Sign up for our newsletter and get the latest HPC news and analysis.
Send me information from insideHPC:


Supercomputing Bioelectric Fields in the Fight Against Cancer

Researchers from of the University of California at Santa Barbara are using TACC supercomputers to study bioelectric effects of cells to develop new anti-cancer strategies.

The research centers around electroporation, the process of applying short, intense electric pulses to living cells. Every cell has a bioelectric physical nature, and it has been established that the bioelectric nature of living organisms plays a pivotal role in the development of their form and growth.

In new research published in the Journal of Computational Physics, Frederic Gibou’s team from UCSB delve into a new computational framework for parallel simulations that models the complex bioelectrical interaction at the tissue scale.

This model, which describes the evolution of transmembrane potential on an isolated cell, has been compared and validated with the response of a single cell in experiments,” said Gibour. “From there, we developed the first computational framework that is able to consider a cell aggregate of tens of thousands of cells and to simulate their interactions. The end goal is to develop an effective tissue-scale theory for electroporation.”

According to Gibou and his colleague, Pouria Mistani, one of the main reasons for the absence of an effective theory at the tissue scale is the lack of data. Specifically, the missing data in the case of electroporation is the time evolution of the transmembrane potential of each individual cell in a tissue environment. Experiments are not able to make those measurements.

Currently, experimental limitations prevent the development of an effective tissue-level electroporation theory,” Mistani said. “Our work has developed a computational approach that can simulate the response of individual cells in a spheroid to an electric field as well as their mutual interactions.”

Each cell behaves according to certain rules. “But when you consider a large number of them together, the aggregate exhibits novel coherent behaviors. It is this emergent phenomenon that is crucial for developing effective theories at the tissue-scale — novel behaviors that emerge from the coupling of many individual elements,” Mistani said.

The effects of electroporation used in cancer treatment, for example, depend on many factors, such as the strength of the electric field, its pulse, and its frequency. “This work could bring an effective theory that helps understand the tissue response to these parameters and thus optimize such treatments,” says Mistani.

The researchers are currently mining this unique dataset to develop an effective tissue-scale theory of cell aggregate electroporation.

Supercomputer allocations on Comet at the San Diego Supercomputer Center and Stampede2 at TACC were awarded to the researchers through XSEDE, the Extreme Science and Engineering Discovery Environment funded by the National Science Foundation (NSF). Additionally, the researchers used TACC’s long-term storage system, Ranch, also an XSEDE resource.

Computer simulations are more and more prominent in the fields of science and engineering because they enable researchers to get data that sometimes cannot be obtained otherwise. State-of-the-art computer architectures, such as Comet and Stampede2, and advanced numerical methods open up new possibilities in advancing the frontiers of science in disciplines that are of high interest to the public, such as cancer treatment, combat wound healing, or the broad field of morphogenesis.

For us, this research would not have been possible without XSEDE because such simulations require over 2,000 cores for 24 hours and terabytes of data to reach time scales and length scales where the collective interactions between cells manifest themselves as a pattern,” Gibou said. “It helped us observe a surprising structure for the behavior of the aggregate out of the inherent randomness. XSEDE provides a truly unique infrastructure for scientific discovery in the era of big data.” Moving forward, the team’s research goal is to develop an effective theory that describes the simulation results.

“This is an example where simulations are not merely used as a predictive tool, but help discover new phenomena,” Gibou said. “Under electroporation, cells respond in surprising synchronicity and it’s beautiful to witness how such levels of order emerge out of inherent randomness.”

Read the Full Story

Sign up for our insideHPC Newsletter

Leave a Comment

*

Resource Links: