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At least 901 records · Page 50
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Direct interaction of DNA repair protein tyrosyl DNA phosphodiesterase 1 and the DNA ligase III catalytic domain is regulated by phosphorylation of its flexible N-terminus

Tyrosyl DNA phosphodiesterase 1 (TDP1) and DNA Ligase IIIα (LigIIIα) are key enzymes in single-strand break (SSB) repair. TDP1 removes 3'-tyrosine residues remaining after degradation of DNA topoisomerase (TOP) 1 cleavage complexes trapped by either DNA lesions or TOP1 inhibitors. It is not known how TDP1 is linked to subsequent processing and LigIIIα-catalyzed joining of the SSB. Here we define a direct interaction between the TDP1 catalytic domain and the LigIII DNA-binding domain (DBD) regulated by conformational changes in the unstructured TDP1 N-terminal region induced by phosphorylation and/or alterations in amino acid sequence. Full-length and N-terminally truncated TDP1 are more effective at correcting SSB repair defects in TDP1 null cells compared with full-length TDP1 with amino acid substitutions of an N-terminal serine residue phosphorylated in response to DNA damage. TDP1 forms a stable complex with LigIII 170-755 , as well as full-length LigIIIα alone or in complex with the DNA repair scaffold protein XRCC1. Small-angle X-ray scattering and negative stain electron microscopy combined with mapping of the interacting regions identified a TDP1/LigIIIα compact dimer of heterodimers in which the two LigIII catalytic cores are positioned in the center, whereas the two TDP1 molecules are located at the edges of the core complex flanked by highly flexible regions that can interact with other repair proteins and SSBs. As TDP1and LigIIIα together repair adducts caused by TOP1 cancer chemotherapy inhibitors, the defined interaction architecture and regulation of this enzyme complex provide insights into a key repair pathway in nonmalignant and cancer cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Stochastic superparameterization in quasigeostrophic turbulence

In this article we expand and develop the authors' recent proposed methodology for efficient stochastic superparameterization algorithms for geophysical turbulence. Geophysical turbulence is characterized by significant intermittent cascades of energy from the unresolved to the resolved scales resulting in complex patterns of waves, jets, and vortices. Conventional superparameterization simulates large scale dynamics on a coarse grid in a physical domain, and couples these dynamics to high-resolution simulations on periodic domains embedded in the coarse grid. Stochastic superparameterization replaces the nonlinear, deterministic eddy equations on periodic embedded domains by quasilinear stochastic approximations on formally infinite embedded domains. The result is a seamless algorithm which never uses a small scale grid and is far cheaper than conventional SP, but with significant success in difficult test problems. Various design choices in the algorithm are investigated in detail here, including decoupling the timescale of evolution on the embedded domains from the length of the time step used on the coarse grid, and sensitivity to certain assumed properties of the eddies (e.g. the shape of the assumed eddy energy spectrum). We present four closures based on stochastic superparameterization which elucidate the properties of the underlying framework: a ‘null hypothesis’ stochastic closure that uncouples the eddies from the mean, a stochastic closure with nonlinearly coupled eddies and mean, a nonlinear deterministic closure, and a stochastic closure based on energy conservation. The different algorithms are compared and contrasted on a stringent test suite for quasigeostrophic turbulence involving two-layer dynamics on a β-plane forced by an imposed background shear. The success of the algorithms developed here suggests that they may be fruitfully applied to more realistic situations. They are expected to be particularly useful in providing accurate and efficient stochastic parameterizations for use in ensemble-based state estimation and prediction.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Constrained approximation of effective generators for multiscale stochastic reaction networks and application to conditioned path sampling

Efficient analysis and simulation of multiscale stochastic systems of chemical kinetics is an ongoing area for research, and is the source of many theoretical and computational challenges. In this paper, we present a significant improvement to the constrained approach, which is a method for computing effective dynamics of slowly changing quantities in these systems, but which does not rely on the quasi-steady-state assumption (QSSA). The QSSA can cause errors in the estimation of effective dynamics for systems where the difference in timescales between the “fast” and “slow” variables is not so pronounced. This new application of the constrained approach allows us to compute the effective generator of the slow variables, without the need for expensive stochastic simulations. This is achieved by finding the null space of the generator of the constrained system. For complex systems where this is not possible, or where the constrained subsystem is itself multiscale, the constrained approach can then be applied iteratively. This results in breaking the problem down into finding the solutions to many small eigenvalue problems, which can be efficiently solved using standard methods. Since this methodology does not rely on the quasi steady-state assumption, the effective dynamics that are approximated are highly accurate, and in the case of systems with only monomolecular reactions, are exact. We will demonstrate this with some numerics, and also use the effective generators to sample paths of the slow variables which are conditioned on their endpoints, a task which would be computationally intractable for the generator of the full system.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Exact and locally implicit source term solvers for multifluid-Maxwell systems

Recently, a family of models that couple multifluid systems to the full Maxwell equations have been used in laboratory, space, and astrophysical plasma modeling. These models are more complete descriptions of the plasma than reduced models like magnetohydrodynamic (MHD) since they are derived more closely from the full kinetic Vlasov-Maxwell system, without assumptions like quasi-neutrality, negligible electron mass, etc. Thus these models naturally retain non-ideal MHD effects like electron inertia, Hall term, pressure anisotropy/nongyrotropy, displacement current, among others. One obstacle to broader application of these model is that an explicit treatment of their source terms leads to the need to resolve rapid processes like plasma oscillation and electron cyclotron motion, even when these are not important. In this paper, we suggest two ways to address this issue. First, we derive the analytic solutions to the source update equations, which can be implemented as a practical, but less generic solver. We then develop a time-centered, locally implicit algorithm to update the source terms, allowing stepping over the fast kinetic time-scales. For a plasma with S species, the locally implicit algorithm involves inverting a local (3 S + 3) × (3 S + 3) matrix only, thus is very efficient. The performance can be further increased by using the direct update formulas to skip null calculations. In this paper, we present benchmarks illustrating the exact energy-conservation of the locally implicit solver, as well as its efficiency and robustness for both small-scale, idealized problems and largescale, complex systems. The locally implicit algorithm can be also easily extended to include other local sources, like collisions and ionization, which are difficult to solve analytically.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2014

Effects of magnetic configuration on divertor power and particle deposition for long pulse operation in EAST

The magnetic configuration exhibits a strong influence on the dynamics of Edge Localized Modes (ELMs), as demonstrated in the EAST superconducting tokamak. Here we find that poloidal drifts play an important role in particle deposition during the ELMs, leading to a strong up/down asymmetry in the double null divertor configuration, favoring the upper divertor for normal toroidal field, Bt, i.e., with the ion ∇B drift towards the bottom, while the heat flux distribution appears to be rather uniform during ELMs. These observations are well reproduced by the boundary plasma turbulence code, BOUT++. As divertor pumping was only available at the bottom, the preferential particle flow towards the bottom divertor associated with reverse Bt led to a preferred scenario for long pulse operation in EAST.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2015

MSH1 Is a Plant Organellar DNA Binding and Thylakoid Protein under Precise Spatial Regulation to Alter Development

As metabolic centers, plant organelles participate in maintenance, defense, and signaling. MSH1 is a plant-specific protein involved in organellar genome stability in mitochondria and plastids. Plastid depletion of MSH1 causes heritable, non-genetic changes in development and DNA methylation. We investigated the msh1 phenotype using hemi-complementation mutants and transgene-null segregants from RNAi suppression lines to sub-compartmentalize MSH1 effects. We show that MSH1 expression is spatially regulated, specifically localizing to plastids within the epidermis and vascular parenchyma. The protein binds DNA and localizes to plastid and mitochondrial nucleoids, but fractionation and protein–protein interactions data indicate that MSH1 also associates with the thylakoid membrane. Plastid MSH1 depletion results in variegation, abiotic stress tolerance, variable growth rate, and delayed maturity. Depletion from mitochondria results in 7%–10% of plants altered in leaf morphology, heat tolerance, and mitochondrial genome stability. MSH1 does not localize within the nucleus directly, but plastid depletion produces non-genetic changes in flowering time, maturation, and growth rate that are heritable independent of MSH1. MSH1 depletion alters non-photoactive redox behavior in plastids and a sub-set of mitochondrially altered lines. Ectopic expression produces deleterious effects, underlining its strict expression control. Unraveling the complexity of the MSH1 effect offers insight into triggers of plant-specific, transgenerational adaptation behaviors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Neutron-fragment and Neutron-neutron Correlations in Low-energy Fission

A computational method has been developed to simulate neutron emission from thermal-neutron induced fission of {sup 235}U and from spontaneous fission of {sup 252}Cf. Measured pre-emission mass-yield curves, average total kinetic energies and their variances, both as functions of mass split, are used to obtain a representation of the distribution of fragment velocities. Measured average neutron multiplicities as a function of mass split and their dependence on total kinetic energy are used. Simulations can be made to reproduce measured factorial moments of neutron-multiplicity distributions with only minor empirical adjustments to some experimental inputs. The neutron-emission spectra in the rest-frame of the fragments are highly constrained by ENDF/B-VII.1 prompt-fission neutron-spectra evaluations. The n-f correlation measurements of Vorobyev et al. (2010) are consistent with predictions where all neutrons are assumed to be evaporated isotropically from the rest frame of fully accelerated fragments. Measured n-f and n-n correlations of others are a little weaker than the predictions presented here. These weaker correlations could be used to infer a weak scission-neutron source. However, the effect of neutron scattering on the experimental results must be studied in detail before moving away from a null hypothesis that all neutrons are evaporated from the fragments.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2014

Damping of unwanted modes in SRF deflecting/crabbing cavities

As deflecting and crab cavities do not use the fundamental acceleration mode for their operation, the spectrum of unwanted modes is significantly different from that of accelerating cavities. The fundamental acceleration mode is now unwanted and can cause energy spread in the beam; in addition this mode frequency is often close to or lower than that of the deflecting mode, making it difficult to damp. This is made more complex in some of the compact crab cavities as there small beampipes often attenuate the fields very sharply. In addition in some crab cavities there can be an orthogonal transverse mode similar to the deflecting mode, known as the same order mode. The degeneracy of these modes must be split by polarising the cavity and if the polarisation is not large enough, dampers should be placed at either an electric or magnetic field null of the crabbing mode to effectively damp the unwanted polarisation. Various concepts for dealing with unwanted modes in various SRF deflecting cavities will be reviewed.

43 PARTICLE ACCELERATORS↗
DOE OSTI2022

A signal packet router for the upgrade of the Muon spectrometer at the ATLAS experiment

Here, we present the design, characterization, and production of a signal packet router for the upgrade of the ATLAS forward muon detector. The router serves as a packet switch in one of the primary trigger paths. It handles up to 12 serial inputs at 4.8 Gbps/input from on-detector electronics and outputs four 4.8 Gbps to the trigger processing circuits. In the 12-to-4 packet switching process, the input streams are decoded and synchronized to a common clock domain for data packets forwarding and NULL packets suppression. Challenges in the design include operations of multi-giga hertz serial links with low and constant latency (<100 ns) for packet routing, as well as mitigation of radiation-induced effects in the harsh radiation environment over 10 years of detector operation. The Router design has been fully characterized and demonstrated to meet all specifications. In total 256 Routers were installed in the detector. Its design concept can be used in other similar applications, particularly in a radiation environment.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

Numerical simulation study of impurity B transport during real-time B powder injection in EAST

To understand the beneficial effects of impurity boron (B) on the plasma, the transport of B species in both atomic and ionic states in the edge plasma and the ensuing evolution of the background plasma are simulated during real-time B powder injection by using two-dimensional fluid code SOLPS-ITER. The initial background plasma profiles for the simulation are reconstructed based on an EAST upper-single null discharge (shot No. 70601). With the injection rate of B atoms, 4.0 × 10 21 atoms/s, the simulation shows that effective charge number is less than 1.1 at the inner boundary R - R sep = -5.2 cm (background plasma density, 5.1 × 10 19 m -3 ) at the outer mid-plane indicating that the B impurity does not have much influence on the energy confinement. The present work finds that the impurity B exhibits very specific features in the edge plasma, mostly present in the narrow region just outside the separatrix. The particular distribution pattern can reduce the heat flux greatly, leading to the divertor detachment. The divertor detachment can be achieved easily under an injection rate of B powder in a reasonable range. This study suggests that the impurity B has a promising potential application in future tokamaks.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Fuel recycling control in long pulse operation with full tungsten divertors in EAST tokamak

Fuel recycling control in long pulse discharges is studied in EAST tokamak with tungsten divertors by particle balance. Double null configuration, proper Resonant Magnetic Perturbation (RMP), divertor cryopumps and realtime lithium injection, are all very effective for recycling control. High heating power discharge leads to low recycling due to the enhancement of particle exhausting. High external gas injection is required in a low fuel recycling discharge to keep a constant density, and Dα emission is increased by external injection, therefore a higher Dα emission may indicate low fuel recycling for the same plasma density. Reproducible long pulse discharges of over 100 s with core electron temperature >10 keV, and 1056 s discharge with ~1.5 MW heating power were obtained in the EAST 2021 campaign, fuel recycling was well controlled by divertor cryopumps and realtime lithium injection. The results provide a valuable reference for the high power and long pulse operation in future fusion reactors, such as ITER and CFETR.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Active wall conditioning through boron powder injection compatible $\mathrm{ELM}$ control in $\mathrm{EAST}$

Real-time wall conditioning and edge-localized mode (ELM) suppression through real-time boron powder injection into high-confinement mode discharges of the Experimental Advanced Superconducting Tokamak (EAST) have been investigated. The boron powder injection effectively conditioned the plasma-facing components, as shown by the reductions in low-Z and high-Z impurities and the global recycling level in the whole inner vessel, and suppressed the strong magnetohydrodynamic (MHD) activity in the plasma core. The improved wall conditions also resulted in an earlier transition from L- to H-mode. Boron powder injection also effectively suppressed ELM in the lower single null configuration with BT in the favorable direction while leaving the plasma density and stored energy largely unaffected.

36 MATERIALS SCIENCE↗
DOE OSTI2018

A simple procedure for construction of the orthonormal basis vectors of irreducible representations of O(5) in the O T ( 3 ) Ⓧ O N ( 2 ) basis

We report a simple and effective algebraic isospin projection procedure for constructing orthonormal basis vectors of irreducible representations of O(5) ⊃ OT(3) Ⓧ O$_\mathscr{N}$ (2) from those in the canonical O(5) ⊃ SU Λ (2) Ⓧ SU I (2) basis is outlined. The expansion coefficients are components of null space vectors of the projection matrix with four nonzero elements in each row in general. Explicit formulae for evaluating O T (3)-reduced matrix elements of O(5) generators are derived.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2013

Test of Lorentz and CPT violation with Short Baseline Neutrino Oscillation Excesses

The sidereal time dependence of MiniBooNE $ν_e$ and $\bar{ν}_e$ appearance data is analyzed to search for evidence of Lorentz and CPT violation. An unbinned Kolmogorov–Smirnov (K–S) test shows both the $ν_e$ and $\bar{ν}_e$ appearance data are compatible with the null sidereal variation hypothesis to more than 5%. Using an unbinned likelihood fit with a Lorentz-violating oscillation model derived from the Standard Model Extension (SME) to describe any excess events over background, we find that the $ν_e$ appearance data prefer a sidereal time-independent solution, and the $\bar{ν}_e$ appearance data slightly prefer a sidereal time-dependent solution. Limits of order 10-20 GeV are placed on combinations of SME coefficients. These limits give the best limits on certain SME coefficients for $ν_μ$→$ν_e$ and $\bar{ν}_μ$→$\bar{ν}_e$ oscillations. The fit values and limits of combinations of SME coefficients are provided.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Do atoms age?

Time evolution generically entangles a quantum state with environmental degrees of freedom. The resulting increase in entropy changes the properties of that quantum system leading to “aging”. It is interesting to ask if this familiar property also applies to simple, single particle quantum systems such as the decay of a radioactive particle. We propose a test of such aging in an ion clock setup where we probe for temporal changes to the energies of the electronic state of an ion containing a radioactive nucleus. Such effects are absent in standard quantum mechanics and this test is thus a potent null test for violations of quantum mechanics. As a proof of principle, we show that these effects exist in causal non-linear modifications of quantum mechanics.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Search for the lepton flavor violating τ → 3μ decay in proton-proton collisions at s = 13 TeV

A search for the lepton flavor violating τ → 3 μ decay is performed using proton-proton collision events at a center-of-mass energy of 13 TeV collected by the CMS experiment at the LHC in 2017–2018, corresponding to an integrated luminosity of 97.7 fb − 1 . Tau leptons produced in both heavy-flavor hadron and W boson decays are exploited in the analysis. No evidence for the decay is observed. The results of this search are combined with an earlier null result based on data collected in 2016 to obtain a total integrated luminosity of 131 fb − 1 . The observed (expected) upper limits on the branching fraction B ( τ → 3 μ ) at confidence levels of 90 and 95% are 2.9 × 10 − 8 ( 2.4 × 10 − 8 ) and 3.6 × 10 − 8 ( 3.0 × 10 − 8 ), respectively.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗