Reorientational dynamics of molecules in liquid methane: A molecular dynamics simulation study, W.A. Monika Madhavi, Samantha Weerasinghe, Konstantin I. Momot, Journal of Molecular Liquids, 2020, 114727, ISSN 0167-7322

Shalini Thiruchittampalam, Samantha Weerasinghe, Plausible compounds drawn from plants as curative agents for neurodegeneration: An in‑silico approach, Journal of Computer-Aided Molecular Design, 2020, 34:1003–1011

Effects of Hydrogen Bonding on the Rotational Dynamics of Water-Like Molecules in Liquids: Insights from Molecular Dynamics Simulations, Madhavi W. A. Monika, Weerasinghe Samantha, Momot Konstantin I.  Australian Journal of Chemistry, 2020, 73, 734-742. https://doi.org/10.1071/CH19537

Cracking a cancer code histone deacetylation in epigenetic: the implication from molecular dynamics simulations on efficacy assessment of histone deacetylase inhibitors, Dushanan R, Weerasinghe S, Dissanayake DP, Senthilinithy R.  Journal of Biomolecular Structure & Dynamics, 2020 Nov:1-17. DOI: 10.1080/07391102.2020.1838328.

Structure and Dynamics of Collagen Hydration Water from Molecular Dynamics Simulations: Implications of Temperature and Pressure. Madhavi, W. A. M., Weerasinghe, S., Fullerton, G. D., & Momot, K. I.,  J.  Phys. Chem. B, 2019, 123(23), 4901–4914. doi:10.1021/acs.jpcb.9b03078

Exploring the binding properties of agonists interacting with glucocorticoid receptor: an in silico approach, Samith Rathnayake & Samantha Weerasinghe, J Mol Model. (2018) 24:342

Development of an Information System of Structures and Force Field Parameters of Chemical Compounds from Sri Lankan Flora, Samith Rathnayake and Samantha Weerasinghe,   ‎Comb. Chem. High Throughput Screen, 2018, 21, 1-7

“Expression, Docking, and Molecular Dynamics of Endo-?-1,4-xylanase I Gene of Trichoderma virens in Pichia stipites”, G. H. Ishan Maduka Wickramasinghe,  Samith Indika Rathnayake N. V. Chandrasekharan, Samantha Weerasinghe, R. L. C. Wijesundera and W. S. Sulochana Wijesundera, BioMed Research International 2017;11pages, Article ID 4658584 (2017)

“Trichoderma virens β-glucosidase I (BGLI) gene; expression in Saccharomyces cerevisiae including docking and molecular dynamics studies”, G. H. Ishan Maduka Wickramasinghe, Samith Indika Rathnayake N. V. Chandrasekharan, Samantha Weerasinghe, R. L. C. Wijesundera and W. S. Sulochana Wijesundera, BMC Microbiology, 17:137 (2017)

Madhavi, W. A. M.; Weerasinghe, S.; Momot, K. I., Rotational-Diffusion Propagator of the Intramolecular Proton–Proton Vector in Liquid Water: A Molecular Dynamics Study.,  J. Phys. Chem. B 2017, 121 (48), 10893–10905.

“An In Silico Approach of Coumarin-Derived Inhibitors for Human DNA Topoisomerase I”,  Amali G. Guruge, Chandani Udawatte, and Samantha Weerasinghe, Aust. J. Chem. 69, 1005–1015 (2016)

“Interaction of caffeine dimers with water molecules”, Rajendram Senthilnithy, Samantha Weerasingha and Dhammika Dissanayake, Computational and Theoretical Chemistry, 1028, 60-64 (2014)

“Theory and Simulation of Multicomponent Osmotic Systems”,Sadish Karunaweera, Moon Bae Gee, Samantha Weerasinghe and Paul E. Smith, Chem. Theory Comput, 8, 3493-3503 (2012)

“Study of aggregate formation of caffeine in water by molecular dynamics simulation”, Rangana Sanjeewa and Samantha Weerasinghe, Computational and Theoretical Chemistry, 966 140-148 (2011)

“A Kirkwood-Buff Derived Force Field for Aqueous Alkali Halides”, Moon Bae Gee, Nicholas R. Cox, Yuanfang Jiao, Nikolaos Bentenitis, Samantha Weerasinghe, and Paul E. Smith, J. Chem. Theory Comput., 7 (5),1369–1380 (2011)

“Development of a molecular mechanics force field for caffeine to investigate the interactions of caffeine in different solvent media”, Rangana Sanjeewa and Samantha Weerasinghe, J. Mol. Struc. (THEOCHEM), 944, 116-123 (2010)

“Simulation of structural and functional properties of mevalonate diphosphate decarboxylase (MVD)”, Samantha Weerasinghe Ranil S. Dassanayake, J. Mol. Model, (accepted for publication, 2009)

“Stability of hydroxamate ions in aqueous medium”, R. Senthilnithy, S. Weerasinghe & D.P. Dissanayake, J. Mol. Struc. (Theochem), 851, 109-114 (2008)

“Recent applications of Kirkwood-Buff theory to biological systems”, Veronica Pierce, Myungshim Kang, Mahalaxmi Aburi, Samantha Weerasinghe and Paul E. Smith, Cell Biochem. Biophys. 50:1-22, (2008)

“A Kirkwood-Buff derived force field for methanol and aqueous methanol solutions”, S. Weerasinghe and Paul E. Smith, J. Phys. Chem. B, 109, 15080-15086 (2005).

“A Kirkwood-Buff derived force field for the simulation of aqueous guanidium chloride solutions”, S. Weerasinghe and Paul E. Smith, J. Chem. Phys., 121, 2120-2186 (2004)

“Kirkwood-Buff derived force field for mixtures of urea and water”, S. Weerasinghe and Paul E. Smith, J. Phys. Chem. B, 107, 3891-3898 (2003)

“Kirkwood-Buff derived force field for mixtures of sodium chloride in water”, S. Weerasinghe and Paul E. Smith, J. Chem. Phys., 119(21), 11342-11349 (2003)

“Kirkwood-Buff derived force field for mixtures of acetone and water”, S. Weerasinghe and Paul E. Smith, J. Chem. Phys., 118(23), 10663-10670 (2003)

“Cavity formation and preferential interaction in urea solutions: Dependence on urea aggregation” S. Weerasinghe and Paul E. Smith, J. Chem. Phys. 118(13), 5901-5910 (2003)

“Structure and stability of model pyrimidine-purine-purine DNA triple helix with a GC.T mismatch by simulation”, S. Weerasinghe, P.E. Smith and B.M. Pettitt, Biochemistry, 34, 16269 (1995).

“Nanosecond dynamics and structure of a model DNA triple helix in saltwater solution”, S. Weerasinghe, P.E. Smith, V. Mohan, Y.K. Cheng and B.M. Pettitt, J. Am. Chem. Soc. 177, 2147 (1995).

“Dielectric response of triplex DNA in ionic solution from simulations”, L. Yang, S. Weerasinghe, P.E. Smith and P.M. Pettitt, Biophy. Journal, 69, 1519 (1995).

“Ideal chemical potential contribution in molecular dynamics simulations of grand canonical ensemble”, S. Weerasinghe and B.M. Pettitt, Mol. Phys. 82, 897 (1994).

“Absolute classical densities of states for very anharmonic systems and application to evaporation of rare gas clusters” S. Weerasinghe and F.G. Amar, J. Chem. Phys. 98, 4967 (1993).