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At least 1,027 records · Page 57
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Down-selection of biomolecules to assemble “reverse micelle” with perovskites

Abstract Biological molecule-semiconductor interfacing has triggered numerous opportunities in applied physics such as bio-assisted data storage and computation, brain-computer interface, and advanced distributed bio-sensing. The introduction of electronics into biological embodiment is being quickly developed as it has great potential in providing adaptivity and improving functionality. Reciprocally, introducing biomaterials into semiconductors to manifest bio-mimetic functionality is impactful in triggering new enhanced mechanisms. In this study, we utilize the vulnerable perovskite semiconductors as a platform to understand if certain types of biomolecules can regulate the lattice and endow a unique mechanism for stabilizing the metastable perovskite lattice. Three tiers of biomolecules have been systematically tested and the results reveal a fundamental mechanism for the formation of a “reverse-micelle” structure. Systematic exploration of a large set of biomolecules led to the discovery of guiding principle for down-selection of biomolecules which extends the classic emulsion theory to this hybrid systems. Results demonstrate that by introducing biomaterials into semiconductors, natural phenomena typically observed in biological systems can also be incorporated into semiconducting crystals, providing a new perspective to engineer existing synthetic materials.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Kinetically controlled metal-elastomer nanophases for environmentally resilient stretchable electronics

Nanophase mixtures, leveraging the complementary strengths of each component, are vital for composites to overcome limitations posed by single elemental materials. Among these, metal-elastomer nanophases are particularly important, holding various practical applications for stretchable electronics. However, the methodology and understanding of nanophase mixing metals and elastomers are limited due to difficulties in blending caused by thermodynamic incompatibility. Here, we present a controlled method using kinetics to mix metal atoms with elastomeric chains on the nanoscale. We find that the chain migration flux and metal deposition rate are key factors, allowing the formation of reticular nanophases when kinetically in-phase. Moreover, we observe spontaneous structural evolution, resulting in gyrified structures akin to the human brain. The hybridized gyrified reticular nanophases exhibit strain-invariant metallic electrical conductivity up to 156% areal strain, unparalleled durability in organic solvents and aqueous environments with pH 2–13, and high mechanical robustness, a prerequisite for environmentally resilient devices.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Structural insights into GABA A receptor potentiation by Quaalude

Methaqualone, a quinazolinone marketed commercially as Quaalude, is a central nervous system depressant that was used clinically as a sedative-hypnotic, then became a notorious recreational drug in the 1960s-80s. Due to its high abuse potential, medical use of methaqualone was eventually prohibited, yet it persists as a globally abused substance. Methaqualone principally targets GABA A receptors, which are the major inhibitory neurotransmitter-gated ion channels in the brain. The restricted status and limited accessibility of methaqualone have contributed to its pharmacology being understudied. Here, we use cryo-EM to localize the GABA A receptor binding sites of methaqualone and its more potent derivative, PPTQ, to the same intersubunit transmembrane sites targeted by the general anesthetics propofol and etomidate. Both methaqualone and PPTQ insert more deeply into subunit interfaces than the previously-characterized modulators. Binding of quinazolinones to this site results in widening of the extracellular half of the ion-conducting pore, following a trend among positive allosteric modulators in destabilizing the hydrophobic activation gate in the pore as a mechanism for receptor potentiation. These insights shed light on the underexplored pharmacology of quinazolinones and further elucidate the molecular mechanisms of allosteric GABA A receptor modulation through transmembrane binding sites.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Diversity of visual inputs to Kenyon cells of the Drosophila mushroom body

The arthropod mushroom body is well-studied as an expansion layer representing olfactory stimuli and linking them to contingent events. However, 8% of mushroom body Kenyon cells in Drosophila melanogaster receive predominantly visual input, and their function remains unclear. Here, we identify inputs to visual Kenyon cells using the FlyWire adult whole-brain connectome. Input repertoires are similar across hemispheres and connectomes with certain inputs highly overrepresented. Many visual neurons presynaptic to Kenyon cells have large receptive fields, while interneuron inputs receive spatially restricted signals that may be tuned to specific visual features. Individual visual Kenyon cells randomly sample sparse inputs from combinations of visual channels, including multiple optic lobe neuropils. These connectivity patterns suggest that visual coding in the mushroom body, like olfactory coding, is sparse, distributed, and combinatorial. However, the specific input repertoire to the smaller population of visual Kenyon cells suggests a constrained encoding of visual stimuli.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Collective dynamics and long-range order in thermal neuristor networks

Abstract In the pursuit of scalable and energy-efficient neuromorphic devices, recent research has unveiled a novel category of spiking oscillators, termed “thermal neuristors.” These devices function via thermal interactions among neighboring vanadium dioxide resistive memories, emulating biological neuronal behavior. Here, we show that the collective dynamical behavior of networks of these neurons showcases a rich phase structure, tunable by adjusting the thermal coupling and input voltage. Notably, we identify phases exhibiting long-range order that, however, does not arise from criticality, but rather from the time non-local response of the system. In addition, we show that these thermal neuristor arrays achieve high accuracy in image recognition and time series prediction through reservoir computing, without leveraging long-range order. Our findings highlight a crucial aspect of neuromorphic computing with possible implications on the functioning of the brain: criticality may not be necessary for the efficient performance of neuromorphic systems in certain computational tasks.

Science & Technology - Other Topics↗
DOE OSTI2024

Fast and deep phosphoproteome analysis with the Orbitrap Astral mass spectrometer

Owing to its roles in cellular signal transduction, protein phosphorylation plays critical roles in myriad cell processes. That said, detecting and quantifying protein phosphorylation has remained a challenge. We describe the use of a novel mass spectrometer (Orbitrap Astral) coupled with data-independent acquisition (DIA) to achieve rapid and deep analysis of human and mouse phosphoproteomes. With this method, we map approximately 30,000 unique human phosphorylation sites within a half-hour of data collection. The technology is benchmarked to other state-of-the-art MS platforms using both synthetic peptide standards and with EGF-stimulated HeLa cells. We apply this approach to generate a phosphoproteome multi-tissue atlas of the mouse. Altogether, we detect 81,120 unique phosphorylation sites within 12 hours of measurement. With this unique dataset, we examine the sequence, structural, and kinase specificity context of protein phosphorylation. Finally, we highlight the discovery potential of this resource with multiple examples of phosphorylation events relevant to mitochondrial and brain biology.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

The neurobench framework for benchmarking neuromorphic computing algorithms and systems

Neuromorphic computing shows promise for advancing computing efficiency and capabilities of AI applications using brain-inspired principles. However, the neuromorphic research field currently lacks standardized benchmarks, making it difficult to accurately measure technological advancements, compare performance with conventional methods, and identify promising future research directions. This article presents NeuroBench, a benchmark framework for neuromorphic algorithms and systems, which is collaboratively designed from an open community of researchers across industry and academia. NeuroBench introduces a common set of tools and systematic methodology for inclusive benchmark measurement, delivering an objective reference framework for quantifying neuromorphic approaches in both hardware-independent and hardware-dependent settings. For latest project updates, visit the project website (neurobench.ai).

Yik, Jason [Harvard Univ., Cambridge, MA (United S↗
DOE OSTI2025

PCM1 coordinates centrosome asymmetry with polarized endosome dynamics to regulate daughter cell fate

Vertebrate radial glia progenitors (RGPs) balance self-renewal and differentiation through asymmetric cell division (ACD), which involves unequal centrosome inheritance. How centrosome asymmetry directs cell fate remains poorly understood. Here, we identify Pericentriolar material 1 (Pcm1) as a key player in this process. In zebrafish embryonic RGPs, Pcm1 is asymmetrically associated with Cep83, a mother centrosome marker. Using in vivo time-lapse imaging and nanoscale-resolution expansion microscopy, we detect Pcm1 on Notch ligand-containing endosomes, where it interacts–either directly or indirectly–with Par-3 and dynein. Loss of pcm1 disrupts endosome dynamics, increasing neuronal differentiation at the expense of RGP self-renewal. Mechanistically, Pcm1 facilitates the transition from Rab5b to Rab11a and promotes the assembly of Par-3 and dynein macromolecular complexes on recycling endosomes. Furthermore, we find conserved PARD3-PCM1-CEP83-RAB11 associations in human cortical brain organoids. Our findings uncover that Pcm1 links centrosome asymmetry to polarized endosome trafficking, thereby regulating RGP fate decisions.

Cell fate and cell lineage↗
DOE OSTI2026

Non-coding structural variants disrupt FOXG1 transcriptional regulation in early neurodevelopment

The FOXG1 transcription factor is a crucial regulator of embryonic brain development. Pathogenic FOXG1 variants cause FOXG1 syndrome. Although structural variants in the non-coding region downstream of FOXG1 have been reported in 38 individuals with similar characteristics, the regulatory pathomechanisms remain unknown. Here, we identify two non-coding structural variants in individuals with FOXG1 syndrome-like features, allowing us to delineate a ~ 124 kb commonly affected regulatory region. Using epigenomic profiling and in vivo enhancer assays, we characterize and validate regulatory elements within the commonly affected regulatory region and wider FOXG1 TAD. We see strong activation of previously validated forebrain enhancers, and identify an enhancer cluster and progenitor-specific enhancer region that are strongly activated during forebrain-directed neural progenitor cell differentiation, a process in which FOXG1 is an important regulator. Perturbation of these elements results in varying degrees of reduced FOXG1 transcription in forebrain neural progenitor cells and in population shifts within these cells, while removal of the TAD boundary leads to aberrant expression of the neighbouring PRKD1 gene. Our findings characterize enhancer and architectural elements essential for proper FOXG1 transcription during neurodevelopment, therefore improving variant interpretation in this region.

Hamerlinck, Lisa↗
DOE OSTI2020

Toward nanoscale molecular mass spectrometry imaging via physically constrained machine learning on co-registered multimodal data

Mass spectrometry imaging (MSI) plays a pivotal role in investigating the chemical nature of complex systems that underly our understanding in biology and medicine. Multiple fields of life science such as proteomics, lipidomics and metabolomics benefit from the ability to simultaneously identify molecules and pinpoint their distribution across a sample. However, achieving the necessary submicron spatial resolution to distinguish chemical differences between individual cells and generating intact molecular spectra is still a challenge with any single imaging approach. Here, we developed an approach that combines two MSI techniques, matrix-assisted laser desorption/ionization (MALDI) and time-of-flight secondary ion mass spectrometry (ToF-SIMS), one with low spatial resolution but intact molecular spectra and the other with nanometer spatial resolution but fragmented molecular signatures, to predict molecular MSI spectra with submicron spatial resolution. The known relationships between the two MSI channels of information are enforced via a physically constrained machine-learning approach and directly incorporated in the data processing. We demonstrate the robustness of this method by generating intact molecular MALDI-type spectra and chemical maps at ToF-SIMS resolution when imaging mouse brain thin tissue sections. This approach can be readily adopted for other types of bioimaging where physical relationships between methods have to be considered to boost the confidence in the reconstruction product.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Tomographic detection of photon pairs produced from high-energy X-rays for the monitoring of radiotherapy dosing

Measuring the radiation dose reaching a patient’s body is difficult. Here we report a technique for the tomographic reconstruction of the location of photon pairs originating from the annihilation of positron–electron pairs produced by high-energy X-rays travelling through tissue. We used Monte Carlo simulations on pre-recorded data from tissue-mimicking phantoms and from a patient with a brain tumour to show the feasibility of this imaging modality, which we named ‘pair-production tomography’, for the monitoring of radiotherapy dosing. We simulated three image-reconstruction methods, one applicable to a pencil X-ray beam scanning through a region of interest, and two applicable to the excitation of tissue volumes via broad beams (with temporal resolution sufficient to identify coincident photon pairs via filtered back projection, or with higher temporal resolution sufficient for the estimation of a photon’s time-of-flight). In addition to the monitoring of radiotherapy dosing, we show that image contrast resulting from pair-production tomography is highly proportional to the material’s atomic number. The technique may thus also allow for element mapping and for soft-tissue differentiation.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2026

Operando microscopy for neuromorphic hardware

Microscopy techniques can uncover the physical properties and dynamic behaviours of materials, driving the discovery of emergent phenomena and guiding the design of next-generation computing hardware. As artificial intelligence becomes pervasive, the demand for high-performance materials to support sustainable information technologies is growing. Here, this Review highlights state-of-the-art imaging from electron and X-ray to optical techniques to probe the dynamics of neuromorphic materials, including operando characterization of devices. We examine design principles for neuromorphic materials, along with obstacles that hinder their development. Emphasis is placed on spatially and temporally resolved approaches that capture state changes including phase transitions, ferroic switching and spin-wave propagation that emulate biological components such as neurons, synapses and their connectivity. We discuss challenges in operando characterization and the integration of artificial intelligence-driven analysis for feedback-guided material discovery. Finally, we outline opportunities for real-time imaging of neuromorphic systems, paving the way towards adaptive, brain-inspired hardware.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Direct observation of a dynamical glass transition in a nanomagnetic artificial Hopfield network

Spin glasses, generally defined as disordered systems with randomized competing interactions, are a widely investigated complex system. Theoretical models describing spin glasses are broadly used in other complex systems, such as those describing brain function, error-correcting codes5 or stock-market dynamics. This wide interest in spin glasses provides strong motivation to generate an artificial spin glass within the framework of artificial spin ice systems. Here we present the experimental realization of an artificial spin glass consisting of dipolar coupled single-domain Ising-type nanomagnets arranged onto an interaction network that replicates the aspects of a Hopfield neural network. Using cryogenic X-ray photoemission electron microscopy (XPEEM), we performed temperature-dependent imaging of thermally driven moment fluctuations within these networks and observed characteristic features of a two-dimensional Ising spin glass. Specifically, the temperature dependence of the spin glass correlation function follows a power-law trend predicted from theoretical models on two-dimensional spin glasses. As a result, we observe clear signatures of the hard-to-observe rugged spin glass free energy in the form of sub-aging, out-of-equilibrium autocorrelations and a transition from stable to unstable dynamics.

36 MATERIALS SCIENCE↗
DOE OSTI2021

cAMP binding to closed pacemaker ion channels is non-cooperative

Electrical activity in the brain and heart depends on rhythmic generation of action potentials by pacemaker ion channels (HCN) whose activity is regulated by cAMP binding. Previous work has uncovered evidence for both positive and negative cooperativity in cAMP binding, but such bulk measurements suffer from limited parameter resolution. Efforts to eliminate this ambiguity using single-molecule techniques have been hampered by the inability to directly monitor binding of individual ligand molecules to membrane receptors at physiological concentrations. Here we overcome these challenges using nanophotonic zero-mode waveguides4 to directly resolve binding dynamics of individual ligands to multimeric HCN1 and HCN2 ion channels. We show that cAMP binds independently to all four subunits when the pore is closed, despite a subsequent conformational isomerization to a flip state at each site. The different dynamics in binding and isomerization are likely to underlie physiologically distinct responses of each isoform to cAMP and provide direct validation of the ligand-induced flip-state model. Furthermore, this approach for observing stepwise binding in multimeric proteins at physiologically relevant concentrations can directly probe binding allostery at single-molecule resolution in other intact membrane proteins and receptors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Limited cross-variant immunity from SARS-CoV-2 Omicron without vaccination

SARS-CoV-2 Delta and Omicron are globally relevant variants of concern. Although individuals infected with Delta are at risk of developing severe lung disease, infection with Omicron often causes milder symptoms, especially in vaccinated individuals. The question arises of whether widespread Omicron infections could lead to future cross-variant protection, accelerating the end of the pandemic. Here we show that without vaccination, infection with Omicron induces a limited humoral immune response in mice and humans. Sera from mice overexpressing the human ACE2 receptor and infected with Omicron neutralize only Omicron, but not other variants of concern, whereas broader cross-variant neutralization was observed after WA1 and Delta infections. Unlike WA1 and Delta, Omicron replicates to low levels in the lungs and brains of infected animals, leading to mild disease with reduced expression of pro-inflammatory cytokines and diminished activation of lung-resident T cells. Sera from individuals who were unvaccinated and infected with Omicron show the same limited neutralization of only Omicron itself. By contrast, Omicron breakthrough infections induce overall higher neutralization titres against all variants of concern. Our results demonstrate that Omicron infection enhances pre-existing immunity elicited by vaccines but, on its own, may not confer broad protection against non-Omicron variants in unvaccinated individuals.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Network-level encoding of local neurotransmitters in cortical astrocytes

Abstract Astrocytes, the most abundant non-neuronal cell type in the mammalian brain, are crucial circuit components that respond to and modulate neuronal activity through calcium (Ca 2+ ) signalling 1–7 . Astrocyte Ca 2+ activity is highly heterogeneous and occurs across multiple spatiotemporal scales—from fast, subcellular activity 3,4 to slow, synchronized activity across connected astrocyte networks 8–10 —to influence many processes 5,7,11 . However, the inputs that drive astrocyte network dynamics remain unclear. Here we used ex vivo and in vivo two-photon astrocyte imaging while mimicking neuronal neurotransmitter inputs at multiple spatiotemporal scales. We find that brief, subcellular inputs of GABA and glutamate lead to widespread, long-lasting astrocyte Ca 2+ responses beyond an individual stimulated cell. Further, we find that a key subset of Ca 2+ activity—propagative activity—differentiates astrocyte network responses to these two main neurotransmitters, and may influence responses to future inputs. Together, our results demonstrate that local, transient neurotransmitter inputs are encoded by broad cortical astrocyte networks over a minutes-long time course, contributing to accumulating evidence that substantial astrocyte–neuron communication occurs across slow, network-level spatiotemporal scales 12–14 . These findings will enable future studies to investigate the link between specific astrocyte Ca 2+ activity and specific functional outputs, which could build a consistent framework for astrocytic modulation of neuronal activity.

Science & Technology - Other Topics↗
DOE OSTI2024

Structure of the human dopamine transporter and mechanisms of inhibition

Abstract The neurotransmitter dopamine has central roles in mood, appetite, arousal and movement 1 . Despite its importance in brain physiology and function, and as a target for illicit and therapeutic drugs, the human dopamine transporter (hDAT) and mechanisms by which it is inhibited by small molecules and Zn 2+ are without a high-resolution structural context. Here we determine the structure of hDAT in a tripartite complex with the competitive inhibitor and cocaine analogue, (–)-2-β-carbomethoxy-3-β-(4-fluorophenyl)tropane 2 (β-CFT), the non-competitive inhibitor MRS7292 3 and Zn 2 + (ref. 4 ). We show how β-CFT occupies the central site, approximately halfway across the membrane, stabilizing the transporter in an outward-open conformation. MRS7292 binds to a structurally uncharacterized allosteric site, adjacent to the extracellular vestibule, sequestered underneath the extracellular loop 4 (EL4) and adjacent to transmembrane helix 1b (TM1b), acting as a wedge, precluding movement of TM1b and closure of the extracellular gate. A Zn 2+ ion further stabilizes the outward-facing conformation by coupling EL4 to EL2, TM7 and TM8, thus providing specific insights into how Zn 2+ restrains the movement of EL4 relative to EL2 and inhibits transport activity.

Science & Technology - Other Topics↗
DOE OSTI2025

In vivo mapping of mutagenesis sensitivity of human enhancers

Distant-acting enhancers are central to human development1. However, our limited understanding of their functional sequence features prevents the interpretation of enhancer mutations in disease2. Here we determined the functional sensitivity to mutagenesis of human developmental enhancers in vivo. Focusing on seven enhancers that are active in the developing brain, heart, limb and face, we created over 1,700 transgenic mice for over 260 mutagenized enhancer alleles. Systematic mutation of 12-base-pair blocks collectively altered each sequence feature in each enhancer at least once. We show that 69% of all blocks are required for normal in vivo activity, with mutations more commonly resulting in loss (60%) than in gain (9%) of function. Using predictive modelling, we annotated critical nucleotides at the base-pair resolution. The vast majority of motifs predicted by these machine learning models (88%) coincided with changes in in vivo function, and the models showed considerable sensitivity, identifying 59% of all functional blocks. Taken together, our results reveal that human enhancers contain a high density of sequence features that are required for their normal in vivo function and provide a rich resource for further exploration of human enhancer logic.

Kosicki, Michael↗