Saeid Ekrami, PhD
Computational and physical chemist
Enthusiastic about advancing research in chemistry, bringing a unique blending of theoretical skills, artificial intelligence, and hands-on laboratory experience.
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Computational skills
Operating systems:
β€ Unix, GNU/Linux, Windows
Programming and scripting:
β€ Python, Bash, Julia, C/C++, Tcl
Software packages:
β€ Gaussian, Quantum Espresso, Lammps, NAMD, Gromacs
Computational tools:
β€ ASE, RDKit, MDAnalysis, Open Babel, Packmol, Moltemplate
Data Science:
β€ Numpy, SciPy, Pandas, Matplotlib, Beautiful Soup
ML/DL:
β€ SciKit-Learn, Pytorch, PyTorch Geometric, YOLOv8, TorchANI
Software Development:
β€ Git, Github, Docker
HPC systems:
β€ Experienced with HPC systems and parallel computing (OpenMP, Open MPI, CUDA)
Experiences:
π Modeling and simulation
Extensive experience in molecular dynamics (MD) simulation and quantum mechanics (QM) in chemical/biological systems
- Modeling polymers and macromolecules (e.g., hyaluronic acid, Polyallylamine, etc.)
- Modeling chemical reactions (bond breaking/formation) in classical molecular dynamics
- Compute molecular and solid-state materials' electronic, electrochemical, and optical properties
- Predict molecular energies, forces, vibrational frequencies, and thermodynamic quantities using Potential Neural Networks
- Implementing various molecular descriptors (e.g., Graph NN) in ML/DL models
- Experienced with generative models in deep learning (e.g., VAE, GAN, etc.)
π Data processing/analysis
Extensive expertise in processing and analysis of experimental/computational data
- Development of fully automated code to analyze AFM force curves
- Statistics and Chemometrics analysis on Infrared spectra
- Image processing (object detection and segmentation) on microscopic data
π Experimental skills
Comprehensive hands-on laboratory skills
- Synthesizing hydrogels and polyelectrolyte multilayers (PEM) films
- Vibrational spectroscopy using Fourier Transform Infrared (FTIR) and Raman (Transmission, Reflectance, ATR techniques)
- Atomic Force Microscopy (AFM) for imaging and mechanical investigation (Contact mode and tapping mode)
- Imaging using scanning electron microscopy (SEM)
- Surface functionalization using SAMs