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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.

Scientists Perform First Basic Physics Simulation of Spontaneous Transition of the Edge of Fusion Plasma to Crucial High-Confinement Mode

PPPL physicists have simulated the spontaneous transition of turbulence at the edge of a fusion plasma to the high-confinement mode that sustains fusion reactions. The research was achieved with the extreme-scale plasma turbulence code XGC developed at PPPL in collaboration with a nationwide team.

Green Fleet Technology

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How Scientists Turned a Flag Into a Loudspeaker

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Assembling Life's Molecular Motor

As part of a project dedicated to modeling how single-celled purple bacteria turn light into food, a team of computational scientists from the University of Illinois at Urbana-Champaign (UIUC) simulated a complete ATP synthase in all-atom detail. The work builds on the project's first phase--a 100-million atom photosynthetic organelle called a chromatophore--and gives scientists an unprecedented glimpse into a biological machine whose energy efficiency far surpasses that of any artificial system.

Engineering Researchers Apply Data Science to Better Predict Effect of Weather and Other Conditions on Solar Panels

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New Model of Plasma Stability Could Help Researchers Predict and Avoid Disruptions in Fusion Machines

PPPL physicists have helped develop a new computer model of plasma stability in doughnut-shaped fusion machines known as tokamaks. The model could help scientists predict when a plasma might become unstable and then avoid the underlying conditions.

Can the Motion of Checking Your Smartwatch Charge It?

Triboelectric nanogenerators (TENGs) are small devices that convert movement into electricity, and might just be what bring us into an era of energy-harvesting clothes and implants. But could TENGs, even theoretically, give us wearable electronics powered solely by the wearer's day-to-day body motion? The short answer is yes. New research published this week in APL Materials demonstrates the ability of mechanical energy produced by typical body motions to power a watch or smartphone.


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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

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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

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SurfTec Receives $1.2 Million Energy Award to Develop Novel Coating

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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.

Penn State Wind Energy Club Breezes to Victory in Collegiate Wind Competition

The Penn State Wind Energy Club breezed through the field at the U.S. Department of Energy Collegiate Wind Competition 2017 Technical Challenge, held April 20-22 at the National Wind Technology Center near Boulder, Colorado--earning its third overall victory in four years at the Collegiate Wind Competition.


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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

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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.

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

Opening Efficient Routes to Everyday Plastics

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

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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.


Assembling Life's Molecular Motor

Article ID: 674750

Released: 2017-05-15 15:05:39

Source Newsroom: Oak Ridge National Laboratory

  • Credit: Barry Isralewitz, University of Illinois at Urbana-Champaign

    ATP hydrolysis-driven rotation of the central stalk in the V-type ATP synthase of the bacteria Enterococcus hirae depicts chemo-mechanical coupling of the molecular motor. These simulations were carried out on the Titan supercomputer using NAMD2.12. Visualization and movie rendering were completed on VMD1.9.3.

Despite the grand diversity among living organisms, the molecule used to store and transmit energy within aerobic, or oxygen-using, cells is remarkably the same. From bacteria to fungi, plants, and animals, adenosine triphosphate (ATP) serves as the universal energy currency of life, fueling the processes cells need to survive and function.

Over the course of a day, an individual will typically use the equivalent of his or her bodyweight in ATP; however, the human body carries only a small amount of the molecule at any one time. That means cells must constantly recycle or replenish their limited capacity, relying on a highly efficient molecular motor called ATP synthase to do the job.

As part of a project dedicated to modeling how single-celled purple bacteria turn light into food, a team of computational scientists from the University of Illinois at Urbana-Champaign (UIUC) simulated a complete ATP synthase in all-atom detail. The work builds on the project’s first phase—a 100-million atom photosynthetic organelle called a chromatophore—and gives scientists an unprecedented glimpse into a biological machine whose energy efficiency far surpasses that of any artificial system.

First proposed under the leadership of the late Klaus Schulten, a pioneer in the field of computational biophysics and the founder of the Theoretical and Computational Biophysics Group at UIUC, the research has progressed under the stewardship of Abhishek Singharoy, co-principal investigator and a National Science Foundation postdoctoral fellow with UIUC’s Center for the Physics of Living Cells.

In addition to Singharoy, the team includes members from the groups of UIUC professors Emad Tajkhorshid, Zaida Luthey-Schulten and Aleksei Aksimentiev; research scientist Melih Sener; and developers Barry Isralewitz, Jim Phillips, and John Stone. Experimental collaborator Neil Hunter of the University of Sheffield in England also took part in the project.

The UIUC-led team built and tested its mega-model under a multiyear allocation awarded through the Innovative and Novel Computational Impact on Theory and Experiment program on the Titan supercomputer, a Cray XK7 managed by the US Department of Energy’s (DOE’s) Oak Ridge Leadership Computing Facility (OLCF), a DOE Office of Science User Facility located at DOE’s Oak Ridge National Laboratory.

Using Titan, the team produced a virtual tool that can predict in exacting detail the chemical energy output of a photosynthetic system based on the amount of sunlight absorbed. The research could one day contribute to advanced clean energy technology that incorporates biological concepts.

“Nature has designed the chromatophore in such a way that it can generate enough ATPs for these bacteria to survive in low-light environments such as the bottom of ponds and lakes,” Singharoy said. “Our work captured this energy conversion process in all-atom detail and allowed us to predict its efficiency.”

Light in motion

Often referred to as the power plant of the cell, ATP synthase is a complex enzyme that speeds up the synthesis of its molecular precursors, adenosine diphosphate (ADP) and phosphate. Embedded within the chromatophore’s inner and outer membrane, the enzymatic motor consists of three major parts—an ion-powered rotor, a central stalk, and a protein ring.

Similar to a waterwheel that’s turned by the force of a flowing stream, the ATP synthase rotor harnesses the electrochemically spurred movement of ions, such as protons or sodium, from high concentration to low concentration across the membrane. The resulting mechanical energy transfers to the central stalk, which assists the protein ring in synthesizing ATP.

Remarkably, the process works just as well in reverse. When too many ions build up on the outer side of the chromatophore, the ATP synthase protein ring will break down ATP into ADP, a process called hydrolysis, and ions will flow back to the inner side.

“Normally, you would expect a lot of energy loss during this process, like in any man-made motor, but it turns out ATP synthase has very little waste,” Singharoy said. “How this motor is designed to minimize energy loss is the question we started asking.”

Similar to a tinkerer disassembling an engine to better understand how it works, Singharoy’s team broke down the 300,000-atom enzyme into its constituent parts. Drawing from decades of research into ATP synthase, past models, and new experimental data supplied by a Japanese team led by Takeshi Murata of the RIKEN Center for Life Science Technologies, the team constructed and simulated the pieces of the ATP synthase puzzle independently and together on Titan.

To capture important processes that play out over millisecond time scales, Singharoy, in collaboration with Christophe Chipot of the French National Center for Scientific Research and Mahmoud Moradi of the University of Arkansas, deployed the molecular dynamics code NAMD strategically. The team executed an ensemble strategy, tracking the motion of around 1,000 replicas of ATP synthase simultaneously with time steps of 2 femtoseconds, or 2,000 trillionths of a second. In total, the team accumulated 65 microseconds (65 millionths of a second) of simulation time, using this information to extrapolate motions that occur over the course of a millisecond (1 thousandth of a second).

As a result, the team identified previously undocumented swiveling motions in the protein ring that help explain the molecular motor’s efficiency. Similarly, the team’s simulations captured the rubber band–like elasticity of the enzyme’s central stalk. Singharoy’s team estimated that when paired with the protein ring, the stalk absorbs about 75 percent of the energy released during hydrolysis.

Additionally, simulations of the protein ring by itself revealed a unit that can function independently, a finding reported in experiments but not in computational detail. “Even in the absence of the center stalk, the protein ring itself is capable of ATP hydrolysis. It’s not very efficient, but it has the capability,” Singharoy said.

The big picture

After simulating its complete ATP synthase model, the UIUC team incorporated the enzyme into its previously constructed chromatophore model to gain the most comprehensive picture of a photosynthetic system to date.

With this virtual biological solar panel, the team could measure each step of the energy conversion process—from light harvesting, to electron and proton transfer, to ATP synthesis—and better understand its mechanical underpinnings.

Nature’s chromatophore is designed for low-light intensity, only absorbing between 3 and 5 percent of sunlight on a typical day. The team, through the efforts of Sener, found this absorption rate translates to around 300 ATPs per second, which is the amount a bacterium needs to stay alive.

Having studied nature’s design, the team now wanted to see if it could improve upon it. Assuming the same amount of light intensity, the team designed an artificial chromatophore with a decidedly unnatural protein composition, boosting the presence of two types of specialized proteins. Analysis of the new design predicted a tripling of the photosynthetic system’s ATP production, opening up the possibility for the chromatophore’s human-guided optimization.

“You could potentially genetically modify a chromatophore or change its concentration of proteins,” Singharoy said. “These predictions promise to bring forth new developments in artificial photosynthesis.”

Under its latest INCITE allocation, the UIUC team is pivoting to energy conversion in a different lifeform: animals. Taking what it has learned from modeling photosynthesis in purple bacteria, the team is modeling cellular respiration, the process animal cells use to convert nutrients to ATP.

“You have at least two proteins in common between respiration and photosynthesis,” said Singharoy, who is continuing his involvement with the project as an assistant professor at Arizona State University. “The question is what design principles carry over into higher organisms?”

Life in situ

Simulation of the chromatophore—complete with ATP synthase—marks an ongoing shift in computational biophysics from analyzing individual cell parts (e.g., single proteins and hundreds of atoms) to analyzing entire cell systems (e.g., hundreds of proteins and millions of atoms).

Schulten, who passed away in October 2016, understood better than most people the significance of using computers to simulate nature. In an interview in 2015, he laid out his rationale for modeling the chromatophore. “The motivation is to understand a very key step of life on Earth on which all life depends today. Energy-wise 95 percent of life on Earth depends on photosynthesis, including humans,” he said.

Schulten also understood the milestone a specialized organelle represented on the road to simulating a complete single-celled organism. “We don’t have anything smaller than a cell that we would call alive,” he said. “It’s the smallest living entity, and we want to understand it.”

With next-generation supercomputers, including the OLCF’s Summit, set to come online in 2018, the research group Schulten founded in 1989 is preparing to take on the grand challenge of simulating a cell.

Under the leadership of Tajkhorshid, the team plans to simulate the first billion-atom cell, including the basic components a cell needs to survive and grow. Improvements to NAMD and work being done under the OLCF’s Center for Accelerated Application Readiness program are helping to make the vision of Schulten and others a reality.

“We keep moving forward,” Singharoy said. “Our exhaustive study of a complete organelle in all-atom detail has opened the door for a full cell in all-atom detail.”

The National Institutes of Health and the National Science Foundation provided the primary support for this work.  Part of the research was performed at the Photosynthetic Antenna Research Center, a DOE Energy Frontier Research Center led by Washington University in St. Louis and supported by DOE’s Office of Science.

Related Publications:

Abhishek Singharoy, Christophe Chipot, Mahmoud Moradi, and Klaus Schulten, “Chemomechanical Coupling in Hexameric Protein–Protein Interfaces Harness Energy Within V–Type ATPases.” Journal of the American Chemical Society 139, no. 1 (2017): 293–310, doi:10.1021/jacs.6b10744.

Abhishek Singharoy, Angela M. Barragan, Sundarapandian Thangapandian, Emad Tajkhorshid, and Klaus Schulten, “Binding Site Recognition and Docking Dynamics of a Single Electron Transport Protein: Cytochrome c2.” Journal of the American Chemical Society 138, no. 37 (2016): 12077–12089, doi:10.1021/jacs.6b01193.

Melih Sener, Johan Strumpfer, Abhishek Singharoy, C. Neil Hunter, and Klaus Schulten, “Overall Energy Conversion Efficiency of a Photosynthetic Vesicle.” eLife 5 (2016): e09541, doi:10.7554/eLife.09541.

Oak Ridge National Laboratory is supported by the US Department of Energy’s Office of Science. The single largest supporter of basic research in the physical sciences in the United States, the Office of Science is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.