NSF: RESEARCHERS INVESTIGATE REMARKABLE APPROACH TO DESALINATION

FROM:  NATIONAL SCIENCE FOUNDATION 

Rice scientists reprogram protein pairs; attempt to modify bacterial decisions

Desalination has come a long way, baby.

On Aug. 3, some 330 years ago, a certain Captain Gifford of His Majesty's Ship Mermaid, was asked to conduct onboard his 24-gun Royal Naval vessel what may have been the first government-sponsored, scientific desalination experiment.

Diarist and later Secretary to the Admiralty Commission in England Samuel Pepys wrote to Gifford saying, "Whereas a Proposal has been made to Us of an Engine to be fixed in one of Our Ships for the making an Experiment of producing fresh water (at Sea) out of Salt."

We do not know whether Gifford actually conducted the experiment, but we do know desalination--the pulling of salt, minerals and other contaminants from soil and water--has become a worldwide concern. Population increases, the scarcity of fresh water in arid regions and a greater need for environmental cleanup has scientists scrambling to improve the process.

Researchers at Rice University in Houston, Texas, for example, are computationally investigating ways to rewire one of desalination's most useful tools: Bacteria.

Bacteria as an environmental cleaning agent is based on the microorganisms' ability to sense its environment, consume pollutants, break them down and excrete different, less-harmful substances than the original contaminant. But bacteria's response mechanisms can do many other things such as provide scientifically discrete information, diagnose levels of toxins in food and water, detect poisonous chemicals, report dangerous compounds in the human body and more.

That's why Jose Onuchic and Herbert Levine, co-directors of Rice's Center for Theoretical Biological Physics are working to treat bacteria like computers with the intention of reprograming them to perform specific activities.

The researchers have a plan to modify the proteins responsible for how bacteria respond to external stimuli, triggering the bacteria to predictably "decide" what actions to take when confronted with targeted environmental conditions.

Directed bacterial responses, the researchers believe, could revolutionize bacteria-based environmental cleanup, modern desalination and a host of medical and industrial applications.

The project, "Molecular Underpinnings of Bacterial Decision-Making" is one of a number of high-risk, potentially high-reward projects in the National Science Foundation's INSPIRE program. INSPIRE funds potentially transformative research that does not fit into a single scientific field, but crosses disciplinary boundaries.

"This research project by two highly respected scientists and their colleagues is an excellent example of basic research that can have tremendous societal benefits," says Kamal Shukla, program director in NSF's Division of Molecular and Cellular Biosciences.

The project is co-funded by NSF's Directorates for Biological Sciences and Mathematical and Physical Sciences.

Special molecules...

"The information encoded in the genome not only contains the blueprint for making proteins that fold into unique 3-D structures," says Onuchic explaining the basis of the research, "but also contains rich information about functional protein-protein interactions." Two-component signaling (TCS) systems, found mainly in bacteria, are an example of this idea.

TCS systems are the dominant means by which bacteria sense the environment and carry out appropriate actions. These signaling pathways, determine how bacteria respond to heat, sunlight, toxins, oxygen and other environmental stimuli.

They also regulate characteristics such as how poisonous bacteria are, their ability to produce disease, their nutrient uptake, their ability to yield secondary organic compounds, etc.

"Our research tries to understand and potentially re-engineer two-component signaling systems," says Ryan Cheng, a postdoctoral fellow at Rice working on the project. "A successful understanding of the special molecules that make up these systems would allow us to take them apart like Lego blocks and start building new blocks or circuits to achieve a specific goal."

Earlier this year in a paper published in the Proceedings of the National Academy of Sciences, the researchers revealed a scoring metric they devised to interpret how TCS proteins interact with each other and to predict how signaling modifications might affect TCS systems.

The metric, based on sequence data from the coevolution of TCS proteins, could form a framework for fine tuning TCS signals and/or mix-matching TCS proteins leading to novel bacterial responses.

"Many proteins have evolved to produce specific behaviors under the additional constraint that they physically bind to another protein," says Faruck Morcos, a postdoctoral fellow at Rice, whose research focuses on computational biology and bioinformatics.

"Random mutations that may occur to one protein over geological timescales need to occur alongside mutations to the second protein in order to maintain their ability to interact with one another."

However, when the signal between two proteins that have evolved together is modified or a protein is matched with a non-evolutionary signaling partner, directed responses can occur.

"Hence, by applying methods from statistical physics, one can quantify and extract the statistical connections associated with amino acid coevolution between families of interacting proteins," Morcos says, and determine which proteins can successfully signal each other to produce predetermined outcomes.

Practical applications...

With this operating premise, Onuchic and Levine, along with a small cadre of colleagues, plan to use the framework to engineer new, predictable behaviors in a model bacterium called Bacillus subtilis. Moreover, they plan to use B. subtilis as the prototype for changes in other protein-based systems.

"The potential applications for sanitation engineers are both numerous and profound," says Joshua Boltz, senior technologist and the biofilm technologies practice leader at CH2M HILL, a U.S. engineering company with major sewerage programs in London and Abu Dhabi, as well as clean water projects in the United States, Europe and Canada.

"Using membranes as a desalination tool to separate solids from liquids has emerged as a mature technology that is widely used globally," says Boltz zeroing in on an area where the research could benefit his industry. But, "A key concern with using membranes is their fouling, or a reduction in filtration capacity due to orifice clogging as a result of biofilms."

The researchers at Rice believe they can help reduce the buildup of biofilms in desalination equipment. Biofilms are thin layers of cells that stick to each other on a surface and have the ability to obstruct the flow of liquids in water purification systems.

"It has been shown experimentally that wrinkle formation in the biofilms of B. subtilis result from localized cell death," says Cheng. "Since cell death is regulated by two-component and related signaling systems, the potential for controlling the morphology and mechanical properties of biofilms exists."

The researchers surmise that this can perhaps be accomplished by introducing engineered bacteria to existing biofilms that can mechanically weaken existing biofilms through programmed cell death.

"While our research so far has exclusively dealt with quantifying the degree of interaction between a single pair of TCS proteins, a significant challenge will be to extend this work to make in vivo predictions," says Levine.

"Extending our methodology to complicated systems containing many potentially competing protein-protein interactions, e.g. living systems, will be a significant challenge for us in the future. We hope to extend this methodology to predictively understand how making a specific site-directed mutation affects the characteristics of an organism."

-- Bobbie Mixon,
Investigators
Jose Onuchic
Herbert Levine
Related Institutions/Organizations
William Marsh Rice University

BEETLE INSPIRES NEW MATERIALS DEVELOPED TO TRAP AND CHANNEL SMALL AMOUNTS OF FLUIDS

FROM:  NATIONAL SCIENCE FOUNDATION 

Quenching the world's water and energy crises, one tiny droplet at a time

In pursuit of beetle biomimicry, NSF-funded engineers develop new, textured materials to trap and channel small amounts of liquid

In the Namib Desert of Africa, the fog-filled morning wind carries the drinking water for a beetle called the Stenocara.

Tiny droplets collect on the beetle's bumpy back. The areas between the bumps are covered in a waxy substance that makes them water-repellant, or hydrophobic (water-fearing). Water accumulates on the water-loving, or hydrophilic, bumps, forming droplets that eventually grow too big to stay put, then roll down the waxy surface.

The beetle slakes its thirst by tilting its back end up and sipping from the accumulated droplets that fall into its mouth. Incredibly, the beetle gathers enough water through this method to drink 12 percent of its body weight each day.

More than a decade ago, news of this creature's efficient water collection system inspired engineers to try and reproduce these surfaces in the lab.

Small-scale advances in fluid physics, materials engineering and nanoscience since that time have brought them close to succeeding.

These tiny developments, however, have the prospect to lead to macro-scale changes. Understanding how liquids interact with different materials can lead to more efficient, inexpensive processes and products, and might even lead to airplane wings impervious to ice and self-cleaning windows.

Beetle bumps in the lab

Using various methods to create intricately patterned surfaces, engineers can make materials that closely mimic the beetle's back.

"Ten years ago no one had the ability to pattern surfaces like this at the nanoscale," says Sumanta Acharya, a National Science Foundation (NSF) program director. "We observed naturally hydrophobic surfaces like the lotus leaf for decades. But even if we understood it, what could we do about it?"

What researchers have done is create surfaces that so excel at repelling or attracting water they've added a "super" at the front of their description: superhydrophobic or superhydrophilic.

Many superhydrophobic surfaces created by chemical coatings are already in the marketplace (water-repellant shoes! shirts! iPhones!).

However, many researchers focus on materials with physical elements that make them superhydrophobic.

These materials have micro or nano-sized pillars, poles or other structures that alter the angles at which water droplets contact their surface. These contact angles determine whether a water droplet beads up like a teeny crystal ball or relaxes a bit and rests on the surface like a spilled milkshake.

By varying the layout of these surfaces, researchers can now trap, direct and repulse small amounts of water for a variety of new purposes.

"We can now do things with fluids we only imagined before," says mechanical engineer Constantine Megaridis at the University of Illinois at Chicago. Megaridis and his team have two NSF grants from the Engineering Directorate's Division of Chemical, Bioengineering, Environmental and Transport Systems.

"The developments have enabled us to create devices -- devices with the potential to help humanity -- that do things much better than have ever been done before," he says.

Megaridis has used his beetle-inspired designs to put precise, textured patterns on inexpensive materials, making microfluidic circuits.

Plastic strips with superhydrophilic centers and superhydrophobic surroundings that combine or separate fluids have the potential to serve as platforms for diagnostic tests (watch "The ride of the water droplets").

"Imagine you want to bring drops of blood or water or any liquid to a certain location," Megaridis explains. "Just like a highway, the road is the strip for the liquid to travel down, and it ends up collecting in a fluid storage tank on the surface." The storage tank could hold a reactive agent. Medical personnel could use the disposable strips to field-test water samples for E. coli, for example.

Devices such as these -- created in engineering labs -- are now working their way to the marketplace.

Water, water in the air

NBD Nanotechnologies, a Boston-based company funded by NSF's Small Business Technology Transfer program, aims to scale up the durability and functionality of surface coatings for industrial use.

One of the most impactful applications for superhydrophobic or hydrophobic research is improved condensation efficiency. When water vapor condenses to a liquid, it typically forms a film. That film is a barrier between the vapor and the surface, making it more difficult for other droplets to form. If that film can be prevented by whisking away droplets immediately after they condense--say, with a superhydrophobic surface--the rate of condensation increases.

Condensers are everywhere. They're in your refrigerator, car and air conditioner. More efficient condensation would let all this equipment function with less energy. Better efficiency is especially important in places where large-scale cooling is paramount, such as power plants.

"NBD makes more durable coatings that span large surface areas," says NBD Nanotechnologies senior scientist Sara Beaini. "Durability is an important factor, because when you're working on the micro level you depend on having a pristine surface structure. Any mechanical or chemical abrasion that distorts the surface structures can significantly reduce or eliminate the advantageous surface properties quickly."

NBD, which you might have guessed stands for Namib Beetle Design, has partnered with Megaridis and others to improve durability, the main challenge in commercializing superhydrophobic research. Power plant condensers with durable hydrophobic or superhydrophobic coatings could be more efficient. And with water and energy shortages looming, partnerships such as theirs that help to transfer this breakthrough from the lab to the outside world are increasingly valuable.

Other groups have applied hydrophobic patterning methods in clever ways.

Kripa Varanasi, mechanical engineer at MIT and NSF CAREER awardee, has applied superhydrophobic coatings to metal, ceramics and glass, including the insides of ketchup bottles. Julie Crockett and Daniel Maynes at Brigham Young University developed extreme waterproofing by etching microscopic ridges or posts onto CD-sized wafers.

With all these cross-country efforts, many are optimistic for a future where people in dry areas can harvest fresh water from a morning wind, and lower their energy needs dramatically.

"If someone comes up with a really cheap solution, then applications are waiting," said Rajesh Mehta, NSF Small Business Innovation Research/Small Business Technology Transfer program director.
-- Sarah Bates
Investigators
Constantine Megaridis
Sara Beaini
Julie Crockett
Kripa Varanasi
Brent Webb
R Daniel Maynes
Related Institutions/Organizations
University of Illinois at Chicago
Iowa State University
Brigham Young University
NBD Nanotechnologies, Inc.
Massachusetts Institute of Technology

NSF LOOKS FOR INTEGRATED COMPUTER MODELING SYSTEM

FROM:  NATIONAL SCIENCE FOUNDATION 

An integrated computer modeling system for water resource management

Water resource management involves numerous and often distinct areas, such as hydrology, engineering, economics, public policy, chemistry, ecology and agriculture, among others. It is a multi-disciplinary field, each with its own set of challenges and, in turn, its own set of computer models.

Jonathan Goodall's mission is "to take all these models from different groups and somehow glue them together," he says.

The National Science Foundation (NSF)-funded scientist and associate professor of civil and environmental engineering at the University of Virginia, is working to design an integrated computer modeling system that will seamlessly connect all the different models, enabling everyone involved in the water resources field to see the big picture.

"We are trying to computationally design models as components within a larger modeling framework so that we can integrate them," he says. "We want to be able to look at connections across the systems. For example, if you grow corn for ethanol for fuel, there are economic, water quality and agricultural aspects. How do you look at the issues and problems holistically? How do you look at all the components of the system and their interactions? We need to have this perspective if we want to understand all the consequences that happen to water, so we can manage it properly."

In doing so, "it will make the models we use to address water resources challenges more accurate and more robust," he says. "There are a lot of current water challenges that require sophisticated computational models."

He lists, among others, the Chesapeake Bay and the Gulf of Mexico, where fertilizer runoff has created dead zones; Southern California, which faces water shortages resulting from an over allocation of the Colorado River, and depleted groundwater resources; and floods along rivers in the Midwest, which prompted difficult decisions about releasing water through levies, and flooding lands, to avoid significant downstream flooding of cities, such as New Orleans.

"Models are used by water resource engineers every day to make predictions, such as when will a river crest following a heavy rain storm, or how long until a city's water supply runs dry during a period of drought," he adds. "One of the problems with our current models is that they often consider only isolated parts of the water cycle. Our work argues that when you look at all the pieces together, you will come up with a more comprehensive picture that will result in more accurate predictions."

His work was motivated and builds off an initiative funded by the European Union called Open Modeling Interface, known as OpenMI, originally conceived to facilitate the simulation of interacting processes, particularly environmental ones, by enabling independent computer models to exchange data as they ran.

Later, it became a generic solution to the problem of data exchange among any models, not just environmental, and soon after, not just models but software components, thereby connecting any combination of models, databases and analytical and visualization tools.

"We are trying to advance the software that bridges all the models," Goodall says. "One of the ways we are trying to strengthen the software is by trying to understand which kinds of problems it can handle."

For example, one challenge with bridging models of different systems is that one system might be more dynamic than another. In water resources, water movement in the atmosphere is more dynamic than water movement in deep aquifers.

"When the models are bridged, you need to allow for the flexibility that allows for these differences, otherwise you may run into significant computationally efficiencies," Goodall says.

"Also, you can quickly get into semantics problems, where different models have different vocabularies in their internal systems," he adds. "You may need to have a variable passed between two different models, but each model might have its own semantics for naming the variable. Computers do not handle this well without very specific runs, such as unified, controlled vocabulary, or clear rules for how to translate terminology between the two models."

These semantic differences can be complex, since variables in models may have slight differences in units or dimensions that, if not properly handled, can cause major problems when linking the models together, he says.

While this work applies generally across water resource modeling challenges, Goodall and his team are applying the work specifically to the challenge of modeling water and nutrient transport within watersheds. They are using the Neuse River Basin in North Carolina as a case study, running widely used models alongside their new modeling framework system in order to test and verify whether the new system reaches the same answers as well-tested models.

"The modeling framework system will then be used to go beyond the capabilities of current models by including new disciplines into the watershed modeling process, and then eventually allowing specialized groups to advance components of the overall modeling system," he says.

Goodall is conducting his research under an NSF Faculty Early Career Development (CAREER) award, which he received in 2009 as part of NSF's American Recovery and Reinvestment Act. The award supports junior faculty who exemplify the role of teacher-scholars through outstanding research, excellent education, and the integration of education and research within the context of the mission of their organization. NSF is funding his work with $408,042 over five years.

Goodall is using the educational component of the grant to plan courses, as well as a workshop for graduate students across different water-related disciplines who "will come up with a water problem that is cross-disciplinary, and then construct a model using the new modeling system that can really test our approach," he says. "We will be talking about the integration we have to do so we can have an integrated system where each person contributes his or her own component."

In 2013, Goodall volunteered as a mentor at a local middle school, where he guided students through design a city of the future and "specifically think about how that city would handle its storm water," he says. "We discussed the general problems cause by storm water," which is runoff caused by heavy rain storms, "falling on impervious surfaces such as roads, roofs and parking lots.

"Because this rain does not infiltrate into the soil, it can cause problems such as flooding or erosion of river beds," he adds. "We talked about the ways engineers handle storm water so that it does not cause these problems, as well as how the philosophy for handling storm water runoff has changed over the years."

While many urban storm water systems were designed in the past simply to remove rain water from a city as quickly as possible--for example, by using large concrete channels--the focus has changed in recent years. Many cities now employ new practices, such as using pervious surfaces for roads or lots, or capturing rainfall in ponds or rain gardens distributed across the city, allowing water to slowly infiltrate into the soil.

"Storm water is something that most people spend very little time thinking about and these students were no different," he says. "But as they began to think about the problem and the challenge of not only solving the problem, but doing it in a sustainable way, they were hooked. You could see their minds go as they tried to come up with solutions to the problem, and that was fun."

WATERSHEDS AFFECTED BY BARK BEETLES

 

Lodgepole Pines.  Credit:  Widimedia.

FROM: NATIONAL SCIENCE FOUNDATION
Ghosts of Forests Past: Bark Beetles Kill Lodgepole Pines, Affecting Entire Watersheds

In mountains across the Western United States, scientists are racing against time--against a tiny beetle--to save the last lodgepole pines.


Forests are bleeding out from the effects of the beetles, their conifers' needles turning crimson before the trees die.

Now, researchers are also hurrying to preserve the region's water quality, affected by the deaths of the pines.

"When these trees die," says hydrologist Reed Maxwell of the Colorado School of Mines, "the loss of the forest canopy affects hydrology and the cycling of essential nutrients."

Maxwell and other scientists recently published results of their study in the journal Biogeochemistry.

Co-authors, in addition to Maxwell, are Kristin Mikkelson, Lindsay Bearup, John McCray and Jonathan Sharp of the Colorado School of Mines, and John Stednick of Colorado State University. Mikkelson is the paper's first author.


Bark beetle numbers: heating up
"The mountain pine beetle outbreak in Western states has reached epidemic proportions," says Maxwell.

Bark beetles, as they're known, are native to the United States. They're so-named as the beetles reproduce in the inner bark of trees. Some species, such as the mountain pine beetle, attack and kill live trees. Others live in dead, weakened or dying hosts.

Massive outbreaks of mountain pine beetles in western North America since the mid-2000s have felled millions of acres of forests from New Mexico to British Columbia, threatening increases in mudslides and wildfires.

Climate change could be to blame. The beetles' numbers were once kept in check by cold winter temperatures and trees that had plenty of water to use as a defense.

But winters have become warmer, and droughts have left trees water-stressed and less able to withstand an onslaught of winged invaders.

"A small change in temperature leads to a large change in the number of beetles--and now to a large change in water quality," says Tom Torgersen, director of the National Science Foundation's (NSF) Water, Sustainability and Climate (WSC) Program, which funded the research.

WSC is part of NSF's Science, Engineering and Education portfolio of investments.

"Bark beetles have killed 95 percent of mature lodgepole pines," says Maxwell.

Death of a lodgepole pine

But the trees don't die immediately.

When beetles invade, a blue fungus spreads inside a tree's trunk, choking off transpiration and killing the tree in about two years.

The trees turn blood-red, then the ashen gray of death, dropping their needles to the forest floor.

"Some of the most important effects of bark beetles may be changes in the hydrologic cycle," says Maxwell, "via snow accumulation under trees and water transpiration from trees and other plants."

Biogeochemical changes may be even more important, he says, with carbon and nitrogen cycles interrupted.

"We're studying these hydrologic and geochemical processes through a combination of field work, lab research and computer modeling," says Maxwell.


Whither the beetles, so the trees, forests...and waters
Changes in tree canopies affect snowpack development and snowmelt.

For example, a lack of needles on branches lets more snow fall through the canopy--snow that would otherwise be caught on branches. A tree without needles also has less shade beneath it.

The result is a shallower snowpack, earlier snowmelt and less water in spring.

"The real question," Maxwell says, "is how these processes translate from individual trees to hillslopes to large watersheds."

Dead trees don't transpire water. Once a forest has died, this important flow of moisture from the ground to the atmosphere ceases.

That can mean a loss of as much as 60 percent of the water budget, although increases in ground evaporation or transpiration from understory shrubs and bushes may compensate for some of the lack.

"Combined with what's happening to snowpack depth," says Maxwell, "it becomes a complicated relationship that can change the timing and magnitude of spring runoff from snowmelt--and an entire year's water resources."

Tree mortality also appears to affect forest carbon and nitrogen cycles through increases in dissolved organic carbon.

"We've seen changes in drinking water quality in beetle-affected watersheds that are almost certainly related to high dissolved organic carbon levels," says Maxwell.

As Maxwell, Mikkelson, Bearup and colleagues discovered, there's a lag time between beetle infestation and water quality declines, "so tree and forest water transport processes are very likely involved," says Maxwell.


All watersheds great and small
The observations prompted the researchers to study processes at the individual tree and hillslope scale to better understand what's happening in watersheds large and small.

"Watersheds are complex, interrelated systems," says Maxwell, "which makes understanding them more challenging.

"We're developing complex, numerical models of bark beetle-infested watersheds that include our best understanding of how and where water flows. The models are allowing us to isolate individual processes by turning them on and off in 'what-if' scenarios."

Along with on-the-ground observations, he says, "they're showing us more of the complex story of pine beetle effects on Western watersheds.

"We now know that healthy watersheds ultimately depend on healthy forests."

Western streams and rivers soon may be part of dead and dying forests, surrounded only by the ghosts of lodgepole pines past.

HYDROLOGY AND CHANGES IN THE ARTIC LANDSCAPE

FROM: LOS ALAMOS NATIONAL LABORATORY

A team of scientists is working to understand how local changes in hydrology might bring about major changes to the Arctic landscape, including the possibility of a large-scale carbon release from thawing permafrost. Bryan Travis, an expert in fluid dynamics, is author of the Mars global hydrology numerical computer model, or MAGHNUM, used for calculating heat and fluid transport phenomena. (MAGHNUM was previously used to model hydrological phenomena under freezing conditions on other planets, including Mars.) Travis advanced the MAGHNUM software with a variety of improvements and additional components into a new program, called ARCHY, a comprehensive Arctic hydrology model. A LANL team's goal is to make ARCHY capable of accurately modeling Arctic topography, thawing, and erosion. Because it includes advective heat transport, ARCHY will help to predict how quickly and how extensively the Arctic permafrost will thaw.  Photo From:  Los Alamos National Laboratory.