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At least 829 records · Page 46

Genetic control of morphological transitions in a coacervating protein template

Nature routinely exploits liquid–liquid phase separation (LLPS) of proteins to control the assembly and mineralization of hybrid materials. Here, we show that fusion of the Car9 silica-binding peptide to an elastin-like polypeptide (ELP) yields temperature- and sequence-programmable soft matter templates for the synthesis of silicified architectures ranging in size from nanometers to micrometers. Specifically, we demonstrate unprecedented control over the diameter of silica nanoparticles (SiNP) in the 30–60 nm range with 4 nm precision, show that a single arginine residue (R4) in the Car9 sequence underpins the transition from micelles to proteinosomes, and find that substitutions in other basic residues modulate electrostatic repulsion and solvation to enable access to kinetically trapped species. These structures, which include interconnected micelles, small (∼200 nm) and large (>5 µm) vesicles, are readily visualized by SEM imaging following silicification. Molecular dynamics (MD) simulations and AlphaFold predictions reveal that mutations in positively charged residues alter interfacial packing, hydration, and conformational freedom of the silica-binding segments. Overall, our results establish sequence and thermal energy as synergistic levers for morphological control across length scales using solid-binding ELPs and establish mineralization as a powerful tool to visualize the structure of dynamic soft matter assemblies.

hierarchy↗

Microstructure-dependent particulate populations in ODS steels revealed by single-particle ICP-TOF-MS

In this work, we evaluated the ability of single-particle inductively coupled plasma time-of-flight mass spectrometry (SP-ICP-TOF-MS) to characterize particulates generated from 300 series stainless steels and oxide dispersion–strengthened (ODS) steels. Particulates were produced using two different rotary tools (cutting disk and grinding bit) to assess the influence of particle generation on effluent particulates. Across all materials and preparation techniques, SP-ICP-TOF-MS detected a substantial population of particles containing the expected constituent elements, with average compositions closely matching the nominal alloy values. A secondary population of Y-bearing particles was evident in ODS steels; their formation is strongly favored in particulates generated using the grinding bit. Specifically, in PM2000, Y-bearing particles were predominantly colocated with Al, whereas in 14YWT, Y-bearing particles were less frequently Fe-free but showed stronger colocation with Ti. These trends are consistent with the known microstructural differences between Y–Al–O oxide particles in PM2000 and finer Y–Ti–O nanoclusters in 14YWT. Together, these results demonstrate that SP-ICP-TOF-MS can resolve distinct particulate populations in complex, multicomponent steels at the femtogram mass scale, enabling particle-resolved insight into microstructure-driven phase separation and preparation-dependent particle generation.

Brubaker, Zach E. [Oak Ridge National Laboratory (↗

Multiphasic droplet microfluidics platform for controlled bacteria and mammalian cell co-culture

Microfluidics has revolutionized high-throughput miniaturized biological assays. However, co-culture of mammalian cells and bacteria remains challenging in microfluidic systems due to incompatible growth requirements, limited spatial control, and the requirement for a mammalian cell adhesion matrix. Here, we present a microfluidic platform that generates multiphasic droplets which encapsulate mammalian and bacterial cells, enabling their direct and indirect co-culture. By combining photopolymerizable hydrogels with polymer phase separation, we generate core–shell droplets composed of a liquid and a hydrogel compartment. The hydrogel compartment supports mammalian cell adhesion and culture, while the liquid compartment sustains bacterial growth. We demonstrate two droplet architectures that allow physical bacteria–mammalian cell contacts or enforce complete physical separation, representing direct and indirect co-culture. Our multiphasic droplets are stable, customizable, able to sustain co-culture for over 24 hours, and compatible with fluorescence-based cell sorting technologies. Overall, our multiphasic droplet microfluidic platform provides a scalable and versatile tool for high-throughput co-culture and screening of host–microbe interactions.

59 BASIC BIOLOGICAL SCIENCES↗

Toward precision cosmochronology

The continuous cooling of a white dwarf is punctuated by events that affect its cooling rate. The most significant of these events is the crystallization of its core, a phase transition that occurs once the C/O interior has cooled down below a critical temperature. This transition releases latent heat, as well as gravitational energy due to the redistribution of the C and O ions during solidification, thereby slowing down the evolution of the white dwarf. The unambiguous observational signature of core crystallization–a pile-up of objects in the cooling sequence–was recently reported. However, existing evolution models struggle to quantitatively reproduce this signature, casting doubt on their accuracy when used to measure the ages of stellar populations. The timing and amount of the energy released during crystallization depend on the exact form of the C/O phase diagram. Using the advanced Gibbs–Duhem integration method and state-of-the-art Monte Carlo simulations of the solid and liquid phases, we obtained a very accurate version of this phase diagram that allows a precise modeling of the phase transition. Despite this improvement, the magnitude of the crystallization pile-up remains underestimated by current evolution models. We conclude that latent heat release and O sedimentation alone are not sufficient to explain the observations, and that other unaccounted physical mechanisms, possibly 22 Ne phase separation, play an important role.

79 ASTRONOMY AND ASTROPHYSICS↗

Dam-Break Flow Measurements of Liquid–Granular Mixtures in a Channelized Reservoir

Dam-break flows of granular materials exhibit a complex non-Newtonian rheology, which is strongly influenced by various factors, such as the characteristics of the granular material, the degree of initial compaction, and saturation level of the granular matrix. Specially adapted nonintrusive techniques are required to investigate these flows in the laboratory. This paper investigated the nonintrusive technique of image analysis. The methodologies used in the measurement of bulk flow parameters, such as flow depth, front velocity, and flow rate, and the extraction of detailed flow characteristics such as velocity profiles, were discussed in the context of a series of granular dam-break flow experiments. These experiments were performed under three types of initial conditions: dry, saturated (water filling the pore space), and submerged (a layer of saturated granular material submerged under water) using four types of granular materials—PET pellets, crushed walnut shells, urea, and sand—with grain sizes ranging from 200 μm to 2.9 mm. High-speed cameras were used to capture the evolution and local properties of the flow, such as velocity fields using particle image velocimetry (PIV). Bulk properties of the flow were obtained by tracking the surface profile of the granular matrix and the water table. The extracted profiles were used to measure the evolution of the volume of the granular matrix and the fluid phase separately upstream and downstream of the gate, which allowed measuring the dilatancy (increase in pore space). The study showed that the image analysis techniques are versatile and can be adapted to measure different flow parameters in a variety of granular flows to better understand and analyze their complex behavior. Finally, the advantages and drawbacks of each image analysis technique were discussed and best-practice recommendations were provided.

42 ENGINEERING↗

Toward using collective x-ray Thomson scattering to study C–H demixing and hydrogen metallization in warm dense matter conditions

The insulator–metal transition in liquid hydrogen is an important phenomenon to understand the interiors of gas giants, such as Jupiter and Saturn, as well as the physical and chemical behavior of materials at high pressures and temperatures. Here, the path toward an experimental approach is detailed based on spectrally resolved x-ray scattering, tailored to observe and characterize hydrogen metallization in dynamically compressed hydrocarbons in the regime of carbon–hydrogen phase separation. With the help of time-dependent density functional theory calculations and scattering spectra from undriven carbon samples collected at the European x-ray Free-Electron Laser Facility (EuXFEL), we demonstrate sufficient data quality for observing C–H demixing and investigating the presence of liquid metallic hydrogen in future experiments using the reprated drive laser systems at EuXFEL.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Debris-induced consequences on turbulence and vorticity in solar photovoltaic module-generated array wakes

Particle-laden flows in solar photovoltaic (PV) systems are inevitable, where wind-swept debris in open environments are carried by high winds and turbulence, coating panel surfaces or damaging structures. Particle deposition, or soiling, is a well-known issue for large-scale plants which rely on uninhibited solar rays for optimal production. But understanding the mechanisms leading to soiling requires a physical and fluid dynamics-centered focus, since turbulence dominates PV panel wakes and is also known to alter particle concentration and trajectories. This study presents an experimental campaign toward consequences of particle-laden flow between two model PV panels using time-resolved particle image velocimetry. The model array was subjected to varied particle volume fractions, including a tracer particle case and a water droplet case. Characterization of mean velocity, turbulence statistics, and mean kinetic energy within the single phase and, separately, particle phase flows showed modified features due to particle inertia. Images captured at a frequency of 1 kHz in the near wake of the upstream panel allow for a first experimental look at vorticity and convective velocity of vortex structures for single-phase and particle-phase flows which are crucial to debris transport and soiling in PV environments.

Energy & Fuels↗

Dynamic density functional theory of polymers with salt in electric fields

Here we present a dynamic density functional theory for modeling the effects of applied electric fields on the local structure of polymers with added salt (polymer electrolytes). Time-dependent equations for the local electrostatic potential and volume fractions of polymer, cation, and anion of added salt are developed using the principles of linear irreversible thermodynamics. For such a development, a field theoretic description of the free energy of polymer melts doped with salts is used, which captures the effects of local variations in the dielectric function. Connections of the dynamic density functional theory with experiments are established by relating the three phenomenological Onsager’s transport coefficients of the theory to the mutual diffusion of electrolyte, ionic conductivity, and transference number of one of the ions. The theory is connected with a statistical mechanical model developed by Bearman and Kirkwood [J. Chem. Phys. 28, 136 (1958)] after relating the three transport coefficients to friction coefficients. The steady-state limit of the dynamic density functional theory is used to understand the effects of dielectric inhomogeneity on the phase separation in polymer electrolytes. The theory developed here provides not only a way to connect with experiments but also to develop multi-scale models for studying connections between local structure and ion transport in polymer electrolytes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Epitaxial (Al x Ga 1-x-y In y ) 2 O 3 Alloys Lattice Matched to Monoclinic Ga 2 O 3 Substrates

We have epitaxially stabilized a series of monoclinic (Al x Ga 1-x-y In y ) 2 O 3 alloys by careful choice of molecular beam epitaxy growth conditions, which balance alloy growth with suboxide desorption. The films are pseudomorphic to (010) β-Ga 2 O 3 substrates at thicknesses up to 150 nm with compositions ranging from (Al 0.01 Ga 0.83 In 0.16 ) 2 O 3 to (Al 0.24 Ga 0.75 In 0.03 ) 2 O 3 . The absorption edge shifts from approximately 4.62-5.14 eV with coincidently increasing Al and decreasing In mole fractions. J-V measurements reveal an increase in resistivity over four orders of magnitude with a maximum value of 4.2 x 10 5 Ω-cm for (Al 0.17 Ga 0.76 In 0.07 ) 2 O 3 , which has nearly identical lattice parameters (both in-plane and out-of-plane) to the underlying β-Ga 2 O 3 . Scanning transmission electron microscopy of this sample reveals a mostly uniform and single crystalline film, though we identify areas of non-uniform In incorporation and some γ-phase inclusions. This work demonstrates the feasibility of thick layers lattice-matched to β-Ga 2 O 3 with increased bandgap compared to phase-separation limited (Al,Ga) 2 O 3 . These alloys can enable higher bandgap epitaxial dielectrics and high sheet charge density transistors by increasing the conduction band offset with respect to β-Ga 2 O 3 .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Spherical and sessile droplet dynamics by fluctuating hydrodynamics

We simulate the mesoscopic dynamics of droplets formed by phase-separated fluids at nanometer scales where thermal fluctuations are significant. Both spherical droplets fully immersed in a second fluid and sessile droplets which are also in contact with a solid surface are studied. Our model combines a Cahn–Hilliard formulation with incompressible fluctuating hydrodynamics; for sessile droplets, the fluid–solid contact angle is specified as a boundary condition. Deterministic simulations with an applied body force are used to measure the droplets' mobility from which a diffusion coefficient is obtained using the Einstein relation. Stochastic simulations are independently used to obtain a diffusion coefficient from a linear fit of the variance of a droplet's position with time. In some scenarios, these two measurements give the same value but not in the case of a spherical droplet initialized near a slip wall or in the case of sessile droplets with large contact angles (≥90°) on both slip and no-slip surfaces.

Bell, John B↗

Machine-learning force-field models for dynamical simulations of metallic magnets

We review recent advances in machine-learning (ML) force-field methods for Landau–Lifshitz–Gilbert simulations of itinerant electron magnets, focusing on their scalability and transferability. Built on the principle of locality, a deep neural-network model is developed to efficiently and accurately predict electron-mediated forces governing spin dynamics. Symmetry-aware descriptors constructed through a group-theoretical approach ensure rigorous incorporation of both lattice and spin-rotation symmetries. The framework is demonstrated using the prototypical s-d exchange model widely employed in spintronics. ML-enabled large-scale simulations reveal novel nonequilibrium phenomena, including anomalous coarsening of tetrahedral spin order on the triangular lattice and the freezing of phase-separation dynamics in lightly hole-doped, strong-coupling square-lattice systems. These results establish ML force-field frameworks as scalable, accurate, and versatile tools for modeling nonequilibrium spin dynamics in itinerant magnets.

Artificial neural networks↗

Four-dimensional chromosome reconstruction elucidates the spatiotemporal reorganization of the mammalian X chromosome

Significance Breakthrough technological advances such as Hi-C have enabled large-scale sequencing of pairwise genomic contacts. However, translating the 2D contacts to 3D spatial models remains challenging. Here we develop the “4DHiC” modeling method to infer 3D information from 2D datasets across time and construct a 3D model of the inactive X-chromosome (Xi). Our model not only demonstrates a spatial phase-separation between A/B and S1/S2 compartments to form “hemispheres,” but also reveals persistent smaller-scale structures hidden under the Xi superstructure. We also simulate Xist RNA spreading dynamics and deduce that the RNA spreads between hemispheres via both surface and core to establish the Xi. Our 4DHiC will serve a growing demand for data-driven methodologies that extract spatial information from biochemical interaction data.

Lappala, Anna↗

Collective behavior of “flexicles”

In recent years the functionality of synthetic active microparticles has edged even closer to that of their biological counterparts. However, we still lack the understanding needed to recreate at the microscale key features of autonomous behavior exhibited by microorganisms or swarms of macroscopic robots. In this study, we propose a model for a three-dimensional deformable cellular composite particle consisting of self-propelled rod-shaped colloids confined within a flexible vesicle—representing a superstructure we call a “flexicle” that couples particle deformation to the internal dynamics of the internal active components. Using molecular dynamics simulations, we investigate the collective behavior of dense systems composed of many flexicles. We show that individual flexicles exhibit shape changes upon collisions with other flexicles that lead to rearrangements of the internal active rods, which slows flexicle motion. This shape deformability gives rise to a diverse set of motility-induced phase separation phenomena and the spontaneous flow of flexicles reminiscent of the migration of cells in dense tissues. Our findings establish a foundation for designing responsive, cell-like active particles and developing strategies for controlling swarm migration and other autonomous swarm behaviors at cellular and colloidal scales.

Science & Technology - Other Topics↗

Hard x-ray methods for studying the structure of amorphous thin films and bulk glassy oxides

High-energy photon diffraction minimizes many of the corrections associated with laboratory x-ray diffractometers, and enables structure factor measurements to be made over a wide range of momentum transfers. The method edges us closer toward an ideal experiment, in which coordination numbers can be extracted without knowledge of the sample density. Three case studies are presented that demonstrate new hard x-ray methods for studying the structure of glassy and amorphous materials. First, the methodology and analysis of high-energy grazing incidence on thin films is discussed for the case of amorphous In 2 O 3 . Additionally, the connectivity of irregular InO 6 polyhedra are shown to exist in face-, edge- and corner-shared configurations in the approximate ratio of 1:2:3. Secondly, the technique of high-energy small and wide angle scattering has been carried out on laser heated and aerodynamically levitated samples of silica-rich barium silicate (20BaO:80SiO 2 ), from the single phase melt at 1500 C-o to the phase separated glass at room temperature. Based on Ba-O coordination numbers of 6 to 7, it is argued that the although the potential of Ba is ionic, it is weak enough to cause the liquid-liquid immiscibility to become metastable. Lastly, high-energy small and wide angle scattering has also been applied to high water content (up to 12 wt.%) samples of hydrous SiO 2 glass quenched from 1500 C-o at 4 GPa. An increase of Si 1 O 2 correlations at 4.3 angstrom is found to be consistent with an increase in the population of three-membered SiO 4 rings at the expense of larger rings.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Overview and status of the Long-Baseline Neutrino Facility Far Site cryogenics system

The Sanford Underground Research Facility (SURF) will host the Far Detector of the Deep Underground Neutrino Experiment (DUNE), an international multi-kiloton Long-Baseline neutrino experiment that will be installed about one and a half kilometers underground in Lead, SD. Detectors will be located inside four cryostats filled with almost 70,000 metric tons of ultrapure liquid argon, with a level of impurities lower than 100 parts per trillion of oxygen equivalent contamination. The cryogenics infrastructure supporting this experiment is provided by the Long-Baseline Neutrino Facility (LBNF). This contribution presents modes of operation, layout, and main features of the LBNF Far Site cryogenic system, which is composed of three subsystems: Infrastructure, Proximity, and Internal cryogenics. The Infrastructure cryogenics supports the needs of the cryostat and Proximity cryogenics. It includes the equipment to receive the argon in liquid phase, vaporize it and transfer it underground as a gas, the nitrogen system (composed of the refrigeration system, liquid nitrogen buffer tanks and liquid and gaseous nitrogen distribution), liquid and gaseous argon distribution and process controls. The Proximity cryogenics receives fluids from the Infrastructure cryogenics and delivers them to the Internal cryogenics at the required temperature, pressure, purity and mass flow rate. It includes the argon condensers, liquid and gaseous argon purification and regeneration systems, nitrogen and argon phase separators, piping, valves, and instrumentation. The Internal cryogenics comprises the liquid and gaseous argon distribution inside the cryostats for the commissioning, cool down, fill, and steady state operations of the cryostats and detectors. An international engineering team is designing these systems and will manufacture, install, commission, and qualify them. This contribution describes the main features, performance, functional requirements, and modes of operation of the LBNF Far Site cryogenics system. It also presents the status of the design, along with present and future needs to support the DUNE experiment.

43 PARTICLE ACCELERATORS↗

Ensemble Kalman inversion of induced polarization data

SUMMARY This paper explores the applicability of ensemble Kalman inversion (EKI) with level-set parametrization for solving geophysical inverse problems. In particular, we focus on its extension to induced polarization (IP) data with uncertainty quantification. IP data may provide rich information on characteristics of geological materials due to its sensitivity to characteristics of the pore–grain interface. In many IP studies, different geological units are juxtaposed and the goal is to delineate these units and obtain estimates of unit properties with uncertainty bounds. Conventional inversion of IP data does not resolve well sharp interfaces and tends to reduce and smooth resistivity variations, while not readily providing uncertainty estimates. Recently, it has been shown for DC resistivity that EKI is an efficient solver for inverse problems which provides uncertainty quantification, and its combination with level set parametrization can delineate arbitrary interfaces well. In this contribution, we demonstrate the extension of EKI to IP data using a sequential approach, where the mean field obtained from DC resistivity inversion is used as input for a separate phase angle inversion. We illustrate our workflow using a series of synthetic and field examples. Variations with uncertainty bounds in both DC resistivity and phase angles are recovered by EKI, which provides useful information for hydrogeological site characterization. Although phase angles are less well-resolved than DC resistivity, partly due to their smaller range and higher percentage data errors, it complements DC resistivity for site characterization. Overall, EKI with level set parametrization provides a practical approach forward for efficient hydrogeophysical imaging under uncertainty.

Geochemistry & Geophysics↗

Mechanism of efficient double-strand break repair by a long non-coding RNA

Mechanistic studies in DNA repair have focused on roles of multi-protein DNA complexes, so how long non-coding RNAs (lncRNAs) regulate DNA repair is less well understood. Yet, lncRNA LINP1 is over-expressed in multiple cancers and confers resistance to ionizing radiation and chemotherapeutic drugs. Here, we unveil structural and mechanistic insights into LINP1’s ability to facilitate non-homologous end joining (NHEJ). We characterized LINP1 structure and flexibility and analyzed interactions with the NHEJ factor Ku70/Ku80 (Ku) and Ku complexes that direct NHEJ. LINP1 self-assembles into phase-separated condensates via RNA–RNA interactions that reorganize to form filamentous Ku-containing aggregates. Structured motifs in LINP1 bind Ku, promoting Ku multimerization and stabilization of the initial synaptic event for NHEJ. Significantly, LINP1 acts as an effective proxy for PAXX. Collective results reveal how lncRNA effectively replaces a DNA repair protein for efficient NHEJ with implications for development of resistance to cancer therapy.

59 BASIC BIOLOGICAL SCIENCES↗

A phage nucleus-associated RNA-binding protein is required for jumbo phage infection

Abstract Large-genome bacteriophages (jumbo phages) of the proposed family Chimalliviridae assemble a nucleus-like compartment bounded by a protein shell that protects the replicating phage genome from host-encoded restriction enzymes and DNA-targeting CRISPR-Cas nucleases. While the nuclear shell provides broad protection against host nucleases, it necessitates transport of mRNA out of the nucleus-like compartment for translation by host ribosomes, and transport of specific proteins into the nucleus-like compartment to support DNA replication and mRNA transcription. Here, we identify a conserved phage nuclear shell-associated protein that we term Chimallin C (ChmC), which adopts a nucleic acid-binding fold, binds RNA with high affinity in vitro, and binds phage mRNAs in infected cells. ChmC also forms phase-separated condensates with RNA in vitro. Targeted knockdown of ChmC using mRNA-targeting dCas13d results in accumulation of phage-encoded mRNAs in the phage nucleus, reduces phage protein production, and compromises virion assembly. Taken together, our data show that the conserved ChmC protein plays crucial roles in the viral life cycle, potentially by facilitating phage mRNA translocation through the nuclear shell to promote protein production and virion development.

59 BASIC BIOLOGICAL SCIENCES↗