I am a computational biophysicist and scientific software engineer interested in high-performance molecular simulation, cheminformatics, and the application of machine learning to drug discovery. During my doctorate I ran multi-year atomistic molecular-dynamics simulations of biological membranes — in particular galactolipid systems modelling thylakoid membranes — studying the formation of inverse-phase water channels and the properties of the lipid/water interface. More recently I have focused on GPU-accelerated algorithms for protein–glycan systems, on-chain protection of conformational intellectual property, and ML methods for virtual screening and molecular property prediction. I combine a strong foundation in molecular dynamics and statistical analysis with hands-on skills in high-performance computing, GPU programming, and production-grade Python and C++ development.
Educational Background
PhD in Biophysics (Biological Sciences)
Dept. of Computational Biophysics and Bioinformatics, Jagiellonian University, Kraków, Poland (2018–2025)
- Topic: Investigation of the mechanism of water-channel formation in galactolipid systems modelling thylakoid membranes and the characterisation of their interface
- Supervisor: Prof. Dr. hab. Marta Pasenkiewicz-Gierula
- Discovered that stacks of monogalactolipid bilayers can reorganise into a lattice of water channels; characterised the lipid/water interface across lyotropic liquid-crystalline phases.
- Ran simulations on national (Prometheus, Athena, Ares) and European (Mahti, Puhti) HPC infrastructure under four PLGrid grants and an HPC-Europa3 fellowship.
Master of Science in Biology
Dept. of Glycoconjugate Biochemistry, Jagiellonian University, Kraków, Poland (2016–2018)
- Topic: Detection of O-GlcNAcylated proteins in melanoma
- Supervisor: Dr. hab. Dorota Hoja-Łukowicz
Bachelor of Science in Biology
Dept. of Glycoconjugate Biochemistry, Jagiellonian University, Kraków, Poland (2013–2016)
- Topic: Analysis of the sugar residues of the L1 adhesion molecule in the WM266-4 melanoma cell line
- Supervisor: Dr. hab. Dorota Hoja-Łukowicz
Professional Experience
Scientific Software Engineer
Małopolska Centre of Biotechnology UJ, Dioscuri Centre, Kraków, Poland (07/2026–present)
Computational Biology Software Developer
Małopolska Centre of Biotechnology UJ, Freelance (02/2025–06/2026)
- Designed and implemented from scratch the GlycoSASA algorithm for the GlycoSHIELD project (MCB UJ / MPCDF Munich), computing solvent-accessible surface area for protein–glycan systems.
- Built a GPU backend (Numba CUDA) with grid-based spatial partitioning — ~5× faster than single-threaded CPU — enabling terabyte-scale MD trajectory processing.
- Developed Ray-analysis and buriedness methods, glycan-only trajectory optimisation (~5× file-size reduction) and parallelised glycan-grafting pipelines integrated with the GROMACS C++ codebase.
- Ran GROMACS scaling benchmarks on the Ares cluster (PLGrid/Cyfronet) and tuned enhanced-sampling (REST/RECT) protocols for glycopeptide systems.
Data Researcher
PeakData, Zug, Switzerland, Remote (02/2024–07/2026)
- Managed large-scale healthcare-professional (HCP) datasets across multiple international markets; automated data acquisition in Python.
- Performed quality assurance and correction of LLM-generated data; conducted market-feasibility research on data-protection compliance, source quality and KOL identification.
Teaching and Research Assistant
Jagiellonian University, Kraków, Poland (09/2021–02/2024)
- Ran large-scale atomistic MD simulations (GROMACS) on national and European HPC clusters, managing jobs via SLURM and PBS schedulers.
- Wrote Bash automation and C++/Python analysis pipelines for membrane modelling; authored scientific articles.
- Taught bioinformatics, molecular modelling and Linux fundamentals.
Selected Publications
Grants and Fellowships
- HPC-Europa3 fellowship (EC H2020, grant 730897) — peer-reviewed transnational access to CSC Finland; research collaboration with the University of Helsinki (2020–2022)
- Four PLGrid computing grants (Cyfronet AGH) — principal investigator and manager (Prometheus, Ares, Athena)
- Faculty research grant (WBBiB / FBBB) for PhD students and young researchers — “Dynamic model of the inverted hexagonal phase (HII) of MGDG” (2021–2022)
Certifications and Additional Training
- Machine Learning in Drug Discovery — EMBL-EBI (2025)
- Building LLM Applications with Prompt Engineering — NVIDIA (2025)
- AI in Business Development — Google (2025)
- C++ from Basic to Expert; Mastering Critical Skills using C++17 — Udemy
Technical Skills
- Molecular dynamics: GROMACS (atomistic & coarse-grained / MARTINI), MDAnalysis, VMD, PyMOL
- HPC: SLURM/PBS, Linux/Bash, Prometheus, Ares, Athena, Mahti, Puhti
- Programming: Python (NumPy, Pandas, SciPy, Numba, CUDA), C/C++, SQL, Git
- ML & cheminformatics: PyTorch, TensorFlow, RDKit, QSAR, virtual screening, AutoDock Vina
- Other: AWS, smart contracts (Solidity, web3.py, Hardhat)
- Languages: Polish (native), English (C1)
Other Activities
- Participant in eight national and international scientific conferences; three-week research stay at the University of Helsinki
- Open-source software: GlycoSHIELD / GlycoSASA (GitLab, MPCDF) and the Conformational Soft Hash registry (GitHub)
- Teaching experience: bioinformatics, molecular modelling, Linux/Bash, C++