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👋 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 harness 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 |
| 🏢 Company & Role | 🌐 Situation | 🎯 Task | 🛠️ Action | 🌟 Result |
|---|---|---|---|---|
| Los Alamos National Laboratory (LANL) Los Alamos, NM, USA Postdoctoral Research Associate |
Aiming to enhance X-ray technology and implement ML-NAMD for energy transfer processes. | Developing advanced methods for X-ray Circular Dichroism (XCD) and accelerating Non-Adiabatic Molecular Dynamics (NAMD) using Interatomic Machine Learning Potentials and Active Learning techniques. | Pending | Anticipatin advancements in X-ray technology and ML-NAMD |
| Frontier Medicines South San Francisco, CA, USA Intern, CADD |
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 Merced, CA, USA Doctoral Researcher |
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, coming soon | Full-stack UV-Visible Spectroscopy, Code development, hybrid QM/MM sampling methods, Excitation Energy Transfer Processes |
🌟 Featured Publications | Google Scholar, Cite: 43 | RGScore: 60.6 | ORCID: 0000-0002-8313-1393
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Deconstructing Chirality: Probing Local and Non-local Effects in Azobenzene Derivatives with X-ray Circular Dichroism
Ajay Khanna, Victor M. Freixas, Lei Xu, Jeremy R. Rouxel, Niranjan Govind, Marco Garavelli, Shaul Mukamel, and Sergei Tretiak, 2025Site-specific X-ray spectroscopy to deconstruct molecular chirality, establishing a new framework for engineering chiroptical signals to design functional molecular machines.
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Calculating Absorption and Fluorescence Spectra for Chromophores in Solution with Ensemble Franck-Condon Methods
Ajay Khanna, Sapana V. Shedge, Tim J. Zuehlsdorff, Christine M. Isborn, Journal of Chemical Physics (2024)Novel computational approach for accurate prediction of absorption and fluorescence spectra in solution, advancing spectroscopic analysis techniques.
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Molecular Polariton Electroabsorption
Chiao-Yu Cheng, Nina Krainova, Alyssa Brigeman, Ajay Khanna, Sapana Shedge, Christine Isborn, Joel Yuen-Zhou, Noel C. Giebink, Nature Communication (2022)Novel study on molecular polariton electroabsorption, opening new avenues in optoelectronics and quantum technology.
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Explicit Environmental and Vibronic Effects in Simulations of Linear and Nonlinear Optical Spectroscopy Sapana V. Shedge, Tim J. Zuehlsdorff, Ajay Khanna, Stacey Conley, Christine M. Isborn, Journal of Chemical Physics (2021)
Comprehensive exploration of environmental and vibronic effects in optical spectroscopy simulations, enhancing accuracy in molecular property predictions.
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Resonance Energy Transfer Processes in Explicit Solvent Environment: Going Beyond Traditional FRET
Ajay Khanna, Christine M. Isborn, 2024Exploring advanced FRET processes in complex solvent environments to enhance energy transfer predictions in molecular systems.
| Degree | Institution | Year | Focus |
|---|---|---|---|
| 🔬 Ph.D. Computational Chemistry |
University of California, Merced |
2018 - 2024 | AIMD, Fluorescence Spectroscopy, AIMD, Quantum Mechanics, High Throughput Screening, Machine Learning, and Resonance Energy Transfer |
| 🔬 M.Sc. Chemistry |
National Institute of Technology, Rourkela |
2015 - 2017 | Advanced Experimental Chemistry, Computaitonal Chemistry, and Zintl Clusters |
| 💻 Diploma Web Design and Development |
eZone Academy, New Delhi |
2012-2013 | Web Development, UI/UX Design |
| Certification | Issuing Organization | Year | Skills Acquired |
|---|---|---|---|
| 🧪 Introduction to Cheminformatics and Medicinal Chemistry |  Udemy |
2023 | Cheminformatics, Drug Discovery, QSAR |
| 📊 Data Science with Python |  Simplilearn |
2022 | Python, Data Analysis, Machine Learning |
| 🚀 Fundamentals of Accelerated Computing with CUDA Python |  NVIDIA |
2022 | CUDA, Parallel Computing, GPU Programming |