Featured Projects

VorPy3

VorPy3 delivers optimized geometric algorithms for weighted Voronoi and power-diagram partitioning. It computes structural metrics, such as volume, surface area, curvature, and connectivity, for molecular and materials datasets alike. Designed for reproducibility and clarity, VorPy3 produces standardized data and publication-ready visualizations for integration into research and analytical pipelines.

  • Weighted Voronoi Analysis
  • Molecular Ensemble Modeling
  • Geometric & Surface Metrics
  • Curvature & Topology
  • Publication-Ready Visuals
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Foamify

Foamify generates customizable 3D sphere ensembles for modeling disordered or porous materials. It provides full control over geometric and statistical parameters such as density, polydispersity, and overlap to simulate realistic foam microstructures. Designed for scientific modeling and reproducible output, Foamify exports standardized coordinate data compatible with visualization and Vorpy-based analysis.

  • Randomized 3D Foams
  • Analysis-Ready Data
  • PyMOL Visualization
  • VorPy3-Compatible
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Coarsify

Coarsify aggregates molecular structures into coarse-grained models using configurable geometric algorithms and residue-level heuristics. It offers mass-weighted centers, thermal-cushion adjustments, and hydrogen-handling options for precision control. The program outputs PDBs and visualizations compatible with PyMOL, Vorpy, and standard molecular analysis workflows.

  • Multiple Input Formats
  • Configurable Schemes
  • Thermal Cushioning
  • PyMOL Visualization
  • VorPy3-Compatible
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Publications

Comparing Weighted and Additively Weighted Voronoi Decompositions of Polydisperse Ensembles

Ericson, J. (2025). Physical Chemistry Chemical Physics.

The paper analyzes how power vs additive weighting change Voronoi partitions in polydisperse systems (foams, powders, atomic ensembles). Systematic tests across polydispersity, density, and overlap show why the schemes diverge—and identify small-particle subpopulations as key drivers via larger, more aspherical power cells. The result is a practical framework linking weighting choice to physical heterogeneity and measurable volumetric/shape metrics.

  • Voronoi Geometry
  • Polydisperse Systems
  • Geometric Metrics
  • Computational Modeling
  • Experimental Comparison
Read at Journal (DOI)

Voronoi Methods for Molecular Dynamics & Coarse-Graining (in preparation)

Manuscript in progress

Extends weighted/power analyses to MD trajectories and coarse-grained models, connecting geometric descriptors to structure–function signals and simulation-ready pipelines.