Graphene Is Strongest Material in the World Even with Defects

Graphene remains the strongest material ever measured and, as Professor Hone once put it, so strong that "it would take an elephant, balanced on a pencil, to break through a sheet of graphene the thickness of Saran Wrap.” —Illustration by Andrew Shea for Columbia Engineering

In a new study, published in Science May 31, 2013, Columbia Engineering researchers demonstrate that graphene, even if stitched together from many small crystalline grains, is almost as strong as graphene in its perfect crystalline form. This work resolves a contradiction between theoretical simulations, which predicted that grain boundaries can be strong, and earlier experiments, which indicated that they were much weaker than the perfect lattice.

Graphene consists of a single atomic layer of carbon, arranged in a honeycomb lattice. “Our first Science paper, in 2008, studied the strength graphene can achieve if it has no defects—its intrinsic strength,” says James Hone, professor of mechanical engineering, who led the study with Jeffrey Kysar, professor of mechanical engineering. “But defect-free, pristine graphene exists only in very small areas. Large-area sheets required for applications must contain many small grains connected at grain boundaries, and it was unclear how strong those grain boundaries were. This, our second Science paper, reports on the strength of large-area graphene films grown using chemical vapor deposition (CVD), and we’re excited to say that graphene is back and stronger than ever.”

The study verifies that commonly used methods for post-processing CVD-grown graphene weaken grain boundaries, resulting in the extremely low strength seen in previous studies. The Columbia Engineering team developed a new process that prevents any damage of graphene during transfer. “We substituted a different etchant and were able to create test samples without harming the graphene,” notes the paper’s lead author, Gwan-Hyoung Lee, a postdoctoral fellow in the Hone lab. “Our findings clearly correct the mistaken consensus that grain boundaries of graphene are weak. This is great news because graphene offers such a plethora of opportunities both for fundamental scientific research and industrial applications.”

                                              Profs. James Hone and Jeffrey Kysar
In its perfect crystalline form, graphene (a one-atom-thick carbon layer) is the strongest material ever measured, as the Columbia Engineering team reported in Science in 2008—so strong that, as Hone observed, “it would take an elephant, balanced on a pencil, to break through a sheet of graphene the thickness of Saran Wrap.” For the first study, the team obtained small, structurally perfect flakes of graphene by mechanical exfoliation, or mechanical peeling, from a crystal of graphite. But exfoliation is a time-consuming process that will never be practical for any of the many potential applications of graphene that require industrial mass production.

Currently, scientists can grow sheets of graphene as large as a television screen by using chemical vapor deposition (CVD), in which single layers of graphene are grown on copper substrates in a high-temperature furnace. One of the first applications of graphene may be as a conducting layer in flexible displays.

“But CVD graphene is ‘stitched’ together from many small crystalline grains—like a quilt—at grain boundaries that contain defects in the atomic structure,” Kysar explains. “These grain boundaries can severely limit the strength of large-area graphene if they break much more easily than the perfect crystal lattice, and so there has been intense interest in understanding how strong they can be.”

The Columbia Engineering team wanted to discover what was making CVD graphene so weak. In studying the processing techniques used to create their samples for testing, they found that the chemical most commonly used to remove the copper substrate also causes damage to the graphene, severely degrading its strength.

WATCH VIDEO
Click on the Video to watch Prof. James Hone take us on a tour of his synthesis lab in the Northwest Corner Building, where he grows graphene and nanotubes.

Their experiments demonstrated that CVD graphene with large grains is exactly as strong as exfoliated graphene, showing that its crystal lattice is just as perfect. And, more surprisingly, their experiments also showed that CVD graphene with small grains, even when tested right at a grain boundary, is about 90% as strong as the ideal crystal.

“This is an exciting result for the future of graphene, because it provides experimental evidence that the exceptional strength it possesses at the atomic scale can persist all the way up to samples inches or more in size,” says Hone. “This strength will be invaluable as scientists continue to develop new flexible electronics and ultrastrong composite materials.”

Strong, large-area graphene can be used for a wide variety of applications such as flexible electronics and strengthening components—potentially, a television screen that rolls up like a poster or ultrastrong composites that could replace carbon fiber. Or, the researchers speculate, a science fiction idea of a space elevator that could connect an orbiting satellite to Earth by a long cord that might consist of sheets of CVD graphene, since graphene (and its cousin material, carbon nanotubes) is the only material with the high strength-to-weight ratio required for this kind of hypothetical application.

The team is also excited about studying 2D materials like graphene. “Very little is known about the effects of grain boundaries in 2D materials,” Kysar adds. “Our work shows that grain boundaries in 2D materials can be much more sensitive to processing than in 3D materials. This is due to all the atoms in graphene being surface atoms, so surface damage that would normally not degrade the strength of 3D materials can completely destroy the strength of 2D materials. However with appropriate processing that avoids surface damage, grain boundaries in 2D materials, especially graphene, can be nearly as strong as the perfect, defect-free structure.”

The study was supported by grants from the Air Force Office of Scientific Research and the National Science Foundation.

—by Holly Evarts

Source: Columbia University

3-D culture system for pancreatic cancer has potential to change therapeutic approaches

A team of researchers has developed a method to grow pancreatic tissue in a three-dimensional culture system, called organoids. The scientists are able to use tissue not only from laboratory mouse models, but also from human patients. The technology promises to change the way pancreatic cancer research is done, offering a path to personalized treatment approaches in the future. Credit: D. Tuveson/ Cold Spring Harbor Laboratory

Cold Spring Harbor and Bethpage, N.Y. -- Pancreatic cancer is one of the most deadly forms of cancer, with only 6 percent of patients surviving five years after diagnosis. Today, Cold Spring Harbor Laboratory (CSHL) and The Lustgarten Foundation jointly announce the development of a new model system to grow both normal and cancerous pancreatic cells in the laboratory. Their work offers the potential to change the way pancreatic cancer research is done, allowing scientists to interrogate the pathways driving this devastating disease while searching for new drug targets.

In work published in Cell, the research team describes a three-dimensional "organoid" culture system for pancreatic cancer. Co-led by David Tuveson, CSHL Professor and Director of Research for The Lustgarten Foundation, and Hans Clevers, Professor and Director of the Hubrecht Institute and President of the Royal Netherlands Academy of Arts and Sciences, the team developed a method to grow pancreatic tissue not only from laboratory mouse models, but also from human patient tissue, offering a path to personalized treatment approaches in the future.

All cancer research relies on a steady supply of cells -- both normal and cancerous -- that can be grown in the laboratory. By comparing normal cells to cancer cells, scientists can then identify the changes that lead to disease. However, both types of pancreatic cells have been extremely difficult to culture in the laboratory.

Furthermore, the normal ductal cells that are able to develop into pancreatic cancer represent about 10 percent of the cells in the pancreas, complicating efforts to pinpoint the changes that occur as the tumor develops. Until now, scientists have been entirely unable to culture human normal ductal pancreatic cells under standard laboratory conditions. 

Because of these limitations, most pancreatic cancer research relies on genetically engineered mouse models of the disease, which can take up to one year to generate. "With this development, we are now able to culture both mouse and human organoids, providing a very powerful tool in our fight against pancreatic cancer," explains Tuveson.

The organoids are entirely made up of ductal cells, eliminating the surrounding cell types that often contaminate samples from the pancreas. They grow as hollow spheres within a complex gel-like substance filled with growth-inducing factors and connecting fibers. Once they have grown to a sufficient size, the organoids can be transplanted back into mice, where they fully recapitulate pancreatic cancer. "We now have a model for each stage in the progression of the disease," says Chang-Il Hwang, Ph.D., one of the lead authors working in The Lustgarten Foundation's Pancreatic Cancer Research Lab at CSHL directed by Dr. Tuveson.

Traditionally, cancer cells are isolated during surgery or autopsies. Unfortunately, approximately 85 percent of cancer patients are ineligible for surgery at the time of diagnosis, either because the tumor is entwined in critical vasculature or the disease has progressed too far. Researchers therefore have had limited access to patient samples. The new research provides a way for scientists to grow organoids from biopsy material, which is comparatively easy to obtain. "Biopsies are the standard for diagnosis," says Dannielle Engle, Ph.D., also a lead author on the paper. "We can now rapidly generate organoids from any patient, which offers us the potential to study the disease in a much wider population."

The team is now working to create a repository of pancreatic tumor samples, coordinating with the National Cancer Institute. "We hope to make this available to the entire pancreatic cancer research community," says Tuveson. Additionally, Lindsey Baker, Ph.D., another lead author of the paper, has started holding an "organoid school" for other researchers, and has already taught six laboratories from around the world this technique.

Source: Cold Spring Harbor Laboratory

3-D printed Shelby Cobra

This Shelby Cobra sports car, 3D-printed at Department of Energy's Manufacturing Demonstration Facility at Oak Ridge National Laboratory, will be on display this week at the Detroit Auto Show Technology Showcase. Credit: Image courtesy of Oak Ridge National Laboratory

With a 3-D printed twist on an automotive icon, the Department of Energy's Oak Ridge National Laboratory is showcasing additive manufacturing research at the 2015 North American International Auto Show in Detroit.

ORNL's newest 3-D printed vehicle pays homage to the classic Shelby Cobra in celebration of the racing car's 50th anniversary. The 3-D printed Shelby will be on display January 12-15 as part of the show's inaugural Technology Showcase.

Researchers printed the Shelby car at DOE's Manufacturing Demonstration Facility at ORNL using the Big Area Additive Manufacturing (BAAM) machine, which can manufacture strong, lightweight composite parts in sizes greater than one cubic meter. The approximately 1400-pound vehicle contains 500 pounds of printed parts made of 20 percent carbon fiber.
Recent improvements to ORNL's BAAM machine include a smaller print bead size, resulting in a smoother surface finish on the printed pieces. Subsequent work by Knoxville-based TruDesign produced a Class A automotive finish on the completed Shelby.

"Our goal is to demonstrate the potential of large-scale additive manufacturing as an innovative and viable manufacturing technology," said Lonnie Love, leader of ORNL's Manufacturing Systems Research group. "We want to improve digital manufacturing solutions for the automotive industry."

The team took six weeks to design, manufacture and assemble the Shelby, including 24 hours of print time. The new BAAM system, jointly developed by ORNL and Cincinnati Incorporated, can print components 500 to 1000 times faster than today's industrial additive machines. ORNL researchers say the speed of next-generation additive manufacturing offers new opportunities for the automotive industry, especially in prototyping vehicles.

"You can print out a working vehicle in a matter of days or weeks," Love said. "You can test it for form, fit and function. Your ability to innovate quickly has radically changed. There's a whole industry that could be built up around rapid innovation in transportation."

The Shelby project builds on the successful completion of the Strati, a fully 3-D printed vehicle created through a collaboration between Local Motors and ORNL.

The lab's manufacturing and transportation researchers plan to use the 3-D printed Shelby as a laboratory on wheels. The car is designed to "plug and play" components such as battery and fuel cell technologies, hybrid system designs, power electronics, and wireless charging systems, allowing researchers to easily and quickly test out new ideas.

Source: Oak Ridge National Laboratory

Sculpting costumes with 3-D printers is 'the way theater is headed,' say theater education experts

Baylor junior Mackenzie Dobbs, a theatre performance major, in a witch's costume decorated with beans and mushrooms produced from a 3D printer. Credit: Drapers: Sylvia Fuhrken and Ryan Schapp, Photo by Jared Tseng

Three-dimensional printers, which already have churned out jewelry, prosthetic limbs and one fully functioning car, are taking the stage -- literally -- in another arena: live theater.

They allow greater speed, flexilibity, creativity -- and can appease directors who change their minds mid-rehearsal.

Synthetic beans and mushrooms -- accessories for the cursed, hump-backed witch in a Baylor University production of the musical "Into the Woods" -- recently emerged from a little machine tucked away in a corner of the costume shop at Baylor. And that's only the beginning for the new printer, says former Disneyland costume designer/wardrobe coordinator Joe Kucharski, assistant professor of theatre arts at Baylor.

Using his computer mouse and some free software, Kucharski tugged, flattened and pinched a digital "ball of clay" into the desired shapes: rotting vegetables, including two dozen beans and a dozen mushrooms. That done, the 3D printer heated and spun plastic cord into the delicate thread to create the costume elements for the witchy wardrobe.

Depending on the size and how complicated a design is, 3D printing may take 20 minutes to a couple hours.

"You can set a few buttons and walk away during printing," Kucharski said. "You can customize and print multiples, and you can use colors that are the whole range of the rainbow.

"Designers are always thinking, 'How can we design quickly but keep it adjustable so we're ready if the director says, 'Well, we're kinda there. . .'? We can go back and tweak quickly."

The printers have been used in film and fashion, and "it's a great application for scenic design in theater, too," he said. "You can use miniatures created on a small-scale model and save time instead of carving little details."

The 3D printer is rapidly becoming part of the "designer tool bag." While students still need to learn traditional drawing and creating, incorporating 3D technology into curriculum for costume and prop design can give them an edge in the job market.

"This is the way theatre is going," said Stan Denman, Ph.D., chair and professor of theatre arts at Baylor. "This even lets us create items that are no longer being produced -- like brooches or hatpins -- for period plays. Otherwise, because those things are antiques, the cost is prohibitive.

"This also can be helpful if you have an item that has to be broken in a scene," he said. "You can have multiple items to replace it for repeat performances."

Source: Baylor University

Printing in the hobby room: Paper-thin and touch-sensitive displays on various materials

Paper- thin and touch-sensitive displays on various materials.
Credit: Image courtesy of University Saarland

Until now, if you want to print a greeting card for a loved one, you can use colorful graphics, fancy typefaces or special paper to enhance it. But what if you could integrate paper-thin displays into the cards, which could be printed at home and which would be able to depict self-created symbols or even react to touch? Those only some of the options computer scientists in Saarbrücken can offer. They developed an approach that in the future will enable laypeople to print displays in any desired shape on various materials and therefore could change everyday life completely.

For example: A postcard depicts an antique car. If you press a button, the back axle and the steering wheel rim light up in the same color. Two segments on a flexible display, which have the same shape as those parts of the car, can create this effect. Computer scientists working with Jürgen Steimle printed the post card using an off-the-shelf inkjet printer. It is electro-luminescent: If it is connected to electric voltage, it emits light. This effect is also used to light car dashboards at night.

Steimle is leader of the research group "Embodied Interaction" at the Cluster of Excellence "Multimodal Computing and Interaction." Simon Olberding is one of his researchers. "Until now, this was not possible," explains Olberding. "Displays were mass-produced, they were inflexible, they always had a rectangular shape." Olberding and Steimle want to change that. The process they developed works as follows: The user designs a digital template with programs like Microsoft Word or Powerpoint for the display he wants to create.

By using the methods the computer scientists from Saarbrücken developed, called "Screen Printing" and "Conductive Inkjet Printing," the user can print those templates. Both approaches have strengths and weaknesses, but a single person can use them within either a few minutes or two to four hours. The printing results are relatively high-resolution displays with a thickness of only 0.1 millimeters. It costs around €20 to print on a DIN A4 page; the most expensive part is the special ink. Since the method can be used to print on materials like paper, synthetic material, leather, pottery, stone, metal and even wood, two-dimensional and even three-dimensional shapes can be realized. Their depiction can either consist of one segment (surface, shape, pattern, raster graphics), several segments or variously built-up matrixes. "We can even print touch-sensitive displays," says Olberding.

The possibilities for the user are various: displays can be integrated into almost every object in daily life -- users can print not only on paper objects, but also on furniture or decorative accessories, bags or wearable items. For example, the strap of a wristwatch could be upgraded so that it lights up if a text message is received. "If we combine our approach with 3D printing, we can print three-dimensional objects that display information and are touch-sensitive," explains Steimle.

Source: University Saarland

Smelly discovery challenges effectiveness of antimicrobial textiles

University of Alberta textiles scientist Rachel McQueen has found that anti-odor clothing may not be living up to its promise. Credit: University of Alberta

Anti-odour clothing may not be living up to its promise, and an ALES researcher is saying it could all be a matter of how the product was tested.

In two separate experiments, Human Ecology researcher Rachel McQueen and her team found that some antimicrobial textiles were far more effective at performing their advertised tasks in the lab than in testing on humans. In one experiment, the fabrics were designed to help lower the risk of infection; in the second, the fabric was treated with a silver compound, which can be marketed preventing odour in clothing.

"We aren't necessarily seeing the same results in the lab about antimicrobial activity translating into antimicrobial activity when we're wearing them next to our bodies in real life," she said.

The first experiment analyzed the effectiveness of three different textiles coated in antimicrobials triclosan, a zinc pyrithione derivative and a silver chloride-titanium dioxide compound. After putting the fabric on people's arms under plastic film for 24 hours, the silver-chloride titanium dioxide compound hardly eliminated any bacteria. Overall, they found the in vivo -- tested on humans -- results were not comparable with in vitro -- tested in the lab -- results in how they prevented microorganisms from surviving in the textile.

The second test had similar results, and tested whether polyester textiles treated with bioactive concentrations of an antimicrobial silver chloride compound reduced armpit odour and bacterial populations. Although lab testing showed antimicrobial activity, the treated fabrics did not lower odour or bacterial intensity in in vivo testing.

McQueen said that anything from sweat to the proteins in the human body can disrupt the antimicrobial properties of a fabric.

"In reality, when it goes to the point that it gets put on a textile... it may not have the same level of effectiveness as the ones they studied," she said.

McQueen said these findings highlight the importance of in vivo testing, which is less common than in vitro testing, in textile product development. But, because the textiles appear to be effective at reducing bacteria in the lab, she said they may be advertised as being anti-odourous, although they may not necessarily be so when actually worn.

So, for now, McQueen suggests thinking twice before trusting textile's advertised claims.

"It's just a real spectrum to how effective they may truly be. So I'd probably say, from a consumer's point of view, if you're actually buying something that says it's antimicrobial, it may not be," she said. "I think that's important to consider in relation to a lot of claims made about textiles, that is, to be skeptical about the claims marketers make."

McQueen's research was recently published in the International Journal of Clothing Science and Technology.

Source: University of Alberta

Live adaptation of organ models in the OR

The non-deformed liver model (red) adapts to the deformed surface profile (blue). Credit: Graphics: Dr. Stefanie Speidel, KIT, in Medical Physics, 41

During minimally invasive operations, a surgeon has to trust the information displayed on the screen: A virtual 3D model of the respective organ shows where a tumor is located and where sensitive vessels can be found. Soft tissue, such as the tissue of the liver, however, deforms during breathing or when the scalpel is applied. Endoscopic cameras record in real time how the surface deforms, but do not show the deformation of deeper structures such as tumors. Young scientists of the Karlsruhe Institute of Technology (KIT) have now developed a real-time capable computation method to adapt the virtual organ to the deformed surface profile.

The principle appears to be simple: Based on computer tomography image data, the scientists construct a virtual 3D model of the respective organ, including the tumor, prior to operation. During the operation, cameras scan the surface of the organ and generate a stiff profile mask. To this virtual mold, the 3D model then is to fit snuggly, like jelly to a given form. The Young Investigator Group of Dr. Stefanie Speidel analyzed this geometrical problem of shape adaptation from the physical perspective. "We model the surface profile as electrically negative and the volume model of the organ as electrically positive charged," Speidel explains. "Now, both attract each other and the elastic volume model slides into the immovable profile mask." The adapted 3D model then reveals to the surgeon how the tumor has moved with the deformation of the organ.

Simulations and experiments using a close-to-reality phantom liver have demonstrated that the electrostatic-elastic method even works when only parts of the deformed surface profile are available. This is the usual situation at the hospital. The human liver is surrounded by other organs and, hence, only partly visible by endoscopic cameras. "Only those structures that are clearly identified as parts of the liver by our system are assigned an electric charge," says Dr. Stefan Suwelack who, as part of Speidel's group, wrote his Ph.D. thesis on this subject. Problems only arise, if far less than half of the deformed surface is visible. To stabilize computation in such cases, the KIT researchers can use clear reference points, such as crossing vessels. Their method, however, in contrary to others does not rely on such references from the outset.

In addition, the model of the KIT researchers is more precise than conventional methods, because it also considers biomechanical factors of the liver, such as the elasticity of the tissue. So for instance, the phantom liver used by the scientists consists of two different silicones: A harder material for the capsule, i.e. the outer shell of the liver, and a softer material for the inner liver tissue.

As a result of their physical approach, the young scientists also succeeded in accelerating the computation process. As shape adaptation was described by electrostatic and elastic energies, they found a single mathematical formula. Using this formula, even conventional computers equipped with a single processing unit only work so quickly that the method is competitive. Contrary to conventional computation methods, however, the new method is also suited for parallel computers. Using such a computer, the Young Investigator Group now plans to model organ deformations stably in real time.

Source: Karlsruhe Institute of Technology

Self-repairing software tackles malware

Eric Eide, University of Utah research assistant professor of computer science, stands in the computer science department's "Machine Room" where racks of web servers sit. It is on these computers that Eide, U computer science associate professor John Regehr, and their research team created and tested A3, a suite of computer applications that defeat malware and automatically repair the damage it causes. The project could help lead to better consumer software defenses.
Credit: Dan Hixson/University of Utah College of Engineering

University of Utah computer scientists have developed software that not only detects and eradicates never-before-seen viruses and other malware, but also automatically repairs damage caused by them. The software then prevents the invader from ever infecting the computer again.

A3 is a software suite that works with a virtual machine -- a virtual computer that emulates the operations of a computer without dedicated hardware. The A3 software is designed to watch over the virtual machine's operating system and applications, says Eric Eide, University of Utah research assistant professor of computer science leading the university's A3 team with U computer science associate professor John Regehr. A3 is designed to protect servers or similar business-grade computers that run on the Linux operating system. It also has been demonstrated to protect military applications.

The new software called A3, or Advanced Adaptive Applications, was co-developed by Massachusetts-based defense contractor, Raytheon BBN, and was funded by Clean-Slate Design of Resilient, Adaptive, Secure Hosts, a program of the Defense Advanced Research Projects Agency (DARPA). The four-year project was completed in late September.

There are no plans to adapt A3 for home computers or laptops, but Eide says this could be possible in the future.

"A3 technologies could find their way into consumer products someday, which would help consumer devices protect themselves against fast-spreading malware or internal corruption of software components. But we haven't tried those experiments yet," he says.

U computer scientists have created "stackable debuggers," multiple de-bugging applications that run on top of each other and look inside the virtual machine while it is running, constantly monitoring for any out-of-the-ordinary behavior in the computer.

Unlike a normal virus scanner on consumer PCs that compares a catalog of known viruses to something that has infected the computer, A3 can detect new, unknown viruses or malware automatically by sensing that something is occurring in the computer's operation that is not correct. It then can stop the virus, approximate a repair for the damaged software code, and then learn to never let that bug enter the machine again.

While the military has an interest in A3 to enhance cybersecurity for its mission-critical systems, A3 also potentially could be used in the consumer space, such as in web services like Amazon. If a virus or attack stops the service, A3 could repair it in minutes without having to take the servers down.

To test A3's effectiveness, the team from the U and Raytheon BBN used the infamous software bug called Shellshock for a demonstration to DARPA officials in Jacksonville, Florida, in September. A3 discovered the Shellshock attack on a Web server and repaired the damage in four minutes, Eide says. The team also tested A3 successfully on another half-dozen pieces of malware.

Shellshock was a software vulnerability in UNIX-based computers (which include many web servers and most Apple laptops and desktop computers) that would allow a hacker to take control of the computer. It was first discovered in late September. Within the first 24 hours of the disclosure of Shellshock, security researchers reported that more than 17,000 attacks 

by hackers had been made with the bug.

"It is a pretty big deal that a computer system could automatically, and in a short amount of time, find an acceptable fix to a widespread and important security vulnerability," Eide says. 

"It's pretty cool when you can pick the Bug of the Week and it works."

Now that the team's project into A3 is completed and proves their concept, Eide says the U team would like to build on the research and figure out a way to use A3 in cloud computing, a way of harnessing far-flung computer networks to deliver storage, software applications and servers to a local user via the Internet.

The A3 software is open source, meaning it is free for anyone to use, but Eide believes many of the A3 technologies could be incorporated into commercial products.

Other U members of the A3 team include research associate David M. Johnson, systems programmer Mike Hibler and former graduate student Prashanth Nayak.

Source: University of Utah

Software models more detailed evolutionary networks from genetic data

Phylogenetic networks depict the movement of genetic sequences from one species to another as a means of showing where horizontal gene transfer may have taken place. Software by scientists at Rice University aims to reveal far more about species’ evolutionary histories than traditional tree models are able to. Credit: Luay Nakhleh/Rice University

The tree has been an effective model of evolution for 150 years, but a Rice University computer scientist believes it's far too simple to illustrate the breadth of current knowledge.

Rice researcher Luay Nakhleh and his group have developed PhyloNet, an open-source software package that accounts for horizontal as well as vertical inheritance of genetic material among genomes. His "maximum likelihood" method, detailed this month in the Proceedings of the National Academy of Sciences, allows PhyloNet to infer network models that better describe the evolution of certain groups of species than do tree models.

"Inferring" in this case means analyzing genes to determine their evolutionary history with the highest probability -- the maximum likelihood -- of connections between species. Nakhleh and Rice colleague Christopher Jermaine recently won a $1.1 million National Science Foundation grant to analyze evolutionary patterns using Bayesian inference, a statistics-based technique to estimate probabilities based on a data set.

To build networks that account for all of the genetic connections between species, the software infers the probability of variations that phylogenetic trees can't illustrate, such as horizontal gene transfers. These transfers circumvent simple parent-to-offspring evolution and allow genetic variations to move from one species to another by means other than reproduction.

Biologists want to know when and how these transfers happened, but tree structures conceal such information. "When horizontal transfer occurs, as with the hybridization of two species, the tree model becomes inadequate to describe the evolutionary history, and networks that incorporate horizontal gene transfer become the more appropriate model," Nakhleh said.

Nakhleh's Java-based software accounts for incomplete lineage sorting, in which clues to gene evolution that don't match the established lineage of species appear in the genetic record.

"We are the first group to develop a general model that will allow biologists to estimate hybridization while accounting for all these complexities in evolution," Nakhleh said.

Most existing programs for phylogenetics (the study of evolutionary relationships) ignore such complexities. "They end up overestimating the amount of hybridization," Nakhleh said. 

"They start seeing lots of complexities in the data and say, 'Oh, it's complex here; it must be hybridization,' and end up inferring too much. Our method acknowledges that part of the complexity has nothing to do with hybridization; it has to do with other random processes that happened during evolution."

The Rice researchers used two data sets to test the new program. One, a computer-generated set of data that mimics a realistic model of evolution, allowed them to evaluate the accuracy of the program. The second involved multiple genomes of mice found across Europe and Asia. "There have been stories about mice hybridizing," Nakhleh said. "Now that we have the first method to allow for systematic analysis, we ran it on a very large amount of data from five mouse samples and we detected hybridization" -- most notably in the presence of a genetic signal from a mouse in Kazakhstan that found its way to mice in France and Germany, he said.

Nakhleh hopes evolutionary biologists will use PhyloNet to take a fresh look at the massive amount of genomic data collected over the past few decades. "The exciting thing for me about this is that biologists can now systematically go through lots of data they have generated and check to see if there has been hybridization."

Source: Rice University

Cheaper 3-D virtual reality system: Powerful enough for a gamer, made for an engineer

It's like a scene from a gamer's wildest dreams: 12 high-definition, 55-inch 3D televisions all connected to a computer capable of supporting high-end, graphics-intensive gaming.
Credit: Image courtesy of Brigham Young University

It's like a scene from a gamer's wildest dreams: 12 high-definition, 55-inch 3D televisions all connected to a computer capable of supporting high-end, graphics-intensive gaming.

On the massive screen, images are controlled by a Wii remote that interacts with a Kinnect-like Bluetooth device (called SmartTrack), while 3D glasses worn by the user create dizzying added dimensions.

But this real-life, computer-powered mega TV is not for gaming. It's for engineering.

Welcome to Brigham Young University's VuePod, a 3D immersive visualization environment run by BYU's Department of Civil and Environmental Engineering. Student-built and operated, under the supervision of civil engineering professor Dan Ames, the VuePod is changing the way engineers are viewing environmental engineering challenges.

"This is gold," said fellow BYU civil engineering professor Kevin Franke. "This technology has the ability to revolutionize my job as an earthquake engineer."

That's because the VuePod allows users to virtually fly over, wander through or hover above 3D environments that are otherwise difficult to visit. The images are created by point data from aircraft equipped with LIDAR (think RADAR, but with lasers). The LIDAR scans the landscape and records millions of data points that are then viewed as an image on the VuePod. Point data can also be created from stitched-together photographs taken from low-cost drones, which is Franke's research focus.

One set of data currently available for study in the VuePod captured a canyon area beneath a plateau in southern Idaho. With 3D glasses and the Wii controller, a user can virtually drop down into the canyon from above, and then fly from one end to the other.

As cool as it is to fly through a canyon, the real engineering application comes in when you combine two sets of data for the same canyon, taken five years a part. With the second set of data, changes in the natural landscape that are invisible to the human eye become clear as day. Thanks to the VuePod's massive 108-square-foot screen, all of the image-making data can be presented for viewing.

"Our eyes and our brains are so amazing; we need to take full advantage of them," Ames said. "That's the value of this project: we're presenting more information for the human eyes to detect changes."

In addition to natural change detection, the VuePod has the potential to assist in infrastructure monitoring -- such as tracking how highways hold up (or slough and crack) over time and seeing the affect on buildings after severe weather or earthquakes.

While the VuePod is certainly not the first immersive visualization system in academia, it may just be the most cost efficient built to date. Some systems cost as much as $10 million to build and maintain, while BYU's VuePod just barely topped the $30,000 mark.

Ames details how BYU was able to build such a powerful system for so little in a new paper published by the Journal of Computing in Civil Engineering.

"Our question has been: How can we make this technology accessible?" Ames said. "We're trying to determine the threshold for getting the most function at the most affordable cost. Ultimately, the goal is to take an expensive tool and make it cheaper for an everyday engineering firm to use."

And even though Ames and his students have achieved that, they believe much more can be done.

"We want whoever reads this paper to be able to build a better system than we built," he said.

Source: Brigham Young University