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The Carbonate supercomputer in the Indiana University Data Center

A research career in HPC: IU student, Maryam Zahedian, advances using IU HPC resources

Under IU chemistry PhD advisor Bogdan Dragnea, Maryam Zahedian deployed the Karst and Carbonate supercomputers with high performance storage systems to help overcome anomalies in her research.

IU Chemistry researcher Dr. Maryam Zahedian is a veteran of IU’s high-powered computing resources. She says two important papers published so far in her career are the result of research using two generations of high performance computing (HPC) allocated by the National Science Foundation. Two IU supercomputers, Karst, a recently retired computing system, and Carbonate, IU’s recently upgraded HPC resource helped her advance her research.

The Karst supercomputer was in service until December 2020

Broadly, Zahedian’s research aims to build models which help explain how small, but important, components of cells and viruses function, and aims to better inform fundamentals of biomedical science.

At the beginning of her career as an HPC researcher using Karst, Zahedian developed simulations testing whether or not a virus, once it is pulled into a cell membrane, experiences changes in shape. “Addressing this question by systematic experimentation with virus-like probes of the type proposed in our research is important,” said Zahedian, “not only for understanding virus translocation and transformation but also for the new knowledge it could provide for further development of therapeutic delivery technologies.” Such technologies include gene therapy, as well as vaccine development based on biological particles such as viruses and bacteriophages.

Maryam Zahedian

The memory capacity and parallel processors [in Carbonate and Karst] are a requisite to enable our team [to analyze] with a higher level of precision.

Maryam Zahedian, chemistry research at Indiana University

Initially, without HPC resources, an anomaly in the team’s data called the research method into question. Working under her PhD advisor, Professor Bogdan Dragnea, “We were at the stage of wrapping up our results for publication, and we observed an anomaly in our simulation results which we later found out to be caused due to the lack of accuracy in the choice of mesh size,” explained Zahedian. “The memory capacity and parallel processors [of IU supercomputers Karst and Carbonate] are a requisite to enable our team [to analyze] with a higher level of precision,” she continued.

Using Carbonate, Zahedian has continued to conduct research using complex simulations. In a paper published in the American Chemistry Journal of Photonics in 2020, Zahedian and her collaborators conducted research looking at the heat regulation in nanoscale using plasmonic nanoparticles (NPs), with tunable optical properties. Plasmonic NPs have been developed into sensors and local heat nanosources (a source of nanoparticles) for various applications, from cancer therapy to new bolometers,” said Zahedian. A bolometer is a device for measuring radiant heat by means of a material having a temperature-dependent electrical resistance. “The main inspiration of this work was to probe the local induced heat transformation of Polydimethylsiloxane (PDMS), one of the most important thermal interface materials, which is widely used for the fabrication and prototyping of microfluidic chips,” she continued.

IU Graduate, Maryam Zahedian

I highly recommend IU's research supercomputers. They are powerful and I received so much assistance from IU's research supercomputer team to run my simulation on these clusters. In simple words, HPC has enabled me to conduct two of my main projects which otherwise would lack enough accuracy to be completed and published.

Dr. Maryam Zahedian, Philosophy PhD, Indiana University

To achieve this modeling on Carbonate, her colleagues Zachary Lee and Eun Sohl Koh made a library of gold nanoparticles consisting of spherical gold NPs of size 12-120 nm. This work simultaneously computes photothermal amplitude/phase and compares the results with experimental data to quantitatively identify local heat transformation. “Specifically, it becomes possible to extract the temperature-dependent properties of the photo-annealed medium,” said Zahedian.

Zahedian, who is currently pursuing postdoctoral research at the University of Wisconsin-Madison in the group of Prof Choy, encourages everyone at IU to deploy HPC- powered resources. “I would recommend Karst and other IU research supercomputers like Carbonate. They are powerful and I have received so much assistance from IU's research supercomputer team [Research Technologies] to run my simulation on these clusters,” she said.