ArticleMethods in molecular biology (Clifton, N.J.)2023
Calculating Binodals and Interfacial Tension of Phase-Separated Condensates from Molecular Simulations with Finite-Size Corrections.
Article in Methods in molecular biology (Clifton, N.J.), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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5 citing papers in PubMed.
- Modeling biomolecular condensates across scales: Atomistic, coarse-grained, and data-driven approaches.Advances in physics: X · 2025Article
- Fundamental Aspects of Phase-Separated Biomolecular Condensates.Chemical reviews · 2024Review
- Atomistic modeling of liquid-liquid phase equilibrium explains dependence of critical temperature on γ-crystallin sequence.Communications biology · 2023Article
- Atomistic Modeling of Liquid-Liquid Phase Equilibrium Explains Dependence of Critical Temperature on γ-Crystallin Sequence.bioRxiv : the preprint server for biology · 2023Article
- SpiDec: Computing binodals and interfacial tension of biomolecular condensates from simulations of spinodal decomposition.Frontiers in molecular biosciences · 2022Article
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3 authors.
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Abstract
We illustrate three methods for calculating the binodals of phase-separated condensates from molecular simulations. Because molecular simulations can only be carried out for small system sizes, correction for finite sizes may be required for making direct comparison between calculated results and experimental data. We first summarize the three methods and then present detailed implementation of each method on a Lennard-Jones fluid. In the first method, chemical potentials are calculated over a range of particle densities in canonical-ensemble simulations; the densities of the dilute and dense phases at the given temperature are then found by a Maxwell equal-area construction. In Gibbs-ensemble Monte Carlo, the exchange between separated dilute and dense phases is simulated to obtain their densities. Lastly, slab-geometry molecular dynamics simulations model the dilute and dense phases in coexistence and yield not only their densities but also their interfacial tension. The three types of simulations are carried out for a range of system sizes, and the results are scaled to generate the binodals corrected for finite system sizes. Size-corrected interfacial tension is also produced from slab-geometry molecular dynamics simulations.
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