These are the production python scripts for a series of publications using the random-phase approximation (RPA) polymer theory to calculate the liquid-liquid phase separation (LLPS) of charged heteropolymers, particularly intrinsically disordered proteins (IDPs).
The original customized deploy script is not attached. Use the ps_main_ files for calculating the phase diagram of an assigned sequence.
Check the following paper for an overview of the physics theories for LLPS and IDPs:
Y.-H. Lin, J. D. Forman-Kay, and H. S. Chan, Biochemistry 57, 2499–2508 (2018)
Papers based on this algorithm are:
Y.-H. Lin, J. D. Forman-Kay, and H. S. Chan, Phys. Rev. Lett. 117, 178101 (2016)
Y.-H. Lin, J. Song, J. D. Forman-Kay, and H. S. Chan, J. Mol. Liq. 228, 176–193 (2017)
Y.-H. Lin and H. S. Chan, Biophys. J. 112, 2043–2046 (2017)
Y.-H. Lin, J. P. Brady, J. D. Forman-Kay, and H. S. Chan, New J. Phys. 19, 115003 (2017)
Y.-H. Lin, J. P. Brady, H. S. Chan, and K. Ghosh, J. Chem. Phys. 152, 045102 (2020)
Some papers comparing this algorithm with other experimental and numerical/simulation methods:
J. P. Brady, P. J. Farber, A. Sekhar, Y.-H. Lin, R. Huang, A. Bah, T. J. Nott, H. S. Chan, A. J. Baldwin, J. D. Forman-Kay, and L. E. Kay, PNAS 114, E8194–E8203 (2017)
S. Das, A. Eisen, Y.-H. Lin, and H. S. Chan, J. Phys. Chem. B 122, 5418–5431 (2018)
S. Das, A. N. Amin, Y.-H. Lin, and H. S. Chan, Phys. Chem. Chem. Phys. 20, 28558–28574 (2018)
S. P. O. Danielsen, J. McCarty, J.-E. Shea, K. T. Delaney, and G. H. Fredrickson, PNAS 116 8224-8232 (2019)
S. Das, Y.-H. Lin, R. Vernon, J. D. Forman-Kay, and H. S. Chan, PNAS 117, 28795--28805 (2020)
To reproduce the result in PRL 2016, set Gamma = 1 in thermal_1p_1salt.py.