From PNNL: “A New Model for Simulating DNA’s ‘Atmosphere’ of Ions”

PNNL Lab

The study compared two models of very large ions (macroions) that carry an electrical charge, and compared the results to experimental studies. On the left is a model of a cylinder with uniform axial charge density; on the right is the more complex (and useful) discrete charge model.

April 2016

Refined insights into critical ionic interactions with nature’s building blocks

Nucleic acids, large biomolecules essential to life, include the familiar double-stranded deoxyribonucleic acid (DNA), a very stable long molecule that stores genetic information.

In nature, DNA exists within a solution rife with electrostatically charged atoms or molecules called ions. A recent study by researchers at Pacific Northwest National Laboratory (PNNL) proposed a new model of how B-DNA, the form of DNA that predominates in cells, is influenced by the water-and-ions “atmosphere” around it.

Understanding the ionic atmosphere around nucleic acids, and being able to simulate its dynamics, is important. After all, this atmosphere stabilizes DNA’s structure; it impacts how DNA is folded and “packed” in cells, which triggers important biological functions; and it strongly influences how proteins and drugs bind to DNA.

The research combines theoretical modeling and experiments in a study of ion distribution around DNA. It was led by PNNL physical scientist Maria Sushko, computational biologist Dennis Thomas, and applied mathematician Nathan Baker, in concert with colleagues from Cornell University and Virginia Tech.

Earlier approaches have been used to simulate the distribution of ions around biomolecules like DNA. But only roughly. The PNNL-led study goes beyond commonplace electrostatics to propose a more refined but still computationally efficient model of what happens in these critical ionic atmospheres.

“The main idea was to dissect the complex interplay of interactions, and to understand the main forces driving ions deep inside the DNA helix and the forces keeping them on its surface,” said Sushko, the paper’s first author. That interplay includes the correlation of ions within the solution, how they move, how they interact with one another, and how they interact with the DNA.

The new model has two key advantages over older simulations: It allows researchers to turn ion-water and ion-ion interactions on and off at will. “We can calculate important interactions independently,” she said, a flexibility not present in previous simulations. And the new model is computationally efficient, allowing researchers to cheaply simulate a large-scale molecular event over a long time scale.

Results: Importantly, both previous and new experiments by the Cornell colleagues identified the number of bound ions around DNA. Previous simplified models were also able to reproduce this number. But the new model “is richer than that,” said Sushko, because it gives more details on how ions are distributed along the surface of DNA and within DNA’s critical grooves. “DNA interaction will strongly depend on where those ions sit,” she said. For one, the presence of ions in the grooves relates to how compact DNA will be. “The more ions within the grooves,” said Sushko, “the more compact the structure.”

The researchers confirmed that biological “correlation,” a measure of ion affinity, allowed DNA to pack more tightly by effectively neutralizing DNA’s electrostatic charge. Researchers also observed how ions get distributed through a solution, a water-ion interaction called solvation. The stronger the water-ion interaction, the larger the effective ion size, and therefore the less likely the ion was to settle in the DNA’s grooves. More strongly solvated ions, therefore, create a different environment for DNA folding.

Researchers observed results regarding the activity of three types of salts within the simulated ionic environment. Small, single-charge ions did not strongly react with water; about 50 percent of these bond ions could penetrate into DNA grooves. Large ions with triple charges were not strongly hydrated, but their size prevented penetration into the grooves. (“They just decorate the surface,” said Sushko.)

Only 15 to 20 percent of ions with double charges, which were strongly hydrated and strongly correlated, settled in DNA grooves. That showed a “very delicate interplay” of ion-to-ion and ion-to-water interactions, according to Sushko.

Why It Matters: These results highlight important aspects of the properties of electrolyte solutions influencing the ionic atmosphere that impacts DNA condensation. This “packing” of DNA, which is otherwise one of the longest molecules in nature, is essential to DNA’s role in gene regulation. DNA condensation is also the key to protein binding and drug binding. It therefore points to practical applications in medicine and biotechnology.

This research also highlights the impact of the ionic atmosphere on the interaction between biomolecules and a ligand: that is, the molecule, ion, or protein that binds with a protein or the DNA double helix for some biological purpose.

But it is the “methodology itself,” not the designed simulations of DNA, that is most important, said Sushko, in part because it provides a new computational model of how to see into complex molecular systems. “We get a better fundamental understanding of the important forces.”

Methods: Researchers employed two coarse-grained models to simulate the DNA macroion, which is a large colloidal ion carrying a charge. The goal was to capture two versions of detail on how ions spread out in a solvent and how they interact with simulations of DNA topology.

One DNA model posited an infinitely long cylinder with a uniform charge density along one axis. Sushko called it “a very crude model used a lot in the past. It explains quite a lot about ion interactions, but it is deficient in some ways.” The second, more complex “discrete charge” model posited three types of spheres in a helical array that mimics B-form DNA. It had a 3D-like character that allowed ions to penetrate into DNA grooves.

The DNA simulations were run through four computational models of classical density function theory to assess the energetics of different ion-DNA interactions. Results were also compared to data from what Sushko called “state-of-the-art experiments” that used anomalous small-angle x-ray scattering. This technique, used to investigate the spatial dimensions of structures in the nanometer range, always yields a lot of detail about how ions are distributed around a biomolecule.

The uniformly charged cylinder model was not good at simulating the ionic atmosphere around DNA. “This model is a very common simplification,” said Sushko. “You get the same number of ions attached to DNA, but the distribution is completely wrong. In this model, ions will just sit somewhere on the surface.”

But their more complex discrete charge model provided a much more naturalistic portrait of ion distribution in an ionic atmosphere. Its simulations showed ions both clinging to the helical DNA surface and also penetrating into the DNA’s grooves. “The small details of ion penetration are very important for the way DNA will package the chromosome,” she said.

What’s Next? Researchers plan to study the role of the ionic atmosphere in mediating interactions between DNA molecules. They also plan to extend their DNA model to include DNA sequence-specific effects, which often influence ion binding, and DNA sequence-dependent structural variations.

Science paper:
The role of correlation and solvation in ion interactions with B-DNA

See the full article here .

Please help promote STEM in your local schools.

Stem Education Coalition

Pacific Northwest National Laboratory (PNNL) is one of the United States Department of Energy National Laboratories, managed by the Department of Energy’s Office of Science. The main campus of the laboratory is in Richland, Washington.

PNNL scientists conduct basic and applied research and development to strengthen U.S. scientific foundations for fundamental research and innovation; prevent and counter acts of terrorism through applied research in information analysis, cyber security, and the nonproliferation of weapons of mass destruction; increase the U.S. energy capacity and reduce dependence on imported oil; and reduce the effects of human activity on the environment. PNNL has been operated by Battelle Memorial Institute since 1965.

From PNNL: “In Search of Stability: It’s All About Staying Super Cool”

PNNL Lab

March 2016
No writer credit found

While glass might be thought of in terms of holding wine or as a window, the stability of glass affects areas as diverse as nuclear waste storage, pharmaceuticals, and ice cream. Recently, chemical physicists at Pacific Northwest National Laboratory made a key discovery about how glass forms.

They discovered that the temperature at which glass-forming materials are deposited on a substrate affects the stability. Their findings, published in The Journal of Physical Chemistry Letters, show the ability of a technique called inert gas permeation to tell at what temperature a solid “melts.” Their work brings more understanding to the fundamental properties of glass.

“Glasses are metastable materials with the mechanical properties of a solid-you can touch and hold them, versus a gas,” said Dr. Scott Smith, a co-author on the paper. “But they are not like crystalline materials, which are in a perfect array. The molecules in glasses are arranged in a disordered pattern. In liquids the molecules are constantly moving, if you suddenly freeze a liquid, the molecules are randomly oriented and unstructured. In some sense, a glass can be thought of as a frozen liquid.”

Why It Matters: No matter how glass is made, understanding its properties is important. For example, the reason some medications have expiration dates is that their physical state changes from amorphous to crystalline. Once that happens, the medication doesn’t dissolve as readily when taken and is thus ineffective. Finding ways to increase its stability and effectiveness would extend its shelf life. Similarly, when nuclear waste is put into a glass matrix, the glass must remain stable to keep the radionuclides from being released. And as most ice cream lovers know, when you open a carton and see crystals have formed on the surface, it has lost much of its flavor.

Methods: “Our research is fundamental work that could be important for stable glass manufacture by adding to understanding of liquids and liquid behavior,” Smith said. Glasses depend on temperature for stability. At the correct temperature, a glass remains stable because its molecules stay put. At warmer temperatures, it transforms into a supercooled liquid and then crystallizes.

To create a glass, the materials must be cooled rapidly to a temperature low enough that the molecules don’t have enough time or energy to find the lowest energy configuration (a crystal). That temperature is called the glass transition temperature, or Tg, and it varies depending on the experimental conditions and the cooling rate.

Smith and colleagues Dr. Alan May and Dr. Bruce Kay took the glass-forming materials toluene and ethylbenzene and super cooled them by depositing them onto a surface at 30 K. When the materials hit the surface, they formed an amorphous solid—a glass. The researchers then heated the sample. A layer of krypton deposited between two layers of glassy material (a sandwich) remained trapped until the glass transformed into a supercooled liquid (see Figure). The onset of gas release revealed at what temperature the glass transformed into a supercooled liquid.

The researchers varied the material deposition temperature from 40 to 130 K. They observed that the stability of the glass depended on the deposition temperature. They found that for both toluene and ethylbenzene, deposition at a temperature a few degrees less than Tg, created the most stable glass-one that was the most resistant to turning into a supercooled liquid. These results are consistent with the calorimetric studies of Prof. Mark Ediger at the University of Wisconsin-Madison.

“We found we can control one variable: deposition temperature. Even a difference of one Kelvin can result in years of difference in material lifetime and stability,” said Smith.

Acknowledgments:

Sponsors: This work was supported by the U.S. Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. The research was performed using EMSL, a DOE Office of Science User Facility sponsored by the Office of Biological and Environmental Research and located at PNNL.

User Facility: EMSL

Research Team: Scott Smith and Bruce Kay, PNNL; Alan May, Intel Corporation.

Reference: Smith RS, RA May, and BD Kay. “Probing Toluene and Ethylbenzene Stable Glass Formation using Inert Gas Permeation.” Journal of Physical Chemistry Letters 6(18):3639-3644. DOI: 10.1021/acs.jpclett.5b01611

See the full article here .

Please help promote STEM in your local schools.

Stem Education Coalition

From PNNL: “Consorting with the Right Microbes”

PNNL Lab

March 2016
No writer credit found

Microbes

Using microbial consortia may boost success of biotechnologies

Results: Around the world, researchers are studying microbes to see if these tiny organisms can be used to solve a host of problems, from cleaning up toxic waste to providing renewable energy. Unfortunately, attempts to develop biotechnologies often fall short because they focus on a limited set of single, highly engineered organisms. Such organisms frequently do not perform as efficiently or stably in an application as they do in the laboratory.

Now, an internationally recognized group of scientists, organized by Pacific Northwest National Laboratory microbiologists Dr. Stephen Lindemann and Dr. Alexander Beliaev, has reviewed the state of the science to determine how biotechnological use of communities of multiple microbes, or microbial consortia, might transcend the limitations of single organisms.

They posit that the time is ripe for design and control of microbial communities, and that achieving the ability to engineer microbial ecosystems will require a level of understanding of the mechanisms driving microbial community function only possible from combining recent advances in systems biology, computational modeling, and synthetic biology.

These new perspectives stemmed from a panel at the 15th International Symposium on Microbial Ecology in Seoul and appear in the International Society for Microbial Ecology’s (ISME) official publication, The ISME Journal.

Why It Matters: Agriculture has long known that monocultures, or growing only one type of crop, can be susceptible to changes in the environment. For example, relatively small or poorly timed changes in rainfall can cause major losses in production for some crops. In contrast, growing several crops with different tolerances to drought might more stably provide food, no matter the weather for a given year. The same principle applies to microbes, which are drivers of global geochemical cycles and catalysts for renewable fuels and chemicals. Microbial communities can prove to be more reliable than engineered “superbugs” and more robust against unpredictable environment than individual microbes. This reliability is the key to using them for industrial purposes.

“The promise that this field has to offer is great,” said Beliaev. “Transformative biotechnologies will help overcome the energy, health, and environmental problems of the future, and the process of learning to design and control ecological phenomena has and will undoubtedly continue to yield new insights on the fundamentals of life.”

Methods: Seven scientists from PNNL, Montana State University, Fred Hutchinson Cancer Research Center, and the Swiss Federal Institute of Technology brought perspectives from different scientific approaches, research programs, and countries to analyze the state of the science. They used questions posed by experts who attended the ISME symposium to outline key issues.

Drawing on their years of experience and amassed knowledge, the group determined that successful biosystems design is contingent both on the understanding of microbial physiology and accuracy of computational models that describe how organisms interact. An iterative design-build-test approach that can predict interspecies dynamics and analyze energy and material flows in a community will help scientists better understand how these consortia can be used for biotechnologies.

What’s Next? PNNL’s microbial research program continues to expand the foundation of biological systems design. Ideally, advances in this field will allow scientists to control safety, productivity, and stability of natural and designed microbial ecosystems.
Acknowledgments

Sponsors: The U.S. Department of Energy’s Office of Science, Office of Biological and Environmental Research, supported this work via the Genomic Science Program under the PNNL Foundational Scientific Focus Area. MWF is supported by the Scientific Focus Area Program at Lawrence Berkeley National Laboratory. HCB participated with support from the Linus Pauling Distinguished Postdoctoral Fellowship, a Laboratory Directed Research and Development Program at PNNL.

Research Team: Alexander S. Beliaev, Hans C. Bernstein, Jim K. Fredrickson, Stephen R. Lindemann, and Hyun-Seob Song, Pacific Northwest National Laboratory; Matthew W. Fields, Montana State University; Wenying Shou, Fred Hutchinson Cancer Research Center; and David R. Johnson, Swiss Federal Institute of Technology.

Reference: Lindemann SR, HC Bernstein, H-S Song, JK Fredrickson, MW Fields, W Shou, DR Johnson, and AS Beliaev. 2016. “Engineering Microbial Consortia for Controllable Outputs.” The ISME Journal: Multidisciplinary Journal of Microbial Ecology. Advance online publication 11 March 2016. DOI: 10.1038/ismej.2016.26.

See the full article here .

Please help promote STEM in your local schools.

Stem Education Coalition

From PNNL: “Microbes may not be so adaptable to climate change”

PNNL Lab

March 15, 2016
Tom Rickey, PNNL, (509) 375-3732
tom.rickey@pnnl.gov

Microbes in the soil are central players converting carbon into greenhouse gases.
Courtesy of Alice Dohnalkova/PNNL

Microbes in soil — organisms that exert enormous influence over our planet’s carbon cycle — may not be as adaptable to climate change as most scientists have presumed, according to a paper published March 2 in PLOS One.

The finding means that a big piece of the puzzle regarding the future climate of our warming planet just got a little tougher to fit into current computer models.

Soil holds an enormous pool of carbon — in a forest, for instance, usually there is more carbon beneath the surface than in the trees above — and what happens to that carbon is an important factor in the future of our planet. Bacteria, fungi and other microbes are central players, converting carbon and other elements in the soil into carbon dioxide and other gases that are expelled into the atmosphere.

“Soil is the major buffer system for environmental changes, and the microbial community is the basis for that resilience. If the microbial community is not as resilient as we had assumed, then it calls into question the resilience of the overall environment to climate change,” said author Vanessa Bailey of the Department of Energy’s Pacific Northwest National Laboratory.

The findings are based on a unique 17-year study of transplanted soils on a mountain in eastern Washington state. The team moved some samples of soil down the mountainside 500 meters to a warmer, drier climate, and other samples up 500 meters to a cooler, moister climate. After 17 years, they analyzed both sets of soil in the laboratory, as well as “control” samples from both sites that had never been moved.

The scientists analyzed the make-up of the microbial communities, their enzyme activity, and their rates of respiration — how quickly microbes convert carbon in the soil into carbon dioxide which is released to the atmosphere.

The scientists found less adaptability than they expected, even after 17 years. While the microbial make-up of the samples did not change much at all, the microbes in both sets of transplanted soils retained many of the traits they had in their “native” climate, including to a large degree their original rate of respiration.

The message, the authors say, is that scientists can’t simply assume that microbes will nimbly respond to climate change.

“The fact that the soils’ native environment continued to exert profound influence on microbial activity 17 years later is quite surprising,” said co-author Ben Bond-Lamberty, a scientist with the Joint Global Change Research Institute, a partnership between PNNL and the University of Maryland in College Park, Md.

“We can’t assume that soils will respond to climate changes in the ways that many scientific models have assumed,” Bond-Lamberty added.

In their study, the PNNL scientists took advantage of a mountain location where the climate changes quickly as one moves higher. Just 500 meters up the mountain, temperatures cooled about 5 degrees Celsius on average and rainfall increased about 5 centimeters annually. That translates to more vegetation at the higher location and thus more carbon available to microbial communities.

The microbes native to the higher site respired at a higher rate naturally, due to the moister climate and a more plentiful supply of carbon in their environment; when they were moved to the lower, warmer site, they continued to respire at a faster rate than the surrounding “native” soils and microbes. And the microbes transplanted from lower ground to higher ground had an unusually small response to the temperature change, though biological theory and climate models predict a larger change.

“With our changing climate, all microbes will be experiencing new conditions and more extremes,” said Bailey, a soil microbiologist. “Climate change won’t translate simply to steady warming everywhere. There will be storm surges, longer droughts; some places may end up experiencing more mild climates. This study gives us a glimpse of how microbes could weather such changes under one set of conditions. They may be constrained in surprising ways.”

The study was funded by the Department of Energy Office of Science. Measurements of various forms of carbon were done at EMSL, the Environmental Molecular Sciences Laboratory, a DOE Office of Science user facility at PNNL.

Reference: Ben Bond-Lamberty, Harvey Bolton, Sarah Fansler, Alejandro Heredia-Langner, Chongxuan Liu, Lee Ann McCue, Jeffrey Smith, Vanessa Bailey, Soil respiration and bacterial structure and function after 17 years of a reciprocal soil transplant experiment, PLOS One, March 2, 2016, DOI: 10.1371/journal.pone.0150599.

See the full article here .

Please help promote STEM in your local schools.

Stem Education Coalition

From PNNL: “Microbes take their vitamins – for the good of science”

PNNL Lab

January 21, 2016
Tom Rickey

Illustration of the PNNL team’s technology where a vitamin mimic (small blue structure) binds to a protein (larger coiled structure) to gain entry into the bacterium Chloroflexus aurantiacus. Illustration by Nathan Johnson, PNNL

The bacterium Chloroflexus aurantiacus helps give the greenish color to this pool of water in Yellowstone National Park.
Image courtesy of Wikimedia Commons

Chloroflexus aurantiacus under the microscope. Image courtesy of Sylvia Herter and the Joint Genome Institute

Microbes need their vitamins just like people do. Vitamins help keep both organisms healthy and energetic by enabling proteins to do their work. For bacteria, a dearth of vitamins can spell death.

Now scientists at the Department of Energy’s Pacific Northwest National Laboratory have made a “vitamin mimic” — a molecule that looks and acts just like the natural vitamin to bacteria, but can be tracked and measured by scientists in live cells. The research offers a new window into the inner workings of living microbes that are crucial to the world’s energy future, wielding great influence in the planet’s carbon and nutrient cycle and serving as actors in the creation of new fuels.

Vitamins are a powerful currency for researchers seeking to compel microbes to give up their secrets.

“We have a lot to learn about how microbes accumulate and use nutrients that are necessary for their survival and growth. This provides a window for doing so,” said chemist Aaron Wright, the corresponding author of the study published in ACS Chemical Biology.

“Perhaps we will be able to make a microbial community do what we want, by controlling its access to a specific nutrient,” Wright added.

To control the bacteria via vitamins, Wright and his team have to know what other proteins in the cell the vitamins are consorting with, and where and when.

Think of a planner analyzing emergency services for a large city. Knowing that an ambulance enters the city occasionally and transports some people somewhere, for instance, is not nearly as useful as knowing the precise address of the caller, the identity of the injured, and the location of the nearest hospital.

It’s the same for scientists trying to understand microbial cells. While a cell is infinitesimally small, the activity within resembles the hustle and bustle of a large city, with many functions within carried out by thousands of entities. Knowing precisely which vitamins aid which proteins, under what circumstances, to keep things running is a must if scientists are to maximize microorganisms for energy production and other processes.

“Microbial communities are organized based on their ability to get the resources they need to survive and grow,” said Wright. “We need to understand how the availability of nutrients, like vitamins, helps determine the structure of a microbial community as a step toward controlling that community in ways we would like to be able to do.”

An anchor for pond scum

Wright’s team studied the bacterium Chloroflexus aurantiacus J-10-fl, which is a common member of microbial mats — gloopy natural structures (think pond scum) where layers containing different groups of microbes band together. In these collections, C. aurantiacus often plays the role of anchor, helping to hold together an assortment of microbes. The bacteria, which resemble strands of string under the microscope, are usually found in hot springs, since they enjoy temperatures above 100 degrees Fahrenheit.

Wright’s team performed a series of synthetic chemical steps to alter three vitamins that C. aurantiacus needs to survive: vitamin B1 (thiamine), vitamin B2 (riboflavin), and vitamin B7 (biotin). While the bacteria recognized the substances as normal vitamins, the researchers can monitor the mimics much more easily than their natural counterparts.

Wright’s team used the mimics to relay a treasure trove of information about how vitamins enter the cell and interact within the cell, by analyzing the precise location of the molecules’ activity in living cells. Through a system called affinity-based protein profiling, Wright’s group effectively tagged these molecules where they’re active, then used techniques such as mass spectrometry to sort and measure proteins of interest.

One of the team’s findings suggests multiple vitamins may share the same molecular machinery to gain entry into the cell. The team is still investigating these data. These findings can provide a road map for scientists like Wright who are trying to direct microbes as part of broad efforts to create clean, renewable fuels and reduce the effects of climate change.

The work was funded by the U.S. Department of Energy Office of Science. The mass spectrometry-based measurements and microscopy were performed at EMSL, the Environmental Molecular Sciences Laboratory, a DOE Office of Science User Facility at PNNL.

Reference: Lindsey N. Anderson, Phillip K. Koech, Andrew E. Plymale, Elizabeth V. Landorf, Allan Konopka, Frank R. Collart, Mary S. Lipton, Margaret F. Romine and Aaron T. Wright, Live cell discovery of microbial vitamin transport and enzyme-cofactor interactions, ACS Chemical Biology, Dec. 15, 2015, DOI: 10.1021/acschembio.5b00918.

EMSL, the Environmental Molecular Sciences Laboratory, is a national scientific user facility sponsored by the Department of Energy’s Office of Science. Located at Pacific Northwest National Laboratory in Richland, Wash., EMSL offers an open, collaborative environment for scientific discovery to researchers around the world. Its integrated computational and experimental resources enable researchers to realize important scientific insights and create new technologies. Follow EMSL on Facebook, LinkedIn and Twitter.

See the full article here .

Please help promote STEM in your local schools.

Stem Education Coalition

From PNNL: “Creating a Super Lattice: Zipping Electrons, Jumping Holes, and the Quest for Solar Fuels”

PNNL Lab

December 2015
Web Publishing Services

Designing a superlattice of chromium and iron oxides produces a material that allows electrons excited by sunshine to freely move away from their “holes,” answering a fundamental question for material scientists working to create the materials that produce fuels from sunlight. No image credit

Imagine having solar panels turn out fuel, essentially storing the sun’s energy for a rainy day. Scientists are searching for a material that can handle the job. The material must excite electrons when struck by sunlight, easily transport the electrons to where they are needed, and use those electrons to create fuel—and, it must be a material that isn’t in short supply. Rare metals such as platinum need not apply. Hematite, an oxide of readily available iron, is a popular choice. It meets all the requirements but one—it doesn’t let the electrons zip along. Dr. Tiffany Kaspar at Pacific Northwest National Laboratory and her colleagues may have found a way to let the electrons flow—by layering on the oxide of another abundant metal: chromium.

Why It Matters: Solar energy must be used when it is generated, or it is lost. Storing the energy as fuel could allow solar power to play a larger role on the nation’s energy stage. In the simplest case, solar energy would split water, H2O, to generate hydrogen, H2, fuel. This work shows how one of the challenges to solar fuels could be overcome with earth-abundant minerals. This work also shows how abrupt interfaces between hematite and chromium oxide can be controlled in such a way as to move the electricity without requiring added energy.

Methods: When you shine light on hematite, electrons are excited, leaving behind “holes,” which act as the positive charge to the electron’s negative charge. Unfortunately, in hematite the electrons tend to fall back into their “holes.” If the electrons and holes could be quickly separated after the electron was excited, both could move on. Ideally, the holes would migrate to the material’s surface, where they can catalyze the production of fuel.

To create a material where the electrons and holes are forced to separate, the team produced an artificial crystal structure called a superlattice. The team built a thin layer of hematite and then added a layer, three atoms deep, of chromium oxide. They added another layer of hematite, and then chromium oxide, like stacking up the layers on a cake. The abrupt interface between each distinct layer is key to separating the electrons and holes: the electrons prefer to remain in the hematite, while the holes are driven to the chromium oxide layers. The layers were created using the molecular beam epitaxy instrument at EMSL, a DOE scientific user facility.

Now, when light strikes the surface of the superlattice, the interfaces are such that they drive the excited electrons to the hematite and the holes to the chromium oxide. As an added benefit, the superlattice stack generates an internal voltage that is epxected to drive holes to the material’s surface, where they can react to create fuels.

The ability of these superlattice stacks to separate electrons and holes was first predicted in 2000 by Kaspar’s colleague Dr. Scott Chambers, but no practical applications were envisioned at the time. Further study led to an understanding of the interfacial properties between the hematite and chromium oxide layers. This work proved relevant to the recent interest in using hematite to produce solar fuels, prompting Kaspar and colleagues to create and test the superlattice stacks.

Solar panels don’t produce electricity on overcast days, so the energy they produce when the sun shines needs to be stored. Scientists are making progress in the quest for materials that are both readily available and efficient. Stock photo: Dollar Photo Club

What’s Next? Kaspar and her team are now conducting photoelectrochemical studies to take the next step: split water to produce fuel.

See the full article here .

Please help promote STEM in your local schools.

Stem Education Coalition

From PNNL via DOE Pulse: Humble bacterium could advance hydrogen as renewable fuel

PNNL Lab

December 14, 2015
Greg Koller, 509.372.4864,
greg.koller@pnnl.gov

A research team at DOE’s Pacific Northwest National Laboratory has discovered that a common type of cyanobacterium, or blue-green algae, produces hydrogen, via photosynthesis, in two ways. The finding could lead to new approaches for hydrogen production as a renewable energy resource.

Cyanothece 51142, shown here in a bioreactor, has demonstrated that it is a workhorse for natural hydrogen production. No image credit

The PNNL team published the information, which pertains to a cyanobacterium known as Cyanothece 51142, in the Scientific Reports journal. Researchers know that 51142 makes hydrogen by drawing upon sugars that it has stored during growth. In this study, the PNNL team found something new—that the organism also draws on a second source of energy, using sunlight and water directly to make the chemical element.

In its experiment, the team set up Cyanothece 51142 in a bioreactor, limited the supply of nitrogen (which influences hydrogen production), and kept lights on for several weeks. The researchers used an array of high-tech equipment to yield sophisticated minute-by-minute profiles of the organism as it converted light energy to hydrogen. Further, the team “interrogated” the organism’s genes and proteins as they changed while the reactions occurred.

Scientists found that in addition to drawing upon its previously stored energy, the organism captures light and uses that energy to split water to create hydrogen in real time. As one component of the organism is creating energy by collecting light energy, another part is using that energy simultaneously to create hydrogen.

The discovery is another step toward advancing hydrogen as a clean energy source. “This organism can make lots of hydrogen, very fast; it’s a viable catalyst for hydrogen production,” says Hans Bernstein, a Linus Pauling distinguished postdoctoral fellow at PNNL. “The enzyme that makes the hydrogen needs a huge amount of energy. The real question is, what funds the energy budget for this important enzyme and then, how can we design and control it to create renewable fuels and to advance biotechnology?”

The research was supported by the DOE Office of Science (Biological and Environmental Research) and PNNL’s Laboratory Directed Research and Development program, which funds the Linus Pauling Distinguished Postdoctoral Fellowship Program.

See the full article here .

Please help promote STEM in your local schools.

Stem Education Coalition

DOE Pulse highlights work being done at the Department of Energy’s national laboratories. DOE’s laboratories house world-class facilities where more than 30,000 scientists and engineers perform cutting-edge research spanning DOE’s science, energy, National security and environmental quality missions. DOE Pulse is distributed twice each month.

From PNNL: “CENATE: A Computing Proving Ground”

PNNL Lab

October 2015 [This was just made available.]

New center at PNNL will shape future extreme-scale computing systems

PNNL’s Seapearl compute cluster can closely monitor and measure power and temperature in high-performance computing systems

High-performance computing systems at the embedded or extreme scales are a union of technologies and hardware subsystems, including memories, networks, processing elements, and inputs/outputs, with system software that ensure smooth interaction among components and provide a user environment to make the system productive. The recently launched Center for Advanced Technology Evaluation, dubbed CENATE, at Pacific Northwest National Laboratory is a first-of-its-kind computing proving ground. Before setting the next-generation, extreme-scale supercomputers to work solving some of the nation’s biggest problems, CENATE’s evaluation of early technologies to predict their overall potential and guide their designs will help hone future technology, systems, and applications before these high-cost machines make it to production. Funding for CENATE at PNNL is being provided by the U.S. Department of Energy’s Office of Advanced Scientific Computing Research.

Modern computing systems are increasingly complex, incorporating a multitude of leading-edge technologies and nonlinear interactions. This complexity has led to a growing and continuous need to employ advanced methods to reassess; prototype; measure; and anticipate, using performance and power modeling and simulation, the life cycle of new technologies, as well as the co-design of new computing systems and applications.

CENATE uses a multitude of “tools of the trade,” depending on the maturity of the technology under investigation. The scientists in CENATE will conduct research in a complex measurement laboratory setting that allows for measuring performance, power, reliability, and thermal effects. When actual hardware is not available for technologies early in their life cycle, modeling and simulation techniques for power, performance, and thermal modeling will be used. Through its Performance and Architecture Laboratory (PAL)—a key technical capability of the Laboratory—PNNL can offer a unique modeling environment for high-performance computing systems and applications. In a near-turnkey way, CENATE will evaluate both complete system solutions and individual subsystem component technologies, from pre-production boards and technologies to full nodes and systems that pave the way to larger-scale production. CENATE will focus on technology evaluations in the context of workloads of interest to DOE’s Office of Science and build on instrumentation and expertise already gleaned from other programs and PNNL institutional investments.

CENATE stands apart because its overarching goal is to take these advanced technology evaluations out of isolation. CENATE will provide the central point for these once-fragmented investigations, incorporating a user facility type of model where other national laboratories and technology providers will have the opportunity to access CENATE resources and share in the integrated evaluation and prediction processes that can benefit computing research.

“A central focus on examining the prediction of potential future extreme-scale high-performance computing systems has been missing from DOE’s HPC research community,” said Adolfy Hoisie, PNNL’s chief scientist for computing and the principal investigator and director of CENATE. “In PAL, we already have applicable resources and experience amid its considerable modeling and simulation of systems and applications portfolio to undertake the empirical evaluations, and we have steadily invested in dedicated infrastructure. CENATE will allow us to bolster our dedicated laboratory with leading-edge testbeds and measurement equipment for rapidly evolving technology evaluations. We also will make the most of our industry connections, adding ‘loaner’ equipment to CENATE’s technology mix as appropriate.”

CENATE evaluations will mostly concern processors; memory; networks; storage; input/output; and the physical aspects of certain systems, such as sizing and thermal effects. All associated system software will be included in the evaluation and analyses, with some investigations emphasizing system software. Multiple types of testbeds will be employed to examine advanced multi-core designs and memory component technologies, as well as smaller-scale technologies with a small number of nodes that can be interconnected using a commodity-type or proprietary network. CENATE’s testbeds also will accommodate larger-scale advanced scalability platforms with hybrid or homogeneous processor technologies and state-of-the-art network infrastructures, as well as disruptive technologies not typically evaluated as physical testbeds, such as Silicon Photonics or quantum computing.

“We’ll strive for CENATE to become the premier destination for technology evaluation, measurement facilities, testbeds, and predictive exploration—driven by transparency and collaboration—that will shape the design and capabilities of future exascale computing systems and beyond,” Hoisie added.

See the full article here .

Please help promote STEM in your local schools.

Stem Education Coalition

From PNNL: “Proud Model: Rolling on the River”

PNNL Lab

Niagara River. The new model can simulate how water makes it into tributaries and the main river channel by way of runoff and below-surface water you can’t see. The ability to simulate water’s complex paths through the landscape is important to understand how human water use impacts Earth’s water cycle.

Results:Drinking, irrigation and energy production. These are just three uses for freshwater provided by rivers to the world’s people. Understanding the rivers’ flow is important, especially as water uses and sources change. As reported in the Journal of Hydrometeorology, a team led by scientists at Pacific Northwest National Laboratory coupled a newly developed river-routing model with an Earth system model, and the simulated streamflow compared favorably against the observed streamflow from more than 1,600 major river stations worldwide. They also found that the added complexity in the new model adopted in Earth system models improves the model’s ability to capture the variability of the observed streamflow. This new feature allows it to represent human influence on the river systems.

Why It Matters: The quality and quantity of freshwater is being increasingly affected by new demands on the system-not only increased demands for use, but changes in the climate. Drought, floods and changes in weather systems all affect freshwater supply. In many areas, rivers provide the majority of freshwater for important uses. Accurately simulating the ebb and flow of rivers is important for understanding and predicting changes in the river. The global river-routing model described in this study simulates water quantity but it forms the basis for modeling stream temperature, sediments and nutrients that can greatly affect rivers and water quality.

“Evaluating the global streamflow simulation is a major milestone before we take on the next challenges in modeling other aspects of the river system, because water quantity affects the energy and matter flowing in the rivers,” said Dr. Hong-Yi Li, a PNNL hydrologist who led the study.

Methods: In this study, a physically based routing model, the MOdel for Scale Adaptive River Transport (MOSART), was coupled with the land component of Community Earth System Model (CESM) called Community Land Model. The gridded CLM-simulated surface runoff and base flow were provided to MOSART at the end of each time step, and MOSART routed the runoff across hillslope and through tributaries and main channels of the river network. One distinct feature of MOSART compared to the previous river transport model in CLM is that MOSART explicitly simulates through both space and time the variability of flow velocity. The team showed that simulating the spatial and temporal variability of river velocity is necessary for capturing the seasonal nature of streamflow and annual maximum floods.

The PNNL team collaborated with scientists from University of Maryland to develop a comprehensive global hydrography database at 7 different spatial resolutions, ranging from 1/16 to 2 degree resolutions. The team evaluated the simulated streamflow globally against the observations from 1,674 major river gauge stations worldwide and systematically examined possible sources of model biases, which can impact the range of answers in simulations. These included model structure complexity, atmospheric forcing and the human influences on streamflow reflected in the observed streamflow in regulated rivers.

The river-routing model has been added to CESM and the Department of Energy’s new Earth system model called Accelerated Climate Modeling for Energy (ACME) to support a wide range of research.

What’s Next? PNNL researchers are testing the implementation of MOSART into CESM and ACME. The team has extended MOSART to simulate stream temperature representing the effects of reservoir operations. In addition, they are now extending MOSART to simulate how sediment, carbon and other nutrients move from the landscape through the rivers and into the ocean.

See the full article here .

Please help promote STEM in your local schools.

Stem Education Coalition

From PNNL- “Good Is Not Enough: Improving Measurements of Atmospheric Particles”

PNNL Lab

September 2015
No Writer Credit

Results: When it comes to understanding how atmospheric particles affect climate, one measurement can’t tell the whole story, especially in areas that haven’t been studied. A research team led by Pacific Northwest National Laboratory developed an approach that links the scattering coefficient, a measure of how much tiny particles suspended in the atmosphere scatter sunlight, with other particle properties. These properties include particle size, chemical composition, and ability to soak up atmospheric water. By linking these measurements, scientists can better understand the effects of a wide range of particles, including those that scatter sunlight (non-absorbing particles) and those that both scatter and absorb sunlight (absorbing particles).

“We found that one property influenced the others,” said Dr. Evgueni Kassianov, PNNL atmospheric scientist and lead author of the article published in Atmosphere. “Using improved airborne measurements of particle scattering and absorbing properties and chemical composition, we can better measure their size distribution as well.”

The U.S. Department of Energy’s Gulfstream-1 aircraft collects data that a team of experts led by PNNL used to develop an approach estimating the properties of tiny airborne particles that can affect climate. Photo courtesy of the ARM Climate Research Facility.

A large aerosol particle plume moves eastward in this “True-color Sea-viewing Wide Field-of-view Sensor (SeaWiFS)” image over the North Atlantic Ocean near Cape Cod. These aerosols are part of the particles suspended in the atmosphere that affect the amount of sunlight reaching the Earth, or scattered in the atmosphere. Image courtesy of the NASA EOS Project Science Office.

Why It Matters: Aerosols, tiny airborne particles of dust and pollution suspended in the atmosphere, affect the atmosphere and the surface of Earth by scattering and absorbing light. The sun’s light scatters when it is reflected off the particles and redistributed. The particles’ absorption of sunlight heats up the atmosphere while at the same time reducing the amount of sunlight reaching Earth. The combined effects of scattering and absorption can either cool or warm Earth’s surface and the atmosphere itself. Understanding the properties associated with these particles gives scientists an edge in estimating the particles’ impact on our climate.

Methods: The PNNL scientists collaborated with colleagues at the University of Nevada and Brookhaven National Laboratory to develop a mathematical framework for calculating the total scattering of both non-absorbing and absorbing particles at ambient conditions based on data collected from aircraft. They then tested the approach using data collected by the U.S. Department of Energy’s Gulfstream-1 aircraft during the recent Atmospheric Radiation Measurement (ARM) Climate Research Facility’s Two-Column Aerosol Project, led by Dr. Larry K. Berg, a PNNL researcher and co-author of the research.

Measurements included optical, microphysical, and chemical properties of weakly absorbing particles. The team compared the scattering coefficient obtained by their approach with the scattering coefficient measured on board the aircraft and found good agreement between the estimated and measured scattering coefficients for a wide range of observational conditions. The new approach will enable scientists to accurately estimate these particle properties, even in areas previously unstudied.

What’s Next? The research team plans to apply their approach to strongly absorbing particles. Given the increasing availability of aerosol composition data collected from aircraft, the team expects that their approach can be successfully applied to improve understanding of a wide range of sophisticated processes and phenomena related to aerosols, including how properties evolve with time and the dynamic interactions between aerosols and clouds.

See the full article here .

Please help promote STEM in your local schools.

Stem Education Coalition