Shashank Shastry

PhD – Biophysics and Quantitative Biology (in progress)

University of Illinois Urbana-Champaign

• Conducting molecular modeling of drugs, proteins, and membranes to understand the mechanisms behind biochemical processes.
• Developing and applying software tools and custom analysis pipelines for molecular simulations, statistical analyses, structural modeling, and machine learning force field prediction.
• Relevant Coursework: Machine Learning for Bioinformatics (CS 582), Statistical Physics (PHYS 504), Physical Chemistry (CHEM 440), Chemical Biology (CHEM 570), Introduction to Biophysics (BIOP 401).
• Fiddler Innovation Fellowship recipient.

Graduate Research Assistant

Pogorelov Lab – University of Illinois Urbana-Champaign (Dr. Taras Pogorelov)

• Developed a tool to reconstruct incomplete lipids from crystallographic protein–lipid structures.
• Quantifying protein–lipid interactions and membrane curvature using atomistic molecular dynamics simulations (GROMACS, NAMD3) to elucidate structural mechanisms driving membrane remodeling.
• Investigating cancer-relevant receptor tyrosine kinase assemblies via multi-scale simulations (MARTINI, GROMACS).
• Quantifying drug aggregate stability, drug–protein binding, and lipid–protein interactions using thermodynamic cycle modeling and free energy perturbation (GROMACS, NAMD3).
• Building high-throughput molecular dynamics workflows with automated analysis pipelines (Python, pandas, NumPy, Bash) for multi-terabyte trajectories.
• Contributed software improvements to the MARTINI ecosystem.
• Authored computational quantum chemistry tutorial (Gaussian) for biophysical applications.

Junior Specialist

Collins Lab – UC Davis (Dr. Sean Collins)

• Generated genetically modified human cell lines via molecular cloning, viral transduction, and mammalian tissue culture.
• Characterized fluorescently tagged membrane protein localization and expression using fluorescence and confocal microscopy.
• Developed MATLAB scripts for automated image analysis and quantitative data extraction.
• Performed molecular biology workflows including nucleic acid isolation, PCR, electrophoresis, and bacterial transformations.

Undergraduate Research Assistant

Collins Lab – UC Davis (Dr. Sean Collins)

• Designed plasmids and generated stable cell lines via viral transduction and mammalian cell culture.
• Developed MATLAB scripts for data analysis and quantitative readouts.
• Co-authored Nature Communications paper (A. Hadjitheodorou et al. 2021).

Computational & Analytical

• Molecular Dynamics: proficient in GROMACS, NAMD3, MARTINI3, and MDAnalysis.
• Free Energy Methods: FEP, thermodynamic cycles, and custom force field development.
• Machine Learning: neural network implementations (PyTorch, scikit-learn, TensorFlow) and force field parametrization (OpenFF 2.0).
• Data Analysis: automated pipelines (Python, pandas, NumPy, Bash) for multi-terabyte datasets on HPC clusters.
• Quantum Chemistry: integration of QM calculations (Gaussian) with classical MD workflows.