<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>
<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>
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>
<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>
</p>
</section>
<section>
- <h2>Control: Modular stack</h2>
+ <h2>Control: My modular stack</h2>
<p>
<img src="media/build/pyafm-fw-fh.png" />
</p>
<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>
</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>
\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}
\]
<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>
<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>
<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>
</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>
<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>
+ <h2>Conclusions: Salt</h2>
+ <ul>
+ <li>
+ Prelimiary results show the expected destabilizing
+ effect of CaCl₂
+ </li>
+ <li>More contextual data!
+ <ul>
+ <li>Pulling speeds</li>
+ <li>Salt concentrations (physiological levels)</li>
+ <li>Salt species</li>
+ </ul>
+ </li>
+ <li>Mutated proteins?
+ <ul>
+ <li>Is glutamic acid special?</li>
+ </ul>
+ </li>
+ </ul>
+ </section>
+ <section>
+ <h2>Conclusions: Hardware</h2>
+ <table class="center">
+ <tr>
+ <td style="vertical-align: top;">
+ <img src="media/build/afm-hw-hh.png" />
+ </td>
+ <td>
+ <p>For automatic control, it would be nice to have…</p>
+ <ul>
+ <li>Piezos with capacitive feedback ($10k an axis)</li>
+ <li>Independent 4-segment photodiode readout</li>
+ <li>Control over photodiode positioning</li>
+ <li>Control over laser alignment</li>
+ </ul>
+ </td>
+ </tr>
+ </table>
+ </section>
+ <section>
+ <h2>Conclusions: Software</h2>
+ <p>
+ <img src="media/build/pyafm-hw-hh.png" />
+ </p>
+ <p style="text-align: left;">
+ Everything works for me, and I expect it will work for
+ others… but no software (except
+ maybe <a href="http://en.wikipedia.org/wiki/TeX#Development">TeX</a>)
+ is without bugs. Testers welcome!
+ </p>
+ </section>
</section>
<section>
<section>
- <h1>THE END</h1>
- <p style="text-align: center;">
- Written with <a href="http://lab.hakim.se/reveal-js/">reveal.js</a>
- </p>
+ <h1>The End</h1>
+ </section>
+ <section>
+ <h1>Thanks!</h1>
+ <table>
+ <tr>
+ <td rowspan="2" style="vertical-align: top;">
+ <ul>
+ <li>Guoliang Yang</li>
+ <li>Luis Cruz Cruz</li>
+ <li>Marisa Roman</li>
+ <li>Runcong Liu</li>
+ <li>Jian-Min Yuan</li>
+ <li>Jun Xi</li>
+ <li>Som Tyagi</li>
+ <li>Michel Vallières</li>
+ <li>Everyone else in Drexel physics!</li>
+ <li>
+ <a href="http://dx.doi.org/10.1093/bioinformatics/btp180">Sandal,
+ Benedetti, et al.</a> for initial work on Hooke</li>
+ </ul>
+ </td>
+ <td style="vertical-align: top;">
+ <ul>
+ <li><a href="http://lab.hakim.se/reveal-js/">reveal.js</a></li>
+ <li><a href="http://sourceforge.net/projects/pymol/">PyMOL</a></li>
+ <li><a href="http://asymptote.sourceforge.net/">Asymptote</a></li>
+ <li>…</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td style="vertical-align: top;">
+ <ul>
+ <li>My family!</li>
+ </ul>
+ </td>
+ </tr>
+ </table>
+ </section>
</section>
</div>
</div>
projects / reveal.js.git / blobdiff