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Cancer treatments get a supercomputing boost

Speed read
  • TACC supercomputers are pushing cancer research to new heights
  • MR-linac safely images anatomy while radiating tissue
  • Quantum simulations explore the unseen mechanisms behind proton therapy
  • Computer simulations provide insight without jeopardizing patient health

“Historically, radiation has been a blunt tool.”

So says Matt Vaughn, director of Life Science Computing at the Texas Advanced Computing Center (TACC). Over the last century, however, radiation technologies have improved and have become a highly effective way to treat cancer.

“It's become ever more precise because we understand the physics and biology of systems that we're shooting radiation into, and have improved our ability to target the delivery of that radiation,” Vaughan adds.

Physicians must walk a fine line between delivering enough radiation to kill tumors, while sparing surrounding healthy tissue.

The science of calculating and assessing the radiation dose received by the human body is known as dosimetry — and here, as in many areas of science, advanced computing plays an important role.

Improving radiation therapy with real-time imaging

Current radiation treatments rely on imaging from computed tomography (CT) scans taken prior to treatment to determine a tumor's location. This works well if the tumor lies in an easily detectable and immobile location, but less so if the area is moving, as in the case of lung cancer.

<strong>Look under the hood.</strong> Developed by Elekta in cooperation with UMC Utrecht and Philips, the MR-linac at MD Anderson is the first of its kind in the US. The technology allows doctors to image anatomy while radiation is being delivered. Courtesy Elekta.At the University of Texas MD Anderson Cancer Center, scientists are accurately attacking tumors using magnetic resonance and linear accelerators (MR-linac). 

Imaging a patient's anatomy while the radiation is being delivered, MR-linacs allows doctors to detect and visualize any anatomical changes in a patient during treatment. 

To ensure patient safety, scientists first correct for the influence of the MRI's magnetic field on the measurements used to calibrate the radiation dose.

Researchers use software called Geant4 to simulate radiation within the detectors. Originally developed to simulate high energy particle physics experiments, the MD Anderson team has adapted Geant4 to incorporate magnetic fields into their computer dosimetry model.

Using the Lonestar supercomputer at TACC, the team simulated nearly 17 billion particles of radiation per detector to get the precision that they needed for their study.

To do experiments with human subjects is dangerous, so the best way is through computer simulation.~ Jorge Morales

“Since the ultimate aim of the MR-linac is to treat patients, it is important that our simulations be very accurate and that the results be very precise,” says Daniel O'Brien, a postdoctoral fellow in radiation physics at MD Anderson. 

“Over time, our understanding of these effects has improved considerably, but there is still work to be done and resources like TACC are an invaluable asset in making these new technologies safe and reliable.”

Uncovering the quantum basis of proton cancer therapy

Like many forms of cancer therapy, clinicians know that proton therapy works, but precisely how it works is a bit of a mystery.

The basic principle is not in question: proton ions collide with water molecules, triggering the release of secondary ions, electrons, reactive molecules, and free radicals that damage the DNA of cancerous cells. The proton ions also collide with the DNA directly, breaking bonds and crippling DNA's ability to replicate.

Because of their high rate of division and reduced ability to repair damaged DNA, cancerous cells are much more vulnerable to DNA attacks than normal cells and are killed at a higher rate. Furthermore, a proton beam can be focused on a tumor area, thus causing maximum damage on cancerous cells and minimum damage on surrounding healthy cells.

However, beyond this general microscopic picture, the mechanics of the process have been hard to determine. 

<strong>Quantum leap. </strong> To tease out how proton therapy works, researchers run computer simulations to predict DNA damage reactions during proton cancer therapy. Courtesy Jorge Morales; Texas Tech University.To investigate the fundamentals of the process, Morales has been running quantum dynamic models on TACC's Stampede supercomputer to simulate the chemical reactions that occur between protons and cancer cells.

Computational experiments can mimic the dynamics of the proton-cell interactions at the molecular level without causing damage to a patient.

Quantum simulations are necessary because the electrons and atoms that are the basis for proton cancer therapy's effectiveness do not behave according to the laws of classical physics.

Rather, they are guided by the laws of quantum mechanics which involve probabilities of location, speed, and reactions' occurrences rather than precisely defined versions of those three variables.

Morales' studies on Stampede have determined the basic byproducts of protons colliding with water within the cell, and with nucleotides and clusters of DNA bases — the basic units of DNA. The studies shed light on how the protons and their water radiolysis products damage DNA.

The results of Morales' computational experiments match the limited data from physical chemistry experiments, leading to greater confidence in their ability to capture the quantum behavior in action.

Though fundamental in nature, the insights and data that Morales' simulations produce help researchers understand proton cancer therapy at the microscale, and help modulate factors like dosage and beam direction.

“These simulations will bring about a unique way to understand and control proton cancer therapy,” says Morales. “They will help to drastically improve, — at a very low cost — the treatment of cancer patients without risking human subjects.”

Morales' work is currently supported by a grant from Cancer Prevention Research Institute of Texas and was started with a previous CAREER award from the National Science Foundation. Stampede was developed and deployed with support from the National Science Foundation.

Read the original TACC article here.

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