Conditional Diffusion Models for Protein Trajectories (PyTAO)

Thu, 15 Jan 2026 00:00:00 +0000

Conditional Diffusion Models for Protein Trajectories (PyTAO)

Overview

Sampling continuous molecular dynamics and conformational transitions of proteins typically requires computationally prohibitive quantum mechanical / molecular mechanics (QM/MM) calculations. In collaboration with Dr. Peng Tao’s Proteins and Computers Lab at SMU, we designed and trained conditional diffusion generative models capable of directly generating continuous biomolecular conformational trajectories from boundary structural coordinates, bypassing thousands of CPU/GPU hours of physics simulations.

This work culminated in a research publication in the Journal of Chemical Theory and Computation (ACS, 2026) and the open-source PyTAO computational chemistry and trajectory toolkit.

flowchart LR A[Initial & Target\nConformations] --> B[Conditional Diffusion Model\nNoise Scheduler & Denoiser] B --> C[Slurm HPC Training\nDistributed Data Parallel] C --> D[Continuous Molecular Dynamics\nTrajectory Reconstruction] D --> E[Validated Physical Coordinates\nBypassing QM/MM Cost]

Highlights & Engineering

1. Conditional Generative Diffusion

Implemented deep generative diffusion models conditioned on 3D Cartesian coordinates and learned invariant spatial representations.
Reconstructed high-dimensional protein conformational trajectories with realistic bond angles and non-bonded interactions.

2. High-Performance Distributed Training (DDP)

Developed Slurm parallel batch training scripts leveraging PyTorch Distributed Data Parallel (DDP) across high-performance GPU clusters.
Optimized tensor transformations and memory-mapped trajectory datasets for rapid epoch turnover.

3. Open-Source PyTAO Toolkit

Built, tested, and released the PyTAO open-source Python library, integrating ONIOM calculation automation, coordinate parsing, and Slurm HPC job monitoring for computational chemistry workflows.

Publication

Efficient sampling of short protein trajectories with conditional diffusion models
Chen Xiong, Praveen Kandhan, Dong Chen, Zerui Ma, Eric D. Smith, Peng Tao.
Journal of Chemical Theory and Computation (ACS), 22(1), 78 (2026).
DOI: .

Protein Trajectories | Zerui "Jerry" Ma's personal website

Conditional Diffusion Models for Protein Trajectories (PyTAO)

Conditional Diffusion Models for Protein Trajectories (PyTAO)

Overview

Highlights & Engineering

1. Conditional Generative Diffusion

2. High-Performance Distributed Training (DDP)

3. Open-Source PyTAO Toolkit

Publication