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DOE OSTI2022

SCONCE : a cosmic web finder for spherical and conic geometries

The latticework structure known as the cosmic web provides a valuable insight into the assembly history of large-scale structures. Despite the variety of methods to identify the cosmic web structures, they mostly rely on the assumption that galaxies are embedded in a Euclidean geometric space. Here, we present a novel cosmic web identifier called SCONCE (Spherical and CONic Cosmic wEb finder) that inherently considers the 2D (RA, DEC) spherical or the 3D (RA, DEC, z) conic geometry. The proposed algorithms in sconce generalize the well-known subspace constrained mean shift (SCMS) method and primarily address the predominant filament detection problem. They are intrinsic to the spherical/conic geometry and invariant to data rotations. We further test the efficacy of our method with an artificial cross-shaped filament example and apply it to the SDSS galaxy catalogue, revealing that the 2D spherical version of our algorithms is robust even in regions of high declination. Finally, using N-body simulations from Illustris, we show that the 3D conic version of our algorithms is more robust in detecting filaments than the standard SCMS method under the redshift distortions caused by the peculiar velocities of haloes. Our cosmic web finder is packaged in python as SCONCE-SCMS and has been made publicly available.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

The beyond-halo mass effects of the cosmic web environment on galaxies

ABSTRACT Galaxy properties primarily depend on their host halo mass. Halo mass, in turn, depends on the cosmic web environment. We explore if the effect of the cosmic web on galaxy properties is entirely transitive via host halo mass, or if the cosmic web has an effect independent of mass. The secondary galaxy bias, sometimes referred to as ‘galaxy assembly bias’, is the beyond-mass component of the galaxy–halo connection. We investigate the link between the cosmic web environment and the secondary galaxy bias in simulations. We measure the secondary galaxy bias through the following summary statistics: projected two-point correlation function, $w_{\mathrm{p}}(r_{\mathrm{p}})$, and counts-in-cylinders statistics, $P(N_{\mathrm{CIC}})$. First, we examine the extent to which the secondary galaxy bias can be accounted for with a measure of the environment as a secondary halo property. We find that the total secondary galaxy bias preferentially places galaxies in more strongly clustered haloes. In particular, haloes at fixed mass tend to host more galaxies when they are more strongly associated with nodes or filaments. This tendency accounts for a significant portion, but not the entirety, of the total secondary galaxy bias effect. Secondly, we quantify how the secondary galaxy bias behaves differently depending on the host halo proximity to nodes and filaments. We find that the total secondary galaxy bias is relatively stronger in haloes more associated with nodes or filaments. We emphasize the importance of removing halo mass effects when considering the cosmic web environment as a factor in the galaxy–halo connection.

Astronomy & Astrophysics↗

DOE OSTI2024

Search for interacting galaxy clusters from SDSS DR-17 employing optimized friends-of-friends algorithm and multimessenger tracers

ABSTRACT In the theoretical framework of hierarchical structure formation, galaxy clusters evolve through continuous accretion and mergers of substructures. Cosmological simulations have revealed the best picture of the universe as a 3D filamentary network of dark-matter distribution called the cosmic web. Galaxy clusters are found to form at the nodes of this network and are the regions of high merging activity. Such mergers being highly energetic, contain a wealth of information about the dynamical evolution of structures in the Universe. Observational validation of this scenario needs a colossal effort to identify numerous events from all-sky surveys. Therefore, such efforts are sparse in literature and tend to focus on individual systems. In this work, we present an improved search algorithm for identifying interacting galaxy clusters and have successfully produced a comprehensive list of systems from SDSS DR-17. By proposing a set of physically motivated criteria, we classified these interacting clusters into two broad classes, ‘merging’ and ‘pre-merging/postmerging’ systems. Interestingly, as predicted by simulations, we found that most cases show cluster interaction along the prominent cosmic filaments of galaxy distribution (i.e. the proxy for dark matter filaments), with the most violent ones at their nodes. Moreover, we traced the imprint of interactions through multiband signatures, such as diffuse cluster emissions in radio or X-rays. Although we could not find direct evidence of diffuse emission from connecting filaments and ridges; our catalogue of interacting clusters will ease locating such faintest emissions as data from sensitive telescopes such as eROSITA or SKA, becomes accessible.

Oak, Tejas↗

DOE OSTI2013

Mechanistic insights into the role of Hop2-Mnd1 in meiotic homologous DNA pairing

The Hop2–Mnd1 complex functions with the DMC1 recombinase in meiotic recombination. Hop2–Mnd1 stabilizes the DMC1-single-stranded DNA (ssDNA) filament and promotes the capture of the double stranded DNA partner by the recombinase filament to assemble the synaptic complex. Herein, we define the action mechanism of Hop2–Mnd1 in DMC1-mediated recombination. Small angle X-ray scattering analysis and electron microscopy reveal that the heterodimeric Hop2–Mnd1 is a V-shaped molecule. We show that the protein complex harbors three distinct DNA binding sites, and determine their functional relevance. Specifically, the N-terminal double-stranded DNA binding functions of Hop2 and Mnd1 co-operate to mediate synaptic complex assembly, whereas ssDNA binding by the Hop2 C-terminus helps stabilize the DMC1-ssDNA filament. A model of the Hop2-Mnd1-DMC1-ssDNA ensemble is proposed to explain how it mediates homologous DNA pairing in meiotic recombination.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

The structural OFF and ON states of myosin can be decoupled from the biochemical super- and disordered-relaxed states

Abstract There is a growing awareness that both thick-filament and classical thin-filament regulations play central roles in modulating muscle contraction. Myosin ATPase assays have demonstrated that under relaxed conditions, myosin may reside either in a high-energy-consuming disordered-relaxed (DRX) state available for binding actin to generate force or in an energy-sparing super-relaxed (SRX) state unavailable for actin binding. X-ray diffraction studies have shown that the majority of myosin heads are in a quasi-helically ordered OFF state in a resting muscle and that this helical ordering is lost when myosin heads are turned ON for contraction. It has been assumed that myosin heads in SRX and DRX states are equivalent to the OFF and ON states, respectively, and the terms have been used interchangeably. In this study, we use X-ray diffraction and ATP turnover assays to track the structural and biochemical transitions of myosin heads, respectively, induced with either omecamtiv mecarbil (OM) or piperine in relaxed porcine myocardium. We find that while OM and piperine induce dramatic shifts of myosin heads from the OFF to the ON state, there are no appreciable changes in the population of myosin heads in the SRX and DRX states in both unloaded and loaded preparations. Our results show that biochemically defined SRX and DRX can be decoupled from structurally defined OFF and ON states. In summary, while SRX/DRX and OFF/ON transitions can be correlated in some cases, these two phenomena are measured using different approaches, reflect different properties of the thick filament, and should be investigated and interpreted separately.

Jani, Vivek P. (ORCID:0000000238114973)↗

DOE OSTI2021

Geometric frustration in the myosin superlattice of vertebrate muscle

Geometric frustration results from an incompatibility between minimum energy arrangements and the geometry of a system, and gives rise to interesting and novel phenomena. Here, we report geometric frustration in a native biological macromolecular system---vertebrate muscle. We analyse the disorder in the myosin filament rotations in the myofibrils of vertebrate striated (skeletal and cardiac) muscle, as seen in thin-section electron micrographs, and show that the distribution of rotations corresponds to an archetypical geometrically frustrated system---the triangular Ising antiferromagnet. Spatial correlations are evident out to at least six lattice spacings. The results demonstrate that geometric frustration can drive the development of structure in complex biological systems, and may have implications for the nature of the actin--myosin interactions involved in muscle contraction. Identification of the distribution of myosin filament rotations with an Ising model allows the extensive results on the latter to be applied to this system. It shows how local interactions (between adjacent myosin filaments) can determine long-range order and, conversely, how observations of long-range order (such as patterns seen in electron micrographs) can be used to estimate the energetics of these local interactions. Furthermore, since diffraction by a disordered system is a function of the second-order statistics, the derived correlations allow more accurate diffraction calculations, which can aid in interpretation of X-ray diffraction data from muscle specimens for structural analysis.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2013

The length-tension curve in muscle depends on lattice spacing

Classic interpretations of the striated muscle length–tension curve focus on how force varies with overlap of thin (actin) and thick (myosin) filaments. New models of sarcomere geometry and experiments with skinned synchronous insect flight muscle suggest that changes in the radial distance between the actin and myosin filaments, the filament lattice spacing, are responsible for between 20% and 50% of the change in force seen between sarcomere lengths of 1.4 and 3.4 µm. Thus, lattice spacing is a significant force regulator, increasing the slope of muscle's force–length dependence.

Williams, C. D.↗

DOE OSTI2025

Quantum graph models for transport in filamentary switching

The formation of metallic nanofilaments bridging two electrodes across an insulator is a mechanism for resistive switching. Examples of such phenomena include atomic synapses, which constitute a distinct class of memristive devices the behavior of which is closely tied to the properties of the filament. Until recently, experimental investigation of the low-temperature regime and quantum transport effects has been limited. However, with growing interest in understanding the true impacts of the filament on device conductance, comprehending quantum effects has become crucial for quantum neuromorphic hardware. Here, we discuss quantum transport resulting from filamentary switching in a narrow region where the continuous approximation of the contact is not valid, and only a few atoms are involved. In this scenario, the filament can be represented by a graph depicting the adjacency of atoms and the overlap between atomic orbitals. Using the theory of quantum graphs with locally diffusive node scattering, we calculate the scattering amplitude of charge carriers on this graph and explore the interplay between filamentary formation and quantum transport effects.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2017

Equilibrium properties of superconducting niobium at high magnetic fields: A possible existence of a filamentary state in type-II superconductors [Possible existence of a filamentary state in type-II superconductors]

The standard interpretation of the phase diagram of type-II superconductors was developed in the 1960s and has since been considered a well-established part of classical superconductivity. However, upon closer examination a number of fundamental issues arises that leads one to question this standard picture. To address these issues we studied equilibrium properties of niobium samples near and above the upper critical field H c2 in parallel and perpendicular magnetic fields. The samples investigated were very high quality films and single-crystal disks with the Ginzburg-Landau parameters 0.8 and 1.3, respectively. A range of complementary measurements has been performed, which include dc magnetometry, electrical transport, muon spin rotation spectroscopy, and scanning Hall-probe microscopy. Contrary to the standard scenario, we observed that a superconducting phase is present in the sample bulk above H c2 and the field H c3 is the same in both parallel and perpendicular fields. Our findings suggest that above H c2 the superconducting phase forms filaments parallel to the field regardless of the field orientation. Near H c2 the filaments preserve the hexagonal structure of the preceding vortex lattice of the mixed state, and the filament density continuously falls to zero at H c3 . Finally, our paper has important implications for the correct interpretation of the properties of type-II superconductors and can be essential for practical applications of these materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2023

Effects of baryonic feedback on the cosmic web

Here, we study the effect of baryons on the cosmic web—halos, filaments, walls, and voids. To do so, we apply a modified version of NEXUS, a cosmic web morphological analysis algorithm, to the IllustrisTNG simulations. We find that halos lose more than 10% of their mass due to baryons, mostly to filaments and a small portion to walls and voids. However, the mass transfer does not significantly shift the boundaries of structures, leaving the volume fractions of the cosmic structures largely unaffected. We quantify the effects of baryonic feedback on the power spectrum and the probability density function of the density field for individual cosmic structures. For the power spectrum, most suppression due to feedback can be accounted for by including M ≥ 10 12 M ⊙ /h halos, without considering other cosmic structures. However, when examining the probability density function of the density field, we find nearly 100% suppression of the emptiest regions and 10%-level effects (boost or suppression) in the remaining regions of filaments, walls, and voids. Our results indicate the importance of modeling the effects of baryons in the whole cosmic web, not just halos, for cosmological analysis beyond two-point statistics or field-based inferences.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

ac susceptibility studies of intra- and intergrain properties of high-$J_c$ Bi-2212 wires

Bi 2 Sr 2 CaCu 2 O x (Bi-2212) is the only high-$T_c$ superconductor (HTS) available as a multifilamentary round wire with multiple architectures and it is a very promising conductor for the realization of high-field applications. Despite their relatively simple wire fabrication by the powder-in-tube technique, Bi-2212 wires require a tightly controlled overpressure heat treatment (HT) with a multi-parameter time-temperature schedule to achieve high critical current density, $J_c$. Further, the variation of these HT parameters, changes in the wire design, wire diameter and powder quality can lead to variations in both the microstructure and the superconducting performance. Particularly noticeable are variations in $J_c$ performance and degree of filament bridging. In this work, we focus on the use of different magnetic characterization techniques to estimate the bridging level and assess the balance of INTER-grain and intra-grain superconducting properties including the irreversibility field ($H_{\text{irr}}$) and the pinning energy ($U_0$) in differently processed wires. Regardless of the actual bridging level, we find that the supercurrent flows at the filament bundle level, not just at the individual filament level. Moreover, using AC susceptibility we identify two distinct supercurrent contributions, one related to the intra-grain and one to the INTER-grain properties, whose irreversibility fields are different but without large sample-to-sample variation. Moreover, an additional component of intra-grain pinning mechanism becomes effective at low temperatures with positive effects also on the INTER-grain performance. The work clearly shows that detailed magnetic characterizations can become valuable tools to investigate the performance of differently processed Bi-2212 wires, correlating their microstructure and overall transport $J_c$, to obtain a deeper understanding of the causes of performance variation and paths to achieve further improvement.

2212↗

DOE OSTI2020

High-resolution crystal structures of Escherichia coli FtsZ bound to GDP and GTP

Bacterial cytokinesis is mediated by the Z-ring, which is formed by the prokaryotic tubulin homolog FtsZ. Recent data indicate that the Z-ring is composed of small patches of FtsZ protofilaments that travel around the bacterial cell by treadmilling. Treadmilling involves a switch from a relaxed (R) state, favored for monomers, to a tense (T) conformation, which is favored upon association into filaments. The R conformation has been observed in numerous monomeric FtsZ crystal structures and the T conformation in Staphylococcus aureus FtsZ crystallized as assembled filaments. However, while Escherichia coli has served as a main model system for the study of the Z-ring and the associated divisome, a structure has not yet been reported for E. coli FtsZ. To address this gap, structures were determined of the E. coli FtsZ mutant FtsZ(L178E) with GDP and GTP bound to 1.35 and 1.40 Å resolution, respectively. The E. coli FtsZ(L178E) structures both crystallized as straight filaments with subunits in the R conformation. These high-resolution structures can be employed to facilitate experimental cell-division studies and their interpretation in E. coli .

protofilaments↗

DOE OSTI2014

Fabrication of compact electron gun for 6 MeV X-ray source

The 6 MeV X-Ray source for container cargo scanning application has been designed and developed by the Accelerator and Pulse Power Division, BARC, Mumbai. This compact linac has been designed as a mobile system, to be mounted on a moving container. In linac-based cargo-scanning system, to work electron gun on a movable container, it has to be robust. Electron gun is to work at 10{sup -7} mbar vacuum and 2000 degree Celsius temperature. An effort is made to engineer the gun assembly to make it more robust and aligned. The linac acts as the source of X-rays, which fall on the cargo and are then detected by the detector system. Many components are indigenously developed like grid, insulating ring, Tungsten filament and filament guide, which are made from alumina ceramic and Tantalum which is to work at 1500 degree Celsius. Filament connector is made from Invar to reduce heat loss and to make rigid connection. It was CNC machined and wire cut by EDM. Invar and Copper electrode feed through is shrink fitted with the help of liquid Nitrogen. Shrink fit tolerances of 15 micrometer are achieved by jig boring machining processes. Tantalum cup for LaB6 cathode and heat shield are made from die and punch mechanism. For alignment of electron emitter with beam axis this Tantalum cup is a crucial component. Electron gun is assembled and aligned its components with the help of precision jigs. The whole assembly was Helium leak tested by MSLD up to 4 x 10{sup -10} mbar.l/s vacuum, no leak was found. This paper will describe the machining, Tantalum cup forming, ceramic components development, heat shields, ceramic feed through etc of electron gun. (author)

43 PARTICLE ACCELERATORS↗

DOE OSTI2023

Recent Progress in Developing Nb 3 Sn Conductors With Increased Specific Heat

A possible approach to reducing Nb 3 Sn magnet training is to increase the energy margin of Nb 3 Sn conductors by enhancing their specific heat (C p ). For this study, we have been developing Nb 3 Sn conductors with increased C p by incorporating substances with high C p at 2-10 K based on a conductor design that is compatible with standard Nb 3 Sn strand production. In the past couple of years our efforts have been mainly focused on improving strand design (e.g., position of high- C p filaments, thickness of the Cu tube for the high-C p filaments, ratio of the Cu powder to the high-C p substance, filament spacing, etc.) in order to obtain good strand drawability and to reduce degradation after rolling, which is needed for production of Rutherford cables. We also tried a new high-C p substance, Gd 2 O 2 S, and verified that it has much higher C p over the whole magnetic field range than the Gd 2 O 3 we used before. With that development work we can now produce high-C p strands with good drawability and low levels of degradation after rolling. This paper reports our findings and the current status of the development of high-C p Nb 3 Sn conductors.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2018

Atomically Thin CBRAM Enabled by 2-D Materials: Scaling Behaviors and Performance Limits

Reducing the energy and power dissipation of conductive bridge random access memory (CBRAM) cells is of critical importance for their applications in future Internet of Things (IoT) device and neuromorphic computing platforms. Atomically thin CBRAMs enabled by 2-D materials are studied theoretically by using 3-D kinetic Monte Carlo simulations together with experimental characterization. The results indicate the performance potential of attoJoule energy dissipation for intrinsic filament formation and a filament size of a single atomistic chain in such a CBRAM cell. The atomically thin CBRAM cells also show qualitatively different features from conventional CBRAM cells, including complete rupture of the filament in the reset stage and comparable forming and set voltages. The scaling and variability of the CBRAM cells down to sub-nanometer size of the switching layer as realized in the experiment are systematically studied, which indicates performance improvement and increased relative variability as the switching layer scales down. Finally, the results establish the ultimate limits of the size and energy scaling for CBRAM cells and illustrate the unique application of 2-D materials in ultralow power memory devices.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2020

Auxin‐induced actin cytoskeleton rearrangements require AUX1

Summary The actin cytoskeleton is required for cell expansion and implicated in cellular responses to the phytohormone auxin. However, the mechanisms that coordinate auxin signaling, cytoskeletal remodeling and cell expansion are poorly understood. Previous studies examined long‐term actin cytoskeleton responses to auxin, but plants respond to auxin within minutes. Before this work, an extracellular auxin receptor – rather than the auxin transporter AUXIN RESISTANT 1 (AUX1) – was considered to precede auxin‐induced cytoskeleton reorganization. In order to correlate actin array organization and dynamics with degree of cell expansion, quantitative imaging tools established baseline actin organization and illuminated individual filament behaviors in root epidermal cells under control conditions and after indole‐3‐acetic acid (IAA) application. We evaluated aux1 mutant actin organization responses to IAA and the membrane‐permeable auxin 1‐naphthylacetic acid (NAA). Cell length predicted actin organization and dynamics in control roots; short‐term IAA treatments stimulated denser and more parallel, longitudinal arrays by inducing filament unbundling within minutes. Although AUX1 is necessary for full actin rearrangements in response to auxin, cytoplasmic auxin (i.e. NAA) stimulated a lesser response. Actin filaments became more ‘organized’ after IAA stopped elongation, refuting the hypothesis that ‘more organized’ actin arrays universally correlate with rapid growth. Short‐term actin cytoskeleton response to auxin requires AUX1 and/or cytoplasmic auxin.

AUX1↗

DOE OSTI2021

Cellular remains in a ~3.42-billion-year-old subseafloor hydrothermal environment

Subsurface habitats on Earth host an extensive extant biosphere and likely provided one of Earth’s earliest microbial habitats. Though the site of life’s emergence continues to be debated, evidence of early life provides insights into its early evolution1. Here we present our discovery of exceptionally well-preserved ~3.40-billion-years-old carbonaceous filamentous microfossils that inhabited a paleo-subseafloor hydrothermal vein system of the Barberton greenstone belt (BGB) in South Africa. The distribution of the microfossils in growth position on the walls of the initial conduits created by low- temperature hydrothermal fluid and their morphological and chemical characteristics as investigated over a range of scales, are consistent with an assemblage of methanogens that thrived in an ultramafic volcanic substrate.

Cavalazzi, Barbara↗

DOE OSTI2022

BCL10 Mutations Define Distinct Dependencies Guiding Precision Therapy for DLBCL

Activated B cell–like diffuse large B-cell lymphomas (ABC-DLBCL) have unfavorable outcomes and chronic activation of CARD11–BCL10–MALT1 (CBM) signal amplification complexes that form due to polymerization of BCL10 subunits, which is affected by recurrent somatic mutations in ABC-DLBCLs. Herein, we show that BCL10 mutants fall into at least two functionally distinct classes: missense mutations of the BCL10 CARD domain and truncation of its C-terminal tail. Truncating mutations abrogated a motif through which MALT1 inhibits BCL10 polymerization, trapping MALT1 in its activated filament-bound state. CARD missense mutations enhanced BCL10 filament formation, forming glutamine network structures that stabilize BCL10 filaments. Mutant forms of BCL10 were less dependent on upstream CARD11 activation and thus manifested resistance to BTK inhibitors, whereas BCL10 truncating but not CARD mutants were hypersensitive to MALT1 inhibitors. Therefore, BCL10 mutations are potential biomarkers for BTK inhibitor resistance in ABC-DLBCL, and further precision can be achieved by selecting therapy based on specific biochemical effects of distinct mutation classes.

60 APPLIED LIFE SCIENCES↗