Biophysical Constraints on Chromatin State Space: Simulation and Analysis Code for Feasibility-Based Regulation
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| Format: | Recurso digital |
| Sprache: | Englisch |
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2026
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| _version_ | 1866901700842881024 |
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| author | Rosario Aloma, Enrique |
| author_facet | Rosario Aloma, Enrique |
| contents | <p>This repository provides the data, code, and computational resources supporting the study <em>“Regulatory Information Beyond Sequence: A Feasibility Constraint Framework for Chromatin Organization.”</em> The work introduces a biophysical framework in which regulatory information is constrained by the physical feasibility of chromatin conformations, governed by stability, dynamical restoration, and energetic maintenance.</p> <p>The repository includes scripts for deterministic and stochastic simulations, parameter sweeps, and phase-space analyses illustrating transitions between persistent and non-persistent regulatory regimes. It also contains processed datasets and figure-generation code used to reproduce the results presented in the manuscript.</p> <p>A central prediction of the framework is that regulatory capacity scales sublinearly with non-coding genome size, providing a mechanistic interpretation of the C-value paradox. This prediction is formulated in terms of measurable quantities, enabling direct comparison with chromatin organization data such as Hi-C–defined domains and accessibility states.</p> <p>All materials are organized to ensure reproducibility and transparency, and include the necessary documentation to replicate simulations and figures. This archive serves as a versioned, citable resource for the computational and theoretical components of the study.</p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_19700829 |
| institution | Zenodo |
| language | eng |
| publishDate | 2026 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | Biophysical Constraints on Chromatin State Space: Simulation and Analysis Code for Feasibility-Based Regulation Rosario Aloma, Enrique chromatin organization gene regulation biophysics theoretical biology genome size c-value paradox regulatory networks genome scaling non-coding DNA systems biology stochastic dynamics <p>This repository provides the data, code, and computational resources supporting the study <em>“Regulatory Information Beyond Sequence: A Feasibility Constraint Framework for Chromatin Organization.”</em> The work introduces a biophysical framework in which regulatory information is constrained by the physical feasibility of chromatin conformations, governed by stability, dynamical restoration, and energetic maintenance.</p> <p>The repository includes scripts for deterministic and stochastic simulations, parameter sweeps, and phase-space analyses illustrating transitions between persistent and non-persistent regulatory regimes. It also contains processed datasets and figure-generation code used to reproduce the results presented in the manuscript.</p> <p>A central prediction of the framework is that regulatory capacity scales sublinearly with non-coding genome size, providing a mechanistic interpretation of the C-value paradox. This prediction is formulated in terms of measurable quantities, enabling direct comparison with chromatin organization data such as Hi-C–defined domains and accessibility states.</p> <p>All materials are organized to ensure reproducibility and transparency, and include the necessary documentation to replicate simulations and figures. This archive serves as a versioned, citable resource for the computational and theoretical components of the study.</p> |
| title | Biophysical Constraints on Chromatin State Space: Simulation and Analysis Code for Feasibility-Based Regulation |
| topic | chromatin organization gene regulation biophysics theoretical biology genome size c-value paradox regulatory networks genome scaling non-coding DNA systems biology stochastic dynamics |
| url | https://doi.org/10.5281/zenodo.19700829 |