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Curriculum Vitae Candidate's Name  20241Contacts Mohammad Sadegh Avestan, Street Address  PHONE NUMBER AVAILABLE EMAIL AVAILABLELinkedInVisa Status Permanent ResidentWork Experience Sr. Advanced Software Engineer: Kroger Technology & Digital Sr. Advanced Solutions Architect: Kroger Technology & Digital Research Fellow Intern: Kroger Technology & Digital Mar 2024  presentDec 2021  Mar 2024Jun 2021  Dec 2021Education Ph.D. Computational Biophysics, University of Cincinnati, Ohio. M.Sc. Physical Chemistry, Bu-Ali Sina University (BASU), Hamadan, Iran.B.Sc. Pure Chemistry, University of Tabriz, Tabriz, Iran 2016 - 20212009 -20122005 - 2009Computer Skills  Programming: Python, R, SQL, bash, csh, Tcl scripting Deep Learning & Machine Learning: Scikit-learn, pandas, numpy, scipy, matplotlib, machine learning algorithms (K-Nearest Neighbor, hierarchical clustering, K-means clustering etc) TensorFlow, Keras, CNN, sequence models (RNN, LSTM, GRU), Markov-Model, Bayesian models, Attention models, etc. Natural Language Processing (NLP): NLTK, Transformers (Hugging Face), Sequence models(LSTM, GRU), Bayesian models, Viterbi algorithm, Attention, chatbot, etc. Generative AI: Implemented Generative AI solutions for Q&A applications, leveraging state-of- the-art Large Language Models (LLMs), Prompt Engineering, Retrieval-Augmented Generation(RAG), etc. Data Science: Data cleaning, data shaping, clustering methods (K-means, hierarchical clustering, KNN), exploratory data analysis, feature engineering, statistical analysis Cloud: Azure (AI Studio) and GCP (Vertex AI) Big Data & High-Performance Computing: HPC Administration, Slurm, Kubernetes, NVIDIA DGX Stations, Extreme Science and Engineering Discovery Environment (XSEDE), Kroger Supernode. Web Frameworks & APIs: Flask, REST API, CSS, HTML, and Streamlit Version Control & Development Tools: Git, Docker, Postman, Jupyter Lab/Hub, VS Code, RStudio Computer Science Fundamentals: Data Structures, Algorithms, Computational Theory, Software Engineering Principles Computational Software: CHARMM, NAMD, LAMMPS, Packmol, Gaussian Computer Graphics & Visualization: Inkscape, Blender 3D, Ovito, VMD Responsible AI (RAI): Ethical AI practices, fairness, accountability, transparency, bias mitigation Curriculum Vitae Candidate's Name  20242Research Skillsand experienceSr. Advanced Software Engineer at Kroger Technology & Digital, Mar 2024 - present Associate Assistant use-case app:- Developing a Langchain/streamlit app using Huggingface and OpenAI Embedings.- Developing associate assistant chatbot using GCP Vertex AI (Agent builder) Sr. Advanced Solutions Architect at Kroger Technology & Digital, Dec 2021  Mar 2024 Tech Lead for AI and IoT Groups: Driving R&D initiatives and cutting-edge technology projects, including the development of a cost-effective paper-based freshness sensor (Meat Sensor) with a team of IoT engineers. Freshness Algorithm Development: Developed and implemented multiple freshness algorithms in Python, enhancing real-time freshness assessments to ensure product quality. Kroger Supernode/MLOPS Project: Oversaw the Kroger Supernode/MLOPS project, optimizing machine learning operations on the Kroger Cluster to streamline data processing and model deployment. Queue Vision Project: performed the Queue Vision project to facilitate the customer shopping experience, implementing computer vision technology to optimize store queues and enhance customer satisfaction. Chatbot Contribution: Contributed to the development and improvement of a chatbot, enhancing customer interaction and support through natural language processing and AI technologies. Associate Assistant use-case app: Developing a Langchain/Streamlit app using Huggingface and OpenAI Embedings. Patent Contributions: Contributed to two patents through active participation in research and development efforts, furthering innovation in freshness sensing, machine learning solutions, and customer shopping experiences.Research Fellow Intern at Kroger Technology & Digital, Jun 2021  Dec 2021 GPU accelerated simulation of supercapacitors and sensors (Using LAMMPS software, Python, bash scripting, Docker, and NVIDIA DGX Station)Ph.D. Student (RA & TA), George Stan Group, UC, 2016  2021 Dissertation: Direction-Dependent Protein Unfolding by the 26S Proteasome and Gating Mechanism of ClpP Nanomachine Author Info Cluster Management & Optimization:- Maintained and administered local computational clusters.- Performed CPU/GPU benchmarking to optimize computation efficiency on local clusters and XSEDE Cloud.- Optimized CPU distribution for Multiscale (MSCALE) modeling using Bash scripting for automation and efficiency. Simulation & Modeling:- Conducted Coarse Grained (CG), MSCALE (CG/EEF1), and Explicit Solvent Simulations of Biopolymers on CPU/GPU Local Clusters and XSEDE Cloud.- Developed and tweaked Python scripts to modify Protein Structure Files (PSF) for MSCALE simulations, enhancing the accuracy and efficiency of simulations. Curriculum Vitae Candidate's Name  20243- Modified CHARMM source code (FORTRAN) to adapt to MSCALE and CG simulations, improving compatibility and performance. Data Analysis & Scripting:- Leveraged Python for data preprocessing, analysis, and visualization of simulation results, ensuring accurate interpretation of complex datasets.- Utilized R for statistical analysis and data visualization, producing insightful graphical representations of research data.- Automated repetitive tasks and enhanced workflow efficiency through advanced Bash scripting. Educational Contributions:- Mentored graduate and undergraduate students in computational biology techniques, including programming skills in Python, R, and Tcl.- Successfully completed multiple LinkedIn courses in Python and data science, demonstrating a commitment to continuous learning and skill enhancement. M.Sc. Student, Hosseinali Zarei Group, BASU, Hamedan, Iran, 2010 - 2012 Calculation of thermodynamic properties of gas binary mixtures using quantum mechanics methods.(M.Sc. thesis)PhDProjects Computational Study of the Inter-Domain Stabilization of Tandem Green Fluorescent Substrate Proteins During Proteasomal Degradation Initiated from Internal Sites (1 paper extracted, another one is in preparation). Multiscale Simulation (CG/EEF1) of I27 Unfolding Mediated by ClpY ATPase Nanomachine. Molecular Insight into ClpP Nanomachine Using Explicit Solvent Simulation. Selected JournalPublications(Google ScholarProfile) Avestan, M. S.; Javidi, A.; Ganote, L. P.; Brown, J. M.; Stan, G. Kinetic effects in directional proteasomal degradation of the green fluorescent protein. J. Chem. Phys. (2020), 153, 105101. Dayananda, A., Dennison, H. T. S., Fonseka, H. Y. Y., Avestan, M. S., Wang, Q., Tehver, R., & Stan, G. Allosteric communication in the gating mechanism for controlled protein degradation by the bacterial ClpP peptidase. Journal of Chemical Physics, (2023) 158(12), 125101. Jahanbakhsh-Bonab, P., Sardroodi, J. J., & Avestan, M. S. The pressure effects on the Amine-Based DES performance in NG Sweetening: Insights from molecular dynamics simulation. Fuel, (2022) 323, 124249. Pour, S. B., Sardroodi, J. J., Ebrahimzadeh, A. R., & Avestan, M. S. Structural and dynamic properties of eutectic mixtures based on menthol and fatty acids derived from coconut oil: a MD simulation study. Scientific Reports, (2022) 12(1) Jahanbakhsh-Bonab, P., Sardroodi, J. J., & Avestan, M. S. Electric field effects on the structural and dynamical properties of a glyceline deep eutectic solvent. Journal of Chemical & Engineering Data, (2022) 67(9), 20772087. Pour, S. B., Sardroodi, J. J., Ebrahimzadeh, A. R., & Avestan, M. S. Using molecular dynamics simulations to understand the effect of fatty acids chain length on structural and dynamic properties of deep eutectic solvents based on choline chloride and fatty acids. ChemistrySelect, (2022) 7(47). Curriculum Vitae Candidate's Name  20244 Atabay, M., Sardroodi, J. J., Ebrahimzadeh, A. R., & Avestan, M. S. Modeling the Interaction of Anticancer Protein Azurin with the Nanosheets for Medical Applications. ChemistrySelect,(2022) 7(47). Ghelichkhah, Z., Dehkharghani, F. K., Sharifi-Asl, S., Obot, I. B., Macdonald, D. D., Farhadi, K., Avestan, M. S, Petrossians, A. The inhibition of type 304LSS general corrosion in hydrochloric acid by the New Fuchsin compound. Corrosion Science, (2021) 178, 109072. Pirhadi, S., Damghani, T., Avestan, M. S., & Sharifi, S. Dual potent c-Met and ALK inhibitors: from common feature pharmacophore modeling to structure based virtual screening. Journal of Receptors and Signal Transduction, (2020), 40, 357-364. Mashayekh K, Sharifi S, Damghani T, Elyasi M, Avestan M. S., Pirhadi S. Clustering and Sampling of the c-Met Conformational Space: A Computational Drug Discovery Study. Comb Chem High Throughput Screen. (2019) 22, 63548. Chianeh, F. N., & Avestan, M. S. Application of central composite design for electrochemical oxidation of reactive dye on Ti/MWCNT electrode. Journal of the Iranian Chemical Society, (2019) 17(5), 10731085. Damghani T., Mashayekh K., Pirhadi S., Firuzi O., Sharifi S., Edraki N., Khoshneviszadeh M., and Avestan M. S. Prediction of cytotoxic activity of a series of 1H-pyrrolo[2,3-b] pyridine derivatives as possible inhibitors of c-Met using molecular fingerprints. J Recept Signal Transduct. (2019) 39, 295-303.SelectedConferenceattendance Mohammad Sadegh Avestan, Abdolreza Javidialesaadi and George Stan; Coarse-grained Simulations of Green Fluorescent Protein Unfolding Mediated by 26S Proteasome From Computational Biophysics to Systems Biology (CBSB2017), Cincinnati, OH. Professional Meeting. Level: International Mohammad Sadegh Avestan, George Stan and Abdolreza Javidialesadi (11-17-2017) Computer simulation of mechanical unfolding of tandem Green Fluorescent Protein in bulk or mediated by the 26S proteasome; 2017 Ralph & Helen Oesper Symposium, University of Cincinnati. Professional Meeting. Level: UniversityTeaching  General chemistry recitations and labs, 1030, 1031,1040, 1041 SelectedAdvancedCoursework Applied Statistics I Big Data Science for Chemistry Biopolymers Bioinformatics Statistical Mechanics Advanced Chemical Kinetics Computational Chemistry Advanced Quantum Chemistry Advanced Analytical Chemistry Advanced Organic Chemistry Advanced Physical Chemistry Surface ChemistryAwards  Chemistry Doctoral Enhancement Fellowship for the summer semester 2019 (UC) Henry Hochstetter Prize; For excellence as a graduate teaching assistant; UC, spring 2018 National Entrance Exam for Undergraduate Studies (Iran) Top 1%ile 2005 National Entrance Exam for Graduate Studies, M.Sc., (Iran) Top 1%ile 2009 Certificates  Developing AI Applications with Python and Flask (IBM, Jun. 2024) Generative AI in Business: Applications, Challenges, Ethics, and Governance(University of Cincinnati, Jun. 2024)Curriculum Vitae Candidate's Name  20245 Natural Language Processing Specialization (DeepLearning.AI, May 2024)- Natural Language Processing with Attention Models (May 2024)- Natural Language Processing with Probabilistic Models (Aug. 2023)- Natural Language Processing with Sequence Models (Nov. 2023)- Natural Language Processing with Classification and Vector Spaces (May 2023) Deep Learning Specialization (DeepLearning.AI, Mar 2023)- Sequence Models (Mar. 2023)- Convolutional Neural Networks (Nov. 2022)- Improving Deep Neural Networks: Hyperparameter Tuning, Regularization and Optimization (Sep. 2022)- Structuring Machin Learning Projects (Sep. 2022)- Neural Network and Deep Learning (Jul. 2022) Building and Deploying Deep Learning Applications with TensorFlow (LinkedIn, Feb. 2021) Deep Learning: Image Recognition (LinkedIn, Feb. 2021) Deep Learning: Face Recognition (LinkedIn, Feb. 2021) Building Deep Learning Applications with Keras 2. (LinkedIn, Feb. 2021) Python for Data Science Tips, Tricks, & Techniques (LinkedIn, Feb. 2021) Learning R (LinkedIn, Jan. 2021) Python for Data Science Essential Training Part 2 (LinkedIn, Dec. 2020) Python for Data Science Essential (LinkedIn, Dec. 2019)