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Primeur weekly 2018-03-19

Exascale supercomputing

BSC and Fujitsu to build up an ecosystem for a future exascale supercomputer ...

Quantum computing

New quantum spin liquid predicted by Nobel Laureate prepared for the first time ...

Focus on Europe

New project to plug the software-stack support gap for energy-efficient computing ...

North German scientists receive new supercomputer in the HLRN network ...

Hardware

Cray tapped to deliver largest supercomputer dedicated to fusion science in Japan by National Institutes for Quantum and Radiological Science and Technology ...

Keeping GPUs young ...

Asetek announces ongoing collaboration with Intel on liquid cooling for servers and data centres ...

UC San Diego Center for Microbiome Innovation announces Panasas as Corporate Member ...

Cavium expands industry partnerships to drive OCP NIC 3.0 ...

Applications

How much snow accumulates in North America each year? More than scientists thought. ...

Green light for Galaxy Europe ...

Supercomputer simulation opens prospects for obtaining ultra-dense electron-positron plasmas ...

The complex journey of red bloods cells through microvascular networks ...

The view from inside supersonic combustion ...

A game changer: Metagenomic clustering powered by supercomputers ...

ORNL researchers design novel method for energy-efficient deep neural networks ...

University of Texas researchers develop new visualization tools to explore fusion physics ...

Fishing with simulations for two-dimensional materials ...

The Cloud

IBM helps accelerate AI with fast new data platform and elite team ...

European Commission to adopt Implementation Roadmap for the European Open Science Cloud ...

Univa announces a global partnership and reseller agreement with UberCloud ...

Univa open sources Project Tortuga to accelerate the migration of enterprise HPC workloads to the Cloud ...

USFlash

Xilinx unveils revolutionary adaptable computing product category ...

The complex journey of red bloods cells through microvascular networks


A snapshot showing red blood cells deforming as they flow through another microvascular network geometry. The large deformation of each individual cell is captured to better understand how individual cells behave as they flow through these networks. Credit: Rutgers University.
15 Mar 2018 Austin - If you think of the human body, microvascular networks comprised of the smallest blood vessels are a central part of the body's function. They facilitate the exchange of essential nutrients and gasses between the blood stream and surrounding tissues, as well as regulate blood flow in individual organs.

While the behaviour of blood cells flowing within single, straight vessels is a well-known problem, less is known about the individual cellular-scale events giving rise to blood behaviour in microvascular networks. To better understand this, researchers Peter Balogh and Prosenjit Bagchi published a recent study in the Biophysical Journal . Prosenjit Bagchi resides in the Mechanical and Aerospace Engineering Department at Rutgers University, and Peter Balogh is his PhD student.

To the researchers' knowledge, theirs is the first work to simulate and study red blood cells flowing in physiologically realistic microvascular networks, capturing both the highly complex vascular architecture as well as the 3D deformation and dynamics of each individual red blood cell.

Peter Balogh and Prosenjit Bagchi developed and used a state-of-the-art simulation code to study the behaviour of red blood cells as they flow and deform through microvascular networks. The code simulates 3D flows within complex geometries, and can model deformable cells, such as red blood cells, as well as rigid particles, such as inactivated platelets or some drug particles.

"Our research in microvascular networks is important because these vessels provide a very strong resistance to blood flow", stated Prosenjit Bagchi. "How much energy the heart needs to pump blood, for example, is determined by these blood vessels. In addition, this is where many blood diseases take root. For example, for someone with sickle cell anemia, this is where the red blood cells get stuck and cause enormous pain."

One of the paper's findings involves the interaction between red blood cells and the vasculature within the regions where vessels bifurcate. They observed that as red blood cells flow through these vascular bifurcations, they frequently jam for very brief periods before proceeding downstream. Such behavior can cause the vascular resistance in the affected vessels to increase, temporarily, by several orders of magnitude.

There have been many attempts to understand blood flow in microvascular networks dating back to the 1800s and French physician and physiologist, Jean-Louis-Marie Poiseuille, whose interest in the circulation of blood led him to conduct a series of experiments on the flow of liquids in narrow tubes. He also formulated a mathematical expression for the non-turbulent flow of fluids in circular tubes.

Updating this research, Peter Balogh and Prosenjit Bagchi use computation to enhance the understanding of blood flow in these networks. Like many other groups, they originally modelled capillary blood vessels as small, straight tubes and predicted their behavior.

"But if you look at the capillary-like vessels under the microscope, they are not straight tubes... they are very winding and continuously bifurcate and merge with each other", Prosenjit Bagchi stated. "We realized that no one else had a computational tool to predict the flow of blood cells in these physiologically realistic networks."

"This is the first study to consider the complex network geometry in 3D and simultaneously resolve the cell details in 3D", Peter Balogh stated. "One of the underlying goals is to better understand what is occurring in these very small vessels in these complex geometries. We hope that by being able to model this next level of detail we can add to our understanding of what is actually occurring at the level of these very small vessels."

In terms of cancer research, this model may have tremendous implications. "This code is just the beginning of something really big", Prosenjit Bagchi stated.

In the medical field today, there are advanced imaging systems that image the capillary network of blood vessels, but it's sometimes difficult for those imaging systems to predict the blood flow in every vessel simultaneously. "Now, we can take those images, put them into our computational model, and predict even the movement of each blood cell in every capillary vessel that is in the image", Prosenjit Bagchi stated.

This is a huge benefit because the researchers can see whether the tissue is getting enough oxygen or not. In cancer research, angiogenesis - the physiological process through which new blood vessels form from pre-existing vessels - is dependent upon the tissue getting enough oxygen.

The team is also working on modeling targeted drug delivery, particularly for cancer. In this approach nanoparticles are used to carry drugs and target the specific location of the disease. For example, if someone has cancer in the liver or pancreas, then those specific organs are targeted. Targeted drug delivery allows increased dose of the drug so other organs don't get damaged and the side effects are minimized.

"The size and shape of these nanoparticles determine the efficiency of how they get transported through the blood vessels", Prosenjit Bagchi stated. "We think the architecture of these capillary networks will determine how well these particles are delivered. The architecture varies from organ to organ. The computational code we developed helps us understand how the architecture of these capillary networks affects the transport of these nanoparticles in different organs."

This research used computational simulations to answer questions like: How accurately can a researcher capture the details of every blood cell in complex geometries? How can this be accomplished in 3D? How do you take into account the many interactions between these blood cells and vessels?

"In order to do this, we need large computing resources", Prosenjit Bagchi stated. "My group has been working on this problem using XSEDE resources from the Texas Advanced Computing Center. We used Stampede1 to develop our simulation technique, and soon we will be moving to Stampede2 because we'll be doing even larger simulations. We are using Ranch to store terabytes of our simulation data."

The eXtreme Science and Engineering Discovery Environment (XSEDE) is a National Science Foundation-funded virtual organisation that integrates and coordinates the sharing of advanced digital services - including supercomputers and high-end visualization and data analysis resources - with researchers nationally to support science. Stampede1, Stampede2, and Ranch are XSEDE-allocated resources.

The simulations reported in the paper took a few weeks of continuous simulation and resulted in terabytes of data.

In terms of how this research will help the medical community, Prosenjit Bagchi stated: "Based on an image of capillary blood vessels in a tumor, we can simulate it in 3D and predict the distribution of blood flow and nanoparticle drugs inside the tumor vasculature, and, perhaps, determine the optimum size, shape and other properties of nanoparticles for most effective delivery. This is something we'll be looking at in the future."

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

Back to Table of contents

Primeur weekly 2018-03-19

Exascale supercomputing

BSC and Fujitsu to build up an ecosystem for a future exascale supercomputer ...

Quantum computing

New quantum spin liquid predicted by Nobel Laureate prepared for the first time ...

Focus on Europe

New project to plug the software-stack support gap for energy-efficient computing ...

North German scientists receive new supercomputer in the HLRN network ...

Hardware

Cray tapped to deliver largest supercomputer dedicated to fusion science in Japan by National Institutes for Quantum and Radiological Science and Technology ...

Keeping GPUs young ...

Asetek announces ongoing collaboration with Intel on liquid cooling for servers and data centres ...

UC San Diego Center for Microbiome Innovation announces Panasas as Corporate Member ...

Cavium expands industry partnerships to drive OCP NIC 3.0 ...

Applications

How much snow accumulates in North America each year? More than scientists thought. ...

Green light for Galaxy Europe ...

Supercomputer simulation opens prospects for obtaining ultra-dense electron-positron plasmas ...

The complex journey of red bloods cells through microvascular networks ...

The view from inside supersonic combustion ...

A game changer: Metagenomic clustering powered by supercomputers ...

ORNL researchers design novel method for energy-efficient deep neural networks ...

University of Texas researchers develop new visualization tools to explore fusion physics ...

Fishing with simulations for two-dimensional materials ...

The Cloud

IBM helps accelerate AI with fast new data platform and elite team ...

European Commission to adopt Implementation Roadmap for the European Open Science Cloud ...

Univa announces a global partnership and reseller agreement with UberCloud ...

Univa open sources Project Tortuga to accelerate the migration of enterprise HPC workloads to the Cloud ...

USFlash

Xilinx unveils revolutionary adaptable computing product category ...