Research

Building tools to understand the body

Most of my research lives in the Thomson Lab at Caltech — microfluidics and active matter — alongside computational biology and a study on equity in science itself.

Optically-Controlled Active-Matter Microfluidic Pump

SURF 2025

Thomson Lab, Caltech · Dr. Matt Thomson

A microfluidic pump powered entirely by biocompatible proteins and ATP — generating controllable fluid flow without motors, electric fields, or rigid mechanical parts. Flow is steered with light patterns projected onto the device.

Methods

  • Designed a library of channel geometries (2-Layer, Centipede, Turbo, Whirlpool, Zigzag) varying width (100–400 µm), circle diameter (600–1100 µm), and guidance posts
  • Fabricated PDMS devices: 1:10 catalyst, degassing, dehydration, plasma bonding, acid/base flush
  • Active-matter solution: microtubules + kinesin motors + ATP energy mix + fluorescent beads + hydrogel
  • Microscopy + projector ROI light-patterning over the GFP channel for optical control
  • Python PIV pipeline: average & percentile speed, directionality index, spatiotemporal stability, volumetric flow rate
  • Interactive simulation to draw channel patterns and preview predicted flow; 25× scaled 3D-printed demo model

Outcomes

  • Gee Family SURF Poster Competition — Finalist & First-Place Winner (Gee Prize)
  • Presented at SCURR 2025 and accepted to APS 2025 Mid-Atlantic Section
  • Motivation: animal models poorly capture human physiology (mouse heart rate ~10× human) — motivating non-animal microfluidic models
MicrofluidicsActive matterPDMSOptical controlPIV

Engineering Adaptive Microfluidic Niches for Stem-Cell Cardiac Repair

Sigma Xi GIAR proposal · SURF 2026

Thomson Lab, Caltech · Dr. Matt Thomson

A deformable microfluidic platform that dynamically modulates chamber geometry and perfusion as tissue grows — aiming to keep nutrient delivery and physiological shear stable enough to improve cardiac differentiation and maturation of stem-cell-derived cardiomyocytes.

Methods

  • PDMS devices with a central tissue chamber, perfusion channels, and fluid-actuated 'origami-like' deformable hinges
  • Syringe-pump pressure control switching the niche between discrete volumes
  • Quantify deformation by microscopy/image analysis; flow by fluorescent particle tracking + PIV (velocity, shear)
  • Human iPSCs differentiated toward cardiac lineages; survival, morphology, and contraction assays
  • RT-qPCR (TNNT2, NKX2.5, MYH6/MYH7, ACTN2, GATA4), immunostaining + confocal, Western blot, traction force microscopy

Outcomes

  • Builds on 2025 SURF work (predictable membrane deflection, reversible geometric transitions)
  • Addresses cardiovascular disease — the leading cause of death worldwide (>20.5M deaths/yr)
  • Sigma Xi GIAR draft: $1,000 requested, ~$6,400 total project (advisor review pending)
MicrofluidicsCardiaciPSCTissue engineering

Generative Localization Models for Spatial Gene Expression

Thomson Lab, Caltech

A reference implementation of seven generative models for 3D transcript clouds (MERFISH-style spatial gene-expression data) in embryos, in spherical coordinates centered on the segmentation center of mass.

Methods

  • Single multivariate Gaussian (closed-form MLE baseline)
  • Gaussian Mixture Model fit by Expectation–Maximization
  • Kernel Density Estimation (Scott's / Silverman's bandwidth)
  • Radial × angular factorized density (cortical-vs-central + polarity)
  • Spherical-harmonic angular expansion (ℓ=1 polarity, ℓ=2 quadrupolar) × radial KDE
  • Inhomogeneous Poisson spatial point process; voxelized spherical-grid density

Outcomes

  • Scored against transcript clouds via sliced 3D Wasserstein + spherical-marginal Wasserstein distances
  • Deterministic figure generation and a live 3D comparison viewer
Computational biologySpatial statisticsPython

Geographic Diversity in Medical Publishing

Summer 2021–present

Dr. Smita Bhatia (UAB)

A first-author study abstracting two decades (2001–2021) of publication data from JAMA, NEJM, and The Lancet to quantify geographic diversity in leading medical journals.

Methods

  • Abstracted publication metadata across three journals over 20 years
  • Built Python tooling: data abstraction, name/country dictionaries, analysis scripts

Outcomes

  • First author on a manuscript accepted for publication in General Internal Medicine
  • Title: "Geographic Diversity of Articles Published over Two Decades in Leading Medical Journals"
Health equityData analysisPublication

Publications & conferences

  • Geographic Diversity of Articles Published over Two Decades in Leading Medical Journals

    General Internal Medicine — first author (accepted)

  • Active-matter microfluidic pumping & optical control of autonomous micro-flow

    APS Mid-Atlantic Section Conference, 2025

  • Optically-controlled active-matter microfluidic pump

    SCURR 2025 · Gee Family SURF Poster Competition — First Place (Gee Prize)