RYAN MCGREEVY

Kokomo, IN 46901 | rmcgreevy@protonmail.com | github.com/ryanmcgreevy

Software engineer with 17+ years of professional experience spanning high-performance scientific computing, cloud infrastructure, and applied AI/ML. Spent 9+ years developing C++, Tcl/Tk, and CUDA-based molecular dynamics software (NAMD/VMD) at the University of Illinois’ Theoretical and Computational Biophysics Group, co-authoring 10 peer-reviewed publications. Since 2019, has run an independent practice building and automating AWS cloud infrastructure with Terraform and Ansible. In recent years has expanded into applied machine learning and generative AI with building RAG-based LLM applications, agentic systems, and traditional ML models. Backed by AWS certifications in Solutions Architecture, Machine Learning, and AI. Holds an M.Eng. in Bioinformatics (University of Illinois Chicago) built on a B.A. in Biochemistry and Computer Science (St. Mary’s College of Maryland).

SKILLS

  • AI & Machine Learning: LLM agent frameworks (Google ADK, Amazon Strands), RAG, LangChain, AI-assisted development (GitHub Copilot), PyTorch, scikit-learn, pandas, MLflow, Optuna, AWS SageMaker
  • Cloud, DevOps & Containerization: AWS, IaC (Terraform, CloudFormation, Ansible), Docker, Kubernetes, ECS, CI/CD (GitHub Actions, AWS CodePipeline), Linux systems administration
  • Programming Languages: Python, C++, Tcl/Tk, CUDA, C#
  • Scientific Computing: Molecular dynamics simulation and analysis, HPC/GPU computing, structural biology methods
  • Certifications: AWS Certified Machine Learning Engineer – Associate, AWS Certified Solutions Architect – Associate, AWS Certified AI Practitioner, AWS Certified Cloud Practitioner

EXPERIENCE

Owner and Engineer | Panoptesoft, LLC — Kokomo, IN

Sep 2019 – Present

  • Design, build, and sell Ubuntu Server EC2 AMIs (remote Linux desktop environments) on the AWS Marketplace.
  • Provision and configure infrastructure as code using Terraform and Ansible.

Math Lab Supervisor | Indiana University Kokomo — Kokomo, IN

Jan 2022 – May 2022

  • Supervised and assisted students during math lab sessions for College Algebra.

Research Programmer | UIUC, Beckman Institute — Urbana, IL

Aug 2010 – Sep 2019

  • Developed HPC scientific software in C++, Tcl/Tk, and CUDA for NAMD and VMD, including the Molecular Dynamics Flexible Fitting (MDFF) method for structural biology.
  • Created xMDFF, a novel method for refining low-resolution X-ray crystallography structures.
  • Built GUIs, automation scripts, and analysis methods in Tcl/Tk.
  • Led the group’s cloud computing efforts, deploying simulation software and training AMIs on AWS EC2.
  • Authored 10 peer-reviewed publications; developed training materials and led workshop instruction; mentored REU (Research Experience for Undergraduates) students on computational research projects; contributed to successful grant proposals.

Associate Engineer | Chesapeake Technology International Corp. — California, MD

Jun 2009 – Aug 2010

  • Developed C#/C++ front-end interfaces and C back-end systems for EA-6B Prowler flight simulators; maintained Access/VBA database and performed IT support.

Laboratory Assistant | Chesapeake Biological Laboratory, UMCES — Solomons, MD

May 2006 – Jan 2009

  • Prepared and analyzed environmental samples using CVAFS and ICP-MS systems for analytical geochemistry group.

EDUCATION

  • M.Eng., Bioinformatics — University of Illinois Chicago, 2013
    Coursework including: Machine Learning, Data Mining, Statistics, Databases, Imaging Informatics
  • B.A., Biochemistry and Computer Science — St. Mary’s College of Maryland, 2009
    Honors Thesis: Genetic Algorithm for Pathfinding in Robots; Department Award in Computer Science, 2009

PUBLICATIONS

  1. Phillips, J.C., Hardy, D.J., Maia, J.D.C., Stone, J.E., Ribeiro, J.V., Bernardi, R.C., Buch, R., Fiorin, G., Hénin, J., Jiang, W., McGreevy, R., Melo, M.C.R., Radak, B.K., Skeel, R.D., Singharoy, A., Wang, Y., Roux, B., Aksimentiev, A., Luthey-Schulten, Z., Kalé, L.V., Schulten, K., Chipot, C., Tajkhorshid, E. Scalable molecular dynamics on CPU and GPU architectures with NAMD. J. Chem. Phys. 153, 044130, 2020.
  2. Wang, Y., Shekhar, M., Thifault, D., Williams, C.J., McGreevy, R., Richardson, J., Singharoy, A., Tajkhorshid, E. Constructing atomic structural models into cryo-EM densities using molecular dynamics – Pros and cons. Journal of Structural Biology, 204:319-328, 2018.
  3. Qi, Y., Lee, J., Singharoy, A., McGreevy, R., Schulten, K., Im, W. CHARMM-GUI MDFF/xMDFF Utilizer for Molecular Dynamics Flexible Fitting Simulations in Various Environments. The Journal of Physical Chemistry B, 2017.
  4. Singharoy, A., Teo, I., McGreevy, R., Stone, J.E., Zhao, J., Schulten, K. Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps. eLife, 2016.
  5. Goh, B.C., Hadden, J.A., Bernardi, R.C., Singharoy, A., McGreevy, R., Rudack, T., Cassidy, C.K., Schulten, K. Computational Methodologies for Real-Space Structural Refinement of Large Macromolecular Complexes. Annual Review of Biophysics, 45, 2016.
  6. McGreevy, R., Teo, I., Singharoy, A., Schulten, K. Advances in the molecular dynamics flexible fitting method for cryo-EM modeling. Methods, 100:50-60, 2016.
  7. McGreevy, R., Singharoy, A., Li, Q., Zhang, J., Xu, D., Perozo, E., Schulten, K. xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures. Acta Cryst. D, 70:2344-2355, 2014.
  8. Stone, J.E., McGreevy, R., Isralewitz, B., Schulten, K. GPU-Accelerated Analysis and Visualization of Large Structures Solved by Molecular Dynamics Flexible Fitting. Faraday Disc., 169:265-283 (Chosen for journal cover image), 2014.
  9. Li, Q., Wanderling, S., Paduch, M., Medovoy, D., Singharoy, A., McGreevy, R., Villalba-Galea, C.A., Hulse, R.E., Roux, B., Schulten, K., Kossiakoff, A., Perozo, E. Structural mechanism of voltage-dependent gating in an isolated voltage-sensing domain. Nat. Struct. & Mol. Biol., 21:244-252, 2014.
  10. Chan, K.-Y., Gumbart, J., McGreevy, R., Watermeyer, J.M., Sewell, B.T., Schulten, K. Symmetry-restrained flexible fitting for symmetric EM maps. Structure, 19:1211-1218, 2011.