Machine learning · Simulation · Scientific software

Machine learning, AI systems, and simulation.

I manage the Biomechanics Modeling team at Align Technology and have 10+ years of experience building research software and production systems. I enjoy working across model development, validation, and the software needed to make research useful.

10+ yearsScientific and production software
ML + simulationModels tied to physical systems
FDA-accepted methodML model validation
5 patents pendingBiomedical modeling and AI

Selected work

AI, simulation, and engineering systems

Representative work across private production systems, open-source software, and academic research.

032025–Present

LLM and vision systems

Fine-tuning, inference, and custom harnesses

Fine-tuned task-specific LLMs and VLMs for ranking, classification, structured extraction, and multimodal analysis. Built evaluation datasets, managed local GPU inference with vLLM, and created custom harnesses for Claude Code and OpenAI Codex.

LLMVLMFine-tuningvLLMEvaluation
042026

Representation learning

Geometry and graph-based latent embeddings

Built embeddings for clinical geometry and treatment data to support similarity search, clustering, classification, and prediction.

Geometric MLGraph embeddingsRetrievalClustering
052024

Simulation infrastructure · Align Technology

Distributed simulation platform

Built distributed simulation pipelines on GPU clusters for large-scale analysis and ML training-data generation.

Distributed computeGPU clustersKubernetesData pipelinesSimulation
062023–2025

Open source

RustFEA

Created an open-source finite-element framework in Rust for high-performance, memory-safe scientific computing.

RustFEAScientific computing
View repository
072020–2022

Research and software launch

Nonlinear frictional contact

Researched mesh-independent contact methods for immersed-boundary FEA and implemented analytical geometry for contact detection and stick-slip behavior in OnSimulation.

Contact mechanicsIBFEMNumerical methods
Read thesis
082015–2023

Production software · Catch The Fever

Automated e-commerce platform

Built and operated software for online and retail sales, inventory, fulfillment, shipping, notifications, and advertising for a multi-million-dollar business.

Full stackAutomationOperations

Experience

Professional experience

Engineering management, predictive modeling, AI systems, simulation research, and production software.

View full résumé
Feb 2026—Present

Manager, Biomechanics Modeling

Align Technology

Lead a distributed R&D team developing patient-specific prediction models, biomechanics simulations, and optimization methods. Set technical strategy and model-validation standards across research, clinical, software, and regulatory teams.

2025—Jan 2026

R&D Team Lead, Simulation & Modeling

Align Technology

Led treatment-prediction, shape-optimization, classification, and production-integration work. Built and launched the internal RAG platform.

2023—2025

R&D Engineer III, Simulation & Modeling

Align Technology

Designed transformer models, embeddings, and classifiers for patient-specific treatment data and built distributed simulation pipelines for ML training-data generation.

2022—2023

R&D Engineer II, Simulation & Modeling

Align Technology

Built patient-specific simulation methods, biomechanics metrics, and automated analyses for orthodontic treatment design.

2020—2022

Graduate Research Assistant

University of Florida

Researched nonlinear frictional contact in FEA and contributed analytical geometry methods to the OnSimulation codebase.

2015—2023

Senior Developer

Catch The Fever

Built and automated an e-commerce platform supporting multi-million-dollar revenue, fulfillment, shipping, and ad operations.

Technical range

Core technical areas

Skills used across research prototypes, validated models, and production systems.

01

Machine learning

PyTorch, JAX, TensorFlow, transformers, geometric deep learning, graph embeddings, interpretability, and model validation

02

LLMs, vision, and agents

Fine-tuning, RAG, embeddings, vector search, reranking, agentic workflows, multimodal analysis, and custom harnesses

03

Scientific computing

Optimization, FEA, nonlinear contact, multiphysics, biomechanics, CFD, Abaqus, FEBio, and FEniCS

04

Infrastructure and software

Python, Rust, C++, Go, JavaScript, WebAssembly, Docker, Kubernetes, GPU cluster training, vLLM serving, CUDA, Linux, AWS, GCP, and CI/CD

About

Background

My training is in aerospace engineering, numerical methods, solid mechanics, CFD, and controls. I now apply that foundation to biomedical machine learning, geometry-based models, RAG, agents, and scientific software.

I enjoy work where there is a real system to understand: building the model, finding its failure modes, validating it, and writing the software around it. Personal projects usually involve browser-based simulations, Rust, embedded systems, robotics, 3D printing, or photography.

Education M.S. Aerospace Engineering

University of Florida · 2022 · Custom FEA, CFD, reduced-order modeling, nonlinear mechanics, and uncertainty methods

Education B.S. Aerospace Engineering

University of Florida · 2021 · Cum Laude

Patents Five patent applications pending

Biomedical modeling, simulation, treatment prediction, and optimization · View published WO2023183884A1

What I enjoy

Problems I like working on

I prefer projects with a real system to understand, a model to test, and software to build.

01ML for physical and geometry-rich problems
02RAG, agents, and multimodal systems with measurable quality
03Simulation, scientific computing, and visualization
04Leading technical teams while staying close to implementation
San Jose, CA · Bay Area or remote
john@johndews.com LinkedIn Résumé ↗