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Podcast: Supercomputing Gels with Stampede

Jell-o is one example of a colloidal gel, a liquid dispersed in a solid. Roseanna Zia and colleagues created the largest computer simulation of colloidal gels yet attempted. Credit: Steven Depolo.

Jell-o is one example of a colloidal gel, a liquid dispersed in a solid. Roseanna Zia and colleagues created the largest computer simulation of colloidal gels yet attempted. Credit: Steven Depolo.

In this TACC Podcast, Jorge Salazar looks at how researchers are using the Stampede supercomputer to shed light on the microscale world of colloidal gels — liquids dispersed in a solid medium as a gel.

Cornell Chemical engineering researcher Roseanna Zia says that sometimes the gels act like liquids, and sometimes they act like a solid, such as hair gel that squirts out of a tube like a liquid, but retains its shape sitting in your hand.

“Colloidal gels are actually soft solids, but we can manipulate their structure to produce ‘on-demand’ transitions from liquid-like to solid-like behavior that can be reversed many times,” Zia said. Zia is an Assistant Professor of Chemical and Biomolecular Engineering at Cornell University.

The tiny solid particles in a colloidal gel — invisible to the naked eye — bind together and form a 3-D scaffolding of filaments throughout the medium. One can break that scaffolding by simply squirting the material or dragging a surface across it. For example, toothpaste or hair gel — after it has been squirted — will sit on a toothbrush like a solid because its scaffolding by simply squirting the material or dragging a surface across it. For example, toothpaste or hair gel — after it has been squirted — will sit on a toothbrush like a solid because its scaffold has re-formed on its own due to the attractions between the particles.

Zia and colleagues utilized over seven million service units on the Stampede supercomputer at the Texas Advanced Computing Center (TACC), awarded through an allocation by XSEDE, the eXtreme Science and Engineering Discovery Environment. “Stampede high performance computational access was a game-changer,” Zia said.

Zia used Stampede to simulate how gels evolve over time.

Study co-author Benjamin Landrum, also at Cornell with the Zia Research Group, created the computer model of nearly a million particles using the simulation package called LAMMPS, the Large-scale Atomic/Molecular Massively Parallel Simulator.

“LAMMPS is optimized to spread out the particles onto many, many processors,” Zia said. She explained that the code basically applies a set of rules based on the physics equations that govern the forces acting on the particles, such as attraction, collision, Brownian motion, and so on. Combining LAMMPS and XSEDE was the key to carrying out the massively parallelized large-scale simulations required to accurately model gel behavior.

According to Zia, the insight into how gels break down is having a major impact in areas including the treatment of wounds, artificial tissue scaffolds, and injectable pharmaceuticals.

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