Agent/Parameter	Value	Source/Information
Nucleus
Radius	12 µm	Experimental measurements
Nucleolus
Radius	4.5 µm ±0.2	Experimental measurements
Friction	1	Empirical to obtain diffusion coefficients similar to experimental measurements of nucleoli in Control NSN oocytes
Nucleus repulsion	30	Strength of confinement; empirical to avoid objects leaving the nucleus while allowing small deformation
Sphere repulsion	30	Strength of hard-core repulsion with other agents
Droplet
Initial radius	0.9 µm ± 0.01	Experimental measurements of nuclear speckles in NSN oocytes
Initial number	55	Experimental quantifications of nuclear speckles in NSN oocytes
Nucleus repulsion	30	Strength of confinement; empirical to avoid objects leaving the nucleus while allowing small deformation
Sphere repulsion	10	Hard-core repulsion with other agents; empirical, with values moderated to allow small deformation
Fusion speed	Instantaneous	Simplification based on experimental observations
Friction	0.55	Empirical to obtain diffusion coefficients similar to experimental measurements of speckles in Control NSN oocytes
Obstacle
Radius	0.85 µm ± 0.4	Empirical to confine nucleolus and speckle motion and to obtain similar diffusion coefficients and anomalous MSD exponents as in NSN experiments
Initial number	875	Empirical to confine nucleolus and speckle motion and to obtain similar diffusion coefficients and anomalous MSD exponents as in NSN experiments
Nucleus repulsion	30	Strength of confinement; empirical to avoid objects leaving the nucleus while allowing small deformation
Sphere repulsion	30	Hard-core repulsion with other agents; an empirical value equal to the nucleolus value
Friction	5	Empirical to have lower mobility when compared to other agents
Proportion contact	0 initial 0.4 after switch	Evaluated from experimental NSN vs. SN chromatin area in experiments
Simulation
Time step	0.01 s	For numerical stability
Transition time	12 h	Time when simulation state switches from NSN-like to SN-like
Minimal mobility D0	0.01	Calculated by linear regression of nucleolus diffusion relative to cytoplasmic stirring11
Coefficient of mobility α	0.11	Calculated by linear regression of nucleolus diffusion relative to cytoplasmic stirring11