“Titan” Supercomputer Helps Scientists Analyze the Atoms in a Nanoparticle

Scientists used one of the world’s most powerful electron microscopes to map the precise location and chemical type of 23,000 atoms in an extremely small particle made of iron and platinum. The Cray supercomputer “Titan” was then used to simulate the nanoparticle’s behavior.

The 3-D reconstruction reveals the arrangement of atoms in unprecedented detail. Insights gained from the particle’s structure could lead to new ways to improve its magnetic performance for use in high-density, next-generation hard drives.

What’s more, the technique used to create the reconstruction, atomic electron tomography (which is like an incredibly high-resolution CT scan), lays the foundation for precisely mapping the atomic composition of other useful nanoparticles.

Microscopy data was obtained and analyzed by scientists from the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) at the Molecular Foundry, in collaboration with Foundry users from UCLA, Oak Ridge National Laboratory and the United Kingdom’s University of Birmingham. The research was reported in the Feb. 2 issue of the journal Nature.

Atoms are the building blocks of matter, and the patterns in which they’re arranged dictate a material’s properties. These patterns can also be exploited to greatly improve a material’s function, which is why scientists are eager to determine the 3-D structure of nanoparticles at the smallest scale possible.

“Our research is a big step in this direction,” says Mary Scott, who conducted the research while she was a Foundry user, and who is now a staff scientist. “We can now take a snapshot that shows the positions of all the atoms in a nanoparticle at a specific point in its growth. This will help us learn how nanoparticles grow atom by atom, and it sets the stage for a materials-design approach starting from the smallest building blocks.” Scott and fellow Foundry scientists Peter Ercius and Colin Ophus developed the method in close collaboration with Jianwei Miao, a UCLA professor of physics and astronomy.

The scientists’ latest accomplishment hinged on the use of one of the highest-resolution transmission electron microscopes in the world, called TEAM I.

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Video (0:25).: A closer look at the nanoparticle’s atoms. 

The researchers began growing an iron-platinum nanoparticle from its constituent elements, and then stopped the particle’s growth before it was fully formed. They placed the “partially baked” particle in the TEAM I stage, obtained a 2-D projection of its atomic structure, rotated it a few degrees, obtained another projection, and so on. Each 2-D projection provides a little more information about the full 3-D structure of the nanoparticle.

They sent the projections to Miao at UCLA, who used a sophisticated computer algorithm to convert the 2-D projections into a 3-D reconstruction of the particle. The individual atomic coordinates and chemical types were then traced from the 3-D density based on the knowledge that iron atoms are lighter than platinum atoms. The resulting atomic structure contains 6,569 iron atoms and 16,627 platinum atoms, with each atom’s coordinates precisely plotted to less than the width of a hydrogen atom.

Translating the data into scientific insights

To explore how the various arrangements of atoms affect the nanoparticle’s magnetic properties, scientists from DOE’s Oak Ridge National Laboratory ran computer calculations on the “Titan” supercomputer at ORNL, a Cray® XK-7 system. They used the coordinates and chemical type of each atom to simulate the nanoparticle’s behavior in a magnetic field. This allowed the scientists to see patterns of atoms that are very magnetic, which is ideal for hard drives. They also saw patterns with poor magnetic properties that could sap a hard drive’s performance.

You can read the complete story, “Scientists Determine Precise 3-D Location and Identity of All 23,000 Atoms in a Nanoparticle,” on Berkeley Labs’ News Center.

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