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We simulate a self-avoiding polymer with a fixed fraction of active Ornstein\u2013Uhlenbeck monomers arranged in different sequences and compare free-draining dynamics with simulations including Rotne\u2013Prager\u2013Yamakawa hydrodynamic interactions. Increasing sequence blockiness drives a non-monotonic conformational response from expansion to compaction and then re-expansion. Hydrodynamic interactions preserve this qualitative sequence dependence but shift the compact regime, alter the degree of compaction and mechanical size balance, and render center-of-mass transport sequence-dependent. At intermediate blockiness, the compact state is accompanied by a suppressed active contribution to radial swelling and develops an internally segregated structure with a passive-rich core and active peripheral protrusions. At larger blockiness, the polymer re-expands despite this suppression, with the increase in size arising instead from the growing spatial separation between the active and passive blocks. This block separation is reduced by hydrodynamic interactions, thereby modifying the high-blockiness conformations. Formation of the compact state proceeds through rapid global compaction followed by slower radial reorganization, leaving the active segments dynamically constrained in the compact state. These results show that hydrodynamic interactions do more than renormalize relaxation. They reshape the sequence-selected conformational landscape and couple internal organization to long-time transport in active\u2013passive copolymers.<\/jats:p>","DOI":"10.1063\/5.0354603","type":"journal-article","created":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T10:56:30Z","timestamp":1792061790000},"update-policy":"https:\/\/doi.org\/10.1063\/aip-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["Hydrodynamic modulation of sequence-dependent compaction in active\u2013passive copolymers"],"prefix":"10.1063","volume":"165","author":[{"ORCID":"https:\/\/orcid.org\/0009-0009-4074-4788","authenticated-orcid":false,"given":"Minakshi","family":"Jangir","sequence":"first","affiliation":[{"name":"Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science , Bengaluru, Karnataka 560012,","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7694-0654","authenticated-orcid":false,"given":"Shibananda","family":"Das","sequence":"additional","affiliation":[{"name":"Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science , Bengaluru, Karnataka 560012,","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"317","published-online":{"date-parts":[[2026,10,15]]},"reference":[{"key":"2026101506562700700_c1","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1016\/j.cell.2020.09.014","article-title":"The self-organizing genome: Principles of genome architecture and function","volume":"183","year":"2020","journal-title":"Cell"},{"key":"2026101506562700700_c2","doi-asserted-by":"publisher","first-page":"407","DOI":"10.1038\/nrm.2017.26","article-title":"Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes","volume":"18","year":"2017","journal-title":"Nat. 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