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  • richardmitnick 8:26 am on September 23, 2020 Permalink | Reply
    Tags: "I focus on how electrons behave within solids.", "Think We Already Know Everything About Electrons? Think Again", , , , Emergent phenomena-in which groups of atoms or electrons act in unexpected ways., Groups of electrons collectively behave differently than we would expect from the way each individual electron acts on its own., , , Simons Foundation, Songtian Sonia Zhang, Superconductivity is an example of an emergent phenomenon within physics., , ,   

    From Simons Foundation: Women in STEM-Songtian Sonia Zhang”Think We Already Know Everything About Electrons? Think Again” 

    From Simons Foundation

    1
    Songtian Sonia Zhang. Credit: Rick Soden, Princeton University
    Physicist Songtian Sonia Zhang explores how electrons work within the tiniest objects and finds that they sometimes do unexpected things.

    September 22, 2020
    Marcus Banks

    Songtian Sonia Zhang envisioned a life in finance, until she discovered that learning how electrons work is much more rewarding. A fundamental physicist with a bachelor’s degree from the University of Waterloo in Ontario, Canada, and a doctorate from Princeton University, Zhang has already discovered unexpected behaviors among electrons found in quantum materials like superconductors or magnets. But many mysteries remain about the behavior of these tiny particles. Now beginning a postdoctoral appointment at Columbia University in the physics lab of Dmitri N. Basov, Zhang already has lots of ideas about what she wants to explore next. Our conversation has been edited for clarity.

    You began as a dual major in economics and physics at the University of Waterloo. What prompted the sharper focus on physics instead?

    When I was an undergraduate at Waterloo, I planned to pursue a career in finance, perhaps even on Wall Street. I was interested in physics too, but I never imagined becoming a physicist. That all changed after I completed a physics research project in my third year of college, which happened to overlap with my first job at a financial services firm. This gave me the chance to directly compare finance to physics work — and physics won out handily.

    When I was doing physics, I felt like I was helping to bring new understanding into the world. I know that sounds corny, but it’s true. And it was far more rewarding to me than my work at the financial firm, where I essentially was moving money around. Don’t get me wrong, we need money! But I knew early that physics was for me.

    That sounds clarifying! But the study of physics is broad. How did you narrow your interests?

    During my last semester at Waterloo I researched a special kind of magnet known as ‘spin ice,’ in which the atoms are arranged in a complex lattice pattern. Most magnets have a north and south pole. And if you cut a magnet in two, each new magnet will then also have a north and south pole. But spin ice magnets have such a complex structure that we call them geometrically frustrated. Spin ice magnets can behave like monopoles — that is, a magnet with only one pole instead of the normal two. We still don’t know if monopoles even exist! But the spin ice magnet I studied sure seemed like a monopole, which was fascinating to me. When I first began to study physics, I assumed I would become an astrophysicist. Instead I decided to be more down-to-earth — literally. Today I study the physics of solids, not stars.

    This sounds like quantum physics.

    In many ways, yes. But quantum physics is an extremely broad term that can apply to many things, so in some ways it’s too general. The specific field I work in is condensed matter physics. I focus on how electrons behave within solids. I’m particularly interested in how groups of electrons behave, and especially how their collective behavior cannot be predicted by how each individual in the group acts.

    You’re saying that groups of electrons collectively behave differently than we would expect from the way each individual electron acts on its own?

    Exactly. We call this overall concept ‘emergent phenomena,’ in which groups of atoms or electrons act in unexpected ways. There are many examples of emergent phenomena in nature that go well beyond quantum physics. Think of individual birds migrating together as a cohesive flock, or a school of fish swimming upriver to spawn. Even though each individual bird or fish moves independently, they become entangled in the group and impossible to distinguish from one another.

    Superconductivity is an example of an emergent phenomenon within physics. Regular electrical conductors carry a current known as electricity; this is how we light lightbulbs, for example, by connecting an electricity source to an object that emits light. These kinds of everyday conductors come with inherent inefficiencies — energy is always lost because the electricity faces resistance as it travels. This is why lightbulbs eventually burn out.

    In contrast, a superconductor operating in extremely low temperatures (−450 F) can keep conducting electricity forever, because the electricity meets no resistance at all. Nobody could have predicted that superconductors could do this. It had to be discovered through observation, and it’s an example of how we are constantly learning about new types of emergent phenomena. Sometimes this is purely about developing knowledge for its own sake, but oftentimes this work has practical applications.

    We’ll loop back to the practical applications in a moment. First, though, what was your most exciting discovery at Princeton?

    At Princeton I studied kagome magnets. The atoms that comprise these magnets are arranged in a lattice which evokes the famous Japanese basket lattice pattern of the same name.

    4
    Scanning tunneling microscopy (STM) image of magnetic adatoms deposited on topological superconductor candidate PbTaSe2. Inset: a 2D enlarged view. Each magnetic adatom can host a Majorana zero mode acting as a topological qubit which has the potential to be used for robust quantum computation. Credit: Songtian Zhang.

    Like the spin ice magnets I previously mentioned, kagome magnets are geometrically frustrated. In our research, we did various things to these magnets, such as observing them within magnetic fields of various strengths or alternating their temperatures. This was all to see how the electrons behaved in different conditions. In high magnetic fields the kagome magnets started acting like negative magnets — meaning they exerted more energy when moving in the same direction as a magnetic field and not when going ‘against the wind,’ so to speak.

    We published these unexpected results in Nature Physics last year.

    The fact that we discovered something totally unexpected shows the importance of keeping an open mind, of not being locked into any one idea. Instead, we are always finding new questions to ask.

    As you begin your postdoctoral work at Columbia, what do you plan to focus on, at least initially, until you discover new questions?

    I’m interested in learning more about topological insulators: objects that, on the surface, conduct electricity but in their interior act as an insulator. When the material is cut, the new surface, which was previously the insulating bulk, becomes conductive and can now support surface currents. Besides topological insulators there are topological superconductors, which can superconduct currents of electricity. The physics community has made some headway in understanding these superconductors, but there’s a lot more work that needs to be done.

    And how do you hope this knowledge will inform our understanding of the natural and physical world?

    Topological superconductors come from the math concept of topology. A good way to think about topology is the relationship between a doughnut, with a hole in the middle, and a ball, which has no holes. In this comparison, the doughnut and the ball are topologically distinct.

    By comparison, the doughnut would be topologically identical to a ring, which also has a hole in the middle. In this example, the number of holes is a topological property that can’t be destroyed without changing the underlying nature of the object.

    In physics, we’re interested in electronic behaviors that are similarly robust, such as in topological superconductors. There’s great potential for topological superconductors to be used for powerful, reliable and robust quantum computation, which will be a giant leap past the computers we use today. I can’t say exactly how my work will contribute to this, but I do know I’m excited to be on the journey. And I know I will enjoy it more than working on Wall Street.

    See the full article here.

    five-ways-keep-your-child-safe-school-shootings

    Please help promote STEM in your local schools.

    Stem Education Coalition


    Mission and Model

    The Simons Foundation’s mission is to advance the frontiers of research in mathematics and the basic sciences.

    Co-founded in New York City by Jim and Marilyn Simons, the foundation exists to support basic — or discovery-driven — scientific research undertaken in the pursuit of understanding the phenomena of our world.

    The Simons Foundation’s support of science takes two forms: We support research by making grants to individual investigators and their projects through academic institutions, and, with the launch of the Flatiron Institute in 2016, we now conduct scientific research in-house, supporting teams of top computational scientists.

     
  • richardmitnick 2:00 pm on September 14, 2020 Permalink | Reply
    Tags: "Infinitely Long Chains of Hydrogen Atoms Have Surprising Properties, , Auxiliary-field quantum Monte Carlo, Including a Metallic Phase", Lattice-regularized diffusion Monte Carlo, Moving the hydrogen atoms even closer together the researchers discovered that the hydrogen chain transformed from an insulator into a metal with electrons moving freely between atoms., , , Simons Foundation, Standard and sliced-basis density-matrix renormalization, The Many Electron Problem, Variational Monte Carlo   

    From Simons Foundation: “Infinitely Long Chains of Hydrogen Atoms Have Surprising Properties, Including a Metallic Phase” 

    From Simons Foundation

    September 14, 2020
    Thomas Sumner

    Stacey Greenebaum
    press@simonsfoundation.org.

    Scientists with the Flatiron Institute and the Simons Collaboration on the Many Electron Problem combined cutting-edge computational methods to probe an endless line of protons surrounded by electrons.

    1
    A map of where electrons are most likely to be found around a chain of hydrogen atoms. Brighter colors denote higher probabilities. At this spacing between atoms, the electrons try to link pairs of adjacent atoms to form dihydrogen molecules. Because the protons are fixed in place, these molecules can’t form. Instead, each electron ‘leans’ toward a neighboring atom. M. Motta et al./Physical Review X 2020.

    An infinite chain of hydrogen atoms is just about the simplest bulk material imaginable — a never-ending single-file line of protons surrounded by electrons. Yet a new computational study combining four cutting-edge methods finds that the modest material boasts fantastic and surprising quantum properties.

    By computing the consequences of changing the spacing between the atoms, an international team of researchers from the Flatiron Institute and the Simons Collaboration on the Many Electron Problem found that the hydrogen chain’s properties can be varied in unexpected and drastic ways. That includes the chain transforming from a magnetic insulator into a metal, the researchers report September 14 in Physical Review X.

    The computational methods used in the study present a significant step toward custom-designing materials with sought-after properties, such as the possibility of high-temperature superconductivity in which electrons flow freely through a material without losing energy, says the study’s senior author Shiwei Zhang. Zhang is a senior research scientist at the Center for Computational Quantum Physics (CCQ) at the Simons Foundation’s Flatiron Institute in New York City.

    “The main purpose was to apply our tools to a realistic situation,” Zhang says. “Almost as a side product, we discovered all of this interesting physics of the hydrogen chain. We didn’t think that it would be as rich as it turned out to be.”

    Zhang, who is also a chancellor professor of physics at the College of William and Mary, co-led the research with Mario Motta of IBM Quantum. Motta serves as first author of the paper alongside Claudio Genovese of the International School for Advanced Studies (SISSA) in Italy, Fengjie Ma of Beijing Normal University, Zhi-Hao Cui of the California Institute of Technology, and Randy Sawaya of the University of California, Irvine. Additional co-authors include CCQ co-director Andrew Millis, CCQ Flatiron Research Fellow Hao Shi and CCQ research scientist Miles Stoudenmire.

    The paper’s long author list — 17 co-authors in total — is uncommon for the field, Zhang says. Methods are often developed within individual research groups. The new study brings many methods and research groups together to combine forces and tackle a particularly thorny problem. “The next step in the field is to move toward more realistic problems,” says Zhang, “and there is no shortage of these problems that require collaboration.”

    While conventional methods can explain the properties of some materials, other materials, such as infinite hydrogen chains, pose a more daunting computational hurdle. That’s because the behavior of the electrons in those materials is heavily influenced by interactions between electrons. As electrons interact, they become quantum-mechanically entangled with one another. Once entangled, the electrons can no longer be treated individually, even when they are physically separate.

    The sheer number of electrons in a bulk material — roughly 100 billion trillion per gram — means that conventional brute force methods can’t even come close to providing a solution. The number of electrons is so large that it’s practically infinite when thinking at the quantum scale.

    Thankfully, quantum physicists have developed clever methods of tackling this many-electron problem. The new study combines four such methods: variational Monte Carlo, lattice-regularized diffusion Monte Carlo, auxiliary-field quantum Monte Carlo, and standard and sliced-basis density-matrix renormalization group. Each of these cutting-edge methods has its strengths and weaknesses. Using them in parallel and in concert provides a fuller picture, Zhang says.

    Researchers, including authors of the new study, previously used those methods in 2017 to compute the amount of energy each atom in a hydrogen chain has as a function of the chain’s spacing [Physical Review X]. This computation, known as the equation of state, doesn’t provide a complete picture of the chain’s properties. By further honing their methods, the researchers did just that.

    At large separations, the researchers found that the electrons remain confined to their respective protons. Even at such large distances, the electrons still ‘know’ about each other and become entangled. Because the electrons can’t hop from atom to atom as easily, the chain acts as an electrical insulator.

    As the atoms move closer together, the electrons try to form molecules of two hydrogen atoms each. Because the protons are fixed in place, these molecules can’t form. Instead, the electrons ‘wave’ to one another, as Zhang puts it. Electrons will lean toward an adjacent atom. In this phase, if you find an electron leaning toward one of its neighbors, you’ll find that neighboring electron responding in return. This pattern of pairs of electrons leaning toward each other will continue in both directions.

    Moving the hydrogen atoms even closer together, the researchers discovered that the hydrogen chain transformed from an insulator into a metal with electrons moving freely between atoms. Under a simple model of interacting particles known as the one-dimensional Hubbard model, this transition shouldn’t happen, as electrons should electrically repel each other enough to restrict movement. In the 1960s, British physicist Nevill Mott predicted the existence of an insulator-to-metal transition based on a mechanism involving so-called excitons, each consisting of an electron trying to break free of its atom and the hole it leaves behind. Mott proposed an abrupt transition driven by the breakup of these excitons — something the new hydrogen chain study didn’t see.

    Instead, the researchers discovered a more nuanced insulator-to-metal transition. As the atoms move closer together, electrons gradually get peeled off the tightly bound inner core around the proton line and become a thin `vapor’ only loosely bound to the line and displaying interesting magnetic structures.

    The infinite hydrogen chain will be a key benchmark in the future in the development of computational methods, Zhang says. Scientists can model the chain using their methods and check their results for accuracy and efficiency against the new study.

    The new work is a leap forward in the quest to utilize computational methods to model realistic materials, the researchers say. In the 1960s, British physicist Neil Ashcroft proposed that metallic hydrogen, for instance, might be a high-temperature superconductor. While the one-dimensional hydrogen chain doesn’t exist in nature (it would crumple into a three-dimensional structure), the researchers say that the lessons they learned are a crucial step forward in the development of the methods and physical understanding needed to tackle even more realistic materials.

    See the full article here.

    five-ways-keep-your-child-safe-school-shootings

    Please help promote STEM in your local schools.

    Stem Education Coalition


    Mission and Model

    The Simons Foundation’s mission is to advance the frontiers of research in mathematics and the basic sciences.

    Co-founded in New York City by Jim and Marilyn Simons, the foundation exists to support basic — or discovery-driven — scientific research undertaken in the pursuit of understanding the phenomena of our world.

    The Simons Foundation’s support of science takes two forms: We support research by making grants to individual investigators and their projects through academic institutions, and, with the launch of the Flatiron Institute in 2016, we now conduct scientific research in-house, supporting teams of top computational scientists.

     
  • richardmitnick 8:30 am on August 4, 2020 Permalink | Reply
    Tags: "Empowering the Future of Fusion Energy", , , PPPL NSTX -U tokamak at Princeton Plasma Physics Lab Princeton NJ USA, Simons Foundation   

    From Simons Foundation: “Empowering the Future of Fusion Energy” 

    From Simons Foundation

    Annual Report 2019

    Simons Collaboration on Hidden Symmetries and Fusion Energy

    Since the 1940s, scientists have dreamed of creating fusion energy reactors, which could make energy cheaply and safely, producing less radiation and waste than conventional nuclear-fission reactors. So far, though, no design has managed to generate more energy than was put in, leading cynics to perennially quip that fusion is the energy source of the future — and always will be.

    The Simons Collaboration on Hidden Symmetries and Fusion Energy, using a new design approach and fresh insights into the mathematics of symmetry, may yet prove the cynics wrong.

    Fusing nuclei together in a controlled way requires creating a starlike environment: In stars, high temperatures result in enough kinetic energy to squash hydrogen nuclei together, forming helium and releasing energy.

    Here on Earth, physicists have managed to come up with a few strategies to fuse hydrogen. One method requires heating hydrogen atoms in a container to 100 million degrees to give them enough energy to overcome the mutual repulsion of their nuclei. Under those conditions, hydrogen gas ionizes, which means electrons are stripped from their atoms and float around freely with the nuclei in a mix called plasma.

    One promising early model was first tested out in 1958. In that design, a doughnut-shaped (or toroidal) tokamak holds plasma by pumping electrical currents through a series of metal coils, which create magnetic fields that contain the hydrogen and squeeze it together, causing fusion.

    PPPL NSTX -U tokamak at Princeton Plasma Physics Lab, Princeton, NJ,USA

    ITER Tokamak in Saint-Paul-lès-Durance, which is in southern France

    Tokamaks have a major drawback, however: The magnetic field created by the coils that wrap around the toroidal tokamak also induce a current in the plasma. Researchers usually pulse that current, which makes it difficult to maintain the plasma in the stable steady state necessary for fusion. Furthermore, the system can be disrupted by instability, dissipating the plasma after even a few milliseconds. Scientists have built dozens of experimental tokamaks, but none has yet resulted in a net gain of energy, although research continues.

    Princeton astrophysicist Lyman Spitzer thought of another configuration: a stellarator. A stellarator is also torus-like, but because of a complicated helical structure in its coils, the plasma holds no current and hence can operate in steady state devoid of disruptive instabilities, in principle creating ideal conditions for fusion. The challenge is to build an optimum set of coils that will realize the dream of gains in energy via fusion.

    Wendelstgein 7-X stellarator, built in Greifswald, Germany

    The collaboration hopes that new mathematical and numerical techniques will solve that challenge. This collection of 33 mathematicians, computer scientists and plasma physicists from 16 universities across the globe is working on the next generation of stellarators, whose coils test the limits of design and manufacturing precision.

    “We are developing novel optimization methods that will enable us to design the stellarator of the future with as much engineering simplicity as possible,” says Princeton University professor of astrophysical sciences Amitava Bhattacharjee, director of the collaboration. “When you put physics and the science of precise optimization together, you can come up with sophisticated designs which were impossible before; the ways to do that is the primary focus of the Simons project.”


    Both the tokamak and the stellarator use strong magnetic fields to confine plasma at the high temperatures and pressures needed for nuclear fusion. The tokamak (top) uses an internal transformer to drive a current in the plasma, thereby twisting the magnetic field and containing the plasma. This approach, though, can result in instabilities. The stellarator’s contorted design (bottom) results in a twisted magnetic field without the need for induced current, resulting in improved stability. Credit: © 2020 New Scientist Ltd. All rights reserved. Distributed by Tribune Content Age.

    The theoretical side of hidden symmetries

    Symmetries in objects simplify analyses and allow people to use less energy — think of how circular wheels work better than oval-shaped or square-shaped ones. Unlike those in the doughnut-shaped tokamak, which has an obvious symmetry, the twisting coils of a stellarator don’t appear symmetric in terms of the usual x, y and z coordinates. But when their structures are viewed in relation to magnetic fields instead of those axes, in a coordinate system defined by one of the collaboration’s founding investigators, Columbia University professor of applied physics and applied mathematics Allen Boozer, stellarators do have an approximate ‘hidden’ symmetry, or quasisymmetry.

    “The symmetry is hidden in the sense that if you look at one of these magnetic fields it looks like a Salvador Dali painting: It’s distorted and wobbly,” says co-investigator Matt Landreman, an associate research scientist at the Institute for Research in Electronics and Applied Physics at the University of Maryland. “But the equations tell us that even if you can’t see it by eye, the electrically charged particles in these magnetic fields experience a symmetry. It’s sort of like you trick electrons and protons into thinking they’re in a symmetric system. That’s an exciting and beautiful motivating concept for the project.”

    The containing magnetic field of the stellarator can be described using quasi-symmetric equations. Previous numerical research using computers found around 20 possible configurations for the field that minimize the ‘approximateness’ of the quasi-symmetry. But Landreman says that the black-box solution “was emotionally unsatisfying because we don’t know why the computer takes me to this shape. How many possible shapes are out there?”

    Instead, the collaborators used different numerical methods to approximate the quasi-symmetry equations. They found all possible configurations, ensuring that future stellarator designs won’t overlook a magnetic field alignment that could optimize energy output.

    Experiments to prove the theories

    Unlike a constantly tended tokamak, a stellarator is a steady-state system, which means that “you can turn it on in the morning and turn it off in the evening,” says co-investigator Thomas Sunn Pedersen, a professor of physics at the Max Planck Institute for Plasma Physics, where he runs experiments on one of the largest stellarators in the world, the Wendelstein 7-X (W7-X).

    Although stellarators such as the W7-X were built and optimized to the best extent possible at the time, the collaboration hopes to use more advanced computing power to better optimize the next generation. Thus far, all the results from the theoretical side have been borne out by data from the W7-X.

    “These experiments make me excited,” Pedersen says. “The optimization that was done two decades ago with computers we can laugh about today in terms of computational power works; we can do so much more now.”

    The hub of an international community

    The collaboration’s shared postdocs are also in on the fun. These eight people embody one of the unusual hallmarks of the project: encouraging travel between multiple institutions, ferrying knowledge and achieving collaboration between departments.

    “What I really like about being a shared postdoc is not working by yourself in an office. You really can talk to people and do a lot of interesting problems,” says postdoc Silke Glas, who travels between Cornell University and New York University. “I enjoy the variety I have, and I think it’s a win for the collaboration as well.”

    These postdocs help nail down jargon between different fields, a role also played by the biweekly video chats between the theoretical and experimental collaboration members.

    “Another challenge of the interdisciplinary nature of this work is trying to come up with concepts that are interesting to the people in both theoretical and experimental communities,” says Landreman. “One thing we’ve done a lot of this first year is define precisely stated mathematical problems that numerical optimization people can study that are interesting enough from a physics point of view, but don’t have all the complexities of physical experiments.”

    Nowadays, nonmembers of the collaboration sit in on the biweekly “Simons Hour” as well. The international research community showed up in droves at the first annual meeting of the collaboration, which took place in late March at the Simons Foundation in New York City. Seventy-five researchers came from around the world for research updates from the collaboration and poster presentations from non-collaboration researchers.

    “The general sense of enthusiasm about the hidden symmetries project is very high; I’m very gratified by it,” says Bhattacharjee. “I think what Simons did was support an idea which was very timely in which there were not enough resources invested, and in the process created something that was very much needed by the stellarator community.”

    The collaboration also co-hosted a plasma physics summer school at the Princeton Plasma Physics Laboratory for 33 graduate students and postdocs with backgrounds in optimizing magnetic fields, who will hopefully join the community and continue contributing at the frontier of one of the world’s foremost science problems.

    “You have here a marriage of fundamental science, wonderful mathematics and physics, dedicated to an engineering cause of great importance,” Bhattacharjee says.

    See the full article here.

    five-ways-keep-your-child-safe-school-shootings

    Please help promote STEM in your local schools.

    Stem Education Coalition


    Mission and Model

    The Simons Foundation’s mission is to advance the frontiers of research in mathematics and the basic sciences.

    Co-founded in New York City by Jim and Marilyn Simons, the foundation exists to support basic — or discovery-driven — scientific research undertaken in the pursuit of understanding the phenomena of our world.

    The Simons Foundation’s support of science takes two forms: We support research by making grants to individual investigators and their projects through academic institutions, and, with the launch of the Flatiron Institute in 2016, we now conduct scientific research in-house, supporting teams of top computational scientists.

     
    • Schwarz Christina 5:33 am on October 25, 2021 Permalink | Reply

      Hello,
      I am a student at Erlangen-Nuremberg university in Germany and currently writing my master thesis about the topic ‘Geometric multigrid for the gyrokinetic Poisson equation fromf usion plasma applications’.
      I would kindly like to ask if I may use a picture from this article in my thesis.
      Yours sincerely
      Christina Schwarz

      Like

      • richardmitnick 8:32 am on October 25, 2021 Permalink | Reply

        For some reason, I could not bring up the post for editing/ I saw that some images are missing, but all are usable under “fair use”. so use what you would like.

        Like

  • richardmitnick 2:44 pm on July 30, 2020 Permalink | Reply
    Tags: Antibodies- the proteins of the immune system, , are another challenge for Rosetta., “Rosetta was born in the wild the raw and the unstructured” recalls Richard Bonneau a group leader for systems biology at the Flatiron Institute’s Center for Computational Biology., , , , Communicating all of Rosetta’s capabilities is one of the many challenges of managing a colossal software suite and a community of thousands of users., David Baker had a view early on that this community would meet regularly and that the code would be centralized., , In an internship program college students can spend a summer in a Rosetta lab sandwiched between a week at the Coding Boot Camp at the University of North Carolina and a week at the summer RosettaCon , Macromolecular modeling and design, Maintaining the code takes great effort and coordination. Each time a developer submits a piece of code it has to be integrated into the entire Rosetta suite., , Recently improved structure prediction and a burst of new applications have ballooned Rosetta’s offerings to include over 80 distinct methods for macromolecular modeling., RNA and DNA Studies, Rosetta was first intended as a key for deciphering proteins- the building blocks of life., , Rosetta’s licensing agreement is unique in that most of the fees paid by pharmaceutical companies flow back to the RosettaCommons, Rosetta’s modular nature is its secret weapon: Scientists can build a dizzying array of workflows from the thousands of available code classes., RosettaCommons, Simons Foundation, , With 3.1 million lines of code and over 35000 licenses the Rosetta of 2020 looks very different from the one Bonneau helped craft 25 years ago.   

    From Simons Foundation: “A Software, a Community and a Different Way to Do Science” rosetta@home 

    From Simons Foundation
    July 30, 2020
    Susan Reslewic Keatley, Ph.D.

    1
    Rendering of a composite structure depicting the interaction between the ACE2/BOAT1 complex (blue/yellow) from PDB ID 6M17, and the SARS-CoV-2 spike ectodomain structure (pink, teal) from PDB ID 6VYB. Credit: P. Douglas Renfrew/Flatiron Institute.

    The suite of software tools collectively known Rosetta@home is defined not only by what it does, but also by a community of scientists who are changing how collaborations thrive and move science forward.

    2
    Main laboratories and institutions in the RosettaCommons and basic facts about the software. Figure first appeared in PLOS Computational Biology.

    Rising up against this computational tower of Babel is Rosetta, a suite of software tools for macromolecular modeling and design. Like its namesake, the Rosetta stone, which gave the modern world a key to deciphering ancient hieroglyphs, Rosetta was first intended as a key for deciphering proteins, the building blocks of life. Designed originally to predict individual protein structure, the software has broadened in scope: It can now help scientists map complex interactions between proteins and design novel proteins. It can also boost a whole host of other biological applications in fields from medicine to synthetic materials to climate science. With 500 developers at over 70 academic institutions worldwide, Rosetta is defined not only by what it does, but also by a community of scientists who are changing how science is done and how collaborations thrive and move science forward.

    “Rosetta was born in the wild, the raw and the unstructured,” recalls Richard Bonneau, a group leader for systems biology at the Flatiron Institute’s Center for Computational Biology. As a student in David Baker’s biochemistry lab at the University of Washington in the mid-’90s, he and several members of the lab sat down to write a code that would predict protein structure — solving a problem that had long eluded researchers. With 3.1 million lines of code and over 35,000 licenses, the Rosetta of 2020 looks very different from the one Bonneau helped craft 25 years ago. What remains the same, however, is the intent to build a standardized, shareable code that anyone can use, and to grow a cohesive community to further evolve and strengthen the code base.

    David Baker’s Rosetta@home project, a project running on BOINC software from UC Berkeley

    In an internship program, college students can spend a summer in a Rosetta lab, sandwiched between a week at the Coding Boot Camp at the University of North Carolina and a week at the summer RosettaCon.
    “David Baker had a view early on that this community would meet regularly and that the code would be centralized,” says Roland Dunbrack, a Rosetta principal investigator and a professor in the Molecular Therapeutics Program at the Fox Chase Cancer Center.

    U Washington Dr. David Baker

    Our knowledge of biology has transformed over the last few decades, but the fundamental relationship between a molecule’s structure and function is still a guiding principle of discovery-driven biological research. Rosetta assesses the structure of proteins and other biological molecules — whether natural or designed — by considering all aspects of a molecule’s conformation, from how the individual atoms attract or repel each other to how segments of a molecule can move freely in space. It then selects the structure with the lowest free energy. This information is critical for scientists working to decipher protein structure and function. Recently, improved structure prediction and a burst of new applications have ballooned Rosetta’s offerings to include over 80 distinct methods for macromolecular modeling, as reported on June 1 in Nature Methods — a milestone that represents a boon to the scientific world.

    Communicating all of Rosetta’s capabilities is one of the many challenges of managing a colossal software suite and a community of thousands of users. The recent Nature Methods paper is an important step toward that goal, however, serving as a catalog for the community of Rosetta users and the larger scientific community, says Julia Koehler Leman, one of the paper’s first authors and a research scientist in systems biology in Bonneau’s group at the Flatiron Institute. With over 100 authors, the paper reviews Rosetta’s advances over the last five years, with an emphasis on major scientific applications, user interfaces and usability.

    The Nature Methods resource also highlights Rosetta’s approach to several unique challenges to modeling and understanding in biology. Take membrane proteins, which are targets for 60% of the pharmaceuticals on the market despite making up just 30% of all human proteins. Because they are hard to work with in the lab, they make up a tiny fraction of the proteins available in structure databases, which Rosetta uses for its prediction algorithms. An additional obstacle is that Rosetta was developed for proteins in water rather than those embedded within cell membranes, which are ‘greasy’ and water insoluble. As a postdoctoral fellow who had also worked in an experimental membrane proteins lab during graduate school, Koehler Leman worked with colleagues to adapt Rosetta to the membrane environment. “The training I had experimentally with membrane proteins shaped how I develop code,” Koehler Leman says, and led her to emphasize ease of the user interface in her coding. Rosetta now offers an array of capabilities for modeling the characteristics of membrane proteins, including protein-protein docking and design.

    Antibodies, the proteins of the immune system, are another challenge for Rosetta. Unlike other proteins, they contain loop regions that can confound structure prediction. They are also known to make split-second changes when binding to an antigen, making them difficult to predict and model. A large collaboration of researchers, including Jeffrey Gray, a Rosetta principal investigator and a professor of chemical and biomolecular engineering at Johns Hopkins University, has succeeded in creating Rosetta methods to predict the structure of an antibody from its sequence, and then model the interaction of the antibody with its antigen. Understanding these interactions is critical for developing therapeutic antibodies or vaccines. Motivated by COVID-19, Gray, Dunbrack and other Rosetta developers are thinking about how to most effectively design antibodies to combat this and future pandemics. “Our collaborations through Rosetta have given us deep internal knowledge of antibodies,” says Gray. “The synergistic and positive nature of this community has helped us accelerate science.”

    4
    eXtreme Rosetta Workshops (XRWs) are organized annually and have had a drastic positive impact on both the software and the community. Image first appeared in PLOS Computational Biology.

    Rosetta has expanded beyond proteins, to RNA and DNA. RNA structure in particular presents challenges distinct from those of proteins. Loops with irregular nucleotide pairing abound, and the method Rosetta uses for proteins flounders in the presence of RNA; multiple possible energy minima can confound the overall energetic view of a conformation, much the way deep potholes on a hill might mislead an altimeter. Rosetta developers have demonstrated RNA structure prediction, as well as RNA- and DNA-protein binding, by modeling the molecules in a step-by-step fashion, in essence sacrificing computational expense for accuracy. Several of the leading COVID-19 vaccine candidates, including two of those selected for Operation Warp Speed, initiated by the federal government to accelerate vaccine development against COVID-19, are DNA- or RNA-based. This underscores the importance of making tools available to probe nucleic acids and how they bind to proteins.

    Rosetta’s modular nature is its secret weapon: Scientists can build a dizzying array of workflows from the thousands of available code classes. “There are things we can do with Rosetta that we can’t do otherwise, like design proteins so stable they are more like nonliving materials and integrate high-throughput computation with high-throughput experiments,” says Bonneau. The sheer size of both the software itself and the worldwide community can, at times, feel unwieldy, added Bonneau, but ultimately it is necessary for solving big scientific problems.

    Rosetta’s licensing agreement is unique in that most of the fees paid by pharmaceutical companies flow back to the RosettaCommons, the community of developers, to support code maintenance and community building. “You can think of Rosetta as a multi-institution research group, with money,” says Dunbrack. “There are lots of consortiums out there, but not as many with their own source of funds.” Recently, the corporate licensing agreement was changed so companies can contribute code back to Rosetta. “This change says a lot about where our tools are, and how the community and the science are evolving,” says Brian Weitzner, another of the Nature Methods paper’s first authors and a senior scientist at Lyell Immunopharma, a company Baker co-founded.

    Maintaining the code takes great effort and coordination. Each time a developer submits a piece of code, it has to be integrated into the entire Rosetta suite. “Individual code development branches are merged into the software several times a day,” says Koehler Leman, “so we need to continually test the software to make sure it won’t break.” The benefits make this effort worthwhile, says Bonneau. “For whatever you want to do, whether with DNA, RNA, drugs or surfaces, you might just have two to 10 people in the community writing a code in the same framework.” RosettaCommons issues its own grants to members of the community for code maintenance, something scientific research grants won’t often cover.

    The emphasis on documentation and interface development aims to make Rosetta more user-friendly and a benchmark for how people can develop powerful software in any community, says Koehler Leman. Detailed user instructions, called protocol captures, accompany each new addition of code, and three different language interfaces (C++, Python and command line) are available to developers. For the general public, including K-12 students, the video game Foldit offers a chance to play with protein structure, with terms like ‘rubber bands’ for restraints and ‘shake’ for rotating parts of a molecule. Foldit’s 700,000 regular users routinely solve real-world scientific structure puzzles, including a challenge this past February to design a protein to inhibit the spike protein on the new coronavirus, with the top results selected for experimental testing in labs.

    To rally the community around the arduous tasks of standardized documentation and code curation, RosettaCommons holds a meeting (RosettaCon) each summer and winter, hack-a-thons for code maintenance and improvement, and boot camps to train junior developers. It also grants an annual Rosetta Service Award for contributions to code maintenance or community leadership. A conversation in 2012 between Weitzner and Andrew Leaver-Fay, now an assistant professor of biochemistry and biophysics at the University of North Carolina School of Medicine and Matthew O’Meara, now a research assistant professor of computational medicine and bioinformatics at the University of Michigan Medical School, led to the creation of the boot camp. “We noticed postdocs spent a year and a half learning to program, and we said, let’s have a class. I’ve learned that when you ask, ‘What if we did this differently?’ the community is so supportive and the response is, ‘Yeah, let’s do it,’” says Weitzner, who worked in Dunbrack’s lab in high school and college, in Gray’s lab in graduate school, and in Baker’s lab as a postdoc.

    In an internship program, college students can spend a summer in a Rosetta lab, sandwiched between a week at the Coding Boot Camp at the University of North Carolina and a week at the summer RosettaCon in Washington state. “They start to foster this community right when you come in,” says former intern and current Coding Boot Camp teaching assistant Anna Yaschenko, who graduated from the University of Maryland this year with a dual major in computer science and bioinformatics. “RosettaCon is so casual — it allows people to connect in ways you couldn’t at a typical conference. I was surprised at how tight-knit the community was despite being so large.”

    A post-baccalaureate program starts this summer, Gray says, and all five participants are from groups underrepresented in STEM fields. Rosetta’s diversity, equity and inclusion committee has encouraged Rosetta principal investigators, students and postdocs to attend conferences like the Annual Biomedical Research Conference for Minority Students; oSTEM, a professional society for LGBTQ people in STEM fields; and the Grace Hopper Celebration of Women in Computing conference. “Diversity in research programs is important because it’s fair, and everyone should have the opportunity to participate,” says Dunbrack. RosettaCommons recently put out a statement on Black Lives Matter that included action items for individuals and labs to combat racism. “We had so many people weighing in,” says Gray, “saying ‘this is important,’ or ‘here’s this subtlety.’ There’s still a lot of work to do, but I was very proud of our community for their serious engagement.”

    As a software and a community, Rosetta represents a different way to do science. “We really believe the best idea wins, no matter where it comes from,” says Koehler Leman. “At our conferences, people are less worried about being right or wrong, and more concerned with ‘Does something work or not?’”

    “Other research communities can benefit from this approach,” says Weitzner, “and collaborate more and not worry as much about competing.” The challenge will be to continue to balance innovation with standardization as the software and community grow. “We’ve got to maintain the quality and continuity of the code, while integrating new methods and research into Rosetta,” says Bonneau. “New problems in biology have a scale and complexity that demand this kind of collaboration.”

    [I participated in rosetta@home as a BOINC cruncher for a number of years.]

    My BOINC

    See the full article here.

    five-ways-keep-your-child-safe-school-shootings

    Please help promote STEM in your local schools.

    Stem Education Coalition


    Mission and Model

    The Simons Foundation’s mission is to advance the frontiers of research in mathematics and the basic sciences.

    Co-founded in New York City by Jim and Marilyn Simons, the foundation exists to support basic — or discovery-driven — scientific research undertaken in the pursuit of understanding the phenomena of our world.

    The Simons Foundation’s support of science takes two forms: We support research by making grants to individual investigators and their projects through academic institutions, and, with the launch of the Flatiron Institute in 2016, we now conduct scientific research in-house, supporting teams of top computational scientists.

     
  • richardmitnick 1:05 pm on July 23, 2020 Permalink | Reply
    Tags: , Computational Quantum Physics, , , Flatiron Institute, In the quantum mechanical world electrical resistance is a byproduct of electrons bumping into things., Links to astrophysics, , , Quantum Monte Carlo algorithm, , Simons Foundation, Strange metals are related to high-temperature superconductors and have surprising connections to the properties of black holes.,   

    From Simons Foundation: “Quantum physicists crack mystery of ‘strange metals,’ a new state of matter” 

    From Simons Foundation

    July 23, 2020
    Thomas Sumner

    Strange metals have surprising connections to high-temperature superconductors and black holes.

    1
    A diagram showing different states of matter as a function of temperature, T, and interaction strength, U (normalized to the amplitude, t, of electrons hopping between sites). Strange metals emerge in a regime separating a metallic spin glass and a Fermi liquid. P. Cha et al./Proceedings of the National Academy of Sciences 2020.

    Even by the standards of quantum physicists, strange metals are just plain odd. The materials are related to high-temperature superconductors and have surprising connections to the properties of black holes. Electrons in strange metals dissipate energy as fast as they’re allowed to under the laws of quantum mechanics, and the electrical resistivity of a strange metal, unlike that of ordinary metals, is proportional to the temperature.

    Generating a theoretical understanding of strange metals is one of the biggest challenges in condensed matter physics. Now, using cutting-edge computational techniques, researchers from the Flatiron Institute in New York City and Cornell University have solved the first robust theoretical model of strange metals. The work reveals that strange metals are a new state of matter, the researchers report July 22 in the Proceedings of the National Academy of Sciences.

    “The fact that we call them strange metals should tell you how well we understand them,” says study co-author Olivier Parcollet, a senior research scientist at the Flatiron Institute’s Center for Computational Quantum Physics (CCQ). “Strange metals share remarkable properties with black holes, opening exciting new directions for theoretical physics.”

    In addition to Parcollet, the research team consisted of Cornell doctoral student Peter Cha, CCQ associate data scientist Nils Wentzell, CCQ director Antoine Georges, and Cornell physics professor Eun-Ah Kim.

    In the quantum mechanical world, electrical resistance is a byproduct of electrons bumping into things. As electrons flow through a metal, they bounce off other electrons or impurities in the metal. The more time there is between these collisions, the lower the material’s electrical resistance.

    For typical metals, electrical resistance increases with temperature, following a complex equation. But in unusual cases, such as when a high-temperature superconductor is heated just above the point where it stops superconducting, the equation becomes much more straightforward. In a strange metal, electrical conductivity is linked directly to temperature and to two fundamental constants of the universe: Planck’s constant and Boltzmann’s constant. Consequently, strange metals are also known as Planckian metals.

    Models of strange metals have existed for decades, but accurately solving such models proved out of reach with existing methods. Quantum entanglements between electrons mean that physicists can’t treat the electrons individually, and the sheer number of particles in a material makes the calculations even more daunting.

    Cha and his colleagues employed two different methods to crack the problem. First, they used a quantum embedding method based on ideas developed by Georges in the early ’90s. With this method, instead of performing detailed computations across the whole quantum system, physicists perform detailed calculations on only a few atoms and treat the rest of the system more simply. They then used a quantum Monte Carlo algorithm (named for the Mediterranean casino), which uses random sampling to compute the answer to a problem. The researchers solved the model of strange metals down to absolute zero (minus 273.15 degrees Celsius), the unreachable lower limit for temperatures in the universe.

    The resulting theoretical model reveals the existence of strange metals as a new state of matter bordering two previously known phases of matter: Mott insulating spin glasses and Fermi liquids. “We found there is a whole region in the phase space that is exhibiting a Planckian behavior that belongs to neither of the two phases that we’re transitioning between,” Kim says. “This quantum spin liquid state is not so locked down, but it’s also not completely free. It is a sluggish, soupy, slushy state. It is metallic but reluctantly metallic, and it’s pushing the degree of chaos to the limit of quantum mechanics.”

    The new work could help physicists better understand the physics of higher-temperature superconductors. Perhaps surprisingly, the work has links to astrophysics. Like strange metals, black holes exhibit properties that depend only on temperature and the Planck and Boltzmann constants, such as the amount of time a black hole ‘rings’ after merging with another black hole. “The fact that you find this same scaling across all these different systems, from Planckian metals to black holes, is fascinating,” Parcollet says.

    For more information, please contact Stacey Greenebaum at press@simonsfoundation.org.

    See the full article here.

    five-ways-keep-your-child-safe-school-shootings

    Please help promote STEM in your local schools.

    Stem Education Coalition


    Mission and Model

    The Simons Foundation’s mission is to advance the frontiers of research in mathematics and the basic sciences.

    Co-founded in New York City by Jim and Marilyn Simons, the foundation exists to support basic — or discovery-driven — scientific research undertaken in the pursuit of understanding the phenomena of our world.

    The Simons Foundation’s support of science takes two forms: We support research by making grants to individual investigators and their projects through academic institutions, and, with the launch of the Flatiron Institute in 2016, we now conduct scientific research in-house, supporting teams of top computational scientists.

     
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