Week 1-Journal/Code Club- PKD Paper


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4 months ago by
Hey I wanted to do a weekly journal/code club on the PKD paper since Yuan also had questions on it, and it's the new year!


Week 1-

Discussion on Code/Basics-Focusing on Tubule code
  • The code from the paper is split into 3 folders: IsoCyst, Measure, and tubule.
  • Tubule- creates a kidney tubule with domains and sub cellular parts
    • PKD.py- This imports models and is where you change and input parameters that feed to the Steppables
    • Lines 1-8: Parameters of interest.
      • #PARAMETERS:
        cd=12          #Typical cell diameter
        Lx=10*cd       #Size of lattice - x
        Ly=10*cd       #Size of lattice - y
        Lz=15*cd       #Size of lattice - z
        Trelax=400     #Time for cells to relax boundaries
        debugFreq=100
        • These parameters are the cell diameter and lattice spacing. I believe they correspond to table S3, since this code is making preformed tubules.  
      • Line 10-13 
        • #POTTS PARAMETERS:
          Temp=50               #Potts temperature
          Time=1+20000             #Total number of MCS
          NOrder=4              #NeighborOrder
          • Temp or Tm is in the Potts formula Eq 2
            • T is from the Ising model, which is physics based. More Tm means more interactions I believe, "To mimic cell motility the method iteratively attempts to move the interfaces between adjacent cells, depending on the amplitude of active membrane fluctuations (expressed as a “cellular temperature” [ μ(τ)) and on a force balance of the active forces the cells exert on their environment (e.g. due to chemotaxis or random motility) and the reactive adhesive, cohesive and cellular compression forces. " Source
            • Norder is the number of voxel neighbors that contact energy is calculated over
            • Similar to lines 15- 17 
              • #CONTACT PARAMETERS:
                CNOrder=4             #Distance of interaction
                CINOrder=4            #Internal Distance of interaction
      • Lines 19-20 
        • #VOLUYME PARAMETERS
          LamV=4                #Lambda Volume
          targV=cd*cd*cd        #Target Volume
        • so target is the Vt parameter here in the volume constraint part of the GGH equation.
      • Lines 31-37
        • #CONTACT INHIBITION:
          gFactor=0.8          #Growth factor
          hillCoef=20          #Hill coeficient
          critAlpha=0.35        #Critical alpha
          gFactorSick  =gFactor
          hillCoefSick =hillCoef
          critAlphaSick=critAlpha
        • See the cell contact fraction, under contact inhibition, in the paper for the parameters, and table S4.
          • here K= gfactor which is the max growth rate of the cells (only 1 cell type in this model with 3 sub cellular compartments),ac=critAlpha which is the critical fractional area of cell-cell contact for growth inhibition , n=hillCoefSick. I don't know why critAlphSick and critAlpha are defined separately. The "Sick" is a cell type?
      • Lines 39-41
      • #LUMEN GROWTH:
        Kl=1               
        ApArea=6.*cd*cd*.2  # ApArea=1/Kr
        • Lumen growth, which the tubule module creates in the other stoppable code. Table s2 has info. The growth rate is in volume/time, so voxel/mcs or um3/min. This could be a way to relate experimental results to simulation results.  I think they use this paper from Engelberg as a start for the lumen growth rates (I am trying to figure out which reference Engelberg uses in turn for lumen growth rates).
    • PKDSteppables.py


Community: CompuCell3D
Good job! I have benefited a lot especially for the source of the reference.
written 4 months ago by Yuan  

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