Publications

• Shen, Xinyi, Benjamin M. Gallant, Philippe Holzhey, Joel A. Smith, Karim A. Elmestekawy, Zhongcheng Yuan, P. V. G. M. Rathnayake et al. (2023) Chloride‐Based Additive Engineering For Efficient and Stable Wide‐Bandgap Perovskite Solar Cells. Advanced Materials. 2211742
• Purijjala P.W.C.M., Rathnayake P.V.G.M., Kumara B.T., Gunathunge B.C.M., Ranasinghe R.A.A.P., Karunaratnea D.N., Ranatunga R.J.K.U. (2022) Multiscale Modeling of the Cellular Uptake of C6 Peptide-siRNA Complexes. Computational Biology and Chemistry. 107679
• Kumara, B. T., Wijesiri, N. K., Rathnayake, P. V. G. M., & Ranatunga, R. J. K. U. (2021). A Re-evaluation of the Free Energy Profiles for Cell-Penetrating Peptides Across DOPC Membranes. International Journal of Peptide Research and Therapeutics, 27(4), 2931-2943.
• Rathnayake, P. V. G. M. (2020). Development and evaluation of force fields for studying the formation of metal halide perovskites from solution
• Rathnayake, P. V. G. M., Bernardi, S., & Widmer-Cooper, A. (2020). Evaluation of the AMOEBA force field for simulating metal halide perovskites in the solid state and in solution. The Journal of Chemical Physics, 152(2), 024117.
• Rathnayake, P. V. G. M., Gunathunge, B. G. C. M., Wimalasiri, P. N., Karunaratne, D. N., & Ranatunga, R. J. K. U. (2017). Trends in the binding of cell penetrating peptides to siRNA: A molecular docking study. Journal of Biophysics
• Rathnayake, P. V. G. M. (2016). A comparative study on the binding of cell penetrating peptides to siRNA using molecular docking

Presentations

• Rathnayake P. V. G. M. , Sameera W. M. C. , Watanabe N., (2022) PyQM/MM for subtractive QM/MM calculations with the AMOEBA09 polarisable force field, CECAM Virtual Winter School for Computational Chemistry
• Rathnayake P. V. G. M. , Sameera W. M. C., Watanabe N., (2021) PyQM/MM for modelling chemical processes in the interstellar medium, Workshop on Interstellar Matter 2021, Japan
• Rathnayake, P. V. G. M., Bernardi, S., & Widmer-Cooper, A. (2020) Evaluation of the AMOEBA force field for simulating metal halide perovskites in the solid state and in solution, Statistical Mechanics of Soft Matter 2020, University of Queensland, Australia
• Rathnayake, P. V. G. M., Bernardi, S., & Widmer-Cooper, A. (2019) Evaluating classical force fields to study dissolution and crystallisation of hybrid organometallic halide perovskites, Statistical Mechanics of Soft Matter 2019, University of Adelaide, Adelaide, Australia
• Rathnayake, P. V. G. M., Bernardi, S., & Widmer-Cooper, A. (2019) Evaluating classical force fields to study dissolution and crystallisation of hybrid organometallic halide perovskites, Asia-Pacific Association of Theoretical and Computational Chemists (APATCC), University of Sydney, Sydney, Australia
• Sameera W. M. C., Senevirathne B., Rathnayake P. V. G. M., Al-Ibadi M. A., Miyazaki A., Andersson S., Nyman G., Watanabe N. (2018) Radical species on interstellar ices: some clues from a quantum mechanics/molecular mechanics study, International workshop on interstellar matter, Hokkaido University, Japan
• Rathnayake, P. V. G. M., Bernardi, S., & Widmer-Cooper, A. (2018) Evaluating classical force fields for studying dissolution and crystallisation of organometallic halide perovskites, Statistical Mechanics of Soft Matter 2018, The University of Auckland, New Zealand
• Rathnayake, P. V. G. M., Bernardi, S., & Widmer-Cooper, A. (2018) Simulating Perovskites: New polarizable force field to study dissolution and crystallisation of hybrid lead halide perovskites, Chemistry Postgraduate Symposium, University of Sydney, Australia
• Kumara B. T., Rathnayake P. V. G. M., Ranatunga R. J. K. U. (2018) Computational study on free energy profiles of passively cell penetrating peptides in dioleoylphosphatidylcholine (DOPC) lipid bilayer, PGIS Research Congress, Postgraduate Institute of Science (PGIS), University of Peradeniya, Sri Lanka
• Purijjala P. W. C. M., Rathnayake P. V. G. M., Karunaratne D. N., Ranatunga R. J. K. U. (2016) Membrane translocation energetics of C6 Cell Penetrating Peptides in-silico, PGIS Research Congress, Postgraduate Institute of Science (PGIS), University of Peradeniya, Sri Lanka
• Rathnayake, P. V. G. M., Gunathunge, B. G. C. M., Karunaratne, D. N., Ranatunga, R. J. K. U. (2015) A comparative study on the binding of cell penetrating peptides to siRNA using docking simulations. PGIS Research Congress, Postgraduate Institute of Science (PGIS), University of Peradeniya, Sri Lanka
• Adhihetty, P. K., Rathnayake, P. V. G. M., Pandithavidana, D. R. (2014) Computational investigation of cyclic 8-membered enediyne chemistry. 70th Annual Scientific Sessions: Engage Science, Enrich Society, Sri Lanka Association for the Advancement of Science (SLAAS), University of Colombo, Sri Lanka
• Rathnayaka, R. M. C. S., Rathnayake, P. V. G. M., Pandithavidana, D. R. (2014) Computational investigation of thermodynamic and kinetic feasibilities of cyclopropenone decarbonylation mechanism. 70th Annual Scientific Sessions: Engage Science Enrich Society, Association for the Advancement of Science (SLAAS), University of Colombo, Sri Lanka