Update GMC Proliferation Module

[Jannetty]

Estimated time to review: Medium

Summary of changes:
In general this PR adds volume-sensitive growth for the fly GMC cells (which the Neuroblasts will also use)

• Add default sigmoid volume-based growth for PottsModuleProliferationVolumeBasedDivision if growth rate is set to be volume sensitive
• Add framework for simulating PDE-like growth where cell growth rate is regulated by average cell volume I REMOVED THIS THIS IS NO LONGER IN THIS PR
• Added growth rate updating function for GMCs
• Added necessary parameters for volume-sensitive growth rate and PDE-like growth

How to verify changes:

• run tests (PottsModuleProliferationVolumeBasedDivisionTest and PottsModuleFlyGMCDifferentiationTest)
  Here is a minimal GMC setup file:

<set prefix="2024-10-25-04">
    <series name="dd" start="1" end="1"
            ds=".3" margin="0" height="1" length="302" width="302"
            dt=".083" ticks="576" interval="4">
        <potts>
            <potts.term id="volume" />
            <potts.term id="adhesion" />
            <potts.term id="surface" />
            <!-- <potts.term id="persistence" /> -->
            <!-- <potts.parameter term="adhesion" id="ADHESION" value="80" target="fly-neuron:*"/>
            <potts.parameter term="adhesion" id="ADHESION" value="80" target="fly-gmc:*"/> -->
        </potts>
        <agents>
            <populations>
                <population id="fly-gmc" class="fly-gmc" init="1">
                 <population.link id="fly-neuron" weight="1"/>
                 <population.parameter id="proliferation/BASAL_APOPTOSIS_RATE" value="0"/>
                 <population.parameter id="CRITICAL_VOLUME" value="11" units="um^3" conversion="DS^-3" />
                </population>
                <population id="fly-neuron" class="fly-neuron" init="0">
                <population.parameter id="proliferation/CELL_GROWTH_RATE" value="0"/>
                <population.parameter id="proliferation/BASAL_APOPTOSIS_RATE" value="0"/>
                <population.parameter id="CRITICAL_VOLUME" value="11" units="um^3" conversion="DS^-3" />
                </population>
            </populations>
        </agents>
    </series>
</set>

You can add/adjust the following parameters and run simulations:

<population.parameter id="proliferation/DYNAMIC_GROWTH_RATE_VOLUME" value="1"/>
<population.parameter id="proliferation/GROWTH_RATE_VOLUME_SENSITIVITY" value="4.0"/>

Dynamic growth rate volume is a boolean you can turn on and off. When on (1) small cells grow slower than big cells.
Growth rate volume sensitivity is the exponent that determines the slope of the sigmoid (essentially the hill coefficient) dictating how sensitive the growth rate is to the cell's volume.
PDELIKE is a boolean that, when on, makes the cell growth rate a function of the average GMC volume across all GMCs in the simulation.

[allison-li-1016]

Finished my first pass of reviews - overall looks good but I have a couple of discussion points/questions to be resolved before approving

[kristaphommatha]

LGTM! Just one quick question about one of the changes 😺

[allison-li-1016]

unit tests passed on my end and I ran the model and verified that the sensitivity param is ignored when the boolean is 0. My comments are pretty minor across the board so this looks good to me

[kristaphommatha]

Looks great! Thanks for answering my questions!