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Primeur weekly 2017-05-15

Special

NVIDIA ushers in new era of robotics, with breakthroughs making It easier to build and train intelligent machines ...

NVIDIA and Toyota collaborate to accelerate market introduction of autonomous cars ...

NVIDIA launches GPU Cloud platform to simplify AI development ...

NVIDIA advances AI computing revolution with new Volta-based DGX systems ...

NVIDIA launches revolutionary Volta GPU platform, fueling next era of AI and high performance computing ...

NVIDIA to train 100,000 developers on deep learning in 2017 ...

NVIDIA paves path to AI cities with Metropolis Edge-to-Cloud platform for video analytics ...

NVIDIA Tesla accelerators on IBM Cloud demonstrate advanced performance for training deep learning models ...

BSC and NVIDIA a step forward to the interactive simulation of humans ...

Quantum computing

Refrigerator for quantum computers discovered ...

Focus on Europe

EoCoE service page open for PRACE user community ...

Spring 2017 edition of the e-IRG newsletter available ...

PRACE to issue Annual Report 2016 ...

Middleware

Bright Computing announces 8.0 release - Setting new standard for automation and ease-of-use for Linux-based clusters and public, private and hybrid Clouds ...

CETIAT France chooses Bright Cluster Manager for aerodynamics and fluid mechanics HPC environment ...

2016 National Research Infrastructure Roadmap for Australia is now available ...

Hardware

Cray delivers production-ready AI with new Cray CS-Storm accelerated cluster supercomputers ...

Inspur to unveil 2U 8-GPU AI supercomputer at GTC 2017 ...

Inspur unveiled AIStation, AI deep learning training cluster management software at GTC 2017 ...

Supermicro systems deliver 170 Tflop/s FP16 of peak performance for artificial intelligence, and deep learning at GTC 2017 ...

NCSA's Blue Waters project provides $1.08 billion direct return to Illinois' economy ...

Applications

SDSC's Comet helps replicate brain circuitry to direct a realistic prosthetic arm ...

University of Wyoming graduate student one of 36 selected for CyberGIS Summer School ...

Supercomputing mimics berkelium experiments to validate new find ...

'Inverse designing' spontaneously self-assembling materials ...

Story of silver birch from genomic Big Data ...

Targeted, high-energy cancer treatments get a supercomputing boost ...

Computer accurately identifies and delineates breast cancers on digital tissue slides ...

Sound over silicon: Computing's wave of the future ...

USC Viterbi School of Engineering faculty awarded multiple MURI grants ...

New funding announced for Digital Earth Australia ...

NCSA releases annual report highlighting scientific exploration and breakthroughs enabled by the Blue Waters Project ...

Supercomputer can disprove the theory of sunspot formation ...

The Cloud

Inspur to release InCloud OS 5.0 "F.A.S.T" at the 2017 OpenStack Summit ...

IBM extends data science collaborative workspace to the private Cloud ...

Pointwise and Envenio Join Forces on Demand ...

Targeted, high-energy cancer treatments get a supercomputing boost

The inner ring is the MRI bore which performs the imaging of the patient. The outer ring is the gantry on which the linear accelerator (linac) that produces the radiation for treatment is mounted. The linac gantry can rotate completely around. In the centre is the bed where the patient would lie. Credit: Elekta.10 May 2017 Austin - Radiation therapy shoots high-energy particles into the body to destroy or damage cancer cells, while sparing surrounding healthy tissue. New types of radiation systems are emerging that can better target cancer cells. These include proton beam therapy and MR-linac, which combines real-time imaging and radiation treatment in a single device. Scientists rely on supercomputers at the Texas Advanced Computing Center to virtually test, plan treatments, and understand the basic science of, these radiation therapies.

Over the last century, the technologies used have constantly improved and it has become a highly effective way to treat cancer. However, physicians must still walk a fine line between delivering enough radiation to kill tumours, while sparing surrounding healthy tissue.

"Historically, radiation has been a blunt tool", stated Matt Vaughn, Director of Life Science Computing at the Texas Advanced Computing Center. "However, 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."

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.

Current radiation treatments rely on imaging from computed tomography (CT) scans taken prior to treatment to determine a tumour'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.

At the University of Texas MD Anderson Cancer Center, scientists are tackling the problem of accurately attacking tumors using a new technology known as an MR-linac that combines magnetic resonance (MR) imaging with linear accelerators (linacs). Developed by Elekta in cooperation with UMC Utrecht and Philips, the MR-linac at MD Anderson is the first of its kind in the U.S.

MR-linacs can image a patient's anatomy while the radiation beam is being delivered. This allows doctors to detect and visualize any anatomical changes in a patient during treatment. Unlike CT or other x-ray based imaging modalities, which provide additional ionizing radiation, MRI is harmless to healthy tissue.

The MR-linac method offers a potentially significant improvement over current image-guided cancer treatment technology. However, to ensure patients are treated safely, scientists must first correct for the influence of the MRI's magnetic field on the measurements used to calibrate the radiation dose being delivered.

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

"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", stated Daniel O'Brien, a postdoctoral fellow in radiation physics at MD Anderson. "Geant4 was originally designed to study radiation at much higher energies than what is used to treat patients. We had to perform tests to make sure that we had the accuracy that we needed."

Using the Lonestar supercomputer at the Texas Advanced Computing Center (TACC), the research team simulated nearly 17 billion particles of radiation per detector to get the precision that they needed for their study.

In August 2016, they published magnetic field correction factors in Medical Physics for six of the most-used ionization chamber detectors - gas-filled chambers that are used to ensure the dose delivered from a therapy unit is correct. They are now working on verifying these results experimentally.

"The MR-linac is a very promising technology but it also presents many unique challenges from a dosimetry point of view", Daniel O'Brien stated. "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."

"Our computer simulations are important because their results will serve as the foundation to extend current national and international protocols to perform calibration of conventional linacs to MR-linacs", stated Gabriel Sawakuchi, assistant professor of Radiation Physics at MD Anderson. "However, it is important that our results be validated against measurements and independent simulations performed by other groups before used clinically."

The project was partially funded by Elekta, a Swedish company that provides radiation therapy equipment and clinical management for the treatment of cancer and brain disorders.

X-ray radiation is the most frequently used form of high-energy treatment, but a new treatment is emerging that uses a beam of protons to deliver energy directly to the tumor with minimal damage to surrounding tissues and without the side effects of x-ray therapy.

Like x-ray radiation, proton therapy blasts tumors with beams of particles. But whereas traditional radiation uses photons, or focused light beams, proton therapy uses ions - hydrogen atoms that have lost an electron.

Proton beams have a unique physical characteristic known as the 'Bragg peak' that allows the greatest part of its energy to be transferred to a specific area within the body, where it has maximum destructive effect. X-ray radiation, on the other hand, deposits energy and kills cells along the whole length of the beam. This can lead to unintended cell damage and even secondary cancer that can develop years later.

In comparison with current radiation procedures, proton therapy saves healthy tissue in front of and behind the tumour. Since the patient is irradiated from all directions and the intensity of beams can be well modulated, the method provides further reduction of adverse effects.

Proton therapy is particularly effective when irradiating tumors near sensitive organs - for instance near the neck, spine, brain or lungs - where stray beams can be particularly damaging.

Medical physicists and radiation oncologists from Mayo Clinic in Phoenix, Arizona in collaboration with MD Anderson researchers, recently published a series of papers describing improved planning and use of proton therapy.

Writing in Medical Physics in January 2017, they showed that in the three clinical cases included in this study, their chance-constrained model was better at sparing organs at risk than the current method. The model also provided a flexible tool for users to balance between plan robustness and plan quality and was found to be much faster than the commercial solution.

The research used the Stampede supercomputer at TACC to conduct computationally intensive studies of the hundreds of factors that go into maximizing the effectiveness of, and minimizing the risk and uncertainties involved in, these treatments.

Proton therapy was first developed in the 1950s and came into mainstream in the 1990s. There are currently 12 proton therapy centers nation-wide and the number is growing. However, the cost of the proton beam devices - $200 million dollars, or 30 to 50 times more expensive than a traditional x-ray system - means they are still rare. They are applied only in cases that require extra precision and doctors must maximize their benefit when they are used.

Mayo Clinic and MD Anderson operate the most advanced versions of these devices, which perform scanning beam proton therapy and are able to modulate the intensity of the beam. Wei Liu, one of the lead proton therapy researchers at Mayo Clinic, likens the process to 3D printing, "painting the tumour layer by layer". However, this is accomplished at a distance, through a protocol that must be planned in advance.

The specificity of the proton beam, which is its greatest advantage, means that it must be precisely calibrated and that discrepancies from the ideal must be considered. For instance, hospital staff situate patients on the operating surface of the device, and even placing a patient a few millimeters off-center can impact the success of the treatment.

Moreover, every patient's body has a slightly different chemical composition, which can make the proton beam stop at a different position from what is intended. Even patients' breathing can throw off the location of the beam placement.

"If a patient has a tumor close to the spinal cord and this level of uncertainty exists, then the proton beam can overdose and paralyze the patient", Wei Liu stated.

The solution to these challenges is robust optimization, which uses mathematical techniques to generate a plan that can manage and mitigate the uncertainties and human errors that may arise.

"Each time, we try to mathematically generate a good plan", he stated. "There are many unknown variables. You can choose different beam angles or energy or intensity. There are 25,000 variables or more, so generating a plan that is robust to these mistakes and can still get the proper dose distribution to the tumor is a large-scale optimization problem."

To solve these problems, Wei Liu and his team use supercomputers at the Texas Advanced Computing Center.

"It's very computationally expensive to generate a plan in a reasonable timeframe", he continued. "Without a supercomputer, we can do nothing."

Wei Liu has been working on developing the proton beam planning protocols for many years. Leading commercial companies have adopted methods similar to those that Wei Liu and his collaborators developed as the basis for their radiation planning solutions.

Recently, Wei Liu and his collaborators extended their studies to include the uncertainties presented by breathing patients, which they call "4D robust optimization", since it takes into account the time component and not just spatial orientation.

In the May 2016 issue of the International Journal of Radiation Oncology , they showed that compared to its 3D counterpart, 4D robust optimization for lung cancer treatment provided more robust target dose distribution and better target coverage, while still offering normal tissue protection.

"We're trying to provide the patient with the most effective, most reliable, and most efficient proton therapy", Wei Liu stated. "Because it's so expensive, we have to do the best job to take advantage of this new technology."

Wei Liu's work is supported by grants from the National Institutes of Health's National Cancer Institute and recently received support from the State of Arizona.

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, which make up 70 percent of cells, triggering the release of electrons 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.

"As happens in cancer therapy, they know empirically that it works but they don't know why", stated Jorge A. Morales, a professor of chemistry at Texas Tech University and a leading proponent of the computational analysis of proton therapy. "To do experiments with human subjects is dangerous, so the best way is through computer simulation."

Jorge A. Morales has been running computer simulations of proton-cell chemical reactions using quantum dynamics models on TACC's Stampede supercomputer to investigate the fundamentals of the process. Computational experiments can mimic the dynamics of the proton-cell interactions without causing damage to a patient and can reveal what happens when the proton beam and cells collide from start to finish, with atomic-level accuracy.

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 quantum mechanics which involve probabilities of location, speed and reactions' occurrences rather than to the precisely defined versions of those three variables.

Jorge A. Morales' studies on Stampede, reported in PLOS One in March 2017, as well as in Molecular Physics , and Chemical Physics Letters (both 2014), 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 Jorge A. 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 Jorge A. Morales' simulations produce help researchers understand proton cancer therapy at the microscale, and help modulate factors like dosage and beam direction.

"The results are all very promising and we're excited to extend our research further", Jorge A. Morales stated. "These simulations will bring about a unique way to understand and control proton cancer therapy that, at a very low cost, will help to drastically improve the treatment of cancer patients without risking human subjects."

The 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.

Source: University of Texas at Austin, Texas Advanced Computing Center - TACC

Back to Table of contents

Primeur weekly 2017-05-15

Special

NVIDIA ushers in new era of robotics, with breakthroughs making It easier to build and train intelligent machines ...

NVIDIA and Toyota collaborate to accelerate market introduction of autonomous cars ...

NVIDIA launches GPU Cloud platform to simplify AI development ...

NVIDIA advances AI computing revolution with new Volta-based DGX systems ...

NVIDIA launches revolutionary Volta GPU platform, fueling next era of AI and high performance computing ...

NVIDIA to train 100,000 developers on deep learning in 2017 ...

NVIDIA paves path to AI cities with Metropolis Edge-to-Cloud platform for video analytics ...

NVIDIA Tesla accelerators on IBM Cloud demonstrate advanced performance for training deep learning models ...

BSC and NVIDIA a step forward to the interactive simulation of humans ...

Quantum computing

Refrigerator for quantum computers discovered ...

Focus on Europe

EoCoE service page open for PRACE user community ...

Spring 2017 edition of the e-IRG newsletter available ...

PRACE to issue Annual Report 2016 ...

Middleware

Bright Computing announces 8.0 release - Setting new standard for automation and ease-of-use for Linux-based clusters and public, private and hybrid Clouds ...

CETIAT France chooses Bright Cluster Manager for aerodynamics and fluid mechanics HPC environment ...

2016 National Research Infrastructure Roadmap for Australia is now available ...

Hardware

Cray delivers production-ready AI with new Cray CS-Storm accelerated cluster supercomputers ...

Inspur to unveil 2U 8-GPU AI supercomputer at GTC 2017 ...

Inspur unveiled AIStation, AI deep learning training cluster management software at GTC 2017 ...

Supermicro systems deliver 170 Tflop/s FP16 of peak performance for artificial intelligence, and deep learning at GTC 2017 ...

NCSA's Blue Waters project provides $1.08 billion direct return to Illinois' economy ...

Applications

SDSC's Comet helps replicate brain circuitry to direct a realistic prosthetic arm ...

University of Wyoming graduate student one of 36 selected for CyberGIS Summer School ...

Supercomputing mimics berkelium experiments to validate new find ...

'Inverse designing' spontaneously self-assembling materials ...

Story of silver birch from genomic Big Data ...

Targeted, high-energy cancer treatments get a supercomputing boost ...

Computer accurately identifies and delineates breast cancers on digital tissue slides ...

Sound over silicon: Computing's wave of the future ...

USC Viterbi School of Engineering faculty awarded multiple MURI grants ...

New funding announced for Digital Earth Australia ...

NCSA releases annual report highlighting scientific exploration and breakthroughs enabled by the Blue Waters Project ...

Supercomputer can disprove the theory of sunspot formation ...

The Cloud

Inspur to release InCloud OS 5.0 "F.A.S.T" at the 2017 OpenStack Summit ...

IBM extends data science collaborative workspace to the private Cloud ...

Pointwise and Envenio Join Forces on Demand ...