ajaykhanna/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.

Ajay Khanna

🎓 Ph.D. | 🧪 Computational Chemist | Citations: 24 | RGScore: 48.3

📩 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	📃 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

💼 Work Experience

🏢 Company & Role	📍 Location	🌐 Situation	🎯 Task	🛠️ Action	🌟 Result
Frontier Medicines Intern, CADD	South San Francisco, CA, USA	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	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	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	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	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	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.

🌟 Featured Publications | Google Scholar | ResearchGate | ORCID

1. Resonance Energy Transfer Processes in Explicit Solvent Environment: Going Beyond Traditional FRET (In Progress) Ajay Khanna, Christine M. Isborn Peer-reviewed Journal (Comming soon, 2024)

   Exploring advanced FRET processes in complex solvent environments to enhance energy transfer predictions in molecular systems.

2. 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.

3. 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.

4. 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.

🎓 Education & Academic Journey

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	Advance Experiemental Chemistry, Computaitonal Chemistry, and Zintl Clusters
🧪 B.Sc. Chemistry (Hons.)	University of Delhi	2011 - 2015	Core Experimental Chemistry: Basics to Advanced Synthetic Chemistry
💻 Diploma Full Stack Web Design and Development	eZone Academy, New Delhi	2012-2013	Web Development, UI/UX Design

🎓 Certifications

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
🔒 Information Security & Ethical Hacking	Appin Technology Lab	2011	Cybersecurity, Ethical Hacking, Network Security

🌐 Social Media Presence

• LinkedIn: Ajay Khanna
• Twitter: @Samdig