Ajay Khanna

🎓 Ph.D. Candidate | 🧪 Computational Chemist

📩 Email | 📝 LinkedIn | 🌐 Portfolio

🌟 About Me

👋 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 Name	Brief Summary	🔗 Link	🔧 Skills
🚀 Molecular Dynamics Techniques	Dive deep into the world of Molecular Dynamics with everything MD.	View Repo	Classical MD, Enhanced sampling MD, Ab Initio MD
🧪 Quantum Mechanics Techniques	Explore the intricacies of Quantum Mechanics with methods like HF, DFT, and applications in spectroscopy.	View Repo	HF, DFT, Torsional Analysis, Geometry Optimization, Spectroscopy: IR and UV-Visible, Solvent Chemistry, Charge Analysis
💊 Drug Discovery Techniques	Delve into the innovative techniques behind drug discovery, from ligand docking to structure-based design.	View Repo	Free Energy, Thermodynamics Integration, Ligand Docking, Similarity Search: KRAS-G12C, Structure-based Drug Design
🧬 Chemoinformatics	Harness the power of tools like Rdkit and OEChem in the fascinating domain of Chemoinformatics.	View Repo	Rdkit, CppTraj, OEChem, Open Babel
🤖 Machine Learning	Embark on a machine learning journey tailored for chemistry with models like decision trees and GNNs.	View Repo	Linear regression, Decision Trees, Random Forest, k-mean clustering, GNNs
💻 Programming	Sharpen your programming skills across various languages and scripting tools tailored for scientific computations.	View Repo	Python, C++, Bash, Sed, Awk, and CUDA
📊 Data Analysis	Dive into data analytics for chemistry, mastering tools from MDTraj to Plotly for in-depth insights.	View Repo	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 cutting-edge research.	View Repo	Amber, OpenMM, Gromacs, VMD, MOE, TeraChem, Gaussian, Qubekit, Psi4
🖥️ Operating System and HPC	Master operating systems and high-performance computing tools like Docker and Google Colab for efficient workflows.	View Repo	Linux, Windows, and Mac-OS, Docker, Singularity, Google Colab, and HPC

🎓 Education

• 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

🏆 Certifications

• 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

💼 Work Experience

🏢 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

• Peer-Reviewed Journals (On Going)

  • Ajay Khanna, Christine M. Isborn, Resonance Energy Transfer Processes in Explicit Solvent Environment: Going Beyond Traditional FRET, Fall 2024

• Peer-Reviewed Journals (In Press)

  • 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, In Journal of Chemical Physics (JCP) Press, ChemRxiv, Accepted, Stage: Minor Revisions, ChemRxiv

• Peer-Reviewed Journals (Published)

  • 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, ASAP, DOI:10.1021/acs.jpcb.4c01401
  • 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 13, 7937, 2022, DOI:10.1038/s41467-022-35589-4
  • 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 , J. Chem. Phys. 154, 084116, 2021, DOI: 10.1063/5.0038196
  • 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., Int. J. Hit. Tranc: Eccn. Vol.4: Issue 1A, 2018, ISSN: 0973-6875

🌐 Social Media Presence

• LinkedIn: Ajay Khanna
• Twitter: @Samdig
• ResearchGate: Ajay Khanna, RIScore: 44.4
• Citations: 24