{"id":1084,"date":"2021-03-03T05:40:43","date_gmt":"2021-03-03T05:40:43","guid":{"rendered":"https:\/\/science.sjp.ac.lk\/che\/?page_id=1084"},"modified":"2026-04-23T05:08:09","modified_gmt":"2026-04-23T05:08:09","slug":"dr-tharindu-senapathi","status":"publish","type":"page","link":"https:\/\/science.sjp.ac.lk\/che\/dr-tharindu-senapathi\/","title":{"rendered":"Dr. Tharindu Senapathi"},"content":{"rendered":"<h4><strong><a href=\"https:\/\/science.sjp.ac.lk\/che\/wp-content\/uploads\/sites\/13\/2021\/03\/WhatsApp-Image-2021-10-26-at-8.04.41-PM.jpeg\"><img decoding=\"async\" loading=\"lazy\" class=\"alignnone size-medium wp-image-1146 alignleft\" src=\"https:\/\/science.sjp.ac.lk\/che\/wp-content\/uploads\/sites\/13\/2021\/03\/WhatsApp-Image-2021-10-26-at-8.04.41-PM-209x300.jpeg\" alt=\"whatsapp-image-2021-10-26-at-8-04-41-pm\" width=\"209\" height=\"300\" srcset=\"https:\/\/science.sjp.ac.lk\/che\/wp-content\/uploads\/sites\/13\/2021\/03\/WhatsApp-Image-2021-10-26-at-8.04.41-PM-209x300.jpeg 209w, https:\/\/science.sjp.ac.lk\/che\/wp-content\/uploads\/sites\/13\/2021\/03\/WhatsApp-Image-2021-10-26-at-8.04.41-PM.jpeg 575w\" sizes=\"(max-width: 209px) 100vw, 209px\" \/><\/a><\/strong><\/h4>\n<h4><strong>Senior Lecturer<\/strong><\/h4>\n<p>B.Sc.(Honors) (USJP), M.Sc.(UCT), Ph.D.(UCT)<\/p>\n<h4><a style=\"background-color: #00b4d8;border: none;color: white;padding: 15px 32px;text-align: center;text-decoration: none;font-size: 16px;margin: 4px 2px;cursor: pointer\" href=\"https:\/\/science.sjp.ac.lk\/che\/wp-content\/uploads\/sites\/13\/2026\/04\/Tharindu_Senapathi_CV.pdf\" target=\"_blank\" rel=\"noopener\"><strong>Download Full CV &gt;&gt;<\/strong><\/a><\/h4>\n<h4 style=\"text-align: left\"><\/h4>\n<h4 style=\"text-align: left\"><strong>Biosketch:<\/strong><\/h4>\n<p style=\"text-align: left\">B.Sc. Special Degree (Chemistry) (Honors)\u2013 University of Sri Jayewardenapura, Sri Lanka, 2014<br \/>\nM.Sc. (Computational Science) \u2013 University of Cape Town, South Africa, 2017<br \/>\nPh.D. (Chemistry) \u2013 University of Cape Town, South Africa, 2021<\/p>\n<p><strong>Divisions:<\/strong><\/p>\n<p>Physical Chemistry \/ Theoretical and Computational Chemistry<\/p>\n<p><strong><span style=\"color: #333333\">Undergraduate Teaching:<\/span><\/strong><\/p>\n<blockquote>\n<p class=\"p1\"><strong>Currently Teaching:<\/strong><\/p>\n<p>CHE 106 1.0 Structure and Properties of Matter<\/p>\n<p>CHE 350 0.0 Mathematics for Chemistry<\/p>\n<p>CHE 361 1.0 Advanced Chemical Kinetics<\/p>\n<p>CHE 362 1.0 Advanced Quantum Chemistry<\/p>\n<p>CHE 457 1.0 Molecular Spectroscopy<\/p>\n<p><em>CHE 207 2.0 Chemistry Practical Unit (Physical Chemistry)<\/em><\/p>\n<p><em>CHE 315 2.0 Chemistry Practical Unit (Physical Chemistry)<\/em><\/p>\n<p><em>ICH 373 2.0 Advanced Chemical Kinetics and Thermodynamics<\/em><\/p>\n<p><em>ICH 484 2.0 Quality Assurance, Accreditation, and Project Management (Statistical Methods)<\/em><\/p>\n<p><em>GMB 351 1.0 Advanced Bioinformatics<\/em><\/p>\n<p><em>GMB 422 2.0 Drug Discovery and Development<\/em><\/p>\n<p><em>FST 166 1.0 Structure and Properties of Matter<\/em><\/p>\n<p style=\"font-weight: 400\"><strong>Undergraduate Teaching: Previously Taught<\/strong><\/p>\n<p><em>CHE 103 1.0 Chemical Thermodynamics<\/em><\/p>\n<p><em>CHE 204 1.0\u00a0Electrochemistry<\/em><\/p>\n<p><em>ICH 355 1.0 Solid State Chemistry<\/em><\/p><\/blockquote>\n<h4><strong>Research interest :<\/strong><\/h4>\n<ul>\n<li>Develop and apply quantum chemistry and QM\/MM methods to investigate enzyme catalysis and reactions in glycoenzymes and carbohydrate-active systems, and use molecular dynamics and free-energy methods to study biomolecular and materials behavior.<\/li>\n<li>Integrate AI-driven approaches, including machine learning and automated workflows, into drug discovery and materials design.<\/li>\n<li>Develop open-source computational tools leveraging high-performance computing and GPU acceleration, and apply first-principles and AI-assisted methods to design advanced materials for energy storage and electrochemical technologies.<\/li>\n<\/ul>\n<h4><strong>Selected Publications:<\/strong><\/h4>\n<p>Peer-Reviewed Journal Articles<\/p>\n<ol>\n<li style=\"font-weight: 400\">Nashed, A.; Dilsook, K.; <strong>Senapathi, T.<\/strong>; Naidoo, K. J. An In Vitro Approach for Simulating Divergent Golgi O-Glycosylation of Tumor-Associated MUC1 from Normal MUC1. Nature Communications 2026, 17, 3619. <a href=\"https:\/\/doi.org\/10.1038\/s41467-026-72151-y\">https:\/\/doi.org\/10.1038\/s41467-026-72151-y<\/a><\/li>\n<li style=\"font-weight: 400\">Selvaraj, S.; Perera, M.; Yapa, P.; Munaweera, I.; Perera, I. C.; <strong>Senapathi, T.<\/strong>; Weerasinghe, L. In Vitro Analysis of XLAsp-P2 Peptide-Loaded Cellulose Acetate Nanofiber for Wound Healing. Journal of Pharmaceutical Sciences 2025, 114 (2), 911\u2013922. <a href=\"https:\/\/doi.org\/10.1016\/j.xphs.2024.10.050\">https:\/\/doi.org\/10.1016\/j.xphs.2024.10.050<\/a><\/li>\n<li style=\"font-weight: 400\">Sigera, S.; Theekshana, K. D.; Dinanja, S. G.; Eranga, P.; Karunathilake, N.; Abeywardhana, S.; Weerasinghe, L.; <strong>Senapathi, T.<\/strong>; Peiris, D. C. Molecular Docking and Molecular Dynamics Simulations Reveal the Antidiabetic Potential of a Novel Fucoxanthin Derivative from Chnoospora minima. Marine Drugs 2025, 23, 471. <a href=\"https:\/\/doi.org\/10.3390\/md23120471\">https:\/\/doi.org\/10.3390\/md23120471<\/a><\/li>\n<li style=\"font-weight: 400\">Naidoo, K. J.; Bruce-Chwatt, T.; <strong>Senapathi, T.<\/strong>; Hillebrand, M. Multidimensional Free Energy and Accelerated Quantum Library Methods Provide a Gateway to Glycoenzyme Conformational, Electronic and Reaction Mechanisms. Accounts of Chemical Research 2021, 54 (22), 4120\u20134130. <a href=\"https:\/\/doi.org\/10.1021\/acs.accounts.1c00477\">https:\/\/doi.org\/10.1021\/acs.accounts.1c00477<\/a><\/li>\n<li style=\"font-weight: 400\">Barnett, C. B.; <strong>Senapathi, T.<\/strong>; Naidoo, K. J. Conformational Play in the Binding of Variably Glycosylated MUC1 Antigen to AR20.5 Antibody. Beilstein Journal of Organic Chemistry 2020, 16, 2540\u20132550. <a href=\"https:\/\/doi.org\/10.3762\/bjoc.16.206\">https:\/\/doi.org\/10.3762\/bjoc.16.206<\/a><\/li>\n<li style=\"font-weight: 400\">Bray, S.; <strong>Senapathi, T.<\/strong>; Barnett, C. B.; Gr\u00fcning, B. Intuitive, Reproducible High-Throughput Molecular Dynamics in Galaxy: A Tutorial. Journal of Cheminformatics 2020, 12, 1\u201313. <a href=\"https:\/\/doi.org\/10.1186\/s13321-020-00451-6\">https:\/\/doi.org\/10.1186\/s13321-020-00451-6<\/a><\/li>\n<li style=\"font-weight: 400\"><strong> Senapathi, T.<\/strong>; Barnett, C. B.; Naidoo, K. J. BRIDGE: An Open Platform for Reproducible Protein-Ligand Simulations and Free Energy of Binding Calculations. Bio-protocol 2020, 10 (17), e3731. <a href=\"https:\/\/doi.org\/10.21769\/BioProtoc.3731\">https:\/\/doi.org\/10.21769\/BioProtoc.3731<\/a><\/li>\n<li style=\"font-weight: 400\"><strong> Senapathi, T.<\/strong>; Suruzhon, M.; Barnett, C. B.; Essex, J. W.; Naidoo, K. J. BRIDGE: An Open Platform for Reproducible High-Throughput Free Energy Simulations. Journal of Chemical Information and Modeling 2020, 60 (8), 3731\u20133740. <a href=\"https:\/\/doi.org\/10.1021\/acs.jcim.0c00206\">https:\/\/doi.org\/10.1021\/acs.jcim.0c00206<\/a><\/li>\n<li style=\"font-weight: 400\">Suruzhon, M.; <strong>Senapathi, T.<\/strong>; Bodnarchuk, M. S.; Viner, R.; Wall, I.; Barnett, C. B.; Naidoo, K. J.; Essex, J. W. ProtoCaller: Robust Automation of Binding Free Energy Calculations. Journal of Chemical Information and Modeling 2020, 60 (4), 1917\u20131921. <a href=\"https:\/\/doi.org\/10.1021\/acs.jcim.9b01158\">https:\/\/doi.org\/10.1021\/acs.jcim.9b01158<\/a><\/li>\n<li style=\"font-weight: 400\"><strong> Senapathi, T.<\/strong>; Bray, S.; Barnett, C. B.; Gr\u00fcning, B.; Naidoo, K. J. Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE). Bioinformatics 2019, 35 (18), 3508\u20133509. <a href=\"https:\/\/doi.org\/10.1093\/bioinformatics\/btz107\">https:\/\/doi.org\/10.1093\/bioinformatics\/btz107<\/a><\/li>\n<li style=\"font-weight: 400\">Rathnayake, U. A.; <strong>Senapathi, T.<\/strong>; Sandaruwan, C.; Gunawardene, S.; Karunaratne, V.; Kottegoda, N. Rice Bran Nanofiber Composites for Stabilization of Phytase. Chemistry Central Journal 2018, 12, 1\u20137. <a href=\"https:\/\/doi.org\/10.1186\/s13065-018-0400-y\">https:\/\/doi.org\/10.1186\/s13065-018-0400-y<\/a><\/li>\n<\/ol>\n<p>Book Chapters<\/p>\n<ol>\n<li style=\"font-weight: 400\">Naidoo, K. J.; Bruce-Chwatt, T.; <strong>Senapathi, T.<\/strong> Enzyme Reaction Dynamics from Adaptive Reaction Coordinate Forces. In Comprehensive Computational Chemistry; Elsevier, 2024; pp 544\u2013558. <a href=\"https:\/\/doi.org\/10.1016\/B978-0-12-821978-2.00124-0\">https:\/\/doi.org\/10.1016\/B978-0-12-821978-2.00124-0<\/a><\/li>\n<\/ol>\n<p><strong style=\"font-size: revert\">Current Affiliations:<\/strong><\/p>\n<p>Research Associate: <a href=\"http:\/\/www.scientificomputing.uct.ac.za\/\">Scientific Computing Research Unit, University of Cape Town.<\/a><\/p>\n<p>Deputy Proctor:\u00a0<a href=\"https:\/\/science.sjp.ac.lk\/\">Faculty of Applied Sciences,\u00a0University of Sri Jayewardenepura.<\/a><\/p>\n<p><strong>Contact information<\/strong><\/p>\n<p>Telephone number: 0717 385 385<\/p>\n<p>Web: <a href=\"https:\/\/scholar.google.com\/citations?user=Vv7CYHYAAAAJ&amp;hl=en\">Google Scholar\/Tharindu Senapathi<\/a><\/p>\n<p>Email: <a href=\"mailto:tharindunuwan@sjp.ac.lk\">tharindunuwan@sjp.ac.lk<\/a><\/p>\n<p>Room: 2L027<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Senior Lecturer B.Sc.(Honors) (USJP), M.Sc.(UCT), Ph.D.(UCT) Download Full CV &gt;&gt; Biosketch: B.Sc. Special Degree (Chemistry) (Honors)\u2013 University of Sri Jayewardenapura, &hellip; <a href=\"https:\/\/science.sjp.ac.lk\/che\/dr-tharindu-senapathi\/\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">Dr. Tharindu Senapathi<\/span><\/a><\/p>\n","protected":false},"author":3,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_ti_tpc_template_sync":false,"_ti_tpc_template_id":"","footnotes":""},"_links":{"self":[{"href":"https:\/\/science.sjp.ac.lk\/che\/wp-json\/wp\/v2\/pages\/1084"}],"collection":[{"href":"https:\/\/science.sjp.ac.lk\/che\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/science.sjp.ac.lk\/che\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/science.sjp.ac.lk\/che\/wp-json\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/science.sjp.ac.lk\/che\/wp-json\/wp\/v2\/comments?post=1084"}],"version-history":[{"count":69,"href":"https:\/\/science.sjp.ac.lk\/che\/wp-json\/wp\/v2\/pages\/1084\/revisions"}],"predecessor-version":[{"id":4770,"href":"https:\/\/science.sjp.ac.lk\/che\/wp-json\/wp\/v2\/pages\/1084\/revisions\/4770"}],"wp:attachment":[{"href":"https:\/\/science.sjp.ac.lk\/che\/wp-json\/wp\/v2\/media?parent=1084"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}