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We were able to define which pH and temperature conditions lead to spontaneous reorganization into a stable core\u2010shell architecture in beads, driven by pH\u2010dependent chitosan protonation and thermally induced network restructuring. We elucidate the mechanistic basis of this transformation and show that the resulting shell layer and core structure provide distinct optical signatures that can be tuned through the processing conditions. Leveraging this intrinsic material response, we introduce a single\u2010channel bead coding strategy that enables simultaneous digital PCR amplification and bead identification. As a proof of concept, we demonstrate multiplexed digital PCR of multiple samples in a single run, illustrating how a fundamental structure\u2010forming mechanism in hybrid hydrogels can be translated into a powerful functional capability for bioanalytical assays.<\/jats:p>","DOI":"10.1002\/smll.76008","type":"journal-article","created":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T14:42:28Z","timestamp":1790779348000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Induced Core\u2010Shell Transformation in Agarose\u2010Chitosan Nanoreactor Beads Enable Single Channel Coding for dPCR Multiplexing"],"prefix":"10.1002","author":[{"given":"Katharina","family":"Heise","sequence":"first","affiliation":[{"name":"BLINK AG  Jena Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-6535-4155","authenticated-orcid":false,"given":"Lennart","family":"Gura","sequence":"additional","affiliation":[{"name":"BLINK AG  Jena Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-5738-1024","authenticated-orcid":false,"given":"Emma","family":"Pohl","sequence":"additional","affiliation":[{"name":"BLINK AG  Jena Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lea","family":"Kanitz","sequence":"additional","affiliation":[{"name":"BLINK AG  Jena Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Theresa","family":"Liebe","sequence":"additional","affiliation":[{"name":"BLINK AG  Jena Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-9392-068X","authenticated-orcid":false,"given":"Daniel","family":"Toro","sequence":"additional","affiliation":[{"name":"BLINK AG  Jena Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-9231-8756","authenticated-orcid":false,"given":"Katrin","family":"Steinmetzer","sequence":"additional","affiliation":[{"name":"BLINK AG  Jena Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-6941-5772","authenticated-orcid":false,"given":"Thomas","family":"Ellinger","sequence":"additional","affiliation":[{"name":"BLINK AG  Jena Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susanne","family":"Klingner","sequence":"additional","affiliation":[{"name":"BLINK AG  Jena Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-5701-9355","authenticated-orcid":false,"given":"Stephan","family":"Hubold","sequence":"additional","affiliation":[{"name":"BLINK AG  Jena Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-4249-9473","authenticated-orcid":false,"given":"Oliver","family":"Lemuth","sequence":"additional","affiliation":[{"name":"BLINK AG  Jena Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susanne","family":"T\u00f6pfer","sequence":"additional","affiliation":[{"name":"BLINK AG  Jena Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6876-0565","authenticated-orcid":false,"given":"Eugen","family":"Ermantraut","sequence":"additional","affiliation":[{"name":"BLINK AG  Jena Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,9,30]]},"reference":[{"key":"e_1_2_11_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.biotechadv.2025.108719"},{"key":"e_1_2_11_3_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.96.16.9236"},{"key":"e_1_2_11_4_1","doi-asserted-by":"publisher","DOI":"10.1177\/2472630317705680"},{"key":"e_1_2_11_5_1","first-page":"444","article-title":"Quantitation of Targets for PCR by Use of Limiting Dilution","volume":"13","author":"Sykes P. 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