http://science.energy.gov/ber/highlights/The Office of Science is the single largest supporter of basic research in the physical sciences in the United States, providing more than 40 percent of total funding for this vital area of national importance. It oversees - and is the principal federal funding agency of - the Nation's research programs in high-energy physics, nuclear physics, and fusion energy sciences.en{E48A0243-AEC7-4CD4-9759-C171D5B7FF9A}http://science.energy.gov/ber/highlights/2012/ber-2012-09-a/<img src='/~/media/ber/images/highlights/2012/09/chang-thumb.jpg' align='left' style='height:75px;width:135px;margin-right:10px;margin-bottom:10px;'/>Understanding factors influencing a cyclone’s path and intensity improves our ability to forecast and mitigate impacts.Mon, 18 Mar 2013 10:27:17 -0400 <p>A barrier layer in ocean environments, or Mixed Layer Depth, is defined as the depth where the density increases from the surface value due to a prescribed temperature decrease of some value (e.g., 0.2&deg;C) from the surface value while maintaining constant surface salinity value. Using a combination of observations and model simulations, the team demonstrated that barrier layers, formed through high fresh water input reducing the salinity in the upper tropical oceans, significantly increase the intensity of tropical cyclones. When tropical cyclones pass over these regions, the increased stratification and stability within the layer reduce storm-induced vertical mixing and sea surface temperature cooling. Their findings underscore the importance of observing salinity structure in deep tropical barrier layer regions.  As the hydrological cycle responds to global warming, any associated changes in the barrier layer distribution must be considered in projecting future tropical cyclone activity.</p> {67BFD15D-1E11-4E8E-BD17-650AA2EDEDA6}http://science.energy.gov/ber/highlights/2012/ber-2012-09-b/<img src='/~/media/ber/images/highlights/2012/09/poplar-trees-thumb.jpg' align='left' style='height:75px;width:135px;margin-right:10px;margin-bottom:10px;'/>Knowing how Poplar trees make wood enables us to optimize their use for bioenergy production.Mon, 18 Mar 2013 10:27:16 -0400 <p>Poplar is a promising bioenergy feedstock due to its rapid growth, large biomass and because sugars extracted from the lignocellulosic biomass (wood) of these native trees can be fermented to form renewable biofuels. These sugars are embedded within lignin, a complex, rigid structure that is critical to the overall health of the plant but that also impeded extraction of the sugars. New DOE research is providing insight into how the lignocellulosic material forms in poplar. The process involves the expression of a cascade of genes whose regulation is poorly understood. The researchers at North Carolina State University report their discovery of a single protein (“controller” protein) that regulates this cascade on multiple levels to ensure normal growth, doing so in a way never before seen in plants. The controller protein was found outside the cell nucleus. In the presence of one of four other related proteins, it is carried into the nucleus where the two proteins bind. The newly-formed molecule then suppresses expression of the regulatory gene cascade. </p> {E5F4E881-2738-4AC7-8B30-A6DF89B215DF}http://science.energy.gov/ber/highlights/2012/ber-2012-09-c/<img src='/~/media/ber/images/highlights/2012/09/gregurick-palsson-thumb.jpg' align='left' style='height:75px;width:135px;margin-right:10px;margin-bottom:10px;'/>Enzyme “promiscuity” and “monogamy” play a significant role in myriad biochemical reactions.Mon, 18 Mar 2013 10:27:16 -0400 <p>In biology, some enzymes are highly specialized and catalyze specific reactions with few or only one substrate while other enzymes are promiscuous and can catalyze reactions using a variety of substrates. This phenomenon has also been observed experimentally for microbes involved in bioenergy related processes. However, we don’t understand why, within an organism, some enzymes are highly specialized while others remain generalists. Recently Nam and co-workers have addressed this question using whole genome metabolic reconstructions and analysis, including dynamical simulations of environmental changes to understand microbial responses. The higher flux and higher regulation allows enzymes with very specialized functions to be more responsive and adaptive to environmental surroundings and changes then their less specialized counterparts. This work also illustrates that understanding environmental cellular physiology is greatly enhanced when using a systems biology approach rather than approaches that are focused on single enzymes simulations.</p> {EB315AB0-A12A-4678-9886-4F1FD5465001}http://science.energy.gov/ber/highlights/2012/ber-2012-09-d/<img src='/~/media/ber/images/highlights/2012/09/graber-meeks-thumb.jpg' align='left' style='height:75px;width:135px;margin-right:10px;margin-bottom:10px;'/>Discovering how a microbe makes complex structures to perform complex functions.Mon, 18 Mar 2013 10:27:15 -0400 <p>In comparison to multicellular plants and animals, bacteria are relatively simple, typically existing as single cells. However, some bacteria cooperate to form surprisingly sophisticated  structures. The photosynthetic microbe <em>Nostoc punctiforme</em> forms long filaments of connected cells. At regular spacing along these filaments, individual cells differentiate to form heterocysts, non-photosynthetic cells that convert nitrogen gas into biologically useful nitrogen compounds. This patterning allows these microbes to separately perform both photosynthesis (which produces O₂ as byproduct) and “fix” nitrogen using enzymes that are poisoned by oxygen, cooperatively exchanging the resulting nutrients between the cell types. In a new study, DOE researchers at the University of California, Davis describe genetic mechanisms responsible for the establishment and maintenance of this distinctive pattern in growing filaments. When the expression of a series of regulatory genes (the “pat system”) was experimentally manipulated, filaments formed with abnormal distributions of heterocysts. By analyzing these patterns and tracking the distribution of related proteins in dividing cells, the investigators were able to develop a new model describing the regulatory interactions resulting in the pattern that allows optimal photosynthesis and nitrogen fixation in the filaments.</p> {931D7F26-CAE3-4E2E-8070-B1CC81A6639C}http://science.energy.gov/ber/highlights/2012/ber-2012-08-a/<img src='/~/media/ber/images/highlights/2012/08/koch-barton-thumb.jpg' align='left' style='height:75px;width:135px;margin-right:10px;margin-bottom:10px;'/>Arctic clouds, major controllers of the radiative budget, are now better represented in climate models.Mon, 18 Mar 2013 10:27:18 -0400 <p>The Arctic Ocean’s surface alters between ocean and sea ice. This variation, along with atmospheric dynamics and thermodynamics, affects Arctic cloud properties. DOE scientists at Lawrence Livermore National Laboratory (LLNL) developed a method to evaluate Arctic clouds in the Community Earth System Model’s (CESM) two most recent global atmospheric models that are used in the coupled transient climate projections, the Community Atmospheric Model Version 4 and 5 (CAM4 and CAM5). Clouds were first examined during distinctly separate dynamical and thermo-dynamical conditions, which were called synoptic regimes. Next, clouds fractions for each regime were examined when the regime occurred over open-ocean, sea ice, and land. The scientists ran CAM4 and CAM5 using the DOE Cloud-Associated Parameterizations Testbed (CAPT) framework to ensure the dynamics and thermodynamics in the models were similar to the observations. From CAM4 to CAM5, there was a large community effort to improve the representation of boundary layer clouds, which are prevalent in the Arctic.</p> {34724901-4530-4070-91EA-9629A3EBDF58}http://science.energy.gov/ber/highlights/2012/ber-2012-08-b/<img src='/~/media/ber/images/highlights/2012/08/single-celled-marine-cyanobacterium-cyanothece-thumb.jpg' align='left' style='height:75px;width:135px;margin-right:10px;margin-bottom:10px;'/>A microbe able to produce hydrogen without typical poisoning by oxygen production.Mon, 18 Mar 2013 10:27:17 -0400 <p>One challenge to the commercialization of microbial production of hydrogen using sunlight is that the oxygen produced by photosynthesis decreases hydrogen production. Various biological mechanisms have evolved to separate the two reactions and scientists have been looking for engineering solutions, but the challenge is not yet solved. The bacteria produce hydrogen at relatively high rates without high cell density or inducing circadian rhythms, as required in studies by other researchers. Furthermore, there is little photo-damage and decay of the photosynthesis apparatus, perhaps enabled by the removal of excess electrons by the hydrogen production.</p> {C1979465-F9B1-4C9F-B9EE-4341F32D0B95}http://science.energy.gov/ber/highlights/2012/bes-2012-07-b/<img src='/~/media/34DCFCF74E5649CDA7424992D2865AA9.ashx' align='left' style='height:75px;width:135px;margin-right:10px;margin-bottom:10px;'/>Nanoscale features in rocks enable more carbon dioxide to be trapped as a solid carbonate material underground.Fri, 10 May 2013 16:37:57 -0400<p>Advanced experiments and computations have shown that underground carbonate mineral nucleation and growth is strongly dependent on nanoscale features such as the pore structure and surface topography of permeable rocks and the interfacial energies between rock surfaces and solid carbonates. This research at the Lawrence Berkeley National Laboratory&rsquo;s Center for Nanoscale Control of Geologic CO₂, Washington University in St. Louis, and Oregon State University provides the quantitative parameters necessary to develop advanced models that describe how nucleation and growth of carbonate occur in porous media that contain multiple minerals with different surface properties and micro- to nanoscale pores. In carbon capture and storage, CO₂ is captured from power plant exhaust and other sources and injected underground into porous rock formations where it mixes with ambient salt water and may remain for 1000&rsquo;s of years. Although it is expected that CO₂ can be transformed to carbonate minerals, it is unknown how fast this will occur and how the addition of new carbonate mineral in the rock formations will affect the short and long-term behavior of the system. This research will enable more realistic modeling of mineral formation from the injected CO₂ and thus increase the pace of deployment of this critical energy technology.</p>{5D57B763-F10F-455A-A9DA-9F8F5304AD9B}http://science.energy.gov/ber/highlights/2012/ber-2012-06-a/<img src='/~/media/ber/images/highlights/2012/06/ad-2009-sep-20-amanita-muscaria-thumb.jpg' align='left' style='height:75px;width:135px;margin-right:10px;margin-bottom:10px;'/>Insights into the origin of ligninases can help develop processes to convert biomass into bioenergy.Mon, 18 Mar 2013 10:27:19 -0400 <p>Much of the world’s coal was generated 300–360 million years ago during the Carboniferous period. Wood (a major pool of organic carbon that is highly resistant to decay largely due to its lignin content) was deposited, transformed to peat, and eventually transformed to coal. But coal formation may also have declined from an unlikely source - fungi. These fungi had enzymes (ligninases) capable of degrading lignin, a category of enzyme important for the Department of Energy’s bioenergy mission, since lignin in plant biomass hinders biomass conversion to biofuels. By comparing the genomic sequences of 31 fungi, including 12 sequenced for this study, the researchers showed that genes able to degrade lignin first appeared at the end of this period. Instead of becoming coal, the plant biomass decayed and the carbon was released into the atmosphere as carbon dioxide.</p> {CC675AE6-9F6E-43AD-A1F4-0F1A13A02B43}http://science.energy.gov/ber/highlights/2012/ber-2012-06-b/<img src='/~/media/ber/images/highlights/2012/06/journal-pone-thumb.jpg' align='left' style='height:75px;width:135px;margin-right:10px;margin-bottom:10px;'/>A microbe not known for cellulose degradation has 15 cellulases that may improve biofuel production.Fri, 10 May 2013 16:38:17 -0400 <p>The biotechnology and biofuels industries are particularly interested in cellulases, enzymes that break down cellulose, the most abundant organic compound on Earth and the component that makes up 33 percent of all plant matter. Cellulases from a group of aerobic bacteria called <em>Actinobacteria</em> are of special interest as sources of enzymes useful for biofuel production from lignocellulosic biomass. They have distinct features and cellular organization when contrasted to those in anaerobic bacteria (such as the <em>Clostridia</em>). The DOE Joint Genome Institute (JGI) has sequenced the genomes of eleven diverse strains of these bacteria. Comparative analysis using the JGI’s Integrated Microbial Genomes system followed by experimental verification identified eight cellulolytic Actinobacterial species that were not previously known to degrade cellulose. Of seven organisms tested, six showed activity in assays for cellulases. This work, conducted under the umbrella of the JGI’s Genomic Encyclopedia of Bacteria and Archaea (GEBA) project, broadens the repertoire of useful enzymes beyond those previously recognized.</p> {B048B78A-D799-4A76-A7CF-E14F3637AC64}http://science.energy.gov/ber/highlights/2012/ber-2012-06-c/<img src='/~/media/ber/images/highlights/2012/06/lintner-thumb.jpg' align='left' style='height:75px;width:135px;margin-right:10px;margin-bottom:10px;'/>Impacts of anthropogenic warming on tropical land region rainfall.Fri, 10 May 2013 16:38:22 -0400 <p>Quantifying how global warming impacts the spatiotemporal distribution of precipitation represents a key scientific challenge with profound implications for human systems.  In particular, tropics-wide precipitation frequencies for 25-year periods over the late 21st and 20th centuries show increased late-21st-century occurrence of both extremes in the model ensemble and across individual models.  Similar diagnostics are calculated for two 15-year subperiods from 1979-2008 to assess whether the signature of late-21st-century warming has already emerged in response to recent warming.  While both the observations and CMIP3 ensemble-mean hint at similar amplification in the warmer (1994-2008) subinterval, the changes are not robust, as substantial differences are evident among the observational products and the intraensemble spread is large.  Comparing results from the warmest and coolest years of the observational period further demonstrates effects of internal variability, notably the El Niño/Southern Oscillation, which appear to oppose the impact of quasi-uniform anthropogenic warming on the wet tail of the monthly precipitation distribution.</p> {A76E7315-2A24-46AA-8610-56925C2E5A25}http://science.energy.gov/ber/highlights/2012/ber-2012-05-a/<img src='/~/media/ber/images/highlights/2012/05/drell-blanc-thumb.jpg' align='left' style='height:75px;width:135px;margin-right:10px;margin-bottom:10px;'/>A polar alga with lipid metabolism enzymes may prove useful harnessing algae for biodiesel production.Mon, 18 Mar 2013 10:27:20 -0400 <p>Algae are of major interest to researchers who are developing alternative energy sources. For example, lipids making up algal membranes can be transformed into biodiesel. One photosynthetic alga, <em>Coccomyxa subellipsoidea</em> C-169, was recently isolated in Antarctica and now is the first alga from a polar region to have its genome sequenced. Surprisingly, the alga thrives at temperatures close to 20ºC, though it is tolerant of the cold temperatures in the Antarctic.<em> C. subellipsoidea</em> was sequenced by the DOE Joint Genome Institute and its predicted protein families were compared with those from several other sequenced green algae. This greater versatility of lipid metabolism is thought to have contributed to its adaptation to cold.</p> {A8181AFC-8ECE-4D62-9E2D-9B5876F86778}http://science.energy.gov/ber/highlights/2012/ber-2012-05-b/<img src='/~/media/ber/images/highlights/2012/05/koch-gao-thumb.jpg' align='left' style='height:75px;width:135px;margin-right:10px;margin-bottom:10px;'/>Regional Climate Models predict greater drought resistance in southwest U.S. than General Circulation Models (GCMs).Mon, 18 Mar 2013 10:27:20 -0400 <p>Getting an accurate projection of water cycle changes for the southwestern United States (SW) is becoming increasingly more urgent in light of regional drought trends and changes in the Colorado River flow. A research team, including a DOE scientist from Pacific Northwest National Laboratory, analyzed the future climate from four pairs of regional and global climate models (RCMs and GCMs). The water cycle of the region is dominated by winter storms that maintain a positive annual net precipitation (precipitation minus evapotranspiration). The analysis shows that compared to GCMs, RCMs simulate enhanced transient moisture convergence in the SW, although both robustly simulate large-scale drying due to enhanced moisture divergence by the divergent mean flow in a warmer climate.</p> {D6D61DA6-9190-46CE-9E6C-09E22308F05E}http://science.energy.gov/ber/highlights/2012/ber-2012-05-c/<img src='/~/media/ber/images/highlights/2012/05/liu-mam-thumb.jpg' align='left' style='height:75px;width:135px;margin-right:10px;margin-bottom:10px;'/>Complex aerosol processes accurately captured in climate models with a new, minimal aerosol module.Mon, 18 Mar 2013 10:27:20 -0400 <p>Accurately simulating climate change requires inclusion of full interactions between tiny aerosol particles, clouds and climate. This in turn requires that aerosol size and mixing conditions be resolved and that multiple species be carried in the climate model. A new aerosol scheme that includes these features is now available for the Community Earth System Model (CESM1). DOE researchers at Pacific Northwest National Laboratory led the development of a Modal Aerosol Module (MAM) for the Community Atmospheric Model version 5 (CAM5), the atmospheric component of CESM1. MAM can simulate the aerosol size distribution and mixing states between different aerosol components, and can treat numerous aerosol physical and chemical processes. Two versions of MAM were developed: a complete version with 7 aerosol modes serving as the benchmark and used for detailed aerosol studies, and a simplified version with 3 aerosol modes used for decade to century climate simulations. MAM does a good job of simulating the temporal and spatial distributions of aerosol mass, number and size distribution, and aerosol optical depth compared to observations, although some biases, such as underestimation of black carbon in the Arctic and underestimation of aerosol loading near source regions, will require further development. MAM is being used in CESM1 for the International Panel on Climate Change 5th Assessment Report. MAM has also been adopted by other major global and regional models (e.g., NASA GEOS-5 and the Weather Research Forecast Model).  The complexities of aerosol properties and processes, and limitations of computer resources have made it a challenge for global climate models (GCMs) to realistically represent aerosols.</p> {95EE58C7-FF86-4361-AA38-2322621F2E0A}http://science.energy.gov/ber/highlights/2012/ber-2012-04-a/<img src='/~/media/ber/images/highlights/2012/04/binary-cultivation-in-photobioreactors-thumb.jpg' align='left' style='height:75px;width:135px;margin-right:10px;margin-bottom:10px;'/>New insights into the effect of light quality on bacterial metabolism and respiration.Mon, 18 Mar 2013 10:27:21 -0400 <p>Cyanobacteria are prime candidates for the biological production of biofuels, especially hydrogen. They photosynthesize in sunlight, have relatively fast growth rates, are tolerant to extreme environments, and can accumulate high amounts of intracellular compounds and produce large quantities of H₂. The model and experiments provide new insights into the effect of light quality on metabolism and the bacteria’s mechanisms for balancing reductant and electron flows. The model differs from similar models of other cyanobacteria in its detailed treatment of the photosynthesis and respiratory systems. The photobioreactor features dual sources of monochromatic light that can vary photon flux with wavelengths that are tuned to the two bacterial photosynthesis systems.</p> {332740D4-A9D4-4396-A2B1-5A7C8B340540}http://science.energy.gov/ber/highlights/2012/ber-2012-03-a/<img src='/~/media/ber/images/highlights/2012/03/mt-ruapehu-ash-snow-thumb.jpg' align='left' style='height:75px;width:135px;margin-right:10px;margin-bottom:10px;'/>Snow reflects less solar radiation when contaminated with black carbon.Mon, 18 Mar 2013 10:27:22 -0400 <p>Climate models indicate that the reduction of surface albedo caused by black carbon (BC) contamination of snow contributes to global warming and near-worldwide melting of ice. However, model predictions of BC-caused snow albedo reduction over a range of BC levels and snow grain sizes have not been verified by measurements. The main reason is that the BC effect is typically masked in natural environments by other variables that influence albedo, such as snow grain size, snow density, snow depth and the interaction of sunlight with the underlying surface, tree cover and solar zenith angle. These methods enabled quantification of the snow albedo reduction associated with increasing amounts of BC and as a function of snow grain size. The study verified that black carbon contamination at levels that have been found in natural settings appreciably reduces snow albedo. Increasing the size of snow grains decreased snow albedo and amplified the radiative perturbation of black carbon, which justifies the aging-related positive feedbacks that are included in climate models. Moreover, these data provide an extensive verification of a snow, ice, and aerosol radiation model which will be included in the next assessment of the Intergovernmental Panel on Climate Change.</p> {3E3C967A-612F-4580-937F-FA496AAC1850}http://science.energy.gov/ber/highlights/2012/ber-2012-02-a/<img src='/~/media/ber/images/highlights/2012/02/ivanova-thumb.jpg' align='left' style='height:75px;width:135px;margin-right:10px;margin-bottom:10px;'/>Does polar ice erosion come from atmospheric heating or from oceanic advection of warm waters?Mon, 18 Mar 2013 10:27:23 -0400 <p>The model passes an important test of sea-ice distribution changes: when the model is driven by the observed-reanalysis winds of the 1990’s, it successfully simulates the observed dipole pattern of ice concentration changes characteristic of the changes associated with North Atlantic Oscillation pressure and circulation changes.  The model successfully simulates the first mode of sea ice concentration variability, which is characterized by a dipole pattern of ice concentration anomalies, coherent with the atmospheric North Atlantic Oscillation (NAO) pressure pattern. The model ocean-ice system was forced with NCEP/NCAR atmospheric reanalysis and then run for the two NAO periods during the 1990s.  The upper ocean mixed layer heat budgets were analyzed in the Barents, Nordic, and Irminger Seas to determine the winter-to-winter changes in the ocean heat advection and mixed layer net fluxes and these were then related to the ice changes. The ocean advection anomalies were also closely related to anomalous bottom ice melt rates. However although the oceanic temperature advection is of the same order of magnitude as the net atmospheric heat fluxes, the latter are always larger. Entrainment of heat from the deeper ocean may also play a key role in the upper ocean heat balance and this may be strongly influenced by ocean heat advection. Future research will consider the role of the deeper ocean upwelling, and will continue to investigate the relative importance of atmospheric and oceanic processes in eroding polar sea-ice.</p> {AE569D8A-E975-4A6E-B37D-101194379C74}http://science.energy.gov/ber/highlights/2012/ber-2012-02-b/<img src='/~/media/ber/images/highlights/2012/02/1754-6834-5-5-thumb.jpg' align='left' style='height:75px;width:135px;margin-right:10px;margin-bottom:10px;'/>Researchers develop new assay for ease of converting plant biomass to ethanol.Mon, 18 Mar 2013 10:27:22 -0400 <p>The conversion of plant biomass to liquid transportation fuel using consolidated bioprocessing (CBP) technology is a promising, cost-efficient strategy to develop energy from renewable sources.  CBP takes advantage of the ability of certain microbes to convert sugars contained within the plant cell wall to high-energy chemicals such as ethanol or butanol, but the efficiency can be hampered by the recalcitrance of certain plant materials to deconstruction. While plant cell wall composition and corresponding resistance to breakdown varies considerably within plant species, this genetic diversity can potentially be exploited if plant material is efficiently screened for such properties. The anaerobic bacterium <em>Clostridium phytofermentans</em>, is capable of directly converting a wide array of fermentable biomass components to ethanol without the addition of costly, exogenous, deconstruction enzymes. The assay, which measures ethanol production under the influence of different variables, was tested on both herbaceous grasses and woody plants. Significant differences in ethanol production within individual plant species were found, indicating detection of subtle genetic differences.</p> {99832BE0-0677-4C50-9079-929C389E1EB3}http://science.energy.gov/ber/highlights/2011/bes-2011-02-a/<img src='/~/media/bes/images/highlights/2011/02/kp-uranium-thumb.jpg' align='left' style='height:75px;width:135px;margin-right:10px;margin-bottom:10px;'/>Understanding the interaction of uranium in soils may lead to new ways to clean-up contaminated ground.Fri, 10 May 2013 15:57:05 -0400 <p>Determining how radioactive material sticks to soil and affects its movement into nearby water sources is a major challenge for cleaning up nuclear waste sites. This waste, which may include uranium, can be diffuse as well as difficult to isolate and remove. To reduce the cost and complexity of complete removal, innovative and inexpensive methods are needed to expedite clean-up efforts around the world, especially in sites with vast areas of contamination. Scientists at Pacific Northwest National Laboratory discovered that the surface of a common soil mineral, aluminum oxide, adheres to uranium making it less mobile. The researchers assembled a detailed picture of how uranium adheres to the mineral surface using a computational model. By modeling the behavior of uranium in a complex subsurface environment, they were able to show that uranium sticks to the surface of aluminum oxide without changing it in any way and that a more acidic environment improves how well the two stick together. This cluster model approach used by the researchers allows for a straight forward comparison to be made between different sorption mechanisms and predictions can be directly related to X-ray adsorption experiment measurements. This approach can be used to model surface reactivity and be further utilized in other complex model systems.</p>