Showing posts with label CHEMISTRY. Show all posts
Showing posts with label CHEMISTRY. Show all posts

Wednesday, June 17, 2015

SCIENTISTS STUDY CORAL REEFS AND OCEAN ACIDIFICATION

FROM:  NATIONAL SCIENCE FOUNDATION
Coral reefs defy ocean acidification odds in Palau
Palau reefs show few of the predicted responses

Will some coral reefs be able to adapt to rapidly changing conditions in Earth's oceans? If so, what will these reefs look like in the future?

As the ocean absorbs atmospheric carbon dioxide (CO2) released by the burning of fossil fuels, its chemistry is changing. The CO2 reacts with water molecules, lowering ocean pH (making it more acidic) in a process known as ocean acidification.

This process also removes carbonate, an essential ingredient needed by corals and other organisms to build their skeletons and shells.

Scientists are studying coral reefs in areas where low pH is naturally occurring to answer questions about ocean acidification, which threatens coral reef ecosystems worldwide.

Palau reefs dodge ocean acidification effects

One such place is Palau, an archipelago in the far western Pacific Ocean. The tropical, turquoise waters of Palau's Rock Islands are naturally more acidic due to a combination of biological activity and the long residence time of seawater in their maze of lagoons and inlets.

Seawater pH within the Rock Island lagoons is as low now as the open ocean is projected to reach as a result of ocean acidification near the end of this century.

A new study led by scientists at the Woods Hole Oceanographic Institution (WHOI) found that coral reefs in Palau seem to be defying the odds, showing none of the predicted responses to low pH except for an increase in bio-erosion--the physical breakdown of coral skeletons by boring organisms such as mollusks and worms.

A paper reporting the results is published today in the journal Science Advances.

"This research illustrates the value of comprehensive field studies," says David Garrison, a program director in the National Science Foundation's Division of Ocean Sciences, which funded the research through NSF's Ocean Acidification (OA) Program. NSF OA is supported by the Directorates for Geosciences and for Biological Sciences.

"Contrary to laboratory findings," says Garrison, "it appears that the major effect of ocean acidification on Palau Rock Island corals is increased bio-erosion rather than direct effects on coral species."

Adds lead paper author Hannah Barkley of WHOI, "Based on lab experiments and studies of other naturally low pH reef systems, this is the opposite of what we expected."

Experiments measuring corals' responses to a variety of low pH conditions have shown a range of negative effects, such as fewer varieties of corals, more algae growth, lower rates of calcium carbonate production (growth), and juvenile corals that have difficulty constructing skeletons.

"Surprisingly, in Palau where the pH is lowest, we see a coral community that hosts more species and has greater coral cover than in the sites where pH is normal," says Anne Cohen, co-author of the paper.

"That's not to say the coral community is thriving because of the low pH, rather it is thriving despite the low pH, and we need to understand how."

When the researchers compared the communities found on Palau's reefs with those in other reefs where pH is naturally low, they found increased bio-erosion was the only common feature.

"Our study revealed increased bio-erosion to be the only consistent community response, as other signs of ecosystem health varied at different locations," Barkley says.

The riddle of resilience

How do Palau's low pH reefs thrive despite significantly higher levels of bio-erosion?

The researchers aren't certain yet, but hope to answer that question in future studies.

They also don't completely understand why conditions created by ocean acidification seem to favor bio-eroding organisms.

One theory--that skeletons grown under more acidic conditions are less dense, making them easier for bio-eroding organisms to penetrate--is not the case on Palau, Barkley says, "because we don't see a correlation between skeletal density and pH."

Though coral reefs cover less than one percent of the ocean, these diverse ecosystems are home to at least a quarter of all marine life. In addition to sustaining fisheries that feed hundreds of millions of people around the world, coral reefs protect thousands of acres of coastlines from waves, storms and tsunamis.

"On the one hand, the results of this study are optimistic," Cohen says. "Even though many experiments and other studies of naturally low pH reefs show that ocean acidification negatively affects calcium carbonate production, as well as coral diversity and cover, we are not seeing that on Palau.

"That gives us hope that some coral reefs--even if it is a very small percentage--might be able to withstand future levels of ocean acidification."

Along with Barkley and Cohen, the team included Yimnang Golbuu of the Palau International Coral Reef Center, Thomas DeCarlo and Victoria Starczak of WHOI, and Kathryn Shamberger of Texas A&M University.

The Dalio Foundation, Inc., The Tiffany & Co. Foundation, The Nature Conservancy and the WHOI Access to the Sea Fund provided additional funding for this work.

-NSF-

Thursday, May 28, 2015

OCEAN PHOSPHORUS CYCLE AND THE ROLE OF MICROBES

FROM:  NATIONAL SCIENCE FOUNDATION
Revealing the ocean's hidden fertilizer
Tiny marine plants play major role in phosphorus cycle
Phosphorus is one of the most common substances on Earth.

An essential nutrient for every living organism--humans require approximately 700 milligrams per day--we're rarely concerned about consuming enough because it is in most of the foods we eat.

Despite its ubiquity and living organisms' dependence on it, we know surprisingly little about how it moves, or cycles, through the ocean environment.

Scientists studying the marine phosphorous cycle have known that phosphorus was absorbed by plants and animals and released back to seawater in the form of phosphate as these plants and animals decay and die.

But a growing body of research hints that microbes in the ocean transform phosphorus in ways that remain a mystery.

Hidden role of ocean's microbes

A new study by a research team from the Woods Hole Oceanographic Institution (WHOI) and Columbia University reveals for the first time a marine phosphorus cycle that is much more complex than previously thought.

The work also highlights the important but previously hidden role that some microbial communities play in using and breaking down forms of this essential element.

A paper reporting the findings is published this week in the journal Science.

"A reason to be excited about this elegant study is in the paper's last sentence: 'the environmental, ecological and evolutionary controls ...remain completely unknown,'" says Don Rice, program director in the National Science Foundation's (NSF) Division of Ocean Sciences, which funded the research through its Chemical Oceanography Program. "There's still a lot we don't know about the sea."

The work is also supported by an NSF Dimensions of Biodiversity grant.

"This is an exciting new discovery that closes a fundamental knowledge gap in our understanding of the marine phosphorus cycle," says the paper's lead author Ben Van Mooy, a biochemist at WHOI.

Much like phosphorus-based fertilizers boost the growth of plants on land, phosphorus in the ocean promotes the production of microbes and tiny marine plants called phytoplankton, which compose the base of the marine food chain.

Phosphonate mystery

It's been unclear exactly how phytoplankton are using the most abundant forms of phosphorus found in the ocean--phosphates and a strange form of phosphorus called phosphonates.

"Phosphonates have always been a huge mystery," Van Mooy says.

"No one's been able to figure out exactly what they are, and more importantly, if they're made and consumed quickly by microbes, or if they're just lying around in the ocean."

To find out more about phosphonates and how microbes metabolize them, the researchers took samples of seawater at a series of stations during a research cruise from Bermuda to Barbados.

They added phosphate to the samples so they could see the microbes in action.

The research team used ion chromatography onboard ship for water chemistry analyses, which allowed the scientists to observe how quickly microbes reacted to the added phosphate in the seawater.

"The ion chromatograph [IC] separates out the different families of molecules," explains Van Mooy.

"We added radioactive phosphate, then isolated the phosphonate to see if the samples became radioactive, too. It's the radioactive technique that let us see how fast phosphate was transformed to phosphonate."

Enter the microbes

The researchers found that about 5 percent of the phosphate in the shallow water samples was taken up by the microbes and changed to phosphonates.

In deeper water samples, which were taken at depths of 40 and 150 meters (131 feet and 492 feet), about 15 to 20 percent of the phosphates became phosphonates.

"Although evidence of the cycling of phosphonates has been mounting for nearly a decade, these results show for the first time that microbes are producing phosphonates in the ocean, and that it is happening very quickly," says paper co-author Sonya Dyhrman of Columbia University.

"An exciting aspect of this study was the application of the IC method at sea. In near-real-time, we could tell that the phosphate we added was being transformed to phosphonate."

Better understanding of phosphorus cycle

A better understanding of phosphorus cycling in the oceans is important, as it affects the marine food web and, therefore, the ability of the oceans to absorb atmospheric carbon dioxide.

The researchers say that solving the mystery of phosphonates also reinforces the need to identify the full suite of phosphorus biochemicals being produced and metabolized by marine microbes, and what physiological roles they serve for these cells.

"Such work will help us further resolve the complexities of how this critical element is cycled in the ocean," Dyhrman adds.

Grants from the Simons Foundation also supported the work.

-NSF-
Media Contacts
Cheryl Dybas, NSF

VERY PROMISING QUANTUM DOTS

FROM:  NATIONAL SCIENCE FOUNDATION
Many uses in researching quantum dots

These nanoparticles can achieve higher levels of energy when light stimulates them.

It's easier to dissolve a sugar cube in a glass of water by crushing the cube first, because the numerous tiny particles cover more surface area in the water than the cube itself. In a way, the same principle applies to the potential value of materials composed of nanoparticles.

Because nanoparticles are so small, millions of times smaller than the width of a human hair, they have "tremendous surface area," raising the possibility of using them to design materials with more efficient solar-to-electricity and solar-to-chemical energy pathways, says Ari Chakraborty, an assistant professor of chemistry at Syracuse University.

"They are very promising materials," he says. "You can optimize the amount of energy you produce from a nanoparticle-based solar cell."

Chakraborty, an expert in physical and theoretical chemistry, quantum mechanics and nanomaterials, is seeking to understand how these nanoparticles interact with light after changing their shape and size, which means, for example, they ultimately could provide enhanced photovoltaic and light-harvesting properties. Changing their shape and size is possible "without changing their chemical composition," he says. "The same chemical compound in different sizes and shapes will interact differently with light."

Specifically, the National Science Foundation (NSF)-funded scientist is focusing on quantum dots, which are semiconductor crystals on a nanometer scale. Quantum dots are so tiny that the electrons within them exist only in states with specific energies. As such, quantum dots behave similarly to atoms, and, like atoms, can achieve higher levels of energy when light stimulates them.

Chakraborty works in theoretical and computational chemistry, meaning "we work with computers and computers only," he says. "The goal of computational chemistry is to use fundamental laws of physics to understand how matter interacts with each other, and, in my research, with light. We want to predict chemical processes before they actually happen in the lab, which tells us which direction to pursue."

These atoms and molecules follow natural laws of motion, "and we know what they are," he says. "Unfortunately, they are too complicated to be solved by hand or calculator when applied to chemical systems, which is why we use a computer."

The "electronically excited" states of the nanoparticles influence their optical properties, he says.

"We investigate these excited states by solving the Schrödinger equation for the nanoparticles," he says, referring to a partial differential equation that describes how the quantum state of some physical system changes with time. "The Schrödinger equation provides the quantum mechanical description of all the electrons in the nanoparticle.

"However, accurate solution of the Schrödinger equation is challenging because of large number of electrons in system," he adds. "For example, a 20 nanometer CdSe quantum dot contains over 6 million electrons. Currently, the primary focus of my research group is to develop new quantum chemical methods to address these challenges. The newly developed methods are implemented in open-source computational software, which will be distributed to the general public free of charge."

Solar voltaics, "requires a substance that captures light, uses it, and transfers that energy into electrical energy," he says. With solar cell materials made of nanoparticles, "you can use different shapes and sizes, and capture more energy," he adds. "Also, you can have a large surface area for a small amount of materials, so you don't need a lot of them."

Nanoparticles also could be useful in converting solar energy to chemical energy, he says. "How do you store the energy when the sun is not out?" he says. "For example, leaves on a tree take energy and store it as glucose, then later use the glucose for food. One potential application is to develop artificial leaves for artificial photosynthesis. There is a huge area of ongoing research to make compounds that can store energy."

Medical imaging presents another useful potential application, he says.

"For example, nanoparticles have been coated with binding agents that bind to cancerous cells," he says. "Under certain chemical and physical conditions, the nanoparticles can be tuned to emit light, which allows us to take pictures of the nanoparticles. You could pinpoint the areas where there are cancerous cells in the body. The regions where the cancerous cells are located show up as bright spots in the photograph."

Chakraborty is conducting his research under an NSF Faculty Early Career Development (CAREER) award. 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 $622,123 over five years.

As part of the grant's educational component, Chakraborty is hosting several students from a local high school--East Syracuse Mineoa High School--in his lab. He also has organized two workshops for high school teachers on how to use computational tools in their classrooms "to make chemistry more interesting and intuitive to high school students," he says.

"The really good part about it is that the kids can really work with the molecules because they can see them on the screen and manipulate them in 3-D space," he adds. "They can explore their structure using computers. They can measure distances, angles, and energies associated with the molecules, which is not possible to do with a physical model. They can stretch it, and see it come back to its original structure. It's a real hands-on experience that the kids can have while learning chemistry."

-- Marlene Cimons, National Science Foundation
Investigators
Arindam Chakraborty
Related Institutions/Organizations
Syracuse University

Thursday, March 5, 2015

THE QUEST FOR ECO-FRIENDLY PLASTICS

FROM:  NATIONAL SCIENCE FOUNDATION
From tea bags to Miatas, bioplastics are on the rise
Chemists and other researchers are working up new formulas for greener plastic
March 3, 2015

It's no longer common to hear, "Paper or plastic?" at the supermarket. In many jurisdictions, the plastic option is curbed. Hundreds of local governments around the world--even entire countries, such as China and India--ban or tax lightweight, single-use plastic bags.

Every year in the United States, more governments enact such restrictions, which are part of a larger shift away from petroleum-based plastic. As people grow more concerned about throwaways destined for landfills (or worse, for the open ocean) and the problems associated with fossil fuels, businesses of all sizes are looking beyond "traditional," petroleum-based plastics to alternatives derived from plants, or even synthesized by microorganisms.

The bioplastic revolution

Bioplastics are made wholly or in part from renewable biomass sources such as sugarcane and corn, or from the digest of microbes such as yeast. Some bioplastics are biodegradable or even compostable, under the right conditions.

These new, more eco-friendly plastics are cropping up in all sorts of places, from tea bags to 3D printing media to medical implants.

In Finland, for example, consumers can now buy milk in cartons, made by Tetra Pak, that are 100 percent plant-based. In the United States, a small company called Iris Industries used Kickstarter to get off the ground with "Denimite," a marbleized blue composite made of recycled denim and a thermoset resin binding agent that is partially bio-based. And NSF-funded Ecovative makes a packing material called "Myco Foam" that's designed to replace polystyrene packaging, that bane of environmentally aware consumers who nevertheless buy take-out meals.

The bioplastic revolution

Bio-based plastics are on the rise. The thriving European market for bioplastics is growing by more than 20 percent per year. Global demand is expected to rise by 19 percent annually through 2017, according to market research group Freedonia. Global production capacities are set to increase by 400 percent by 2018, with most bioplastics being produced in Asia, according to European Bioplastics (EUBP), an association that represents the interests of the industry in Europe.

Packaging has been, and still is, one of the most common uses for bioplastics, but there is growth in other areas, such as textiles and automotive applications.

"From functional sports garments with enhanced breathability to fuel lines, bioplastics are constantly spreading into new markets," said EUBP chairman François de Bie.

Even the sports-car market appreciates bioplastics. Mazda announced late last year that it would use a new bioplastic in the interior (and, eventually, exterior) of its MX5 Miata. In a December 2014 press release, the company says the plant-based plastic it developed with Mitsubishi Chemical Corp. can be dyed and has a higher-quality, less-toxic finish than traditional painted surfaces.

Likewise, the Ford Motor Co. said last July that it will work with Heinz to make plastic out of leftover tomato skins, for use in car wiring brackets and storage bins.

How plastics are born

All of this activity is exciting, but most of today's plastic still comes from a nonrenewable resource: crude oil deposits in the earth. The oil is extracted and sent to a refinery to be distilled and yield an intermediate product called naphtha. Intense heat helps "crack" the naphtha into smaller hydrocarbon molecules such as ethylene and propylene. These chemicals are combined with a catalyst and polymerized to form chains of many linked molecules--the materials we know as plastics.

Different kinds of plastic will have varying polymer structures and distinct properties (toughness, stiffness, strength, transparency, etc.). Manufacturers then buy those bulk polymer pellets, granules or liquids for creating plastic in different shapes using processes such as extrusion or injection molding.

The push to use alternative, more renewable feed stocks rests on increasing concerns about the impact of petrochemicals on health and the environment, as well as the wariness people feel about relying on finite fossil-fuel resources. Many petroleum-based plastics don't break down for hundreds, or even thousands, of years--the carbon-carbon bonds that form the polymers are that durable. According to the U.S. Environmental Protection Agency (EPA), in 2012, the U.S. generated almost 32 million tons of plastic waste, but only 9 percent of that was recovered for recycling, leaving about 29 million tons. Much of the rest ends up in landfills, as ground litter or in the ocean.

In addition, petro-based plastics have been linked to health concerns such as endocrine disruption, and studies show some potentially harmful plastic chemicals accumulate in the human body.

Planting the next plastic crop

To spur solutions, some governments are promoting global and national bio-based economies or so-called bioeconomies. In 2012, the Obama administration released a National Bioeconomy Blueprint that calls for increased research and development, technology transfer, training and other steps to drive the nation's bioeconomy. Businesses are interested in following that lead--in fact, they may actually be ahead of consumers, some of whom aren't willing to pay a premium for greener plastics.

"The consumers want these materials, and they want to be more sustainable," said Marc Hillmyer, director of the University of Minnesota's Center for Sustainable Polymers (CSP). "But they're generally not going to do it at a cost. What we hear from industry is, 'Yes, we obviously have businesses that rely on petrochemical feed stocks, and we obviously want to be profitable in those businesses. But we want to be part of the future as well," Hillmyer added.

Nearly three dozen company affiliates support the CSP's work, including 3M, Ashland, BASF, Coca-Cola, General Mills, Henkel, Kimberly-Clark, Natureworks and Schlumberger, which make up the center's Industrial Advisory Board.

Coca-Cola has been one of the big-business leaders in bioplastics development, with a recyclable "PlantBottle" that is made partially from PET (polyethylene terephthalate) derived from sugarcane. PlantBottle packaging accounts for 30 percent of the company's packaging in North America and 7 percent globally, "making Coke the world's largest bioplastics end user," the company has said. The company has also said it wants its bottles to be 100 percent made of plant-based plastic by 2020.

Alternative plastics also show up in niche products. For example, last year, wine cork maker Nomacorc released a recyclable cork made of renewable plant-based polyethylene, and a Finnish company called Ahlstrom sells tea bags made of polylactic acid (PLA), which is derived from resources such as corn starch and sugarcane, and is one of the most commonly used bioplastics.

The cost of green

Researchers working with businesses are challenged to make a material that will not only be biodegradable and nontoxic, but also cost-effective.

"Many people, including us, are very good at making expensive polymers that help us advance basic science but that are not economically all that viable," Hillmyer said. "And so, what we're really trying to emphasize in the center, again with industrial input, is how do we do it economically?"

To date, Hillmyer and his colleagues have had several success stories:

The center developed a biodegradable adhesive, made from PLA and a menthol-based polymer, which could one day make sticky-note recycling more efficient and environmentally friendly. (Most sticky notes are petroleum-based and tend to gum up recycling equipment.)
The center has identified a way to use additives to improve the toughness of PLA by a factor of more than 10.
They've discovered a new high-performance bio-based elastomer (an elastic polymer resembling rubber) that could be an economic, drop-in replacement for current petroleum-based materials.
There are many other challenges in developing new materials and getting them from the lab to the market.

"Our undergraduates, graduate students and postdocs all regularly hear from industry about the challenges that [companies] face when trying to introduce a new material into the marketplace," said CSP Managing Director Laura Seifert. "Can it be scaled up to an industrial process in an economically viable way? Can the material be used in existing infrastructure, or do we have to build an entirely new plant in order to adopt this new technology? And at the end of life … is it going to cause more harm than good to introduce this into our recycling stream?"

"These are hard problems," said Hillmyer. "If it was easy, somebody would have done it."

While the polymer industry is not going to shift overnight, in the long run change is inevitable, he added. "The graduate students and postdoctoral researchers and undergraduates...in the center, they're driven by these principles. So we are not having a hard time convincing them that this is something they should do. They're growing up in this world [asking] 'How do we make our world more sustainable?'"

-- Jacqueline Conciatore, National Science Foundation jconciat@associates.nsf.gov
Investigators
Marc Hillmyer
Related Institutions/Organizations
University of Minnesota-Twin Cities

Tuesday, August 5, 2014

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

Sunday, March 2, 2014

INCREASING FUEL CELL PERFORMANCE USING MATERIAL TECHNOLOGY

FROM:  NATIONAL SCIENCE FOUNDATION 
Material technology that can increase performance of fuel cells
Researcher hopes to create fuel cells that are more durable, efficient and less costly

Fuel cells convert chemical energy stored in fuel into electricity without combustion. They hold great promise as a clean energy alternative to fossil fuels because they use mostly hydrogen gas, and their only byproducts are heat and water, which makes them pollution free. They also have more than two times the efficiency of traditional combustion technologies.

But they still are expensive, with parts that can degrade over time, and--to be widely used in ground transportation, for example--likely would require an overhaul of the nation's infrastructure, among other things, in order to make the switch from gas to hydrogen.

Chulsung Bae is working to develop a key fuel cell component that he hopes will be more durable and efficient than what is currently available, as well as less costly, with the hope of promoting more widespread use of the technology.

The National Science Foundation (NSF)-funded scientist and associate professor of chemistry and chemical biology at the New York State Center for Polymer Synthesis, Rensselaer Polytechnic Institute, predicts that fuel cells ultimately "will be adopted in ground transportation in automobiles, and they will probably replace batteries in such devices as laptops and cell phones."

The fuel cell was invented in 1839 by William Robert Grove, a Welsh scientist, but was not used commercially until the 1960s, according to the Department of Energy. NASA used fuel cells in Project Gemini between 1962 and 1966 to generate power for probes, satellites and space capsules, and still uses them in the space program. Astronauts, in fact, drink water generated from fuel cells, Bae says.

Like batteries, fuel cells have no internal moving parts. Unlike batteries, however, which need a long time to store energy, fuel cells produce electricity instantly and continuously as long as fuel and air are available.

When hydrogen is the fuel, "electrons are drawn from the fuel at the negative side (called anode) of fuel cell and travel to the positive side (called cathode) through external circuit, turning chemical energy into electricity while producing only water and heat as byproducts.

Fuel cells have the potential to revolutionize energy if scientists can make them more affordable and durable.

"It's a complicated technology made of many parts, with two being the most important," Bae says. "These are a catalyst, which converts the fuel to proton and electron by electrochemical reaction, and the other key component of the cell is a membrane that allows the proton to move from the anode to the cathode of the fuel cell to complete the chemical reaction. The proton is known as H+, which is a positive form of the hydrogen created by removing one electron from the hydrogen atom."

Bae's goal is to develop a new membrane through molecular engineering that lasts longer and is more economical than the only commercial product currently available, a material called Nafion,® which has serious drawbacks in addition to its high cost, he says. These include the "rare availability of fluorine-containing precursors," that is, the materials need to produce Nafion,® which are difficult to make, "and reduced proton conductivity above 100 Celsius degree," among others, he says. "It is not ideal for fuel cells."

"If you want to increase the performance of fuel cells, proton conductivity is the key for determining performance," he adds.

To that end, Bae has been studying Nafion® to determine which chemical structures in it are weak so "I can revise them in my design of new membrane chemical structures," he says, and has synthesized a new type of fuel cell membranes in the lab.

In testing, "we make a membrane and, for example, say it is made of five different chemical structures--a, b, c, d, e," he says. "I change 'a' and measure its properties, then change 'b' and measure its properties, and so on. I would like to know what happens to the properties when changing the structure systematically, so I can have a better understanding of the relationship between the chemical structure and its performance in fuel cells."

He has a candidate membrane and is collaborating with the Los Alamos National Laboratory to test it.

"In our lab we discovered key structures that can enhance proton conductivity without adding too much cost by using commercially available plastics as a membrane precursor, changing its structures and measuring its properties," he says.

Bae is conducting his work with an NSF Faculty Early Career Development (CAREER) award, which he received in 2008. 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 about $450,000 over five years. (He received a one-year deadline extension to accommodate his transition in changing schools.)

As part of the grant's educational component, Bae teaches about clean energy technology in his graduate and undergraduate courses, and has sponsored high school students for a month's internship in his lab.

"I usually teach organic chemistry, a large enrollment undergraduate course with 200 or more students," he says. "They mostly are juniors and sophomores who often think that chemistry is just about the periodic table, and not related to real life. They don't get the idea of how chemists can have an impact on our lives. I give them fuel cell demonstrations and talk about our membrane work in order to show how chemistry they learned in the class can change the world and chemistry is an important part of our lives."

-- Marlene Cimons, National Science Foundation
Investigators
Chulsung Bae
Related Institutions/Organizations
University of Nevada Las Vegas

Monday, February 3, 2014

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."

Thursday, May 10, 2012

THE CHEMISTRY MAGICIAN


FROM:  AMERICAN FORCES PRESS SERVICE
Dr. Ron Furstenau during a chemistry magic presentation at the Garden of the Gods Visitor and Nature Center in Colorado Springs, Colo., April 21, 2012. Furstenau is an instructor with the U.S. Air Force Academy's chemistry department. U.S. Air Force photo by Don Branum

Chemistry Whiz Uses Magic to Teach
By Don Branum
U.S. Air Force Academy Public Affairs
COLORADO SPRINGS, Colo., May 9, 2012 - The first thing noticeable about Dr. Ron Furstenau is his apparel. One of his ties displays a bevy of chemical symbols. An American flag, a smiley face and periodic table [of elements] pins grace the lapels of his lab coat, along with a three-eyed fish on one of his pockets.

Furstenau, a chemistry instructor at the U.S. Air Force Academy here, is an enthusiastic person -- whether he's mentoring students in the academy's chemistry labs or performing instructive magic shows for young students in the local community.
The chemistry whiz said he became interested in science during grade school.
"Even as a little kid, I liked to try to understand why things work the way they do," said Furstenau, who grew up in Norfolk, Neb. "I don't think I knew it was science at the time. I just knew it was fun."
It took him a few more years, though, to discover which area of study interested him the most.

"It was my first science class in ninth grade," he recalled. "It was physical science, but mostly chemistry. Once I got into it in high school, I really liked it."
Furstenau went on to graduate from the Air Force Academy with a bachelor's degree in chemistry before earning a master's degree and doctorate at the University of Nebraska.
Between degrees, he served as a chemist at Edwards Air Force Base, Calif., and taught here. He came back to the academy after finishing his doctorate and kept teaching even after he retired from active duty in 2006. He's been involved with the academy's chemistry department magic show the entire time.

Furstenau performed a magic show April 21 at Colorado's Garden of the Gods Visitor and Nature Center as part of the park's observance of Earth Day. Children enthusiastically raised their hands every time he called for volunteers.

Those who were picked got to mix potions of all sorts, including one that switched from blue to gold seemingly in response to cheering from the audience.

The kids didn't care that it was a Briggs-Rauscher oscillating reaction or that it involved malonic acid, hydrogen peroxide and iodine. They just knew it was cool.
As they watched the beaker's liquid cycle through blue, gold and clear states, Furstenau explained the basics: the reaction that turned the solution gold also provided the ingredients needed to turn the solution blue and vice versa.

"I did my first tour here in '84," he added. "I've probably done at least 800 of them over the years."

Furstenau said he and other academy chemistry instructors have performed chemistry magic shows across the state of Colorado, mainly in the Pikes Peak region and the Denver area.

"We'll go to whoever happens to ask," he said. "As a department, we look at getting them interested in science as well as maybe getting them interested in attending the Air Force Academy."

One magic show in particular sticks out in Furstenau's mind more than any other. It was one that he performed for a child who was in the Cadet for a Day program and her family.
"She was recovering from cancer," said Furstenau, who survived prostate cancer in 2007. "There was something about the interaction with her and her family. I don't know exactly what it was, but it's something I'll remember for the rest of my life."

The academy's STEM (science, technology, engineering and mathematics) initiative for young people also offers programs for Girl Scouts, and programs to give middle and high-school teachers hands-on access to the academy's laboratories. They have instruments that measure chemical compounds in almost any way imaginable, from using radio waves and powerful magnetic fields to changing the rotation of an atomic radius, to using x-rays to shear electrons from an atom's outer layers.

"Science is really fun!" Furstenau said. "At some point, someone tells kids science is hard, and that's just not true. Yes, science is work, and it involves a lot of math, but it should always be fun."

His love of chemistry shines in his work, said Air Force Col. Mike Van Valkenburg, the head of the academy's chemistry department.

"I've known Dr. Furstenau since 1991 when I was first assigned here to the department as a captain," Van Valkenburg said. "I've been very fortunate to observe, learn and work alongside this very brilliant educator. He communicates understanding and the 'why' of chemistry superbly to any group of captured listeners. He is no doubt one of the best chemistry educators in the country who can motivate anyone to be interested in the subject and material."

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