Predictability and Dynamics of Hurricane Joaquin (2015) Explored through Convection-Permitting Ensemble Sensitivity Experiments
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Robert G. Nystrom↗
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Wind-Stress Simulations and Equatorial Dynamics in an AGCM: Basic Results from a 1979-1999 Forced SST Experiment - Part 1
This is the first of a two part study examining the connection of the equatorial momentum budget in an AGCM (Atmospheric General Circulation Model), with simulated equatorial surface wind stresses over the Pacific. The AGCM used in this study forms part of a newly developed coupled forecasting system used at NASA's Seasonal- to-Interannual Prediction Project. Here we describe the model and present results from a 20-year (1979-1999) AMIP-type experiment forced with observed SSTs (Sea Surface Temperatures). Model results are compared them with available observational data sets. The climatological pattern of extra-tropical planetary waves as well as their ENSO-related variability is found to agree quite well with re-analysis estimates. The model's surface wind stress is examined in detail, and reveals a reasonable overall simulation of seasonal interannual variability, as well as seasonal mean distributions. However, an excessive annual oscillation in wind stress over the equatorial central Pacific is found. We examine the model's divergent circulation over the tropical Pacific and compare it with estimates based on re-analysis data. These comparisons are generally good, but reveal excessive upper-level convergence in the central Pacific. In Part II of this study a direct examination of individual terms in the AGCM's momentum budget is presented. We relate the results of this analysis to the model's simulation of surface wind stress.
Bacmeister, Julio T.↗
Thermal Evolution of Solar Flares During the First Year of SDO as Seen by the EVE Instrument
It is very evident during the first year of the Solar Dynamics Observatory (SDO) that the Sun awoke from its prolonged minimum and is well into solar cycle 24. There has been tens of moderate M-class flares and a large X-class event (as of abstract submission), with more surely to come as the solar cycle activity increases. With SDO's 24/7 observations, every single flare has been observed through their entire evolution, providing new insights in the thermal evolution of every flare. It is evident that this evolution is extremely different for many of the flares, even for flares with similar X-ray magnitude classifications. Presented and discussed will be these different flares with their varying thermal evolution profiles as observed by the Extreme ultraviolet Variability Experiment (EVE) onboard the Solar Dynamics Observatory (SDO).
Chamberlin, Phillip C.↗
Dynamic Control System Performance during Commissioning of the Space Technology 7-Disturbance Reduction System Experiment of LISA Pathfinder
The Space Technology-7 Disturbance Reduction System (DRS) launched aboard the European Space Agency's LISA Pathfinder spacecraft on December 3, 2015, after more than a decade in development. DRS consists of three primary components: an Integrated Avionics Unit (IAU), Colloidal MicroNewton Thrusters, and Dynamic Control System (DCS) algorithms implemented on the IAU. During the portions of the mission in which the DRS was under control, the DCS was responsible for controlling the spacecraft and the free-floating test masses that were part of the LISA Test Package. The commissioning period was originally divided into two periods: before propulsion separation and after propulsion separation. A recommissioning period was added after an anomaly occurred in the thruster system. The paper will describe the activities used to commission DRS, present results from the commissioning of the DCS and the recommissioning activities per-formed after the thruster anomaly.
Hsu, Oscar↗
Dynamic Nucleation in Zr-2.5Nb During Reduced-Gravity Electromagnetic Levitation Experiments
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Gwendolyn P. Bracker↗
Effects of presenilin-1 familial Alzheimer’s disease mutations on γ-secretase activation for cleavage of amyloid precursor protein
Presenilin-1 (PS1) is the catalytic subunit of γ-secretase which cleaves within the transmembrane domain of over 150 peptide substrates. Dominant missense mutations in PS1 cause early-onset familial Alzheimer’s disease (FAD); however, the exact pathogenic mechanism remains unknown. Here we combined Gaussian accelerated molecular dynamics (GaMD) simulations and biochemical experiments to determine the effects of six representative PS1 FAD mutations (P117L, I143T, L166P, G384A, L435F, and L286V) on the enzyme-substrate interactions between γ-secretase and amyloid precursor protein (APP). Biochemical experiments showed that all six PS1 FAD mutations rendered γ-secretase less active for the endoproteolytic (ε) cleavage of APP. Distinct low-energy conformational states were identified from the free energy profiles of wildtype and PS1 FAD-mutant γ-secretase. The P117L and L286V FAD mutants could still sample the “Active” state for substrate cleavage, but with noticeably reduced conformational space compared with the wildtype. The other mutants hardly visited the “Active” state. The PS1 FAD mutants were found to reduce γ-secretase proteolytic activity by hindering APP residue L49 from proper orientation in the active site and/or disrupting the distance between the catalytic aspartates. Therefore, our findings provide mechanistic insights into how PS1 FAD mutations affect structural dynamics and enzyme-substrate interactions of γ-secretase and APP.
60 APPLIED LIFE SCIENCES↗
Interpretive MHD modeling of dispersive shell pellet injection for rapid shutdown in tokamaks
Dispersive shell pellet (DSP) injection is modeled with the extended-MHD code NIMROD for interpretive insight into the results of recent DIII-D DSP experiments and to explore the dynamics of an inside-out thermal quench for disruption mitigation in tokamaks. Simulations of the pre-thermal quench (TQ) phase indicate that the upper bound for the quantity of ablated carbon shell material that will not perturb the flux surfaces is in the ballpark of, but somewhat below the experimental quantity. Even below this quantity, sufficient electrons are added to the plasma by the shell material to produce significant dilution cooling before the TQ is triggered. Simulations carried through the end of the TQ have very large amplitude MHD fluctuations (δB/B>10 -2 ) at the time of the plasma current spike associated with current profile redistribution. Finally, after the plasma current spike, which is of comparable amplitude to that measured in DIII-D experiments, none of the runaway electron test-particles whose orbits are tracked throughout the simulation remain confined.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Regional and Model-Specific Response Types in A Global Gridded Crop Model Ensemble
Crop models are often employed to project crop yields under changing conditions such as global warming and associated management change for adaptation. Multi-model ensembles are promoted to enhance the robustness of projections, but questions remain on what causes often large differences between projections of individual models. Global Gridded Crop Models (GGCMs) are especially exposed to this question when applied for assessing climate change impacts, adaptation, environmental impacts of agricultural production, because their results are used in downstream analyses, such as in integrated assessment or economic modeling for projecting future land-use change. Even though global gridded crop models are often based on detailed field-scale models or have implemented similar modeling principles in other ecosystem models, global-scale models are subject to substantial uncertainties from both model structure and parametrization as well as from calibration and input data quality. AgMIP’s Global Gridded Crop Model Intercomparison (GGCMI) has thus set out to intercompare GGCMs in order to evaluate model performance, describe model uncertainties, identify inconsistencies within the ensemble and underlying reasons, and to ultimately improve models and modeling capacities. In phase 2 of the GGCMI activities, 12 modeling groups followed a modeling protocol that asked for up to 1404 31-year global simulations at 0.5 arc-degree spatial resolution to assess models’ sensitivities to changes in carbon dioxide (C; 4 different levels) temperature (T; 7 different offset levels), water supply (W; 9 levels), and nitrogen (N; 3 levels), the so-called CTWN experiment (Franke et al. 2020; http://dx.doi.org/10.5194/gmd-13-2315-2020). We here present analyses of model response types using impact response surfaces along the C, T, W, and N dimensions, respectively and collectively. Doing so, we can understand differences in simulated responses per driver rather than aggregated changes in yields. We find that models’ sensitivities to the individual driver dimensions are substantially different and often more different across models than across regions. A cluster analysis finds regional and model-specific patterns. There is some agreement across models with respect to the spatial patterns of response types but strong differences in the distribution of response type clusters across models suggests that models need to undergo further scrutiny. We suggest establishing standards in model process evaluation not only against historical dynamics but also against dedicated experiments across the CTWN dimensions.
crop models↗
Spectral broadening and vibronic dynamics of the S2 state of canthaxanthin in the orange carotenoid protein
We have performed a series of broadband multidimensional electronic spectroscopy experiments to probe the electronic and vibrational dynamics of the canthaxanthin chromophore of the Orange Carotenoid Protein (OCP) from Synechocystis sp. PCC 6803 in its photoactivated red state, OCPR. Cross-peaks observed below the diagonal of the two-dimensional electronic spectrum indicate that absorption transitions prepare the bright S2 state of the ketocarotenoid canthaxanthin near to a sequence of conical intersections, allowing passage to the dark S1 state via the Sx intermediate in <50 fs. Rapid damping of excited-state coherent wavepacket motions suggests that the branching coordinates of the conical intersections include out-of-plane deformation and C=C stretching coordinates of the π-conjugated isoprenoid backbone. The unusual proximity of the Franck–Condon S2 state structure to the conical intersections with Sx and S1 suggests that the protein surroundings of canthaxanthin prepare it to function as an excitation energy trap in the OCPR–phycobilisome complex. Numerical simulations using the multimode Brownian oscillator model demonstrate that the ground-state absorption spectrum of OCPR overlaps with the fluorescence emission spectrum of allophycocyanin due to spectral broadening derived especially from the intramolecular motions of the canthaxanthin chromophore in its binding site.
Yang, Kunwei↗
Dynamic Control System Performance during Commissioning of the Space Technology 7-Disturbance Reduction System Experiment of LISA Pathfinder
The Space Technology-7 Disturbance Reduction System (DRS) launched aboard the European Space Agencys LISA Pathfinder spacecraft on December 3, 2015, after more than a decade in development. DRS consists of three prima-ry components: an Integrated Avionics Unit (IAU), Colloidal MicroNewton Thrusters, and Dynamic Control System (DCS) algorithms implemented on the IAU. During the portions of the mission in which the DRS was under control, the DCS was responsible for controlling the spacecraft and the free-floating test masses that were part of the LISA Test Package. The commissioning period was originally divided into two periods: before propulsion separation and after pro-pulsion separation. A recommissioning period was added after an anomaly oc-curred in the thruster system. The paper will describe the activities used to com-mission DRS, present results from the commissioning of the DCS and the re-commissioning activities performed after the thruster anomaly.
Hsu, Oscar↗
Sensitivity of the FVGCM to Changes in Ozone
We have carried out an experiment with the finite volume general circulation model (FVGCM). This experiment consisted of two different imposed changes in the climatological ozone fields assumed in the radiation code. for conditions with no significant ozone hole. This distribution was obtained from a 50-year simulation of the full stratospheric ozone chemistry, with a time-dependent chlorine loading, done with our off-line chemical transport model (CTM). Three years (1978-1980) of this simulation were averaged to form a monthly, zonal-mean ozone distribution that was used in the 20-year integration of the FVGCM for "unperturbed" conditions. The second 20-year GCM integration included a fully-developed ozone hole. This ozone distribution was from three years, 1998-2000, from the same CTM simulation. The goal of this work is to determine the coupled response of the chemistry and dynamics of the stratosphere. These experiments are the first step in understanding the coupled response. An important initial question concerns the significance of the signals: if 20-year integrations turn out to be too short, the runs will be extended.
Stolarski↗
Synchronous dynamics of a coupled shaft/bearing/housing system with auxiliary support from a clearance bearing: Analysis and experiment
This study examines the response of a flexible rotor supported by load sharing between linear bearings and an auxiliary clearance bearing. The objective of the work is to develop a better understanding of the dynamical behavior of a magnetic bearing supported rotor system interacting with auxiliary bearings during a critical operating condition. Of particular interest is the effect of coupling between the bearing/housing and shaft vibration on the rotordynamical responses. A simulation model is developed and a number of studies are performed for various parametric configurations. An experimental investigation is also conducted to compare and verify the rotordynamic behavior predicted by the simulation studies. A strategy for reducing synchronous shaft vibration through appropriate design of coupled shaft/bearing/housing vibration modes is identified. The results are presented and discussed.
Lawen, James, Jr.↗
Anisotropic X-Ray Scattering of Transiently Oriented Water
We study the structural dynamics of liquid water by time-resolved anisotropic x-ray scattering under the optical Kerr effect condition. In this way, we can separate the anisotropic scattering decay of 160 fs from the delayed temperature increase of ~ 0.1 K occurring at 1 ps and quantify transient changes in the O-O pair distribution function. Polarizable molecular dynamics simulations reproduce well the experiment, indicating transient alignment of molecules along the electric field, which shortens the nearest-neighbor distances. In addition, analysis of the simulated water local structure provides evidence that two hypothesized fluctuating water configurations exhibit different polarizability.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
The Arabidopsis T‐DNA mutant SALK_008491 carries a 14‐kb deletion on chromosome 3 that provides rare insights into the plant response to dynamic light stress
Abstract In nature, plants experience rapid changes in light intensity and quality throughout the day. To maximize growth, they have established molecular mechanisms to optimize photosynthetic output while protecting components of the light‐dependent reaction and CO 2 fixation pathways. Plant phenotyping of mutant collections has become a powerful tool to unveil the genetic loci involved in environmental acclimation. Here, we describe the phenotyping of the transfer‐DNA (T‐DNA) insertion mutant line SALK_008491, previously known as nhd1‐1 . Growth in a fluctuating light regime caused a loss in growth rate accompanied by a spike in photosystem (PS) II damage and increased non‐photochemical quenching (NPQ). Interestingly, an independent nhd1 null allele did not recapitulate the NPQ phenotype. Through bulk sequencing of a backcrossed segregating F 2 pool, we identified an ~14‐kb large deletion on chromosome 3 (Chr3) in SALK_008491 affecting five genes upstream of NHD1 . Besides NHD1 , which encodes for a putative plastid Na + /H + antiporter, the stromal NAD‐dependent D‐3‐phosphoglycerate dehydrogenase 3 ( PGDH3 ) locus was eradicated. Although some changes in the SALK_008491 mutant's photosynthesis can be assigned to the loss of PGDH3, our follow‐up studies employing respective single mutants and complementation with overlapping transformation‐competent artificial chromosome (TAC) vectors reveal that the exacerbated fluctuating light sensitivity in SALK_008491 mutants result from the simultaneous loss of PGDH3 and NHD1. Altogether, the data obtained from this large deletion‐carrying mutant provide new and unintuitive insights into the molecular mechanisms that function to protect the photosynthetic machinery. Moreover, our study renews calls for caution when setting up reverse genetic studies using T‐DNA lines. Although second‐site insertions, indels, and SNPs have been reported before, large deletion surrounding the insertion site causes yet another problem. Nevertheless, as shown through this research, such unpredictable genetic events following T‐DNA mutagenesis can provide unintuitive insights that allow for understanding complex phenomena such as the plant acclimation to dynamic high light stress.
Lopez, Laura S.↗
Molecular Dynamics Investigation of the Relaxation Mechanism of Entangled Polymers after a Large Step Deformation
The chain retraction hypothesis of the tube model for nonlinear polymer rheology has been challenged by the recent small-angle neutron scattering (SANS) experiment. In this study, we further examine the microscopic relaxation mechanism of entangled polymer melts after a large step uniaxial extension by using large-scale molecular dynamics simulation. We show that the unique structural features associated with the chain retraction mechanism of the tube model are absent in our simulations, in agreement with the previous experimental results. In contrast to SANS experiments, molecular dynamics simulations allow us to accurately and unambiguously determine the evolution of the radius of gyration tensor of a long polymer chain after a large step deformation. Contrary to the prediction of the tube model, our simulations reveal that the radius of gyration in the perpendicular direction to stretching increases monotonically toward its equilibrium value throughout the stress relaxation. These results provide a critical step in improving our understanding of nonlinear rheology of entangled polymers.
36 MATERIALS SCIENCE↗
CSI technology validation on an LSS ground experiment facility
The test bed developed at JPL for experimental evaluation of new technologies for the control of large flexible space structures is described. The experiment consists of a flexible spacecraft dynamic simulator, sensors, actuators, a microcomputer, and an advanced programming environment. The test bed has been operational for over a year, and thus far nine experiments were completed or are currently in progress. Several of these experiments were reported at the 1987 CSI conference, and several recent ones are documented in this paper, including high order adaptive control, non-parametric system identification, and mu-synthesis robust control. An aggressive program of experiments is planned for the forseeable future.
Wang, S. J.↗
Characterizing the Effect of Capillary Heterogeneity on Multiphase Flow Pulsation in an Intermediate–Scale Beadpack Experiment using Time Series Clustering and Frequency Analysis
An intermediate-scale beadpack drainage experiment was conducted to investigate how simple layered lamination heterogeneity affects CO 2 flow. Two simple layers of capillary barriers are manually packed in the tank and slow drainage was carried out using analog fluids to mimic the capillary- and gravity-dominated CO 2 upward migration process in deep saline aquifers. Nonwetting phase saturation time series clustering analysis and frequency analysis have been conducted on the experimental data. Additionally, modified invasion percolation numerical simulations were done on a digital model of the beadpack to compare to experimental results. Results show that capillary barriers can lead to strong pulsation behavior, which in turn can cause unexpected early breaching through other barriers. The inlet pressure is found to be able to respond to saturation changes in far regions of the domain, indicating that the wetting phase can transmit pressure changes from the other phase. Although static simulations were not able to capture all the dynamic behavior observed in the experiment, Monte Carlo composite simulation results combining many different realizations can better illustrate how the nonwetting phase will behave in the heterogeneous domain. Furthermore, our results suggest the need for CO 2 storage site selection with preference given to aquifers with more capillary barriers with finer grain sizes to avoid flow pulsation and to retard plume upward migration.
58 GEOSCIENCES↗
Nanopores with dynamic pore opening diameter
Solid state nanopores have emerged as model systems for understanding transport properties on the nanoscale. They serve as templates for both preparing mimics of biological channels and designing biological sensors. Unlike their biological inspirations, the majority of nanopores prepared thus far, however, have been structurally static devices such that the pore opening diameter is fixed. If we could prepare nanopores whose opening diameter fluctuated in time with controlled amplitude at known locations in the pore, we could create ionic memristors as well as achieve new transport modes. Here we present ∼10 nm diameter single nanopores drilled through a 10 nm thick gold layer positioned on top of a 30 nm thick silicon nitride film. Two types of devices were prepared; one containing single stranded DNA and the other containing hairpin DNA attached to the discrete layer of gold using thiol chemistry. When an external electric field was applied across a nanopore with single stranded DNA, the nanoconfined DNA molecules exhibited steric and electrical constraints that led to memristor-like behavior in the current–voltage curves. The degree of hysteresis was controlled by salt concentration, magnitude of voltage and pore diameter. In contrast, nanopores containing DNA hairpins conducted similar currents in forward and reverse bias in agreement with the rigidity of the hairpin molecule. The experiments are explained by Brownian dynamics simulations that reveal voltage and salt concentration induced changes in DNA extension. The degree of DNA extension was also found to be dependent on the location of the molecules along the pore axis. The nanopores presented here provide the first steps towards preparation of non-equilibrium nanopore systems.
Vlassiouk, Ivan [ORNL] (ORCID:0000000254940386)↗