Research

My research uses computational methods: molecular dynamics and electronic structure calculations, to probe systems which are difficult to study experimentally. Below are some of the topics which are under research in our group.

Major Projects

Dendrimer Architecture

Dendrimers are a class of hyperbranched, layered polymer which take tree-like structures. We use multi-scale modelling to probe the behavior of dendrimers of varing architecture. Particular attention is given to trends in drug loading (entrapment) capacity, as a function of structural features.

As a part of this project we have developed a VMD plugin DendriGen to create the initial coordinates of dendrimers.

Contributors: Dhakshita Abeygunawardane, Sajaya Wiraj, Waruni Kulathunga, Rasinindu Kumarachchi, Ruwini Kalhari.
Past Contributors: Zuzana Dujanova, Chamikara Karunasena, Sajith Manjrake, Pubudu Wimalasiri.

Inclusion Complexes of Cylcodextrins

Cyclodextrins are oligosachcharides which have a conical shape, and relatively hydrophobic interior compared to the outer surface. These molecules are extensively used in preparation of drug formulations. We study the interactions and properties of molecules which can successfully make inclusion complexes with these to better inform drug formulation and testing.

Collaborators: Dr. S. O. Nielsen
Contributors: Rumesh Nelumdeniya, Dineli Ranatunga

Cell-Penetrating Peptides

These short peptides are known to spontaneously translocate through plasma membranes into cells. Their high uptake and low cytotoxicity makes them attractive candidates for the delivery of therapeutics. We study factors and structural features that could enhance the adsorption and passive translocation of a variety of peptides using computer simulations.

Collaborators: Prof. D. N. Karunaratne
Contributors: Buddhika Kumara, Chandrika Purijjala, Kithminie Wijesirir
Past contributors: Madhuranga Rathnayake, Charuni Gunathunge, Pubudu Wimalasiri, Amani Ranasinghe

Extension of the SDK-CG Force Field

Extension of the coarse grained force field of Shinoda-De Vane and Klein. We have extended the original force-field to include:

Tri-glycerides
Pluronics

Contributors: Nishani KannangaraPast Contributors: Isuru Ariyaratne, Dineli Ranathunga, Malith Dilhan.

Single-site Coarse Grained Models

For testing theories and interrogating systems using simplified representations of solid particles is advantageous. We are actively developing potentials to represent simple geometric solids using a single interaction site, which are based on continuum models but which faithfully represent the interactions of a solid featuring atomic detail.

Our efforts are three-fold: (1) to develop the actual models, (2) to develop methods and strategies to use these models in unique ways, and (3) to develop software and techniques to utilize these efficiently.

Collaborators: Dr. Steve Nielsen (Uni. Texas at Dallas)

Minor Projects / Collaborations

Molecular Switches: Furylfugides

Relating the steric effect of furylfulgies with reaction rates in the switching of molecules from the closed to open state.

Collaboration with Dr. C. V. Hettiarachchi. Past contributors: Iresh Galindawatte, A. A. D. M. Adhikari

Dispersion of Carbon Nanotubes

Research into finding macromolecular dispersion agents capable of forming stable dispersions of carbon nanotubes. We have investigated a variety of molecules including

Surfactant peptides
Pluronics
Cyclic peptides

Parameterization of Small Molecules

Accurate parameters for small molecules is a prevalent problem in applying molecular dynamics to many industrial and pharmaceutical problems. We look to parameterize important molecules to aid in ready application of molecular mechanics to problem solving.

Science Education

Effectiveness of computer assisted instructions in teaching Structure, properties, bonding nature, synthesis, reactions and mechanisms of aliphatic hydrocarbons G.C.E. (A/L) chemistry. Research Project of Dilhari Karunadasa.
Study of the factors which influence students, in their choice of subject stream for A/Ls. A case study in the Nuwara-Eliya educational zone. Research Project of Premila Illukkumbura

Publications

Journal Publications:

P. V. G. M. Rathnayake, B. G. C. M. Gunathunge, P. N. Wimalasiri, D. N. Karunaratne, R. J. K. U. Ranatunga. Trends in the Binding of Cell Penetrating Peptides to siRNA: A Molecular Docking Study J. Biophys., 2017, 1059216, (2017)
D. N. Karunaratne, M. Jafari, R. J. K. U. Ranatunga, A. Siriwardhana. Natural Carriers for siRNA Delivery. Curr. Pharmaceutical Design, 21, 4529-4540, (2015).
M. J. Shoura, R. J. K. U. Ranatunga, S. A. Harris, S. O. Nielsen, S. D. Levene. Contribution of Fluorophore Dynamics and Solvation to Resonant Energy Transfer in Protein-DNA Complexes: A Molecular-Dynamics Study. Biophy. J., 197, 700–710, (2014)
J. Hao, Y. Cheng, R. J. K. U. Ranatunga, S. Senevirathne, M. C. Biewer, S. O. Nielsen, Q. Wang, and M. C. Stefan. A Combined Experimental and Computational Study of the Substituent Effect on Micellar Behavior of γ-Substituted Thermoresponsive Amphiphilic Poly(ε-caprolactone)s. Macromol., 46, 4829-4838, (2013)
R. J. K. U. Ranatunga, and S. O. Nielsen. Application of a Continuum Mean Field Approximation to Fullerenes in Lipid Bilayers. Curr. Nanosci., 7, 667-673, (2011)
R. J. K. U. Ranatunga, C. T. Nguyen, B. A. Wilson, W. Shinoda, and S. O. Nielsen. Molecular Dynamics Study of Nanoparticles and Non-Ionic Surfactant at an oil/water interface. Soft Matter, 7, 6942-6952, (2011).
R. J. K. U. Ranatunga, R. J. B. Kalescky, C.-c. Chiu, and S. O. Nielsen. Molecular Dynamics Simulations of Surfactant Functionalized Nanoparticles in the Vicinity of an Oil/Water Interface. J. Phys. Chem. C 114, 12151-12157, (2010).
C.-c. Chiu, R. J. K. U. Ranatunga, D. T. Flores, D. V. Perez, P. B. Moore, W. Shinoda, and S. O. Nielsen. A Mean Field Approach for Computing Solid-Liquid Surface Tension for Nanoscale Interfaces. J. Chem. Phys., 132, 054706, (2010).

Book Chapters:

I. R. Perera, C. V. Hettiarachchi, R. J. K. U. Ranatunga, Organic Frameworks in Dye-Sensitized Solar Cells. In, Advances in Solar Energy Research.
D. N. Karunaratne, K. M. G. K. Pamunuwa, and R. J. K. U. Ranatunga. Introductory. Chapter: Microemulsions. In Microemulsions (InTech Open) Chapter 1, 1 –13, (2016).
R. J. K. U. Ranatunga, C. T. Nguyen, C.-c. Chiu, W. Shinoda, and S. O. Nielsen. Molecular Dynamics Simulations of Nanoparticles and Surfactants at Oil/Water Interfaces. In Amphiphiles: Molecular Assembly and Applications (ACS Books Symposium Series) Chapter 18, 295-314, (2011). Edited by R. Nagarajan.

Conference Abstracts:

P. W. C. M. Purijjala, P. V. G. M. Rathnayake, D. N. Karunaratne, R. J. K. U. Ranatunga. Membrane translocation energetics of C6-cell penetrating peptides in silico. Proc. PGIS Res. Congress, Vol 3, (2016).
N. A. P. F. Rizmiya, S. S. Gunathilake, R. J. K. U. Ranatunga. Developing an economical spill-kit for neutralizing harmful liquids.Proc. PGIS Res. Congress, Vol 3, (2016).
M. I. Haseemdeen, R. M. G. Rajapakse, H. M. N. Bandara, R. J. K. U. Ranatunga. Design of a novel protein to bind with Telomere: A possible path towards cancer treatment. Proc. PGIS Res. Congress, Vol 3, (2016).
K. U. Attanayake, A. N. Navaratne, R. J. K. U. Ranatunga. Kinetic and thermodynamics study of photo-induced oxidation of Aloin to Aloe-emodin. iPURSE, 19, (2015).
I. S. W. Galindawatte, A. A. D. M. Adhikari, C. V. Hettiarachchi, R. J. K. U. Ranatunga. Steric effects of substituents on furylfulgide molecular switches. iPURSE, 19, (2015).
P. E. Illukkumbura, R. J. K. U. Ranatunga. Factors affecting the selection of the Advanced Level science stream: A study of students in Nuwara-Eliya zone. iPURSE, 19, (2015).
P. N. Wimalasiri, I. M. Chandrasiri, R. J. K. U. Ranatunga. Dendrigen: A graphical tool for preparing dendrimer models for computer simulation. PGIS Research Congress, 2, (2015)
P. V. G. M. Rathnayake, B. G. C. M. Gunathunge, D. N. Karunaratne, R. J. K. U. Ranatunga. A comparative study on the binding of cell penetrating peptides to siRNA using docking simulations. PGIS Research Congress, 2, (2015)
B. G. C. M. Gunathunge, P. N. Wimalasiri, R. A. A. P. Ranasinghe, M. Jafari, P. Chen, D. N. Karunaratne, R. J. K. U. Ranatunga. Computational Study of the Interaction of the C6 Cell Penetrating Peptides with short-Interfering RNA. PGIS Research Congress, 1, (2014)
D. T. S. Ranathunga, A. D. L. C. Perera, R. J. K. U. Ranatunga. A theoretical study on the stability of designed microemulsions. iPURSE, 18, (2014).

Conference Presentations:

Pluronics and SWCNTs: Modeling and Toxicity, Semiconductor Research Coporation (SRC) Engineering Research Center(ERC) for Environmentally Benign Semiconductor Manufacturing Teleseminar Series (2012)
Utilization of Continuum Models for Soft Matter Simulations, American Chemical Society, Dallas Fort-Worth Chapter, 45th Local Section Meeting, University of Texas at Dallas, Texas (2012)
Predicting, Testing, and Neutralizing Nanoparticle Toxicity, SRC-GRC Engineering Research Center for Environmentally Benign Semiconductor Manufacturing Annual Review Meeting, Tucson, Arizona (2012)
Spherical Fullerenes in Lipid Membranes, SRC TechCon 2011, Austin, Texas (2011)
Non-Ionic Surfacants and Nanoparticles at an Oil-Water Interface, American Chemical Society, Dallas Fort-Worth Chapter, 44th Local Section Meeting, Tarleton State University, Texas (2011)
Nanoparticle Aggregation and Toxicity, SRC ERC for Environmentally Benign Semiconductor Manufacturing, TeleSeminar Series (2011)
Influence of Solvation and Interparticle Interaction on the Aggregation Behavior of Nanoparticles in Membranes, American Chemical Society, 241st National Meeting and Exposition, Anaheim, California (2011)
Surfactants and Nanoparticles at Oil/Water Interfaces, American Chemical Society, 241st National Meeting and Exposition, Anaheim, California (2011)
Aggregation Behavior of Nanoparticles Constrained at Oil/Water Interfaces, American Chemical Society, 241st National Meeting and Exposition, Anaheim, California (2011)
Molecular Dynamics Study of Non-Ionic Surfactant and Nanoparticles at Oil/Water Interfaces, Southwestern Theoretical Chemistry Conference, October 22nd & 23rd, University of North Texas, Texas (2010)
Surfactant Functionalized Nanoparticles, American Chemical Society, Dallas Fort-Worth Chapter, 43rd Local Section Meeting, University of Texas at Dallas, Texas (2010)

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