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Computational & Experimental Materials Science

Thomas J. Barrett, PhD

Research Associate · Brookhaven National Lab
PhDNortheastern University2024
MSNortheastern University2018
BSUniversity of Rochester2016
Focus areas

Research

🏅 2023 PACK International Research Fellowship
Multiscale Modeling

Hierarchical polymer composite simulation

Coarse-grained MD → FEA pipeline for semi-crystalline polymer composites, capturing homo- and heterogeneous crystallization, interphase structure, and continuum mechanical response across length scales.

Scientific Software

Polymer microstructure analysis tools

pothos and mdvoro: open-source Python packages for chain orientation tracking, Voronoi tessellation, and conversion of MD control volumes into FEA representative volume elements.

Digital Twin / Inverse Design

Molecularly imprinted polymer framework

MIPkit: RDKit-driven toolkit for automated vinyl polymerization simulation and in-silico screening of ~100 functional monomers, enabling systematic MIP development without exhaustive synthesis.

Statistical Mechanics

Thermostat and barostat integration

Systematic comparison of Nosé-Hoover integrator schemes, demonstrating that barostat coupling choice has a measurable and underappreciated effect on uniaxial tension results in solid-phase simulations.


Peer-reviewed work

First Author Publications

5
Indications of ZIF-8 promoting cell viability in electrospun tricuspid valve scaffolding.In Preparation
Expected 2026
4
A digital twin for the in-silico screening, polymerization, and rebinding of Molecularly Imprinted Polymers In Preparation
Expected 2026
3
Nosé-Hoover Integrators at-a-glance: Barostat integration has a demonstrable effect on uniaxial tension results of solid materials
Journal of Chemical Theory and Computation, 2025
2
pothos: A Python package for polymer chain orientation and microstructure evolution monitoring
Journal of Chemical Theory and Computation, 2024
1
Fine-scale surface complexity promotes temperature extremes but reduces the spatial extent of refugia on coastal rocks
Ecological Modelling, 501 (110969), 2025
Google Scholar profile

Open source

Tools & Packages

Φ

pothos

Chain orientation and microstructure evolution monitoring for MD trajectories of semi-crystalline polymers.

Python
V

mdvoro

Voronoi tessellation of MD simulation cells for conversion into FEA representative volume elements.

Python
M

MIPkit

Digital twin toolkit for in-silico MIP development — automated polymerization, screening, and rebinding analysis.

Python / RDKit
N

nose-hoover-schemes

LAMMPS scripts benchmarking Nosé-Hoover barostat integration schemes under uniaxial tension.

LAMMPS
+

More on GitHub

Additional simulation utilities, analysis scripts, and experimental tools.

View All →

Technical capabilities

Skills & Methods

Simulation

  • LAMMPS, GROMACS (MD)
  • ORCA (DFT)
  • Abaqus, COMSOL, ANSYS (FEA)
  • Coarse-grained modeling
  • Free energy calculations

Machine Learning

  • PyTorch, E3NN
  • Graph neural networks
  • Surrogate modeling
  • Bayesian optimization
  • Generative models (diffusion)

Characterization

  • SEM, AFM, WAXD
  • DMA, TGA, DSC
  • FTIR-ATR, UV-VIS, RAMAN
  • Nanoindentation
  • Tribometry

Software & Dev

  • Python
  • C++, Fortran
  • RDKit, cheminformatics
  • Docker, Linux, HPC
  • Git, CI/CD

Materials Systems

  • Semi-crystalline polymers
  • Polymer composites
  • MIP development
  • Thin film coatings
  • Biomedical scaffolds

Methodology

  • Multiscale modeling
  • Inverse design
  • Interphase characterization
  • Statistical mechanics
  • Scientific software development