Loom
TUI control center for managing git worktrees and agentic workflows, supporting Claude Code, GitHub, and Linear
Rust
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Granular Hopper
Spherical granular particles falling through a glass hopper
Ray tracing Granular materials
Asteroid Belt Planet
A planet with an asteroid belt and an orbiting satellite
Ray tracing
Optical Matter Array
An assembly of optically bound metal nanoparticles in a tightly focused laser beam.
Electromagnetism
Recent Posts
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Real-time visualization of a large number of circles using OpenGL
November 7, 2020
When using Matplotlib, animations of a large number of circles becomes slow. Using OpenGL, over a million circles can be animated in realtime.
Graphics Performance
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FFT performance using NumPy, PyFFTW, and cuFFT
October 14, 2020
Compare the performance of different FFT implementations, using Python
Performance
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Measuring the overlap of Delaunay tessellations
September 25, 2020
Given two or more Delaunay tessellations, you may be interested in measuring how much they overlap with one another
Data analysis
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Highlighted Publications
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ProT-VAE: Protein Transformer Variational AutoEncoder for Functional Protein Design
Emre Sevgen, Joshua Moller, Adrian Lange, John Parker, Sean Quigley, Jeff Mayer, Poonam Srivastava, Sitaram Gayatri, David Hosfield, Maria Korshunova, Micha Livne, Michelle Gill, Rama Ranganathan, Anthony B. Costa, Andrew L. Ferguson
PNAS (2025)
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DOI: 10.1073/pnas.2408737122
Optical matter machines: angular momentum conversion by collective modes in optically bound nanoparticle arrays
John Parker, Curtis W. Peterson, Yuval Yifat, Stuart A. Rice, Zijie Yan, Stephen K. Gray, Norbert F. Scherer
Optica (2020)
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DOI: 10.1364/OPTICA.396147
Excitation of nonradiating anapoles in dielectric nanospheres
John Parker, Hiroshi Sugimoto, Brighton Coe, Daniel Eggena, Minoru Fujii, Norbert F. Scherer, Stephen K. Gray, Uttam Manna
Physical Review Letters (2020)
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DOI: 10.1103/PhysRevLett.124.097402
Featured Talks
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Emergence of nonreciprocal interactions and phase transitions in optically assembled nanomaterials
Bag Lunch, University of Chicago, August 2020 (August 2020)
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Collective electrodynamic excitations and non-conservative dynamics in optical matter and meta-atom systems
Thesis Defense, University of Chicago, July 2020 (July 2020)
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Interactive tutorial for Miepy and Stoked software
University of Chicago, April 2019 (April 2019)
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