Back to Table of contents

Primeur weekly 2016-05-09

Focus

NIST's Robert Bohn and Oxford University's David Wallom expand on Cloud standards and the Cloud landscape ...

With trust, openness and empowerment, there is a bright future for Cloud computing, according to Microsoft's Elena Bonfiglioli ...

Quantum computing

IBM makes quantum computing available on IBM Cloud to accelerate innovation ...

Quantum logical operations realized with single photons ...

Focus on Europe

Celebrating HPC and research at University College London ...

Still time to save on ISC 2016 registration - Register by May 11 ...

Current status of the Flemish supercomputer ...

Middleware

Bright Computing names Bill Griffin as Chief Financial Officer ...

Hardware

Invitation to participate in HPC Site Census study ...

CSRA to deliver high capacity connectivity to support education priorities in Alabama ...

Cray reports first quarter 2016 financial results ...

Applications

SDSC researchers publish book on using GPU accelerators for nanosciences ...

Movidius announces deep learning accelerator and Fathom software framework ...

GPU-powered systems take top spot and set new record in Student Supercomputer Competition ...

Fine-tuning forecasts of nighttime storms on the plains ...

Sudden collapse: Supercomputing spotlight on gels ...

BSC and IrsiCaixa create bioinformatics method to predict the effectiveness of antiretroviral drugs with different HIV mutations ...

University of Wyoming faculty have until May 22 to apply for supercomputer use ...

Webinar on performance tuning and optimization of GROMACS ...

IBM and SK Holdings C&C Alliance brings Watson and the cognitive era to South Korea ...

Sudden collapse: Supercomputing spotlight on gels


Snapshot of gel simulation, periodic cell. With permission from the Journal of Rheology (Zia et al, Journal of Rheology, 58(5), 2014).
2 May 2016 Austin - What exactly is life? A popular idea with some scientists in the early 1800s held that life was constructed of yet-unseen building blocks of a fundamental life force. The success around that time with microscopes in seeing tiny things for the first time helped drive the idea that through an eyepiece one could find the core of life.

Botanist Robert Brown saw something in 1827 through the single lens microscope he built that astounded him. Pollen grains suspended in water danced around, animated by what he guessed might be the fundamental life force. Like any good scientist, he tested his hypothesis, by watching the motion of non-living things: floating bits of coal and of glass pulverized into microscopic dust. But they too danced in water, seemingly animated by some unseen source. Life didn't cause the motion - but what did was a mystery. As long as the particles were very small, they moved. Robert Brown published his findings in detail with more questions than answers. His zigzag motion of microscopic floating objects would baffle scientists and survive nearly a century of misinterpretation and argument under its enduring name, Brownian motion.

Explanations of Robert Brown's discovery were key to the discoveries that set much of 20th century science in motion. In 1905 the physicist Albert Einstein used the mathematical description of Brownian motion to help prove the existence atoms and molecules. And thus began a scientific field called microrheology, the study of material properties by tracking the Brownian motion of tiny suspended particles.

Looking beyond just particles dancing in water, much study has since followed, focusing on the flow of fluids in which microscopically small particles, droplets, or bubbles are suspended, so-called "colloids". When microscopic forces between the particles causes them to bond together into a network, they form a solid-like scaffold immersed in a fluid, forming a soft solid - which engineers utilize for building artificial tissue scaffolds and injectable pharmaceuticals, for example. But these materials are everywhere around us in nature and common household products as well, in the form of shampoo, Jell-o, and yogurt, to name a few.

Chemical engineering researcher Roseanna Zia has begun to shed light on the microscale world of colloidal gels - liquids dispersed in a solid medium as a gel. Sometimes the gels act like liquids, and sometimes they act like a solid, such as hair gel that squirts out of a tube like a liquid, but retains its shape sitting in your hand.

"Colloidal gels are actually soft solids, but we can manipulate their structure to produce 'on-demand' transitions from liquid-like to solid-like behaviour that can be reversed many times", Roseanna Zia stated. Roseanna Zia is an Assistant Professor of Chemical and Biomolecular Engineering at Cornell University.

The tiny solid particles in a colloidal gel - invisible to the naked eye - bind together and form a 3D scaffolding of filaments throughout the medium. One can break that scaffolding by simply squirting the material or dragging a surface across it. For example, toothpaste or hair gel - after it has been squirted - will sit on a toothbrush like a solid because its scaffold has re-formed on its own due to the attractions between the particles.

New research by Roseanna Zia and colleagues is focused on understanding why gel scaffolding can suddenly collapse on its own. "This research grew out of our initial quest to understand why some gels, once they are formed and placed in a container, remain intact but then later they suddenly, seemingly inexplicably, collapse under their own weight. This unpredictable behaviour has presented a roadblock in the design of technological materials like tissue scaffolds, injectable pharmaceuticals, petroleum drilling fluids, and even commercial household fluids. It's a very broad and technologically pressing problem", Roseanna Zia stated.

A survey of the recent scientific literature surrounding this problem revealed that some basic questions about how colloidal gels behave in general, even without collapse, hadn't yet been answered. Open questions included how does the gel scaffolding evolve over time after it forms, if it evolves at all; what does its structure look like; and do its properties change over time? Even today, the challenges of precisely imaging these microscopic structures as they evolve rapidly over time pushes the limits of imaging techniques.

"This is where dynamic simulations play a really important role in scientific discovery", Roseanna Zia stated. "In these simulations we can track and view changes in the material all the way down to individual particles. There, another challenge computationally is that these gels could form long network-length scales, and the simulation has to capture that. This means that to simulate a realistic system, one must develop a very large simulation."

In reality, even a small sample of a gel comprises billions of of particles that interact to form the gel. Before Roseanna Zia and colleagues began their research, the largest prior simulations included only a few thousand gel particles, which did not produce the full range of structural variations in a gel that give it its unique properties. Using supercomputers, she was able to increase that number to over 750,000 and, in so doing, more faithfully capture the way the complex scaffold rearranges over time.

Roseanna Zia and her colleagues utilized over seven million service units on the Stampede supercomputer at the Texas Advanced Computing Center (TACC), awarded through an allocation by XSEDE, the eXtreme Science and Engineering Discovery Environment. "Stampede high performance computational access was a game-changer", Roseanna Zia stated.

"I often say that I'm Stampede's biggest fan, not just in terms of computational access, but also, the technical staff are world-class in terms of making available the best computational resources, training, and help services. They're literally available 24/7 and always solve problems really quickly. I can't say enough good things about the TACC staff."

Zia used Stampede to simulate how gels evolve over time. The particle strands of a gel scaffolding coarsen and grow thicker as they age, leading to changes in the mechanical properties. "The next question was, how, at a microscopic length scale, do gels rearrange themselves?" Roseanna Zia asked.

"It was already known that gels are built from an interconnected network of strands, with each strand made up of many bonded-together particles. What was not known was, how are these particles packed together? Are individual particles all frozen into place like the solid-like macroscopic scaffold?" Roseanna Zia stated. They discovered that the interior of each strand is a frozen, disordered solid, like a glass. "But on the surface of these strands, the particles are actually a lot more mobile. The surface of each strand is covered with weakly bonded particles - the surface is like a liquid." And it turned out that Brownian motion plays a key role in how they evolve.

Brownian motion allows the particles to break free of their bonds, allowing them to crawl along the network, settling into more energetically favourable positions via a process called diffusion.

"They might temporarily detach from the network due to a Brownian fluctuation, then get pulled back down onto the network and get trapped in a cage of other particles", Roseanna Zia stated. These roving particles migrate from cage to cage and eventually sink down into the strand as more particles get deposited on top of them. "We call that 'cage-trapping', and once they fall down into these energy wells, they rarely come out. They become trapped there essentially forever, and that's how gels coarsen with age", Roseanna Zia stated.

Understanding the theory behind these transitions can translate to real-world applications, such as helping research why the airway mucus - a colloidal gel - of people with cystic fibrosis can thicken, resist flow and possibly threaten life. It will also be a piece of the puzzle in understanding more rapid transitions in gels, such as sudden collapse. Their current work focuses on the response of such gels to imposed flow and to gravity.

The simulated gel aging and coarsening are described in the study, "A micro-mechanical study of coarsening and rheology of colloidal gels: Cage building, cage hopping, and Smoluchowski's ratchet", published in the September/October 2014 issue ofThe Journal of Rheology. Funding was provided by the National Science Foundation Grant No. CBET-0754078 and the Office of Naval Research Grant No. N00014-14-1-0744.

Study co-author Benjamin Landrum, also at Cornell with the Zia Research Group, created the computer model of nearly a million particles using the simulation package called LAMMPS, the Large-scale Atomic/Molecular Massively Parallel Simulator.

"LAMMPS is optimized to spread out the particles onto many, many processors", Roseanna Zia stated. She explained that the code basically applies a set of rules based on the physics equations that govern the forces acting on the particles, such as attraction, collision, Brownian motion, and so on. Combining LAMMPS and XSEDE was the key to carrying out the massively parallelized large-scale simulations required to accurately model gel behaviour.

Roseanna Zia's research group got help from the Campus Champions programme of XSEDE to get started on using its high performance computational resources. Campus Champions are typically but not limited to campus IT faculty and staff that are trained by and maintain close ties to XSEDE. They help researchers access XSEDE resources, get allocations and training, and more.

"Our campus champion is Susan Mehringer, and she's been a tremendous help", stated Roseanna Zia. "I didn't know anything about XSEDE. She's introduced us to XSEDE and guided me through the process of acquiring user credentials and applying for start-up allocations. A champion has their own allocation for researchers to do initial benchmarking, an important step in the proposal process. Most importantly, she gave us guidance for preparing for our first research allocation proposal. Having a campus champion right here made a huge difference for our early success with XSEDE."

Susan Mehringer is the Assistant Director of the Center for Advanced Computing, Cornell University. "As a Campus Champion", stated Susan Mehringer, "I'm always eager to introduce faculty to XSEDE capabilities, from advanced computation to educational opportunities for their students. We enjoy working with Dr. Zia and other researchers to facilitate their timely access to and efficient use of XSEDE resources."

Back in the lab, other work in the Zia Group addresses the difficulties of modelling colloidal dispersions with free-flowing fluid systems that arise from the strong hydrodynamic coupling between particles. In other words, when one particle moves it disturbs and moves other particles, even far away. The coupling decays at a rate of only one over the separation distance, compared to one over the distance squared for say, electrostatic or gravitational interactions. Trying to incorporate those interactions between millions of particles quickly overwhelms even the most powerful supercomputers.

"Sometimes people decide that it's too difficult, and they just throw the hydrodynamic coupling approximations away", Roseanna Zia stated. "There are some situations where that's a reasonable approximation. There are other situations where that leads to major inaccuracies in predicted suspension behaviour. In those cases, we just have to roll up our sleeves and do the physics."

Roseanna Zia and colleagues addressed these ideas in a recent study, "Pair mobility functions for rigid spheres in concentrated colloidal dispersions", published in December 2015 in theJournal of Chemical Physics. In this case she set up a computational scenario to test whether the coupling can be neglected in crowded suspensions. One case where such interactions can be neglected is when particles are fixed in place and block or "screen" the long-distance hydrodynamic interactions. One can think of the particles like the walls of an office cubicle, separating two sides of a fluid allowed to flow around it, a set-up scientists call Brinkmann screening.

"The idea has been proposed that in very crowded systems like the interior of a cell, the dense population leads to a screening effect, and thus one can neglect these difficult-to-model interactions", Roseanna Zia stated. "We know that the more particles you put in a confined space, the less mobile they are. Think of being on a crowded subway. The more people get on, the harder it is to move, and good luck getting out the door when it comes to your stop." So they decided to test whether the restriction of motion from crowding leads to the same "screening" as having fixed particles.

"It turns out that screening does not occur", Roseanna Zia stated. "Crowding does not give the same behaviour as the fixed-particle case. Regardless of how dense the suspension is, as long as the spheres are free to move, they're coupled very strongly, over very long distances. And so we do have to carefully model those hydrodynamic interactions."

Those interactions are guiding what's next in research for the Zia Group. "The most important thing is solving that 'collapse problem'", Roseanna Zia stated. "This is our current top goal, figuring out what's going on with this sudden collapse."

Good things can come from finding out why things go bad quickly for the gel scaffolds. "We have a lot of interest in this, not only from our peers working in this area but also in industry, such as petroleum and personal care products", Roseanna Zia stated.

Colloidal gels and other complex fluids are the materials of the future, according to Roseanna Zia. "People have engineered these materials to chemically control insulin delivery; to control the release of drugs; to stimulate bone formation to repair defects in bones; they're even being used to encapsulate compounds to deliver into cells; to transplant cells; to do tissue repair; and even, if you can imagine post-surgery pain treatments injecting materials that are long-lasting pain treatments, so that a patient doesn't have to take a drug that affects their entire physiology", Roseanna Zia stated. "They're even being sought about for using repair and prevention materials for soldiers in battle to help them with diagnostics in battlefield conditions."

"I'd like people to know that I work with the support of a fantastic research group of my graduate students here at Cornell University, in particular, Ben Landrum, the graduate student who worked closely with me in our initial gel studies and simulations", Roseanna Zia stated, "as well as my collaborator Bill Russel from Princeton University, who played an important role in our first big gel-aging study".

You can find out more about the Zia Group at http://www.icse.cornell.edu/ziagroup/ . Funding resources are the National Science Foundation, the Office of Naval Research, and XSEDE.
Source: University of Texas at Austin - Texas Advanced Computing Center - TACC

Back to Table of contents

Primeur weekly 2016-05-09

Focus

NIST's Robert Bohn and Oxford University's David Wallom expand on Cloud standards and the Cloud landscape ...

With trust, openness and empowerment, there is a bright future for Cloud computing, according to Microsoft's Elena Bonfiglioli ...

Quantum computing

IBM makes quantum computing available on IBM Cloud to accelerate innovation ...

Quantum logical operations realized with single photons ...

Focus on Europe

Celebrating HPC and research at University College London ...

Still time to save on ISC 2016 registration - Register by May 11 ...

Current status of the Flemish supercomputer ...

Middleware

Bright Computing names Bill Griffin as Chief Financial Officer ...

Hardware

Invitation to participate in HPC Site Census study ...

CSRA to deliver high capacity connectivity to support education priorities in Alabama ...

Cray reports first quarter 2016 financial results ...

Applications

SDSC researchers publish book on using GPU accelerators for nanosciences ...

Movidius announces deep learning accelerator and Fathom software framework ...

GPU-powered systems take top spot and set new record in Student Supercomputer Competition ...

Fine-tuning forecasts of nighttime storms on the plains ...

Sudden collapse: Supercomputing spotlight on gels ...

BSC and IrsiCaixa create bioinformatics method to predict the effectiveness of antiretroviral drugs with different HIV mutations ...

University of Wyoming faculty have until May 22 to apply for supercomputer use ...

Webinar on performance tuning and optimization of GROMACS ...

IBM and SK Holdings C&C Alliance brings Watson and the cognitive era to South Korea ...