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Using a coarse-grained computational model, we examine the physical effects of the protein H-NS and molecular crowders on bacterial chromosome organization. In our model, an H-NS dimer with two binding sites cross-links a coarse-grained DNA polymer with a ring topology. Our simulations reveal the complex organizational behavior of the polymer. At low crowder volume fractions (\u22720.2), the polymer adopts a heterogeneous organization, with some regions arranged in parallel, while others remain extended\u2014an effect that becomes more pronounced as the polymer backbone stiffens. At higher crowder volume fractions (\u22730.2), the polymer adopts a circular organization, with multiple turns of the chain aligned in parallel. This organization correlates with enhanced clustering of H-NS at high crowding levels, facilitated by the parallel alignment of DNA segments. Furthermore, H-NS clustering strengthens with increasing backbone stiffness, suggesting cooperative H-NS binding. We also find that chain stiffness enhances the synergistic action of crowders and H-NS. In contrast, H-NS alone induces a more heterogeneous and irregular chain collapse.<\/jats:p>","DOI":"10.1063\/5.0325597","type":"journal-article","created":{"date-parts":[[2026,5,12]],"date-time":"2026-05-12T11:38:36Z","timestamp":1778585916000},"update-policy":"https:\/\/doi.org\/10.1063\/aip-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["Computational study of bacterial chromosome organization by H-NS-mediated cross-linking and molecular crowding"],"prefix":"10.1063","volume":"164","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-3333-3860","authenticated-orcid":false,"given":"Youngkyun","family":"Jung","sequence":"first","affiliation":[{"name":"Supercomputing Center, Korea Institute of Science and Technology Information 1 , Daejeon 34141,","place":["South Korea"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-3073-866X","authenticated-orcid":false,"given":"Amir","family":"Sadeghi","sequence":"additional","affiliation":[{"name":"Department of Physics and Astronomy, University of Waterloo 2 , Waterloo, Ontario N2L 3G1,","place":["Canada"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2089-6759","authenticated-orcid":false,"given":"Bae-Yeun","family":"Ha","sequence":"additional","affiliation":[{"name":"Department of Physics and Astronomy, University of Waterloo 2 , Waterloo, Ontario N2L 3G1,","place":["Canada"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"317","published-online":{"date-parts":[[2026,5,12]]},"reference":[{"key":"2026051207383012300_c1","doi-asserted-by":"publisher","first-page":"661","DOI":"10.1038\/nrg.2016.112","article-title":"Organization and function of the 3D genome","volume":"17","year":"2016","journal-title":"Nat. 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