{"paper":{"title":"A Brownian dynamics study of liquid-liquid phase separation in multi-scale chromatin networks","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"Chromatin fiber networks control the positioning and morphology of phase-separated protein droplets through interactions analogous to wetting transitions.","cross_cats":["physics.bio-ph"],"primary_cat":"cond-mat.soft","authors_text":"Judith Min\\'e-Hattab, L\\'ea Beaul\\`es, Pierre Illien, Vincent Dahirel","submitted_at":"2026-05-14T07:59:51Z","abstract_excerpt":"In living cells, proteins involved in specialized biochemical functions are often spatially organized within biomolecular condensates. Increasing evidence suggests that some of these condensates, including DNA repair condensates, emerge through liquid-liquid phase separation (LLPS). In the nucleus, however, condensates form within a highly heterogeneous environment composed of chromatin fibers, RNA, and additional protein scaffolds such as PAR chains, all of which may interact with phase-separating proteins. Moreover, condensate formation is frequently associated with specific chromatin confor"},"claims":{"count":4,"items":[{"kind":"strongest_claim","text":"We show that protein-fiber interactions strongly influence droplet positioning relative to the substrate, in a manner analogous to wetting transitions in soft condensed matter systems. Both local geometric constraints and global network organization markedly affect droplet size, morphology, and multiplicity. In addition, large-scale asymmetries in fiber organization can induce robust spatial localization of the dense phase.","source":"verdict.strongest_claim","status":"machine_extracted","claim_id":"C1","attestation":"unclaimed"},{"kind":"weakest_assumption","text":"The minimal model of Lennard-Jones particles interacting with fixed fibrous substrates sufficiently captures the dominant physical effects of real chromatin on phase-separating proteins, without needing explicit dynamics of the fibers themselves or additional molecular details.","source":"verdict.weakest_assumption","status":"machine_extracted","claim_id":"C2","attestation":"unclaimed"},{"kind":"one_line_summary","text":"Brownian dynamics simulations demonstrate that multi-scale chromatin fiber geometry and network organization control the positioning, size, morphology, and multiplicity of liquid-liquid phase separated condensates via protein-fiber interactions.","source":"verdict.one_line_summary","status":"machine_extracted","claim_id":"C3","attestation":"unclaimed"},{"kind":"headline","text":"Chromatin fiber networks control the positioning and morphology of phase-separated protein droplets through interactions analogous to wetting transitions.","source":"verdict.pith_extraction.headline","status":"machine_extracted","claim_id":"C4","attestation":"unclaimed"}],"snapshot_sha256":"b06a90e7d2b5e5f9df0f1b34f1617ccd60a5be687658f3654f236a382dcee346"},"source":{"id":"2605.14516","kind":"arxiv","version":1},"verdict":{"id":"a2476bc5-d7d0-46c7-ab46-c586f60b89b4","model_set":{"reader":"grok-4.3"},"created_at":"2026-05-15T01:37:19.097102Z","strongest_claim":"We show that protein-fiber interactions strongly influence droplet positioning relative to the substrate, in a manner analogous to wetting transitions in soft condensed matter systems. Both local geometric constraints and global network organization markedly affect droplet size, morphology, and multiplicity. In addition, large-scale asymmetries in fiber organization can induce robust spatial localization of the dense phase.","one_line_summary":"Brownian dynamics simulations demonstrate that multi-scale chromatin fiber geometry and network organization control the positioning, size, morphology, and multiplicity of liquid-liquid phase separated condensates via protein-fiber interactions.","pipeline_version":"pith-pipeline@v0.9.0","weakest_assumption":"The minimal model of Lennard-Jones particles interacting with fixed fibrous substrates sufficiently captures the dominant physical effects of real chromatin on phase-separating proteins, without needing explicit dynamics of the fibers themselves or additional molecular details.","pith_extraction_headline":"Chromatin fiber networks control the positioning and morphology of phase-separated protein droplets through interactions analogous to wetting transitions."},"references":{"count":80,"sample":[{"doi":"","year":null,"title":"Linear fiber There is a large variety of chromatin geometries within the length scales under study here (nucleosomes to con- densates, 10 nm to 1µm). In order to understand the possible interactions o","work_id":"770fcf99-0436-43ca-9ce2-c99e94a518cc","ref_index":1,"cited_arxiv_id":"","is_internal_anchor":false},{"doi":"","year":null,"title":"There can be intersections within the same fiber if there is a loop [59, 60], or between dif- ferent fibers","work_id":"ed48be9a-21d1-419c-b090-df380c900ab8","ref_index":2,"cited_arxiv_id":"","is_internal_anchor":false},{"doi":"","year":null,"title":"Droplet identification Two proteins are considered as part of the same droplet if they are closer than a threshold distancer cut of each other. The value ofr cut is chosen as the distance at 12 the fi","work_id":"4ca761ad-8916-45ab-8d86-74519b0aab19","ref_index":3,"cited_arxiv_id":"","is_internal_anchor":false},{"doi":"","year":null,"title":"It is estimated from the positionsr i = (rix, riy, riz) of the nparti proteins in each droplet","work_id":"9cc63931-2f0f-475f-a0e3-07ec4bac118b","ref_index":4,"cited_arxiv_id":"","is_internal_anchor":false},{"doi":"","year":null,"title":"Droplet localization To quantify the localization of the droplets with re- spect to the fibers, we calculate the pair correlation func- tiong DN (r) between the center of mass of a droplet and the pos","work_id":"adcc4e5a-a983-43d0-a468-3310f24cf067","ref_index":5,"cited_arxiv_id":"","is_internal_anchor":false}],"resolved_work":80,"snapshot_sha256":"f0f8784ca247c1be172cb6411944051070dd692c6c014b32bf28ed24ff3485f2","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"}