Code and data for: Nonequilibrium protein complexes as molecular automata

DOI

Code and data for the linked publication: https://doi.org/10.1103/dgw7-s8gl . The repository contains the code that was used to obtain results for the article and tidied jupyter notebooks that produce all the figures and data used.- notebooks/classifying_attractors.ipynb produces the main part of Fig. 2 and Fig. S1 along with performance measurements on the needed calculations.- notebooks/example_networks.ipynb produces the example networks shown in Figures 2, 3 and S4.- notebooks/kymographs.ipynb produces all kymographs in Figures 1, 4 and 6.- notebooks/error_correcting.ipynb produces all the network and splitting probability diagrams and coherence time plots for error correcting shown in Figures 5, S2, S3 and S6.- notebooks/FSMs.ipynb produces the analysis of finite state machines, specifically the full network vizualizations from Fig. 6 (a) and the analysis needed for Figures S7 and S8.- notebooks/relaxation_dynamics.ipynb produces the data and plots for relaxation kinetics and coherence times shown in Fig. 4.- notebooks/relaxation_dynamics_SI.ipynb produces the relaxation kinetics analysis for Fig. S5.

Identifier
DOI https://doi.org/10.5522/04/31497577.v1
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Metadata Access https://api.figshare.com/v2/oai?verb=GetRecord&metadataPrefix=oai_datacite&identifier=oai:figshare.com:article/31497577
Provenance
Creator Kocka, Jan; Husain, Kabir; Agudo-Canalejo, Jaime
Publisher University College London UCL
Contributor Figshare
Publication Year 2026
Rights https://creativecommons.org/publicdomain/zero/1.0/
OpenAccess true
Contact researchdatarepository(at)ucl.ac.uk
Representation
Language English
Resource Type Software
Discipline Natural Sciences; Physics