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At least 91 records · Page 5

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DOE OSTI2021

Correlated conformational dynamics of the human GluN1-GluN2A type N-methyl-D-aspartate (NMDA) receptor

N-Methyl-D-aspartate receptors (NMDARs) are glutamate-gated ion channels found in the nerve cell membranes. As a result of overexcitation of NMDARs, neuronal death occurs and may lead to diseases such as epilepsy, stroke, Alzheimer’s disease, and Parkinson’s disease. In this study, human GluN1- GluN2A type NMDAR structure is modeled based on the X-ray structure of the Xenopus laevis template and missing loops are added by ab-initio loop modeling. The final structure is chosen according to two different model assessment scores. To be able to observe the structural changes upon ligand binding, glycine and glutamate molecules are docked into the corresponding binding sites of the receptor. Subsequently, molecular dynamics simulations of 1.3 μs are performed for both apo and ligand-bound structures. Structural parameters, which have been considered to show functionally important changes in previous NMDAR studies, are monitored as conformational rulers to understand the dynamics of the conformational changes. Moreover, principal component analysis (PCA) is performed for the equilibrated part of the simulations. Additionally, from these analyses, the differences in between apo and ligand-bound simulations can be summarized as the following: The girdle right at the beginning of the pore loop, which connects M2 and M3 helices of the ion channel, partially opens. Ligands act like an adhesive for the ligand-binding domain (LBD) by keeping the bi-lobed structure together and consequently this is reflected to the overall dynamics of the protein as an increased correlation of the LBD with especially the amino-terminal domain (ATD) of the protein.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Structure of human TRPV4 in complex with GTPase RhoA

Transient receptor potential (TRP) channel TRPV4 is a polymodal cellular sensor that responds to moderate heat, cell swelling, shear stress, and small-molecule ligands. It is involved in thermogenesis, regulation of vascular tone, bone homeostasis, renal and pulmonary functions. TRPV4 is implicated in neuromuscular and skeletal disorders, pulmonary edema, and cancers, and represents an important drug target. The cytoskeletal remodeling GTPase RhoA has been shown to suppress TRPV4 activity. Here, we present a structure of the human TRPV4-RhoA complex that shows RhoA interaction with the membrane-facing surface of the TRPV4 ankyrin repeat domains. The contact interface reveals residues that are mutated in neuropathies, providing an insight into the disease pathogenesis. We also identify the binding sites of the TRPV4 agonist 4α-PDD and the inhibitor HC-067047 at the base of the S1-S4 bundle, and show that agonist binding leads to pore opening, while channel inhibition involves a π-to-α transition in the pore-forming helix S6. Our structures elucidate the interaction interface between hTRPV4 and RhoA, as well as residues at this interface that are involved in TRPV4 disease-causing mutations. They shed light on TRPV4 activation and inhibition and provide a template for the design of future therapeutics for treatment of TRPV4-related diseases.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

MgO Nanostructures on Cu(111): Understanding Size- and Morphology-Dependent CO 2 Binding and Hydrogenation

To design and optimize cost-effective technologies for the capture, utilization, and storage of carbon dioxide (CO 2 ), we need a fundamental knowledge and control of chemical interactions associated with the capture and conversion of the molecule into high-value chemicals, minerals, and all kinds of materials. Bulk magnesium oxide (MgO) is frequently used for the trapping and storage of CO 2 by generation of magnesium carbonates. In this study, the growth and reactivity of MgO nanostructures on a Cu 2 O/Cu(111) substrate were investigated using scanning tunneling microscopy (STM) and synchrotron-based ambient-pressure X-ray photoelectron spectroscopy (AP-XPS). For extremely small concentrations of Mg (~ 0.01 monolayer (ML)), a well-ordered film of copper oxide with small clusters (0.2-0.5 nm in width, 0.4-0.6 Å in height) of embedded MgO was seen. At a coverage of 0.1 ML, MgO nanoparticles with a width of 0.4 to 1 nm and a height of ~ 1.5 Å were randomly distributed on the copper oxide. Further, random distribution was also observed when the MgO coverage was raised to 0.25 ML, with the width of the MgO particles increasing to 2-2.5 nm and the height reaching 2 Å. These oxide nanostructures displayed a high reactivity towards CO 2 and H 2 that is not seen for bulk MgO. Dissociation of H 2 was observed at room temperature with reaction of the H adatoms with CuO x and C-containing groups. On the small MgO nanostructures (< 1 nm in width), instead of plain carbonate formation, there was dissociation of CO 2 into CO and C species, opening reaction channels for the conversion of this harmful molecule into oxygenates and light alkanes.

03 NATURAL GAS↗

DOE OSTI2021

Hyporheic Exchange Driven by Submerged Rigid Vegetation: A Modeling Study

Flow-vegetation interaction affects fluid flow hydraulics and associated material transport in river corridors. Concomitant changes in pressure within the flow field due to the presence of vegetation may act as a driver for the formation of hyporheic flow across the sediment-water interface. This potentially important process, however, has yet to be studied. In order to investigate vegetation-induced hyporheic exchange, a series of numerical models of interlinked surface-subsurface flow modified by plant stems was conducted. Periodically staggered plant stem arrays on a flat sediment bed were considered within a coupled multiphysics computational fluid dynamics approach. Plants were idealized as rigid cylinders and arranged in different streamwise and spanwise spacing distances. Each vegetation array was then subjected to a broad range of flow Reynolds Numbers (Re). The results showed that hyporheic flow occurs in all conditions with the presence of vegetation. The vegetation-induced hyporheic flux is found to be a function of Re via a power law. The flux increases with interstem space until the space reaches the distance that rigid stems no longer affect the flow structures in the vicinity of each other. Larger intervegetation distances lead to a larger hyporheic zone. A direct comparison with bedforminduced hyporheic flow showed that vegetation can induce higher hyporheic flux through relatively shallower exchange zones. The results of all the simulations were synthesized into predictive models for hyporheic flux, bulk residence time and exchange depth based on drag coefficient, vegetation density, and Reynolds Number.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Non-equilibrium anti-Stokes Raman spectroscopy for investigating Higgs modes in superconductors

Abstract Even before its role in electroweak symmetry breaking, the Anderson-Higgs mechanism was introduced to explain the Meissner effect in superconductors. Spontaneous symmetry-breaking yields massless phase modes representing the low-energy excitations of the Mexican-Hat potential. Only in superconductors the phase mode is shifted towards higher energies owing to the gauge field of the charged condensate. This results in a low-energy excitation spectrum governed by the Higgs mode. Consequently, the Bardeen-Cooper-Schrieffer-like Meissner effect signifies a macroscopic quantum condensate in which a photon acquires mass, representing a one-to-one analogy to high-energy physics. We report on an innovative spectroscopic technique to study symmetries and energies of the Higgs modes in the high-temperature superconductor Bi 2 Sr 2 CaCu 2 O 8 after a soft quench of the Mexican-Hat potential. Population inversion induced by an initial laser pulse leads to an additional anti-Stokes Raman-scattering signal, which is consistent with polarization-dependent Higgs modes. Within Ginzburg-Landau theory, the Higgs-mode energy is connected to the Cooper-pair coherence length. Within a Bardeen-Cooper-Schrieffer weak-coupling model we develop a quantitative and coherent description of single-particle and two-particle channels. This opens the avenue for Higgs Spectroscopy in quantum condensates and provides a unique pathway to control and explore Higgs physics.

Science & Technology - Other Topics↗

DOE OSTI2021

Superconducting neural networks with disordered Josephson junction array synaptic networks and leaky integrate-and-fire loop neurons

Fully coupled randomly disordered recurrent superconducting networks with additional open-ended channels for inputs and outputs are considered the basis to introduce a new architecture to neuromorphic computing in this work. Various building blocks of such a network are designed around disordered array synaptic networks using superconducting devices and circuits as an example, while emphasizing that a similar architectural approach may be compatible with several other materials and devices. A multiply coupled (interconnected) disordered array of superconducting loops containing Josephson junctions [equivalent to superconducting quantum interference devices (SQUIDs)] forms the aforementioned collective synaptic network that forms a fully recurrent network together with compatible neuron-like elements and feedback loops, enabling unsupervised learning. This approach aims to take advantage of superior power efficiency, propagation speed, and synchronizability of a small world or a random network over an ordered/regular network. Additionally, it offers a significant factor of increase in scalability. Here, a compatible leaky integrate-and-fire neuron made of superconducting loops with Josephson junctions is presented, along with circuit components for feedback loops as needed to complete the recurrent network. Several of these individual disordered array neural networks can further be coupled together in a similarly disordered way to form a hierarchical architecture of recurrent neural networks that is often suggested as similar to a biological brain.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2025

On transport of electrons in a magnetized plasma sheath

Electron trajectories are analyzed in the plasma sheath region in a magnetic field that intersects the surface at a shallow angle. Depending on the size of the Debye width relative to the electron gyroradius, λ D /ρ e , an electron either drifts in the sheath electric field or follows a sequence of reflections (“bouncing”) on the surface before reversing its parallel velocity. For thin sheath, λ D /ρ e ≪ 1, the conservation of the electron magnetic moment can be violated, depending on the ratio of the electron perpendicular and parallel velocities V ⊥ /V || and the magnetic field pitch angle with respect to the surface. Small-scale waviness of the surface can strongly amplify this effect, leading to violation of the magnetic moment conservation even for λ D /ρ e ≳ 1, which opens a channel of anomalous radial transport for electrons in plasma devices.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

Bayesian analysis of the 86 Sr ⁢(𝛼,𝛼) reaction to constrain the 86 Sr ⁢(𝛼,𝑛) cross section at astrophysical energies

The alpha optical model potential (𝛼-OMP ) is a phenomenological approach used to describe elastic scattering where multiple reaction channels are open. It is one of the most critical inputs for the calculation of thermonuclear reaction rates in explosive stellar environments, but uncertainties within the 𝛼-OMP lead to imprecise predictions hindering comparisons between calculations and observations. In order to improve the precision of the 𝛼-OMP, additional nuclear physics data are required. In this paper, a measurement of the 86 Sr (𝛼, 𝛼) elastic scattering cross section at multiple energies is reported. Here, a local optical potential is constructed via a fully Bayesian analysis of the elastic scattering data. The resulting uncertainties on the low-energy cross sections relevant to nuclear astrophysics are then calculated and shown to be on the order of 50%.

59 ≤ A ≤ 89↗

DOE OSTI2023

AmeriFlux FLUXNET-1F US-Tw4 Twitchell East End Wetland

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site US-Tw4 Twitchell East End Wetland. This is the FLUXNET version of the carbon flux data for the site US-Tw4 Twitchell East End Wetland produced by applying the standard ONEFlux (1F) software. Site Description - The Twitchell East End Wetland is a newly constructed restored wetland on Twitchell Island, CA. This site and the surrounding region are part of the San Joaquin - Sacramento River Delta drained beginning in the 1850's and subsequently used for agriculture. The site was previously a corn field. The wetland was designed to have a mix of vegetated and open water channels and ponds (due to surface elevation differences). Flooding of the wetland was done gradually beginning in January, 2014. Berms wind throughout the wetland to allow vehicle access. Tule and Cattail plant material from a nearby wetland were spread along the berms immediately prior to flooding to facilitate plant establishment and stabilization of the berms from wind/water erosion. The tower was installed on November 25, 2013.

Eichelmann, Elke↗

DOE OSTI2022

Message-Based SPDK Transport Utility (TED Report) [Slides]

The driving goal is to investigate the feasibility of a message-based data transport for SPDK. All of SPDK’s existing data transport protocols are “connection-based”, requiring a target to hold state for each connected client / initiator. At extreme scale, juggling these connections from a large number of initiators creates a performance bottleneck. Under a message-based paradigm, we can bypass this behavior, as all initiators share a global communication channel, held open for the entire run. In theory, this approach should minimize connection management overhead at extreme scale.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Classification of Intensity Distributions of Transmission Eigenchannels of Disordered Nanophotonic Structures Using Machine Learning

Light-matter interaction optimization in complex nanophotonic structures is a critical step towards the tailored performance of photonic devices. The increasing complexity of such systems requires new optimization strategies beyond intuitive methods. For example, in disordered photonic structures, the spatial distribution of energy densities has large random fluctuations due to the interference of multiply scattered electromagnetic waves, even though the statistically averaged spatial profiles of the transmission eigenchannels are universal. Classification of these eigenchannels for a single configuration based on visualization of intensity distributions is difficult. However, successful classification could provide vital information about disordered nanophotonic structures. Emerging methods in machine learning have enabled new investigations into optimized photonic structures. In this work, we combine intensity distributions of the transmission eigenchannels and the transmitted speckle-like intensity patterns to classify the eigenchannels of a single configuration of disordered photonic structures using machine learning techniques. Specifically, we leverage supervised learning methods, such as decision trees and fully connected neural networks, to achieve classification of these transmission eigenchannels based on their intensity distributions with an accuracy greater than 99%, even with a dataset including photonic devices of various disorder strengths. Simultaneous classification of the transmission eigenchannels and the relative disorder strength of the nanophotonic structure is also possible. Our results open new directions for machine learning assisted speckle-based metrology and demonstrate a novel approach to classifying nanophotonic structures based on their electromagnetic field distributions. These insights can be of paramount importance for optimizing light-matter interactions at the nanoscale.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

Viral Capsid Change upon Encapsulation of Double-Stranded DNA into an Infectious Hypodermal and Hematopoietic Necrosis Virus-like Particle

In this study, we aimed to encapsulate the sizable double-stranded DNA (dsDNA, 3.9 kbp) into a small-sized infectious hypodermal and hematopoietic necrosis virus-like particle (IHHNV-VLP; T = 1) and compared the changes in capsid structure between dsDNA-filled VLP and empty VLP. Based on our encapsulation protocol, IHHNV-VLP was able to load dsDNA at an efficiency of 30–40% (w/w) into its cavity. Structural analysis revealed two subclasses of IHHNV-VLP, so-called empty and dsDNA-filled VLPs. The three-dimensional (3D) structure of the empty VLP produced in E. coli was similar to that of the empty IHHNV-VLP produced in Sf9 insect cells. The size of the dsDNA-filled VLP was slightly bigger (50 Å) than its empty VLP counterpart; however, the capsid structure was drastically altered. The capsid was about 1.5-fold thicker due to the thickening of the capsid interior, presumably from DNA–capsid interaction evident from capsid protrusions or nodules on the interior surface. In addition, the morphological changes of the capsid exterior were particularly observed in the vicinity of the five-fold axes, where the counter-clockwise twisting of the “tripod” structure at the vertex of the five-fold channel was evident, resulting in a widening of the channel’s opening. Whether these capsid changes are similar to virion capsid maturation in the host cells remains to be investigated. Nevertheless, the ability of IHHNV-VLP to encapsulate the sizable dsDNA has opened up the opportunity to package a dsDNA vector that can insert exogenous genes and target susceptible shrimp cells in order to halt viral infection.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Impact of Polymer Rheology on Gel Treatment Performance of Horizontal Wells with Severe Channeling

Summary Gel treatment has been a cost-effective method to control the conformance of a reservoir with severe heterogeneity problems. The water channels in such reservoirs can be classified as open fractures or high permeability porous media with pore-throat network. Many simulation studies have been conducted to discuss gel treatment performance for conformance control. However, nobody considered the polymer rheology difference in open fractures and porous media in simulation. Previous simulation studies also ignored the residual resistance factor as a function of rock permeability rather than a constant parameter. In this study, a conceptual simulation model was established to simulate the linear flow system for the reservoir with horizontal wells considering the two factors mentioned above. The results demonstrate that the gel treatment always provides the better placement results in the open fracture type channel than pore-throat network type channel. Moreover, it is very necessary to consider residual resistance factor as a function of permeability, which is based on the experimental results and can provide much greater plugging efficiency in the higher permeable channels than constant residual resistance factor. Sensitivity analysis studies and multifactor analysis indicate that increasing oil viscosity and permeability ratio has a strong positive influence on conformance control results, which indicate in-situ gel treatment can be better applied in heavy or viscous oil reservoirs with fracture-like channels. Besides, the results also indicate that in reservoirs with severe channeling problem where channel velocity was high, the differences of gelant placement and profile improvement in models with two different types of channels could be enlarged greatly.

Engineering↗

DOE OSTI2023

Open millifluidics based on powder-encased channels

Millifluidics, the manipulation of liquid flow in millimeter-sized channels, has been a revolutionary concept in chemical processing and engineering. The solid channels that contain the liquids, though, are not flexible in their design and modification, and prevent contact with the external environment. All-liquid constructs, on the other hand, while flexible and open, are imbedded in a liquid environment. Here, we provide a route to circumvent these limitations by encasing the liquids in a hydrophobic powder in air that jams on the surface, containing and isolating flowing fluids, offering flexibility and adaptability in design, as manifest in the ability to reconfigure, graft, and segment the constructs. Along with the open nature of these powder-contained channels that allow arbitrary connections/disconnections and substance addition/extraction, numerous applications can be opened in the biological, chemical, and material arenas.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Carbon electrodes based capacitive deionization for the desalination of water

A capacitive deionization system includes first and second electrodes comprising tire derived carbon particles obtained from a carbonaceous waste-tire source material containing carbon black. A conductive polymer coating on the carbon particles forms coated carbon particles. The first electrode and the second electrode define a flow channel there between, having a first opening for conducting saline solution into the flow channel and a second opening for conducting treated saline solution from the flow channel. A first current collector is provided for the first electrode and a second current collector is provided for the second electrode. An electrical connection between the first and second electrodes. A method of making a system for the capacitive deionization of a salt from a liquid, and a method for the capacitive desalination of a saline solution are also disclosed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Rigid stiffener-reinforced flexible neural probes, and methods of fabrication using wicking channel-distributed adhesives and tissue insertion and extraction

A stiffener-reinforced microelectrode array probe and fabrication method using wicking channel-distributed adhesives which temporarily adheres a flexible device onto a rigid stiffener for insertion and extraction. Assembly is by dispensing a liquid adhesive into a narrow open groove wicking channel formed on the stiffener so that the adhesive is wicked along and fills the channel by capillary action, and adhering the adhesive-filled bonding side of the elongated section of the rigid substrate to a flexible device.

Shah, Kedar G.↗

DOE OSTI2023

Influence of extreme fracture flow channels on the thermal performance of open-loop geothermal systems at commercial scale

Abstract Adequate stewardship of geothermal resources requires accurate forecasting of long-term thermal performance. In enhanced geothermal systems and other fracture-dominated reservoirs, predictive models commonly assume constant-aperture fractures, although spatial variations in aperture can greatly affect reservoir permeability, fluid flow distribution, and heat transport. Whereas previous authors have investigated the effects of theoretical random aperture distributions on thermal performance, here we further explore the influence of permeability heterogeneity considering field-constrained aperture distributions from a meso-scale field site in northern New York, USA. Using numerical models of coupled fluid flow and heat transport, we conduct thermal–hydraulic simulations for a hypothetical reservoir consisting of a relatively impervious porous matrix and a single, horizontal fracture. Our results indicate that in highly channelized fields, most well design configurations and operating conditions result in extreme rates of thermal drawdown (e.g., 50% drop in production well temperatures in under 2 years). However, some other scenarios that account for the risks of short-circuiting can potentially enhance heat extraction when mass flow rate is not excessively high, and the direction of geothermal extraction is not aligned with the most permeable features in the reservoir. Through a parametric approach, we illustrate that well separation distance and relative positioning play a major role in the long-term performance of highly channelized fields, and both can be used to help mitigate premature thermal breakthrough.

Rangel-Jurado, Nicolás↗

DOE OSTI2024

Metadynamics simulations reveal mechanisms of Na + and Ca 2+ transport in two open states of the channelrhodopsin chimera, C1C2

Cation conducting channelrhodopsins (ChRs) are a popular tool used in optogenetics to control the activity of excitable cells and tissues using light. ChRs with altered ion selectivity are in high demand for use in different cell types and for other specialized applications. However, a detailed mechanism of ion permeation in ChRs is not fully resolved. Here, we use complementary experimental and computational methods to uncover the mechanisms of cation transport and valence selectivity through the channelrhodopsin chimera, C1C2, in the high- and low-conducting open states. Electrophysiology measurements identified a single-residue substitution within the central gate, N297D, that increased Ca 2+ permeability vs. Na + by nearly two-fold at peak current, but less so at stationary current. We then developed molecular models of dimeric wild-type C1C2 and N297D mutant channels in both open states and calculated the PMF profiles for Na + and Ca 2+ permeation through each protein using well-tempered/multiple-walker metadynamics. Results of these studies agree well with experimental measurements and demonstrate that the pore entrance on the extracellular side differs from original predictions and is actually located in a gap between helices I and II. Cation transport occurs via a relay mechanism where cations are passed between flexible carboxylate sidechains lining the full length of the pore by sidechain swinging, like a monkey swinging on vines. In the mutant channel, residue D297 enhances Ca 2+ permeability by mediating the handoff between the central and cytosolic binding sites via direct coordination and sidechain swinging. We also found that altered cation binding affinities at both the extracellular entrance and central binding sites underly the distinct transport properties of the low-conducting open state. This work significantly advances our understanding of ion selectivity and permeation in cation channelrhodopsins and provides the insights needed for successful development of new ion-selective optogenetic tools.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗