index.html.itex: Claim my stuff (the pyafm stack and sawsim)

[reveal.js.git] / index.html.itex

diff --git a/index.html.itex b/index.html.itex
index 0c3b7af078f9f89aaff1783edbacd8948bc8e2ea..3d9bc48f3633b455fa6e3daf2525407a2417fc53 100644 (file)
--- a/index.html.itex
+++ b/index.html.itex
@@ -53,9 +53,11 @@
                                                        <li><a href="#/3">Single molecule force spectroscopy</a></li>
                                                        <li><a href="#/4">Experiment control</a></li>
                                                        <li><a href="#/5">Cantilever calibration</a></li>
-                                                       <li><a href="#/6">Monte Carlo unfolding simulations</a></li>
-                                                       <li><a href="#/7">Unfolding in salty buffers</a></li>
-                                                       <li><a href="#/8">Conclusions</a></li>
+                                                       <li><a href="#/6">
+                                                                       Modeling: Monte Carlo unfolding simulations</a></li>
+                                                       <li><a href="#/7">
+                                                                       Application: Unfolding in salty buffers</a></li>
+                                                       <li><a href="#/8">Conclusions and future work</a></li>
                                                </ol>
                                        </section>
                                        <section>
@@ -169,9 +171,11 @@ NLKVKEL</pre>
                                                        <li><a href="#/3">Single molecule force spectroscopy</a></li>
                                                        <li><a href="#/4">Experiment control</a></li>
                                                        <li><a href="#/5">Cantilever calibration</a></li>
-                                                       <li><a href="#/6">Monte Carlo unfolding simulations</a></li>
-                                                       <li><a href="#/7">Unfolding in salty buffers</a></li>
-                                                       <li><a href="#/8">Conclusions</a></li>
+                                                       <li><a href="#/6">
+                                                                       Modeling: Monte Carlo unfolding simulations</a></li>
+                                                       <li><a href="#/7">
+                                                                       Application: Unfolding in salty buffers</a></li>
+                                                       <li><a href="#/8">Conclusions and future work</a></li>
                                                </ol>
                                        </section>
                                        <section>
@@ -257,9 +261,11 @@ NLKVKEL</pre>
                                                                        Single molecule force spectroscopy</a></li>
                                                        <li><a href="#/4">Experiment control</a></li>
                                                        <li><a href="#/5">Cantilever calibration</a></li>
-                                                       <li><a href="#/6">Monte Carlo unfolding simulations</a></li>
-                                                       <li><a href="#/7">Unfolding in salty buffers</a></li>
-                                                       <li><a href="#/8">Conclusions</a></li>
+                                                       <li><a href="#/6">
+                                                                       Modeling: Monte Carlo unfolding simulations</a></li>
+                                                       <li><a href="#/7">
+                                                                       Application: Unfolding in salty buffers</a></li>
+                                                       <li><a href="#/8">Conclusions and future work</a></li>
                                                </ol>
                                        </section>
                                        <section>
@@ -311,9 +317,11 @@ NLKVKEL</pre>
                                                        <li><a href="#/3">Single molecule force spectroscopy</a></li>
                                                        <li><a href="#/4" class="active">Experiment control</a></li>
                                                        <li><a href="#/5">Cantilever calibration</a></li>
-                                                       <li><a href="#/6">Monte Carlo unfolding simulations</a></li>
-                                                       <li><a href="#/7">Unfolding in salty buffers</a></li>
-                                                       <li><a href="#/8">Conclusions</a></li>
+                                                       <li><a href="#/6">
+                                                                       Modeling: Monte Carlo unfolding simulations</a></li>
+                                                       <li><a href="#/7">
+                                                                       Application: Unfolding in salty buffers</a></li>
+                                                       <li><a href="#/8">Conclusions and future work</a></li>
                                                </ol>
                                        </section>
                                        <section>
@@ -329,7 +337,7 @@ NLKVKEL</pre>
                                                </p>
                                        </section>
                                        <section>
-                                               <h2>Control: Modular stack</h2>
+                                               <h2>Control: My modular stack</h2>
                                                <p>
                                                        <img src="media/build/pyafm-fw-fh.png" />
                                                </p>
@@ -492,9 +500,11 @@ index 60741c6..e76b118 100644
                                                        <li><a href="#/3">Single molecule force spectroscopy</a></li>
                                                        <li><a href="#/4">Experiment control</a></li>
                                                        <li><a href="#/5" class="active">Cantilever calibration</a></li>
-                                                       <li><a href="#/6">Monte Carlo unfolding simulations</a></li>
-                                                       <li><a href="#/7">Unfolding in salty buffers</a></li>
-                                                       <li><a href="#/8">Conclusions</a></li>
+                                                       <li><a href="#/6">
+                                                                       Modeling: Monte Carlo unfolding simulations</a></li>
+                                                       <li><a href="#/7">
+                                                                       Application: Unfolding in salty buffers</a></li>
+                                                       <li><a href="#/8">Conclusions and future work</a></li>
                                                </ol>
                                        </section>
                                        <section>
@@ -527,30 +537,27 @@ index 60741c6..e76b118 100644
                                        </section>
                                        <section>
                                                <h2>Calibration: Equipartition</h2>
-                                               <p>
-                                                       For a damped harmonic oscillator
-                                               </p>
-
-\[
-  -\kappa x_c
-  - \gamma \frac{\mathrm{d}\! x_c}{\mathrm{d}\! t}
-  + F_\text{ext}(t)
-    = m\frac{\mathrm{d}^2\! x}{\mathrm{d}\! t^2} \;,
-\]
-
-                                               <p>
-                                                       the energy in each degree of freedom is $\frac{1}{2}k_B
-                                                       T$.
-                                               </p>
+                                               <table class="center">
+                                                       <tr>
+                                                               <td style="vertical-align: middle;">
+                                                                       <img src="media/build/calibcant-flow-hw-fh.png" />
+                                                               </td>
+                                                               <td>
+                                                                       <p>
+                                                                               The average spring energy is
+                                                                       </p>
 
 \[
   \frac{1}{2} \kappa \left\langle x_c^2 \right\rangle = \frac{1}{2}k_B T \;,
 \]
 
-                                               <p>
-                                                       where $k_B$ is Boltzmann's constant and $T$ is the
-                                                       temperature.
-                                               </p>
+                                                                       <p>
+                                                                               where $k_B$ is Boltzmann's constant and $T$ is the
+                                                                               temperature.
+                                                                       </p>
+                                                               </td>
+                                                       </tr>
+                                               </table>
                                        </section>
                                        <section>
                                                <h2>Calibration: Vibration</h2>
@@ -575,8 +582,8 @@ index 60741c6..e76b118 100644
   \sqrt{\left\langle x_c^2 \right\rangle}
     &= \sqrt{\frac{\left\langle V_p^2 \right\rangle}{\sigma_p^2}}
     = 0.28 \; \text{nm} \\
-  \kappa &= \frac{k_B T \sigma_p^2}{\left\langle V_p^2 \right\rangle}
-    = 54 \pm 3 \; \text{pN/nm}
+  \kappa = \frac{k_B T \sigma_p^2}{\left\langle V_p^2 \right\rangle}
+    &= 54 \pm 3 \; \text{pN/nm}
 \end{aligned}
 \]
 
@@ -671,9 +678,10 @@ index 60741c6..e76b118 100644
                                                        <li><a href="#/4">Experiment control</a></li>
                                                        <li><a href="#/5">Cantilever calibration</a></li>
                                                        <li><a href="#/6" class="active">
-                                                                       Monte Carlo unfolding simulations</a></li>
-                                                       <li><a href="#/7">Unfolding in salty buffers</a></li>
-                                                       <li><a href="#/8">Conclusions</a></li>
+                                                                       Modeling: Monte Carlo unfolding simulations</a></li>
+                                                       <li><a href="#/7">
+                                                                       Application: Unfolding in salty buffers</a></li>
+                                                       <li><a href="#/8">Conclusions and future work</a></li>
                                                </ol>
                                        </section>
                                        <section>
@@ -713,6 +721,9 @@ index 60741c6..e76b118 100644
                                                        <img src="media/build/sawsim-states-hw-fh.png"
                                                                         style="vertical-align: middle;">
                                                </p>
+                                               <p>
+                                                       My simulation framework.
+                                               </p>
                                        </section>
                                        <section>
                                                <h2>Sawsim: Simulation loop</h2>
@@ -823,10 +834,11 @@ index 60741c6..e76b118 100644
                                                        <li><a href="#/3">Single molecule force spectroscopy</a></li>
                                                        <li><a href="#/4">Experiment control</a></li>
                                                        <li><a href="#/5">Cantilever calibration</a></li>
-                                                       <li><a href="#/6">Monte Carlo unfolding simulations</a></li>
+                                                       <li><a href="#/6">
+                                                                       Modeling: Monte Carlo unfolding simulations</a></li>
                                                        <li><a href="#/7" class="active">
-                                                                       Unfolding in salty buffers</a></li>
-                                                       <li><a href="#/8">Conclusions</a></li>
+                                                                       Application: Unfolding in salty buffers</a></li>
+                                                       <li><a href="#/8">Conclusions and future work</a></li>
                                                </ol>
                                        </section>
                                        <section>
@@ -881,7 +893,7 @@ index 60741c6..e76b118 100644
                                                                </tr>
                                                        </tbody>
                                                </table>
-                                               <p>Ca²⁺ radius ∼1.1 Å, H-bond ∼2 Å.</p>
+                                               <p><small>Ca²⁺ radius ∼1.1 Å, H-bond ∼2 Å.</small></p>
                                        </section>
                                </section>
                                <section>
@@ -893,9 +905,12 @@ index 60741c6..e76b118 100644
                                                        <li><a href="#/3">Single molecule force spectroscopy</a></li>
                                                        <li><a href="#/4">Experiment control</a></li>
                                                        <li><a href="#/5">Cantilever calibration</a></li>
-                                                       <li><a href="#/6">Monte Carlo unfolding simulations</a></li>
-                                                       <li><a href="#/7">Unfolding in salty buffers</a></li>
-                                                       <li><a href="#/8" class="active">Conclusions</a></li>
+                                                       <li><a href="#/6">
+                                                                       Modeling: Monte Carlo unfolding simulations</a></li>
+                                                       <li><a href="#/7">
+                                                                       Application: Unfolding in salty buffers</a></li>
+                                                       <li><a href="#/8" class="active">
+                                                                       Conclusions and future work</a></li>
                                                </ol>
                                        </section>
                                        <section>