CFD Simulations Take Cancer Research to a New Dimension

By Kara L. Gray

June 4, 2008

Sixteen milliseconds — one-fifth the speed of the blink of an eye — can mean the difference between life and death for millions of people. How can such a miniscule amount of time have such a profound effect on so many? That’s about how long it takes for one infinitesimal cancer cell to adhere to a new location within the body. In as little as a day, a new tumor is born in a phenomenon known as metastasizing.

The American Cancer Society forecasts that nearly 1.5 million new cases of cancer will be diagnosed this year alone, and for many patients, fear of metastasis will dominate their treatment. It takes just one cell, measuring about one-fourth the width of a human hair, to begin a new tumor in a secondary site. Often renegade cells travel through the lymphatic system, where they might get caught up in lymph nodes near the primary site. Other times, they travel through the blood stream, where they can make their way to any location within the body.

Exactly what causes cancer cells to break away and travel remains a challenge for cancer researchers, but scientists at The Pennsylvania State University (PSU) are zeroing in on how cells adhere in the new location, and what might be done to influence this adhesion. To do so, they are employing pioneering computational fluid dynamics simulations made possible by Harpoon 3D mesh generator and EnSight extreme visualization software by North Carolina-based CEI Inc.

A Sticky Situation

Meghan Hoskins, a Ph.D. candidate in the Bioengineering program at Penn State, under the advisement of Robert Kunz, Ph.D. and Cheng Dong, Ph.D., is examining how cancer cells stick to white blood cells, the defenders of the blood stream, and how the flow of blood affects this adhesion. Her work, funded by the National Cancer Institute and the PSU Applied Research Laboratory, is based on the theory that, as cancer cells travel through the blood stream, they are attracted to areas where white blood cells are at work fighting inflammation.

“If there is already inflammation in the body, that could actually attract the cancer cells,” Hoskins says, noting that the patient may be totally unaware of the inflammation. “Cancer cells are also capable of secreting certain proteins that can activate the white blood cells, so there’s a possibility that cancer cells can themselves create a localized inflammation, even if there isn’t one there to begin with.”

This frightening concept, that cancer cells can actually use our own immune system against us, is the foundation of Hoskins research. Her goal is to accurately simulate previous experimental conditions of this phenomenon to validate her model, so that it may be used to further study the metastasis process. To do so, Hoskins is developing a simulated system, based on an existing rectangular test chamber in Professor Dong’s lab, designed to study the flow of these proteins to the white blood cells and how this affects the adhesion.

A Model Approach

Existing experimental data suggests that shear rate, the change in flow velocity within the micro capillaries, can affect the adhesion of tumor cells. By devising computational fluid dynamics models of the chamber, Hoskins is calculating velocity profiles throughout the test chamber and attempting to characterize the dynamic forces and biochemistry at work during in vitro cell adhesion.

To develop the model, Hoskins is using Harpoon by Sharc Ltd., a fully automatic extreme mesh generator, to construct a detailed 3D geometric grid of the experimental flow chamber. At each time step, which ranges from 1 to 8 microseconds, Hoskins performs a quasi-steady CFD calculation to ascertain the fluid forces on the tumor cells. She then generates a new Harpoon grid.

“Harpoon has been pretty important in my work because I’m doing such small time steps with so much going on simultaneously,” Hoskins says. “I need something that can work quickly, and Harpoon has been very fast. Each time I make a new grid, it takes less than 30 seconds. Without Harpoon, I would have to generate each grid by hand, which could take hours, depending on the complexity of the grid.”

The results are exported to the AcuSolve flow solver for CFD analysis. Motion is then calculated by solving the six-degrees-of-freedom (6DOF) dynamics system for the cells in a Python script. This calculation allows Hoskins to determine exactly where and how fast the cells move at each step within the three-dimensional field.

“Each AcuSolve calculation goes into an EnSight case file, where the individual steady result files are compiled into one transient EnSight case file,” Hoskins says. “Then, I am able to animate them using the transient tools in EnSight to watch what happens over the course of 100 milliseconds.”

EnSight, CEI’s extreme visualization software, allows Hoskins to view a realistic animation of the model, adjust parameters and generate new animations based on varying conditions. EnSight’s speed and agility with varying file formats has been critical to Hoskins’s work.

“With EnSight, I can watch my full simulation without having to look at just individual time steps,” Hoskins says. “Piecing them together has been very easy, and the fact that AcuSolve files work with EnSight is important.”

Blood is Thicker than Water

So far, Hoskins plans to model two experimental setups. The first is called a migration chamber — a rectangular flow chamber with holes in the bottom surface on which a filter is placed that allows cells to migrate through it. Endothelium cells, like those that form the inside lining of the blood vessels, are cultured on top of the filter. A solution of white blood cells and cancer cells are perfused through the inside. In this model, when only cancer cells are present in the chamber, there is significantly less migration of those cells through the endothelium than when white blood cells are also present. This suggests that the white blood cells influence the migration.

In the second model, the chamber is sealed. Researchers can watch as the cells interact, collide and adhere to one another, and measure how much of this activity takes place. In this instance, it has been found that shear rate, or velocity, affects the cancer cell’s adhesion to white blood cells. But, the adhesion of white blood cells to the endothelial cells is affected by both shear rate and shear stress, or the force produced by the flow.

Where the Model Meets Medicine

Hoskins’ mission is to understand why and how the migration of cancer cells is affected by the fluid dynamics of the system. This knowledge could help determine targets for future therapeutic research. For example, if she can identify that cancer-produced proteins carried through the blood stream do significantly activate the white blood cells, perhaps medical researchers can devise a way to block the activity of those proteins.

For right now, though, Hoskins’ is laying the groundwork for future research by providing insight into the adhesion process. She continues to make improvements to the model to more accurately simulate in vivo metastasis.
 
“In early models, for simplicity, I kept the cells rigid. But, in reality both the cancer cell and white blood cells are flexible. I’m working on a new model that allows the cells to deform. Both the flow and the collision between the two affects the shape of the cells,” Hoskins says. “This could change how the adhesion takes place. If the cells can deform, there might be a larger area for adhesion bonds to form.”

For future study, Hoskins hopes that her model will see continued improvement, particularly with regard to simulating adhesion within the geometry of actual blood vessel shapes. Once her model is validated, the options for future study are open to many possibilities. For the 10.5 million people now living with a history of cancer in the United States alone, this offers a glimmer of hope that some day future generations will not have to live in fear of metastasizing cancer.

Subscribe to HPCwire's Weekly Update!

Be the most informed person in the room! Stay ahead of the tech trends with industy updates delivered to you every week!

SC19 Student Cluster Competition: Know Your Teams

November 19, 2019

I’m typing this live from Denver, the location of the 2019 Student Cluster Competition… and, oh yeah, the annual SC conference too. The attendance this year should be north of 13,000 people, with the majority attende Read more…

By Dan Olds

Top500: US Maintains Performance Lead; Arm Tops Green500

November 18, 2019

The 54th Top500, revealed today at SC19, is a familiar list: the U.S. Summit (ORNL) and Sierra (LLNL) machines, offering 148.6 and 94.6 petaflops respectively, remain in first and second place. The only new entrants in t Read more…

By Tiffany Trader

ScaleMatrix and Nvidia Launch ‘Deploy Anywhere’ DGX HPC and AI in a Controlled Enclosure

November 18, 2019

HPC and AI in a phone booth: ScaleMatrix and Nvidia announced today at the SC19 conference in Denver a joint offering that puts up to 13 petaflops of Nvidia DGX-1 compute power in an air conditioned, water-cooled ScaleMa Read more…

By Doug Black

HPE and NREL Collaborate on AI Ops to Accelerate Exascale Efficiency and Resilience

November 18, 2019

The ever-expanding complexity of high-performance computing continues to elevate the concerns posed by massive energy consumption and increasing points of failure. Now, the AI Ops collaboration between Hewlett Packard En Read more…

By Oliver Peckham

Intel Debuts New GPU – Ponte Vecchio – and Outlines Aspirations for oneAPI

November 17, 2019

Intel today revealed a few more details about its forthcoming Xe line of GPUs – the top SKU is named Ponte Vecchio and will be used in Aurora, the first planned U.S. exascale computer. Intel also provided a glimpse of Read more…

By John Russell

AWS Solution Channel

Making High Performance Computing Affordable and Accessible for Small and Medium Businesses with HPC on AWS

High performance computing (HPC) brings a powerful set of tools to a broad range of industries, helping to drive innovation and boost revenue in finance, genomics, oil and gas extraction, and other fields. Read more…

IBM Accelerated Insights

Data Management – The Key to a Successful AI Project

 

Five characteristics of an awesome AI data infrastructure

[Attend the IBM LSF & HPC User Group Meeting at SC19 in Denver on November 19!]

AI is powered by data

While neural networks seem to get all the glory, data is the unsung hero of AI projects – data lies at the heart of everything from model training to tuning to selection to validation. Read more…

SC19: Welcome to Denver

November 17, 2019

A significant swath of the HPC community has come to Denver for SC19, which began today (Sunday) with a rich technical program. As is customary, the ribbon cutting for the Expo Hall opening is Monday at 6:45pm, with the Read more…

By Tiffany Trader

Top500: US Maintains Performance Lead; Arm Tops Green500

November 18, 2019

The 54th Top500, revealed today at SC19, is a familiar list: the U.S. Summit (ORNL) and Sierra (LLNL) machines, offering 148.6 and 94.6 petaflops respectively, Read more…

By Tiffany Trader

ScaleMatrix and Nvidia Launch ‘Deploy Anywhere’ DGX HPC and AI in a Controlled Enclosure

November 18, 2019

HPC and AI in a phone booth: ScaleMatrix and Nvidia announced today at the SC19 conference in Denver a joint offering that puts up to 13 petaflops of Nvidia DGX Read more…

By Doug Black

Intel Debuts New GPU – Ponte Vecchio – and Outlines Aspirations for oneAPI

November 17, 2019

Intel today revealed a few more details about its forthcoming Xe line of GPUs – the top SKU is named Ponte Vecchio and will be used in Aurora, the first plann Read more…

By John Russell

SC19: Welcome to Denver

November 17, 2019

A significant swath of the HPC community has come to Denver for SC19, which began today (Sunday) with a rich technical program. As is customary, the ribbon cutt Read more…

By Tiffany Trader

SC19’s HPC Impact Showcase Chair: AI + HPC a ‘Speed Train’

November 16, 2019

This year’s chair of the HPC Impact Showcase at the SC19 conference in Denver is Lori Diachin, who has spent her career at the spearhead of HPC. Currently deputy director for the U.S. Department of Energy’s (DOE) Exascale Computing Project (ECP), Diachin is also... Read more…

By Doug Black

Cray, Fujitsu Both Bringing Fujitsu A64FX-based Supercomputers to Market in 2020

November 12, 2019

The number of top-tier HPC systems makers has shrunk due to a steady march of M&A activity, but there is increased diversity and choice of processing compon Read more…

By Tiffany Trader

Intel AI Summit: New ‘Keem Bay’ Edge VPU, AI Product Roadmap

November 12, 2019

At its AI Summit today in San Francisco, Intel touted a raft of AI training and inference hardware for deployments ranging from cloud to edge and designed to support organizations at various points of their AI journeys. The company revealed its Movidius Myriad Vision Processing Unit (VPU)... Read more…

By Doug Black

IBM Adds Support for Ion Trap Quantum Technology to Qiskit

November 11, 2019

After years of percolating in the shadow of quantum computing research based on superconducting semiconductors – think IBM, Rigetti, Google, and D-Wave (quant Read more…

By John Russell

Supercomputer-Powered AI Tackles a Key Fusion Energy Challenge

August 7, 2019

Fusion energy is the Holy Grail of the energy world: low-radioactivity, low-waste, zero-carbon, high-output nuclear power that can run on hydrogen or lithium. T Read more…

By Oliver Peckham

Using AI to Solve One of the Most Prevailing Problems in CFD

October 17, 2019

How can artificial intelligence (AI) and high-performance computing (HPC) solve mesh generation, one of the most commonly referenced problems in computational engineering? A new study has set out to answer this question and create an industry-first AI-mesh application... Read more…

By James Sharpe

Cray Wins NNSA-Livermore ‘El Capitan’ Exascale Contract

August 13, 2019

Cray has won the bid to build the first exascale supercomputer for the National Nuclear Security Administration (NNSA) and Lawrence Livermore National Laborator Read more…

By Tiffany Trader

DARPA Looks to Propel Parallelism

September 4, 2019

As Moore’s law runs out of steam, new programming approaches are being pursued with the goal of greater hardware performance with less coding. The Defense Advanced Projects Research Agency is launching a new programming effort aimed at leveraging the benefits of massive distributed parallelism with less sweat. Read more…

By George Leopold

AMD Launches Epyc Rome, First 7nm CPU

August 8, 2019

From a gala event at the Palace of Fine Arts in San Francisco yesterday (Aug. 7), AMD launched its second-generation Epyc Rome x86 chips, based on its 7nm proce Read more…

By Tiffany Trader

D-Wave’s Path to 5000 Qubits; Google’s Quantum Supremacy Claim

September 24, 2019

On the heels of IBM’s quantum news last week come two more quantum items. D-Wave Systems today announced the name of its forthcoming 5000-qubit system, Advantage (yes the name choice isn’t serendipity), at its user conference being held this week in Newport, RI. Read more…

By John Russell

Ayar Labs to Demo Photonics Chiplet in FPGA Package at Hot Chips

August 19, 2019

Silicon startup Ayar Labs continues to gain momentum with its DARPA-backed optical chiplet technology that puts advanced electronics and optics on the same chip Read more…

By Tiffany Trader

Crystal Ball Gazing: IBM’s Vision for the Future of Computing

October 14, 2019

Dario Gil, IBM’s relatively new director of research, painted a intriguing portrait of the future of computing along with a rough idea of how IBM thinks we’ Read more…

By John Russell

Leading Solution Providers

ISC 2019 Virtual Booth Video Tour

CRAY
CRAY
DDN
DDN
DELL EMC
DELL EMC
GOOGLE
GOOGLE
ONE STOP SYSTEMS
ONE STOP SYSTEMS
PANASAS
PANASAS
VERNE GLOBAL
VERNE GLOBAL

Intel Confirms Retreat on Omni-Path

August 1, 2019

Intel Corp.’s plans to make a big splash in the network fabric market for linking HPC and other workloads has apparently belly-flopped. The chipmaker confirmed to us the outlines of an earlier report by the website CRN that it has jettisoned plans for a second-generation version of its Omni-Path interconnect... Read more…

By Staff report

Kubernetes, Containers and HPC

September 19, 2019

Software containers and Kubernetes are important tools for building, deploying, running and managing modern enterprise applications at scale and delivering enterprise software faster and more reliably to the end user — while using resources more efficiently and reducing costs. Read more…

By Daniel Gruber, Burak Yenier and Wolfgang Gentzsch, UberCloud

Dell Ramps Up HPC Testing of AMD Rome Processors

October 21, 2019

Dell Technologies is wading deeper into the AMD-based systems market with a growing evaluation program for the latest Epyc (Rome) microprocessors from AMD. In a Read more…

By John Russell

Cray, Fujitsu Both Bringing Fujitsu A64FX-based Supercomputers to Market in 2020

November 12, 2019

The number of top-tier HPC systems makers has shrunk due to a steady march of M&A activity, but there is increased diversity and choice of processing compon Read more…

By Tiffany Trader

Rise of NIH’s Biowulf Mirrors the Rise of Computational Biology

July 29, 2019

The story of NIH’s supercomputer Biowulf is fascinating, important, and in many ways representative of the transformation of life sciences and biomedical res Read more…

By John Russell

Xilinx vs. Intel: FPGA Market Leaders Launch Server Accelerator Cards

August 6, 2019

The two FPGA market leaders, Intel and Xilinx, both announced new accelerator cards this week designed to handle specialized, compute-intensive workloads and un Read more…

By Doug Black

When Dense Matrix Representations Beat Sparse

September 9, 2019

In our world filled with unintended consequences, it turns out that saving memory space to help deal with GPU limitations, knowing it introduces performance pen Read more…

By James Reinders

With the Help of HPC, Astronomers Prepare to Deflect a Real Asteroid

September 26, 2019

For years, NASA has been running simulations of asteroid impacts to understand the risks (and likelihoods) of asteroids colliding with Earth. Now, NASA and the European Space Agency (ESA) are preparing for the next, crucial step in planetary defense against asteroid impacts: physically deflecting a real asteroid. Read more…

By Oliver Peckham

  • arrow
  • Click Here for More Headlines
  • arrow
Do NOT follow this link or you will be banned from the site!
Share This