MolSSI - Nanocar

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# MolSSI Research Proposal
## .red[Computational Design of Artificial Molecular Machines]
### Kutay B. Sezginel
#### July 30, 2018

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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: 50%; text-align: center; float:left; padding: 0px 0px 0px 0px;">
  <p style="text-align:center;"><b>Kinesin</b></p>
<img src="/assets/img/presentations/molssi/kinesin-walker.gif" height=280>
</div>

<div style="width: 50%; text-align: center; float:left; padding: 0px 0px 50px 0px;">
  <p style="text-align:center;"><b>RNA Polymerase</b></p>
<img src="/assets/img/presentations/molssi/rna-polymerase-animation.gif" height=280>
</div>

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## 1. Project

.red[**Developing a computer-aided design tool to build and study artficial molecular machine systems at different length scales.**]

### Artificial Molecular Machines

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## 2. Phase I Goal - Nanocar builder

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## 2. Phase I Goal - Nanocar builder

- **Atomic coordinates of wheels and chassis**

- Experimental and hypothetical

- **Geometric operations to assemble Nanocars**
  - Manipulating wheel and chassis sizes
  - Connecting wheels to chassis
  - Placing nanocars on surfaces

- **Energetic calculations and force field assignment**
  - Surface interaction energy
  - Topological analysis and simulation setup

- **UI Integration**
  - Interactive Nanocar builder

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## 3. Audience

- Academia (Experimental & Computational)

- Outreach and education (high school students and undergraduates)

- Nanocar racers

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## 4. MolSSI Support

- How to contribute code to larger open source projects

- UI Integration

.col3[<p align="center"><img src="/assets/img/presentations/molssi/avogadro-logo.png" height=150></p>]
.col3[<p align="center"><img src="/assets/img/presentations/molssi/ase-logo.png" height=150></p>]
.col3[<p align="center"><img src="/assets/img/presentations/molssi/blender-logo.png" height=150></p>]

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## 5. Similar Work

.col2L[
- **ASE**
  - Nanotubes, nanoribbons
  - Crystals
  - Building tools
]
.col2[<img src="/assets/img/presentations/molssi/ase-builder.png" height=140>]

.col2L[
- **Avogadro**
  - Molecule drawing
  - Nanotubes
]
.col2[<img src="/assets/img/presentations/molssi/avogadro-builder.png" height=140>]

.col2L[
- **Blender**
  - Nanoparticles
]
.col2[<img src="/assets/img/presentations/molssi/blender-builder.png" height=150>]

.col2[<br>    - `STK` (Dr. Kim Jelfs - Imperial College London)]
.col2[<br>    - `mBuild` (Dr. Peter Cummings - Vanderbilt University)]

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# <div class="font-effect-anaglyph">Thank you!<div>