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At least 145 records · Page 8

An Application of the "Virtual Spacecraft" Concept in Evaluation of the Mars Pathfinder Lander Low Gain Antenna

The virtual spacecraft concept is embodied in a set of subsystems, either in the form of hardware or computational models, which together represent all, or a portion of, a spacecraft. For example, the telecommunications transponder may be a hardware prototype while the propulsion system may exist only as a simulation. As the various subsystems are realized in hardware, the spacecraft becomes progressively less virtual. This concept is enabled by JPL's Mission System Testbed which is a set of networked workstations running a message passing operating system called "TRAMEL" which stands for Task Remote Asynchronous Message Exchange Layer. Each simulation on the workstations, which may in fact be hardware controlled by the workstation, "publishes" its operating parameters on TRAMEL and other simulations requiring those parameters as input may "subscribe" to them. In this manner, the whole simulation operates as a single virtual system. This paper describes a simulation designed to evaluate a communications link between the earth and the Mars Pathfinder Lander module as it descends under a parachute through the Martian atmosphere toward the planet's surface. This link includes a transmitter and a low gain antenna on the spacecraft and a receiving antenna and receiver on the earth as well as a simulation of the dynamics of the spacecraft. The transmitter, the ground station antenna, the receiver and the dynamics are all simulated computationally while the spacecraft antenna is implemented in hardware on a very simple spacecraft mockup. The dynamics simulation is a record of one output of the ensemble of outputs of a Monte Carlo simulation of the descent. Additionally, the antenna/spacecraft mock-up system was simulated using APATCH, a shooting and bouncing ray code developed by Demaco, Inc. The antenna simulation, the antenna hardware, and the link simulation are all physically located in different facilities at JPL separated by several hundred meters and are linked via the local area network (LAN).

Pogorzelski, R. J.↗

Toward Integrated Seasonal Predictions of Land and Ocean Carbon Flux: Lessons from the 2015-16 El Nino

Seasonal forecasts made by coupled atmosphere-ocean general circulation models (GCMs) are increasingly able to provide skillful forecasts of climate anomalies. At some centers, the capabilities of these models are being expanded to represent carbon-climate feedbacks including ocean biogeochemistry (OB), terrestrial biosphere (TB) interactions, and fires. These advances raise the question of whether such models can support skillful forecasts of carbon fluxes.Here, we examine whether land and ocean carbon flux anomalies associated with the 2015-16 El Nino could have been predicted months in advance. This El Nino was noteworthy for the magnitude of the ocean temperature perturbation, the skill with which this perturbation was predicted, and the extensive satellite observations that can be used to track its impact. We explore this topic using NASA's Goddard Earth Observing System (GEOS) model, which routinely produces an ensemble of seasonal climate forecasts, and a suite of offline dynamical and statistical models that estimate carbon flux processes. Using GEOS forecast fields from 2015-16 to force flux model hindcasts shows that these models are able to reproduce significant features observed by satellites. Specifically, OB hindcasts are able to predict anomalies in chlorophyll distributions with lead times of 3-4 months. The ability of TB hindcasts to reproduce NDVI anomalies is driven by the skill of the climate forecast, which is greatest at short lead times over tropical landmasses. Statistical fire forecasts driven by ocean climate indices are able to predict burned area in the tropics with lead times of 3-12 months. We also integrate the ocean and land hindcast fluxes into the GEOS GCM to examine the magnitude of the atmospheric carbon dioxide anomaly and compare with satellite and ground-based observations.While seasonal forecasting remains an active area of research, these results demonstrate that forecasts of carbon flux processes can support a variety of applications, potentially allowing scientists to understand carbon-climate feedbacks as they happen and to capitalize on more flexible satellite technologies that allow areas of interest to be targeted with lead times of weeks to months. We also provide a first glimpse at the spring 2019 carbon forecast using the GEOS-based forecasting system.

Ott, L.↗

An Alternative Ensemble Streamflow Prediction Approach Using Improved Subseasonal Precipitation Forecasts from the North America Multi-Model Ensemble Phase II

In this article, streamflow forecasting at a subseasonal time scale (10–30 days into the future) is important for various human activities. The ensemble streamflow prediction (ESP) is a widely applied technique for subseasonal streamflow forecasting. However, ESP’s reliance on the randomly resampled historical precipitation limits its predictive capability. Available dynamical subseasonal precipitation forecasts provide an alternative to the randomly resampled precipitation in ESP. Prior studies found the predictive performance of raw subseasonal precipitation forecast is limited in many regions such as the central south of the United States, which raises questions about its effectiveness in assisting streamflow forecasting. To further assess the hydrologic applicability of dynamical subseasonal precipitation forecasts, we test the subseasonal precipitation forecast from North America Multi-Model Ensemble Phase II (NMME-2) at four watersheds in the central south region of the United States. The subseasonal precipitation forecasts are postprocessed with bias correction and spatial disaggregation (BCSD) to correct bias and improve spatial resolution before replacing the randomly resampled precipitation in ESP for streamflow predictions. The performance of the resulting streamflow predictions is benchmarked with ESP. Evaluation is conducted using Kling–Gupta Efficiency (KGE), continuous ranked probability score (CRPS), probability of detection (POD), false alarm ratios (FARs), as well as reliability diagrams. Our results suggest that BCSD-corrected subseasonal precipitation forecasts lead to overall improved streamflow predictions due to added skills in winter and spring. Our results also suggest that BCSD-corrected subseasonal precipitation forecasts lead to improved predictions on the occurrence of high-percentile streamflow values above 75%. Overall, BCSD-corrected subseasonal precipitation has shown promising performance, highlighting its potential broader applications for river and flood forecasting.

54 ENVIRONMENTAL SCIENCES↗

Assessment of ESM Readiness Level for Exascale HPC

Advancement of Earth System Models (ESMs) is becoming increasingly challenging due to a confluence of factors including increasing model complexity – to more fully represent the earth system, increasing spatial resolution - to achieve higher accuracy by resolving fine-scale dynamical to physical, biological, and chemical processes and their interaction, increasing ensemble size - to more accurately represent predictive uncertainty, and increased computing requirements – to enable more accurate and timely weather predictions and climate projections for societal benefit. The belief by many that computing will take care of itself is no longer valid given the disruptive changes in HPC that are driving up the cost of computing, increasing the difficulty of using emerging HPC effectively, and exposing limits in parallelism, portability and scalability of the ESM applications themselves.

54 ENVIRONMENTAL SCIENCES↗

Behavior of Filters and Smoothers for Strongly Nonlinear Dynamics

The Kalman filter is the optimal filter in the presence of known gaussian error statistics and linear dynamics. Filter extension to nonlinear dynamics is non trivial in the sense of appropriately representing high order moments of the statistics. Monte Carlo, ensemble-based, methods have been advocated as the methodology for representing high order moments without any questionable closure assumptions. Investigation along these lines has been conducted for highly idealized dynamics such as the strongly nonlinear Lorenz model as well as more realistic models of the means and atmosphere. A few relevant issues in this context are related to the necessary number of ensemble members to properly represent the error statistics and, the necessary modifications in the usual filter situations to allow for correct update of the ensemble members. The ensemble technique has also been applied to the problem of smoothing for which similar questions apply. Ensemble smoother examples, however, seem to be quite puzzling in that results state estimates are worse than for their filter analogue. In this study, we use concepts in probability theory to revisit the ensemble methodology for filtering and smoothing in data assimilation. We use the Lorenz model to test and compare the behavior of a variety of implementations of ensemble filters. We also implement ensemble smoothers that are able to perform better than their filter counterparts. A discussion of feasibility of these techniques to large data assimilation problems will be given at the time of the conference.

Zhu, Yanqui↗

From sequence to protein structure and conformational dynamics with artificial intelligence/machine learning

The 2024 Nobel Prize in Chemistry was awarded in part for de novo protein structure prediction using AlphaFold2, an artificial intelligence/machine learning (AI/ML) model trained on vast amounts of sequence and three-dimensional structure data. AlphaFold2 and related models, including RoseTTAFold and ESMFold, employ specialized neural network architectures driven by attention mechanisms to infer relationships between sequence and structure. At a fundamental level, these AI/ML models operate on the long-standing hypothesis that the structure of a protein is determined by its amino acid sequence. More recently, AlphaFold2 has been adapted for the prediction of multiple protein conformations by subsampling multiple sequence alignments. Herein, we provide an overview of the deterministic relationship between sequence and structure, which was hypothesized over half a century ago with profound implications for the biological sciences ever since. We postulate that protein conformational dynamics are also determined, at least in part, by amino acid sequence and that this relationship may be leveraged for construction of AI/ML models dedicated to predicting protein conformational ensembles. Accordingly, we describe a conceptual model architecture, which may be trained on sequence data in combination with conformationally sensitive structural information, coming primarily from nuclear magnetic resonance (NMR) spectroscopy. Notwithstanding certain limitations in this context, NMR offers abundant structural heterogeneity conducive to conformational ensemble prediction. As NMR and other data continue to accumulate, sequence-informed prediction of protein structural dynamics with AI/ML has the potential to emerge as a transformative capability across the biological sciences.

Artificial intelligence↗

MoSST DAS: The First Working Geomagnetic Data Assimilation System

The Earth possesses an internal magnetic field (geomagnetic field) generated by convection in the outer core (geodynamo). Previous efforts have been focused along two distinct paths: (1) numerical geodynamo modeling to understand the origin of the geomagnetic field, and the mechanisms of geomagnetic secular variations (SV); and (2) geomagnetic field modeling to map the spatial/temporal variations of the field from geomagnetic data, and to derive core properties, e.g. inversion of core flow near the core-mantle boundary (CMB). Geomagnetic data assimilation is a new approach emerged over the past 5 years: surface observations are assimilated with geodynamo models for better understanding of the core dynamical state, and accurately prediction of SV. In collaboration with several geomagnetic research groups, we have developed the first working geomagnetic data assimilation system, Modular, Scalable, Self-consistent, and Three-dimensional (MoSST) DAS, that includes the MoSST numerical dynamo model; 7000 years of geomagnetic field maps from several field models utilizing satellite and ground observatory data, historical magnetic records and archeo/paleo magnetic data; and an ensemble based optimal interpolation (01) assimilation algorithm. With this system, we have demonstrated clearly that the assimilated core dynamical state is substantially different from those of pure geodynamo simulations. Ensemble assimilation runs also show the convergence of the assimilated solutions inside the core, suggesting that the simulation state is pulled closer to the truth via data assimilation. The forecasts from this system are also very accurate: the 5-year forecast of the geomagnetic field agrees very well with the observations; and the 5-year secular variation forecast is more accurate than the IGRF SV forecast models in the past. Using geomagnetic records up to 2009, we have made an SV forecast for the period from 2010-2015, and is a candidate SV model for IGRF-11.

Kuang, Weijia↗

Signal amplification in a solid-state sensor through asymmetric many-body echo

Electronic spins of nitrogen–vacancy centres in diamond constitute a promising system for micro- and nanoscale magnetic sensing, because of their operation under ambient conditions, ease of placement in close proximity to sensing targets and biological compatibility. At high densities, the electronic spins interact through dipolar coupling, which typically limits but can also potentially enhance sensing performance. Here we report the experimental demonstration of many-body signal amplification in a solid-state, room-temperature quantum sensor. Our approach uses time-reversed two-axis-twisting interactions, engineered through dynamical control of the quantization axis and Floquet engineering in a two-dimensional ensemble of nitrogen–vacancy centres. We observe that optimal amplification occurs when the backward evolution time equals twice the forward evolution time, in sharp contrast to the conventional Loschmidt echo. These observations can be understood as resulting from an underlying time-reversed mirror symmetry of the microscopic dynamics, providing key insights into signal amplification and opportunities for practical entanglement-enhanced quantum sensing.

quantum information↗

Inter-Oligomer Interaction Influence on Photoluminescence in Cis-Polyacetylene Semiconductor Materials

Semiconducting conjugated polymers (CPs) are pivotal in advancing organic electronics, offering tunable properties for solar cells and field-effect transistors. Here, we carry out first-principle calculations to study individual cis-polyacetylene (cis-PA) oligomers and their ensembles. The ground electronic structures are obtained using density functional theory (DFT), and excited state dynamics are explored by computing nonadiabatic couplings (NACs) between electronic and nuclear degrees of freedom. We compute the nonradiative relaxation of charge carriers and photoluminescence (PL) using the Redfield theory. Our findings show that electrons relax faster than holes. The ensemble of oligomers shows faster relaxation compared to the single oligomer. The calculated PL spectra show features from both interband and intraband transitions. The ensemble shows broader line widths, redshift of transition energies, and lower intensities compared to the single oligomer. This comparative study suggests that the dispersion forces and orbital hybridizations between chains are the leading contributors to the variation in PL. It provides insights into the fundamental behaviors of CPs and the molecular-level understanding for the design of more efficient optoelectronic devices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Quantifying Groundwater Response and Uncertainty in Beaver‐Influenced Mountainous Floodplains Using Machine Learning‐Based Model Calibration

Abstract Beavers ( Castor canadensis ) alter river corridor hydrology by creating ponds and inundating floodplains, and thereby improving surface water storage. However, the impact of inundation on groundwater, particularly in mountainous alluvial floodplains with permeable gravel/cobble layers overlain by a soil layer, remains uncertain. Numerical modeling across various floodplain structures considers topographic and sediment complexity and multidirectional flow, linking inundation to groundwater response. This study develops a model‐data integration workflow to address uncertainty in groundwater response to beaver‐induced inundations in a mountainous alluvial floodplain in the Upper Colorado River Basin. Uncertain factors include seasonal hydrologic dynamics, hydraulic conductivities, floodplain structures, and meteorological forcings. We employed an ensemble of groundwater models, based on geophysical and hydrologic data, with machine learning‐based calibration using a neural density estimator. This allowed us to quantify the vertical flux from the soil layer to the permeable gravel bed, the down‐valley underflow within the gravel bed, and their ratios. Results show a significant increase in the vertical flux relative to down‐valley underflow, from 2 during dry pond periods to 20 during wet periods, serving as an analogy for conditions without and with beaver ponds. The study highlights the influence of floodplain structure on groundwater storage, water balance, and water quality impacted by beaver ponds. A thick gravel bed layer, with a large down‐valley underflow, minimizes the effect of beaver‐induced inundation on water quality. We emphasize the need for field‐scale measurements of floodplain structure and improved characterization of evapotranspiration changes to reduce uncertainty in groundwater response. Plain Language Summary Beavers change the flow of water in river corridors by creating ponds, expanding wetlands, and flooding floodplains. This increases surface water area, promotes plant growth, and enhances biodiversity. However, the impact of this flooding on groundwater flow is not well understood, especially in mountainous areas with gravel layers where water moves easily beneath soil. In this study, we used numerical modeling to investigate how beaver ponds influence groundwater in a mountainous floodplain of the Upper Colorado River Basin. We adapted a machine learning method to validate our numerical models using multiple field data sets. Our findings show that beaver ponds significantly increase vertical water flow from the soil to the gravel during wet periods, compared to when the ponds are fully drained. The study also highlights the importance of floodplain structure in controlling both water flow in gravel layers along the river direction and vertical flow from the soil to the gravel with the presence of beavers. To reduce uncertainty in groundwater response, we emphasize the need for more field‐scale measurements of floodplain structure, hydraulic properties, and evapotranspiration changes. Key Points Floodplain structures and hydraulic conductivities are important for groundwater response with beaver ponds in mountainous floodplains Large down‐valley underflow in permeability‐stratified floodplains reduces beaver‐induced impacts on groundwater storage and water quality Machine learning‐based model calibration methods are effective for estimating posterior distributions of groundwater model parameters

Wang, Lijing↗

Computational chaos in massively parallel neural networks

A fundamental issue which directly impacts the scalability of current theoretical neural network models to massively parallel embodiments, in both software as well as hardware, is the inherent and unavoidable concurrent asynchronicity of emerging fine-grained computational ensembles and the possible emergence of chaotic manifestations. Previous analyses attributed dynamical instability to the topology of the interconnection matrix, to parasitic components or to propagation delays. However, researchers have observed the existence of emergent computational chaos in a concurrently asynchronous framework, independent of the network topology. Researcher present a methodology enabling the effective asynchronous operation of large-scale neural networks. Necessary and sufficient conditions guaranteeing concurrent asynchronous convergence are established in terms of contracting operators. Lyapunov exponents are computed formally to characterize the underlying nonlinear dynamics. Simulation results are presented to illustrate network convergence to the correct results, even in the presence of large delays.

Barhen, Jacob↗

The Behavior of Filters and Smoothers for Strongly Nonlinear Dynamics

The Kalman filter is the optimal filter in the presence of known Gaussian error statistics and linear dynamics. Filter extension to nonlinear dynamics is non trivial in the sense of appropriately representing high order moments of the statistics. Monte Carlo, ensemble-based, methods have been advocated as the methodology for representing high order moments without any questionable closure assumptions (e.g., Miller 1994). Investigation along these lines has been conducted for highly idealized dynamics such as the strongly nonlinear Lorenz (1963) model as well as more realistic models of the oceans (Evensen and van Leeuwen 1996) and atmosphere (Houtekamer and Mitchell 1998). A few relevant issues in this context are related to the necessary number of ensemble members to properly represent the error statistics and, the necessary modifications in the usual filter equations to allow for correct update of the ensemble members (Burgers 1998). The ensemble technique has also been applied to the problem of smoothing for which similar questions apply. Ensemble smoother examples, however, seem to quite puzzling in that results of state estimate are worse than for their filter analogue (Evensen 1997). In this study, we use concepts in probability theory to revisit the ensemble methodology for filtering and smoothing in data assimilation. We use Lorenz (1963) model to test and compare the behavior of a variety implementations of ensemble filters. We also implement ensemble smoothers that are able to perform better than their filter counterparts. A discussion of feasibility of these techniques to large data assimilation problems will be given at the time of the conference.

Zhu, Yanqiu↗

Structural switching dynamically controls the doubly pseudoknotted Rous sarcoma virus–programmed ribosomal frameshifting element

A hallmark of retrovirus replication is the translation of two different polyproteins from one RNA through programmed –1 frameshifting. This is a mechanism in which the actively translating ribosome is induced to slip in the 5′ direction at a defined codon and then continues translating in the new reading frame. Programmed frameshifting controls the stoichiometry of viral proteins and is therefore under stringent evolutionary selection. Forty years ago, the first frameshifting stimulatory element was discovered in the Rous sarcoma virus. The ~120 nt RNA segment was predicted to contain a pseudoknot, but its 3D structure has remained elusive. Now, we have determined cryoEM and X-ray crystallographic structures of this classic retroviral element, finding that it adopts a butterfly-like double-pseudoknot fold. One “wing” contains a dynamic pyrimidine-rich helix, observed crystallographically in two conformations and in a third conformation via cryoEM. The other wing encompasses the predicted pseudoknot, which interacts with a second unexpected pseudoknot through a toggle residue, A2546. This key purine switches conformations between structural states and tunes the stability of interacting residues in the two wings. We find that its mutation can modulate frameshifting by as much as 50-fold, likely by altering the relative abundance of different structural states in the conformational ensemble of the RNA. Taken together, our structure–function analyses reveal how a dynamic double pseudoknot junction stimulates frameshifting by taking advantage of conformational heterogeneity, supporting a multistate model in which high Shannon entropy enhances frameshifting efficiency.

Science & Technology - Other Topics↗

Influences of Local Sea-Surface Temperatures and Large-scale Dynamics on Monthly Precipitation Inferred from Two 10-year GCM-Simulations

Two parallel sets of 10-year long: January 1, 1982 to December 31, 1991, simulations were made with the finite volume General Circulation Model (fvGCM) in which the model integrations were forced with prescribed sea-surface temperature fields (SSTs) available as two separate SST-datasets. One dataset contained naturally varying monthly SSTs for the chosen period, and the oth& had the 12-monthly mean SSTs for the same period. Plots of evaporation, precipitation, and atmosphere-column moisture convergence, binned by l C SST intervals show that except for the tropics, the precipitation is more strongly constrained by large-scale dynamics as opposed to local SST. Binning data by SST naturally provided an ensemble average of data contributed from disparate locations with same SST; such averages could be expected to mitigate all location related influences. However, the plots revealed: i) evaporation, vertical velocity, and precipitation are very robust and remarkably similar for each of the two simulations and even for the data from 1987-ENSO-year simulation; ii) while the evaporation increased monotonically with SST up to about 27 C, the precipitation did not; iii) precipitation correlated much better with the column vertical velocity as opposed to SST suggesting that the influence of dynamical circulation including non-local SSTs is stronger than local-SSTs. The precipitation fields were doubly binned with respect to SST and boundary-layer mass and/or moisture convergence. The analysis discerned the rate of change of precipitation with local SST as a sum of partial derivative of precipitation with local SST plus partial derivative of precipitation with boundary layer moisture convergence multiplied by the rate of change of boundary-layer moisture convergence with SST (see Eqn. 3 of Section 4.5). This analysis is mathematically rigorous as well as provides a quantitative measure of the influence of local SST on the local precipitation. The results were recast to examine the dependence of local rainfall on local SSTs; it was discernible only in the tropics. Our methodology can be used for computing relationship between any forcing function and its effect(s) on a chosen field.

Sud, Y. C.↗

Structure-Based Design of Small-Molecule Inhibitors of Human Interleukin-6

Human Interleukin-6 (hIL-6) is a pro inflammatory cytokine that binds to its receptor, IL-6Rα followed by binding to gp130 and subsequent dimerization to form a hexamer signaling complex. As a critical inflammation mediator, hIL-6 is associated with a diverse range of diseases and monoclonal antibodies in clinical use that either target IL-6Rα or hIL-6 to inhibit signaling. Here, we perform high-throughput structure-based computational screening using ensemble docking for small-molecule antagonists for which the target conformations were taken from 600 ns long molecular dynamics simulations of the apo protein. Prior knowledge of the contact sites from binary complex studies and experimental work was incorporated into the docking studies. The top 20 scoring ligands from the in silico studies after post analysis were subjected to in vitro functional assays. Among these compounds, the ligand with the second-highest calculated binding affinity experimentally showed an ~84% inhibitory effect on IL6-induced STAT3 reporter activity at 10 μM concentration. This finding may pave the way for designing small-molecule inhibitors of hIL-6 of therapeutic significance.

Human Interleukin-6↗

A Localized Ensemble Kalman Smoother

Numerous geophysical inverse problems prove difficult because the available measurements are indirectly related to the underlying unknown dynamic state and the physics governing the system may involve imperfect models or unobserved parameters. Data assimilation addresses these difficulties by combining the measurements and physical knowledge. The main challenge in such problems usually involves their high dimensionality and the standard statistical methods prove computationally intractable. This paper develops and addresses the theoretical convergence of a new high-dimensional Monte-Carlo approach called the localized ensemble Kalman smoother.

recursive estimation↗

Architecture and Dynamics of Kepler's Multi-Transiting Planet Systems.III. Comprehensive Investigation Using All Four Years of Kepler Mission Data

We study the orbital architectures of planetary systems orbiting within ∼1 AU of their stars by analyzing the ensemble of Kepler systems having two or more planet candidates. We use data from the entire Kepler mission, and in many cases we apply improved analysis techniques (e.g., replacing histograms by top-hat Kernel Density Estimators that avoid the loss of information resulting from choosing a particular phase for the bin boundaries) to extend and enhance the studies of Lissauer et al. (2011, ApJS 197, 8) and Fabrycky et al. (2014, ApJ 790, 146).These data show ~ 1700 transiting planet candidates in > 600 multiple-planet systems, far more than were available for our previous two studies. The increased numbers and better information about planetary radii and the properties of stellar hosts made possible by Gaia DR2 allow more statistically-robust analyses of the entire ensemble of Kepler multis as well as independent analyses of subsets of the population. We are thus able to contrast the dynamical configurations of small and large planets, short-period and longer-period planets, and planets orbiting various types of host stars. We reinforce our previous findings that most pairs of planets within the same system are neither in nor near low-order mean motion resonances and that there is a substantial excess of planets having period ratios slightly larger than those of first-order mean-motion resonances. However, neglecting three systems whose planets are locked in 3- body resonances and summing over all first-order mean motion resonances, the deficit of planet pairs with period ratios just narrow of resonance is as large as the excess of planets wide of resonance (within statistical uncertainties), suggesting that overall there is no overall excess of planet pairs in the vicinity of resonance. Other aspects of our study, including estimates of the typical relative inclinations of planetary orbits and their variations as functions of orbital period, planet sizes and stellar properties, are in progress, with results expected to be available for presentation by the time of the conference.

Lissauer, Jack↗