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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Involving the new generations in Fermilab endeavors

Since 1984 the Italian groups of the Istituto Nazionale di Fisica Nucleare (INFN) and Italian Universities, collaborating with the DOE laboratory of Fermilab (US) have been running a two-month summer training program for Italian university students. While in the first year the program involved only four physics students of the University of Pisa, in the following years it was extended to engineering students. This extension was very successful and the engineering students have been since then extremely well accepted by the Fermilab Technical, Accelerator, and Scientific Computing Division groups. Over the many years of its existence, this program has proven to be the most effective way to engage new students in Fermilab endeavors. Many students have extended their collaboration with Fermilab with their Master’s Thesis and PhD. Since 2004 the program has been supported in part by DOE in the frame of an exchange agreement with INFN. Over its almost 40 years of history, the program has grown in scope and size and has involved more than 550 Italian students from more than 20 Italian Universities, Several Institutes of Research, including ASI and INAF in Italy, and the ISSNAF Foundation in the US, have provided additional financial support. Since the program does not exclude appropriately selected non-Italian students, a handful of students from European and non-European Universities were also accepted over the years. Each intern is supervised by a Fermilab Mentor responsible for performing the training program. Training programs spanned from Tevatron, CMS, Muon (g-2), Mu2e, and Short Baseline Neutrino Experiments and DUNE design and experimental data analysis, development of particle detectors (silicon trackers, calorimeters, drift chambers, neutrino and dark matter detectors), design of electronic and accelerator components, development of infrastructures and software for exascale data handling, research on superconductive elements and on accelerating cavities, and theory of particle accelerators. Since 2010, within an extended program supported by the Italian Space Agency and the Italian National Institute of Astrophysics, a total of 30 students in physics, astrophysics, and engineering have been hosted for two months in the summer at US space science Research Institutes and laboratories. In 2015 the University of Pisa included these programs within its educational programs. Accordingly, Summer School students are enrolled at the University of Pisa for the duration of the internship and are identified and ensured as such. At the end of the internship, the students are required to write summary reports on their achievements. After positive evaluation by a University Examining Board, interns are acknowledged credits for their Diploma Supplement. The program was canceled in 2020 and 2021 due to the pandemic but restarted successfully in 2022. We believe this program can be taken as a model and easily adopted by interested institutions.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2024

Computing in AEC Education: Hindsight, Insight, and Foresight

In the architecture, engineering, and construction (AEC) fields, computing and information technologies play an increasingly prevalent and complex role in day-to-day work. Consequently, educators must adjust and, in many cases, reimagine curricula and teaching methodologies to adapt to the changing landscape. Past research efforts led by the ASCE Computing Division Education Committee, formerly called the Task Committee on Computing Education of the Technical Council on Computing and Information Technology (TCCIT), have regularly surveyed AEC educators to understand computing trends in AEC curricula, with the latest survey taking place nearly a decade ago. This work presents the results of an updated survey that used this prior work as a springboard, providing timely insights into the computing skills and curricular barriers faced by AEC educators today. The results showed that the technical skills used by students have evolved, but the barriers faced in incorporating new skills into curricula have remained largely the same. In addition to comparisons with prior surveys, this work presents the results of an expanded, open-ended portion of the survey that explores educator perspectives on the future of the AEC workforce in a broader lens than used in previous surveys. Thematic analysis of these open-ended responses revealed themes that were common among responses and provided organization to the findings. For example, educators provided their vision of what competencies the future AEC workforce would need, which were thematically organized into a continuum based on the level of interaction between humans and technology. These results suggest an increasingly complex and evolving relationship between the AEC workforce and emerging technology, highlighting the need for educators to encourage the development of technological adaptability and agility. Overall, this work provides a systematic comparison of current educational practices in AEC computing with a decade ago to illustrate educational shifts and adds a prediction of AEC trends from experts in AEC education, providing crucial discussion of curricular transformations that will better position students for success in the workforce.

42 ENGINEERING↗
DOE OSTI2020

CP2K: An Electronic Structure and Molecular Dynamics Software Package - Quickstep: Efficient and Accurate Electronic Structure Calculations

CP2K is an open source electronic structure and molecular dynamics software package to perform atomistic simulations of solid-state, liquid, molecular and biological systems. It is especially aimed at massively-parallel and linear-scaling electronic structure methods and state-of-the-art ab-initio molecular dynamics simulations. Excellent performance for electronic structure calculations is achieved using novel algorithms implemented for modern high-performance computing systems. This review revisits the main capabilities of CP2K to perform efficient and accurate electronic structure simulations. The emphasis is put on density functional theory and multiple post-Hartree-Fock methods using the Gaussian and plane wave approach and its augmented all-electron extension. TDK has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement No. 716142). VRR has been supported by the Swiss National Science Foundation in the form of Ambizione grant No. PZ00P2 174227 and RZK by the Natural Sciences and Engineering Research Council of Canada (NSERC) through Discovery Grants (RGPIN-2016-0505). GKS and CJM are supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. UK based work was funded under the embedded CSE programme of the ARCHER UK National Supercomputing Service (http://www.archer.ac.uk), grants eCSE03-011, eCSE06-6, eCSE08-9, eCSE13-17 and the EPSRC (EP/P022235/1) grant “Surface and Interface Toolkit for the Materials Chemistry Community". Computational resources were provided by the Swiss National Supercomputing Centre (CSCS) and Compute Canada. The generous allocation of computing time on the FPGA-based supercomputer “Noctua" at PC2 is kindly acknowledged.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

A pushered capsule implosion as an alternate approach to the ignition regime for inertial confinement fusion

We report in inertial confinement fusion, the threshold for ignition is a highly dynamic quantity as the sources and sinks of power in the hot spot can vary rapidly. In this article, we consider the ignition condition as a race between heating and disassembly rates and make use of a prior solution to the fusion hot-spot thermodynamics to develop a Lawson-like ignition criteria for pressure × confinement time (p-τ) vs temperature. Low-Z capsule designs reach the temperature for this threshold using as much of the shell as feasible as ablator but then are limited in τ by low stagnated mass. An alternate approach, the pushered single shell (PSS) design [D. D.-M. Ho, S. MacLaren, and Y. Wang, “High-yield implosions via radiation trapping and high rho-R,” paper presented at the 60th Annual Meeting of the APS Division of Plasma Physics, 2018], introduces a dense inner layer of Mo-Be alloy that is smoothly graded outward to pure Be, increasing the confinement time at stagnation and lowering the temperature requirement at the ignition threshold. Here, we describe a PSS ignition design for the National Ignition Facility and use the theory as well as simulations to compare it with the low-Z capsule approach. Additionally, we show how an adjustment to the design is used to anticipate the effects of mixing at the fuel–ablator interface.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Preface to special topic: The High Repetition Rate Frontier in High-Energy-Density Physics

High-repetition-rate (HRR) experiments can collect large datasets with high temporal, spatial, and/or parametric resolution or large numbers of repeat measurements for statistics. HRR experiments also enable new experimental designs, including active feedback control loops and novel diagnostics, that can improve the reproducibility as well as the quantity of measurements. Together, these attributes make HRR experiments ideal for performing high-quality repeatable science. Until recently, these techniques have not been applied to high-energy-density–physics (HEDP) experiments, which are typically restricted to repetition rates of a few per day. However, recent advancements in lasers, pulsed-power drivers, target fabrication, and diagnostics are starting to change this fact, opening an exciting new frontier of HRR HEDP experiments. A mini-conference on this subject at the 2021 meeting of the American Physical Society Division of Plasma Physics brought together members of this growing community. As a result, the “High Repetition Rate Frontier in High-Energy-Density Physics” special topic in Physics of Plasmas highlights current progress in this exciting area.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Summary report from the mini-conference on workforce development through research-based, plasma-focused activities

This report is a summary of the mini-conference on Workforce Development Through Research-Based, Plasma-Focused Science Education and Public Engagement held during the 2022 American Physical Society Division of Plasma Physics annual meeting. The motivation for organizing this mini-conference originates from recent studies and community-based reports highlighting important issues with the current state of the plasma workforce. Here, we summarize the main findings presented in the two speaker sessions of the mini-conference, the challenges, and recommendations identified in the discussion sessions and the results from a post-conference survey. Here, we further provide information on initiatives and studies presented at the mini-conference, along with references to further resources.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

A GHz-frequency multistrip acoustic beam splitter for quantum applications

Here we demonstrate a microwave-frequency, two-track acoustic beam splitter, based on a multistrip coupler design matched to four unidirectional transducers, two on each of the two acoustic tracks that make up the device. We explain the device design and its experimental implementation, showing good agreement between our model and the measured device scattering spectra. The beam splitter regime, dividing an input signal at port 1 into closely equal outputs at ports 2 and 3, is reached over a 94.7 MHz bandwidth centered at 4.79 GHz, with an output power division ratio |S 21 /S 31 | 2 = 1.1 ± 0.2. The measured bandwidth of the device is limited by the bandwidth of the transducers, rather than that of the multistrip coupler.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Charged-particle transport in high energy density plasmas

This Special Topic Collection grew out of two gatherings of researchers active in the high energy density (HED) physics community: a mini-conference on charged-particle transport in HED plasma held during the 64th annual meeting of the American Physical Society's Division of Plasma Physics (Spokane, WA, November 2022) and a dedicated charged-particle transport coefficient code comparison workshop (Livermore, CA, July 2023). These gatherings provided opportunities for theoretical, computational, and experimental researchers to discuss the state of the field, including current capabilities and methods, needs of hydrodynamic simulations, and frontiers for future research. Finally, this special issue collects a total of 13 research and review articles on charged-particle transport in HED plasmas.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Application of neural networks to determine the discrete spectrum of the direct Zakharov – Shabat problem

A neural network architecture is proposed to determine the number of solitons generated by random processes in optical wavelength-division multiplexed telecommunication systems with QPSK, 16-QAM, 64-QAM, and 1024-QAM modulation. The dependence of the prediction quality of a neural network with a special architecture on the number of soliton modes in the signal and the parameters of this signal is studied. (paper)

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Cryogenic single-molecule fluorescence annotations for electron tomography reveal in situ organization of key proteins in Caulobacter

Superresolution fluorescence microscopy and cryogenic electron tomography (CET) are powerful imaging methods for exploring the subcellular organization of biomolecules. Superresolution fluorescence microscopy based on covalent labeling highlights specific proteins and has sufficient sensitivity to observe single fluorescent molecules, but the reconstructions lack detailed cellular context. CET has molecular-scale resolution but lacks specific and nonperturbative intracellular labeling techniques. Here, we describe an imaging scheme that correlates cryogenic single-molecule fluorescence localizations with CET reconstructions. Our approach achieves single-molecule localizations with an average lateral precision of 9 nm, and a relative registration error between the set of localizations and CET reconstruction of ∼30 nm. We illustrate the workflow by annotating the positions of three proteins in the bacterium Caulobacter crescentus : McpA, PopZ, and SpmX. McpA, which forms a part of the chemoreceptor array, acts as a validation structure by being visible under both imaging modalities. In contrast, PopZ and SpmX cannot be directly identified in CET. While not directly discernable, PopZ fills a region at the cell poles that is devoid of electron-dense ribosomes. We annotate the position of PopZ with single-molecule localizations and confirm its position within the ribosome excluded region. We further use the locations of PopZ to provide context for localizations of SpmX, a low-copy integral membrane protein sequestered by PopZ as part of a signaling pathway that leads to an asymmetric cell division. Our correlative approach reveals that SpmX localizes along one side of the cell pole and its extent closely matches that of the PopZ region.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Scaling relationships for the elastic moduli and viscosity of mixed lipid membranes

The elastic and viscous properties of biological membranes play a vital role in controlling cell functions that require local reorganization of the membrane components as well as dramatic shape changes such as endocytosis, vesicular trafficking, and cell division. These properties are widely acknowledged to depend on the unique composition of lipids within the membrane, yet the effects of lipid mixing on the membrane biophysical properties remain poorly understood. Here, we present a comprehensive characterization of the structural, elastic, and viscous properties of fluid membranes composed of binary mixtures of lipids with different tail lengths. We show that the mixed lipid membrane properties are not simply additive quantities of the single-component analogs. Instead, the mixed membranes are more dynamic than either of their constituents, quantified as a decrease in their bending modulus, area compressibility modulus, and viscosity. While the enhanced dynamics are seemingly unexpected, we show that the measured moduli and viscosity for both the mixed and single-component bilayers all scale with the area per lipid and collapse onto respective master curves. This scaling links the increase in dynamics to mixing-induced changes in the lipid packing and membrane structure. More importantly, the results show that the membrane properties can be manipulated through lipid composition the same way bimodal blends of surfactants, liquid crystals, and polymers are used to engineer the mechanical properties of soft materials, with broad implications for understanding how lipid diversity relates to biomembrane function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Dual-action kinase inhibitors influence p38α MAP kinase dephosphorylation

Reversible protein phosphorylation directs essential cellular processes including cell division, cell growth, cell death, inflammation, and differentiation. Because protein phosphorylation drives diverse diseases, kinases and phosphatases have been targets for drug discovery, with some achieving remarkable clinical success. Most protein kinases are activated by phosphorylation of their activation loops, which shifts the conformational equilibrium of the kinase toward the active state. To turn off the kinase, protein phosphatases dephosphorylate these sites, but how the conformation of the dynamic activation loop contributes to dephosphorylation was not known. To answer this, we modulated the activation loop conformational equilibrium of human p38α ΜΑP kinase with existing kinase inhibitors that bind and stabilize specific inactive activation loop conformations. From this, we identified three inhibitors that increase the rate of dephosphorylation of the activation loop phospho-threonine by the PPM serine/threonine phosphatase WIP1. Hence, these compounds are “dual-action” inhibitors that simultaneously block the active site and promote p38α dephosphorylation. Our X-ray crystal structures of phosphorylated p38α bound to the dual-action inhibitors reveal a shared flipped conformation of the activation loop with a fully accessible phospho-threonine. In contrast, our X-ray crystal structure of phosphorylated apo human p38α reveals a different activation loop conformation with an inaccessible phospho-threonine, thereby explaining the increased rate of dephosphorylation upon inhibitor binding. These findings reveal a conformational preference of phosphatases for their targets and suggest a unique approach to achieving improved potency and specificity for therapeutic kinase inhibitors.

Science & Technology - Other Topics↗
DOE OSTI2025

3D pattern formation of a protein–membrane suspension

Many essential cellular processes, including cell division and the establishment of cell polarity during embryogenesis, are regulated by pattern-forming proteins. These proteins often need to bind to a substrate, such as the cell membrane, onto which they interact and form two-dimensional (2D) patterns. It is unclear how the membrane’s continuity and dimensionality impact pattern formation. Here, we address this gap using the MinDE system, a prototypical example of pattern-forming membrane proteins. We show that when the lipid substrate is fragmented into submicrometer-sized diffusive liposomes, adenosine triphosphate-driven protein–protein interactions generate three-dimensional (3D) spatially extended patterns, despite the complete loss of membrane continuity. Remarkably, these 3D patterns emerge at scales four orders of magnitude larger than the individual liposomes. By systematically varying protein concentration, liposome size, and density, we observed and characterized a variety of 3D dynamical patterns not seen on continuous 2D membranes, including traveling waves, dynamical spirals, and a coexistence phase. Simulations and linear stability analysis of a coarse-grained model revealed that the physical properties of the dispersed membrane effectively rescale both the protein–membrane binding rates and diffusion, two key parameters governing pattern formation and wavelength selection. These findings highlight the robustness of Min’s pattern-forming ability, suggesting that protein–membrane suspensions could serve as an adaptable template for studying out-of-equilibrium self-organization in 3D, beyond in vivo contexts.

36 MATERIALS SCIENCE↗
DOE OSTI2021

APS: High-Energy X-rays Expediting Applied and Fundamental Research

The Advanced Photon Source (APS) at Argonne National Laboratory (ANL) was designed and built as one of the first large 3rd generation synchrotrons operated at 7 GeV. The United States Department of Energy (DOE) Office of Science funded the construction and continues to fund the operation of this national facility. Furthermore, the beamlines were originally operated by Collaborative Access Teams (CAT), which allowed a strong involvement of research institutes, universities, and industry. Today 43 of 68 beamlines are operated by the X-ray Science Division (XSD) and 35 beamlines are directly funded by the DOE Office of Science. The APS became operational in 1995, and was planned right from the beginning with 4 beamlines dedicated to high-energy x-rays above 40 keV: 1-ID designed to study engineering materials science, 6-ID-D for magnetism and condensed matter research, 11-ID-B dedicated to magnetic Compton scattering using an Elliptical Multipole Wiggler, and 11-ID-C for materials science and condensed matter physics. These stations were later joined by the bending magnet beamlines 6-BM for white beam studies and 17-BM for rapid powder diffraction. CAT operated beamlines such as 15-ID for crystallography or 16-ID for high-pressure studies also use the high-energy x-ray regime frequently. The program in Compton scattering ended in 2004 and the wiggler was replaced by an undulator. 11-ID-B became the first dedicated station for Pair Distribution Function (PDF) Analysis.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Cellulose synthase-like D movement in the plasma membrane requires enzymatic activity

Cellulose Synthase-Like D (CSLD) proteins, important for tip growth and cell division, are known to generate β-1,4-glucan. However, whether they are propelled in the membrane as the glucan chains they produce assemble into microfibrils is unknown. To address this, we endogenously tagged all eight CSLDs in Physcomitrium patens and discovered that they all localize to the apex of tip-growing cells and to the cell plate during cytokinesis. Actin is required to target CSLD to cell tips concomitant with cell expansion, but not to cell plates, which depend on actin and CSLD for structural support. Like Cellulose Synthase (CESA), CSLD requires catalytic activity to move in the plasma membrane. We discovered that CSLD moves significantly faster, with shorter duration and less linear trajectories than CESA. In contrast to CESA, CSLD movement was insensitive to the cellulose synthesis inhibitor isoxaben, suggesting that CSLD and CESA function within different complexes possibly producing structurally distinct cellulose microfibrils.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Torques within and outside the human spindle balance twist at anaphase

At each cell division, nanometer-scale motors and microtubules give rise to the micron-scale spindle. Many mitotic motors step helically around microtubules in vitro, and most are predicted to twist the spindle in a left-handed direction. However, the human spindle exhibits only slight global twist, raising the question of how these molecular torques are balanced. Here, we find that anaphase spindles in the epithelial cell line MCF10A have a high baseline twist, and we identify factors that both increase and decrease this twist. The midzone motors KIF4A and MKLP1 are together required for left-handed twist at anaphase, and we show that KIF4A generates left-handed torque in vitro. The actin cytoskeleton also contributes to left-handed twist, but dynein and its cortical recruitment factor LGN counteract it. Together, our work demonstrates that force generators regulate twist in opposite directions from both within and outside the spindle, preventing strong spindle twist during chromosome segregation.

Cell Biology↗
DOE OSTI2021

Roadmap on emerging concepts in the physical biology of bacterial biofilms: from surface sensing to community formation

Abstract Bacterial biofilms are communities of bacteria that exist as aggregates that can adhere to surfaces or be free-standing. This complex, social mode of cellular organization is fundamental to the physiology of microbes and often exhibits surprising behavior. Bacterial biofilms are more than the sum of their parts: single-cell behavior has a complex relation to collective community behavior, in a manner perhaps cognate to the complex relation between atomic physics and condensed matter physics. Biofilm microbiology is a relatively young field by biology standards, but it has already attracted intense attention from physicists. Sometimes, this attention takes the form of seeing biofilms as inspiration for new physics. In this roadmap, we highlight the work of those who have taken the opposite strategy: we highlight the work of physicists and physical scientists who use physics to engage fundamental concepts in bacterial biofilm microbiology, including adhesion, sensing, motility, signaling, memory, energy flow, community formation and cooperativity. These contributions are juxtaposed with microbiologists who have made recent important discoveries on bacterial biofilms using state-of-the-art physical methods. The contributions to this roadmap exemplify how well physics and biology can be combined to achieve a new synthesis, rather than just a division of labor.

Wong, Gerard C. L. (ORCID:0000000308936383)↗
DOE OSTI2021

Let it rip: The mechanics of self-bisection in asexual planarians determines their population reproductive strategies

Asexual freshwater planarians reproduce by transverse bisection (binary fission) into two pieces. This process produces a head and a tail, which fully regenerate within 1-2 weeks. How planarians split into two offspring - using only their musculature and substrate traction – is a challenging biomechanics problem. We found that three different species, Dugesia japonica, Girardia tigrina and Schmidtea mediterranea, have evolved three different mechanical solutions to self-bisect. Using time lapse imaging of the fission process, we quantitatively characterize the main steps of division in the three species and extract the distinct and shared key features. Across the three species, planarians actively alter their body shape, regulate substrate traction, and use their muscles to generate tensile stresses large enough to overcome the ultimate tensile strength of the tissue. Moreover, we show that how each planarian species divides dictates how resources are split among its offspring. This ultimately determines offspring survival and reproductive success. Furthermore, heterospecific differences in the mechanics of self-bisection of individual worms explain the observed differences in the population reproductive strategies of different planarian species.

59 BASIC BIOLOGICAL SCIENCES↗