anchor.diff:  // :revealjsdir: https://cdnjs.cloudflare.com/ajax/libs/reveal.js/3.0.0/
   :stem: latexmath
   :imagesdir: imgs
  +:toc:
   
   == Topics
   
  - * Janus Particle Propulsion
  - * Flow through the Nucleoid
  - * Activity Simulations
  +[discrete]
  +=== Flow through the Nucleoid
  +
  +[discrete]
  +=== Janus Particle Propulsion
  +
  +[discrete]
  +=== Active Particle Simulations
  +
  +== Flow through the Nucleoid
  +
  +// cropped images created with
  +// convert SCinner-cellshape.png -crop 50x100%+0+0 +repage -flop SCinner-cellshape-crop.png 
  +
  +[cols="^a,^a",grid="none",frame="none"]
  +|==================================
  +| Hard Inner Spherocylinder | Soft Potential
  +
  +| image::SCinner2-flow.svg[Spherocylinder Flow, 100%, title="", caption="", align=center]
  +| image::SCforces6-flow.svg[Spherocylinder Flow, 100%, title="", caption="", align=center]
  +
  +| image::SCinner-cellshape-crop.png[Spherocylinder Shape, 55%, title="", caption="", align=center]
  +| image::SCforces-cellshape-crop.png[Spherocylinder Shape, 55%, title="", caption="", align=center]
  +|==================================
  +
  +=== Flow through the Nucleoid
  +
  +
  +[cols="^55a,^45a",grid="none",frame="none"]
  +|==================================
  +| Wiggins | Soft Potential
  +
  +| image::wiggins-nucleoidexclusion-drift.png[Spherocylinder Flow, 100%, title="", caption="", align=center]
  +| image::SCforces6-flow.svg[Spherocylinder Flow, 100%, title="", caption="", align=center]
  +
  +| image::wiggins-nucleoidexclusion-cell.png[Spherocylinder Shape, 100%, title="", caption="", align=center]
  +| image::SCforces-cellshape-crop.png[Spherocylinder Shape, 65%, title="", caption="", align=center]
  +|==================================
  +
  +=== Passive Model
  +
  +[quote, 'Stylianidou, Kuwada, and Wiggins [cite:stylianidou_cytoplasmic_2014]']
  +If we combine the predicted drift velocity maps for the nucleoid exclusion and membrane confinement
  +models, we see striking agreement with the qualitative shape and quantitative scale of the observed
  +drift velocity map throughout the entire cell.
  +
  + * They use an entirely _passive_ model, like ours, to predict the same nucleoid flow
  +
  +=== Position Dependent Diffusion Constant
  +
  +[cols="^2a,^3a",grid="none",frame="none"]
  +|==================================
  +
  +| image::wiggins-diffusion-B.png[title="Fig. 4B from Wiggins", caption=""]
  +
  +|
  + * "`The nucleoid-exclusion model would naively predict both decreased occupancy over the nucleoid as
  + well as a decreased diffusion coefficient. Strikingly, our results show exactly the opposite
  + phenomenology: comparison between the occupancy of MS2-mRNA (Fig. 2 A) and the position
  + dependent diffusion coefficient (Fig. 4 B) reveals that *the highest diffusion coefficients are
  + observed in regions with the lowest MS2-mRNA occupancy and the highest nucleoid density.*`"
  +
  +|==================================
  +
  +=== Position Dependent Diffusion Constant
  +
  +[cols="^.>52a,^.>48a",grid="none",frame="none"]
  +|==================================
  +| Fig. 4B from Wiggins | Soft Potential
  +
  +| image::wiggins-diffusion-B.png["", 75%, title="", caption="", align=center]
  +| image::SCforces6-diffusion.svg["", 75%, title="", caption="", align=center]
  +
  +.<| image::wiggins-nucleoidexclusion-cell.png[Spherocylinder Shape, 60%, title="", caption="", align=center]
  +.<| image::SCforces-cellshape-crop.png[Spherocylinder Shape, 35%, title="", caption="", align=center]
  +
  +|
  +<| Diffusion constant calculated from
  +
  +\[
  +    D \sim \frac{\left< \Delta x^2 \right>}{\Delta t}
  +\]
  +
  +|==================================
  +
  +=== Step Size Distribution
  +
  +[cols="^.>a,^.>a",grid="none",frame="none"]
  +|==================================
  +| Wiggins | Soft Potential
  +
  +| image::wiggins-expsteps.png["", 100%, title="", caption="", align=center]
  +| image::SCforces6-dxdistrib.svg["", 100%, title="", caption="", align=center]
  +
  +| image::wiggins-nucleoidexclusion-cell.png[Spherocylinder Shape, 100%, title="", caption="", align=center]
  +| image::SCforces-cellshape-crop.png[Spherocylinder Shape, 50%, title="", caption="", align=center]
  +
  +|==================================
   
   == Janus Particle Propulsion
   
  
positive.code: 2+| image::randkicktest-MSD-f0.64-R200-N100.svg[title="", caption="", align=center]
  |==================================
  
  == Bibliography
  
  [bibliography]
negative.code: * Particles in H~2~O~2~ move much farther
  --
  
  == Active Particle Simulations
  
  * Metabolic activity does not significantly raise the temperature of the cell (right?)
  * ATP, the main energy source of metabolism, has energy \(E_\mathrm{ATP} \sim 20 k_B T\)
  