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Hi, I'm Harith Ayodya Kulathunga
Computational Chemistry Researcher
I’m passionate about combining computational chemistry, molecular modeling, and software development to solve real world scientific problems.
Current occupation: Temporary Teaching Assistant, Faculty of Science, University of Colombo
Education: BSc Honors in Computational Chemistry, University of Colombo (June, 2025)
Work Experience: Web Developer at ITSC, University of Colombo
Scholarly Interests:
- Computational Drug Discovery
- Molecular Modeling
- Molecular Dynamics Simulations
- Protein Biology
- QM/MM Theories
Research Experience:
- Computational Chemistry Researcher at Dr. W. M. C. Sameera’s Research Group
- Researcher at Dr. Gayathri N. Silva’s Research Group
Undergraduate Research Summary:
Project Title: Screening for High-Affinity DNA Aptamers Targeting the Extracellular Domain of CD36 Using In-Silico Methods (April 2024 – April 2025)
This project focuses on developing a computational pipeline to design and evaluate DNA aptamers that can recognize the extracellular domain of CD36, a biomarker associated with exosome-based cancer detection.
My work includes preparing protein and aptamer structures, generating mutated aptamer libraries, running molecular dynamics simulations, and performing docking studies to assess binding interactions.
The project also involves analyzing aptamer–protein interfaces to understand key interaction regions.
Project: Automated Quantum Chemistry Workflow
Developed a Python-based workflow to automate quantum chemical simulations of hydrogen molecules using Gaussian 16.
The system automatically generates input files, submits batch jobs, and parses SCF energy values from Gaussian log files for efficient data analysis.
Tools Used: Python, Gaussian 16, Zsh (Linux)
Project GitHub Repository