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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. My pipelines screen 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, 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

  • 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 A lot, Coming Soon.
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

🌐 Social Media Presence

Ajay Khanna's Projects

amber-organic-solvent-box icon amber-organic-solvent-box

This repo contains custom made preequilibrated organic solvent boxes and droplets based on Amber software. More information about each organic solvent can be found in their separate directory.

awesome-python icon awesome-python

A curated list of awesome Python frameworks, libraries, software and resources

black icon black

The uncompromising Python code formatter

cheminformatics icon cheminformatics

A tutorial set for applying cheminformatics in Virtual Screening, Similarity Search, Conformers Generation and Presentation

cuda_with_coffee icon cuda_with_coffee

Cplusplus CUDA Programming Examples This repository contains example programs written in Cplusplus CUDA programming language. The examples demonstrate how to use the language for general purpose programming tasks.

denstq icon denstq

calculate transition charges using spatial densities

drug_discovery icon drug_discovery

Computational Chemistry methods applied to drug discovery processes

excitonic_coupling icon excitonic_coupling

How to Compute Excitonic Coupling Between Molecules Using Various Excitonic Coupling Schemes

excitonichamiltonian icon excitonichamiltonian

The scripts in this repository can be used to generate an excitonic Hamiltonian of a molecular aggregate. The protocol for running this code to generate such a Hamiltonian is described in the paper "Excitonic Hamiltonians for Calculating Optical Absorption Spectra and Optoelectronic Properties of Molecular Aggregates and Solids" by A.A. Kocherzhenko, S.V. Shedge, P.F. Germaux, M. Heidarian, C.M. Isborn, J. Vis. Exper., 2020, Issue 159, e60598, doi: 10.3791/60598.

hydrogen_bonding_analysis icon hydrogen_bonding_analysis

This is Analysis Hydrogen bonding pattern that includes bond length and bond angle between a dye and solvent.

literaturereviews icon literaturereviews

This repository contains notes on a selection of quantum chemistry (and related theory) literature.

machine_learning_with_chemistry icon machine_learning_with_chemistry

This repository contains tutorials on using machine learning methods to predict chemical properties. These tutorials represents using ML as tool and not core implementation of any ML method. The goal from these tutorials is to see how ML helps in making better predictions while keep the chemical intuition as the base.

manim icon manim

Animation engine for explanatory math videos

molecular_dynamics_101 icon molecular_dynamics_101

Molecular Dynamics 101, this repository contains lessons and things I learned during the course of my PhD. The topics includes fundamental topics to some important algorithms to propagate the systems. This repository will serves as an examples repository for the future MD online courses I'll generate

nglview icon nglview

Jupyter widget to interactively view molecular structures and trajectories

parmed icon parmed

Parameter/topology editor and molecular simulator

python icon python

All Algorithms implemented in Python

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