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At least 1,639 records · Page 91

Relationship between molecular structure and corrugations in self-assembled polypeptoid nanosheets revealed by cryogenic electron microscopy

Designing conformationally dynamic molecules that self-assemble into predictable nanostructures remains an important unmet challenge. This paper describes how atomic-scale cryogenic transmission electron microscopy (cryo-TEM) can be used to explore the relationship between molecular structure and self-assembly of block copolymers. We examined sheetlike micelles formed in water using a series of diblock copolypeptoids with the same hydrophilic block and three distinct crystalline hydrophobic blocks. Our cryo-TEM images revealed all the structures share nansoscale features, but differ in their intermolecular packing geometries. Different molecular arrangements, parallel and antiparallel V-shaped crystal motifs, were revealed by two-dimensional atomic-scale through-plane images. However, images from tilted samples revealed an unexpected feature when the hydrophobic polypeptoid block comprised phenyl rings with substituted bromine atoms at the para position. The nanosheets contained atomic-scale corrugations that were absent in the other systems which comprised unsubstituted aliphatic and aromatic side chains. We hypothesize that these corrugations are due to the dipolar characteristics of the brominated phenyl group and interactions between this group and water molecules. Published by the American Physical Society 2024

36 MATERIALS SCIENCE↗

Coordinated Self-Assembly of Networked Microgrids Using Irving’s Algorithm

Abstract— Microgrid installations have regained significant interest, driven by the increasing adoption of distributed energy resources, decentralized controls, and ongoing technological advancements. While the number of microgrids increases, there are opportunities to coordinate networks of microgrids. In this study, Irving’s algorithm is applied to a framework for the coordinated self-assembly of networked microgrids. Compared with the authors’ previous work, this new study relaxes the constraint on participated microgrids to have a single global objective. Thus, each microgrid can rank others according to its local preference. This reduces the amount of shared information, improves the privacy, and enhances the flexibility. The adaptability to that proposed framework is also maintained. Examples are presented to illustrate the networking processes and self-assembly operations.

Xie, Jing↗

Assembly and Tests of Mechanical Models of the 15-T Nb 3 Sn Dipole Demonstrator

Within the US Magnet Development Program, Fermilab is developing a 15-T Nb 3 Sn dipole demonstrator. Prior to the construction of the real magnet model, short sections and the whole structure were instrumented with strain gauges and assembled to confirm the results of structural analysis, check tooling and to gain experience with the assembly of the real magnet components. We summarize the lessons learned from these mechanical models and compares the measured data with the finite element analysis.

43 PARTICLE ACCELERATORS↗

Magnetic Measurements of $\mathrm{HL-LHC AUP}$ Cryo-Assemblies at Fermilab

LQXFA/B production series cryogenic assemblies are being built for the LHC upgrade by the HL-LHC Accelerator Upgrade Project (AUP). These contain a pair of MQXFA quadrupole magnets combined as a cold mass within a vacuum vessel, and are to be installed in the IR regions of the LHC. The LQXFA/B are being tested at 1.9 K to assess alignment and magnetic performance at Fermilab's horizontal test facility. The ~10 m long assembly must meet stringent specifications for quadrupole strength and harmonic field integrals determination, magnetic axis location, and for variations in axis position and local field profiles. A multi-probe, PCB-based rotating coil and a Single Stretched Wire system are employed for these measurements. To accurately determine rotating coil location and angles within the cold mass, a laser tracker is utilized to record multiple targets at one end of the probe. Here this paper describes the measurements, probes/equipment, and techniques used to perform the necessary characterization of the cold mass.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Design and Assembly of a Large-Aperture Nb 3 Sn Cos-Theta Dipole Coil With Stress Management in Dipole Mirror Configuration

The stress-management cos-theta (SMCT) coil is a new concept which has been proposed and is being developed at Fermilab in the framework of US Magnet Development Program (US-MDP) for high-field and/or large-aperture accelerator magnets based on low-temperature and high-temperature superconductors. The SMCT structure is used to reduce large coil deformations under the Lorentz forces and, thus, the excessively large strains and stresses in the coil. A large-aperture Nb 3 Sn SMCT dipole coil has been developed and fabricated at Fermilab to demonstrate and test the SMCT concept including coil design, fabrication technology and performance. The first SMCT coil has been assembled with 60-mm aperture Nb 3 Sn coil inside a dipole mirror configuration and will be tested separately and in series with the insert coil. Here this paper summarizes the large-aperture SMCT coil design and parameters and reports the coil fabrication steps and its assembly in dipole mirror configuration.

43 PARTICLE ACCELERATORS↗

Magnetic Measurements and Alignment Results of LQXFA/B Cold Mass Assemblies at Fermilab

MQXFA production series quadrupole magnets are being built for the Hi-Lumi (HL) LHC upgrade by the U.S. Accelerator Upgrade Project (US-HL-LHC AUP). These magnets are being placed in pairs, as a cold mass, within cryostats at Fermilab, and are being tested to assess alignment and magnetic performance at Fermilab's horizontal test stand facility. The ~10 m - long assembly must meet stringent specifications for quadrupole strength and harmonic field integrals determination, magnetic axis position, and for magnet variations in positioning and local field profile. Here this paper describes the results of the magnetic and alignment measurements which characterize the first LQXFA/B assembly.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

AUP First Pre-Series Cryo-Assembly Design Production and Test Overview

New high field and large-aperture quadrupole magnets for the low-beta inner triplets (Q1, Q2, Q3) have been built and tested as part of the high-luminosity upgrade of the Large Hadron Collider (HL-LHC). These new quadrupole magnets are based on Nb3Sn superconducting technology. The US Accelerator Upgrade Project (US-AUP) is producing the Q1 and Q3 Cryo-Assemblies: a pair of ~5 m long magnet structures installed in a stainless-steel helium vessel (Cold Mass) and surrounded by cryostat shields, piping, and a vacuum vessel. In conclusion, this paper gives an overview of the design, production, and the results of the horizontal test of the first pre-series Q1/Q3 Cryo-Assembly.

43 PARTICLE ACCELERATORS↗

Assembly of the MOLLER Toroidal Magnets at Jefferson Lab

The MOLLER experiment at the Thomas Jefferson National Accelerator Facility (JLab) aims to precisely measure the weak interaction between electrons. This experiment leverages the 12 GeV electron beam and will run for three years. A crucial component of MOLLER is a system of five uniquely shaped water-cooled toroidal magnets. These magnets, possessing seven-fold symmetry, are designed to focus particles by separating electrons scattered off hydrogen in a liquid hydrogen target. The five magnets separate electrons scattered off electrons (Møller scattering) and protons (elastic e-p scattering) within target into approximately circular rings at the detector. Here, this paper presents the assembly process for these five toroidal magnets, detailing critical steps including epoxy application, pin insertion, soldering and brazing, coil assembly, and alignment, all performed to meet stringent magnet specifications. Additionally, it discusses challenges encountered during construction and highlights lessons learned, offering insights for future magnet development projects.

Lamont, Joseph [Thomas Jefferson National Accelera↗

Design of a Structure for Assembly and Cooling the Magnet of the Next-Generation 45 GHz ECR Ion Source MARS-D

Here, the current Electron Cyclotron Resonance Ion Sources (ECRISs), constructed with Nb-Ti wires and the conventional racetrack-and-solenoid structure, have achieved operating frequencies up to 28 GHz and utilized about 90% of the critical current of the Nb-Ti wire. A Mixed Axial and Radial field System Demonstrator (MARS-D) is being developed at Lawrence Berkeley National Laboratory (LBNL). This system, which consists of an innovative hexagonal Closed-Loop Coil (CLC) and a set of solenoids, can generate higher magnetic fields (up to 150% ) while requiring only about 50% of the superconducting wire, enabling Nb-Ti wires to be used in the next-generation 45 GHz ECRIS. However, the assembly and cooling of such an efficient and compact magnet are particularly challenging due to the small radial gap between the CLC and solenoids, as well as the tight operating temperature margin. To address these challenges, a structure was developed that combines a three-section radially split solenoid mandrel with a series of shrink-fit reinforcement rings and cooling channels. This paper presents the detailed structure, manufacturing method, assembly procedure, impregnation method, mechanical Finite Element Analysis (FEA) comparison, and thermal FEA comparison.

ECR ion sources↗

Phylogenetic analyses and reclassification of the oleaginous marine species Nannochloris sp. “desiccata" (Trebouxiophyceae, Chlorophyta), formerly Chlorella desiccata , supported by a high-quality genome assembly

Microalgae are diverse, with many gaps remaining in phylogenetic and physiological understanding. Thus, studying new microalgae species increases our broader comprehension of biological diversity, and evaluation of new candidates as algal production platforms can lead to improved productivity under a variety of cultivation conditions. Chlorella is a genus of fast-growing species often isolated from freshwater habitats and cultivated as a source of nutritional supplements. However, the use of freshwater increases competition with other freshwater needs. We identified Chlorella desiccata to be worthy of further investigation as a potential algae production strain, due to its isolation from a marine environment and its promising growth and biochemical composition properties. Long-read genomic sequencing was conducted for C. desiccata UTEX 2526, resulting in a high-quality, near chromosome level, diploid genome with an assembly length of 21.55 Mbp in only 18 contigs. We also report complete circular mitochondrial and chloroplast genomes. Phylogenomic and phylogenetic analyses using nuclear, chloroplast, 18S rRNA, and actin sequences revealed that this species clades within strains currently identified as Nannochloris (Trebouxiophyceae, Chlorophyta), leading to its reclassification as Nannochloris sp. “desiccata” UTEX 2526. The mode of cell division for this species is autosporulation, differing from the type species N. bacillaris. As has occurred across multiple microalgae genera, there are repeated examples of Nannochloris species reclassification in the literature. This high-quality genome assembly and phylogenetic analysis of the potential algal production strain Nannochloris sp. “desiccata” UTEX 2526 provides an important reference and useful tool for further studying this region of the phylogenetic tree.

59 BASIC BIOLOGICAL SCIENCES↗

The Cu chaperone CopZ is required for Cu homeostasis in Rhodobacter capsulatus and influences cytochrome cbb 3 oxidase assembly

We present that Cu homeostasis depends on a tightly regulated network of proteins that transport or sequester Cu, preventing the accumulation of this toxic metal while sustaining Cu supply for cuproproteins. In Rhodobacter capsulatus, Cu-detoxification and Cu delivery for cytochrome c oxidase (cbb 3 -Cox) assembly depend on two distinct Cu-exporting P 1B -type ATPases. The low-affinity CopA is suggested to export excess Cu and the high-affinity CcoI feeds Cu into a periplasmic Cu relay system required for cbb 3 -Cox biogenesis. In most organisms, CopA-like ATPases receive Cu for export from small Cu chaperones like CopZ. However, whether these chaperones are also involved in Cu export via CcoI-like ATPases is unknown. Here we identified a CopZ-like chaperone in R. capsulatus, determined its cellular concentration and its Cu binding activity. Our data demonstrate that CopZ has a strong propensity to form redox-sensitive dimers via two conserved cysteine residues. A ΔcopZ strain, like a ΔcopA strain, is Cu-sensitive and accumulates intracellular Cu. In the absence of CopZ, cbb 3 -Cox activity is reduced, suggesting that CopZ not only supplies Cu to P 1B -type ATPases for detoxification but also for cuproprotein assembly via CcoI. In conclusion, this finding was further supported by the identification of a ~150 kDa CcoI-CopZ protein complex in native R. capsulatus membranes.

59 BASIC BIOLOGICAL SCIENCES↗

The Sec1/Munc18‐like proteins TgSec1 and TgVps45 play pivotal roles in assembly of the pellicle and sub‐pellicle network in Toxoplasma gondii

Summary Post‐Golgi vesicle trafficking is indispensable for precise movement of proteins to the pellicle, the sub‐pellicle network and apical secretory organelles in Apicomplexa. However, only a small number of molecular complexes involved in trafficking, tethering and fusion of vesicles have been identified in Toxoplasma gondii . Consequently, it is unclear how complicated vesicle trafficking is accomplished in this parasite. Sec1/Munc18‐like (SM) proteins are essential components of protein complexes involved in vesicle fusion. Here, we found that depletion of the SM protein TgSec1 using an auxin‐inducible degron‐based conditional knockout strategy led to mislocalization of plasma membrane proteins. By contrast, conditional depletion of the SM protein TgVps45 led to morphological changes, asymmetrical loss of the inner membrane complex and defects in nucleation of sub‐pellicular microtubules, polarization and symmetrical assembly of daughter parasites during repeated endodyogeny. TgVps45 interacts with the SNARE protein TgStx16 and TgVAMP4‐1. Conditional ablation of TgStx16 causes the similar growth defect like TgVps45 deficiency suggested they work together for the vesicle fusion at TGN. These findings indicate that these two SM proteins are crucial for assembly of pellicle and sub‐pellicle network in T. gondii respectively.

Cao, Shinuo↗

Cellulose assembles into helical bundles of uniform handedness in cell walls with abnormal pectin composition

Plant cells and organs grow into a remarkable diversity of shapes, as directed by cell walls composed primarily of polysaccharides such as cellulose and multiple structurally distinct pectins. The properties of the cell wall that allow for precise control of morphogenesis are distinct from those of the individual polysaccharide components. For example, cellulose, the primary determinant of cell morphology, is a chiral macromolecule that can self-assemble in vitro into larger-scale structures of consistent chirality, and yet most plant cells do not display consistent chirality in their growth. One interesting exception is the Arabidopsis thaliana rhm1 mutant, which has decreased levels of the pectin rhamnogalacturonan-I and causes conical petal epidermal cells to grow with a left-handed helical twist. Here, we show that in rhm1 the cellulose is bundled into large macrofibrils, unlike the evenly distributed microfibrils of the wild type. This cellulose bundling becomes increasingly severe over time, consistent with cellulose being synthesized normally and then self-associating into macrofibrils. We also show that in the wild type, cellulose is oriented transversely, whereas in rhm1 mutants, the cellulose forms right-handed helices that can account for the helical morphology of the petal cells. Furthermore, our results indicate that when the composition of pectin is altered, cellulose can form cellular-scale chiral structures in vivo, analogous to the helicoids formed in vitro by cellulose nano-crystals. We propose that an important emergent property of the interplay between rhamnogalacturonan-I and cellulose is to permit the assembly of nonbundled cellulose structures, providing plants flexibility to orient cellulose and direct morphogenesis.

59 BASIC BIOLOGICAL SCIENCES↗

Insight into the assembly of lipid-hyaluronan complexes in osteoarthritic conditions

Interactions between molecules in the synovial fluid and the cartilage surface may play a vital role in the formation of adsorbed films that contribute to the low friction of cartilage boundary lubrication. Osteoarthritis (OA) is the most common degenerative joint disease. Previous studies have shown that in OA-diseased joints, hyaluronan (HA) not only breaks down resulting in a much lower molecular weight (MW), but also its concentration is reduced ten times. Here, we have investigated the structural changes of lipid-HA complexes as a function of HA concentration and MW to simulate the physiologically relevant conditions that exist in healthy and diseased joints. Small angle neutron scattering and dynamic light scattering were used to determine the structure of HA-lipid vesicles in bulk solution, while a combination of atomic force microscopy and quartz crystal microbalance was applied to study their assembly on a gold surface. We infer a significant influence of both MW and HA concentrations on the structure of HA-lipid complexes in bulk and assembled on a gold surface. Our results suggest that low MW HA cannot form an amorphous layer on the gold surface, which is expected to negatively impact the mechanical integrity and longevity of the boundary layer and could contribute to the increased wear of the cartilage that has been reported in joints diseased with OA.

59 BASIC BIOLOGICAL SCIENCES↗

High-resolution chemical patterns from negative tone resists for the integration of extreme ultraviolet patterns of metal-oxide resists with directed self-assembly of block copolymers

Extreme ultraviolet (EUV) lithography faces significant challenges in designing suitable resist materials that can provide adequate precision, while maintaining economically viable throughput. These challenges in resist materials have led to printing failures and high roughness in EUV patterns, compromising the performance of semiconductor devices. Integrating directed self-assembly (DSA) of block copolymers (BCPs) with EUV lithography offers a promising solution because, while the BCPs register to the EUV-defined chemical guiding pattern, the thermodynamically determined structures of the BCPs automatically rectify defects and roughness in the EUV pattern. Despite the superior resolution of metal-oxide EUV resists (MORs), their application to DSA is limited by the difficulty in converting them into chemical patterns that allow effective transfer of the rectified patterns of DSA films into inorganic materials. To address this challenge, this study introduces a novel strategy for fabricating chemical patterns using hydrogen silsesquioxane (HSQ), a high-resolution negative tone inorganic resist, as a model system for MORs. Initially, a sacrificial Cr pattern is generated from HSQ patterns via reactive ion etching. The sacrificial Cr pattern is converted into a chemical pattern by first grafting a water-soluble polyethylene oxide brush onto the substrate, then wet etching the Cr, and finally grafting nonpolar polystyrene brushes. Assembling polystyrene-block-poly(methyl methacrylate) on these patterns results in structures oriented and registered with the underlying pattern, achieving 24 nm full-pitch resolutions. In conclusion, this approach has the potential to integrate MOR patterns into the DSA process, thereby enabling the generation of high-quality sub-10 nm patterns with high-χ BCPs.

Atomic force microscopy↗

A D53 repression motif induces oligomerization of TOPLESS corepressors and promotes assembly of a corepressor-nucleosome complex

TOPLESS are tetrameric plant corepressors of the conserved Tup1/Groucho/TLE (transducin-like enhancer of split) family. Herein, we show that they interact through their TOPLESS domains (TPDs) with two functionally important ethylene response factor–associated amphiphilic repression (EAR) motifs of the rice strigolactone signaling repressor D53: the universally conserved EAR-3 and the monocot-specific EAR-2. We present the crystal structure of the monocot-specific EAR-2 peptide in complex with the TOPLESS-related protein 2 (TPR2) TPD, in which the EAR-2 motif binds the same TPD groove as jasmonate and auxin signaling repressors but makes additional contacts with a second TPD site to mediate TPD tetramer-tetramer interaction. We validated the functional relevance of the two TPD binding sites in reporter gene assays and in transgenic rice and demonstrate that EAR-2 binding induces TPD oligomerization. Moreover, we demonstrate that the TPD directly binds nucleosomes and the tails of histones H3 and H4. Higher-order assembly of TPD complexes induced by EAR-2 binding markedly stabilizes the nucleosome-TPD interaction. These results establish a new TPD-repressor binding mode that promotes TPD oligomerization and TPD-nucleosome interaction, thus illustrating the initial assembly of a repressor-corepressor-nucleosome complex.

59 BASIC BIOLOGICAL SCIENCES↗

Guiding kinetic trajectories between jammed and unjammed states in 2D colloidal nanocrystal-polymer assemblies with zwitterionic ligands

Mesostructured matter composed of colloidal nanocrystals in solidified architectures abounds with broadly tunable catalytic, magnetic, optoelectronic, and energy storing properties. Less common are liquid-like assemblies of colloidal nanocrystals in a condensed phase, which may have different energy transduction behaviors owing to their dynamic character. Limiting investigations into dynamic colloidal nanocrystal architectures is the lack of schemes to control or redirect the tendency of the system to solidify. We show how to solidify and subsequently reconfigure colloidal nanocrystal assemblies dimensionally confined to a liquid-liquid interface. Our success in this regard hinged on the development of competitive chemistries anchoring or releasing the nanocrystals to or from the interface. With these chemistries, it was possible to control the kinetic trajectory between quasi–two-dimensional jammed (solid-like) and unjammed (liquid-like) states. In future schemes, it may be possible to leverage this control to direct the formation or destruction of explicit physical pathways for energy carriers to migrate in the system in response to an external field.

36 MATERIALS SCIENCE↗

Allosteric modulation of nucleoporin assemblies by intrinsically disordered regions

Intrinsically disordered regions (IDRs) of proteins are implicated in key macromolecular interactions. However, the molecular forces underlying IDR function within multicomponent assemblies remain elusive. By combining thermodynamic and structural data, we have discovered an allostery-based mechanism regulating the soluble core region of the nuclear pore complex (NPC) composed of nucleoporins Nup53, Nic96, and Nup157. We have identified distinct IDRs in Nup53 that are functionally coupled when binding to partner nucleoporins and karyopherins (Kaps) involved in NPC assembly and nucleocytoplasmic transport. We show that the Nup53·Kap121 complex forms an ensemble of structures that destabilize Nup53 hub interactions. Our study provides a molecular framework for understanding how disordered and folded domains communicate within macromolecular complexes.

59 BASIC BIOLOGICAL SCIENCES↗