{"id":29,"date":"2025-05-16T11:14:06","date_gmt":"2025-05-16T11:14:06","guid":{"rendered":"https:\/\/www.bio.iitb.ac.in\/ranjithp\/?page_id=29"},"modified":"2026-04-19T04:26:29","modified_gmt":"2026-04-19T04:26:29","slug":"publications","status":"publish","type":"page","link":"https:\/\/www.bio.iitb.ac.in\/~ranjith\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"\n<p class=\"is-style-default has-text-color has-link-color wp-elements-0f6f02b51939f9fc08701e1406d746e8 wp-block-paragraph\" style=\"color:#1808f6\">Find all my papers in <a href=\"http:\/\/scholar.google.co.in\/citations?hl=en&amp;user=FWxnJn8AAAAJ&amp;view_op=list_works&amp;sortby=pubdate\" target=\"_blank\" rel=\"noreferrer noopener\">Google scholar<\/a><br><br><strong><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/?term=Ranjith+Padinhateeri&amp;sort=date\">Find all my papers in Pubmed<\/a><\/strong><\/p>\n\n\n\n<p class=\"has-contrast-color has-text-color has-link-color wp-elements-cabe6d82fa2b1c5405ed7dbb8ddaa861 wp-block-paragraph\"><strong>My <\/strong>selected papers<strong> are listed below:<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li class=\"has-contrast-color has-text-color has-link-color wp-elements-9ed0fd5af5cc66b5a5aa80f9549ebfca\">Polymer simulations of chromatin: connecting 3D organization and dynamics to function<br>Shuvadip Dutta , <strong>Ranjith Padinhateeri<\/strong><br><a href=\"https:\/\/doi.org\/10.1016\/j.gde.2025.102429\">Curr. Opin. Genet. Dev 96:102429 (2026)<\/a><br><br><\/li>\n\n\n\n<li>Dynamical properties of chromatin provide insights into key folding principles.<br>Sangram Kadam, S Sahoo , PBS Kumar , <strong>Ranjith Padinhateeri<\/strong><br><strong><a href=\"https:\/\/doi.org\/10.1016\/j.bpj.2025.08.018\">Biophys J. 124(19):3189-3205 (2025)<\/a><\/strong><br><br><\/li>\n\n\n\n<li>Role of diffusion and reaction of the constituents in spreading of histone modification marks<br>Vinoth Manivannan, MM Inamdar MM, <strong>Ranjith Padinhateeri <\/strong><br><strong><a href=\"https:\/\/doi.org\/10.1371\/journal.pcbi.1012235\">PLoS Comput Biol.  20(7):e1012235 (2024)<\/a><\/strong><br><\/li>\n\n\n\n<li>Predicting scale-dependent chromatin polymer properties from systematic coarse-graining<br>Sangram Kadam, K Kumari, S Dutta, MK Mitra,&nbsp;<strong>Ranjith Padinhateeri<\/strong><br><strong><a href=\"https:\/\/doi.org\/10.1038\/s41467-023-39907-2\">Nature Communications, 14, 4108 (2023)<\/a><\/strong><br><\/li>\n\n\n\n<li>Nucleosome sliding can influence the spreading of histone modifications<br>Shantanu Kadam, T Bameta,&nbsp;<strong>R Padinhateeri<\/strong><br><strong><a href=\"https:\/\/journals.aps.org\/pre\/abstract\/10.1103\/PhysRevE.106.024408\">Physical Review E 106 (2), 024408 (2022)<\/a><\/strong><br><\/li>\n\n\n\n<li>Heterogeneous interactions and polymer entropy decide organization and dynamics of chromatin domains.<br>Kiran Kumari, J. Ravi Prakash, and&nbsp;<strong>Ranjith Padinhateeri<\/strong><br><strong><a href=\"https:\/\/doi.org\/10.1016\/j.bpj.2022.06.008\">Biophysical Journal 121, 2794-2812, (2022)<\/a><\/strong><br><\/li>\n\n\n\n<li>Role of non-specific interactions in the phase-separation and maturation of macromolecules.<br>Rakesh Krishnan, Srivastav Ranganathan, Samir K Maji, and&nbsp;<strong>Ranjith Padinhateeri<\/strong><br><strong><a href=\"https:\/\/doi.org\/10.1371\/journal.pcbi.1010067\">PLoS Comput Biol. 18(5):e1010067 (2022)<\/a><\/strong><br><\/li>\n\n\n\n<li>High fidelity epigenetic inheritance: Information theoretic model predicts threshold filling of histone modifications post replication<br>Nithya Ramakrishnan, Sibi Raj B. Pillai and&nbsp;<strong>Ranjith Padinhateeri<\/strong><br><a href=\"https:\/\/doi.org\/10.1371\/journal.pcbi.1009861\"><strong>PLoS Comput. Biol. 18(2) e1009861 (2022)<\/strong><\/a><br><\/li>\n\n\n\n<li>Continuous variable responses and signal gating form kinetic bases for pulsatile insulin signaling and emergence of resistance<br>Namrata Shukla, Shantanu Kadam,&nbsp;&nbsp;<strong>Ranjith Padinhateeri<\/strong>, and Ullas Kolthur-Seetharam<br><a href=\"https:\/\/doi.org\/10.1073\/pnas.2102560118\"><strong>Proc. Natl. Acad. Sci. (USA) , 118, e2102560118 (2021)<\/strong><\/a><br><\/li>\n\n\n\n<li>Nucleosome positioning and chromatin organization<br>Jyotsana Parmar and&nbsp;<strong>Ranjith Padinhateeri<\/strong><br><strong><a href=\"https:\/\/doi.org\/10.1016\/j.sbi.2020.06.021\">Current Opinion in Structural Biology, 64, 111-118 (2020)<\/a><\/strong><br><\/li>\n\n\n\n<li>Irregular Chromatin: Packing density, fiber width, and occurrence of heterogeneous clusters<br>Gaurav Bajpai and&nbsp;<strong>Ranjith Padinhateeri<\/strong><br><strong><a href=\"https:\/\/doi.org\/10.1016\/j.bpj.2019.11.004\">Biophysical Journal 118, 207-218&nbsp;(2020)<\/a><\/strong><\/li>\n<\/ul>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Computing 3D chromatin configurations from contact probability maps by Inverse Brownian Dynamics<br>Kiran Kumari, B Duenweg,&nbsp;<strong>R Padinhateeri<\/strong>, JR Prakash.<br><strong><a href=\"https:\/\/doi.org\/10.1016\/j.bpj.2020.02.017\" target=\"_blank\" rel=\"noreferrer noopener\">Biophysical Journal 118: 2193-2208 (2020)<br><\/a><\/strong><\/li>\n\n\n\n<li>Computational model for studying breakage-dependent amyloid growth<br>Jennifer Joseph, Samir K Maji and Ranjith Padinhateeri<br><a href=\"https:\/\/pubs.acs.org\/doi\/abs\/10.1021\/acschemneuro.0c00481\"><strong><em>ACS Chem. Neurosci.<\/em>&nbsp;11, 21, 3615 (2020)<\/strong><\/a><br><\/li>\n\n\n\n<li>R<em>ole of nucleosome positioning in 3D chromatin organization and loop formation.<br>Kharerin H, Bhat PJ,&nbsp;<strong>Padinhateeri R<\/strong>.<br><\/em><strong><a href=\"https:\/\/link.springer.com\/article\/10.1007\/s12038-019-9976-1\" target=\"_blank\" rel=\"noreferrer noopener\"><em>Journal of&nbsp;Biosciences&nbsp;45 (14) (2020)<\/em><\/a><\/strong><br><br><\/li>\n\n\n\n<li>Coupling of replisome movement with nucleosome dynamics can contribute to parent-daughter information transfer<br>Tripti Bameta, Dibyendu Das &amp;&nbsp;<strong>Ranjith Padinhateeri<br><a href=\"https:\/\/doi.org\/10.1093\/nar\/gky207\">Nucleic Acids Research, 46, 4991-5000 (2018)<\/a><\/strong><br><\/li>\n\n\n\n<li>Binding of DNA-bending non-histone proteins destabilizes regular 30-nm chromatin structure<br>Gaurav Bajpai, Ishutesh Jain, Mandar Inamdar, Dibyendu Das &amp;&nbsp;<strong>Ranjith Padinhateeri<br><a href=\"http:\/\/dx.doi.org\/10.1371\/journal.pcbi.1005365\">PLoS Computational Biology, 13, e1005365 (2017)<\/a><\/strong><br><\/li>\n\n\n\n<li>Defining a physical basis for diversity in protein self-assemblies using a minimal model<br>Srivastav Ranganathan, Samir Maji and&nbsp;<strong>Ranjith Padinhateeri<br><em><a href=\"http:\/\/pubs.acs.org\/doi\/abs\/10.1021\/jacs.6b06433\">J. Am. Chem. Soc. 138, 13911-13922 (2016)<\/a><\/em><\/strong><br><\/li>\n\n\n\n<li>Role of transcription factor-mediated nucleosome disassembly in&nbsp;<em>PHO5<\/em>&nbsp;gene expression<br>Hungyo Kharerin, Paike J Bhat, John F Marko and&nbsp;<strong>Ranjith Padinhateeri<br><\/strong><a href=\"http:\/\/www.nature.com\/articles\/srep20319\"><em>Scientific Reports, 6, 20319 (2016)<\/em><\/a><br><\/li>\n\n\n\n<li>Theoretical estimates of exposure timescales of protein binding sites on DNA regulated by nucleosome kinetics<br>Jyotsana Parmar,&nbsp;Dibyendu&nbsp;Das, and&nbsp;<strong>Ranjith Padinhateeri<\/strong><br><a href=\"http:\/\/nar.oxfordjournals.org\/content\/44\/4\/1630\"><em>Nucleic Acids Research, 44, &nbsp;(2016)<\/em><\/a><br><\/li>\n\n\n\n<li>Statistical mechanics provides novel insights into microtubule stability and mechanism of shrinkage<br>Ishutesh Jain<strong>,&nbsp;<\/strong>Mandar Inamdar<strong>,&nbsp;<\/strong>and<strong>&nbsp;Ranjith Padinhateeri<br><\/strong><a href=\"http:\/\/journals.plos.org\/ploscompbiol\/article?id=10.1371%2Fjournal.pcbi.1004099\">PLOS Computational Biology 11(2): e1004099 (2015)<\/a><\/li>\n<\/ul>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Branching influences force-velocity curves and length fluctuations in actin networks<br>Deepak Hansda, Shamik Sen<strong>,&nbsp;<\/strong>and<strong>&nbsp;Ranjith Padinhateeri<br><\/strong><a href=\"http:\/\/link.aps.org\/doi\/10.1103\/PhysRevE.90.062718\">Phys. Rev. E., 90, 062718, (2014)<\/a><br><br><br><a href=\"http:\/\/link.aps.org\/doi\/10.1103\/PhysRevE.90.062718\"><\/a><\/li>\n\n\n\n<li>Force-induced dynamical properties of multiple cytoskeletal filaments are distinct from that of single filaments<br>Dipjyoti Das, Dibyendu Das<strong>,&nbsp;<\/strong>and<strong>&nbsp;Ranjith Padinhateeri<br><\/strong><a href=\"http:\/\/www.plosone.org\/article\/info%3Adoi%2F10.1371%2Fjournal.pone.0114014\">PLoS One 9(12): e114014 (2014)<\/a><br><\/li>\n\n\n\n<li>Collective force generated by multiple biolfilaments can exceed the sum of forces due to individual filaments<br>Dipjyoti Das, Dibyendu Das<strong>,&nbsp;<\/strong>and<strong>&nbsp;Ranjith Padinhateeri<\/strong><br><a href=\"http:\/\/iopscience.iop.org\/1367-2630\/16\/6\/063032\/\" target=\"_blank\" rel=\"noreferrer noopener\">New J. Phys., 16, 063032 (2014)<\/a><br><\/li>\n\n\n\n<li>Nuecleosome positioning and kinetics near transcription-start-site barriers<br>are controlled by interplay between active remodeling and DNA sequence<br>Jyotsana Parmar, John F Marko, and<strong>&nbsp;Ranjith Padinhateeri<br><\/strong><a href=\"http:\/\/nar.oxfordjournals.org\/content\/early\/2013\/09\/24\/nar.gkt854.abstract?keytype=ref&amp;ijkey=31gmdHomoWmY6Mx\" target=\"_blank\" rel=\"noreferrer noopener\">Nucleic Acids Research, 42, 128-146, (2014)<\/a><br><\/li>\n\n\n\n<li>Forces due to curving protofilaments in microtubules<br>Shirish Vichare, Ishutesh Jain, Mandar Inamdar, and<strong>&nbsp;Ranjith Padinhateeri<\/strong><br><a href=\"http:\/\/pre.aps.org\/abstract\/PRE\/v88\/i6\/e062708\">Phys. Rev. E. 88, 062708 (2013)<\/a><br><\/li>\n\n\n\n<li>Force generation and step-size fluctuations in a dynein motor<br>Tripti Bameta,&nbsp;<strong>Ranjith Padinhateeri<\/strong>&nbsp;and Mandar M Inamdar<br><a href=\"http:\/\/iopscience.iop.org\/1742-5468\/2013\/02\/P02030\">J. Stat. Mech. P02030 (2013)<\/a><br><\/li>\n\n\n\n<li>Stretching and bending fluctuations of short DNA molecules,<br><strong>Ranjith Padinhateeri<\/strong>&nbsp;and Gautam I. Menon<br><a href=\"http:\/\/www.cell.com\/biophysj\/abstract\/S0006-3495(12)05067-9\">Biophys. J., 104, 463-271 (2013)<\/a><br><\/li>\n\n\n\n<li>History-dependent depolymerization of actin filaments<br>Ishutesh Jain, David Lacoste, Dulal Panda and&nbsp;<strong>Ranjith Padinhateeri<\/strong><br><a href=\"http:\/\/pubs.acs.org\/doi\/abs\/10.1021\/bi300629f\">Biochemistry, 51, 7580-7587 (2012)<\/a><br><\/li>\n\n\n\n<li>Random hydrolysis controls the dynamics instability of microtubules<br><strong>Ranjith Padinhateeri<\/strong>, A. B. Kolomeisky, and David Lacoste<br><a href=\"http:\/\/www.cell.com\/biophysj\/abstract\/S0006-3495(12)00161-0\">Biophys. J., 102, 1274-1283 (2012<\/a><br><\/li>\n\n\n\n<li>Molecular interpretation of ACTH\u2013endorphin coaggregation: relevance to&nbsp;&nbsp;secretory granule biogenesis<br>S Ranganathan&nbsp;P. K. Singh, U. Singh, P. S. Singru,&nbsp;<strong>R. Padinhateeri<\/strong>&nbsp;and S. K. Maji<br><a href=\"http:\/\/www.plosone.org\/article\/info%3Adoi%2F10.1371%2Fjournal.pone.0031924\">PLoS ONE, 7, e31924 (2012)<\/a><br><\/li>\n\n\n\n<li>Nucleosome positioning in a model of active chromatin remodeling enzymes<br><strong>Ranjith Padinhateeri<\/strong>&nbsp;and John F. Marko<br><a href=\"http:\/\/www.pnas.org\/cgi\/doi\/10.1073\/pnas.1015206108\">Proc. Natl. Acad. Sci. USA, 108, 7799-7803&nbsp; (2011)<\/a><\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Pre-IITB period<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Role of ATP-hydrolysis in the dynamics of a single actin filament<br><strong>P. Ranjith<\/strong>, K. Mallick, J-F. Joanny, and&nbsp; D. Lacoste<br><a href=\"http:\/\/www.cell.com\/biophysj\/abstract\/S0006-3495%2810%2900007-X\">Biophysical Journal 98, 1418-1427 (2010)<\/a><\/li>\n\n\n\n<li>Equilibrium properties of a grafted polyelectrolyte with explicit counterions<br><em>K. Jayasree,&nbsp;<strong>P. Ranjith<\/strong>, Madan Rao and P. B. Sunil Kumar<br><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/19275418\">J. Chem. Phy. 130, 094901 (2009)<\/a><\/em><\/li>\n\n\n\n<li>Non-equilibrium self-assembly of a filament coupled to ATP\/GTP hydrolysis<br><strong>P. Ranjith<\/strong>, D. Lacoste, K. Mallick and J-F. Joanny<br><a href=\"http:\/\/www.cell.com\/biophysj\/retrieve\/pii\/S0006349509003786\">Biophysical Journal 96, 2146-2159, (2009<\/a>)<\/li>\n\n\n\n<li>Nucleosome hopping and sliding&nbsp; kinetics determined from dynamics of single chromatin fibers in Xenopus egg extracts<br><strong>P. Ranjith<\/strong>, J. Yan and John F. Marko<br><a href=\"http:\/\/www.pnas.org\/content\/104\/34\/13649.abstract\">Proc. Natl. Acad. Sci. USA, 104, 13649-13654 (2007<\/a>)<\/li>\n\n\n\n<li>Filling of a one-dimensional lattice by k-mers proceeds via fast power-law-like kinetics<br><strong>P. Ranjith<\/strong>&nbsp;and John F. Marko<br><a href=\"http:\/\/pre.aps.org\/abstract\/PRE\/v74\/i4\/e041602\">Phys. Rev. E. 74, 041602 (2006)<\/a><\/li>\n\n\n\n<li>Distribution Functions, Loop Formation Probabilities and Force-Extension Relations in a Model for Short Double-Stranded DNA Molecules<br><strong>P. Ranjith<\/strong>, P. B. Sunil Kumar and Gautam I. Menon<br><a href=\"http:\/\/prl.aps.org\/abstract\/PRL\/v94\/i13\/e138102\">Phys. Rev. Lett. 94, 138102 (2005)<\/a><\/li>\n\n\n\n<li>Dynamics of a Semiflexible filament under external force<br><strong>P. Ranjith<\/strong>&nbsp;and P.B. Sunil Kumar<br><a href=\"http:\/\/www.sciencedirect.com\/science?_ob=ArticleURL&amp;_udi=B6TVG-46V4TR2-R&amp;_user=10&amp;_coverDate=02%2F01%2F2003&amp;_rdoc=1&amp;_fmt=high&amp;_orig=gateway&amp;_origin=gateway&amp;_sort=d&amp;_docanchor=&amp;view=c&amp;_searchStrId=1694134119&amp;_rerunOrigin=scholar.google&amp;_acct=C000050221&amp;_version=1&amp;_urlVersion=0&amp;_userid=10&amp;md5=a246f7f24c89e7f8b2d9f27c94c47360&amp;searchtype=a\">Physica A 318, 220-229 (2003)<\/a><\/li>\n\n\n\n<li>Dynamics of folding in Semiflexible filaments<br><strong>P. Ranjith<\/strong>&nbsp;and P. B. Sunil Kumar<br><a href=\"http:\/\/prl.aps.org\/abstract\/PRL\/v89\/i1\/e018302\">Phys. Rev. Lett. 89, 018302 (2002)<\/a><\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Find all my papers in Google scholar Find all my papers in Pubmed My selected papers are listed below: Pre-IITB period<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-29","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.bio.iitb.ac.in\/~ranjith\/wp-json\/wp\/v2\/pages\/29","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.bio.iitb.ac.in\/~ranjith\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.bio.iitb.ac.in\/~ranjith\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.bio.iitb.ac.in\/~ranjith\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.bio.iitb.ac.in\/~ranjith\/wp-json\/wp\/v2\/comments?post=29"}],"version-history":[{"count":15,"href":"https:\/\/www.bio.iitb.ac.in\/~ranjith\/wp-json\/wp\/v2\/pages\/29\/revisions"}],"predecessor-version":[{"id":66,"href":"https:\/\/www.bio.iitb.ac.in\/~ranjith\/wp-json\/wp\/v2\/pages\/29\/revisions\/66"}],"wp:attachment":[{"href":"https:\/\/www.bio.iitb.ac.in\/~ranjith\/wp-json\/wp\/v2\/media?parent=29"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}