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Scientists Set Record Resolution for Drawing at the One-Nanometer Length Scale

Using a specialized electron microscope outfitted with a pattern generator, scientists turned an imaging instrument into a lithography tool that could be used to create and study materials with new properties.

For First Time, Researchers Measure Forces That Align Crystals and Help Them Snap Together

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Video Captures Bubble-Blowing Battery in Action

PNNL researchers have created a unique video that shows oxygen bubbles inflating and later deflating inside a tiny lithium-air battery. The knowledge gained from the video could help make lithium-air batteries that are more compact, stable and can hold onto a charge longer.

Study Offers New Theoretical Approach to Describing Non-Equilibrium Phase Transitions

Two physicists at Argonne offered a way to mathematically describe a particular physics phenomenon called a phase transition in a system out of equilibrium. Such phenomena are central in physics, and understanding how they occur has been a long-held and vexing goal; their behavior and related effects are key to unlocking possibilities for new electronics and other next-generation technologies.

Berkeley Lab Scientists Discover New Atomically Layered, Thin Magnet

Berkeley Lab scientists have found an unexpected magnetic property in a 2-D material. The new atomically thin, flat magnet could have major implications for a wide range of applications, such as nanoscale memory, spintronic devices, and magnetic sensors.

Stabilizing Molecule Could Pave Way for Lithium-Air Fuel Cell

Lithium-oxygen fuel cells boast energy density levels comparable to fossil fuels and are thus seen as a promising candidate for future transportation-related energy needs.

Scientists Identify Chemical Causes of Battery "Capacity Fade"

Researchers at Argonne National Laboratory identified one of the major culprits in capacity fade of high-energy lithium-ion batteries.

Modeling Reveals How Policy Affects the Adoption of Solar Energy Photovoltaics in California

Researchers at the University of California, Riverside, inspired by efforts to promote green energy, are exploring the factors driving commercial customers in Southern California, both large and small, to purchase and install solar photovoltaic (PV) systems. As the group reports this week in the Journal of Renewable and Sustainable Energy, they built a model for commercial solar PV adoption to quantify the impact of government incentives and solar PV costs.

Machine Learning Dramatically Streamlines Search for More Efficient Chemical Reactions

A catalytic reaction may follow thousands of possible paths, and it can take years to identify which one it actually takes so scientists can tweak it and make it more efficient. Now researchers at the Department of Energy's SLAC National Accelerator Laboratory and Stanford University have taken a big step toward cutting through this thicket of possibilities.

Freezing Lithium Batteries May Make Them Safer and Bendable

Columbia Engineering Professor Yuan Yang has developed a new method that could lead to lithium batteries that are safer, have longer battery life, and are bendable, providing new possibilities such as flexible smartphones. His new technique uses ice-templating to control the structure of the solid electrolyte for lithium batteries that are used in portable electronics, electric vehicles, and grid-level energy storage. The study is published online April 24 in Nano Letters.


OU Engineering Professor Receives National Science Foundation Early CAREER Award

A University of Oklahoma Gallogly College of Engineering professor, Steven P. Crossley, is the recipient of a five-year, National Science Foundation Early CAREER Award in the amount of $548,829 for research that can be used to understand catalysts that are important for a broad range of chemical reactions ranging from the production of renewable fuels and chemicals for natural gas processing. The research will be integrated with educational and outreach programs intended for American Indian students, emphasizing the importance of sustainable energy.

3 Small Energy Firms to Collaborate with PNNL

Pacific Northwest National Laboratory is collaborating with three small businesses to address technical challenges concerning hydrogen for fuel cell cars, bio-coal and nanomaterial manufacturing.

ORNL to Collaborate with Five Small Businesses to Advance Energy Tech

Five small companies have been selected to partner with the Department of Energy's Oak Ridge National Laboratory to move technologies in commercial refrigeration systems, water power generation, bioenergy and battery manufacturing closer to the marketplace.

U.S. Department of Energy's INCITE Program Seeks Advanced Computational Research Proposals for 2018

The Department of Energy's INCITE program will be accepting proposals for high-impact, computationally intensive research campaigns in a broad array of science, engineering, and computer science domains.

New Berkeley Lab Project Turns Waste Heat to Electricity

A new Berkeley Lab project seeks to efficiently capture waste heat and convert it to electricity, potentially saving California up to $385 million per year. With a $2-million grant from the California Energy Commission, Berkeley Lab scientists will work with Alphabet Energy to create a cost-effective thermoelectric waste heat recovery system.

New SLAC Theory Institute Aims to Speed Research on Exotic Materials at Light Sources

A new institute at the Department of Energy's SLAC National Accelerator Laboratory is using the power of theory to search for new types of materials that could revolutionize society - by making it possible, for instance, to transmit electricity over power lines with no loss.

Lenvio Inc. Exclusively Licenses ORNL Malware Behavior Detection Technology

Virginia-based Lenvio Inc. has exclusively licensed a cyber security technology from the Department of Energy's Oak Ridge National Laboratory that can quickly detect malicious behavior in software not previously identified as a threat.

Argonne Scientist and Nobel Laureate Alexei Abrikosov Dies at 88

Alexei Abrikosov, an acclaimed physicist at the U.S. Department of Energy's Argonne National Laboratory who received the 2003 Nobel Prize in Physics for his work on superconducting materials, died Wednesday, March 29. He was 88.

Jefferson Lab Accomplishes Critical Milestones Toward Completion of 12 GeV Upgrade

The Continuous Electron Beam Accelerator Facility (CEBAF) at the U.S. Department of Energy's Thomas Jefferson National Accelerator Facility has achieved two major commissioning milestones and is now entering the final stretch of work to conclude its first major upgrade. Recently, the CEBAF accelerator delivered electron beams into two of its experimental halls, Halls B and C, at energies not possible before the upgrade for commissioning of the experimental equipment currently in each hall. Data were recorded in each hall, which were then confirmed to be of sufficient quality to allow for particle identification, a primary indicator of good detector operation.

Valerie Taylor Named Argonne National Laboratory's Mathematics and Computer Science Division Director

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Fast Electrons and the Seeds of Disruption

Physicists measured fast electron populations. They achieved this first-of-its-kind result by seeing the effect of the fast electrons on the ablation rate of small frozen argon pellets.

Plasma Turbulence Generates Flow in Fusion Reactors

Heating the core of fusion reactors causes them to develop sheared rotation that can improve plasma performance.

The Roadmap to Quark Soup

Scientists discover new signposts in the quest to determine how matter from the early universe turned into the world we know today.

Neutrons Play the Lead to Protons in Dance Around "Double-Magic" Nucleus

Electric and magnetic properties of a radioactive atom provide unique insight into the nature of proton and neutron motion.

Ultrafast Imaging Reveals the Electron's New Clothes

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One Small Change Makes Solar Cells More Efficient

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Electronic "Cyclones" at the Nanoscale

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Deciphering Material Properties at the Single-Atom Level

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New Computer Model Could Explain how Simple Molecules Took First Step Toward Life

Article ID: 637835

Released: 2015-07-28 10:05:00

Source Newsroom: Brookhaven National Laboratory

  • Credit: Brookhaven National Laboratory

    Brookhaven researchers Sergei Maslov (left) and Alexi Tkachenko developed a theoretical model to explain molecular self-replication.

  • Credit: Brookhaven National Laboratory

    A schematic drawing of template-assisted ligation, shown in this model to give rise to autocatalytic systems.

New Computer Model Could Explain how Simple Molecules Took First Step Toward Life

Two Brookhaven researchers developed theoretical model to explain the origins of self-replicating molecules

July 28, 2015

UPTON, NY—Nearly four billion years ago, the earliest precursors of life on Earth emerged. First small, simple molecules, or monomers, banded together to form larger, more complex molecules, or polymers. Then those polymers developed a mechanism that allowed them to self-replicate and pass their structure on to future generations.

We wouldn't be here today if molecules had not made that fateful transition to self-replication. Yet despite the fact that biochemists have spent decades searching for the specific chemical process that can explain how simple molecules could make this leap, we still don't really understand how it happened.

Now Sergei Maslov, a computational biologist at the U.S. Department of Energy's Brookhaven National Laboratory and adjunct professor at Stony Brook University, and Alexei Tkachenko, a scientist at Brookhaven's Center for Functional Nanomaterials (CFN), have taken a different, more conceptual approach. They've developed a model that explains how monomers could very rapidly make the jump to more complex polymers. And what their model points to could have intriguing implications for CFN's work in engineering artificial self-assembly at the nanoscale. Their work is published in the July 28, 2015 issue of The Journal of Chemical Physics.

To understand their work, let's consider the most famous organic polymer, and the carrier of life's genetic code: DNA. This polymer is composed of long chains of specific monomers called nucleotides, of which the four kinds are adenine, thymine, guanine, and cytosine (A, T, G, C). In a DNA double helix, each specific nucleotide pairs with another: A with T, and G with C. Because of this complementary pairing, it would be possible to put a complete piece of DNA back together even if just one of the two strands was intact.

While DNA has become the molecule of choice for encoding biological information, its close cousin RNA likely played this role at the dawn of life. This is known as the RNA world hypothesis, and it's the scenario that Maslov and Tkachenko considered in their work.

The single complete RNA strand is called a template strand, and the use of a template to piece together monomer fragments is what is known as template-assisted ligation. This concept is at the crux of their work. They asked whether that piecing together of complementary monomer chains into more complex polymers could occur not as the healing of a broken polymer, but rather as the formation of something new.

"Suppose we don't have any polymers at all, and we start with just monomers in a test tube," explained Tkachenko. "Will that mixture ever find its way to make those polymers? The answer is rather remarkable: Yes, it will! You would think there is some chicken-and-egg problem—that, in order to make polymers, you already need polymers there to provide the template for their formation. Turns out that you don't really."

Instilling memory

Maslov and Tkachenko's model imagines some kind of regular cycle in which conditions change in a predictable fashion—say, the transition between night and day. Imagine a world in which complex polymers break apart during the day, then repair themselves at night. The presence of a template strand means that the polymer reassembles itself precisely as it was the night before. That self-replication process means the polymer can transmit information about itself from one generation to the next. That ability to pass information along is a fundamental property of life.

"The way our system replicates from one day cycle to the next is that it preserves a memory of what was there," said Maslov. "It's relatively easy to make lots of long polymers, but they will have no memory. The template provides the memory. Right now, we are solving the problem of how to get long polymer chains capable of memory transmission from one unit to another to select a small subset of polymers out of an astronomically large number of solutions."

According to Maslov and Tkachenko's model, a molecular system only needs a very tiny percentage of more complex molecules—even just dimers, or pairs of identical molecules joined together—to start merging into the longer chains that will eventually become self-replicating polymers. This neatly sidesteps one of the most vexing puzzles of the origins of life: Self-replicating chains likely need to be very specific sequences of at least 100 paired monomers, yet the odds of 100 such pairs randomly assembling themselves in just the right order is practically zero.

"If conditions are right, there is what we call a first-order transition, where you go from this soup of completely dispersed monomers to this new solution where you have these long chains appearing," said Tkachenko. "And we now have this mechanism for the emergence of these polymers that can potentially carry information and transmit it downstream. Once this threshold is passed, we expect monomers to be able to form polymers, taking us from the primordial soup to a primordial soufflé."

While the model's concept of template-assisted ligation does describe how DNA—as well as RNA—repairs itself, Maslov and Tkachenko's work doesn't require that either of those was the specific polymer for the origin of life.

"Our model could also describe a proto-RNA molecule. It could be something completely different," Maslov said.

Order from disorder

The fact that Maslov and Tkachenko's model doesn't require the presence of a specific molecule speaks to their more theoretical approach.

"It's a different mentality from what a biochemist would do," said Tkachenko. "A biochemist would be fixated on specific molecules. We, being ignorant physicists, tried to work our way from a general conceptual point of view, as there's a fundamental problem."

That fundamental problem is the second law of thermodynamics, which states that systems tend toward increasing disorder and lack of organization. The formation of long polymer chains from monomers is the precise opposite of that.

"How do you start with the regular laws of physics and get to these laws of biology which makes things run backward, which make things more complex, rather than less complex?" Tkachenko queried. "That's exactly the jump that we want to understand."

Applications in nanoscience

The work is an outgrowth of efforts at the Center for Functional Nanomaterials, a DOE Office of Science User Facility, to use DNA and other biomolecules to direct the self-assembly of nanoparticles into large, ordered arrays. While CFN doesn't typically focus on these kinds of primordial biological questions, Maslov and Tkachenko's modeling work could help CFN scientists engaged in cutting-edge nanoscience research to engineer even larger and more complex assemblies using nanostructured building blocks.

"There is a huge interest in making engineered self-assembled structures, so we were essentially thinking about two problems at once," said Tkachenko. "One is relevant to biologists, and second asks whether we can engineer a nanosystem that will do what our model does."

The next step will be to determine whether template-aided ligation can allow polymers to begin undergoing the evolutionary changes that characterize life as we know it. While this first round of research involved relatively modest computational resources, that next phase will require far more involved models and simulations.

Maslov and Tkachenko's work has solved the problem of how long polymer chains capable of information transmission from one generation to the next could emerge from the world of simple monomers. Now they are turning their attention to how such a system could naturally narrow itself down from exponentially many polymers to only a select few with desirable sequences.

"What we needed to show here was that this template-based ligation does result in a set of polymer chains, starting just from monomers," said Tkachenko. "So the next question we will be asking is whether, because of this template-based merger, we will be able to see specific sequences that will be more 'fit' than others. So this work sets the stage for the shift to the Darwinian phase."

This work was supported by the DOE Office of Science.

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

One of ten national laboratories overseen and primarily funded by the Office of Science of the U.S. Department of Energy (DOE), Brookhaven National Laboratory conducts research in the physical, biomedical, and environmental sciences, as well as in energy technologies and national security. Brookhaven Lab also builds and operates major scientific facilities available to university, industry and government researchers. Brookhaven is operated and managed for DOE's Office of Science by Brookhaven Science Associates, a limited-liability company founded by the Research Foundation for the State University of New York on behalf of Stony Brook University, the largest academic user of Laboratory facilities, and Battelle, a nonprofit applied science and technology organization.

Related Links

Scientific Paper: "Spontaneous emergence of autocatalytic information-coding polymers" http://scitation.aip.org/content/aip/journal/jcp/143/2/10.1063/1.4922545

Media contact: Peter Genzer, 631-344-3174, genzer@bnl.gov