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At least 325 records · Page 18

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DOE OSTI2025

Generating forces in confinement via polymerization

Understanding how to produce forces using biomolecular building blocks is essential for the development of adaptive synthetic cells and living materials. Here we ask whether a dynamic polymer system can generate deformation forces in soft shells by pure self-assembly, motivated by the fact that biological polymer networks like the cytoskeleton can exert forces, move objects, and deform membranes by simply growing, even in the absence of molecular motors. We address this question by investigating polymer force generation by varying the release rate, the structure, and the interactions of self-assembling monomers. First, we develop a toy computational model of polymerization in a soft elastic shell that reveals the emergence of spontaneous bundling which enhances shell deformation. We then extend our model to account more explicitly for monomer binding dynamics. We find that the rate at which monomers are released into the interior of the shell is a crucial parameter for achieving deformation through polymer growth. Lastly, we demonstrate that the introduction of multivalent particles that can join polymers can either improve or impede polymer performance, depending on the amount and on the structure of the multivalent particles. Our results provide guidance for the experimental realization of polymer systems that can perform work at the nanoscale, for example through rationally designed self-assembling proteins or nucleic acids.

Osmanović, Dino [University of California at Los A↗

DOE OSTI2023

A group finder algorithm optimised for the study of local galaxy environments

Context. The majority of galaxy group catalogues available in the literature use the popular friends-of-friends algorithm which links galaxies using a linking length. One potential drawback to this approach is that clusters of points can be linked with thin bridges which may not be desirable. In order to study galaxy groups, it is important to obtain realistic group structures. Aim. Here, in this study, we present a new simple group finder algorithm, TD-ENCLOSER, that finds the group that encloses a target galaxy of interest. Methods. TD-ENCLOSER is based on the kernel density estimation method which treats each galaxy, represented by a zero-dimensional particle, as a two-dimensional circular Gaussian. The algorithm assigns galaxies to peaks in the density field in order of density in descending order (‘top down’) so that galaxy groups ‘grow’ around the density peaks. Outliers in under-dense regions are prevented from joining groups by a specified hard threshold, while outliers at the group edges are clipped below a soft (blurred) interior density level. Results. The group assignments are largely insensitive to all free parameter variations apart from the hard density threshold and the kernel standard deviation, although this is a known feature of density-based group finder algorithms and it operates with a computing speed that increases linearly with the size of the input sample. In preparation for a companion paper, we also present a simple algorithm to select unique representative groups when duplicates occur. Conclusions. TD-ENCLOSER is tested on a mock galaxy catalogue using a smoothing scale of 0.3 Mpc and is found to be able to recover the input group distribution with sufficient accuracy to be applied to observed galaxy distributions.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

The MeerKAT Fornax Survey: II. The rapid removal of H I from dwarf galaxies in the Fornax cluster

We present MeerKAT Fornax Survey atomic hydrogen (H I) observations of the dwarf galaxies located in the central ~2.5 × 4 deg 2 of the Fornax galaxy cluster (R vir ~2°). The H I images presented in this work have a 3σ column density sensitivity between 2.7 and 50 × 10 18 cm –2 over 25 km s –1 for spatial resolution between 4 and 1 kpc. We are able to detect an impressive M HI = 5 × 10 5 M ⊙ 3σ point source with a line width of 50 km s –1 at a distance of 20 Mpc. We detected H I in 17 out of the 304 dwarfs in our field, with 14 out of the 36 late-type dwarfs (LTDs) and three out of the 268 early-type dwarfs (ETDs). The H I-detected LTDs have likely just joined the cluster and are on their first infall as they are located at large clustocentric radii, with comparable MHI and mean stellar surface brightness at fixed luminosity as blue, star-forming LTDs in the field. By contrast, the H I-detected ETDs have likely been in the cluster longer than the LTDs and acquired their H I through a recent merger or accretion from nearby H I. Eight of the H I-detected LTDs host irregular or asymmetric H I emission and disturbed or lopsided stellar emission. There are two clear cases of ram pressure shaping the H I, with the LTDs displaying compressed H I on the side closest to the cluster centre and a one-sided, starless tail pointing away from the cluster centre. The H I-detected dwarfs avoid the most massive potentials (i.e. cluster centre and massive galaxies), consistent with massive galaxies playing an active role in the removal of H I. We created a simple toy model to quantify the timescale of H I stripping in the cluster by reproducing the observed M r' –M HI relation. We find that a M HI = 10 8 M ⊙ dwarf is stripped in ~240 Myr. The model is consistent with our observations, where low-mass LTDs are directly stripped of their H I from a single encounter and more massive LTDs can harbour a disturbed H I morphology due to longer times or multiple encounters being required to fully strip their H I. This is the first time dwarf galaxies with M HI ≲ 1 × 10 6 M ⊙ have been detected and resolved beyond the local group and in a galaxy cluster.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

On-the-fly data set combinations with RNTuple

With the expected data volume increase for HL-LHC and the even more complex computing challenges set by future colliders, the need for efficient data storage and processing becomes more pressing. ROOT’s next-generation data format and I/O subsystem, RNTTuple, is designed to address these challenges. RNTTuple already demonstrates a clear improvement in storage and I/O efficiency, as well as overall stability and robustness with respect to its predecessor, TTTree. These improvements provide a solid baseline to introduce novel extensions to common high-energy and nuclear physics (HENP) workflows. Notably, many workflows could benefit from the ability to arbitrarily join and chain data set samples at runtime, which could reduce overall storage requirements and improve application runtime and ergonomics. In this paper, we present the RNTupleProcessor, which enables HENP data set combinations with RNTuple. We will discuss the main design considerations, present the interfaces to support data set combinations and show how they integrate in typical workflows.

de Geus, Florine Willemijn [CERN; Twente U., Ensch↗

DOE OSTI2022

Developing Novel Performance Measures for Traffic Congestion Management and Operational Planning Based on Connected Vehicle Data

In this study, the authors present their efforts in exploring a new type of traffic data, referred to as internet-connected vehicle (ICV) data, for traffic congestion management and operational planning. Most currently manufactured vehicles contain onboard GPS and cellular modules, and they constantly connect to automobile manufacturers' clouds via cellular networks and upload their status. Some automobile manufacturers have recently redistributed the nonpersonal part of such data, such as geolocation, to third-party organizations for innovative applications. Compared with the traditional vehicle GPS data, the ICV data contain high-resolution GPS waypoints accompanied with the vehicles' abnormal moving events (e.g., hard braking). The ICV data also have huge potential in congestion management and operational planning. They explore to identify and analyze traffic congestion on both freeways and arterials using the ICV data. The ICV data adopted for this research are redistributed by Wejo Data Service, representing 10%-15% of all moving vehicles in the Dallas-Fort Worth (DFW) area in Texas. Through one case study for a freeway segment and one for an arterial segment, new traffic performance metrics based on the characteristics of ICV data have been presented. The highlights of these efforts are as follows: (I) queue length and propagation at freeway bottlenecks can be directly measured based on where and when most internet-connected vehicles slow down and join the queue; (II) an internet-connected vehicle's actual delay time on arterials can be directly measured according to its slow movement percentage, without assuming the nondelay travel speed; and (III) the ICV data set are also combined with the high-resolution traffic signal events to generate a ground-truth time-space diagram (TSD) on arterials - a common visualization of arterial signal performance for transportation planning and operations.

33 ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2020

Intrinsic thermal interfacial resistance measurement in bonded metal–polymer foils

Heat conduction through bonded metal–polymer interfaces often limits the overall heat transfer in electronic packaging, batteries, and heat recovery systems. To design the thermal circuit in such systems, it is essential to measure the thermal interfacial resistance (TIR) across ~1 µm to 100 µm junctions. Previously reported TIR of metal–polymer junctions utilize ASTM E1530-based two-block systems that measure the TIR by applying pressure across the interface through external heating and cooling blocks. Here, we report a novel modification of the ASTM-E1530 technique that employs integrated heaters and sensors to provide an intrinsic TIR measurement of an adhesively bonded metal–polymer junction. We design the measurement technique using finite element simulations to either passively suppress or actively compensate the lateral heat diffusion through the polymer, which can minimize the systematic error to ≲5%. Through proof-of-concept experiments, we report the TIR of metal–polymer interfaces made from DuPont’s Pyralux double-side copper-clad laminates, commonly used in flexible printed circuit boards. Our TIR measurement errors are <10%. We highlight additional sources of errors due to non-idealities in the experiment and discuss possible ways to overcome them. Our measurement technique is also applicable to interfaces that are electrically insulating such as adhesively joined metal–metal junctions and sputter-coated or welded metal–polymer junctions. Altogether, the technique is capable of measuring TIR ≳10 –5 m 2 KW –1 in bonded metal–polymer foils and can be tailored for in situ measurements in flexible electronics, circuit packaging, and other hybrid metal–polymer systems.

47 OTHER INSTRUMENTATION↗

DOE OSTI2022

Controlling superconductivity of CeIrIn 5 microstructures by substrate selection

Superconductor/metal interfaces are usually fabricated in heterostructures that join these dissimilar materials. A conceptually different approach has recently exploited the strain sensitivity of heavy-fermion superconductors, selectively transforming regions of the crystal into the metallic state by strain gradients. The strain is generated by differential thermal contraction between the sample and the substrate. Here, we present an improved finite-element model that reliably predicts the superconducting transition temperature in CeIrIn 5 even in complex structures. Different substrates are employed to tailor the strain field into the desired shapes. Using this approach, both highly complex and strained as well as strain-free microstructures are fabricated to validate the model. This enables a high degree of control over the microscopic strain fields and forms the basis for more advanced structuring of superconductors as in Josephson junctions yet also finds natural use cases in any material class in which a modulation of the physical properties on a chip is desirable.

36 MATERIALS SCIENCE↗

DOE OSTI2023

The dynamics, mixing, and thermonuclear burn of compressed foams with varied gas fills

Inertial confinement fusion (ICF) implosions involve highly coupled physics and complex hydrodynamics that are challenging to model computationally. Due to the sensitivity of such implosions to small features, detailed simulations require accurate accounting of the geometry and dimensionality of the initial conditions, including capsule defects and engineering features such as fill tubes used to insert gas into the capsule, yet this is computationally prohibitive. It is therefore difficult to evaluate whether discrepancies between the simulation and experiment arise from inadequate fidelity to the capsule geometry and drive conditions, uncertainties in physical data used by simulations, or inadequate physics. We present results from detailed high-resolution three-dimensional simulations of ICF implosions performed as part of the MARBLE campaign on the National Ignition Facility [Albright et al., Phys. Plasmas 29, 022702 (2022)]. These experiments are foam-filled separated-reactant experiments, where deuterons reside in the foam and tritons reside in the capsule gas fill and deuterium–tritium (DT) fusion reactions only occur in the presence of mixing between these materials. Material mixing in these experiments is primarily seeded by shock interaction with the complex geometry of the foam and gas fill, which induces the Richtmyer–Meshkov instability. We compare results for experiments with two different gas fills (ArT and HT), which lead to significant differences in the hydrodynamic and thermodynamic developments of the materials in the implosion. Our simulation results show generally good agreement with experiments and demonstrate a substantial impact of hydrodynamic flows on measured ion temperatures. The results suggest that viscosity, which was not included in our simulations, is the most important unmodeled physics and qualitatively explains the few discrepancies between the simulation and experiment. The results also suggest that the hydrodynamic treatment of shocks is inadequate to predict the heating and yield produced during shock flash, when the shock converges at the center of the implosion. Alternatively, underestimation of the level of radiative preheat from the shock front could explain many of the differences between the experiment and simulation. Nevertheless, simulations are able to reproduce many experimental observables within the level of experimental reproducibility, including most yields, time-resolved X-ray self-emission images, and an increase in burn-weighted ion temperature and neutron down-scattered ratio in the line of sight that includes a jet seeded by the glue spot that joins capsule hemispheres.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2021

Molecular mechanisms of assembly and TRIP13-mediated remodeling of the human Shieldin complex

The Shieldin complex, composed of REV7, SHLD1, SHLD2, and SHLD3, protects DNA double-strand breaks (DSBs) to promote nonhomologous end joining. The AAA + ATPase TRIP13 remodels Shieldin to regulate DNA repair pathway choice. Here we report crystal structures of human SHLD3–REV7 binary and fused SHLD2–SHLD3–REV7 ternary complexes, revealing that assembly of Shieldin requires fused SHLD2–SHLD3 induced conformational heterodimerization of open (O-REV7) and closed (C-REV7) forms of REV7. We also report the cryogenic electron microscopy (cryo-EM) structures of the ATPγS-bound fused SHLD2–SHLD3–REV7–TRIP13 complexes, uncovering the principles underlying the TRIP13-mediated disassembly mechanism of the Shieldin complex. We demonstrate that the N terminus of REV7 inserts into the central channel of TRIP13, setting the stage for pulling the unfolded N-terminal peptide of C-REV7 through the central TRIP13 hexameric channel. The primary interface involves contacts between the safety-belt segment of C-REV7 and a conserved and negatively charged loop of TRIP13. This process is mediated by ATP hydrolysis-triggered rotatory motions of the TRIP13 ATPase, thereby resulting in the disassembly of the Shieldin complex.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Decorating chromatin for enhanced genome editing using CRISPR-Cas9

CRISPR-associated (Cas) enzymes have revolutionized biology by enabling RNA-guided genome editing. Homology-directed repair (HDR) in the presence of donor templates is currently the most versatile method to introduce precise edits following CRISPR-Cas-induced double-stranded DNA cuts, but HDR efficiency is generally low relative to end-joining pathways that lead to insertions and deletions (indels). We tested the hypothesis that HDR could be increased using a Cas9 construct fused to PRDM9, a chromatin remodeling factor that deposits histone methylations H3K36me3 and H3K4me3 to mediate homologous recombination in human cells. Our results show that the fusion protein contacts chromatin specifically at the Cas9 cut site in the genome to increase the observed HDR efficiency by threefold and HDR:indel ratio by fivefold compared with that induced by unmodified Cas9. HDR enhancement occurred in multiple cell lines with no increase in off-target genome editing. These findings underscore the importance of chromatin features for the balance between DNA repair mechanisms during CRISPR-Cas genome editing and provide a strategy to increase HDR efficiency.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

NTRC regulates CP12 to activate Calvin–Benson cycle during cold acclimation

NADPH-dependent thioredoxin reductase C (NTRC) is a chloroplast redox regulator in algae and plants. Here, we used site-specific mutation analyses of the thioredoxin domain active site of NTRC in the green alga Chlamydomonas reinhardtii to show that NTRC mediates cold tolerance in a redox-dependent manner. By means of coimmunoprecipitation and mass spectrometry, a redox- and cold-dependent binding of the Calvin–Benson Cycle Protein 12 (CP12) to NTRC was identified. NTRC was subsequently demonstrated to directly reduce CP12 of C. reinhardtii as well as that of the vascular plant Arabidopsis thaliana in vitro. As a scaffold protein, CP12 joins the Calvin–Benson cycle enzymes phosphoribulokinase (PRK) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) to form an autoinhibitory supracomplex. Using size-exclusion chromatography, NTRC from both organisms was shown to control the integrity of this complex in vitro and thereby PRK and GAPDH activities in the cold. Thus, NTRC apparently reduces CP12, hence triggering the dissociation of the PRK/CP12/GAPDH complex in the cold. Like the ntrc::aphVIII mutant, CRISPR-based cp12::emx1 mutants also exhibited a redox-dependent cold phenotype. In addition, CP12 deletion resulted in robust decreases in both PRK and GAPDH protein levels implying a protein protection effect of CP12. Both CP12 functions are critical for preparing a repertoire of enzymes for rapid activation in response to environmental changes. This provides a crucial mechanism for cold acclimation.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

P2M Simulation Exercise on Past Fuel Melting Irradiation Experiments

This paper presents the results of the Power To Melt and Maneuverability (P2M) Simulation Exercise on past fuel melting irradiation experiments, organized within the Organisation for Economic Co-operation and Development/Nuclear Energy Agency Framework for IrraDiation ExperimentS (FIDES) framework by the Core Group (CEA, EDF, and SCK·CEN) and open to all FIDES members. The exercise consisted in simulating two past power ramps where fuel melting was detected: (1) the xM3 staircase power transient [ramp terminal level (RTL) 70 kW·m -1 , average burnup 27 GWd·tU -1 ], carried out in 2005 in the R2 reactor at Studsvik (Sweden), where the rodlet maintained its integrity, and (2) the HBC4 fast power transient (RTL 66 kW·m -1 , average burnup 48 GWd·tU -1 ), carried out in 1987 in the BR2 reactor at SCK·CEN (Belgium), where the cladding failed during the experiment. The exercise was joined by 13 organizations from 9 countries using 11 different fuel performance codes. In this paper, the main results of the Simulation Exercise are presented and compared to available postirradiation examinations (PIE) or on-line measurements during the power ramps (fuel and clad diameters, rod elongation, pellet-clad gap, and fission gas release). Since the focus of the Simulation Exercise is on fuel melting assessment, determination of the boundary between melted/nonmelted fuel and the consequent definition of a melting radius from PIE are first discussed. During the HBC4 ramp, fuel melting was predicted by most of the codes despite differences in the melting models. Higher discrepancies were observed for the xM3 rod that can be attributed partly to power uncertainty and partly to the limited capability of the models to describe partial melting of the fuel during this ramp. Finally, possible code developments to improve simulation results are presented.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

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 OSTI2021

High pressure stability of β-Zr: no evidence for isostructural phase transitions

Isostructural transitions have been reported to occur in several pure elements; however, most of these have been disproven. Zr is one of those elements which remains controversial with two reports of an isostructural bcc-to-bcc transition at ~56–60 GPa at an ambient temperature and a more recent report proposing a second bcc-to-bcc transition at 110 GPa. Here, we report a detailed experimental and theoretical study of zirconium in the pressure region of the proposed isostructural transition(s). We conducted three room temperature static compression experiments using Ne as a pressure transmitting medium up to 80 GPa. We see no evidence for an isostructural transition finding a smooth compression curve for β-Zr. We determined the theoretical volume, elastic parameters, and Poisson’s ratio for β-Zr up to 717 GPa and no obvious anomalies are identified. Furthermore, our new results join the growing body of evidence that does not find evidence of isostructural transitions in β-Zr.

36 MATERIALS SCIENCE↗

DOE OSTI2022

On reading Youden: Learning about the practice of statistics and applied statistical research from a master applied statistician

From reading William John “Jack” Youden’s books and articles, Youden (1900-1971), an analytical chemist, becomes an applied statistician by the time he joins the National Bureau of Standards (NBS) in 1948. Here, this article traces his transition from chemist to applied statistician and what his body of work mostly at NBS (1948-1965) demonstrates about his practice of statistics and the role that applied statistical research plays in it. There is much we can learn from a master applied statistician.

42 ENGINEERING↗

DOE OSTI2023

Friction stir welding of thick 7175 aluminium alloy plates for deepwater riser applications

To substantially reduce the cost of extracting petroleum from ultra-deepwater sources, manufacturing risers from 7175 aluminium (Al) alloys rather than steels is being considered. Friction stir welding (FSW), a solid-phase joining technique, is widely applied to 7XXX Al alloys because its mechanical properties are retained within the nugget zone. And, the primary technical objective of the current study is the development of high-strength, corrosion-resistant weldments that connect 7175 Al riser flanges and pipes. However, as the welding thickness increases, the welding speed can be greatly impeded, which lowers the manufacturing efficiency and weakens the mechanical properties in the heat affected zone (next to the nugget). Therefore, obtaining high-performance thick plate 7175 Al alloy joints via FSW is challenging. To overcome this dilemma, the current work optimises the tool design and welding parameters for achieving high-performance joints between 25.4 mm thick 7175 Al alloy plates in butt joint configuration.

Wang, Tianhao↗

DOE OSTI2022

Characterization of a novel HIV-1 circulating recombinant form, CRF91_cpx, comprising CRF02_AG, G, J, and U, mostly among men who have sex with men

Prospective molecular studies of HIV-1 pol region (2253–5250 in HXB2 genome) sequences from sequenced samples of 269 HIV-1-infected patients in Cyprus (2017–2021) revealed a transmission cluster of 14 unknown HIV-1 recombinants that were not classified as previously established CRFs. The earliest recombinant was collected in September 2017, and the transmission cluster continued to grow until November 2020. Near full-length HIV-1 genome sequences of the 11 of the 14 recombinants were successfully obtained (790–8795 in HXB2 genome) and aligned against a reference dataset of HIV-1 subtypes and CRFs. We employed MEGAX for maximum-likelihood tree construction (GTR model, 1000 bootstrap replicates), Cluster-Picker for phylogenetic clustering analysis (genetic distance ≤0.045, bootstrap support value ≥70%), and REGA-3.0 for subtype determination. Bootscan and similarity plot analyses (sliding window of 400 nucleotides overlapped by 40 nucleotides) were conducted using SimPlot-v3.5.1, and subregion confirmatory neighbour-joining tree analyses were conducted using MEGAX (Kimura two-parameter model, 1000 bootstrap replicates, ≥70% bootstrap-support value). Exclusive clustering of the HIV-1 recombinants revealed their uniqueness. The recombination analyses illustrated the same unique mosaic pattern with six putative intersubtype recombination breakpoints, seven fragments of subtypes CRF02_AG, G, J and an unclassified fragment. We conclusively characterized the mosaic structure of the novel HIV-1 CRF, named CRF91_cpx, by the Los Alamos HIV Sequence Database. Additionally, we identified a URF of CRF91_cpx with two additional recombination sites, generated by a recombination event between subtype B and CRF91_cpx. Since the identification of CRF91_cpx, two additional patient samples have been entered into the CRF91_cpx transmission cluster, demonstrating active growth.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Baby universes and worldline field theories

The quantum gravity path integral involves a sum over topologies that invites comparisons to worldsheet string theory and to Feynman diagrams of quantum field theory. However, the latter are naturally associated with the non-abelian algebra of quantum fields, while the former has been argued to define an abelian algebra of superselected observables associated with partition-function-like quantities at an asymptotic boundary. We resolve this apparent tension by pointing out a variety of discrete choices that must be made in constructing a Hilbert space from such path integrals, and arguing that the natural choices for quantum gravity differ from those used to construct QFTs. We focus on one-dimensional models of quantum gravity in order to make direct comparisons with worldline QFT. Finally, we also restrict attention to models in which worldlines do not split apart or join together.

79 ASTRONOMY AND ASTROPHYSICS↗