About

Allison H. Squires is the Neubauer Family Assistant Professor of Molecular Engineering at The University of Chicago. She completed her postdoctoral research in Chemistry at Stanford University under the mentorship of W.E. Moerner. She earned her Ph.D. in Biomedical Engineering from Boston University, where she worked with Amit Meller, and holds a Bachelor of Science in Engineering in Mechanical and Aerospace Engineering from Princeton University. Professor Squires leads a research group that values diverse training and perspectives, fostering an inclusive and equitable environment to pursue collaborative scientific goals. Her lab is located at the Gordon Center for Integrative Sciences, and she actively mentors graduate students, postdoctoral scholars, and undergraduate researchers across multiple disciplines including engineering, chemistry, physics, and biological sciences. The group focuses on innovative experimental and analytical approaches in molecular engineering, with an emphasis on training and collaboration to advance their scientific objectives.

Research topics

• Physics
• Genetics
• Biology
• Optics
• Computer Science
• Evolutionary biology
• Medicine
• Nuclear physics
• Chemistry
• Computational biology
• Cell biology
• Nanotechnology
• Computational physics
• Atomic physics
• Telecommunications
• Materials science
• Ecology

Selected publications

• BPS2026 – Multiplexing single-molecule biosensing with FRETfluors

  Biophysical Journal · 2026-02-01

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• BPS2026 – TetrathymosinBeta (TTH-1) inhibits actin assembly through the coordinated function of 4 tandem WH2 domains

  Biophysical Journal · 2026-02-01

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• BPS2026 - Optimizing multimodal data collection on the ABEL trap for classification of DNA-fluorophore constructs

  Biophysical Journal · 2026-02-01

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• BPS2025 – Single-molecule imaging reveals C. elegans tetrathymosin beta's effect on actin assembly

  Biophysical Journal · 2025-02-01

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• BPS2025 - Disaggregation of biomolecular condensates by molecular chaperones is heterogeneous at the single-condensate level

  Biophysical Journal · 2025-02-01

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• Phycobilisome core architecture influences photoprotective quenching by the Orange Carotenoid Protein

  Proceedings of the National Academy of Sciences · 2025-10-07 · 2 citations

  articleOpen accessSenior authorCorresponding

  Photosynthetic organisms rely on sophisticated photoprotective mechanisms to prevent oxidative damage under high or fluctuating solar illumination. Cyanobacteria, which have evolved a unique, water-soluble light-harvesting complex—the phycobilisome—achieve photoprotection through a photoactivatable quencher called the Orange Carotenoid Protein (OCP). Phycobilisomes are highly symmetric and modular, formed by hierarchical assembly of conserved subunits into diverse geometries ranging from simple bundles to elaborate fan- or bouquet-like macromolecular architectures. Although OCP is known to provide photoprotection across species of cyanobacteria with different phycobilisome structures, it is not known whether or how these structural variations relate to changes in the photoprotective function of OCP. For example, OCP was recently discovered to bind as a dimer at two specific instances of an abundant structural motif on the tricylindrical phycobilisome of Synechocystis sp. PCC 6803, yet these sites are sterically inaccessible on a more common pentacylindrical phycobilisome ( Anabaena sp. PCC 7120). To understand how structural modularity and binding specificity contribute to conservation of OCP binding sites and function across different phycobilisome architectures, here we compare experimentally measured photophysical states accessible to these prototypical tricylindrical and pentacylindrical phycobilisomes, with and without OCP, at the single-molecule level. Together with Monte Carlo simulations of exciton transfer in OCP-quenched phycobilisomes, our results suggest that OCP binds at distinct and specific sites in each type of phycobilisome, yet provides nearly identical quenching strength to both phycobilisomes. Our findings highlight the utility of modular phycobilisome structures in balancing robust conservation of photoprotective function with adaptability of site-specific binding across species.

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• BPS2025 - Disaggregation of biomolecular condensates by molecular chaperones is heterogeneous at the single-condensate level

  Biophysical Journal · 2025-02-01

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• BPS2025 - Spatial mapping of the cellular redox environment by magnetically manipulated quantum sensors

  Biophysical Journal · 2025-02-01

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• BPS2025 - Molecular simulation of cyanine-labeled DNA dynamics towards enabling rational FRET design for single-molecule immunoassays

  Biophysical Journal · 2025-02-01

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• BPS2025 - Probing the effects of heat shock proteins on the rheology of in vitro heat shock-induced ribosomal protein condensates

  Biophysical Journal · 2025-02-01

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Frequent coauthors

• A. Meller

  Technion – Israel Institute of Technology

  23 shared

• W. E. Moerner

  Stanford University

  19 shared

• Peter D. Dahlberg

  Stanford Synchrotron Radiation Lightsource

  13 shared

• Ayesha Ejaz

  University of Chicago

  12 shared

• Abhijit A. Lavania

  Stanford University

  9 shared

• Jiachong Chu

  University of Chicago

  8 shared

• Kyle Lin

  University of Chicago

  7 shared

• Kepler Domurat‐Sousa

  University of Chicago

  6 shared

Labs

• Squires LabPI

  The Squires group is a diverse team of scholars at all levels including graduate students, undergraduates, and summer researchers.

Awards & honors

• NSF Fellow at Boston University