Senior Lecturer
B.Sc.(Honors) (USJP), M.Sc.(UCT), Ph.D.(UCT)
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Biosketch:
B.Sc. Special Degree (Chemistry) (Honors)– University of Sri Jayewardenapura, Sri Lanka, 2014
M.Sc. (Computational Science) – University of Cape Town, South Africa, 2017
Ph.D. (Chemistry) – University of Cape Town, South Africa, 2021
Divisions:
Physical Chemistry / Theoretical and Computational Chemistry
Undergraduate Teaching:
Currently Teaching:
CHE 106 1.0 Structure and Properties of Matter
CHE 350 0.0 Mathematics for Chemistry
CHE 361 1.0 Advanced Chemical Kinetics
CHE 362 1.0 Advanced Quantum Chemistry
CHE 457 1.0 Molecular Spectroscopy
CHE 207 2.0 Chemistry Practical Unit (Physical Chemistry)
CHE 315 2.0 Chemistry Practical Unit (Physical Chemistry)
ICH 373 2.0 Advanced Chemical Kinetics and Thermodynamics
ICH 484 2.0 Quality Assurance, Accreditation, and Project Management (Statistical Methods)
GMB 351 1.0 Advanced Bioinformatics
GMB 422 2.0 Drug Discovery and Development
FST 166 1.0 Structure and Properties of Matter
Undergraduate Teaching: Previously Taught
CHE 103 1.0 Chemical Thermodynamics
CHE 204 1.0 Electrochemistry
ICH 355 1.0 Solid State Chemistry
Research interest :
- 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.
- Integrate AI-driven approaches, including machine learning and automated workflows, into drug discovery and materials design.
- 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.
Selected Publications:
Peer-Reviewed Journal Articles
- Nashed, A.; Dilsook, K.; Senapathi, T.; 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. https://doi.org/10.1038/s41467-026-72151-y
- Selvaraj, S.; Perera, M.; Yapa, P.; Munaweera, I.; Perera, I. C.; Senapathi, T.; Weerasinghe, L. In Vitro Analysis of XLAsp-P2 Peptide-Loaded Cellulose Acetate Nanofiber for Wound Healing. Journal of Pharmaceutical Sciences 2025, 114 (2), 911–922. https://doi.org/10.1016/j.xphs.2024.10.050
- Sigera, S.; Theekshana, K. D.; Dinanja, S. G.; Eranga, P.; Karunathilake, N.; Abeywardhana, S.; Weerasinghe, L.; Senapathi, T.; 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. https://doi.org/10.3390/md23120471
- Naidoo, K. J.; Bruce-Chwatt, T.; Senapathi, T.; 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), 4120–4130. https://doi.org/10.1021/acs.accounts.1c00477
- Barnett, C. B.; Senapathi, T.; Naidoo, K. J. Conformational Play in the Binding of Variably Glycosylated MUC1 Antigen to AR20.5 Antibody. Beilstein Journal of Organic Chemistry 2020, 16, 2540–2550. https://doi.org/10.3762/bjoc.16.206
- Bray, S.; Senapathi, T.; Barnett, C. B.; Grüning, B. Intuitive, Reproducible High-Throughput Molecular Dynamics in Galaxy: A Tutorial. Journal of Cheminformatics 2020, 12, 1–13. https://doi.org/10.1186/s13321-020-00451-6
- Senapathi, T.; 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. https://doi.org/10.21769/BioProtoc.3731
- Senapathi, T.; 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), 3731–3740. https://doi.org/10.1021/acs.jcim.0c00206
- Suruzhon, M.; Senapathi, T.; 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), 1917–1921. https://doi.org/10.1021/acs.jcim.9b01158
- Senapathi, T.; Bray, S.; Barnett, C. B.; Grüning, B.; Naidoo, K. J. Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE). Bioinformatics 2019, 35 (18), 3508–3509. https://doi.org/10.1093/bioinformatics/btz107
- Rathnayake, U. A.; Senapathi, T.; Sandaruwan, C.; Gunawardene, S.; Karunaratne, V.; Kottegoda, N. Rice Bran Nanofiber Composites for Stabilization of Phytase. Chemistry Central Journal 2018, 12, 1–7. https://doi.org/10.1186/s13065-018-0400-y
Book Chapters
- Naidoo, K. J.; Bruce-Chwatt, T.; Senapathi, T. Enzyme Reaction Dynamics from Adaptive Reaction Coordinate Forces. In Comprehensive Computational Chemistry; Elsevier, 2024; pp 544–558. https://doi.org/10.1016/B978-0-12-821978-2.00124-0
Current Affiliations:
Research Associate: Scientific Computing Research Unit, University of Cape Town.
Deputy Proctor: Faculty of Applied Sciences, University of Sri Jayewardenepura.
Contact information
Telephone number: 0717 385 385
Web: Google Scholar/Tharindu Senapathi
Email: tharindunuwan@sjp.ac.lk
Room: 2L027