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Fungal Enzymes Team Up to More Efficiently Break Down Cellulose

Cost-effectively breaking down bioenergy crops into sugars that can then be converted into fuel is a barrier to commercially producing sustainable biofuels. Enabled by DOE User Facilities, a team reports that early lineages of fungi can form enzyme complexes capable of degrading plant biomass.

Argonne Scientists Make Vanadium Into a Useful Catalyst for Hydrogenation

In a new study, Argonne chemist Max Delferro boosted and analyzed the unprecedented catalytic activity of an element called vanadium for hydrogenation - a reaction that is used for making everything from vegetable oils to petrochemical products to vitamins.

Printed, Flexible and Rechargeable Battery Can Power Wearable Sensors

Nanoengineers at the University of California San Diego have developed the first printed battery that is flexible, stretchable and rechargeable. The zinc batteries could be used to power everything from wearable sensors to solar cells and other kinds of electronics. The work appears in the April 19, 2017 issue of Advanced Energy Materials.

Neutrons Provide the First Nanoscale Look at a Living Cell Membrane

A research team from the Department of Energy's Oak Ridge National Laboratory has performed the first-ever direct nanoscale examination of a living cell membrane. In doing so, it also resolved a long-standing debate by identifying tiny groupings of lipid molecules that are likely key to the cell's functioning.

How X-Rays Helped to Solve Mystery of Floating Rocks

Experiments at Berkeley Lab's Advanced Light Source have helped scientists to solve a mystery of why some rocks can float for years in the ocean, traveling thousands of miles before sinking.

Special X-Ray Technique Allows Scientists to See 3-D Deformations

In a new study published last Friday in Science, researchers at Argonne used an X-ray scattering technique called Bragg coherent diffraction imaging to reconstruct in 3-D the size and shape of grain defects. These defects create imperfections in the lattice of atoms inside a grain that can give rise to interesting material properties and effects.

Neptune: Neutralizer-Free Plasma Propulsion

The most established plasma propulsion concepts are gridded-ion thrusters that accelerate and emit a larger number of positively charged particles than those that are negatively charged. To enable the spacecraft to remain charge-neutral, a "neutralizer" is used to inject electrons to exactly balance the positive ion charge in the exhaust beam. However, the neutralizer requires additional power from the spacecraft and increases the size and weight of the propulsion system. Researchers are investigating how the radio-frequency self-bias effect can be used to remove the neutralizer altogether, and they report their work in this week's Physics of Plasmas.

Report Sheds New Insights on the Spin Dynamics of a Material Candidate for Low-Power Devices

In a report published in Nano LettersArgonne researchers reveal new insights into the properties of a magnetic insulator that is a candidate for low-power device applications; their insights form early stepping-stones towards developing high-speed, low-power electronics that use electron spin rather than charge to carry information.

Researchers Find Computer Code That Volkswagen Used to Cheat Emissions Tests

An international team of researchers has uncovered the mechanism that allowed Volkswagen to circumvent U.S. and European emission tests over at least six years before the Environmental Protection Agency put the company on notice in 2015 for violating the Clean Air Act. During a year-long investigation, researchers found code that allowed a car's onboard computer to determine that the vehicle was undergoing an emissions test.

Physicists Discover That Lithium Oxide on Tokamak Walls Can Improve Plasma Performance

A team of physicists has found that a coating of lithium oxide on the inside of fusion machines known as tokamaks can absorb as much deuterium as pure lithium can.


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University of Wisconsin-Milwaukee Joins Energy-Focused National Science Foundation Research Center

The University of Wisconsin-Milwaukee is joining a National Science Foundation-backed research center that will develop new technologies for storing, controlling and distributing energy that could ward off cybersecurity threats and lower energy bills.

Rensselaer Polytechnic Institute Graduates Urged to Embrace Change at 211th Commencement

Describing the dizzying pace of technological innovation, former United States Secretary of Energy Ernest J. Moniz urged graduates to "anticipate career change, welcome it, and manage it to your and your society's benefit" at the 211th Commencement at Rensselaer Polytechnic Institute (RPI) Saturday.

ORNL Welcomes Innovation Crossroads Entrepreneurial Research Fellows

Oak Ridge National Laboratory today welcomed the first cohort of innovators to join Innovation Crossroads, the Southeast region's first entrepreneurial research and development program based at a U.S. Department of Energy national laboratory.

Department of Energy Secretary Recognizes Argonne Scientists' Work to Fight Ebola, Cancer

Two groups of researchers at Argonne earned special awards from the office of the U.S. Secretary of Energy for addressing the global health challenges of Ebola and cancer.

Jefferson Science Associates, LLC Recognized for Leadership in Small Business Utilization

Jefferson Lab/Jefferson Science Associates has a long-standing commitment to doing business with and mentoring small businesses. That commitment and support received national recognition at the 16th Annual Dept. of Energy Small Business Forum and Expo held May 16-18, 2017 in Kansas City, Mo.

Rensselaer Polytechnic Institute President's Commencement Colloquy to Address "Criticality, Incisiveness, Creativity"

To kick off the Rensselaer Polytechnic Institute Commencement weekend, the annual President's Commencement Colloquy will take place on Friday, May 19, beginning at 3:30 p.m. The discussion, titled "Criticality, Incisiveness, Creativity," will include the Honorable Ernest J. Moniz, former Secretary of Energy, and the Honorable Roger W. Ferguson Jr., President and CEO of TIAA, and will be moderated by Rensselaer President Shirley Ann Jackson.

ORNL, University of Tennessee Launch New Doctoral Program in Data Science

The Tennessee Higher Education Commission has approved a new doctoral program in data science and engineering as part of the Bredesen Center for Interdisciplinary Research and Graduate Education.

SurfTec Receives $1.2 Million Energy Award to Develop Novel Coating

The Department of Energy has awarded $1.2 million to SurfTec LLC, a company affiliated with the U of A Technology Development Foundation, to continue developing a nanoparticle-based coating to replace lead-based journal bearings in the next generation of electric machines.

Ames Laboratory Scientist Inducted Into National Inventors Hall of Fame

Iver Anderson, senior metallurgist at Ames Laboratory, has been inducted into the National Inventors Hall of Fame.

DOE HPC4Mfg Program Funds 13 New Projects to Improve U.S. Energy Technologies Through High Performance Computing

A U.S. Department of Energy (DOE) program designed to spur the use of high performance supercomputers to advance U.S. manufacturing is funding 13 new industry projects for a total of $3.9 million.


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Casting a Wide Net

Designed molecules will provide positive impacts in energy production by selectively removing unwanted ions from complex solutions.

New Software Tools Streamline DNA Sequence Design-and-Build Process

Enhanced software tools will accelerate gene discovery and characterization, vital for new forms of fuel production.

The Ultrafast Interplay Between Molecules and Materials

Computer calculations by the Center for Solar Fuels, an Energy Frontier Research Center, shed light on nebulous interactions in semiconductors relevant to dye-sensitized solar cells.

Supercapacitors: WOODn't That Be Nice

Researchers at Nanostructures for Electrical Energy Storage, an Energy Frontier Research Center, take advantage of nature-made materials and structure for energy storage research.

Groundwater Flow Is Key for Modeling the Global Water Cycle

Water table depth and groundwater flow are vital to understanding the amount of water that plants transmit to the atmosphere.

Finding the Correct Path

A new computational technique greatly simplifies the complex reaction networks common to catalysis and combustion fields.

Opening Efficient Routes to Everyday Plastics

A new material from the Inorganometallic Catalyst Design Center, an Energy Frontier Research Center, facilitates the production of key industrial supplies.

Fight to the Top: Silver and Gold Compete for the Surface of a Bimetallic Solid

It's the classic plot of a buddy movie. Two struggling bodies team up to drive the plot and do good together. That same idea, when it comes to metals, could help scientists solve a big problem: the amount of energy consumed by making chemicals.

Saving Energy Through Light Control

New materials, designed by researchers at the Center for Excitonics, an Energy Frontier Research Center, can reduce energy consumption with the flip of a switch.

Teaching Perovskites to Swim

Scientists at the ANSER Energy Frontier Research Center designed a two-component layer protects a sunlight-harvesting device from water and heat.


Saturday May 20, 2017, 12:05 PM

Rensselaer Polytechnic Institute Graduates Urged to Embrace Change at 211th Commencement

Rensselaer Polytechnic Institute (RPI)

Monday May 15, 2017, 01:05 PM

ORNL, University of Tennessee Launch New Doctoral Program in Data Science

Oak Ridge National Laboratory

Friday April 07, 2017, 11:05 AM

Champions in Science: Profile of Jonathan Kirzner

Department of Energy, Office of Science

Wednesday April 05, 2017, 12:05 PM

High-Schooler Solves College-Level Security Puzzle From Argonne, Sparks Interest in Career

Argonne National Laboratory

Tuesday March 28, 2017, 12:05 PM

Champions in Science: Profile of Jenica Jacobi

Department of Energy, Office of Science

Friday March 24, 2017, 10:40 AM

Great Neck South High School Wins Regional Science Bowl at Brookhaven Lab

Brookhaven National Laboratory

Wednesday February 15, 2017, 04:05 PM

Middle Schoolers Test Their Knowledge at Science Bowl Competition

Argonne National Laboratory

Friday January 27, 2017, 04:00 PM

Haslam Visits ORNL to Highlight State's Role in Discovering Tennessine

Oak Ridge National Laboratory

Tuesday November 08, 2016, 12:05 PM

Internship Program Helps Foster Development of Future Nuclear Scientists

Oak Ridge National Laboratory

Friday May 13, 2016, 04:05 PM

More Than 12,000 Explore Jefferson Lab During April 30 Open House

Thomas Jefferson National Accelerator Facility

Monday April 25, 2016, 05:05 PM

Giving Back to National Science Bowl

Ames Laboratory

Friday March 25, 2016, 12:05 PM

NMSU Undergrad Tackles 3D Particle Scattering Animations After Receiving JSA Research Assistantship

Thomas Jefferson National Accelerator Facility

Tuesday February 02, 2016, 10:05 AM

Shannon Greco: A Self-Described "STEM Education Zealot"

Princeton Plasma Physics Laboratory

Monday November 16, 2015, 04:05 PM

Rare Earths for Life: An 85th Birthday Visit with Mr. Rare Earth

Ames Laboratory

Tuesday October 20, 2015, 01:05 PM

Meet Robert Palomino: 'Give Everything a Shot!'

Brookhaven National Laboratory

Tuesday April 22, 2014, 11:30 AM

University of Utah Makes Solar Accessible

University of Utah

Wednesday March 06, 2013, 03:40 PM

Student Innovator at Rensselaer Polytechnic Institute Seeks Brighter, Smarter, and More Efficient LEDs

Rensselaer Polytechnic Institute (RPI)

Friday November 16, 2012, 10:00 AM

Texas Tech Energy Commerce Students, Community Light up Tent City

Texas Tech University

Wednesday November 23, 2011, 10:45 AM

Don't Get 'Frosted' Over Heating Your Home This Winter

Temple University

Wednesday July 06, 2011, 06:00 PM

New Research Center To Tackle Critical Challenges Related to Aircraft Design, Wind Energy, Smart Buildings

Rensselaer Polytechnic Institute (RPI)

Friday April 22, 2011, 09:00 AM

First Polymer Solar-Thermal Device Heats Home, Saves Money

Wake Forest University

Friday April 15, 2011, 12:25 PM

Like Superman, American University Will Get Its Energy from the Sun

American University

Thursday February 10, 2011, 05:00 PM

ARRA Grant to Help Fund Seminary Building Green Roof

University of Chicago

Tuesday December 07, 2010, 05:00 PM

UC San Diego Installing 2.8 Megawatt Fuel Cell to Anchor Energy Innovation Park

University of California San Diego

Monday November 01, 2010, 12:50 PM

Rensselaer Smart Lighting Engineering Research Center Announces First Deployment of New Technology on Campus

Rensselaer Polytechnic Institute (RPI)

Friday September 10, 2010, 12:40 PM

Ithaca College Will Host Regional Clean Energy Summit

Ithaca College

Tuesday July 27, 2010, 10:30 AM

Texas Governor Announces $8.4 Million Award to Create Renewable Energy Institute

Texas Tech University

Friday May 07, 2010, 04:20 PM

Creighton University to Offer New Alternative Energy Program

Creighton University

Wednesday May 05, 2010, 09:30 AM

National Engineering Program Seeks Subject Matter Experts in Energy

JETS Junior Engineering Technical Society

Wednesday April 21, 2010, 12:30 PM

Students Using Solar Power To Create Sustainable Solutions for Haiti, Peru

Rensselaer Polytechnic Institute (RPI)

Wednesday March 03, 2010, 07:00 PM

Helping Hydrogen: Student Inventor Tackles Challenge of Hydrogen Storage

Rensselaer Polytechnic Institute (RPI)

Thursday February 04, 2010, 02:00 PM

Turning Exercise into Electricity

Furman University

Thursday November 12, 2009, 12:45 PM

Campus Leaders Showing the Way to a Sustainable, Clean Energy Future

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Tuesday November 03, 2009, 04:20 PM

Furman University Receives $2.5 Million DOE Grant for Geothermal Project

Furman University

Thursday September 17, 2009, 02:45 PM

Could Sorghum Become a Significant Alternative Fuel Source?

Salisbury University

Wednesday September 16, 2009, 11:15 AM

Students Navigating the Hudson River With Hydrogen Fuel Cells

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Wednesday September 16, 2009, 10:00 AM

College Presidents Flock to D.C., Urge Senate to Pass Clean Energy Bill

National Wildlife Federation (NWF)

Wednesday July 01, 2009, 04:15 PM

Northeastern Announces New Professional Master's in Energy Systems

Northeastern University

Friday October 12, 2007, 09:35 AM

Kansas Rural Schools To Receive Wind Turbines

Kansas State University

Thursday August 17, 2006, 05:30 PM

High Gas Prices Here to Stay, Says Engineering Professor

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Wednesday May 17, 2006, 06:45 PM

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University of Maryland, College Park




A Fresh Math Perspective Opens New Possibilities for Computational Chemistry

Article ID: 675068

Released: 2017-05-19 15:05:51

Source Newsroom: Lawrence Berkeley National Laboratory

  • Credit: Bert de Jong, Berkeley Lab

    This image shows the structure of berkelium in oxidation state +IV. Researchers used the new Berkeley Lab algorithm to calculate the absorption spectrum and confirm what what several experimental results have been hinting—that the element berkelium breaks form with its heavy element peers by taking on an extra positive charge when bound to a synthetic organic molecule. This property could help scientists develop better methods for handling and purifying nuclear materials.

  • Credit: Chao Yang, Berkeley Lab

    This plot shows how the absorption spectrum of p3b2 molecule computed by the Lanczos algorithm matches with the real-time TDDFT result.

Glow-in-the-dark objects seem magical when you’re a kid—they can brighten up a dark room without the need for electricity, batteries or a light bulb. Then at some point you learn the science behind this phenomenon. Chemical compounds called chromophores become energized, or excited, when they absorb visible light. As they return to their normal state, the stored energy is released as light, which we perceive as a glow. In materials science, researchers rely on a similar phenomenon to study the structures of materials that will eventually be used in chemical catalysis, batteries, solar applications and more.

When a molecule absorbs a photon—the fundamental particle of light—electrons in the molecular system are promoted from a low-energy (ground) state to a higher-energy (excited) state. These responses resonate at specific light frequencies, leaving “spectral fingerprints” that illuminate the atomic and electronic structures of the system being studied.

In experiments, the “spectral fingerprints” or absorption spectrum, are measured with state-of-the-art facilities like the Advanced Light Source (ALS) at the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab). In computer simulations, these measurements are typically captured with a quantum mechanical method called Time Dependent Density Functional Theory (TDDFT). The computational models are critical in helping researchers make the most of their experiments by predicting and validating results.

Yet despite its usefulness, there are times when TDDFT cannot not be used to calculate the absorption spectrum of a system because it would require too much time and computer resources. This is where a new mathematical “shortcut” developed by researchers in Berkeley Lab’s Computational Research Division (CRD) comes in handy. Their algorithm speeds up absorption calculations by a factor of five, so simulations that used to take 10 to 15 hours to compute can now be done in approximately 2.5 hours.

A paper describing this method was published in the Journal of Chemical Theory and Computation (JCTC). And the new approach for computing the absorption spectrum will be incorporated in an upcoming release of the widely used NWChem computational chemistry software suite later this year.

New Algorithms Lead to Computational Savings

To study the chemical structure of new molecules and materials, scientists typically probe the system with an external stimulus—typically a laser—then look for small electronic changes. Mathematically, this electronic change can be expressed as an eigenvalue problem. By solving this eigenvalue problem, researchers can get a good approximation of the absorption spectrum, which in turn reveals the resonant frequencies of the system being studied. Meanwhile, the corresponding eigenvector is used to calculate how intensely the system responded to the stimulus. This is essentially the principle behind the TDDFT approach, which has been implemented in several quantum chemistry software packages, including the open-source NWChem software suite.

While this approach has proven to be successful, it does have limitations for large systems. The wider the energy range of electronic responses a researcher tries to capture in a system, the more eigenvalues and eigenvectors need to be computed, which also means more computing resources are necessary. Ultimately, the absorption spectrum of a molecular system with more than 100 atoms becomes prohibitively expensive to compute with this method.

To overcome these limitations, mathematicians in CRD developed a technique to compute the absorption spectrum directly without explicitly computing the eigenvalues of the matrix.

“Traditionally, researchers have had to compute the eigenvalues and eigenvectors of very large matrices in order to generate the absorption spectrum, but we realized that you don’t have to compute every single eigenvalue to get an accurate view of the absorption spectrum,” says Chao Yang, a CRD mathematician who led the development of the new approach.

By reformulating the problem as a matrix function approximation, making use of a special transformation and taking advantage of the underlying symmetry with respect to a non-Euclidean metric, Yang and his colleagues were able to apply the Lanczos algorithm and a Kernal Polynomial Method (KPM) to approximate the absorption spectrum of several molecules. Both of these algorithms require relatively low-memory compared to non-symmetrical alternatives, which is the key to the computational savings. 

Because this method requires less computing power to achieve a result, researchers can also easily calculate the absorption spectrum for molecular systems with several hundreds of atoms.

“This method is a significant step forward because it allows us to model the absorption spectrum of molecular systems of hundreds of atoms at lower computational cost.” says Niranjan Govind, a computational chemist at the Pacific Northwest National Laboratory who collaborated with the Berkeley Lab team on the development of the method in the NWChem computational chemistry program.

Recently Berkeley Lab scientists used this method to calculate the absorption spectrum and confirm what several experimental results have been hinting—that the element berkelium breaks form with its heavy element peers by taking on an extra positive charge when bound to a synthetic organic molecule. This property could help scientists develop better methods for handling and purifying nuclear materials. A paper highlighting this result appeared April 10 in the journal Nature Chemistry.

 “The experimental results were hinting at this unusual behavior in berkelium, but there wasn’t enough experimental evidence to say yes, 100 percent, this is what we’re seeing,” says study co-author Wibe Albert de Jong, a CRD scientist. “To be 100 percent sure, we did large computational simulations and compared them to the experimental data and determined that they were, indeed, seeing berkelium in an unusual oxidation state.”

This new algorithm was developed through a DOE Office of Science-supported Scientific Discovery through Advanced Computing (SciDAC) project focused on advancing software and algorithms for photochemical reactions. SciDAC projects typically bring together an interdisciplinary team of researchers to develop new and novel computational methods for tackling some of the most challenging scientific problems.

“The interdisciplinary nature of SciDAC is a very effective way to facilitate breakthrough science, as each team member brings a different perspective to problem solving,” says Yang. “In this dynamical environment, mathematicians, like me, team up with domain scientists to identify computational bottlenecks, then we use cutting-edge mathematical techniques to address and overcome those challenges.”

 In addition to Yang and Govind, other authors on the JCTC paper are Jiri Brabec, Lin Lin, Meiyue Shao and Esmond Ng of Berkeley Lab; and Yousef Saad of the University of Minnesota. 

The development of the new algorithm benefited from computing resources provided by the National Energy Research Scientific Computing Center (NERSC) and the Environmental Molecular Sciences Laboratory. ALS and NERSC at Berkeley Lab and EMSL at Pacific Northwest National Laboratory are all DOE Office of Science User Facilities.