anchor.diff:  \]
   ** WCA potential / repulsive Lennard-Jones for \(U\)
   ** Damping \(\gamma\) to simulate solution viscosity
  -** Random, instantaneous "kicks" to the particles
  -*** \(\vec \Gamma_T\) for the thermostat; balanced by \(\gamma\)
  -*** \(\vec \Gamma_k\) for metabolism
  +** *Random, instantaneous "kicks"* to the particles
  +*** \(\vec \Gamma_T\) *for the thermostat*; balanced by \(\gamma\), the drag force
  +*** \(\vec \Gamma_k\) *for metabolism*
   
   === Random Kicks
   
  
positive.code: |
  * \(\Gamma_T \sim \Delta t k_B T \sim {10}^{-5} k_B T\)
  * Every timestep
  * Correlated: satisfy FDT
  * Gaussian distribution
  * Balanced by \(-\gamma \vec v\)
  |
  * \(0 \le E_k \le 20 k_B T\)
  * Instantaneous
  
negative.code: // :revealjsdir: https://cdnjs.cloudflare.com/ajax/libs/reveal.js/3.0.0/
  :stem: latexmath
  :imagesdir: imgs
  :toc:
  
  == Topics
  
  [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
  
  