Source Code - RNA gradients can guide condensates toward promoters: Implications for enhancer–promoter contacts and condensate-promoter kissing

Directories Content Directory GitHub Finite Volume Simulations FVM https://github.com/gohdavid/CoupledEPCondensates Theoretical Calculations Theory https://github.com/gohdavid/CoupledEPCondensatesTheory Brownian Dynamics Simulations BD https://github.com/gohdavid/active-polymers Finite Element Method FEM https://github.com/gohdavid/CoupledEPCondensatesFEM Jupyter Notebooks Figure Notebook Fig. 1B FVM/workspace/01_Analysis/Fig_1B.ipynb and FVM/workspace/01_Analysis/Fig_1B_I-II-III.ipynb Fig. 1C Theory/Fig_1C_CSV.ipynb Fig. 2B Theory/Fig_2B-4B.ipynb Fig. 2C BD/Fig_2C-S16.ipynb Fig. 2D BD/Fig_2D-S15.ipynb Fig. 2E FVM/workspace/04_Analysis/Fig_2E.ipynb Fig. 3B FVM/workspace/05_Analysis/Fig_3B-3C.ipynb Fig. 3C FVM/workspace/05_Analysis/Fig_3B-3C.ipynb Fig. 3D FVM/workspace/05_Analysis/Fig_3D.ipynb Fig. 4B Theory/Fig_2B-4B.ipynb Fig. 4C FVM/workspace/05_Analysis/Fig_4C-4D.ipynb Fig. 4D FVM/workspace/05_Analysis/Fig_4C-4D.ipynb Fig. S1 FVM/workspace/00_Misc/Fig_S1-S8-S9-S10.ipynb Fig. S2 Theory/Fig_S2-S3-S5-S6.ipynb Fig. S3 Theory/Fig_S2-S3-S5-S6.ipynb Fig. S5 Theory/Fig_S2-S3-S5-S6.ipynb Fig. S6 Theory/Fig_S2-S3-S5-S6.ipynb Fig. S7 FEM/Fig-S7.ipynb Fig. S8 FVM/workspace/00_Misc/Fig_S1-S8-S9-S10.ipynb Fig. S9 FVM/workspace/00_Misc/Fig_S1-S8-S9-S10.ipynb Fig. S10 FVM/workspace/00_Misc/Fig_S1-S8-S9-S10.ipynb Fig. S11 FVM/workspace/05_Analysis/Fig-S11-S12-S13.ipynb Fig. S12 FVM/workspace/05_Analysis/Fig-S11-S12-S13.ipynb Fig. S13 FVM/workspace/05_Analysis/Fig-S11-S12-S13.ipynb Fig. S14 FVM/Fig_S14.ipynb Fig. S15 BD/Fig_2D-S15.ipynb Fig. S16 BD/Fig_2C-S16.ipynb