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Primeur weekly 2013-07-15

Special

Supercomputer acting as a discovery machine for neuroscience ...

Exascale supercomputing

Jack Dongarra helps design software for the next generation of supercomputers receiving $1 million grant ...

The Cloud

e-Infrastructures for e-Sciences 2013 ...

EastWest Bank chooses HP to build private Cloud ...

IBM accelerates Cloud computing on System z with acquisition of CSL International ...

IBM closes acquisition of SoftLayer Technologies ...

L'Oréal Uruguay consolidates IT infrastructure into the private Cloud and reduces power consumption with IBM PureSystems ...

Oracle announces availability of Cloud Application Foundation, the #1 application foundation across conventional and Cloud environments ...

Oracle expands support for mobile and Cloud technologies with the latest Java development tools and framework ...

US Ignite recognizes RENCI and NC State for innovative app for monitoring power grids ...

EuroFlash

MINES ParisTech selects Bright Cluster Manager for materials science research cluster ...

European Commission to launch survey about Future Internet Assembly ...

Bull launches StoreWay Optima 4600: reaffirming its presence in the new-generation data handling market ...

DANTE celebrates 20 years of networking excellence ...

Oracle Enterprise Manager 12c deployed by CERN to manage its Oracle infrastructure ...

PRACE Winter School 2014 to be held in Tel Aviv, Israel ...

USFlash

Professor Jack Dongarra announces new supercomputer benchmark ...

CASL milestone validates reactor model using TVA data ...

DOST to strengthen weather forecasting to benefit farmers ...

Fujitsu M10 achieves world-record result on two-tier SAP SD standard application benchmark ...

Fujitsu integrates internal database platform using SPARC M10 servers ...

1Wealth Trading Company opines on IBM's foray into global banking ...

Golf Channel selects Oracle's Pillar Axiom Storage System to support rapid growth and new reality programming ...

Stephen F. Austin State University readies for growth; speeds registration, adds 8X capacity and unlocks IT for strategic projects ...

TACC supercomputers help microfluidics researchers make waves at the microscopic level ...

TACC supercomputers help microfluidics researchers make waves at the microscopic level

Baskar Ganapathysubramanian, Iowa State University12 Jul 2013 Austin - Have you ever noticed the way water flows around boulders in a fast-moving river, creating areas of stillness and intense motion? What if those forces of fluid flow could be controlled at the smallest levels? In May 2013, researchers from the University of California at Los Angeles (UCLA), Iowa State and Princeton reported results inNature Communicationsabout a new way of sculpting tailor-made fluid flows by placing tiny pillars in microfluidic channels. By altering the speed of the fluid, and stacking many pillars, with different widths, placements and orientations, in the fluid's path, they showed that it is possible to create an impressive array of controlled flows.

Why does this matter? Because such a method will allow clinicians to separate white blood cells from other cells in a blood sample, increase mixing in industrial applications, and more quickly perform lab-on-a-chip-type operations, like DNA sequencing and chemical detection. Each of these could form the foundation for a multi-million dollar industry. Together, they could revolutionize microfluidics.

"Most microfluidic flow is at a very low speed", stated Baskar Ganapathysubramaniam, assistant professor of mechanical engineering at Iowa State and one of the lead researchers. "At that speed, the flow hugs the cylinder and there's fore-aft symmetry. Whatever's happening upstream is exactly mirrored downstream. But if you increase the speed - or more technically, the Reynolds number - slightly, you can break this symmetry and get wakes, vortices, and non-trivial deformations." All of which create distinct flows.

Hashing out the idea with Dino Di Carlo, associate professor of bioengineering at UCLA, the two researchers asked themselves if they could control the flow of fluids in microfluidic channels by placing pillars in specific locations in the path. Using both experimental methods and numerical simulations, they explored the possibilities offered by this approach and found that they could indeed create a range of predictable flows.

"Each pillar has a unique deformation signature to it", Baskar Ganapathysubramaniam stated. "By stacking these pillars together, we can create an astounding variety of deformations, and these can be tuned for specific purposes."

"Engineering tools like this allow a scientists to easily develop and manipulate a flow to a shape of their interest", Dino Di Carlo stated. "There hasn't been that platform available in the fluids community."

The equations used to determine the fluid flows are fairly straightforward, but the number of configurations needed to solve the problem required them to use the Ranger supercomputer at the Texas Advanced Computing Center (TACC). Ranger, funded by the National Science Foundation (NSF), served the national open science community for five years and was replaced by Stampede - the sixth most powerful supercomputer in the world - in January 2013.

Using several thousand processors concurrently, the researchers ran more than a 1,000 different problems, each representing a combination of different speeds, thicknesses, heights or offsets.

"Each of these gives us one transformation and together, they form what we call a library of transformations", Dino Di Carlo described.

With this method, Baskar Ganapathysubramaniam said it's possible to create a sequence of pillars that would push white cells to the boundaries of a channel to separate them, and then return them to the centre to be recaptured. He is also excited to study the potential of pillars to enhance mixing, which would be useful for removing heat from microprocessor fabrication as well as nano- and micro-scale controlled manufacturing.

Eventually, Dino Di Carlo and Baskar Ganapathysubramanian want to crowd-source the identification of critical flow transportations that will have implications to industry.

"Once we have the library, we envision creating a video game where we ask the player to design a specific kind of flow transformation", Baskar Ganapathysubramaniam explained. "They pick different pillars, stack them together, and see if they can get that configuration."

It's this kind of out-of-the-box thinking that characterizes the Iowa State scientist's research. Recently, partnering with Manish Parashar, the director of the Rutgers Discovery Informatics Institute (RDI2) at Rutgers University, and with Rutgers research professor Jaroslaw Zola, Baskar Ganapathysubramaniam undertook another experiment typical of his knack for creative problem-solving.

Using Federated Computing enabled by Comet Cloud, the project brought together a team of researchers with access to 10 supercomputers at six high performance computing (HPC) centres across three continents to continue and extend Baskar Ganapathysubramaniam's microfluidics simulations. The consortium included TACC's new Stampede system, as well as resources from the Department of Energy, FutureGrid, and international HPC centres.

Using the Comet Cloud, the researchers ran 12,845 flow simulations, consuming more than 2.5 million core-hours and generating 400 gigabytes of data over the course of 16 days. Initial results of the work are published on the Comet Cloud website and a paper about the project is under review.

"The experiment allowed us to explore an alternate paradigm for doing computational science and demonstrate that we can support applications using this paradigm", Manish Parashar stated. "Many applications have a similar work flow so this could be a model for supporting researchers without all of them going to one resource or another. This could be used to provide compute resources to a wide-range of applications."

The computations enabled by Comet Cloud brought Baskar Ganapathysubramaniam halfway to his dream of a complete library of microscopic fluid flows. However, the entire library would take much more computing. Fortunately, supercomputers are getting relentlessly faster, and with new technologies come new opportunities for industry, science and medicine.
Source: University of Texas at Austin, Texas Advanced Computing Center

Back to Table of contents

Primeur weekly 2013-07-15

Special

Supercomputer acting as a discovery machine for neuroscience ...

Exascale supercomputing

Jack Dongarra helps design software for the next generation of supercomputers receiving $1 million grant ...

The Cloud

e-Infrastructures for e-Sciences 2013 ...

EastWest Bank chooses HP to build private Cloud ...

IBM accelerates Cloud computing on System z with acquisition of CSL International ...

IBM closes acquisition of SoftLayer Technologies ...

L'Oréal Uruguay consolidates IT infrastructure into the private Cloud and reduces power consumption with IBM PureSystems ...

Oracle announces availability of Cloud Application Foundation, the #1 application foundation across conventional and Cloud environments ...

Oracle expands support for mobile and Cloud technologies with the latest Java development tools and framework ...

US Ignite recognizes RENCI and NC State for innovative app for monitoring power grids ...

EuroFlash

MINES ParisTech selects Bright Cluster Manager for materials science research cluster ...

European Commission to launch survey about Future Internet Assembly ...

Bull launches StoreWay Optima 4600: reaffirming its presence in the new-generation data handling market ...

DANTE celebrates 20 years of networking excellence ...

Oracle Enterprise Manager 12c deployed by CERN to manage its Oracle infrastructure ...

PRACE Winter School 2014 to be held in Tel Aviv, Israel ...

USFlash

Professor Jack Dongarra announces new supercomputer benchmark ...

CASL milestone validates reactor model using TVA data ...

DOST to strengthen weather forecasting to benefit farmers ...

Fujitsu M10 achieves world-record result on two-tier SAP SD standard application benchmark ...

Fujitsu integrates internal database platform using SPARC M10 servers ...

1Wealth Trading Company opines on IBM's foray into global banking ...

Golf Channel selects Oracle's Pillar Axiom Storage System to support rapid growth and new reality programming ...

Stephen F. Austin State University readies for growth; speeds registration, adds 8X capacity and unlocks IT for strategic projects ...

TACC supercomputers help microfluidics researchers make waves at the microscopic level ...