DOE News
    Doe Science news source
    The DOE Science News Source is a Newswise initiative to promote research news from the Office of Science of the DOE to the public and news media.
    • 2015-07-28 10:05:00
    • Article ID: 637835

    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

    • 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

    X
    X
    X
    • Filters

    • × Clear Filters

    New PMLD Technique Improves Tools to Form Organic Multilayers

    Researchers have developed a new class of molecular layer deposition chemistry that paves the way for a new photoactivated molecular layer deposition technique. They report that their new method will expand the tool kit for forming covalently bound organic multilayers at surfaces. These emerging deposition techniques have enabled engineers to produce organic thin films with improved conformality. Richard Closser, Stanford University, will present the findings at the AVS 65th International Symposium and Exhibition, Oct. 21-26, 2018.

    Spotlighting Differences in Closely-Related Species

    Aspergillus fungi play roles in fields including bioenergy, health, and biotechnology. In Nature Genetics, a team led by scientists at the Technical University of Denmark, the DOE Joint Genome Institute, and the Joint Bioenergy Institute, present the first large analysis of an Aspergillus fungal subgroup, section Nigri.

    Researchers switch material from one state to another with a single flash of light

    Scientists from the Department of Energy's SLAC National Accelerator Laboratory and the Massachusetts Institute of Technology have demonstrated a surprisingly simple way of flipping a material from one state into another, and then back again, with single flashes of laser light.

    The Stories Behind the Science: How Does the Ocean's Saltiness Affect Tropical Storms?

    Two researchers with personal experience of hurricanes set out to investigate the role of an underestimated factor in storm's strength - salinity. They found that salinity plays a larger role than anyone thought, including them.

    Surprise finding: Discovering a previously unknown role for a source of magnetic fields

    Feature describes unexpected discovery of a role the process that seeds magnetic fields plays in mediating a phenomenon that occurs throughout the universe and can disrupt cell phone service and knock out power grids on Earth.

    Genetic behavior reveals cause of death in poplars essential to ecosystems, industry

    Scientists studying a valuable, but vulnerable, species of poplar have identified the genetic mechanism responsible for the species' inability to resist a pervasive and deadly disease. Their finding could lead to more successful hybrid poplar varieties for increased biofuels and forestry production and protect native trees against infection.

    Pushing the (Extra Cold) Frontiers of Superconducting Science

    Ames Laboratory has developed a method to measure magnetic properties of superconducting and magnetic materials that exhibit unusual quantum behavior at very low temperatures in high magnetic fields.

    Scientists Find Unusual Behavior in Topological Material

    Argonne scientists have identified a new class of topological materials made by inserting transition metal atoms into the atomic lattice of a well-known two-dimensional material.

    Wind Farms and Reducing Hurricane Precipitation

    New research reveals an unexpected benefit of large-scale offshore wind farms: the ability to lessen precipitation from hurricanes.

    New simulations confirm efficiency of waste-removal process in plasma device

    PPPL scientists have found evidence suggesting that a process could remove the unwanted ash produced during fusion reactions and make the fusion processes more efficient within a type of fusion facility known as a field-reversed configuration device.


    • Filters

    • × Clear Filters

    Physicist Takes Cues from Artificial Intelligence

    In the world of computing, there's a groundswell of excitement for what is perceived as the impending revolution in artificial intelligence. Like the industrial revolution in the 19th century and the digital revolution in the 20th, the AI revolution is expected to change the way we live and work. Now, Cristiano Fanelli aims to bring the AI revolution to nuclear physics.

    Engineering professor receives Department of Energy grant

    New Mexico State University Department of Civil Engineering Assistant Professor Ehsan Dehghan Niri has received a United States Department of Energy grant. This is a three-year award for $400,000 and is a collaboration with Arizona State University.

    Argonne and Capstone receive funding to advance thermal energy storage technology

    The U.S. Department of Energy's (DOE) Argonne National Laboratory and Capstone Turbine Corp. have received $380,000 in DOE Technology Commercialization Funding to refine Argonne's high-efficiency, fast charging/discharging latent heat thermal energy storage system (TESS) for use in building applications and process/manufacturing industries.

    AVS and AIP Publishing Expand Partnership to Launch AVS Quantum Science

    AIP Publishing and AVS: Science and Technology of Materials, Interfaces, and Processing (AVS) today announced an agreement to publish AVS Quantum Science, a new online interdisciplinary journal. The announcement coincides with the AVS 65th International Symposium & Exhibition in Long Beach, California, from October 21-26, 2018.

    Prototype Solar Energy, Battery Systems to Fuel Commercialization

    Designing, building and testing prototype systems that show how renewable energy can power devices, such as a weather and soil sensor station, can help bridge the gap between basic science research and commercialization.

    Argonne to Advance High Performance Computing in Manufacturing

    Argonne awarded funding to partner with Industry to advance the use of high performance computing in manufacturing.

    "Invisible Glass" Wins 2018 Create the Future Design Contest Grand Prize

    Scientists from the Center for Functional Nanomaterials developed a technique for making nonreflecting glass, silicon, and plastic surfaces.

    Missouri S&T researchers win multimillion dollar grant to build fast-charging stations for electric cars

    Researchers from Missouri S&T and three private companies will combine their expertise to create charging stations for electric vehicles that could charge a car in less than 10 minutes - matching the time it takes to fill up a conventional vehicle with gasoline."The big problem with electric vehicles is range, and it's not so much range as range anxiety.

    Making batteries store more energy, last longer

    A new solid polymer electrolyte may help make cell phone batteries store more energy and last longer.

    Three Brookhaven Lab Scientists Named Fellows of American Physical Society

    The American Physical Society (APS), the world's largest physics organization, has elected three scientists from the U.S. Department of Energy's (DOE) Brookhaven National Laboratory as 2018 APS fellows.


    • Filters

    • × Clear Filters

    Cryocooler Cools an Accelerator Cavity

    Researchers demonstrated cryogen-free operation of a superconducting radio-frequency cavity that might ease barriers to its use in societal applications.

    Shining Light on the Separation of Rare Earth Metals

    New studies identify key molecular characteristics to potentially separate rare earth metals cleanly and efficiently with light.

    Placing Atoms for Optimum Catalysts

    Precise positioning of oxygens could help engineer faster, more efficient energy-relevant chemical transformations.

    How to Make Soot and Stardust

    Scientists unlock mystery that could help reduce emissions of fine particles from combustion engines and other sources.

    Breaking the Symmetry Between Fundamental Forces

    Scientists improve our understanding of the relationship between fundamental forces by re-creating the earliest moments of the universe.

    Water Plays Unexpected Role in Forming Minerals

    Water molecules line up tiny particles to attach and form minerals; understanding how this happens impacts energy extraction and storage along with waste disposal.

    Heavy Particles Get Caught Up in the Flow

    First direct measurement show how heavy particles containing a charm quark get caught up in the flow of early universe particle soup.

    Seeing Between the Atoms

    New detector enables electron microscope imaging at record-breaking resolution.

    Scaling Up Single-Crystal Graphene

    New method can make films of atomically thin carbon that are over a foot long.

    Discovered: Optimal Magnetic Fields Suppress Instabilities in Tokamak Plasmas

    U.S. and Korean scientists show how to find and use beneficial 3-D field perturbations to stabilize dangerous edge-localized modes in plasma.


    Spotlight

    Thursday October 11, 2018, 04:00 PM

    Research on Light-Matter Interaction Could Lead to Improved Electronic and Optoelectronic Devices

    Rensselaer Polytechnic Institute (RPI)

    Wednesday October 03, 2018, 07:05 PM

    Innovating Our Energy Future

    Oregon State University, College of Engineering

    Tuesday October 02, 2018, 03:05 PM

    Physics graduate student takes her thesis research to a Department of Energy national lab

    University of Alabama at Birmingham

    Friday September 21, 2018, 01:05 PM

    "Model" students enjoy Argonne campus life

    Argonne National Laboratory

    Thursday September 06, 2018, 01:05 PM

    Writing Code for a More Skilled and Diverse STEM Workforce

    Brookhaven National Laboratory

    Tuesday September 04, 2018, 11:30 AM

    New graduate student summer school launches at Princeton Plasma Physics Laboratory

    Princeton Plasma Physics Laboratory

    Friday August 31, 2018, 06:05 PM

    The Gridlock State

    California State University (CSU) Chancellor's Office

    Friday August 31, 2018, 02:05 PM

    Meet Jasmine Hatcher and Trishelle Copeland-Johnson

    Brookhaven National Laboratory

    Friday August 24, 2018, 11:05 AM

    Argonne hosts Modeling, Experimentation and Validation Summer School

    Argonne National Laboratory

    Wednesday August 22, 2018, 01:05 PM

    Students affected by Hurricane Maria bring their research to SLAC

    SLAC National Accelerator Laboratory

    Wednesday August 22, 2018, 10:05 AM

    Brookhaven Lab Pays Tribute to 2018 Summer Interns

    Brookhaven National Laboratory

    Monday August 20, 2018, 12:05 PM

    Changing How Buildings Are Made

    Washington University in St. Louis

    Thursday August 16, 2018, 12:05 PM

    CSUMB Selected to Host Architecture at Zero Competition in 2019

    California State University, Monterey Bay

    Friday July 20, 2018, 03:00 PM

    Department of Energy Invests $64 Million in Advanced Nuclear Technology

    Rensselaer Polytechnic Institute (RPI)

    Thursday July 19, 2018, 05:00 PM

    Professor Miao Yu Named the Priti and Mukesh Chatter '82 Career Development Professor

    Rensselaer Polytechnic Institute (RPI)

    Tuesday July 03, 2018, 11:05 AM

    2018 RHIC & AGS Annual Users' Meeting: 'Illuminating the QCD Landscape'

    Brookhaven National Laboratory

    Friday June 29, 2018, 06:05 PM

    Argonne welcomes The Martian author Andy Weir

    Argonne National Laboratory

    Monday June 18, 2018, 09:55 AM

    Creating STEM Knowledge and Innovations to Solve Global Issues Like Water, Food, and Energy

    Illinois Mathematics and Science Academy (IMSA)

    Friday June 15, 2018, 10:00 AM

    Professor Emily Liu Receives $1.8 Million DoE Award for Solar Power Systems Research

    Rensselaer Polytechnic Institute (RPI)

    Thursday June 07, 2018, 03:05 PM

    Celebrating 40 years of empowerment in science

    Argonne National Laboratory

    Monday May 07, 2018, 10:30 AM

    Introducing Graduate Students Across the Globe to Photon Science

    Brookhaven National Laboratory

    Wednesday May 02, 2018, 04:05 PM

    Students from Massachusetts and Washington Win DOE's 28th National Science Bowl(r)

    Department of Energy, Office of Science

    Thursday April 12, 2018, 07:05 PM

    The Race for Young Scientific Minds

    Argonne National Laboratory

    Wednesday March 14, 2018, 02:05 PM

    Q&A: Al Ashley Reflects on His Efforts to Diversify SLAC and Beyond

    SLAC National Accelerator Laboratory

    Thursday February 15, 2018, 12:05 PM

    Insights on Innovation in Energy, Humanitarian Aid Highlight UVA Darden's Net Impact Week

    University of Virginia Darden School of Business

    Friday February 09, 2018, 11:05 AM

    Ivy League Graduate, Writer and Activist with Dyslexia Visits CSUCI to Reframe the Concept of Learning Disabilities

    California State University, Channel Islands

    Wednesday January 17, 2018, 12:05 PM

    Photographer Adam Nadel Selected as Fermilab's New Artist-in-Residence for 2018

    Fermi National Accelerator Laboratory (Fermilab)

    Wednesday January 17, 2018, 12:05 PM

    Fermilab Computing Partners with Argonne, Local Schools for Hour of Code

    Fermi National Accelerator Laboratory (Fermilab)

    Wednesday December 20, 2017, 01:05 PM

    Q&A: Sam Webb Teaches X-Ray Science from a Remote Classroom

    SLAC National Accelerator Laboratory

    Monday December 18, 2017, 01:05 PM

    The Future of Today's Electric Power Systems

    Rensselaer Polytechnic Institute (RPI)

    Monday December 18, 2017, 12:05 PM

    Supporting the Development of Offshore Wind Power Plants

    Rensselaer Polytechnic Institute (RPI)

    Tuesday October 03, 2017, 01:05 PM

    Stairway to Science

    Argonne National Laboratory

    Thursday September 28, 2017, 12:05 PM

    After-School Energy Rush

    Argonne National Laboratory

    Thursday September 28, 2017, 10:05 AM

    Bringing Diversity Into Computational Science Through Student Outreach

    Brookhaven National Laboratory

    Thursday September 21, 2017, 03:05 PM

    From Science to Finance: SLAC Summer Interns Forge New Paths in STEM

    SLAC National Accelerator Laboratory

    Thursday September 07, 2017, 02:05 PM

    Students Discuss 'Cosmic Opportunities' at 45th Annual SLAC Summer Institute

    SLAC National Accelerator Laboratory

    Thursday August 31, 2017, 05:05 PM

    Binghamton University Opens $70 Million Smart Energy Building

    Binghamton University, State University of New York

    Wednesday August 23, 2017, 05:05 PM

    Widening Horizons for High Schoolers with Code

    Argonne National Laboratory

    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





    Showing results

    0-4 Of 2215