WLAB GM - Nanocar

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## Research Update | .red[Nanocar]
### Kutay B. Sezginel
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### WilmerLab Group Meeting
#### September 10, 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: 40%; text-align: center; float:left; padding: 0px 0px 0px 0px;">
 Kinesin
<img src="/assets/img/presentations/molssi/kinesin-walker.gif" height=250>
</div>

<div style="width: 60%; text-align: center; float:left; padding: 0px 0px 0px 0px;">
 RNA Polymerase
<img src="/assets/img/presentations/molssi/rna-polymerase-animation.gif" height=250>
</div>

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### Research Objective

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

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### Artificial Molecular Machines

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## Nanocars

.col2[<img src="/assets/img/presentations/avogadro/Nanocar2.png" height=200>]

.col2[<img src="/assets/img/presentations/avogadro/nanocar-feringa.png" height=200>]
--

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## Nanocar objectives

### .red[1 | Nanocar structure-property relationships]

- **Properties:** speed (diffusivity), directionality, cargo (capacity / type)
- **Structure:** wheels, chassis, surface interactions

### .red[2 | Nanocar builder]

**Avogadro 2 Plug-in**
- Select parts (chassis and wheels) and assemble
- Parametric building (chassis size / wheel diameter)
- Surface builder (ASE)
- Energy minimization
- Force field assignment

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**Body Parts - Wheels / Chassis**
<img src="/assets/img/presentations/avogadro/nanocar-bodyparts.png" height=230>

**Nanocar Assembly**
<img src="/assets/img/presentations/avogadro/nanocar-assembly.png" height=310>

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## Diffusion

### 1 | Transition State Theory (Umbrella Sampling)

### 2 | Molecular Dynamics

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### Surface diffusion of large molecules

.col3[DC<img src="/assets/img/presentations/DC.png" height=150>]
.col3[HtBDC<img src="/assets/img/presentations/HtBDC.png" height=150>]
.col3[Violet .red[Lander]<img src="/assets/img/presentations/VL.png" height=150>]

.col3[C60<img src="/assets/img/presentations/C60.png" height=150>]
.col3[.red[p-Carborane]<img src="/assets/img/presentations/PCARBORANE.png" height=150>]
.col3[PVBA<img src="/assets/img/presentations/PVBA.png" height=150>]

.col3[BtPHD<img src="/assets/img/presentations/BtPHD.png" height=150>]
.col3[DNHD<img src="/assets/img/presentations/DNHD.png" height=150>]
.col3[TPEE<img src="/assets/img/presentations/TPEE.png" height=150>]

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## MD Simulation Setup

- **NVT | Temperature:** 200 K
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- **Length:** 10 ns (2 ns equilibration + 8 ns production) | Δt: 1 fs
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- **Sampling:** 10 runs (different velocity distribution)
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- **Force field:** UFF
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- **Surface**
 - Rigid and vdW interactions are multiplied by 5 (25 εCu)
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 - **Molecule**
 - Flexible
 - Rigid

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## Diffusion coefficient calculation

$$MSD = \langle (x - x_0)^2 \rangle = \frac{1}{N} \sum^N_i [x_n(t) - x_n(0)]^2 $$

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## Diffusion coefficient calculation

.col2[DC Flexible Runs<img src="/assets/img/presentations/nanocar/dc_flexible_msd_fft_molecule_plots.png" height=390>]

.col2[DC Flexible Average<img src="/assets/img/presentations/nanocar/dc_flexible_msd_fft_all_plot.png" height=390>]

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## Diffusion coefficient directionality

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## Diffusion coefficient directionality

.col2[x-direction <img src="/assets/img/presentations/tst-fcc-110-x.png" height=150>]
.col2[y-direction <img src="/assets/img/presentations/tst-fcc-110-y.png" height=150>]

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#### Trajectory for each molecule (flexible)

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#### Trajectory for each molecule (rigid)

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### vdW Energy

<img src="/assets/img/presentations/nanocar/md-thermo-epair-t0.png" height=500>
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### Molecular Energy

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### Energy vs Diffusion

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### Temperature

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### Energy Equilibration

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### Effect of sampling

Averaged x & y directions | Standard Error = $\frac{\sigma}{\sqrt{n}}$

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### Individual runs

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## Next Steps

- Calculate other molecular properties
- Finish analyzing dcTST results
- Compare dcTST with MD results
- Avogadro Nanocar builder

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

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### Molecule trajectories (flexible)

<a class="tooltip">PCARBORANE | MW: 144.23 g/mol
 <img src="/assets/img/presentations/nanocar/pcarborane-md-flexible-trajectory.png" height=300>
</a>

<a class="tooltip">BtPHD | MW: 340.50 g/mol
 <img src="/assets/img/presentations/nanocar/btphd-md-flexible-trajectory.png" height=300>
</a>

<a class="tooltip">HtBDC | MW: 787.17 g/mol
 <img src="/assets/img/presentations/nanocar/htbdc-md-flexible-trajectory.png" height=300>
</a>