Aug. 24, 2012

Failure the only option at the Mechanics Lab

BREAK TIME — Helena Jin and Kevin Nelson (both 8526) inspect the test setup for upcoming experiments to determine the breaking strength of weapon case lugs. (Photo by Dino Vournas) View large image.

by Patti Koning

For most people, breaking something is unplanned and unwelcome. But for Bonnie Antoun (8256) and the rest of the Micromechanics & Materials Mechanics Experimental Facilities staff, also known as the Mechanics Lab, it’s all in a day’s work.

Bonnie and the rest of the staff — Wei-Yang Lu, Bo Song, Helena Jin, Kevin Connelly, Andy Kung, and Kevin Nelson (8256) — will stretch, squeeze, torque, heat, cool, and pound any material to failure. Material systems of interest include metals, ceramics, structural foams, polymers, and composites.

They do this using equipment that can apply from 2 million pounds of load to less than 1 micronewton (µN) of load or 1 micrometer (µm) displacement; apply load at a rate of 220 inches per second; enforce strain rates of 1,000-5,000 per second; and capture it all with high speed and ultra-high speed optical cameras, and high-speed, high-resolution thermal imaging cameras.

To study the effects of complex stress history, Bonnie might subject a specific material to stress and twisting on the MTS 100 Kip axial and torsional test frame. “To see the effects of deformation history, we would apply tension and torsion to failure, then reverse the order on another sample, and continue repeating the experiment with different configurations,” she says.

Other equipment includes Hopkinson Bar test systems for testing materials at very high strain rates, flexible Endura Tech axial/torsional systems, atomic force microscope (AFM), scanning electronic microscope (SEM) loading stage for in-situ experiments under microscopes, and an extensive variety of loading frames and diagnostic equipment.

“All of our work is toward development of constitutive models that describe materials as a function of loading, rates, temperatures, environments, and other conditions,” Bonnie says.

The Mechanics Lab works closely with modeling and simulation in designing experiments. The physical experiment must exactly match the modeling boundary conditions so that the data can be used to then validate the model. 

“Our end-users are the material modelers, finite element analysts, and, finally, the weapons component and systems engineers,” she says. “Ultimately, we’re always trying to improve our understanding and modeling of complex events. As modeling and simulation capabilities have grown, they can handle more information. We are moving toward more volume measurements to study what goes on beneath the surface.”

Assessing the accuracy of models

Lu and Helena are developing X-ray computed tomography (XCT) techniques to understand what happens inside a material as it is loaded to failure. This new experimental capability is necessary to keep pace with advances in modeling and simulation. The Mechanics Lab hopes to acquire a high-resolution XCT device to gain more data for the modelers from these experiments.

Arthur Brown (8259) often turns to the Mechanics Lab for projects with experimental needs for material characterization, validation, or both. “They have helped me populate constitutive models for metals and composites over various loading rates and temperatures.  They have also performed complex experiments that I have used to assess the accuracy of model predictions,” he explains.

The Mechanics Lab may be physically located at the California site, but the group works equally with New Mexico organizations. The lab has teamed with the solid mechanics staff of the Engineering Sciences Center (1500) for many years.

“We have formed a uniquely integrated team of analysts and experimentalists, all working toward a common goal to better understand, design, assess, and predict physical response characteristics of our components and systems for many environmental threats,” says Frank Dempsey (1526).

“With computers getting larger and faster, enhancements to our predictive physics code capabilities require experimental validation. The Mechanics Lab staff is now an essential part of the analyst community with increasingly more challenges to predict, assess, design, and capture the physics correctly.”

About 75 percent of the group’s work is nuclear weapons-related. This has led to development of specific diagnostics and capabilities.

“There are few industries where you need to test to completely quantify materials to failure,” says Bonnie. “We need to understand not just when and how materials fail, but every step along the way.”

Much of the rest of the group’s work is Work for Others. In 2003, the Mechanics Lab played a key role in the space shuttle Columbia accident investigation (See the Sept. 5, 2003, issue of Sandia Lab News.)

Lu, Bonnie, and John Korellis (8254-1) led studies on the reinforced carbon-carbon (RCC) panels, thermal protection system (TPS) tiles, and foam impacting materials that provided data for the material response models critical to the computational studies. This led to a follow-on project with NASA for return-to-flight testing.

The Mechanics Lab has also worked on projects for the US Army, the US Navy, and DOE (non-nuclear weapons), and has been involved in several CRADAs, including Goodyear. In 2009, the group was involved in a DOE project to study liquid natural gas (LNG) cascading damage. “One concern is what would happen to the integrity of the tankers if there was a fire followed by rupturing of the tanks. The LNG is extremely cold, so it would quench the hot tanker steel immediately,” Bonnie says.

Currently, the group is studying potential materials for tubes on solar receivers for DOE. This project is unusual because of the duration of each experiment.

“Many of our experiments are finished in less than a minute,” says Bonnie. “The material in the solar receivers would be used for 30 years, so this is a test that will be going on for weeks.” To speed the aging process, researchers are imposing day and night cycles on materials of about a minute each.

The experiments may be fast, but the design and set-up are not. A new experiment can easily be more than a year in the making. Setting up experiments is a painstaking process as special fixtures often have to be designed to handle unusually shaped components.

Still, Bonnie says there is never a dull day in the Mechanics Lab.

“There is a balance between developing our own capabilities for the future and working on experiments happening right away,” she says. “Our work is all about helping others do their jobs better.”

-- Patti Koning

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Island hopping, bacterial style

The dark areas on this visualization of 40 genomes of the bacteria Brucella represent genomic islands — gene clusters that bacteria swap horizontally. Kelly Williams (8623, above) is studying genomic islands to better understand how pathogenicity naturally evolves in bacteria, which will aid in recognizing the unnatural pathogenicity of a synthesized bioweapon. (Photo by Dino Vournas) View large image.

by Patti Koning

We often think of evolution as a slow, orderly process. Over generations, incremental genomic changes are passed from parent to child through the tree of life. Not so with bacteria — their form of evolution is more akin to paper trading on the floor of the New York Stock Exchange, with genes being swapped horizontally in a tree of life that would be better described as a tumbleweed.

We know about the “Wild West” environment of bacterial evolution thanks to genomic sequencing. “More than 6,000 bacterial genomes have been sequenced to date, so we’re beginning to get a really good picture of what they look like,” says staff bioinformaticist Kelly Williams (8623).

Bacteria have a slow mutation rate, about one in a billion changes per base pair per generation, but genetic change can, in fact, occur rapidly in these organisms because of their ability to swap genes horizontally via mobile DNA elements called genomic islands. Genomic islands are a focus of Sandia bioinformatics research because they are the main source of bacterial genes of interest to biodefense and bioenergy applications, such as pathogenicity genes underlying microbial virulence and biodegrading enzyme genes that could be tailored for use in the biofuels industry.

Shedding light on how islands move

In an LDRD project, Kelly is using comparative genomics to better understand the structure and content of genomic islands. His first step was to write a computer algorithm that aligns multiple bacterial genomes in chromosomal order for easy visualization of their mobile elements. He has used this algorithm to order and visualize 40 genomes of the bacteria Brucella, and is now moving onto Rickettsia and other bacteria of interest.

“It’s a quick, visual way to focus on the islands and begin in-depth analysis of island genomic sites and arrangements, as well as their phylogenetic distributions,” says Kelly. “This analysis will shed light on how islands move, evolve, and cooperate combinatorially to promote pathogenicity.”

Together with developing visualization tools, Kelly also is building a database of known pathogenicity islands and more basic reference databases for Sandia’s growing program in biology and bioinformatics. “The ultimate goal is to use this information to machine learn the ability to predict pathogenicity genes,” he says.

This is where Kelly’s research interest in bacterial evolution via genomic islands fits into Sandia’s broader national security mission. The understanding of how pathogenicity naturally evolves in bacteria can be used to identify unnatural evolution of pathogenicity, in other words, a synthesized bioweapon.

Bioengineering used to leave behind “toolmarks” that enabled researchers to identify engineered biological agents (EBA) as such. Today’s biosecurity challenge is that EBAs are more sophisticated and can escape such detection, but even in the “Wild West” there are still rules governing the horizontal gene transfer that occurs in genomic islands.

Kelly, together with collaborators Owen Solberg and Joe Schoeniger (both 8623), is working toward a computational tool to measure the “naturalness” of a suspect organism in terms of novel gene combinations.

“This is just one critical area where bioinformatics can aid in biodefense,” says Cathy Branda, manager of Systems Biology Department 8623. “We are harnessing the incredible amount of data made available by advanced genetic sequencing technology to further our understanding of basic biology, which in turn allows us to pinpoint certain processes like horizontal gene transfer.”

Makes sense to focus on genomic solutions

Sandia, like other research institutions, is developing a bioinformatics capability hand-in-hand with the technological revolution in genomic sequencing. “Sequencing has become so fast and sophisticated that it makes sense to focus on genomic solutions to problems in biodefense, energy, and the clinical world,” she says.

Kelly brings to Sandia deep expertise in phylogenetic characterization of sequence datasets. He earned his bachelor’s degree from the University of California, Santa Barbara in physiology and cell biology and his doctorate from University of California, San Diego in biology. Before joining Sandia, Kelly spent seven years as an assistant professor of biology at Indiana University and five years as a research investigator at the Virginia Bioinformatics Institute at Virginia Tech.

Kelly initially joined Sandia to work on the RapTOR Grand Challenge, which helped lay important groundwork in bioinformatics. “This is an area in which we’d all like to see Sandia grow,” says Cathy.

-- Patti Koning

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DNA fingerprinting to go

Summer interns Harrison Edwards and Daniel Lee (both 8125) work with the Battlefield DNA Analysis amplification module. (Photo by Dino Vournas) View large image.

by Patti Koning

On popular television shows like CSI, it often seems that detectives send DNA crime scene evidence to the forensic lab and have their results in hand after a single commercial break.

“In real life, an entire laboratory filled with technicians and PhD-level scientists using equipment worth thousands and even millions of dollars is at work analyzing those samples, a process that can take hours if not days,” says Michael Bartsch (8125). “That fade-to-commercial glosses over a lot of time, effort, and expertise.

Mike is leading a project for the US Army Criminal Investigation Laboratory (USACIL) that aims to make the practical process of forensic DNA analysis more closely match the duration of that commercial break, at least in part. Over the last year, Mike and the science and engineering team in Advanced Systems Engineering & Deployment Dept. 8125 have been developing a prototype Battlefield Automated DNA Analysis Sampling System, an instrument designed to enable rapid DNA fingerprinting (genotyping) in a field-portable package.

Currently, DNA samples collected in Afghanistan, for example, may be sent to a containerized laboratory at a US or Coalition base in-theater, or to the USACIL headquarters outside Atlanta for forensic analysis. The Battlefield DNA Analysis System will ultimately help bring that laboratory capability to investigation sites near the front lines and provide results in about an hour.

“It takes time to transport a sample back to the lab,” says Ken Patel (8125). “The forward-deployed forensics labs reduce the travel time, but still require highly trained scientists and specialized equipment. The Army has a real interest in rapidly processing DNA samples to aid decision-making for emerging military and intelligence needs” And, as in the case of confirming the identity of Osama Bin Laden, the turnaround time required for DNA analysis can be critical.

In particular, the Army wants to use rapid DNA analysis in investigations of improvised explosive devices (IEDs) to identify bomb-makers and their associates. Even after an explosion, investigators can often collect usable DNA from IED remnants. Other potential applications include screening at checkpoints and detention centers or determining which individuals may have been present at places of interest, such as terrorist training camps.

The Battlefield DNA System brings together four traditional benchtop DNA sample preparation steps: extraction, quantification, amplification, and separation. Amplification, or polymerase chain reaction (PCR), is critical for touch and trace DNA samples like those collected from IED components.

“You can start with a very small amount of DNA, even just one copy, and amplify it until you have thousands of copies that you can readily measure,” says Mike. “It’s a very powerful technique that makes it possible to obtain DNA analysis from an actual fingerprint. It’s also very challenging to implement outside a laboratory environment.”

Digital Microfluidic Hub

Key to bringing together these four steps in an automated, portable platform is the Sandia Digital Microfluidic Hub, a tool for manipulating and transporting microliter-scale sample droplets using electrostatic forces. Initially developed for the RapTOR (Rapid Threat Organism Recognition) Grand Challenge, this technology won an R&D 100 Award this year (Lab News, June 29, 2012) and last year garnered the Society for Laboratory Automation and Screening’s innovation award (Lab News, April 22, 2011).

The Hub acts like a network router, directing, assembling, translating, and scheduling the movement of discrete packets — in this case DNA and reagent droplets — to and from the four sample processing modules.

“The Microfluidic Hub allows us to optimize each of those modules independently. They don’t need to be compatible with each other, only with the Hub,” says Ken. “It really streamlines what would otherwise be an almost intractable engineering problem.”

This difficult, multidisciplinary problem requires a diverse and well-integrated project team.

“Engineering team lead Ron Renzi [8125] contributes a strong mechanical design and systems engineering ethic. Electrical engineer Jim Van DeVreudge [8125] has the expertise to seamlessly interface hardware controls with the software developed by our programmer, Dan Knight [independent contractor]. And Mark Claudnic’s [8233-1] CAD designs and assemblies are brought to life by Jerry Inman [8125], an expert technologist in electronic and microfluidic systems,” Ken says.

With a couple months remaining on the project, the team has built and tested prototype hardware for most elements of the DNA analysis platform. Summer interns are currently testing an automated DNA extraction module that uses a commercially available protocol for isolating DNA from cheek swab samples, but adapts it to work without a benchtop centrifuge or other bulky laboratory equipment — all in a footprint smaller than a shoebox.

The PCR amplification component also is nearing completion. This module uses a novel rapid thermal cycling approach for which the team has filed a technical advance and hopes to submit a patent application. “We’ve got the testbed PCR prototype integrated to a level where you introduce the sample, push a button, and walk away. Ninety minutes later, you have a result,” says Mike.

Even the separation module, a fairly typical capillary electrophoresis design, uses unconventional components to enhance capability. In this case, a low-cost spectrometer the size of two decks of playing cards allows the system to work with virtually any commercially available DNA fingerprinting kit without the need to reconfigure system optics or include multiple kit-specific filter sets.

In the next few months, the modules will be connected through the Microfluidic Hub and the proof of concept prototype will be delivered to USACIL. “It will be a benchtop-integrated prototype that they can test and give us feedback,” says Mike. “Moving forward, we will optimize for size, speed, and performance.”

Forensics is not a traditional area of research for Sandia, but Ken expects that to change. “It plays well to our strengths in microfluidics, bioassays, and system integration,” he says. “This opportunity could open new areas of business for Sandia in developing sample preparation platforms for field and laboratory use. The FBI, for example, may not need portable analysis, but they have huge casework backlogs that could make the speed of our system very attractive.” -- Patti Koning

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