What I bring
A scientist-developer mindset: I care about the accuracy of a model, the quality of its implementation, and the clarity of the scientific decision it enables.
12+Years in computational chemistry and predictive modeling
124+Early-stage pharmaceutical drug-development projects supported
Ph.D.Chemistry (specialized in computational chemistry), UT Dallas
10+Peer-reviewed publications and scientific contributions
About
Turning molecular insight into practical scientific decisions.
I develop computational approaches that help scientists understand molecular behavior, interactions, and properties, enabling informed scientific and practical decisions. My work integrates computational chemistry, molecular simulation, data-driven modeling, and scientific software development across drug discovery, drug delivery, formulation, biophysics, materials science, and engineering.
How I work
I collaborate across pharmaceutical science, medicine, chemistry, biology, engineering, and materials science to translate complex computational results into reproducible workflows, practical tools, and actionable scientific insights.
Research focus
Questions I like to work on.
My research spans multiple scales, from small molecules to large biomolecular systems.
Accurate molecular models
Developing and applying atomistic, coarse-grained, polarizable, and machine-learning force-field workflows for chemically diverse systems.
Free energy and enhanced sampling
Using FEP, umbrella sampling, metadynamics, ABF, and SMD to study binding, permeation, folding, adsorption, and molecular recognition.
Drug development platforms
Building MD, QM, AI/ML, QSAR/QSPR, and PBPK-linked workflows for solubility, dissolution, permeability, formulation, delivery, and ADMET questions.
Biomolecular systems
Modeling proteins, peptides, ligands, membranes, nucleosomes, transport-related systems, and protein-surface interactions.
Materials and interfaces
Connecting molecular-level structure and dynamics to polymers, ionic liquids, nanoparticles, titanium implants, self-assembled monolayers, and surfaces.
Scalable scientific computing
Developing reproducible Python and C/C++ tools for Linux, HPC, GPU-enabled, and cloud workflows using MPI, CUDA, AWS, and Rescale.
Research & development work
Computational research across molecular systems.
Explore selected research themes and the computational methods used to address them. Select a visualization to read the detailed project history.
Implant therapeutics and molecular interactionsDrug design and delivery · View research details
Bio-based ionic liquidsForce fields, MD, and QM
Protein–surface interactionsHMGB1 delivery systems
Titanium implant coatingsDrug-release and adsorption studies
Ionic-liquid property predictionThermophysical properties and green chemistry
Breast-cancer therapeuticsMD, FEP, PROTACs, and PTMs
Nucleosomal histone dynamicsMolecular recognition and interactions
Nanoparticles and imaging systemsOncology drug-development research
Polymer sensors and molecular recognitionIn silico modeling in water
Protein folding and encapsulationCoarse-grained molecular dynamics
Wettability and condensationWater harvesting and thermal management
Experience
Research, development, and scientific leadership.
Selected milestones from industry and academic research.
2025 — Present
Computational Chemist, Scientist III · Thermo Fisher Scientific
Lead computational chemistry work across early-stage drug development projects; Develop and apply MD, QM, FEP, force-field, AI/ML, QSAR/QSPR, and statistical modeling workflows to support compound-lead selection, solubility and bioavailability enhancement, nitrosamine risk-prediction, drug delivery, formulation development, and ADMET evaluation.
2022 — 2025
Computational Chemist, Scientist II · Thermo Fisher Scientific
Integrated MD, QM, AI/ML, and PBPK approaches; Developed workflows for dissolution and permeability predictions; Optimized HPC and cloud workflows and supported computational drug-development decisions.
2021 — 2022
Postdoctoral Research Associate · The University of Texas at Dallas
Developed AMOEBA polarizable force fields for bio-based ionic liquids using MD and QM methods; Applied MD/FEP approaches approaches to support large-molecule drug development, including breast-cancer therapeutics and nucleosomal systems.
2016 — 2021
Research Assistant · The University of Texas at Dallas
Conducted computational research across drug discovery, formulation, drug delivery, and materials applications; Developed and applied molecular modeling workflows using atomistic and coarse-grained MD, QM, FEP, docking, homology modeling, mutation analysis, force-field development, QSAR/QSPR, AI/ML, and statistical modeling;Studied complex biological and chemical systems, span from small molecules to large bio-molecules; Integrated computational insights into medicinal-chemistry workflows; Edited LAMMPS source code to support coarse-grained simulations.
2014-2016
Quality Assurance Analyst and Tiger Brewer · Heineken
Led quality-assurance laboratory operations, including chemical and microbiological testing, routine analysis, sensory evaluation, and training of technical staff and tasting panels. Supported the first Sri Lankan production of Tiger beer to Heineken quality standards; maintained HARA, HAMRA, and ISO compliance; and completed a research project to reduce dissolved oxygen levels in beer.
2014-2015
Visiting Lecturer · ESOFT Metro Campus, Sri Lanka
2014-2015
Teaching Temporary Lecturer · University of Peradeniya
2012-2013
Undergraduate Research Assistant · University of Peradeniya
Topical drug development: MD simulations on lipid-based drug delivery systems (SEDDs); Developed SDK coarse-grained forcefields for triolein and beta-carotene.
2012
Intern · Riagam Marketing (Pvt) Ltd and Dream Life Science (Pvt) Ltd
Identification systems for ingredients/raw materials used in cosmetic industry
Technical toolkit
Tools I use to turn ideas into reproducible workflows.
Programming and infrastructure
Proficient in rapidly adapting to new programming languages and leveraging AI-assisted development tools for efficient code generation, optimization, and scientific computing.
Computational chemistry tools
Data analysis, visualization, and utility tools
Scientific community
Awards, leadership, mentorship, service, and professional memberships.
Awards and recognition
- Outstanding Poster Award, Southwest Theoretical and Computational Chemistry Meeting (2019)
- Third Place, Oral Presentation, Graduate Session, 52nd ACS Local Section Meeting (2019)
- ACS Postdoc to Faculty Award (2022)
- NVIDIA GPU Award Presentation, 264th ACS National Meeting and Exposition (2022)
- Two research grants, Office of the Vice President for Research, UT Dallas (2019–2020)
- Natural Sciences and Mathematics Outstanding Graduate Teaching Award (2018 and 2019)
- President’s Award for Natural Sciences and Mathematics Outstanding Graduate Teaching nomination (2019–2020)
- Research supported by the NIDDK, NSF, Welch Foundation, and other funders (2016–2022)
Leadership, mentorship, and service
- Guest Editor, Pharmaceutics, MDPI (2023–Present)
- Peer reviewer: Journal of Molecular Modeling and Journal of Physical Chemistry (2020–Present)
- Peer reviewer: Kotalawala Defence University (2021–Present)
- Peer reviewer: American Association of Pharmaceutical Scientists (2023–Present)
- Editor, Series of Clinical and Biomedical Research Journal (2023–2024)
- Editor, Innovative Medicines & Omics International Journal (2023–2024)
- Judge and presider, ACS national and local meetings (2021–2022)
- Mentored 11 graduate students and 10 undergraduates; trained 3 experimental postdocs in computational methods (2016–2021)
Professional memberships
- American Chemical Society, including the COMP Division (2018–Present)
- American Association of Pharmaceutical Scientists (2022–Present)
- Biophysical Society (2022–Present)
- Affiliate Member, Royal Society of Chemistry (2023–Present)
Publications
Scientific work in print and in progress.
Selected peer-reviewed journal articles, conference papers, and contributions.
2014
Ranathunga, D. T. S.; Ranatunga U.; et al. “A theoretical study on the stability of designed microemulsions.” Proceedings of the Peradeniya University International Research Session, 18. First author.
2018
Karim, M. R.; Li, X.; Kang, P.; Randrianalisoa, J.; Ranathunga, D. T. S.; Nielsen, S.; Qin, Z.; Qian, D. “Ultrafast pulsed laser-induced nanocrystal transformation in colloidal plasmonic vesicles.” Advanced Optical Materials, 6, 1800726.
2019
Kam, H. C.; Ranathunga, D. T. S.; Payne, E. R.; Smaldone, R. A.; Nielsen, S. O.; Dodani, S. C. “Spectroscopic characterization and in silico modelling of polyvinylpyrrolidone as an anion-responsive fluorescent polymer in aqueous media.” Supramolecular Chemistry, 31, 514–522. Co-first author.
2020
Ranathunga, D. T. S.; Shamir, A.; Dai, X.; Nielsen, S. O. “Molecular dynamics simulations of water condensation on surfaces with tunable wettability.” Langmuir, 36, 7383–7391. First author.
2020
Kuhn, B. L.; Osmari, B. F.; Heinen, T. M.; Bonacorso, H. G.; Zanatta, N.; Nielsen, S. O.; Ranathunga, D. T. S.; Villetti, M. A.; Frizzo, C. P. “Dicationic imidazolium-based dicarboxylate ionic liquids: Thermophysical properties and solubility.” Journal of Molecular Liquids, 308.
2020
Nelumdeniya, N. R. M.; Ranathunga, D. T. S.; et al. “Size dependence of host–guest interactions of β-cyclodextrin in silico.” Proceedings of the PGIS Research Congress, 7.
2020
Dharmadasa, A. G. S. V. B.; Ranathunga, D. T. S.; et al. “Effect of hydrophobicity on entrapment efficiency of dendrimers.” Proceedings of the PGIS Research Congress, 7.
2020
Kannangara, D. N. M.; Nelumdeniya, N. R. M.; Ranathunga, D. T. S.; et al. “Generation of a coarse-grained molecular mechanics model for poloxamer molecules.” Proceedings of the PGIS Research Congress, 7.
2021
Ranathunga, D. T. S.; Arteaga, A.; Biguetti, C. C.; Rodrigues, D. C.; Nielsen, S. O. “Molecular-level understanding of the influence of ions and water on HMGB1 adsorption induced by surface hydroxylation of titanium implants.” Langmuir, 37, 10100–10114. First author.
2022
Vieira, J. C. B.; Ranathunga, D. T. S.; Nielsen, S. O.; Villetti, M. A.; Frizzo, C. P. “Experimental and theoretical heat capacity of mono- and dicationic long alkyl chain imidazolium-based ionic liquids.” Journal of Ionic Liquids, 2, 100048. Co-first author.
2023
Ranathunga, D. T. S.; Torabifard, H. “Histone tail electrostatics modulate E2–E3 enzyme dynamics: A gateway to regulate ubiquitination machinery.” Physical Chemistry Chemical Physics, 25, 3361–3374. First author.
2023
Arteaga, A.; Ranathunga, D. T. S.; Qu, J.; Biguetti, C. C.; Nielsen, S. O.; Rodrigues, D. C. “Exogenous protein delivery of ionic liquid-mediated HMGB1 coating on titanium implants.” Langmuir, 39, 2204–2217. Co-first author.
2026
Konagurthu, S.; Ranathunga, D. T. S.; Buchanan, S.; Mehta, N. M.; Reynolds, T. “The predictive edge: modeling and simulation in drug product development.” Advanced Drug Delivery Reviews, 230, 115784. Co-first author.
2026
Ranathunga, D. T. S.; Reynolds, T.; Konagurthu, S. “Predicting drug dissolution performance using molecular dynamics simulations.” White paper in progress. First author.
2026
Ranathunga, D. T. S.; Relix, D.; Torabifard, H. “Computational design, modeling, and properties determination of novel greener ionic liquids from biomolecules using AMOEBA polarizable force fields.” Manuscript in progress; target journal: Journal of Physical Chemistry B. Co-first author.
2026
Ranathunga, D. T. S.; Rodrigues, D. C.; Nielsen, S. O. “Immunomodulatory surface approach for titanium implants.” Manuscript in progress; target journal: Nature Biomedical Engineering. First author.
Presentations
Scientific work shared with the community.
Selected oral, and poster presentations.
Oral presentations
- 2025 · Invited Interview — AI/ML Model-Informed Early-Stage Drug Development.
- 2024 · Invited Webinar, Thermo Fisher Scientific — Solubility and Bioavailability Enhancement Leveraging AI/ML.
- 2023 · Thermo Fisher Scientific Pharma Services Group Science Hour — Quadrant 2® Advancements Using Molecular Modeling and AI/ML.
- 2022 · 26th Annual Green Chemistry & Engineering Conference — Computational Design, Modeling, and Properties Determination of Novel Greener Ionic Liquids from Biomolecules.
- 2022 · 263rd ACS National Meeting and Exposition — Computational Modeling of Bio-based Ionic Liquids.
- 2022 · 54th ACS Meeting in Miniature — Histone Tail Dynamics Regulate the Ubiquitination Machinery.
- 2021 · ACS Southwest Regional Meeting — Tumor Suppressor BRCA1/BARD1 Interactions with Nucleosome Histones.
- 2021 · 20th World Congress on Material Chemistry and Nanomaterials — Role of Surface Hydrophobicity in Water Condensation.
- 2021 · 261st ACS National Meeting and Exposition — Immunomodulatory Surface Approach for Titanium Implants.
- 2020 · TACC Symposium for Texas Researchers — Simulation Insight into Water Condensation as a Function of Surface Hydrophobicity.
- 2020 · 260th ACS National Meeting and Exposition — Molecular Dynamics Simulation of Water Condensation on Surfaces with Tunable Wettability.
- 2020 · 259th ACS National Meeting and Exposition — Molecular Dynamics Simulation Insight into Water Condensation as a Function of Surface Hydrophobicity.
- 2019 · 52nd ACS Meeting in Miniature — Molecular Dynamics Simulations to Characterize Polyvinylpyrrolidone as a Turn-off Fluorescent Sensor for Anions in Water.
- 2018 · 51st ACS Meeting in Miniature — Molecular Dynamics Simulations of Glutathione-Coated Gold Nanoparticles.
- 2017 · 50th ACS Meeting in Miniature — A General Method to Prepare Ligand-Coated Gold Nanoparticles for Molecular Dynamics Simulations.
- 2014 · IPURSE — A Theoretical Study on the Stability of Designed Microemulsions.
Poster presentations
- 2026 · AAPS Pharmsci 360 Conference — Supporting Lipid Formulation Development Through Computational Solubility Predictions.
- 2025 · AAPS Pharmsci 360 Conference — AI/ML Model-Informed Early-Stage Drug Development.
- 2025 · AAPS Pharmsci 360 Conference — Evaluation of Spray-Dried and Nanomilled Formulations on Pharmacokinetics Using Predictive Modeling.
- 2024 · AAPS Pharmsci 360 Conference — Novel Inter-Polymer Complexes in the Development of Spray-Dried Dispersions: A Computational and Experimental Study.
- 2024 · AAPS Pharmsci 360 Conference — Evaluating Food Effects in Oral Drug Delivery Using PBPK Modeling and Molecular Dynamics Simulations.
- 2023 · AAPS Pharmsci 360 Conference — Predicting Drug Dissolution Performance Using Molecular Dynamics Simulations.
- 2022 · 264th ACS National Meeting and Exposition, NVIDIA GPU Award — GPU-Based Computer Simulations for Novel Immuno-Interactive Surface Strategies to Induce Implant Osseointegration.
- 2022 · 264th ACS National Meeting and Exposition, COMP Sci-Mix — GPU-Based Computer Simulations for Novel Immuno-Interactive Surface Strategies to Induce Implant Osseointegration.
- 2021 · ACS Southwest Regional Meeting — Immunomodulatory Surface Approach for Titanium Implants.
- 2020 · 260th ACS National Meeting and Exposition — Characterization of HMGB1-Immobilized Dicationic Imidazolium-Based Ionic Liquid Coatings on Titanium Surfaces.
- 2020 · 259th ACS National Meeting and Exposition — In silico Modeling for Characterization of Polyvinylpyrrolidone as a Turn-off Fluorescent Sensor for Anions in Water.
- 2019 · Southwest Theoretical and Computational Chemistry Meeting — In silico Modeling for Characterization of Polyvinylpyrrolidone as a Turn-off Fluorescent Sensor for Anions in Water.
- 2019 · TACC Symposium for Texas Researchers — Characterization of Polyvinylpyrrolidone as a Turn-off Fluorescent Sensor.
- 2018 · Annual WOW Poster Competition, University of Texas at Dallas — Molecular Dynamics Simulations to Probe pH-Dependent Emission.
- 2014 · Peradeniya University International Research Sessions — A Theoretical Study on the Stability of Designed Microemulsions.