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Updated: Jul 11, 2026

Sedimentation Equilibrium of a Small Oligomer-forming Membrane Protein: Effect of Histidine Protonation on Pentameric Stability
Published on: April 2, 2015
Finite-size shifts in simulated protein droplet phase diagrams
Daniel Nilsson1, Anders Irbäck1
1Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden.
Abstract:
Computer simulation can provide valuable insight into the forces driving biomolecular liquid-liquid phase separation. However, the simulated systems have a limited size, which makes it important to minimize and control finite-size effects. Here, using a phenomenological free-energy ansatz, we investigate how the single-phase densities observed in a canonical system under coexistence conditions depend on the system size and the total density. We compare the theoretical expectations with results from Monte Carlo simulations based on a simple hydrophobic/polar protein model. We consider both cubic systems with spherical droplets and elongated systems with slab-like droplets. The results presented suggest that the slab simulation method greatly facilitates the estimation of the coexistence densities in the large-system limit.

