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PDB‐101: Molecular Explorations through Biology and Medicine

PDB‐101 is an online portal for teachers, students, and the general public to promote exploration of the structural biology of proteins and nucleic acids ( pdb101.rcsb.org ). Learning about the diverse shapes and functions of these biological macromolecules helps to understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease to biological energy. Why PDB‐101? Researchers around the world are studying these molecules at the atomic level. These 3D structures are freely available at the Protein Data Bank (PDB), the central storehouse of biomolecular structures. This website builds introductory materials to help beginners get started in the basics of biomolecular structure and function (“101”, as in an entry level course) as well as resources for extended learning. Since 2011, PDB‐101 has been developed by the RCSB PDB , a global resource for the advancement of research and education in biology and medicine. Along with our Worldwide PDB collaborators, RCSB PDB curates, annotates, and makes publicly available the PDB data deposited by scientists around the globe. The RCSB PDB then provides a window to these data through a rich online resource with powerful searching, reporting, and visualization tools for researchers. This information is then streamlined for students and teachers at PDB‐101. Features include the ongoing Molecule of the Month series, educational materials such as paper models, posters, molecular animations, educational curricula and more. The section “Guide to Understanding PDB Data” is a primer for detailed PDB‐specific information: PDB Data, Visualizing Structures, Reading Coordinate Files, scientific methods for structure determination, and more. PDB‐101 also runs annual Video Challenges for high school students. Participants create short videos that tell molecular stories that connect structural biology and medicine. Previous topics have included HIV/AIDS, diabetes, and antimicrobial resistance. The 2022 challenge will focus on Molecular Mechanisms of Cancer. PDB‐101 activities are evaluated using user surveys, feedback from in‐person activities, and website analytics. In 2020, PDB‐101 hosted >850,000 users and >2.6 million page views.

Zardecki, Christine↗

Phase diagram of the anisotropic triangular lattice Hubbard model

In a recent study [Phys. Rev. X 10, 021042 (2020)], we showed using large-scale density matrix renormalization group (DMRG) simulations on infinite cylinders that the triangular lattice Hubbard model has a chiral spin liquid phase. In this work, we introduce hopping anisotropy in the model, making one of the three distinct bonds on the lattice stronger or weaker compared with the other two. We implement the anisotropy in two inequivalent ways, one which respects the mirror symmetry of the cylinder and one which breaks this symmetry. In the full range of anisotropy, from the square lattice to weakly coupled one-dimensional chains, we find a variety of phases. Near the isotropic limit we find the three phases identified in our previous work: metal, chiral spin liquid, and 120$^\circ$ spiral order; we note that a recent paper suggests the apparently metallic phase may actually be a Luther-Emery liquid, which would also be in agreement with our results. Furthermore, when one bond is weakened by a relatively small amount, the ground state quickly becomes the square lattice N\'{e}el order. When one bond is strengthened, the story is much less clear, with the phases that we find depending on the orientation of the anisotropy and on the cylinder circumference. While our work is to our knowledge the first DMRG study of the anisotropic triangular lattice Hubbard model, the overall phase diagram we find is broadly consistent with that found previously using other methods, such as variational Monte Carlo and dynamical mean field theory.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Ergodic and nonergodic many-body dynamics in strongly nonlinear lattices

The study of nonlinear oscillator chains in classical many-body dynamics has a storied history going back to the seminal work of Fermi et al. [Los Alamos Scientific Laboratory Report No. LA-1940, 1955 (unpublished)]. Here, we introduce a family of such systems which consist of chains of N harmonically coupled particles with the nonlinearity introduced by confining the motion of each individual particle to a box or stadium with hard walls. The stadia are arranged on a one-dimensional lattice but they individually do not have to be one dimensional, thus permitting the introduction of chaos already at the lattice scale. For the most part we study the case where the motion is entirely one dimensional. We find that the system exhibits a mixed phase space for any finite value of N . Computations of Lyapunov spectra at randomly picked phase space locations and a direct comparison between Hamiltonian evolution and phase space averages indicate that the regular regions of phase space are not significant at large system sizes. While the continuum limit of our model is itself a singular limit of the integrable sinh Gordon theory, we do not see any evidence for the kind of nonergodicity famously seen in the work of Fermi et al. Finally, we examine the chain with particles confined to two-dimensional stadia where the individual stadium is already chaotic and find a much more chaotic phase space at small system sizes.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Electrical control of magnetism by electric field and current-induced torques

The remanent magnetization of ferromagnets has long been studied and used to store binary information. While early magnetic memory designs relied on magnetization switching by locally generated magnetic fields, key insights in condensed matter physics later suggested the possibility of doing it by electrical means instead. In the 1990s, Slonczewski and Berger formulated the concept of current-induced spin torques in magnetic multilayers through which a spin-polarized current generated by a first ferromagnet may be used to switch the magnetization of a second one. This discovery drove the development of spin-transfer-torque magnetic random-access memories (MRAMs). More recent fundamental research revealed other types of current-induced torques named spin-orbit torques (SOTs) and will lead to a new generation of devices including SOT MRAMs and skyrmion-based devices. Parallel to these advances, multiferroics and their magnetoelectric coupling, first investigated experimentally in the 1960s, experienced a renaissance. Dozens of multiferroic compounds with new magnetoelectric coupling mechanisms were discovered and high-quality multiferroic films were synthesized (notably of BiFeO 3 ), also leading to novel device concepts for information and communication technology such as the magnetoelectric spin-orbit (MESO) transistor. The story of the electrical switching of magnetization, which is discussed in this review, is that of a dance between fundamental research (in spintronics, condensed matter physics, and materials science) and technology (MRAMs, MESO transistors, microwave emitters, spin diodes, skyrmion-based devices, components for neuromorphics, etc.). This pas de deux has led to major scientific and technological breakthroughs in recent decades (such as the conceptualization of pure spin currents, the observation of magnetic skyrmions, and the discovery of spin-charge interconversion effects). As a result, this field has not only propelled MRAMs into consumer electronics products but also fueled discoveries in adjacent research areas such as ferroelectrics or magnonics. Here, in this review, recent advances in the control of magnetism by electric fields and by current-induced torques are covered. Fundamental concepts in these two directions are reviewed first, their combination is then discussed, and finally current various families of devices harnessing the electrical control of magnetic properties for various application fields are addressed. The review concludes by giving perspectives in terms of both emerging fundamental physics concepts and new directions in materials science.

36 MATERIALS SCIENCE↗

The COVID-19 High-Performance Computing Consortium

In March of 2020, recognizing the potential of High Performance Computing (HPC) to accelerate understanding and the pace of scientific discovery in the fight to stop COVID-19, the HPC community assembled the largest collection of worldwide HPC resources to enable COVID-19 researchers worldwide to advance their critical efforts. Amazingly, the COVID-19 HPC Consortium was formed within one week through the joint effort of the Office of Science and Technology Policy (OSTP), the U.S. Department of Energy (DOE), the National Science Foundation (NSF), and IBM to create a unique public–private partnership between government, industry, and academic leaders. This article is the Consortium's story–how the Consortium was created, its founding members, what it provides, how it works, and its accomplishments. We will reflect on the lessons learned from the creation and operation of the Consortium and describe how the features of the Consortium could be sustained as a National Strategic Computing Reserve to ensure the nation is prepared for future crises.

97 MATHEMATICS AND COMPUTING↗

Accelerating Hydraulic Fracture Imaging by Deep Transfer Learning

Deep transfer learning has a great success story in computer vision (CV), natural language processing, and many other fields. In this communication, we are going to push forward the deep transfer learning to the hydraulic fracture imaging problem by proposing a two-step approach: 1) train a convolutional neural network (CNN) to reconstruct target geometries by a relatively large amount of approximated field patterns generated from a simplified model and 2) fine-tune the top layers of transferred CNN by a small amount of true field patterns generated through a full model. The advantages include the rapid generation of large amount of data through the simplified model and the high reconstruction accuracy through a careful design of the deep transfer learning. Here, the CNN trained through the deep transfer learning can accurately reconstruct the lateral extent and direction of fractures with unseen conductivity and white Gaussian noise, showing a notable acceleration/accuracy enhancement over the previous CNN trained by mixing a small number of true data into the approximated data as data augmentation.

02 PETROLEUM↗

Technical and personal remembrances of David A. Shirley in studies of surface magnetism, photoelectron spectroscopy, EUV lithography, and hydrogen storage

This article describes the influence of Professor David A. Shirley on the research science of one of his Ph.D. students in the diverse areas of surface magnetism, x-ray photoelectron spectroscopy (XPS), spin-resolved XPS (SRXPS), extreme ultraviolet (EUV) lithography, and hydrogen storage materials science. Examples are given from the author's work on Cr(001) surface magnetism, XPS, and SRXPS studies of multiplet-splitting in core-level photoemission from Fe. In addition, Dave's influence in understanding the radiation-induced deposition of carbon on EUV optics is described, along with the use of XPS in deciphering how hydrogen storage materials are modified by repeated hydrogen adsorption/desorption cycling. The current status of these particular topics is briefly summarized. These technical remembrances are combined with some fond personal stories about Dave, in recognition of his passing on March 29, 2021.

Klebanoff, L. E.↗

Does Antimatter Fall Up?

Antimatter is one of those things that sound like science fiction, rather than science fact. Yet it is a very real substance, predicted in 19281 and discovered in 19322. While the story of antimatter is rich and complex3, there is a common question often asked by introductory students, which is “Does antimatter fall up?” This question is far more subtle than appears at first blush, with unexpected facets that can lead to interesting classroom discussion involving the nature and definition of matter. Furthermore, while the theory of general relativity weighs in on the topic, as with all serious physics questions, the definitive answer requires an empirical test. In this article, I will briefly introduce what antimatter is, describe some of the interesting intellectual exercises that can arise from considering the effect of gravity on antimatter, and finally conclude with the results of a recent experiment that definitively answer the question.

Lincoln, Don [Fermilab] (ORCID:0000000205997407)↗

Surrogate-Based Autotuning for Randomized Sketching Algorithms in Regression Problems

Algorithms from Randomized Numerical Linear Algebra (RandNLA) are known to be effective in handling high-dimensional computational problems, providing high-quality empirical performance as well as strong probabilistic guarantees. However, their practical application is complicated by the fact that the user needs to set various algorithm-specific tuning parameters which are different from those used in traditional NLA. This paper demonstrates how a surrogate-based autotuning approach can be used to address fundamental problems of parameter selection in RandNLA algorithms. In particular, we provide a detailed investigation of surrogate-based autotuning for sketch-and-precondition (SAP)-based randomized least squares methods, which have been one of the great success stories in modern RandNLA. Empirical results show that our surrogate-based autotuning approach can achieve near-optimal performance with much less tuning cost than a random search (up to about 7.6x fewer trials of different parameter configurations). Moreover, while our experiments focus on least squares, our results demonstrate a general-purpose autotuning pipeline applicable to any kind of RandNLA algorithm.

Cho, Younghyun↗

Hybrid Organic Inorganic Perovskites: Physical Properties and Applications (in 4 Volumes)

This four-volume handbook gives a state-of-the-art overview of hybrid organic inorganic perovskites, both two dimensional (2D) and three dimensional (3D), from synthesis and characterization and simulation to optoelectronic devices (such as solar cells and light emitting diodes), spintronics devices and catalysis application. The editors, coming from academia and national laboratory, are known for their didactic skills as well as their technical expertise. Coordinating the efforts of 30 expert authors in 21 chapters, they construct the story of hybrid perovskite structural and optical properties, electronic and spintronic response, laser action, and catalysis from varied viewpoints: materials science, chemical engineering, and energy engineering. The four volumes are arranged according to the focus material properties. Volume 1 is focused on the material physical properties including structure, deposition characteristic and the structure of the electronic bands and excitons of these compounds. Volume 2 covers the hybrid perovskite optical properties including the ultrafast optical response, photoluminescence and laser action. Volume 3 contains the spin response of these compounds including application such as spin valves, photogalvanic effect, and magnetic response of light emitting diodes and solar cell devices. Finally, and highly relevant to tomorrow's energy challenges, volume 4 is focused on the physics and device properties of the most relevant applications of the hybrid perovskites, namely photovoltaic solar cells. The text contains many high-quality colorful illustrations and examples, as well as thousands of up-to-date references to peer-reviewed articles, reports and websites for further reading. This comprehensive and well-written handbook is a must-have reference for universities, research groups and companies working with the hybrid organic inorganic perovskites.

applications↗

Neutrinos in Stellar Astrophysics (in The Encyclopedia of Cosmology)

The physics of the mysterious and stealthy neutrino is at the heart of many phenomena in the cosmos. These particles interact with matter and with each other through the aptly named weak interaction. At typical astrophysical energies the weak interaction is some twenty orders of magnitude weaker than the electromagnetic interaction. However, in the early universe and in collapsing stars neutrinos can more than make up for their feeble interaction strength with huge numbers. Neutrinos can dominate the dynamics in these sites and set the conditions that govern the synthesis of the elements. Here we journey through the history of the discovery of these particles and describe their role in stellar evolution and collapse, the big bang, and multi-messenger astrophysics. Neutrino physics is at the frontier of elementary particle physics, nuclear physics, astrophysics and cosmology. All of these fields overlap in the neutrino story.

Haxton, Wick↗

Big Advances at the Nano Scale in the Nanocarbons Division

In this issue of ECS Interface, we highlight some exciting success stories for low-dimensional materials in technologically critical fields. These are areas where emergent properties and processes within quantum-confined low-dimensional materials (and heterostructures) enable novel applications beyond what can be achieved in bulk materials.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Learning Universal Authorship Representations

This code contains all the utilities required to reproduce the results of our EMNLP 2021 paper "Learning Universal Authorship Representations". It contains the utilities required for download the datasets, training our model, and performing all evaluations necessary for reproducing the results in the paper. Here's the abstract of our work: Determining whether two documents were composed by the same author, also known as authorship verification, has traditionally been tackled using statistical methods. Recently, authorship representations learned using neural networks have been found to outperform alternatives, particularly in large-scale settings involving hundreds of thousands of authors. But do such representations learned in a particular domain transfer to other domains? Or are these representations inherently entangled with domain-specific features? To study these questions, we conduct the first large-scale study of cross-domain transfer for authorship verification considering zero-shot transfers involving three disparate domains: Amazon reviews, fanfiction short stories, and Reddit comments. We find that although a surprising degree of transfer is possible between certain do- mains, it is not so successful between others. We examine properties of these domains that influence generalization and propose simple but effective methods to improve transfer.

Rivera Soto, RafaelA↗

Repometer v.1.0

SAND2022-4256 O Online version control platforms offer insight into traffic and engagement with source code repositories, but only in limited ways and over short windows of time. Scientific software teams at Sandia National Laboratories and elsewhere want to collect and store engagement data to help tell their story and the impact their work has on the community. Repometer aims to supplement existing capabilities by collecting timely and insightful data from GitHub and GitLab repositories and passing it to a database for longer-term storage. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Mundt, Miranda↗

Observations of Boundary Layer Convergence Lines and Associated Updrafts in the U.S. Southern Great Plains

Abstract Boundary layer convergence lines (CLs) are highly effective at deep-convection initiation (DCI), suggesting that their associated updraft properties differ from those of more widespread turbulent updrafts in the planetary boundary layer (PBL). This study exploits observations at the Atmospheric Radiation Measurement Southern Great Plains (ARM SGP) observatory in Oklahoma from 2011 to 2016 to quantify CL properties and their relation to turbulent PBL eddies preceding CL arrival. Two independent methods for estimating CL properties are developed at two locations in the SGP region, both relying on the assumption of a 2D circulation in the CL-normal plane but using different combinations of instruments. The first (the radar method) relies mainly on scanning radar data and is applied to 61 CLs passing near a high-resolution scanning radar based in Nardin, Oklahoma, while the second (the surface method) relies mainly on surface wind data and is applied to 68 CLs crossing the SGP facility in nearby Lamont, Oklahoma. Mean daytime (1000–1900 LST) CL width (∼2 km) and convergence magnitude (∼0.003 s −1 ) are similar for both methods, and mean daytime CL depth is ∼0.75 km. The two methods disagree at night (0000–1000 and 1900–2400 LST), where the surface method estimates wider and weaker CLs than the radar method. This difference may stem from the radar beam overshooting the shallow, highly stable nocturnal PBL. The largest CL updrafts are slightly wider (∼20%) and stronger (∼40%) than the largest PBL updrafts in the pre-CL period, generating 50%–100% larger updraft mass fluxes over most of the PBL depth. Significance Statement Deep convection is commonly initiated by boundary layer convergence lines (CLs), which are associated with intense surface-based wind convergence and strong updrafts that may lift air to saturation. Although CLs form regularly, they are far less common than ordinary, short-lived turbulent thermals in the daytime boundary layer. To better understand why CLs are so effective at deep-convection initiation, we observationally quantify their morphologies and strengths and compare these properties to those of surrounding turbulent updrafts. Perhaps surprisingly, the CLs are found to exhibit only slightly larger scales and strengths as the turbulent updrafts. Although these marginal increases help to explain the preference for storms to initiate along CLs, they likely are not the whole story.

54 ENVIRONMENTAL SCIENCES↗

TECHNOLOGY: A Lesson In LED Adoption: Understanding the hurdles faced by K–12 schools

PK-12 schools lag in upgrading fluorescent lighting. Surprised? So were we; spurring a journey to understand the reasons for lagging adoption of LED. During conversations with school facility managers and other lighting professionals the reasons became clearer. What follows is a synopsis of what has been uncovered so far, yet there remains much to learn. Here, these stories are not the product of imagination; they represent real experiences, real decisions, and real concerns from 9 school districts in 7 states from coast to coast.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

What is the Right Size for a Residential Building Parcel Locker?

Common-carrier parcel lockers present a solution for decreasing delivery times, traffic congestion, and emissions in dense urban areas through consolidation of deliveries. Multi-story residential buildings with large number of residents, and thus a high volume of online package orders, are one of the best venues for installing parcel lockers. But what is the right size for a residential building locker that would suit the residents’ and building managers’ needs? Because of the novelty of parcel lockers, there is no clear guideline for determining the right locker size and configuration for a residential building given the resident population. A small locker would result in packages exceeding capacity and being left in the lobby, increasing the building manager’s workload and confusing and inconveniencing users. On the other hand, a large locker is more expensive, more difficult to install, and unappealing to residents. To answer this question, we installed a common-carrier parcel locker in a residential building in downtown Seattle, WA, U.S.A. Through collecting detailed data on locker usage from the locker provider company, we studied and quantified carriers’ delivery patterns and residents’ online shopping and package pickup behaviors. We then used this information to model the locker delivery and pickup process, and simulated several locker configurations to find the one that best suits the delivery needs of the building. These findings could aid urban planners and building managers in choosing the right size for residential building lockers that meet delivery demand while minimizing costs and contributing to environmental benefits.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Quantification and prediction of error in MIMO tests

Dynamic testing of systems is most realistic of real-world conditions when multiple input and multiple output (MIMO) techniques are used. To replicate measured environmental conditions, a series of desired outputs (responses) on the system must be realized by inverting the frequency response functions (FRF) matrix for input estimation. System identification is dependent on the number of inputs and outputs, which affect the type of solutions. In input estimation, the auto spectra of the determined inputs are affected by both the auto spectra and cross spectra of the desired outputs. This research evaluates errors and investigates two sources in an experimental setting. The first significant error source is test-to-test variability in FRFs from system identification tests, quantified by magnitude variability from long-duration tests. The second significant error source is the realization of time histories from frequency domain inputs. The spectral content of the realized random process deviates from the desired content and is also quantified. The structure is a linear three-story frame fixed at the base; two inputs are provided uniaxially with the use of suspended electrodynamic shakers. The proposed model for error sources was found to be effective in predicting errors in a SISO (single-input single-output) and a square (2-input 2-output) MIMO test.

Yousef, Odey↗