Literature DB >> 36227466

Calculating Binodals and Interfacial Tension of Phase-Separated Condensates from Molecular Simulations with Finite-Size Corrections.

Konstantinos Mazarakos1, Sanbo Qin2, Huan-Xiang Zhou3,4.   

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.
© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

Entities:  

Keywords:  Binodals; Biomolecular condensates; FMAP; Finite-size scaling; Interfacial tension; Lennard-Jones fluid; Molecular dynamics simulation; Monte-Carlo simulation; Phase separation

Year:  2023        PMID: 36227466      PMCID: PMC9577455          DOI: 10.1007/978-1-0716-2663-4_1

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  21 in total

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Authors:  Eun Jin Cho; Jun Soo Kim
Journal:  J Phys Chem B       Date:  2012-03-12       Impact factor: 2.991

2.  Critical phenomena in colloid-polymer mixtures: interfacial tension, order parameter, susceptibility, and coexistence diameter.

Authors:  R L C Vink; J Horbach; K Binder
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2005-01-10

3.  Role of solvent in protein phase behavior: Influence of temperature dependent potential.

Authors:  Jianguo Li; Raj Rajagopalan; Jianwen Jiang
Journal:  J Chem Phys       Date:  2008-06-21       Impact factor: 3.488

4.  A Simple Explicit-Solvent Model of Polyampholyte Phase Behaviors and Its Ramifications for Dielectric Effects in Biomolecular Condensates.

Authors:  Jonas Wessén; Tanmoy Pal; Suman Das; Yi-Hsuan Lin; Hue Sun Chan
Journal:  J Phys Chem B       Date:  2021-04-23       Impact factor: 2.991

5.  Valence and patterning of aromatic residues determine the phase behavior of prion-like domains.

Authors:  Erik W Martin; Alex S Holehouse; Ivan Peran; Mina Farag; J Jeremias Incicco; Anne Bremer; Christy R Grace; Andrea Soranno; Rohit V Pappu; Tanja Mittag
Journal:  Science       Date:  2020-02-07       Impact factor: 47.728

6.  Small ion effects on self-coacervation phenomena in block polyampholytes.

Authors:  Scott P O Danielsen; James McCarty; Joan-Emma Shea; Kris T Delaney; Glenn H Fredrickson
Journal:  J Chem Phys       Date:  2019-07-21       Impact factor: 3.488

7.  Complete Phase Diagram for Liquid-Liquid Phase Separation of Intrinsically Disordered Proteins.

Authors:  James McCarty; Kris T Delaney; Scott P O Danielsen; Glenn H Fredrickson; Joan-Emma Shea
Journal:  J Phys Chem Lett       Date:  2019-03-27       Impact factor: 6.475

8.  Removing Thermostat Distortions of Protein Dynamics in Constant-Temperature Molecular Dynamics Simulations.

Authors:  Alan Hicks; Matthew MacAinsh; Huan-Xiang Zhou
Journal:  J Chem Theory Comput       Date:  2021-08-31       Impact factor: 6.578

9.  Calculation of Second Virial Coefficients of Atomistic Proteins Using Fast Fourier Transform.

Authors:  Sanbo Qin; Huan-Xiang Zhou
Journal:  J Phys Chem B       Date:  2019-09-19       Impact factor: 2.991

10.  Further Development of the FFT-based Method for Atomistic Modeling of Protein Folding and Binding under Crowding: Optimization of Accuracy and Speed.

Authors:  Sanbo Qin; Huan-Xiang Zhou
Journal:  J Chem Theory Comput       Date:  2014-05-06       Impact factor: 6.006

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