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At least 163 records · Page 9

Binding Affinity Prediction by Pairwise Function Based on Neural Network

In this paper, we present a new approach to estimate the binding affinity from given three-dimensional poses of protein–ligand complexes. In this scheme, every protein–ligand atom pair makes an additive free-energy contribution. The sum of these pairwise contributions then gives the total binding free energy or the logarithm of the dissociation constant. The pairwise contribution is calculated by a function implemented via a neural network that takes the properties of the two atoms and their distance as input. The pairwise function is trained using a portion of the PDBbind 2018 data set. The model achieves good accuracy for affinity predictions when evaluated with PDBbind 2018 and with the CASF-2016 benchmark, comparing favorably to many scoring functions such as that of AutoDock Vina. The framework here may be extended to incorporate other factors to further improve its accuracy and power.

59 BASIC BIOLOGICAL SCIENCES↗

FCC-ee interaction region backgrounds

The FCC-ee machine induced backgrounds on the two proposed detectors (CLD and IDEA) have been studied in detail. Synchrotron Radiation (SR) considerations dictate the Interaction Region (IR) optimization. An asymmetric IR design limits the final bend critical energy to 100 keV. Masks placed before the final focus quadrupole protect the detector from direct hits, and a shield placed around the beam pipe from secondary particles, keeping the effect of SR on the detector to negligible levels. The most important source of background is expected to be the Incoherent Pair Creation (IPC). Its effect has been studied in full simulation and reconstruction, and it was shown that it will not pose a problem for the detector, even if conservative estimations for the time resolution of the detector sensors are assumed. Moreover, the γγ → hadrons, radiative Bhabhas and beam-gas interaction induced backgrounds were studied. All were found to have small to negligible effect on the detector. Finally overall, the FCC–ee interaction region backgrounds are not expected to compromise the detector performance.

47 OTHER INSTRUMENTATION↗

Effects of gamma-Radiation on Select Lipids and Antioxidants

Radiation encountered on an extended duration space mission (estimates of 3 Sieverts for a mission to Mars) poses a threat not only to human health, but also to the quality, nutritional value, and palatability of the food system. Free radicals generated by radiation interaction with foods may initiate many unwanted reactions including: 1) autoxidation in lipids that alters flavor, odor, and concentrations of essential fatty acids, and 2) depletion of antioxidants food products and dietary supplements. Studies have shown that antioxidants may provide long term health protection from oxidative stress caused by radiation exposure; therefore, consumption of antioxidants will be important. Stability of essential fatty acids is also important for astronauts long-term health status. The objectives of this study were to characterize the effects of low dose gamma-radiation on lipids and antioxidants by monitoring oxidation and reducing power, respectively, in model systems. Select oils and antioxidants were exposed to levels of gamma-radiation ranging from 0 to 1000 Gy (1 Gy = 1 Sv) using a Gammacell 220 and stored at ambient or elevated temperatures (65 C) for up to 3 months prior to analysis. A Fricke dosimeter was used to verify differences between the radiation doses administered. Primary and secondary products of lipid oxidation in soybean and peanut oils were monitored using conjugated diene and 2-thiobarbituric acid (TBARs) assays. Changes in fatty acid composition and formation and vitamin E levels were also measured. The reducing power of antioxidant compounds, including vitamins C and E and beta-carotene, was determined using the ferric reducing antioxidant power (FRAP) assay. Significant differences (alpha =0.05) were present between all radiation doses tested using the Fricke dosimeter. Increasing radiation doses above 3 Sv resulted in significantly (alpha =0.05) elevated levels of oxidation and free fatty acids in soybean and peanut oils. Decreases in concentrations of essential fatty acids upon increasing radiation doses were also observed. Increasing radiation doses caused significant (alpha =0.05) decreases in reducing power and hence the effectiveness of vitamins C and E as well as beta-carotene. This work establishes a need for quantifying the effects of space relevant radiation doses in the development of a food system for an extended duration mission and for identifying threshold radiation levels that will impact the useful shelf-life of the variety of foods that will be sent. Eventual rancidity of lipids and the loss of antioxidant bioprotective effects are major concerns for the acceptability and nutritional profile of a food system.

Gandolph, Jacob↗

Variance Decomposition of MEDLI2 Reconstructed Heating Using Neural Networks

The Mars Entry, Descent, and Landing Instrumentation (MEDLI2) sensor suite collected data during entry of the Mars 2020 Perseverance rover into Mars’ atmosphere. This suite included a network of MEDLI2 Instrumented Sensor Plugs (MISPs). Each MISP was comprised of a cylinder made of Thermal Protection System (TPS) material with 1-3 embedded thermocouples (TCs), and it was flush mounted into the heatshield or backshell. Data from these in-depth TCs were used to reconstruct the aeroheating environment of the vehicle throughout entry. Surface heating was posed as an inverse problem, with the goal of estimating the surface heating by minimizing an objective function of the difference between MISP temperature measurements during flight and the temperature predictions derived from the Fully Implicit Ablation and Thermal response (FIAT) program. Given an aerothermal environment, FIAT calculates the material response and provides in-depth temperatures throughout the TPS material. To achieve the reverse, an internal tool called FIAT_Opt runs through multiple different environments until the output temperature at the TC depth closely matches the flight data. 95% confidence intervals on the reconstructed surface heating were obtained using Monte Carlo analysis, in which uncertainties in the thermocouple depth and the TPS material properties (e.g., density, thermal conductivity, heat capacity, emissivity) based on flight-lot material testing were included. A variance decomposition method using Sobol indices was employed to assess the sensitivity of the reconstructed peak heating to the TC placement and material property uncertainties. Variance decomposition was found to require tens of thousands of FIAT_Opt runs in order for the Sobol indices to converge. With a single FIAT_Opt run taking on the order of 40 minutes, the required number of computations would take months to complete, even if using multiple CPUs. To mitigate this problem, three machine learning models (ridge regression with cross-validation, random forest regression, and a deep neural network) were trained and tested using the 2000 Monte Carlo runs that were already completed. A subset of 1600 runs were used to train the model (i.e., training set), while the remaining 400 runs were used as the test set. The predictions from the deep neural network (DNN) on the test set showed nearly perfect agreement to the actual values computed with FIAT_Opt (R2 > 0.99). Using the DNN as a surrogate model, the variance decomposition using 50,000 runs was completed within minutes. The resulting Sobol indices showed that the reconstructed peak surface heating was most sensitive to the uncertainties in the thermal conductivity (ST = 0.37) and heat capacity (ST = 0.26). This method can be leveraged to provide requirements for material property measurements needed to improve the accuracy of surface heating prediction and ultimately lead to the reduction of design margins in the future. This presentation will include background on the MEDLI2 suite; the method used for inverse heating estimation; the way that material property uncertainties were accounted for using Monte Carlo analysis; a brief background on variance decomposition; the motivation for using machine learning in this context; how a neural network was trained on the data to enable variance decomposition in a fraction of the time; and the variance decomposition results for one of the MISPs.

Hannah Alpert↗

Hyporheic‐Zone Processes and Stream Oxygen Dynamics: Insights From a Multiscale Reactive Transport Model

Aquatic ecosystem metabolism encapsulates the daily fixation (gross primary production, GPP d ) and mineralization (ecosystem respiration, ER d ) of organic carbon. In fluvial systems, these are commonly estimated by inverse solutions to field observations using a model that describes oxygen concentrations varying in the water column in response to metabolic fluxes and air‐water gas exchange controlled by a rate coefficient (K 600 ). The most common conceptual model is the single‐station metabolism (SSM) model. The simplicity and flexibility of this conceptualization make it attractive; however, it implicitly assumes that all the processes that consume oxygen in fluvial systems can be lumped into a bulk estimate of respiration with poorly understood consequences for estimates of GPP d , ER d , and K 600 . Here, we focus on the implications of using SSM conceptualization when estimating metabolic fluxes from oxygen dynamics in channels where hyporheic exchange occurs. We use a new multiscale numerical model for reactive transport in streams that represents hyporheic exchange and streambed heterotrophic respiration. Nondimensionalization of this model reveals dimensionless groups that collectively control oxygen dynamics. Numerical experiments offer a mechanistic understanding of the impacts of hyporheic exchange on diel oxygen dynamics revealing that potential biases arise from neglecting mass transfer limitations. Specifically, we found that hyporheic exchange significantly affects diel oxygen dynamics, even for nonreactive streambed sediments. Moreover, while the SSM performs well in many situations, we find conditions where significant bias is produced by hyporheic exchange, even when oxygen data are well‐fitted. These situations pose a major challenge in the interpretation of metabolism assessment estimates.

Gomez‐Velez, Jesus D. [Oak Ridge National Laborato↗

Hardware-Efficient Quantum Phase Estimation via Local Control

Quantum phase estimation plays a central role in quantum simulation as it enables the study of spectral properties of many-body quantum systems. Most variants of the phase estimation algorithm require the application of the global unitary evolution conditioned on the state of one or more auxiliary qubits, posing a significant challenge for current quantum devices. In this work, we present an approach to quantum phase estimation that uses only locally controlled operations, resulting in a significantly reduced circuit depth. At the heart of our approach are efficient routines to measure the complex phase of the expectation value of the time-evolution operator, the so-called Loschmidt echo, for both circuit dynamics and Hamiltonian dynamics. By tracking changes in the phase during the dynamics, the routines trade circuit depth for increased sampling cost and classical postprocessing. Our approach does not rely on reference states and is applicable to any efficiently preparable state, regardless of its correlations. We provide a comprehensive analysis of the sample complexity and illustrate the results with numerical simulations. Our methods offer a practical pathway for measuring spectral properties in large many-body quantum systems using current quantum devices.

Schiffer, Benjamin F. [Max Planck Institute of Qua↗

Bayesian learning with Gaussian processes for low-dimensional representations of time-dependent nonlinear systems

This work presents a data-driven method for learning low-dimensional time-dependent physics-based surrogate models whose predictions are endowed with uncertainty estimates. We use the operator inference approach to model reduction that poses the problem of learning low-dimensional model terms as a regression of state space data and corresponding time derivatives by minimizing the residual of reduced system equations. Standard operator inference models perform well with accurate training data that are dense in time, but producing stable and accurate models when the state data are noisy and/or sparse in time remains a challenge. Another challenge is the lack of uncertainty estimation for the predictions from the operator inference models. Our approach addresses these challenges by incorporating Gaussian process surrogates into the operator inference framework to (1) probabilistically describe uncertainties in the state predictions and (2) procure analytical time derivative estimates with quantified uncertainties. The formulation leads to a generalized least-squares regression and, ultimately, reduced-order models that are described probabilistically with a closed-form expression for the posterior distribution of the operators. The resulting probabilistic surrogate model propagates uncertainties from the observed state data to reduced-order predictions. Furthermore, we demonstrate the method is effective for constructing low-dimensional models of two nonlinear partial differential equations representing a compressible flow and a nonlinear diffusion–reaction process, as well as for estimating the parameters of a low-dimensional system of nonlinear ordinary differential equations representing compartmental models in epidemiology.

Data-driven model reduction↗

An Inductor Current Estimation Approach for DC/DC Converters Based on Bisection Method

The trends toward higher power density and efficiency for the DC/DC converters has posed more strict requirements for inductors. The inductor current in turn affect the operating characteristics of the converters significantly and thus needs to be accurately estimated. In this paper, a new bisection-method-based inductor current estimation approach considering the variation of inductance is proposed. The proposed approach can be adapted and applied for various DC/DC converters, including the widely used buck and boost converters and etc. Comparing to the conventional estimation method using constant inductance, the proposed method can obtain more precise estimations of both the inductor current waveform and the power loss. Experimental results on a buck converter with a ferrite-core inductor are presented to validate the effectiveness of the proposed approach.

Zhao, Zhe↗

Near Real-Time Flood Monitoring and Impact Assessment Systems

Floods are the costliest natural disaster, causing approximately 6.8 million deaths in the twentieth century alone. Worldwide economic flood damage estimates in 2012 exceed $19 Billion USD. Extended duration floods also pose longer term threats to food security, water, sanitation, hygiene, and community livelihoods, particularly in developing countries. Projections by the Intergovernmental Panel on Climate Change (IPCC) suggest that precipitation extremes, rainfall intensity, storm intensity, and variability are increasing due to climate change. Increasing hydrologic uncertainty will likely lead to unprecedented extreme flood events. As such, there is a vital need to enhance and further develop traditional techniques used to rapidly assess flooding and extend analytical methods to estimate impacted population and infrastructure. Measuring flood extent in situ is generally impractical, time consuming, and can be inaccurate. Remotely sensed imagery acquired from space-borne and airborne sensors provides a viable platform for consistent and rapid wall-to-wall monitoring of large flood events through time. Terabytes of freely available satellite imagery are made available online each day by NASA, ESA, and other international space research institutions. Advances in cloud computing and data storage technologies allow researchers to leverage these satellite data and apply analytical methods at scale. Repeat-survey earth observations help provide insight about how natural phenomena change through time, including the progression and recession of floodwaters. In recent years, cloud-penetrating radar remote sensing techniques (e.g., Synthetic Aperture Radar) and high temporal resolution imagery platforms (e.g., MODIS and its 1-day return period), along with high performance computing infrastructure, have enabled significant advances in software systems that provide flood warning, assessments, and hazard reduction potential. By incorporating social and economic data, researchers can develop systems that automatically quantify the socioeconomic impacts resulting from flood disaster events.

Ahamed, Aakash↗

Real-time rapid leakage estimation for deep space habitats using exponentially-weighted adaptively-refined search

The recent accelerated growth in space-related research and development activities makes the near-term need for long-term extraterrestrial habitats evident. Such habitats must operate under continuous disruptive conditions arising from extreme environments like meteoroid impacts, extreme temperature fluctuations, galactic cosmic rays, destructive dust, and seismic events. Loss of air or atmospheric leakage from a habitat poses safety challenges that demand proper attention. Such leakage may arise from micro-meteoroid impacts, crack growth, bolt/rivet loosening, and seal deterioration. In this paper, leakage estimation in deep space habitats is posed as an inverse problem. A forward pressure-based dynamical model is formulated for atmospheric leakage. Experiments are performed on a small-scaled pressure chamber where different leakage scenarios are emulated and corresponding pressure values are measured. An exponentially-weighted adaptively-refined search (EWARS) algorithm is developed and validated for the inverse problem of real-time leakage estimation. It is demonstrated that the proposed methodology can achieve real-time estimation and tracking of constant and variable leaks with accuracy.

Deep space habitats↗

Machine learning models for estimating contamination across different curbside collection strategies

Contaminated recyclables, which are frequently discarded as waste, pose a significant challenge to the implementation of a circular economy. These contaminated recyclables impede the circulation of resources, resulting in higher processing costs at material recovery facilities (MRFs). Over the past few decades, machine learning (ML) models such as linear regression (LR), support vector machine (SVM), and random forest (RF) have evolved to provide new methods for predicting inbound contamination rates in addition to traditional statistical models. In this study, we applied ML models to predict inbound contamination rates using demographic features from 15 counties in the U.S. with different curbside collection strategies. In general, we found that ML models outperformed linear mixed models. Specifically, SVM models had the highest performance (R 2 = 0.75; mean absolute error (MAE) = 0.06), which may be due to their ability to model nonlinear relationships between features and inbound contamination rates. Further, the key predictor was population, with poverty rate being positively correlated and median age negatively correlated with inbound contamination rates. To improve the management of contamination and enhance the implementation of a circular economy, better models are needed to understand and estimate inbound contamination rates as well as identify critical factors in the present and future.

54 ENVIRONMENTAL SCIENCES↗

Identifying snowfall elevation patterns by assimilating satellite-based snow depth retrievals

Precipitation in mountain regions is highly variable and poorly measured, posing important challenges to water resource management. Traditional methods to estimate precipitation include in-situ gauges, Doppler weather radars, satellite radars and radiometers, numerical modeling and reanalysis products. Each of these methods is unable to adequately capture complex orographic precipitation. Here, we propose a novel approach to characterize orographic snowfall over mountain regions. We use a particle batch smoother to leverage satellite information from Sentinel-1 derived snow depth retrievals and to correct various gridded precipitation products. This novel approach is tested using a simple snow model for an alpine basin located in Trentino Alto Adige, Italy. Here, we quantify the precipitation biases across the basin and found that the assimilation method (i) corrects for snowfall biases and uncertainties, (ii) leads to cumulative snowfall elevation patterns that are consistent across precipitation products, and (iii) results in overall improved basin-wide snow variables (snow depth and snow cover area) and basin streamflow estimates.

54 ENVIRONMENTAL SCIENCES↗

Fertilizer management for global ammonia emission reduction

Crop production is a large source of atmospheric ammonia (NH 3 ), which poses risks to air quality, human health and ecosystems. However, estimating global NH 3 emissions from croplands is subject to uncertainties because of data limitations, thereby limiting the accurate identification of mitigation options and efficacy. In this report we develop a machine learning model for generating crop-specific and spatially explicit NH 3 emission factors globally (5-arcmin resolution) based on a compiled dataset of field observations. We show that global NH 3 emissions from rice, wheat and maize fields in 2018 were 4.3 ± 1.0 Tg N yr -1 , lower than previous estimates that did not fully consider fertilizer management practices. Furthermore, spatially optimizing fertilizer management, as guided by the machine learning model, has the potential to reduce the NH3 emissions by about 38% (1.6 ± 0.4 Tg N yr -1 ) without altering total fertilizer nitrogen inputs. Specifically, we estimate potential NH3 emissions reductions of 47% (44–56%) for rice, 27% (24–28%) for maize and 26% (20–28%) for wheat cultivation, respectively. Under future climate change scenarios, we estimate that NH3 emissions could increase by 4.0 ± 2.7% under SSP1–2.6 and 5.5 ± 5.7% under SSP5–8.5 by 2030–2060. However, targeted fertilizer management has the potential to mitigate these increases.

54 ENVIRONMENTAL SCIENCES↗

Flight Results from the HST SM4 Relative Navigation Sensor System

On May 11, 2009, Space Shuttle Atlantis roared off of Launch Pad 39A enroute to the Hubble Space Telescope (HST) to undertake its final servicing of HST, Servicing Mission 4. Onboard Atlantis was a small payload called the Relative Navigation Sensor experiment, which included three cameras of varying focal ranges, avionics to record images and estimate, in real time, the relative position and attitude (aka "pose") of the telescope during rendezvous and deploy. The avionics package, known as SpaceCube and developed at the Goddard Space Flight Center, performed image processing using field programmable gate arrays to accelerate this process, and in addition executed two different pose algorithms in parallel, the Goddard Natural Feature Image Recognition and the ULTOR Passive Pose and Position Engine (P3E) algorithms

Naasz, Bo↗

On-board Absolute Localization Based on Orbital Imagery for a Future Mars Science Helicopter

Future Mars Rotorcraft require advanced navigationcapabilities to enable all terrain access over long distance flightsthat are executed fully autonomously. A critical component toenable precision navigation during long traverses is the abilityto perform on-board absolute localization to eliminate drift inposition estimates of the on-board odometry algorithm. Inthis paper, we present an approach for on-board map-basedlocalization to provide global reference position based on orbitalor aerial image maps. Our approach builds on a vision-basedlocalization method to localize against a map derived fromHiRISE image products – an ortho-projected image (orthoimage) and a corresponding digital elevation map. The mapis pre-computed using a feature-based approach. Features arestored with their 3D world coordinates, and a descriptor to codethe local image intensity information in the vicinity of the featurelocation. An on-board matching algorithm uses this informationto match visual features in a query image acquired during flight,guided by a pose prior from the on-board range-visual-inertialstate estimator (Range-VIO). Valid matches are then used bya perspective-n-point (PnP) algorithm to estimate the absolutepose of the vehicle in a global frame. We demonstrate andevaluate our approach on simulated data, and data from UASflights.

Balaram, J. Bob↗

Tracking Coastal Change in American Samoa By Mapping Local Vertical Land Motion with PS-InSAR

Characterizingdiverse contributionsto coastal land change is a key step to mitigating the effects ofrising sea levels that threaten coastal communities. This taskis particularly critical for small island communities in tectonically active regions, which are highlyvulnerableto the effects of sea level rise. We highlight here a case study to extract regional estimates of vertical land motion (VLM) over American Samoa, which in recent years has observedincreased nuisance flooding.Weusedpersistent scatterer Interferometric Synthetic Aperture Radar (PS-InSAR)to derive high-resolutionestimates of crustaldeformationinpopulated regions overTutuila Island from 2015 to 2021. While the area is small and highly vegetatedand poses challenges for InSAR, we wereable to construct a regional map of the estimated deformation ratein these areasandvalidate the time-series with alocal GPS station. Our preliminary results suggest that PS-InSAR has the ability to capture the local and regional deformation patterns, although further workis needed to compensate formore complexatmospheric effects, estimate error margins,and integrate ourresults intomodels of sea-level change that can be used local stakeholders

Stacey A Huang↗

Local models for scatter estimation and descattering in polyenergetic X-ray tomography

We propose a new modeling approach for scatter estimation and descattering in polyenergetic X-ray computed tomography (CT) based on fitting models to local neighborhoods of a training set. X-ray CT is widely used in medical and industrial applications. X-ray scatter, if not accounted for during reconstruction, creates a loss of contrast in CT reconstructions and introduces severe artifacts including cupping, shading, and streaks. Even when these qualitative artifacts are not apparent, scatter can pose a major obstacle in obtaining quantitatively accurate reconstructions. Our approach to estimating scatter is, first, to generate a training set of 2D radiographs with and without scatter using particle transport simulation software. To estimate scatter for a new radiograph, we adaptively fit a scatter model to a small subset of the training data containing the radiographs most similar to it. We compared local and global (fit on full data sets) versions of several X-ray scatter models, including two from the recent literature, as well as a recent deep learning-based scatter model, in the context of descattering and quantitative density reconstruction of simulated, spherically symmetrical, single-material objects comprising shells of various densities. Our results show that, when applied locally, even simple models provide state-of-the-art descattering, reducing the error in density reconstruction due to scatter by more than half.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

State Estimation for K9

The goal of 'Estimate' is to take advantage of attitude information to produce better pose while staying flexible and robust. Currently there are several instruments that are used for attitude: gyros, inclinometers, and compasses. However, precise and useful attitude information cannot come from one instrument. Integration of rotational rates, from gyro data for example, would result in drift. Therefore, although gyros are accurate in the short-term, accuracy in the long term is unlikely. Using absolute instruments such as compasses and inclinometers can result in an accurate measurement of attitude in the long term. However, in the short term, the physical nature of compasses and inclinometers, and the dynamic nature of a mobile platform result in highly volatile and therefore useless data. The solution then is to use both absolute and relative data. Kalman Filtering is known to be able to combine gyro and compass/inclinometer data to produce stable and accurate attitude information. Since the model of motion is linear and the data comes in as discrete samples, a Discrete Kalman Filter was selected as the core of the new estimator. Therefore, 'Estimate' can be divided into two parts: the Discrete Kalman Filter and the code framework.

Xu, Ru-Gang↗