Research

Simple Models | Complex Behavior

My work involves creating coarse-grained models of biological systems. For example, here's a crawling cell built with the deformable particle model. The cell crawls by protruding its perimeter in the direction of motion, which resembles the crawling of real cells, but lacks specific microscopic details like organelles or explicit signaling pathways.

This approach allows us to ask fundamental questions about a wide variety of biological pheneomena.

Previous Work

Mesophyll development

The spongy mesophyll, a complex porous tissue found within leaves and flowers, captures atmospheric carbon during photosynthesis and provides important structural stability. But how does this complex tissue develop its vital airspace?

In our paper, we use deformable particles to show that airspace can emerge from growth and remodelling of cell walls near void space. The colorbar on the right represents the shape parameter \( {\cal A}= p^2 / 4\pi a \), where \(p \) is the cell perimeter and \(a \) is the cell area.

Deformability and response

Complex soft solids like emulsions (e.g. mayonnaise), foams (e.g. capuccino froth) and tissues (e.g. your epidermis) are composed of inherently deformable objects like droplets, bubbles or cells, yet how deformability affects collective behavior is poorly understood. In our recent paper, we studied the effect of single-particle deformability on global vibrational and mechanical response near jamming. We found that stiff, weakly deformable particles reach a rigid-particle limit, but increasing deformability leads to anomalous normal mode spectra and shear moduli.

On the right are some examples of normal modes found in jammed packings of highly deformable particles. These packings contain a few "quartic modes" which are higher-order and much floppier than standard, quadratic modes. Floppy quartic modes can be either extended (black, left) or localized (black, right), while the quadratic modes (red and blue) vary in extent, but predominantly change particle shape.

Jamming in globular protein cores

Globular proteins rely on a core of hydrophobic amino acids for thermodynamic stability. It's been known since the dawn of x-ray crystallography that these structures are densely packed, but our recent work has shown that crystal structures resemble jammed packings of hard particles shaped like amino acids. Interestingly, cryogenic (~77 K) crystal structures resemble packings prepared with athermal protocols, but structures resolved at room temperaure by NMR spectroscopy resemble denser packings formed by thermal protocols like the one shown here. We conjecture that NMR structures in aqueous, room-temperature solutions allow core amino acids to find denser configurations.

Press:
MIT Technology Review
In The Pipeline (Science Translational Medicine)
Yale SEAS website

Clogging of deformable particles

Arrested flow in the presence of confinement (clogging) is important throughout nature and industry. While there is a long history of studying clogging of hard particles (think grains in a silo), less attention has been payed to clogging of deformable objects. In particular, if deformable particles form a clog, can't they always change shape to resume flow?

We address this question, as well as the differences between clogs of deformable and non-deformable particles, in our recent paper, performed in collaboration with Yuxuan Cheng of Corey O'Hern's group at Yale University, and members of Eric Week's group at Emory University.

Publications

2022

J. D. Treado, A. B. Roddy, G. Théroux-Rancourt, C. Ambrose, C. Brodersen, M. D. Shattuck, and C. S. O'Hern, "Localized growth drives spongy mesophyll morphogenesis.'' J. R. Soc. Interface 19, 20220602 (2022)

Y. Cheng, J. D. Treado, B. Lonial, P. Habdas, E. R. Weeks, M. D. Shattuck, and C. S. O'Hern, "Hopper flows of deformable particles.'' Soft Matter 17, 8071 (2022)

2021

D. Wang, J. D. Treado, A. Boromand, B. Norwick, M. P. Murrell, M. D. Shattuck, and C. S. O’Hern, "The structural, vibrational, and mechanical properties of jammed packings of deformable particles in three dimensions." Soft Matter 17, 9901-9915 (2021)

J. D. Treado*, D. Wang*, A. Boromand, M. P. Murrell, M. D. Shattuck, and C. S. O’Hern, "Bridging particle deformability and collective response in soft solids." Phys. Rev. Materials 5, 055605 (2021)

2020

A. T. Grigas, Z. Mei, J. D. Treado, Z. A. Levine, L. Regan, and C. S. O'Hern, "Using physical features of protein core packing to distinguish real proteins from decoys." Protein Science 29, 1931 (2020)

Z. Mei*, J. D. Treado*, A. T. Grigas, Z. A. Levine, L. Regan, and C. S. O'Hern, "Analyses of protein cores reveal fundamental differences between solution and crystal structures." Proteins: Structure, Function, and Bioinformatics 88 (9), 1154-1161 (2020)

2019

J. D. Treado, Z. Mei, L. Regan, and C. S. O'Hern, "Void distributions reveal structural link between jammed packings and protein cores." Phys. Rev. E 99, 022416 (2019)

2018

C. Oi, J. D. Treado, Z. A. Levine, C. S. Lim, K. M. Knecht, Y. Xiong, C. S. O'Hern, and L. Regan, "A threonine zipper that mediates protein-protein interactions: Structure and prediction." Protein Science 27, 1969 (2018)

Commentary

J. D. Treado, D. Wang, Y. Chen, M. D. Shattuck, and C. S. O’Hern, "Determining dynamics from statics in living tissue" Journal Club for Condensed Matter Physics, March 2021

John D. (Jack) Treado

Visiting Postdoc | Max Planck Institute for the Physics of Complex Systems

About Me