As mentioned in the introduction, liquid-liquid phase separation drives the forma-
tion of membrane-less compartments in eukaryotic cells. The droplet-like compartments
possess a large concentration of biopolymers. Now you are asked to study how the size
of polymers (which is closely linked to multivalency) impacts the clustering, and thus
also the formation of organelles.
In the last large scale simulation, you are asked to calculate two quantities related
to phase-separation, as a function of L. The first being the average cluster size divided
by L, ⟨d⟩/L. The second quantity is the average number of clusters, denoted ⟨m⟩. Each
cluster represents an organelle/compartment.
Use T = 300 K, t_r = 1000, N = 30 and M = 5 to calculate ⟨d⟩/L and ⟨m⟩
as a function of L. For L, use 13 evenly spaced values between 3 and 39. Use the
medium flexibility move. You decide yourself the values of t_equil and n, but justify your
choices. Plot ⟨d⟩/L and ⟨m⟩ as a function of L. Discuss your results. How and why
do you think your results would change if you used the rigid move? Because the initial
grid in each system is randomly generated, redoing the simulations might yield quite
different quantitative results. For which values of L do you expect the results to vary
the most? Lastly, choose a different system parameter than L, and discuss qualitatively
how changing this parameter will induce/destroy aggregate formation.
As mentioned in the introduction, liquid-liquid phase separation drives the forma- tion of membrane-less compartments in eukaryotic cells. The droplet-like compartments possess a large concentration of biopolymers. Now you are asked to study how the size of polymers (which is closely linked to multivalency) impacts the clustering, and thus also the formation of organelles.
In the last large scale simulation, you are asked to calculate two quantities related to phase-separation, as a function of L. The first being the average cluster size divided by L, ⟨d⟩/L. The second quantity is the average number of clusters, denoted ⟨m⟩. Each cluster represents an organelle/compartment.
Use T = 300 K, t_r = 1000, N = 30 and M = 5 to calculate ⟨d⟩/L and ⟨m⟩ as a function of L. For L, use 13 evenly spaced values between 3 and 39. Use the medium flexibility move. You decide yourself the values of t_equil and n, but justify your choices. Plot ⟨d⟩/L and ⟨m⟩ as a function of L. Discuss your results. How and why do you think your results would change if you used the rigid move? Because the initial grid in each system is randomly generated, redoing the simulations might yield quite different quantitative results. For which values of L do you expect the results to vary the most? Lastly, choose a different system parameter than L, and discuss qualitatively how changing this parameter will induce/destroy aggregate formation.