Search NASA⌕ Search

SEARCH · Search NASA

Results for “Loop closure”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

14 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Conformational Dynamics and Catalytic Backups in a Hyper-thermostable Engineered Archaeal Protein Tyrosine Phosphatase

Protein tyrosine phosphatases (PTPs) are a family of enzymes that play important roles in regulating cellular signaling pathways. The activity of these enzymes is regulated by the motion of a catalytic loop that places a critical conserved aspartic acid side chain into the active site for acid–base catalysis upon loop closure. These enzymes also have a conserved phosphate-binding loop that is typically highly rigid and forms a well-defined anion-binding nest. The intimate links between loop dynamics and chemistry in these enzymes make PTPs an excellent model system for understanding the role of loop dynamics in protein function and evolution. In this context, archaeal PTPs, which have often evolved in extremophilic organisms, are highly understudied, despite their unusual biophysical properties. We present here an engineered chimeric PTP (ShufPTP) generated by shuffling the amino acid sequence of five extant hyperthermophilic archaeal PTPs. Despite ShufPTP’s high sequence similarity to its natural counterparts, it presents a suite of unique properties, including high flexibility of the phosphate binding P-loop, facile oxidation of the active-site cysteine, mechanistic promiscuity, and, most notably, hyperthermostability, with a denaturation temperature likely >130 °C (>8 °C higher than the highest recorded growth temperature of any archaeal strain). Our combined structural, biochemical, biophysical, and computational analysis provides insight both into how small steps in evolutionary space can radically modulate the biophysical properties of an enzyme and showcases the tremendous potential of archaeal enzymes for biotechnology, to generate novel enzymes capable of operating under extreme conditions.

archaea↗
DOE OSTI2025

Future Opportunities for LWR Irradiations in US Test Reactors

After several years of relatively low activity in the field of Light Water Reactor (LWR) fuel development, the Department of Energy again began to engage in developing new fuel technologies and irradiation performance data prompted by the Fukushima Daichi nuclear accidents. New competencies for irradiation testing in material test reactors in the United States began to be developed at this time using the Advanced Test Reactor (ATR), High Flux Isotope Reactor (HFIR), Massachusetts Institute of Technology Reactor (MITR), and the Transient Reactor Test Facility (TREAT). Capsules for testing fuel and cladding materials in ATR and HFIR were deployed, a Pressurized Water Reactor (PWR) condition loop for testing fuel rods was established in ATR, cladding corrosion studies were performed using a water loop in MITR, and TREAT pulse testing capabilities were commissioned for fuel rods in water capsules. The more recent and unexpected closure of the Halden Boiling Water Reactor (HBWR) also prompted further investments in Loss of Coolant Accident (LOCA) testing capabilities at TREAT. New configurations of these test devices show further potential in enhanced steam condition control and other investigations are building toward a flowing water loop for testing transient to dryout conditions. The closure of HBWR also prompted a major project currently underway to construct additional water loops in ATR where a novel approach is being pursued to enable Boiling Water Reactor (BWR) conditions. A meaningful collaborative project was awarded to MITR which, amidst an unexpected major overhaul of the reactor, has expanded cladding corrosion test capabilities at MITR. New explorations have led to methods for unique experiments at HFIR including channel box irradiations. New device developments are also bridging toward future potential for instrumented capsule irradiation tests in ATR and HFIR. Finally, a new project referred to as the System Physics Advanced Reactor Critical facility (SPARC) is gaining traction towards a large zero-power reactor able to produce physics validation data for LWR fuel bundle designs with increased enrichment and enhanced absorbers for 24-month operation cycles. This paper provides a brief summary of the status of these irradiation testbed capabilities with an emphasis on current efforts toward future capabilities to obtain new data and maximize the performance potential of LWR fuel technologies.

Woolstenhulme, Nicolas [Idaho National Laboratory ↗
DOE OSTI2025

Flux-Closure Domain Structures in Ferroelectric K 0.5 Na 0.5 NbO 3 Thin Films

Topological domain structures in ferroelectric materials have garnered increasing attention due to their intriguing physical properties and promising applications. While most existing topological structures in ferroelectric perovskite oxides originate from tetragonal or rhombohedral bulk phases, much less is understood about their counterparts in orthorhombic ferroelectrics. Here, in this work, we employ ferroelectric K 0.5 Na 0.5 NbO 3 (KNN) thin films as a model system and leverage phase-field simulations to theoretically predict the static structures and dynamic behaviors of three types of flux-closure domain configurations: in-plane (Type-I), out-of-plane (Type-II), and superdomain (Type-III) flux-closure structures. We systematically investigate the effects of finite size, misfit strains, and electrical boundary conditions on the formation and switching of these topological structures. For the Type-I structure, size reduction or small misfit strain facilitates a transition of the flux-closure pattern to polar vortices. Type-II structures emerge under open-circuit electrical boundary conditions of the film, forming at the junctions of specific domain walls with the film surface or the film–substrate interface. The formation mechanisms of these two flux-closure structures are rationalized from an energy perspective. We demonstrated switching capabilities of Type-II and Type-III structures by obtaining polarization–electric field hysteresis loops. Our simulations also reveal a reversible electric-field-induced transition between the orthorhombic and rhombohedral ferroelectric phases with a checkerboard domain pattern, during which the integrity of the flux-closure structure is preserved. These findings provide theoretical insights and practical guidance for identifying and manipulating topological structures in low-symmetry ferroelectrics, paving the way for developing energy-efficient microelectronic devices based on topological structures.

P-E loop↗
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

On reduced modelling of the modulational dynamics in magnetohydrodynamics

This paper explores structure formation in two-dimensional magnetohydrodynamic (MHD) turbulence as a modulational instability (MI) of turbulent fluctuations. We focus on the early stages of structure formation and consider simple backgrounds that allow for a tractable model of the MI while retaining the full chain of modulational harmonics. This approach allows us to systematically examine the validity of popular closures such as the quasilinear approximation and other low-order truncations. We find that, although such simple closures can provide quantitatively accurate approximations of the MI growth rates in some regimes, they can fail to capture the modulational dynamics in adjacent regimes even qualitatively, falsely predicting MI when the system is actually stable. We find that this discrepancy is due to the excitation of propagating spectral waves (PSWs) which can ballistically transport energy along the modulational spectrum, unimpeded until dissipative scales, thereby breaking the feedback loops that would otherwise sustain MIs. The PSWs can be self-maintained as global modes with real frequencies and drain energy from the primary structure at a constant rate until the primary structure is depleted. To describe these waves within a reduced model, we propose an approximate spectral closure that captures them and MIs on the same footing. We also find that introducing corrections to ideal MHD, conservative or dissipative, can suppress PSWs and reinstate the accuracy of the quasilinear approximation. In this sense, ideal MHD is a ‘singular’ system that is particularly sensitive to the accuracy of the closure within mean-field models.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Autonomous Multistate Nanoencoding Using Combinatorial Ferroelectric Closure Domains in BiFeO 3

Recent advances in ferroic materials have identified topological defects as promising candidates for enabling additional functionalities in future electronic systems. The generation of stable and customizable polar topologies is needed to achieve multistates that enable beyond-binary device architectures. Here, in this study, we show how to autonomously pattern on-demand highly tunable striped closure domains in pristine rhombohedral-phase BiFeO 3 thin films through precise scanning of a biased atomic force microscopy tip along carefully designed paths. By employing this strategy, we generate and manipulate closed-loop structures with high spatial resolution in an automated manner, allowing the creation of highly tunable and intricate topological domain structures that exhibit distinct polarization configurations without the need for electrode deposition or complex heterostructure growth. As a proof-of-concept for ferroelectric beyond-binary memory devices, we use such topological domains as multistates, engineering an alphabet and automating the symbolic writing/reading process using autonomous microscopy. The resulting information density is compared with that of current commercially available memory devices, demonstrating the potential of ferroelectric topological domains for multistate information storage applications.

BiFeO3↗
DOE OSTI2025

Decay of skeins of dislocations in cholesterics: rewiring Conway's tangles into necklaces of bangles

Knotted and linked skeins of vortices and disclinations generated, respectively, by symmetry-breaking normal → superfluid and isotropic → nematic phase transitions are known to untie, by rewiring of their crossings, into independent unknots that finally shrink and collapse until the defect-free ground state is reached. We demonstrate that the decay of skeins of dislocations, generated by the isotropic → cholesteric phase transition within a cylinder/cylinder gap, leads to stable necklace-like states made of numerous minimal loops, called bangles, tethered to kinks of much larger loops called cargo. We analyze the topological decay of skeins of dislocations in terms of the Conway–Kauffman theory of knots, showing that the necklace state results from rewiring of crossings triggered by collisions of tangles with their numerator closure. We point out that, in general, for symmetry reasons, kinks on edge dislocations are chiral. Their handedness, right or left, directly depends on the sign of kinks on which they are localized. In cholesterics with intrinsic chirality, the energy of kinks bearing bangles depends on their handedness. For this reason, within necklaces, all bangles are tethered to kinks of the same sign.

Lee, Jun-Yong [International Institute for Sustain↗
DOE OSTI2026

Test of Harmonic Coil Accuracy Using a Multi Vertex Probe

Magnets are integral components of particle accelerators, with different multipoles used to perform various beam conditioning functions, like steering and focusing. Testing accelerator magnets to ensure compliance with specification is a crucial step of fabrication. One of the most popular techniques for verifying magnetic field strength and integrity is the harmonic coil probe. Harmonic coil probes are comprised of passive loops that are rotated around the aperture of a magnet and are used to measure magnetic flux. Oftentimes the measurements of the harmonic coil probe are affected by transverse vibrations along the axis of rotation and torsional vibrations of the position closure sensor, both causing spurious harmonics. To make matters challenging, it is difficult to distinguish between the real harmonics of the magnet and the spurious harmonics during analysis. This research explores the use of a novel configuration of harmonic coil probe, Multi-Vertex Probe (MVP), to address multiple factors that affect the accuracy and repeatability of harmonic coil probe measurement. Most of the results are based on simulation data, in which artificial torsional distortions are introduced and removed with the proposed processing method. In addition to implementing torsional vibration removal in simulation, laboratory analysis regarding the source of vibrations was performed using a pre-fabricated MVP. More specifically, various mechanical conditions were used to explore the standard deviation of main harmonic’s flux amplitude. The conditions included: coupling type (rigid or soft), rotation speed, probe starting position within magnetic field, and cabling location inside the magnetic field. Along with this, the MVP’s measured noise floor in and outside a magnetic field was quantified.

Lofquist, Claire [Northern Illinois U.]↗
DOE OSTI2026

Modeling and Power-Hardware-in-the-Loop Validation of Synchronous Machine Governor

This paper introduces the development of a high-fidelity gas turbine governor model using a programmable logic controller for power-hardware-in-the-loop (PHIL) validation. The governor model is integrated with the National Renewable Energy Laboratory's (NREL) PHIL test bed, featuring a 2-MVA synchronous machine and a 2.5-MW variable-speed drive, to emulate NG-driven HRSGs and CTs under various operational scenarios. The primary objective of this research is to study the grid-connected and islanding operations of conventional generation sources, with representative startup sequences including turbine purge, ignition, speed ramp-up, synchronization, and breaker closure. Preliminary results of the generator governor model on NREL PHIL platform, particularly using the 2.5-MW dynamometer system, offered significant insights into the modeling techniques, hardware integration, scaling, and real-world simulation dynamics.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2025

Integrated Molten Salt Reactor Modeling Capabilities in NEAMS Thermal Hydraulics Tools

The DOE neams program supports a full range of computational thermal fluids analysis capabilities and code developments for a broad range of advanced reactor concepts. The research and development approach under the thermal fluids technical area synergistically combines three length and time scales in a hierarchical multi-scale approach. To enable multi-scale thermal fluids capability using these codes, a key joint effort has been underway to develop an integrated system- and engineering-scale thermal fluids analysis capability, through integration of SAM and Pronghorn codes, both based on the MOOSE framework. This report summarizes recent advances in developing an integrated system- and engineering-scale modeling capability for the msr concept, which has gained significant interest in recent years. A consistent framework was established by coupling Pronghorn and SAM through the Saline interface, with thermophysical properties provided by the Molten Salt Thermal Property Database (MSTDB-TP). Further improvements were made to the coupling schemes and domain-overlapping strategies, enhancing the stability and robustness of multi-code simulations. Verification and validation efforts demonstrate the accuracy of this integration across a range of benchmark problems, including one-dimensional heated pipe flows, three-dimensional natural convection loops with evolving isotopic compositions, and \gls{msre} demonstration cases. Within Pronghorn, new capabilities were introduced to model corrosion and noble-metal plating phenomena, supported by an extended thermal-hydraulics framework and refined turbulence treatments. To capture two-phase flow behavior, a multiphase Euler–Euler model was implemented in Pronghorn, including advanced closure relations, high-resolution advection techniques, and capillary force reconstruction. Preliminary verification cases confirm the fidelity of the approach, while planned validation efforts target canonical multiphase benchmarks and application to msr components such as the msre pump bowl. Finally, updates to SAM’s msr mass transfer modeling were extended to consider noble gas migration into porous structures like graphite. The point kinetics model was updated to include reactivity feedback contributions from any defined species, such as xenon. The gas transport model was expanded for applicability to gas mixtures, bubble efflux phenomena, and species transport between liquid and gas phases. A selection of multi-scale Sherwood number correlations from MOSCATO/NekRS and multi-phase correlations from literature have been added for improved accuracy in calculating mass transfer coefficients. A companion effort on developing system-level redox corrosion has also been incorporated into SAM. Collectively, these enhancements strengthen the predictive capability of SAM and Pronghorn for simulating MSR thermal-hydraulics, corrosion, multiphase behavior, and fission-product transport, providing a more complete toolset for design, safety analysis, and licensing support of next-generation \gls{msr}s.

42 - ENGINEERING↗
DOE OSTI2025

MELCOR Deposition Models Applied to Noble Metals

Noble metals are chemically inert elements that form particles that can circulate around the fuel loop of a liquid-fueled molten salt reactor (LF-MSR). Due to their health-hazardous abilities, it is important to track these elements and to understand their contributions to source term during a reaction, particularly for Te as it decays into iodine. This report describes three solid deposition models that were implemented into the MELCOR reactor modeling code. The models that were implemented were Dittus-Boelter for turbulent fluid deposition, Talbot thermophoretic transport equation and Richardson-Zaki gravitational deposition. These closures were used to calculate the mass transfer coefficient and was compared to those reported for the Molten Salt Reactor Experiment (MSRE). The impacts of salt, operation and particle parameters on how they affect solid deposition are described, and found that solid deposition is strongly dependent on salt flow and viscosity, as well as particle diffusion rate and size. The conclusions form the basis for activities to be carried out in FY26 and for pursuit of future activities.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2025

Crystal structures of Salmonella enterica FraB deglycase reveal a conformational heterodimer with remarkable structural plasticity at the active site

Abstract Thefralocus ofSalmonella entericaencodes five genes for metabolism of fructose‐asparagine, an Amadori product formed by condensation of asparagine with glucose. In the last step of this pathway, the FraB deglycase cleaves 6‐phospho‐fructose‐aspartate into glucose‐6‐phosphate and aspartate. In homology models, FraB forms a homodimer with two equivalent active sites located at the dimer interface. E214 and H230, two invariant residues essential for catalysis, project into each active site cleft from opposing subunits of the dimer. Here, we have determined six crystal structures of FraB, three of a variant containing an N‐terminal His 6 tag and two mutations needed for crystallization (hereafter referred to as WT′), two with additional mutations to active site residues (E214A and P232A), and one of a variant with C‐terminal residues 313–325 deleted. Surprisingly, in the WT′ FraB structure, the two catalytic residues, E214 (general base) and H230 (general acid), are positioned ~22 Å apart. In the E214A and C‐terminus‐truncated FraB variants, however, a conformational change in the E214‐residing helix brings E214 and H230* to ~7 Å (* indicates residue from the second protomer that creates the inter‐subunit catalytic center). The loop bearing H230 also exhibits significant variation, ranging from being completely disordered to adopting open or closed states, with the nearby P232* residue being eithercisortrans. The C‐terminal residues 313–325 form a flexible “C‐tail” that can be fully disordered, bind in the active site to block access of substrate, or angle across the active site to wrap across the other subunit of the dimer and potentially close over substrate. Collectively, these structures reveal that FraB is a conformational heterodimer with two chemically identical subunits that are constrained to adopt different structures as they come together for catalysis. This plasticity likely involves correlated opening and closure of the two active sites for their respective binding and release of substrates and ligands.

Biochemistry & Molecular Biology↗
DOE OSTI2025

Cryo-EM structures of the small-conductance Ca 2+ -activated K Ca 2.2 channel

Small-conductance Ca 2+ -activated K + (K Ca 2.1-K Ca 2.3) channels modulate neuronal and cardiac excitability. We report cryo-electron microscopy structures of the K Ca 2.2 channel in complex with calmodulin and Ca 2+ , alone or bound to two small molecule inhibitors, at 3.18, 3.50, 2.99 and 2.97 angstrom resolution, respectively. Extracellular S3-S4 loops in β-hairpin configuration form an outer canopy over the pore with an aromatic box at the canopy’s center. Each S3-S4 β-hairpin is tethered to the selectivity filter in the neighboring subunit by inter-subunit hydrogen bonds. This hydrogen bond network flips the aromatic residue (Tyr362) in the filter’s GYG signature by 180°, causing the outer selectivity filter to widen and water to enter the filter. Disruption of the tether by a mutation narrows the outer selectivity filter, realigns Tyr362 to the position seen in other K + channels, and significantly increases unitary conductance. UCL1684, a mimetic of the bee venom peptide apamin, sits atop the canopy and occludes the opening in the aromatic box. AP14145, an analogue of a therapeutic for atrial fibrillation, binds in the central cavity below the selectivity filter and induces closure of the inner gate. These structures provide a basis for understanding the small unitary conductance and pharmacology of K Ca 2.x channels.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Hysteresis area at the canopy level during and after a drought event in the Central Amazon

Understanding forest water limitation during droughts within a warming climate is essential for accurate predictions of forest-climate interactions. In hyperdiverse ecosystems like the Amazon forest, the mechanisms shaping hysteresis patterns in transpiration relative to environmental factors are not well understood. From this perspective, we investigated these dynamics by conducting in situ leaf-level measurements throughout and after the 2015 El Niño-Southern Oscillation (ENSO) drought. Our findings indicate a substantial increase in the hysteresis area (H area ) among transpiration (E), vapor pressure deficit (VPD), and stomatal conductance (g s ) at canopy level during the ENSO peak, attributed to both temporal lag and differences in magnitude between g s and VPD peaks. Specifically, the canopy species Pouteria anomala exhibited an increased H area , due to earlier maximum g s rates leading to a greater temporal lag with VPD compared to the post-drought period. Additionally, leaf water potential (ψ L ) and canopy temperature (T canopy ) showed larger H area during the ENSO peak compared to post-drought conditions across all studied species, suggesting that stomatal closure, particularly during the afternoon, acts to minimize water loss and may explain the counterclockwise hysteresis observed between ψ L and T canopy . Here, the pronounced H area during the drought points to a potential imbalance between water supply and demand, underlining the role of stomatal behavior of isohydric species in response to drought.

54 ENVIRONMENTAL SCIENCES↗