11-ensembles.html">Lecture 11: Ensembles and Ergodicity</a></li>
 <li class="toctree-l1"><a class="reference internal" href="lecture-12-monte-carlo.html">Lecture 12: The Monte Carlo Method</a></li>
 <li class="toctree-l1"><a class="reference internal" href="lecture-13-mc-integration.html">Lecture 13: Monte Carlo Integration</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-14-metropolis.html">Lecture 14: A Basic Monte Carlo Algorithm</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-15-nanoparticles.html">Lecture 15: Nanoparticle Shape and Simulated Annealing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-16-tech-details.html">Lecture 16: Technical Details: Boundary Conditions, Truncation of Interactions, <em>Etc.</em></a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-17-lipids.html">Lecture 17: Lipid Interactions in Membranes and Monte Carlo Simulations</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-18-adsorption.html">Lecture 18: Introduction to Project 1: Monte Carlo Simulations of Adsorption on Surfaces</a></li>
 </ul>
 
     </div>

diff --git a/lecture-08-calibration.html b/lecture-08-calibration.html
@@ -196,6 +196,11 @@
 <li class="toctree-l1"><a class="reference internal" href="lecture-11-ensembles.html">Lecture 11: Ensembles and Ergodicity</a></li>
 <li class="toctree-l1"><a class="reference internal" href="lecture-12-monte-carlo.html">Lecture 12: The Monte Carlo Method</a></li>
 <li class="toctree-l1"><a class="reference internal" href="lecture-13-mc-integration.html">Lecture 13: Monte Carlo Integration</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-14-metropolis.html">Lecture 14: A Basic Monte Carlo Algorithm</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-15-nanoparticles.html">Lecture 15: Nanoparticle Shape and Simulated Annealing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-16-tech-details.html">Lecture 16: Technical Details: Boundary Conditions, Truncation of Interactions, <em>Etc.</em></a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-17-lipids.html">Lecture 17: Lipid Interactions in Membranes and Monte Carlo Simulations</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-18-adsorption.html">Lecture 18: Introduction to Project 1: Monte Carlo Simulations of Adsorption on Surfaces</a></li>
 </ul>
 
     </div>

diff --git a/lecture-09-thermo.html b/lecture-09-thermo.html
@@ -196,6 +196,11 @@
 <li class="toctree-l1"><a class="reference internal" href="lecture-11-ensembles.html">Lecture 11: Ensembles and Ergodicity</a></li>
 <li class="toctree-l1"><a class="reference internal" href="lecture-12-monte-carlo.html">Lecture 12: The Monte Carlo Method</a></li>
 <li class="toctree-l1"><a class="reference internal" href="lecture-13-mc-integration.html">Lecture 13: Monte Carlo Integration</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-14-metropolis.html">Lecture 14: A Basic Monte Carlo Algorithm</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-15-nanoparticles.html">Lecture 15: Nanoparticle Shape and Simulated Annealing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-16-tech-details.html">Lecture 16: Technical Details: Boundary Conditions, Truncation of Interactions, <em>Etc.</em></a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-17-lipids.html">Lecture 17: Lipid Interactions in Membranes and Monte Carlo Simulations</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-18-adsorption.html">Lecture 18: Introduction to Project 1: Monte Carlo Simulations of Adsorption on Surfaces</a></li>
 </ul>
 
     </div>

diff --git a/lecture-10-stat-thermo.html b/lecture-10-stat-thermo.html
@@ -196,6 +196,11 @@
 <li class="toctree-l1"><a class="reference internal" href="lecture-11-ensembles.html">Lecture 11: Ensembles and Ergodicity</a></li>
 <li class="toctree-l1"><a class="reference internal" href="lecture-12-monte-carlo.html">Lecture 12: The Monte Carlo Method</a></li>
 <li class="toctree-l1"><a class="reference internal" href="lecture-13-mc-integration.html">Lecture 13: Monte Carlo Integration</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-14-metropolis.html">Lecture 14: A Basic Monte Carlo Algorithm</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-15-nanoparticles.html">Lecture 15: Nanoparticle Shape and Simulated Annealing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-16-tech-details.html">Lecture 16: Technical Details: Boundary Conditions, Truncation of Interactions, <em>Etc.</em></a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-17-lipids.html">Lecture 17: Lipid Interactions in Membranes and Monte Carlo Simulations</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-18-adsorption.html">Lecture 18: Introduction to Project 1: Monte Carlo Simulations of Adsorption on Surfaces</a></li>
 </ul>
 
     </div>

diff --git a/lecture-11-ensembles.html b/lecture-11-ensembles.html
@@ -196,6 +196,11 @@
 <li class="toctree-l1 current active"><a class="current reference internal" href="#">Lecture 11: Ensembles and Ergodicity</a></li>
 <li class="toctree-l1"><a class="reference internal" href="lecture-12-monte-carlo.html">Lecture 12: The Monte Carlo Method</a></li>
 <li class="toctree-l1"><a class="reference internal" href="lecture-13-mc-integration.html">Lecture 13: Monte Carlo Integration</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-14-metropolis.html">Lecture 14: A Basic Monte Carlo Algorithm</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-15-nanoparticles.html">Lecture 15: Nanoparticle Shape and Simulated Annealing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-16-tech-details.html">Lecture 16: Technical Details: Boundary Conditions, Truncation of Interactions, <em>Etc.</em></a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-17-lipids.html">Lecture 17: Lipid Interactions in Membranes and Monte Carlo Simulations</a></li>
+<li class="toctree-l1"><a class="reference internal" href="lecture-18-adsorption.html">Lecture 18: Introduction to Project 1: Monte Carlo Simulations of Adsorption on Surfaces</a></li>
 </ul>
 
     </div>