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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Integrative visualization of the molecular structure of a cellular microdomain

Abstract An integrative approach to visualization is used to create a visual snapshot of the structural biology of the polar microdomain of Caulobacter crescentus . The visualization is based on the current state of molecular and cellular knowledge of the microdomain and its cellular context. The collaborative process of researching and executing the visualization has identified aspects that are well determined and areas that require further study. The visualization is useful for dissemination, education, and outreach, and the study lays the groundwork for future 3D modeling and simulation of this well‐studied example of a cellular condensate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

HDX–MS finds that partial unfolding with sequential domain activation controls condensation of a cellular stress marker

Eukaryotic cells form condensates to sense and adapt to their environment [S. F. Banani, H. O. Lee, A. A. Hyman, M. K. Rosen,Nat. Rev. Mol. Cell Biol.18, 285–298 (2017), H. Yoo, C. Triandafillou, D. A. Drummond,J. Biol. Chem.294, 7151–7159 (2019)]. Poly(A)-binding protein (Pab1), a canonical stress granule marker, condenses upon heat shock or starvation, promoting adaptation [J. A. Ribacket al.,Cell168, 1028–1040.e19 (2017)]. The molecular basis of condensation has remained elusive due to a dearth of techniques to probe structure directly in condensates. We apply hydrogen–deuterium exchange/mass spectrometry to investigate the mechanism of Pab1’s condensation. Pab1’s four RNA recognition motifs (RRMs) undergo different levels of partial unfolding upon condensation, and the changes are similar for thermal and pH stresses. Although structural heterogeneity is observed, the ability of MS to describe populations allows us to identify which regions contribute to the condensate’s interaction network. Our data yield a picture of Pab1’s stress-triggered condensation, which we term sequential activation (Fig. 1A), wherein each RRM becomes activated at a temperature where it partially unfolds and associates with other likewise activated RRMs to form the condensate. Subsequent association is dictated more by the underlying free energy surface than specific interactions, an effect we refer to as thermodynamic specificity. Our study represents an advance for elucidating the interactions that drive condensation. Furthermore, our findings demonstrate how condensation can use thermodynamic specificity to perform an acute response to multiple stresses, a potentially general mechanism for stress-responsive proteins.

Science & Technology - Other Topics↗
DOE OSTI2021

Designer membraneless organelles sequester native factors for control of cell behavior

Subcellular compartmentalization of macromolecules increases flux and prevents inhibitory interactions to control biochemical reactions. Inspired by this functionality, we sought to build designer compartments that function as hubs to regulate the flow of information through cellular control systems. Here we report a synthetic membraneless organelle platform to control endogenous cellular activities through sequestration and insulation of native proteins. We engineer and express a disordered protein scaffold to assemble micron size condensates and recruit endogenous clients via genomic tagging with high-affinity dimerization motifs. By relocalizing up to ninety percent of a targeted enzymes to synthetic condensates, we efficiently control cellular behaviors, including proliferation, division, and cytoskeletal organization. Further, we demonstrate multiple strategies for controlled cargo release from condensates to switch cells between functional states. These synthetic organelles offer a powerful and generalizable approach to modularly control cell decision-making in a variety of model systems with broad applications for cellular engineering.

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

Incorporation and Assembly of a Light-Emitting Enzymatic Reaction into Model Protein Condensates

Eukaryotic cells partition enzymes and other cellular components into distinct subcellular compartments to generate specialized biochemical niches. A subclass of these compartments form in the absence of lipid membranes, via liquid-liquid phase separation of proteins to form biomolecular condensates or “membraneless organelles” such as nucleoli, stress granules, and P-bodies. Because of their ability to form compartments from simple starting materials, membraneless organelles are an attractive target for engineering new functionalities in both living cells and protocells. In this work, we demonstrate incorporation of novel enzymatic activity in protein coacervates with a light-generating enzyme, NanoLuc, to produce bioluminescence. Using condensates comprised of the disordered RGG domain of C. elegans LAF-1, we show functionalization of condensates with enzymatic activity in vitro and that localization to protein coacervates enhances the assembly and activity of split enzymes. To build condensates that function as light emitting reactors, we designed a NanoLuc enzyme flanked by RGG domains. Furthermore, the resulting condensates concentrated NanoLuc by 10-fold over bulk solution and display significantly increased net reaction rates. We further show that condensate viscosity impacts light emission due to diffusion-limited behavior. By splitting NanoLuc enzyme into its constituent components, we demonstrate that NanoLuc activity can be reconstituted via co-condensation. Further, we demonstrate control of the spatial localization of enzyme within condensates by targettng NanoLuc to the surface of in vitro condensates. Collectively, this work demonstrates that membraneless organelles can be endowed with localized enzymatic activity, and that this activity can be spatially and temporally controlled via enzyme reconstitution and design of protein surfactants.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

p14 ARF forms meso-scale assemblies upon phase separation with NPM1

NPM1 is an abundant nucleolar chaperone that, in addition to facilitating ribosome biogenesis, contributes to nucleolar stress responses and tumor suppression through its regulation of the p14 Alternative Reading Frame tumor suppressor protein (p14 ARF ). Oncogenic stress induces p14 ARF to inhibit MDM2, stabilize p53 and arrest the cell cycle. Under non-stress conditions, NPM1 stabilizes p14 ARF in nucleoli, preventing its degradation and blocking p53 activation. However, the mechanisms underlying the regulation of p14 ARF by NPM1 are unclear because the structural features of the p14 ARF -NPM1 complex were elusive. Here we show that p14 ARF assembles into a gel-like meso-scale network upon phase separation with NPM1. This assembly is mediated by intermolecular contacts formed by hydrophobic residues in an α-helix and β-strands within a partially folded N-terminal portion of p14 ARF . These hydrophobic interactions promote phase separation with NPM1, enhance p14 ARF nucleolar partitioning, restrict NPM1 diffusion within condensates and nucleoli, and reduce cellular proliferation. Our structural analysis provides insights into the multifaceted chaperone function of NPM1 in nucleoli by mechanistically linking the nucleolar localization of p14 ARF to its partial folding and meso-scale assembly upon phase separation with NPM1.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Structural Heterogeneity and Hydrodynamics of an Intrinsically Disordered Protein Condensate

Biology demonstrates precise control over the free-energy landscape through the selective partitioning of biomacromolecules into membraneless organelles, enabling essential functions such as biochemical transformations, signaling cascades, and mechanical reinforcement. Although the function of these condensates depends on their underlying structure and hydrodynamics, molecular-scale information on these systems remains sparse. Here, in this study, neutron scattering is used to probe the organization and dynamics of the intrinsically disordered N-terminal domain of Galectin-3, an extracellular lectin responsible for facilitating liquid–liquid phase separation on the cellular surface, in both dilute and condensed phases. Dilute solutions contain isolated protein chains in equilibrium with mesoscopic clusters, whereas the condensed phase adopts a bicontinuous, microemulsion-like morphology. The dilute phase behavior is quantitatively described by coarse-grained polymer models from soft-matter physics, demonstrating their predictive power for complex biological proteins. At elevated concentrations, the proteins self-assemble akin to block copolymers, microphase separating through the aggregation of hydrophobic domains along the protein contour. The resulting condensate remains fluid-like despite a 25-fold increase in concentration; its internal hydrodynamics slow by only a factor of 3 relative to dilute protein chains. These results provide a molecular-level framework for how disordered proteins achieve both the structural complexity and dynamic fluidity of biomolecular condensates.

Carrick, Brian R. [Massachusetts Inst. of Technolo↗
DOE OSTI2022

Fracton Hydrodynamics without Time-Reversal Symmetry

Here, we present an effective field theory for the nonlinear fluctuating hydrodynamics of a single conserved charge with or without time-reversal symmetry, based on the Martin-Siggia-Rose formalism. Applying this formalism to fluids with only charge and multipole conservation, and with broken time-reversal symmetry, we predict infinitely many new dynamical universality classes, including some with arbitrarily large upper critical dimensions. Using large scale simulations of classical Markov chains, we find numerical evidence for a breakdown of hydrodynamics in quadrupole-conserving models with broken time-reversal symmetry in one spatial dimension. Our framework can be applied to the hydrodynamics around stationary states of open systems, broadening the applicability of previously developed ideas and methods to a wide range of systems in driven and active matter.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Evaluation of the Thermal and Moisture Performance of Insulating Shades

Heat transfer through windows accounts for a significant percentage of a building’s energy use and adds substantially to the peak heating and cooling loads of a home. Over the past 20 years, residential window attachment retrofit technologies have been developed that significantly increase the number of options available to home builders, homeowners, and utilities when considering upgrades of overall window performance. Within the interior window attachments category, honeycomb cellular shades typically have the highest R-values because of their layered or concentric designs. During the winter when the window is fully covered, however, the added insulation reduces the amount of warm indoor air that reaches the window surface, thereby lowering the temperature of the window glass and frame and increasing the potential for condensation to collect on the interior surface of the window. The degree to which this potential is realized depends on the indoor and outdoor conditions as well as the overall thermal resistance of the window and the shades. To examine the condensation buildup potential on the interior surface of the window and the conditions under which this occurs, this report describes experimental research conducted by Pacific Northwest National Laboratory in collaboration with Hunter Douglas, using a a controlled environmental test chamber at the Hunter Douglas facility in Broomfield, Colorado. The results will be used to inform the Attachments Energy Rating Council, which provides energy performance information on all rated window attachments products.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2023

Fredkin Staircase: An Integrable System with a Finite-Frequency Drude Peak

We introduce and explore an interacting integrable cellular automaton, the Fredkin staircase, that lies outside the existing classification of such automata, and has a structure that seems to lie beyond that of any existing Bethe-solvable model. The Fredkin staircase has two families of ballistically propagating quasiparticles, each with infinitely many species. Despite the presence of ballistic quasiparticles, charge transport is diffusive in the d.c. limit, albeit with a highly non- gaussian dynamic structure factor. Remarkably, this model exhibits persistent temporal oscillations of the current, leading to a delta-function singularity (Drude peak) in the a.c. conductivity at nonzero frequency. Here, we analytically construct an extensive set of operators that anticommute with the time-evolution operator; the existence of these operators both demonstrates the integrability of the model and allows us to lower-bound the weight of this finite-frequency singularity.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Tau and Membranes: Interactions That Promote Folding and Condensation

Tau misfolding and assembly is linked to a number of neurodegenerative diseases collectively described as tauopathies, including Alzheimer’s disease (AD) and Parkinson’s disease. Anionic cellular membranes, such as the cytosolic leaflet of the plasma membrane, are sites that concentrate and neutralize tau, primarily due to electrostatic interactions with tau’s microtubule binding repeat domain (RD). In addition to electrostatic interactions with lipids, tau also has interactions with membrane proteins, which are important for tau’s cellular functions. Tau also interacts with lipid tails to facilitate direct translocation across the membrane and can form stable protein-lipid complexes involved in cell-to-cell transport. Concentrated tau monomers at the membrane surface can form reversible condensates, change secondary structures, and induce oligomers, which may eventually undergo irreversible crosslinking and fibril formation. These β-sheet rich tau structures are capable of disrupting membrane organization and are toxic in cell-based assays. Given the evidence for relevant membrane-based tau assembly, we review the emerging hypothesis that polyanionic membranes may serve as a site for phase-separated tau condensation. Membrane-mediated phase separation may have important implications for regulating tau folding/misfolding, and may be a powerful mechanism to spatially direct tau for native membrane-mediated functions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Quantum many-body scars from Einstein-Podolsky-Rosen states in bilayer systems

Quantum many-body scar states are special eigenstates of nonintegrable models with distinctive entanglement features that give rise to infinitely long-lived coherent dynamics under quantum quenches from certain initial states. Here, we elaborate on a construction of quantum many-body scar states in which they emerge from Einstein-Podolsky-Rosen states in systems with two layers, wherein the two layers are maximally entangled. We apply this construction to spin systems as well as systems of itinerant fermions and bosons and demonstrate how symmetries can be harnessed to enhance its versatility. We show that several well-known examples of quantum many-body scars, including the tower of states in the spin-1 XY model and the η-pairing states in the Fermi-Hubbard model, can be understood within this formalism. We also demonstrate how an infinite tower of many-body scar states can emerge in bilayer Bose-Hubbard models with charge conservation.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Fracton phases via exotic higher-form symmetry-breaking

We study p-string condensation mechanisms for fracton phases from the viewpoint of higher-form symmetry, focusing on the examples of the X-cube model and the rank-two symmetric-tensor scalar charge theory. This work is motivated by questions of the relationship between fracton phases and continuum quantum field theories, and also provides general principles to describe p-string condensation independent of specific lattice model constructions. We give a perspective on higher-form symmetry in lattice models in terms of cellular homology. Applying this perspective to the coupled-layer construction of the X-cube model, we identify a foliated 1-form symmetry that is broken in the X-cube phase, but preserved in the phase of decoupled toric code layers. Similar considerations for the scalar charge theory lead to a framed 1-form symmetry. These symmetries are distinct from standard 1-form symmetries that arise, for instance, in relativistic quantum field theory. Here, we also give a general discussion on interpreting p-string condensation, and related constructions involving gauging of symmetry, in terms of higher-form symmetry.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Nonlocal Finite-Depth Circuits for Constructing Symmetry-Protected Topological States and Quantum Cellular Automata

Whether a given target state can be prepared by starting with a simple product state and acting with a finite-depth quantum circuit is a key question in condensed matter physics and quantum information science. It underpins classifications of topological phases, as well as the understanding of topological quantum codes, and has obvious relevance for device implementations. Traditionally, this question assumes that the quantum circuit is made up of unitary gates that are . Inspired by the advent of noisy intermediate-scale quantum devices, we reconsider this question with k - gates, i.e., gates that act on no more than k degrees of freedom but are not restricted to be geometrically local. First, we construct explicit finite-depth circuits of symmetric k -local gates that create symmetry-protected topological (SPT) states from an initial product state. Our construction applies to SPT states protected by global symmetries or subsystem symmetries but not to those with higher-form symmetries, which we conjecture remain nontrivial. Next, we show how to implement arbitrary translationally invariant quantum cellular automata in any dimension using finite-depth circuits of k -local gates. These results imply that the topological classifications of SPT phases and quantum cellular automata both collapse to a single trivial phase in the presence of k -local interactions. We furthermore argue that SPT phases are fragile to k -local symmetric perturbations. We conclude by discussing the implications for other phases, such as fracton phases, and surveying future directions. Our analysis opens a new experimentally motivated conceptual direction examining the stability of phases and the feasibility of state preparation without the assumption of geometric locality. Published by the American Physical Society 2024

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Covalent Drug Binding in Live Cells Monitored by Mid-Infrared Quantum Cascade Laser Spectroscopy: Photoactive Yellow Protein as a Model System

The detection of drug-target interactions in live cells enables analysis of therapeutic compounds in a native cellular environment. Recent advances in spectroscopy and molecular biology have facilitated the development of genetically encoded vibrational probes like nitriles that can sensitively report on molecular interactions. Nitriles are powerful tools for measuring electrostatic environments within condensed media like proteins, but such measurements in live cells have been hindered by low signal-to-noise ratios. In this study, we design a spectrometer based on a double-beam quantum cascade laser (QCL)-based transmission infrared (IR) source with balanced detection that can significantly enhance sensitivity to nitrile vibrational probes embedded in proteins within cells compared to a conventional FTIR spectrometer. Here, using this approach, we detect small-molecule binding in Escherichia coli, with particular focus on the interaction between para-Coumaric acid (pCA) and nitrile-incorporated photoactive yellow protein (PYP). This system effectively serves as a model for investigating covalent drug binding in a cellular environment. Notably, we observe large spectral shifts of up to 15 cm –1 for nitriles embedded in PYP between the unbound and drug-bound states directly within bacteria, in agreement with observations for purified proteins. Such large spectral shifts are ascribed to the changes in the hydrogen-bonding environment around the local environment of nitriles, accurately modeled through high-level molecular dynamics simulations using the AMOEBA force field. Our findings underscore the QCL spectrometer’s ability to enhance sensitivity for monitoring drug–protein interactions, offering new opportunities for advanced methodologies in drug development and biochemical research.

chromophores↗
DOE OSTI2026

Dynamic crushing of metal lattice metamaterials: Shock mode diagrams and transition to topology-independent compaction regime

Additively manufactured lattice metamaterials offer design versatility in strength and energy absorption and provide an additional degree of freedom through the selection of the lattice topology. Under quasistatic loading, the unit cell structure can strongly affect the stiffness, yield, and post-yield behavior, but whether and to what degree the effect of lattice topology persists into dynamic loading scenarios, up to the compaction shock regime, has not been established. LLNL’ s ALE3D hydrocode was used to perform a computational investigation of dynamic loading in multiple lattice types, including the gyroid, octet, Schwarz D, and rhombic dodecahedron, under impact velocities from 0.25 to 2.25 km/s. Shock Hugoniots for each lattice topology are generated and compared, suggesting that above a critical velocity, distinctions between architectures may not persevere and compacted lattices behave similarly. Here, to investigate the transition between topology-dependent quasistatic compression and the topology-independent regime above the critical velocity, a one-dimensional elastic-linear hardening plasticity-densified solid (E-LHP-DS) shock model for lattice materials was developed that relies upon confined compression to link the quasistatic and shock mechanics. Unlike similar works, the model does not assume rigid behavior prior to yield or locking behavior at densification, allowing a richer exploration of lattice mechanics. With only six parameters, the analytical model simultaneously fit quasistatic confined compression simulations for relative densities 0.1 $≤ \bar{ρ} ≤$ 0.9 and predicted dynamic compaction behavior to traverse several distinct shock modes, each defined by a critical impact speed (equivalently, critical stresses). Comparing the numerical results to the one-dimensional E-LHP-DS shock model predictions suggests that the topology-independence under strong shocks is linked to the onset of densification, which can be predicted based on quasistatic confined compression results.

Cellular material↗
DOE OSTI2021

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

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

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

Out of the Dark and Into the Light: A New View of Phytochrome Photobodies

Light is a critical environmental stimulus for plants, serving as an energy source via photosynthesis and a signal for developmental programming. Plants perceive light through various light-responsive proteins, termed photoreceptors. Phytochromes are red-light photoreceptors that are highly conserved across kingdoms. In the model plant Arabidopsis thaliana , phytochrome B serves as a light and thermal sensor, mediating physiological processes such as seedling germination and establishment, hypocotyl growth, chlorophyll biogenesis, and flowering. In response to red light, phytochromes convert to a biologically active form, translocating from the cytoplasm into the nucleus and further compartmentalizes into subnuclear compartments termed photobodies. PhyB photobodies regulate phytochrome-mediated signaling and physiological outputs. However, photobody function, composition, and biogenesis remain undefined since their discovery. Based on photobody cellular dynamics and the properties of internal components, photobodies have been suggested to undergo liquid-liquid phase separation, a process by which some membraneless compartments form. Here, we explore photobodies as environmental sensors, examine the role of their protein constituents, and outline the biophysical perspective that photobodies may be undergoing liquid-liquid phase separation. Understanding the molecular, cellular, and biophysical processes that shape how plants perceive light will help in engineering improved sunlight capture and fitness of important crops.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Combinatorial gene inactivation of aldehyde dehydrogenases mitigates aldehyde oxidation catalyzed by E. coli resting cells

Aldehydes are attractive chemical targets both as end products in the flavors and fragrances industry and as synthetic intermediates due to their propensity for C–C bond formation. Here, in this study, we identify and address unexpected oxidation of a model collection of aromatic aldehydes, including many that originate from biomass degradation. When diverse aldehydes are supplemented to E. coli cells grown under aerobic conditions, as expected they are either reduced by the wild-type MG1655 strain or stabilized by a strain engineered for reduced aromatic aldehyde reduction (the E. coli RARE strain). Surprisingly, when these same aldehydes are supplemented to resting cell preparations of either E. coli strain, under many conditions we observe substantial oxidation. By performing combinatorial inactivation of six candidate aldehyde dehydrogenase genes in the E. coli genome using multiplexed automatable genome engineering (MAGE), we demonstrate that this oxidation can be substantially slowed, with greater than 50% retention of 6 out of 8 aldehydes when assayed 4 h after their addition. Given that our newly engineered strain exhibits reduced oxidation and reduction of aromatic aldehydes, we dubbed it the E. coli ROAR strain. We applied the new strain to resting cell biocatalysis for two kinds of reactions – the reduction of 2-furoic acid to furfural and the condensation of 3-hydroxybenzaldehyde and glycine to form a non-standard β-hydroxy-α-amino acid. In each case, we observed substantial improvements in product titer 20 h after reaction initiation (9-fold and 10-fold, respectively). Moving forward, the use of this strain to generate resting cells should allow aldehyde product isolation, further enzymatic conversion, or chemical reactivity under cellular contexts that better accommodate aldehyde toxicity.

59 BASIC BIOLOGICAL SCIENCES↗