Dataset: Active Transport as a Mechanism of Microphase Selection in Biomolecular Condensates

Overview This repository contains the raw simulation data and plotting scripts accompanying the manuscript: > Le Qiao, Peter Gispert, Lukas S. Stelzl, and Friederike Schmid. "Active Transport as a Mechanism of Microphase Selection in Biomolecular Condensates." Submitted 2026. Preprint: arXiv:2604.08316 [physics.bio-ph], https://arxiv.org/abs/2604.08316 The simulation source code used to generate the raw data will be added upload upon manuscript acceptance (see "Code availability" below). Repository structure ``` . ├── README.md ├── LICENSE <- CC-BY 4.0 ├── CITATION.cff <- machine-readable citation metadata ├── requirements.txt ├── 3D_data_full_model/ <- full-model 3D simulations (phi1, phi2), main text Fig. 2, Fig. 3 and SI Sec. VI Fig. S3 ├── 3D_data_approximate_model/ <- approximate-model 3D simulations (F -> F(phi1) only), SI comparison runs ├── 3D_data_approximate_model_above_spinodal/ <- approximate-model runs with e slightly above the spinodal (noise-induced structure formation, SI Sec. V Fig. S1) ├── 3D_Data_approximate_model_phic0.000_check_noise/ <- noise-level check runs at phi_c = 0.000 (SI Sec. V Fig. S2) ├── 3D_Data_approximate_model_phic0.400_check_noise/ <- noise-level check runs at phi_c = 0.400 (SI Sec. V Fig. S2) ├── 3D_data_ani_full_model/ <- anisotropic-transport full-model runs, morphology phase diagram (Fig. 4) ├── movie/ <- simulation movies / time-series snapshots ├── plotting/ <- scripts used to generate manuscript figures from the data above ├── e_0.2.log <- run log, e = 0.2, C0 = 0 (no noise) ├── e_0.2_C0_0.5.log <- run log, e = 0.2, C0 = 0.5 ├── e_0.5.log <- run log, e = 0.5, C0 = 0 (no noise) ├── e_0.5_C0_0.5.log <- run log, e = 0.5, C0 = 0.5 └── visitlog.py <- VisIt session/visualization log (used for rendering 3D movies) ``` Data description File formats: VTR Simulation parameters: note key parameters (box size, resolution, timestep, noise amplitude, etc.) are encoded in filenames. Requirements See `requirements.txt`. Typical dependencies: numpy, scipy, matplotlib. Code availability The simulation code used to generate the raw data is currently private during peer review. It will be: - Deposited separately and linked here via DOI, upon acceptance of the manuscript. This README will be updated with the corresponding DOI/link at that time. License Data and scripts in this repository are released under the Creative Commons Attribution 4.0 International License (CC-BY 4.0) .See `LICENSE` for details. You are free to share and adapt this material for any purpose, provided appropriate credit is given. Citation If you use this data or scripts, please cite both the dataset and the associated paper. See `CITATION.cff` for structured metadata, or cite as: Qiao, L., Gispert, P., Stelzl, L. S., & Schmid, F. (2026). Dataset for "Active Transport as a Mechanism of Microphase Selection in Biomolecular Condensates" [Data set]. Zenodo. https://doi.org/10.5281/zenodo.21780549 Please also cite the associated preprint: Qiao, L., Gispert, P., Stelzl, L. S., & Schmid, F. (2026). Active Transport as a Mechanism of Microphase Selection in Biomolecular Condensates. arXiv:2604.08316. https://arxiv.org/abs/2604.08316 Funding This research was funded by the Deutsche Forschungsgemeinschaft (DFG), Germany — Project numbers 465145163 (CRC 1552), 248882694 (CRC 1551), and 465886476 (CRC 1551). L.S.S. acknowledges support by M3ODEL and the Forschungsinitiative des Landes Rheinland-Pfalz. Simulations were performed on the MOGON2 supercomputer at Johannes Gutenberg University Mainz (https://hpc.uni-mainz.de). Contact Le Qiao — [e-mail] Friederike Schmid — [e-mail] Institute of Physics, Johannes Gutenberg University Mainz, D-55099 Mainz, Germany