ACS 2019 | Nanocar Builder

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# .red[Tools for computational design of artificial molecular machines]
### Kutay B. Sezginel, Jessica Nash, Christopher E. Wilmer
#### Chemical Engineering, University of Pittsburgh
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### ACS 2019
### .gray[Sustainable Software for Computational Molecular Science]
#### April 4, 2019 | Orlando, FL

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## Nanocar Race

???
I am sure some of you have heard about the Nanocar Race two years ago.
6 six teams from all over the world came together in France and raced their tiny molecular cars.
Obviously this race was much more different than a regular car race.
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## Molecular Machines

*An assembly of a distinct number of molecular components that are designed to perform machinelike
movements (output) as a result of an appropriate external stimulation (input).*

<div style="width: 40%; text-align: center; float:left; position: relative; right: 35px;">
  <p style="text-align:center;"><b>Kinesin</b></p>
<img src="/assets/img/presentations/molssi/kinesin-walker.gif" height=280>
</div>

???
Kinesins are amazing biomolecular machines which walk on microtubules that span across the cell to
carry precious molecular cargo such as enzymes, proteins...

<div style="width: 60%; text-align: center; float:left; position: relative; right: 20px;">
  <p><b>RNA Polymerase</b></p>
<img src="/assets/img/presentations/molssi/rna-polymerase-animation.gif" height=280>
</div>

???
RNA polymerase is another biomolecular machine which can synthesize RNA molecular from a DNA molecule
by reading the base pairs. So it's basically like a chef reading a recipe.
And I would argue this is much more complex and efficient than any catalyst we can design today.
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## Artificial Molecular Machines

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<div style=" position: relative; top: -20px; bottom: 800px;">
  <h2>Computer-aided design</h2>
</div>

<div style="width: 50%; text-align: center; float:left; position: relative; top: -40px; right: 50px;">
  <img src="/assets/img/presentations/acs-2019/combustion-engine.gif" height=220>
  <p><b>Macroscopic Machines</b></p>
</div>

<div style="width: 50%; text-align: center; float:left; position: relative; top: -265px; right: 20px;">
  <img src="/assets/img/presentations/acs-2019/molecular-motor-rotation.gif" height=220>
  <p><b>Molecular Machines</b></p>
</div>

???
The industrial revolution and the development of complex macroscopi machinery has revolutinized
our lives. As these macroscopic machines became more complex people started using computers to design
them and today computer-aided design is a crucial part of the machine design.

I believe a similar approach could be used to design molecular machines as well.
Obviously, the scale and the physics would be very different but we already have software
which can provide proper physics.

Developing computer-aided design (CAD) tools to build and study artificial
molecular machine systems at different time/length scales.

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<div style=" position: relative; top: -20px;">
  <h2>Nanocars</h2>
</div>

<div style="width: 50%; text-align: center; float:left; position: relative; top: -40px; right: 30px;">
  <img src="/assets/img/presentations/avogadro/Nanocar2.png" height=210>
  <p style="font-size:12px">Shirai, Yasuhiro, et al. Nano Letters 5.11 (2005): 2330-2334.</p>
</div>

<div style="width: 50%; text-align: center; float:left; position: relative; top: -40px; left: 30px;">
  <img src="/assets/img/presentations/avogadro/nanocar-feringa.png" height=210>
  <p style="font-size:12px">Kudernac, Tibor, et al. Nature 479.7372 (2011): 208.</p>
</div>

<div style="width: 100%; text-align: center; float:left; position: relative; top: -30px;">
  <img src="/assets/img/presentations/avogadro/nanocar-light.gif" height=250>
  <p style="font-size:12px">Chiang, Pinn-Tsong, et al. ACS Nano 6.1 (2011): 592-597.</p>
</div>

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<div style="width: 100%; text-align: center; position: relative; top: -15px; right: 20px;">
  <p style="font-weight: bold;">Body Parts - Wheels / Chassis</p>
  <img src="/assets/img/presentations/avogadro/nanocar-bodyparts.png" height=240>
</div>

<div style="width: 100%; text-align: center; position: relative; top: -40px;">
  <p style="font-weight: bold;">Nanocar Assembly</p>
  <img src="/assets/img/presentations/avogadro/nanocar-assembly.png" height=325>
</div>

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<div style=" position: relative; top: -20px;">
  <h2>Nanocar builder</h2>
</div>

<div style="width: 50%; text-align: center; float:left; position: relative; top: -50px; right: 40px;">
  <p style="font-weight: bold;">Wheels</p>
  <img src="/assets/img/presentations/acs-2019/nanocar_wheels.png" height=130>
</div>

<div style="width: 50%; text-align: center; float:left; position: relative; top: -50px; left: 0px;">
  <p style="font-weight: bold;">Chassis</p>
  <img src="/assets/img/presentations/acs-2019/nanocar_chassis.png" height=130>
</div>

<div style="width: 50%; float:left; position: relative; top: -40px; right: 30px;">
  <ul>
    <li>Build metal surfaces</li>
    <li>Test drive your nanocar (LAMMPS)</li>
  </ul>
  <p style="font-weight: bold;">Coming soon</p>
  <ul>
    <li>Multibody rigid MD (Open PR)</li>
    <li>Simulate rotation of wheels</li>
  </ul>
</div>

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<div style=" position: relative; top: -20px;">
  <h2>Nanocar MD trajectory</h2>
</div>

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<div style="width: 100%; text-align: center; float:left; position: relative; top: -30px;">
  <h2><div class="font-effect-anaglyph">Thank you!<div></h2>
</div>

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