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At least 721 records · Page 40
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Structural basis of RNA conformational switching in the transcriptional regulator 7SK RNP

7SK non-coding RNA (7SK) negatively regulates RNA polymerase II (RNA Pol II) elongation by inhibiting positive transcription elongation factor b (P-TEFb), and its ribonucleoprotein complex (RNP) is hijacked by HIV-1 for viral transcription and replication. Methylphosphate capping enzyme (MePCE) and La-related protein 7 (Larp7) constitutively associate with 7SK to form a core RNP, while P-TEFb and other proteins dynamically assemble to form different complexes. Here, we present the cryo-EM structures of 7SK core RNP formed with two 7SK conformations, circular and linear, and uncover a common RNA-dependent MePCE-Larp7 complex. Further, together with NMR, biochemical, and cellular data, these structures reveal the mechanism of MePCE catalytic inactivation in the core RNP, unexpected interactions between Larp7 and RNA that facilitate a role as an RNP chaperone, and that MePCE-7SK-Larp7 core RNP serves as a scaffold for switching between different 7SK conformations essential for RNP assembly and regulation of P-TEFb sequestration and release.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1978

The observability of the celestial pole and its nutations

The expected motion characteristics of the real earth are systematically analysed based on available dynamical theories for the rigid model, the elastic earth model and the earth model with liquid core. The various axes which are implicit in the dynamical theories are investigated regarding observability on the basis of astronomical observations and suitability for defining reference directions. The observational insignificance of the ''diurnal polar motion'' is demonstrated. A special effort is made to clarify customarily used terminology.

Leick, A.↗
DOE OSTI2016

Dissipative dark matter and the rotation curves of dwarf galaxies

There is ample evidence from rotation curves that dark matter halos around disk galaxies have nontrivial dynamics. Of particular significance are: a) the cored dark matter profile of disk galaxies, b) correlations of the shape of rotation curves with baryonic properties, and c) Tully-Fisher relations. Dark matter halos around disk galaxies may have nontrivial dynamics if dark matter is strongly self interacting and dissipative. Multicomponent hidden sector dark matter featuring a massless 'dark photon' (from an unbroken dark U(1) gauge interaction) which kinetically mixes with the ordinary photon provides a concrete example of such dark matter. The kinetic mixing interaction facilitates halo heating by enabling ordinary supernovae to be a source of these 'dark photons'. Dark matter halos can expand and contract in response to the heating and cooling processes, but for a sufficiently isolated halo could have evolved to a steady state or 'equilibrium' configuration where heating and cooling rates locally balance. This dynamics allows the dark matter density profile to be related to the distribution of ordinary supernovae in the disk of a given galaxy. In a previous paper a simple and predictive formula was derived encoding this relation. Here we improve on previous work by modelling the supernovae distribution via the measured UV and H α fluxes, and compare the resulting dark matter halo profiles with the rotation curve data for each dwarf galaxy in the LITTLE THINGS sample. The dissipative dark matter concept is further developed and some conclusions drawn.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS2014

Proteins with Novel Structure, Function and Dynamics

Recently, a small enzyme that ligates two RNA fragments with the rate of 10(exp 6) above background was evolved in vitro (Seelig and Szostak, Nature 448:828‐831, 2007). This enzyme does not resemble any contemporary protein (Chao et al., Nature Chem. Biol. 9:81‐83, 2013). It consists of a dynamic, catalytic loop, a small, rigid core containing two zinc ions coordinated by neighboring amino acids, and two highly flexible tails that might be unimportant for protein function. In contrast to other proteins, this enzyme does not contain ordered secondary structure elements, such as alpha‐helix or beta‐sheet. The loop is kept together by just two interactions of a charged residue and a histidine with a zinc ion, which they coordinate on the opposite side of the loop. Such structure appears to be very fragile. Surprisingly, computer simulations indicate otherwise. As the coordinating, charged residue is mutated to alanine, another, nearby charged residue takes its place, thus keeping the structure nearly intact. If this residue is also substituted by alanine a salt bridge involving two other, charged residues on the opposite sides of the loop keeps the loop in place. These adjustments are facilitated by high flexibility of the protein. Computational predictions have been confirmed experimentally, as both mutants retain full activity and overall structure. These results challenge our notions about what is required for protein activity and about the relationship between protein dynamics, stability and robustness. We hypothesize that small, highly dynamic proteins could be both active and fault tolerant in ways that many other proteins are not, i.e. they can adjust to retain their structure and activity even if subjected to mutations in structurally critical regions. This opens the doors for designing proteins with novel functions, structures and dynamics that have not been yet considered.

Proteins↗
DOE OSTI2016

User-Assisted Store Recycling for Dynamic Task Graph Schedulers

The emergence of the multi-core era has led to increased interest in designing effective yet practical parallel programming models. Models based on task graphs that operate on single-assignment data are attractive in several ways: they can support dynamic applications and precisely represent the available concurrency. However, they also require nuanced algorithms for scheduling and memory management for efficient execution. In this paper, we consider memory-efficient dynamic scheduling of task graphs. Specifically, we present a novel approach for dynamically recycling the memory locations assigned to data items as they are produced by tasks. We develop algorithms to identify memory-efficient store recycling functions by systematically evaluating the validity of a set of (user-provided or automatically generated) alternatives. Because recycling function can be input data-dependent, we have also developed support for continued correct execution of a task graph in the presence of a potentially incorrect store recycling function. Experimental evaluation demonstrates that our approach to automatic store recycling incurs little to no overheads, achieves memory usage comparable to the best manually derived solutions, often produces recycling functions valid across problem sizes and input parameters, and efficiently recovers from an incorrect choice of store recycling functions.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Cooling Delays from Iron Sedimentation and Iron Inner Cores in White Dwarfs

Do white dwarfs have inner cores made of iron? Neutron-rich nuclei like 56 Fe experience a net gravitational force and sediment toward the core. Using new phase diagrams and molecular dynamics simulations, we show that 56 Fe should separate into mesoscopic Fe-rich crystallites due to its large charge relative to the background. At solar abundances, these crystallites rapidly precipitate and form an inner core of order 100 km and 10 -3 M ⊙ that may be detectable with asteroseismology. Associated cooling delays could be up to a Gyr for low-mass white dwarfs but are only ~0.1 Gyr for massive white dwarfs, so while this mechanism may contribute to the Q-branch the heating is insufficient to fully explain it.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Slip-free multiplication and complexity of dislocation networks in FCC metals

Abstract During plastic deformation of crystalline solids, intricate networks of dislocation lines form and evolve. To capture dislocation density evolution, prominent theories of crystal plasticity assume that 1) multiplication is driven by slip in active slip systems and 2) pair-wise slip system interactions dominate network evolution. In this work, we analyze a massive database of over 100 discrete dislocation dynamics simulations (with cross-slip suppressed), and our findings bring both of these assumptions into question. We demonstrate that dislocation multiplication is commonly observed on slip systems with no applied stress and no plastic strain rate, a phenomenon we refer to as slip-free multiplication. We show that while the formation of glissile junctions provides one mechanism for slip-free multiplication, additional mechanisms which account for the influence of coplanar interactions are needed to fully explain the observations. Unlike glissile junction formation which results from a binary reaction between a pair of slip systems, these new multiplication mechanisms require higher order reactions that lead to complex network configurations. While these complex configurations have not been given much attention previously, they account for about 50% of the line intersections in our database.

36 MATERIALS SCIENCE↗
DOE OSTI2018

ATF Transient Prescription Tests in TREAT

EXECUTIVE SUMMARY The Transient Reactor Test facility (TREAT) was constructed in the late 1950’s and provided thousands of transient irradiations before being placed in standby mode in 1994. In 2017, it resumed operation in order to reclaim its crucial role in nuclear-heated safety research. TREAT is a transient reactor where inherently-safe core physics, a nimble transient rod drive system, and a philosophy of continual facility improvement work together to enable flexible power maneuvers for fuel safety research. While the facility’s flexible design and multi-mission nature saw historic experiments for numerous transient types, TREAT was not specifically adapted to optimize or demonstrate its full performance capability for Light Water Reactor (LWR) postulated accidents including Hot Zero Power Reactivity Initiated Accidents (HZP-RIA) and Loss of Coolant Accidents (LOCA). The physics of HZP-RIA drive very brief pulses with fairly large energy excursions. TREAT is currently capable of approaching HZP-RIA pulse widths through transients initiated on a large step insertion of reactivity and terminated shortly thereafter by rapid re-insertion of the transient rods (“clipping”). LOCAs are postulated to occur quite differently, starting from normal power operations followed by a long period of lower power decay heat. TREAT is able to simulate LOCA events with an initial flattop transient for tens of seconds, followed by a sizeable power reduction, to a longer segment where specimen fission heating represents internal decay heat generation. Two reactor physics testing campaigns were undertaken to address the HZP-RIA type transients, neither of which had been performed in any great measure historically to address data gaps in the timing, repeatability of clipping and effect of dynamic transient rod motions on core-to-specimen fission power coupling. The first campaign, referred to as the Accident Tolerant Fuel (ATF) transient prescription tests, employed dosimeters in the core to characterize the effect of rod motions on specimen power coupling for clipped, unclipped, and low-level steady state operations each with approximately the same moderate core energy release. This campaign was accompanied by efforts to measure dosimetry and compare results to analytic predictions. The other HZP-RIA campaign, referred to as Narrow Pulse Width (NPW) transient prescriptions, employed higher step insertions with increased core energy release to demonstrate TREAT’s capability in achieving the narrowest-possible pulse width. Additionally, a series of LOCA transient prescriptions were also performed to demonstrate how well TREAT could perform long-duration shaped transients. Both NPW and LOCA transient prescriptions did not include dosimeters but used existing plant power instrumentation to produce transient power data. All three transient prescription campaigns were successfully carried out in TREAT. The ATF-3 transient prescriptions showed that TREAT can perform clipped transients with remarkable repeatability. Measurement and modeling both showed that the power coupling in small, fissile dosimeters does not change by more than 8% between clipped, unclipped, and steady state runs while uncertainty sources in both the modeling and measurement methods were identified and found to be on the order of 20% in total. Overall, the ATF-3 transient prescription tests were successful in determining repeatability and consistency of dosimeter power coupling, developing processes for modeling and measuring this crucial parameter, and demonstrating the need for continued efforts in transient prescription work at TREAT in support of future experiment design and post test data interpretation. The NPW and LOCA transient prescriptions were also successfully performed to exhibit TREAT’s capability for these important LWR accident categories. The NPW transients showed pulse widths of ~90 ms, which were the narrowest ever achieved in TREAT to date and relevant for the upper end range of HZP-RIA simulation. This effort provided crucial data for calibrating kinetic models to be used in enhanced pulse-narrowing strategies in upcoming irradiations. Similarly, The LOCA transient prescriptions showed that TREAT can simulate the needed nuclear heating and event time scales for LOCA fuel safety research and provided essential data for future experiment design.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2017

Global Crustal Dynamics of Magnetars in Relation to Their Bright X-Ray Outbursts

This paper considers the yielding response of a neutron star crust to smooth, unbalanced Maxwell stresses imposed at the core–crust boundary, and the coupling of the dynamic crust to the external magnetic field. Stress buildup and yielding in a magnetar crust are global phenomena: an elastic distortion radiating from one plastically deforming zone is shown to dramatically increase the creep rate in distant zones. Runaway creep to dynamical rates is shown to be possible, being enhanced by in situ heating and suppressed by thermal conduction and shearing of an embedded magnetic field. A global and time-dependent model of elastic, plastic, magnetic, and thermal evolution is developed. Fault-like structures develop naturally, and a range of outburst timescales is observed. Transient events with time profiles similar to giant magnetar flares (millisecond rise, ∼0.1 s duration, and decaying power-law tails) result from runaway creep that starts in localized sub-kilometer-sized patches and spreads across the crust. A one-dimensional model of stress relaxation in the vertically stratified crust shows that a modest increase in applied stress allows embedded magnetic shear to escape the star over ∼3–10 ms, dissipating greater energy if the exterior field is already sheared. Several such zones coupled to each other naturally yield a burst of duration ∼0.1 s, as is observed over a wide range of burst energies. The collective interaction of many plastic zones forces an overstability of global elastic modes of the crust, consistent with quasi-periodic oscillation (QPO) activity extending over ∼100 s. Giant flares probably involve sudden meltdown in localized zones, with high-frequency (≫100 Hz) QPOs corresponding to standing Alfvén waves within these zones.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

Ni-based nanoalloys: Towards thermally stable highly magnetic materials

Molecular dynamics simulations and density functional theory calculations have been used to demonstrate the possibility of preserving high spin states of the magnetic cores within Ni-based core-shell bimetallic nanoalloys over a wide range of temperatures. We show that, unlike the case of Ni–Al clusters, Ni–Ag clusters preserve high spin states (up to 8 μ{sub B} in case of Ni{sub 13}Ag{sub 32} cluster) due to small hybridization between the electronic levels of two species. Intriguingly, such clusters are also able to maintain geometrical and electronic integrity of their cores at temperatures up to 1000 K (e.g., for Ni{sub 7}Ag{sub 27} cluster). Furthermore, we also show the possibility of creating ordered arrays of such magnetic clusters on a suitable support by soft-landing pre-formed clusters on the surface, without introducing much disturbance in geometrical and electronic structure of the cluster. We illustrate this approach with the example of Ni{sub 13}Ag{sub 38} clusters adsorbed on the Si(111)–(7×7) surface, which, having two distinctive halves to the unit cell, acts as a selective template for cluster deposition.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Dynamic properties of superconductors: Anderson-Bogoliubov mode and Berry phase in the BCS and BEC regimes

We analyze the evolution of the dynamics of a neutral s-wave superconductor between BCS and BEC regimes. We consider 2d case, when BCS-BEC crossover occurs already at weak coupling as a function of the ratio of the two scales – the Fermi energy E F and the bound state energy for two fermions in a vacuum, E 0 . BCS and BEC limits correspond to E F » E 0 and E F « E 0 , respectively. The chemical potential μ = E F - E 0 changes the sign between the two regimes. We use the effective action approach, derive the leading terms in the expansion of the effective action in the spatial and time derivative of the slowly varying superconducting order parameter Δ(r, τ), and express the action in terms of derivative of the phase Φ(r, τ) of Δ(r, τ) = Δe iΦ(r,τ) . The action contains (∇Φ) 2 and $\dot{Φ}$ 2 terms, which determine the dispersion of collective phase fluctuations, and iπA$\dot{Φ}$ term. For continuous Φ(r, τ), the latter reduces to the contribution from the boundary and does not affect the dynamics. We show that this longwavelength action does not change through BCS-BEC crossover. We apply our approach to a moving vortex, for which Φ is singular at the center of the vortex core, and iπA vort $\dot{Φ}$ term affects vortex dynamics. We find that this term has two contributions. One comes from the states away from the vortex core and has Avort,1 = n/2, where n is the fermion density. The other comes from electronic states inside the vortex core and has A vort,2 = -n 0 /2, where n 0 is the fermion density at the vortex core. This last term comes from the continuous part of the electronic spectrum and has no contribution from discrete levels inside the core; it also does not change if we add impurities. We interpret this term as the contribution to vortex dynamics in the continuum limit, when the spacing between energy levels ω is set to zero, while fermionic lifetime τ can be arbitrary. The total Avort = (n-n 0 )/2 determines the transversal force acting on the vortex core, πA vort $\dot{R}$ × $\hat{z}$, where $\dot{R}$ is the velocity of the vortex core and $\hat{z}$ a unit vector perpendicular to the 2d sample. The difference (n - n 0 )/2 changes through the BEC-BCS crossover as n 0 nearly compensates n in the BCS regime, but vanishes in the BEC regime.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

The core-cusp problem in cold dark matter halos and supernova feedback: effects of oscillation

This study investigates the dynamical response of dark matter (DM) halos to recurrent starbursts in forming less-massive galaxies to solve the core-cusp problem. The gas, which is heated by supernova feedback after a starburst, expands and the star formation then terminates. This expanding gas loses energy by radiative cooling and then falls back toward the galactic center. Subsequently, the starburst is enhanced again. This cycle of expansion and contraction of the interstellar gas leads to a repetitive change in the gravitational potential of the gas. The resonance between DM particles and the density wave excited by the oscillating potential plays a key role in understanding the physical mechanism of the cusp-core transition of DM halos. DM halos effectively gain kinetic energy from the baryon potential through the energy transfer driven by the resonance between the particles and density waves. We determine that the critical condition for the cusp-core transition is such that the oscillation period of the gas potential is approximately the same as the local dynamical time of DM halos. We present the resultant core radius of a DM halo after the cusp-core transition induced by the resonance by using the conventional mass density profile predicted by the cold dark matter models. Moreover, we verify the analytical model by using N-body simulations, and the results validate the resonance model.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Scale effects on core design, fuel costs, and spent fuel volume of pressurized water reactors

The desire to improve the economic competitiveness and deployment pace of nuclear energy through modularization, manufacturing, and series production had led to the development of smaller size reactors. As the standard 17x17 fuel technology is mainly maintained in the pressurized water reactors (PWRs) category, this translates into a lower number of fuel assemblies in the core and sometimes a reduced fuel height. To assess the impact of such scale change in core design on fuel cycle cost and spent fuel volume, a scoping analysis tool is developed based on infinite lattice calculations, leakage, fuel management reduced models, and levelized unit cost of electricity (LCOE) estimate. As such, cost dynamics driven by fuel specific power, burnup, core leakage, feed, cycle length, fuel assembly height as well as uranium market data are captured with consistent set of assumptions and analysis methods. A selection of 5 reactor designs representative of leading PWR developers is assessed and compared. Pursuing higher specific powers and optimal burnups are highlighted as the main fuel cost reduction drivers, nevertheless, practical limitations and opportunities must be evaluated to establish the feasibility of such enhanced fuel operation. In consequence, a detailed core design is performed using SIMULATE3 code for 5 PWR variations including natural and forced coolant circulation modes, two reactor scales, power densities of 73, 112, and 123 kW/l and higher discharge burnups. Design and optimization are performed at the lattice level, for the reflector, and at the core loading level. Satisfactory steady-state operation including power distribution, coolant operating limits, and reactivity requirements are analyzed and reported in this paper. The fuel economics of the detailed core designs confirm the scoping analysis findings. Despite the unlocked power uprates in small PWRs, the achievable burnup for a given fuel specific power requires more enrichment and shorter fuel height results in higher fabrication costs per mass of fuel, which makes scaling down core size a more expensive endeavor on the fuel cycle front. Spent fuel volumes are reported for the PWRs designed in this paper. Furthermore, these volumes are driven by the core average discharge burnup regardless of the scale in consideration. Additional cost and core performance aspects related to heavy reflector gains, fuel-reflector substitution, and disposal cost policy in the U.S. are examined.

42 ENGINEERING↗
DOE OSTI2021

Observation of Defect-Assisted Magnetic Vortex Core Reversal at Ultralow Critical Velocity

The stability of structures with nontrivial topology is a subject of great interest, both from fundamental and technological perspectives. The topology of a magnetic vortex, for example, results in high stability of the vortex core polarity, which is attractive for applications. This high stability, however, greatly impedes the required deterministic polarity switching, which is typically only achieved with large magnetic fields or strong dynamic driving. Here, we show that the interaction between the vortex core and manufactured nanoscale defects in the magnetic material lowers the required driving strength for core polarity reversal by more than an order of magnitude. We excite vortex dynamics in thin permalloy disks, and map the twodimensional (2D) vortex core trajectory using 3D time-resolved Kerr microscopy. In pristine samples, we observe normal gyrotropic motion of the vortex core. After laser-induced generation of defects, however, we observe repeated vortex core reversal at much-reduced driving strength. Micromagnetic simulations reveal how local reduction of exchange coupling and saturation magnetization can create vortex core reversal sites for deterministic vortex core switching.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
NASA NTRS1988

An investigation into force-moment calibration techniques applicable to a magnetic suspension and balance system

The problem of determining the forces and moments acting on a wind tunnel model suspended in a Magnetic Suspension and Balance System is addressed. Two calibration methods were investigated for three types of model cores, i.e., Alnico, Samarium-Cobalt, and a superconducting solenoid. Both methods involve calibrating the currents in the electromagnetic array against known forces and moments. The first is a static calibration method using calibration weights and a system of pulleys. The other method, dynamic calibration, involves oscillating the model and using its inertia to provide calibration forces and moments. Static calibration data, found to produce the most reliable results, is presented for three degrees of freedom at 0, 15, and -10 deg angle of attack. Theoretical calculations are hampered by the inability to represent iron-cored electromagnets. Dynamic calibrations, despite being quicker and easier to perform, are not as accurate as static calibrations. Data for dynamic calibrations at 0 and 15 deg is compared with the relevant static data acquired. Distortion of oscillation traces is cited as a major source of error in dynamic calibrations.

Eskins, Jonathan↗
DOE OSTI2018

Theory and Simulation of Attractive Nanoparticle Transport in Polymer Melts

We theoretically study the diffusion of a single attractive nanoparticle (NP) in unentangled and entangled polymer melts based on combining microscopic “core–shell” and “vehicle” mechanisms in a dynamic bond percolation theory framework. A physical picture is constructed which addresses the role of chain length (N), degree of entanglement, nanoparticle size, and NP–polymer attraction strength. The nanoparticle diffusion constant is predicted to initially decrease with N due to the dominance of the core–shell mechanism, then to cross over to the vehicle diffusion regime with a weaker N dependence, and eventually plateau at large enough N. This behavior corresponds to decoupling of NP diffusivity from the macroscopic melt viscosity, which is reminiscent of repulsive NPs in entangled melts, but here it occurs for a distinct physical reason. Specifically, it reflects a crossover to a transport mechanism whereby nanoparticles adsorb on polymer chains and diffuse using them as “vehicles” over a characteristic desorption time scale. Repetition of random desorption events then leads to Fickian long time NP diffusion. Complementary simulations for a range of chain lengths and low to moderate NP–polymer attraction strengths are also performed. They allow testing of the proposed diffusion mechanisms and qualitatively support the theoretically predicted dynamic crossover behavior. In conclusion, when the desorption time is smaller than or comparable to the onset of entangled polymer dynamics, the NP diffusivity becomes almost chain length independent.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2014

Simultaneous in-situ synthesis and characterization of Co@Cu core-shell nanoparticle arrays

Core-shell nanostructures have attracted much attention due to their unique and tunable properties relative to bulk structures of the same materials, making core-shell nanoparticles candidates for a variety of applications with multiple functionalities. [1,2] Intriguing magnetic behavior can be tailored by variation of size, interface, crystal orientation, and composition, and core-shell nanostructures with noble-metal shells yield novel optical responses [3] and enhanced electrocatalytic activity. [4]

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2018

Multi‐dimensional lock‐free arrays for multithreaded mode‐directed tabling in Prolog

Summary This work proposes a new design for the supporting data structures used to implement multithreaded tabling in Prolog systems. Tabling is an implementation technique that improves the expressiveness of traditional Prolog systems in dealing with recursion and redundant computations. Mode‐directed tabling is an extension to the tabling technique that supports the definition of alternative criteria for specifying how answers are aggregated, thus being very suitable for problems where the goal is to dynamically calculate optimal or selective answers. In this work, we leverage the intrinsic potential that mode‐directed tabling has to express dynamic programming problems by creating a new design that improves the representation of multi‐dimensional arrays in the context of multithreaded tabling. To do so, we introduce a new mode for indexing arguments in mode‐directed tabled evaluations, named dim , where each dim argument features a uni‐dimensional lock‐free array. Experimental results using well‐known dynamic programming problems on a 32‐core machine show that the new design introduces less overheads and clearly improves the execution time for sequential and multithreaded tabled evaluations.

Areias, Miguel↗