📩 Email | 📝 LinkedIn | 🌐 Portfolio |
👋 Hi, there welcome to my GitHub! I'm a computational chemistry wizard 🧙♂️ obsessed with understanding molecules through data 📊! I perform quantum calculations 🤯 to see electrons dance, run molecular simulations 🔬 to watch molecules move, and build ML models 📈 to predict chemical properties. The computational pipelines I develop screens thousands of compounds 🎛️ and crunch big chemical data 📌 to discover new insights. I develop tools in Python and C++ 🛠️ to analyze all the things about molecules! My chemistry spells and algorithms transform raw data into molecular insights. Let's use the power of computation to advance medicines, materials and more! 🚀
| 💼 Repository | 📃 Brief Summary | 🔧 Skills |
|---|---|---|
| Molecular Dynamics (MD) 🚀 | Dive deep into the world of Molecular Dynamics with everything MD. | Classical MD, Enhanced sampling MD, Ab Initio MD |
Quantum Mechanics (QM)  |
Explore the intricacies of Quantum Mechanics with methods like HF, DFT, and applications in spectroscopy. | HF, DFT, Torsional Analysis, Geometry Optimization, Spectroscopy: IR and UV-Visible, Solvent Chemistry, Charge Analysis |
| Drug Discovery 💊 | Delve into the innovative techniques behind drug discovery, from ligand docking to structure-based design. | Free Energy, Thermodynamics Integration, Ligand Docking, Similarity Search: KRAS-G12C, Structure-based Drug Design |
| Cheminformatics 🧬 | Harness the power of tools like Rdkit and OEChem in the fascinating domain of Chemoinformatics. | Rdkit, CppTraj, OEChem, Open Babel |
| Machine Learning 🤖 | Embark on a machine learning journey tailored for chemistry with models like decision trees and GNNs. | Linear regression, Decision Trees, Random Forest, k-mean clustering GNNs |
| Programming 💻 | Computer programs and scripting tools tailored for scientific computations | Python, C++, Bash, Sed, Awk, and CUDA |
| Data Analysis 📊 | Dive into data analytics for high throughput chemistry, mastering tools from Python datastack, MDTraj, Matplotlib, and Plotly for in-depth insights. | NumPy, Pandas, Scikit-learn, SciPy, Plotly, Matplotlib, MDTraj, Excel, and Vortex |
| MD & QM Software 🧮 | Get hands-on with popular software in molecular dynamics and quantum mechanics for high throughput research. | Amber, OpenMM, Gromacs, VMD, MOE, TeraChem, Gaussian, Qubekit, Psi4 |
| OS and HPCs 🖥️ | Master operating systems and high-performance computing tools like Docker and Google Colab for efficient workflows. | Linux, Windows, and Mac-OS, Docker, Singularity, Google Colab, and HPC |
- Ph.D. Candidate in Computational Chemistry, University of California, Merced
- M.Sc. Chemistry and Chemical Biology, University of California, Merced
- M.Sc. Chemistry, National Institute of Technology (NIT), Rourkela, India
- B.Sc. Chemistry (Hons.), University of Delhi, New Delhi, India
- Diploma in Full Stack Web Design and Development, eZone Academy, New Delhi, India
- Introduction to Cheminformatics and Medicinal Chemistry, Udemy
- Data Science with Python Simplilearn
- Fundamental of Accelerated Computing with CUDA Python NVIDIA
- Information Security & Ethical Hacking Appin Technology Lab
| 🏢 Company & Role | 📍 Location & Date | 🌐 Situation | 🎯 Task | 🛠️ Action | 🌟 Result |
|---|---|---|---|---|---|
| Frontier Medicines Intern, CADD |
South San Francisco, CA, USA (May 2023 – Aug 2023) |
Needed a streamlined process for SMILES to desolvation energy and ligand-binding free energy calculations for BTK inhibitors. | Develop Python programs and pipelines. | Created Python programs using AFEP/TI techniques and OpenMM; learned ligand-based docking in MOE. | Streamlined ligand-binding free energy calculations. |
| UC Merced Graduate Student Researcher |
Merced, CA, USA (Aug.2018 - Spring.2024) |
Gap in understanding environmental effects on molecular properties. | Develop computational methods to model experimental spectra. | Developed methods using AIMD, Collaborated on the Polariton project, performed MD and QM simulations and much more, comming soon | Full-stack UV-Visible Spectroscopy, Code development, hybrid QM/MM sampling methods, Excitation Energy Transfer Processes |
| UC Merced Teaching Assistant |
Merced, CA, USA (Aug.2018 – Dec.2022) |
First-generation students needed guidance in chemistry courses. | Teach and prepare materials. | Taught courses and developed worksheet materials. | Successfully educated first-generation students over four years. |
| Indian Institute of Science Research Intern |
Bangalore, India (Jan.2018 – July.2018) |
Need to reproduce experimental spectra of Alexa Fluor dyes. | Reproduce spectra using computational techniques. | Used fundamental spectroscopy and Gaussian calculations. | Successfully reproduced experimental spectra. |
| Indian Association for the Cultivation Science Research Intern |
Kolkata, India (Aug.2017 – Nov.2017) |
Need a method to generate unique metal clusters. | Develop computational procedure for 3D DNA origami structures. | Used Cadnano and oxDNA. | Successfully generated unique DNA origami structures and computational procedure. |
| National Institute of Technology Research Assistant |
Rourkela, India (July 2016 – July.2017) |
Proving 18-electron rule's ability for Zintl ions was unproven. | Conduct quantum mechanical investigations. | Conducted study of Zintl phases. | Demonstrated 18-electron rule's ability to design better Zintl ions. |
📚 Publications Google Scholar | ResearchGate | ORCID
| 📚 Title | 📒 Journal | 📆 Year | 📈 Citations |
|---|---|---|---|
| Ajay Khanna, Christine M. Isborn, Resonance Energy Transfer Processes in Explicit Solvent Environment: Going Beyond Traditional FRET (In Progress) | Journal of Physical Chemistry | 2024 | - |
| Ajay Khanna, Sapana V. Shedge, Tim J. Zuehlsdorff, and Christine M. Isborn, Calculating Absorption and Fluorescence Spectra for Chromophores in Solution with Ensemble Franck-Condon Methods | Journal of Chemical Physics | 2024 | - |
| Christopher A. Myers, Shao-Yu Lu, Sapana Shedge, Arthur Pyuskulyan, Katherine Donahoe, Ajay Khanna, Liang Shi, and Christine M. Isborn, Axial H-bonding Solvent Controls Inhomogeneous Spectral Broadening, Peripherial H-bonding Solvent Controls Vibronic Broadening: Cresyl Violet in Methanol | The Journal of Physical Chemistry B | 2024 | - |
| Chiao-Yu Cheng, Nina Krainova, Alyssa Brigeman, Ajay Khanna, Sapana Shedge, Christine Isborn, Joel Yuen-Zhou, and Noel C. Giebink, Molecular Polariton Electroabsorption | Nature Communication | 2022 | 8 |
| Sapana V. Shedge, Tim J. Zuehlsdorff, Ajay Khanna, Stacey Conley, and Christine M. Isborn, Explicit Environmental and Vibronic Effects in Simulations of Linear and Nonlinear Optical Spectroscopy | Journal of Chemical Physics | 2021 | 14 |
| Rakesh Parida, G. Naresh Reddy, Ajay Khanna, Gourisankar Roymahapatra and Santanab Giri, Ligand Driven Electron Counting Rule Selection: A Case Study for Ge5R Complex | Int. J. Hit. Tranc: Eccn. | 2018 | 1 |
- LinkedIn: Ajay Khanna
- Twitter: @Samdig
- ResearchGate: Ajay Khanna, RIScore: 46.3
- Citations: 24
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