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fr-0zt/README.md

Hi, I'm Senal Liyanage

Computational chemist focused on molecular simulation, quantum-chemical analysis, and research software development.

My work uses computation to study chemically and biologically relevant systems, with particular interests in molecular dynamics, electronic-structure methods, soft matter, polymer and nanoparticle systems, and reproducible workflows for high-performance computing.


Research areas

  • Molecular dynamics simulations of complex chemical and biomolecular systems
  • Polymer, nanoparticle, and ionic-liquid modeling
  • TDDFT and quantum-chemical post-processing
  • Scientific Python tools for chemistry and simulation analysis
  • Reproducible HPC workflows for computational chemistry

Selected open-source repositories

  • qctddft — A command-line toolkit for TDDFT post-processing from Q-Chem, including spectral analysis, region assignment, and clustering of representative structures.
  • chemistry-analysis-tools — Python utilities for chemistry data handling, molecule-file cleanup, and partial-charge analysis.
  • AmberMD-Scripting — Shell-based utilities for preparing and running AMBER molecular dynamics simulations.

Current focus

I am especially interested in computational studies of chemically tunable soft-material systems, including polymers, nanoparticles, and ionic-liquid-containing environments, as well as in building practical tools that make simulation workflows more robust, transparent, and scalable.


Methods and platforms

Molecular simulation: GROMACS, AMBER
Quantum chemistry: Q-Chem, Gaussian, GAMESS, TDDFT
Analysis and scripting: Python, Bash, Pandas, Matplotlib, MDAnalysis
Computing: SLURM, Linux, workflow automation, reproducible HPC practice


Collaboration interests

I am interested in collaborations involving molecular simulation, mechanism-driven modeling, quantum-chemical analysis, simulation workflow design, and computational chemistry software.


Get in touch

Pinned Loading

  1. qctddft qctddft Public

    Command-line toolkit for post-processing Q-Chem TDDFT calculations, from excitation extraction and spectrum generation to spectral-region assignment and structural clustering.

    Python

  2. chemistry-analysis-tools chemistry-analysis-tools Public

    Lightweight Python utilities for MOL2 cleanup and partial-charge analysis using Open Babel.

    Python

  3. AmberMD-Scripting AmberMD-Scripting Public

    Bash helpers for generating staged AMBER MD input files and running membrane-oriented AMBER simulation workflows.

    Shell