Hue Sun CHAN Research Group
    Software for Analytical Theories of
    Biomolecular Condensates

    First published online: May 2021 | home | group publications | group webpages |

    Software developed by our group members for numerical solutions to analytical theories and field-theoretic simulations of sequence-dependent phase separation is available from the Github respository via the following links.

    Links to useful computational resources for coarse-grained explicit-chain simulations of sequence-dependent phase behaviors are also provided further below.



            RPA rationalizes the signficantly different
            liquid-liquid phase separation propensities of
            wildtype Ddx4 intrinsically disordered region
            Ddx4N1 and its charge-scrambled variant
            Ddx4N1CS; see Lin, Forman-Kay & Chan,
            Phys Rev Lett (2016) 117:178101.




    Construction of Phase Diagrams from Analytical Free Energy Functions,
    Random Phase Approximation (RPA), renormalized Gaussian-RPA (rG-RPA)
    Github link:
    https://github.com/laphysique/Protein_RPA

    References (partial list):
    Lin, Forman-Kay & Chan (2016) Sequence-specific polyampholyte phase separation in membraneless organelles. Phys Rev Lett 117:178101.
    Lin, Song, Forman-Kay & Chan (2017) Random-phase-approximation theory for sequence-dependent, biologically functional liquid-liquid phase separation of intrinsically disordered proteins. J Mol Liq 228:176-193.
    Lin, Brady, Forman-Kay & Chan (2017) Charge pattern matching as a "fuzzy" mode of molecular recognition for the functional phase separations of intrinsically disordered proteins. New J Phys 19;115003.
    Lin, Brady, Chan & Ghosh (2020) A unified analytical theory of heteropolymers for sequence-specific phase behaviors of polyelectrolytes and polyampholytes. J Chem Phys 152:045102.


    Complex Langevin (fictitious) time evolution of
    the real parts of the FTS bead-density operators
    showing partial demixing of polyampholyte
    sequences sv9 and sv28 in the condensed droplet;
    see
    Pal, Wessén, Das & Chan, Phys Rev E (2021)
    103:042406
    .






    Field-Theoretic Simulation (FTS),
    Complex Langevin (CL) sampling, Chemical Potentials, Osmotic Pressure
    Github links:
    https://github.com/jwessen/IDP_phase_separation
    https://github.com/mmTanmoy/IDP_phase_separation
    https://github.com/laphysique/FTS_polyampholyte_water

    References (partial list):
    McCarty, Delaney, Danielsen, Fredrickson & Shea (2019) Complete phase diagram for liquid-liquid phase separation of intrinsically disordered proteins. J Phys Chem Lett 10:1644-1652.
    Pal, Wessén, Das & Chan (2021) Subcompartmentalization of polyampholyte species in organelle-like condensates is promoted by charge-pattern mismatch and strong excluded-volume interaction. Phys Rev E 103:042406.
    Wessén, Pal, Das, Lin & Chan (2021) A simple explicit-solvent model of polyampholyte phase behaviors and its ramifications for dielectric effects in biomolecular condensates. J Phys Chem B 125:4337-4358 (journal cover).


            Real Langevin molecular dynamics
            time evolution of a condensed droplet
            showing subcompartmentalization-like
            demixing of polyampholyte sequences
            sv1 (cyan/pink) and sv28 (blue/red)
            with significantly different sequence
            charge patterns; see Pal, Wessén,
            Das & Chan, Phys Rev E (2021)
            103:042406.







    Coarse-Grained Molecular Dynamics,
    "Slab" Sampling

    Useful links:

    http://glotzerlab.engin.umich.edu/hoomd-blue/
    https://lammps.sandia.gov/
    https://www.ks.uiuc.edu/Research/vmd/


    References (partial list):
    Dignon, Zheng, Kim, Best & Mittal (2018) Sequence determinants of protein phase behavior from a coarse-grained model. PLoS Comput Biol 14:e1005941.
    Das, Amin, Lin & Chan (2018) Coarse-grained residue-based models of disordered protein condensates: Utility and limitations of simple charge pattern parameters. Phys Chem Chem Phys 20:28558-28574.
    Das, Lin, Vernon, Forman-Kay & Chan (2020) Comparative roles of charge, π, and hydrophobic interactions in sequence-dependent phase separation of intrinsically disordered proteins. Proc Natl Acad Sci USA 117:28795-28805.