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DOE OSTI2020

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↗

NASA NTRS1981

Computer program documentation for a subcritical wing design code using higher order far-field drag minimization

A subsonic, linearized aerodynamic theory, wing design program for one or two planforms was developed which uses a vortex lattice near field model and a higher order panel method in the far field. The theoretical development of the wake model and its implementation in the vortex lattice design code are summarized and sample results are given. Detailed program usage instructions, sample input and output data, and a program listing are presented in the Appendixes. The far field wake model assumes a wake vortex sheet whose strength varies piecewise linearly in the spanwise direction. From this model analytical expressions for lift coefficient, induced drag coefficient, pitching moment coefficient, and bending moment coefficient were developed. From these relationships a direct optimization scheme is used to determine the optimum wake vorticity distribution for minimum induced drag, subject to constraints on lift, and pitching or bending moment. Integration spanwise yields the bound circulation, which is interpolated in the near field vortex lattice to obtain the design camber surface(s).

Kuhlman, J. M.↗

NASA NTRS1992

Self-learning fuzzy controllers based on temporal back propagation

This paper presents a generalized control strategy that enhances fuzzy controllers with self-learning capability for achieving prescribed control objectives in a near-optimal manner. This methodology, termed temporal back propagation, is model-insensitive in the sense that it can deal with plants that can be represented in a piecewise-differentiable format, such as difference equations, neural networks, GMDH structures, and fuzzy models. Regardless of the numbers of inputs and outputs of the plants under consideration, the proposed approach can either refine the fuzzy if-then rules if human experts, or automatically derive the fuzzy if-then rules obtained from human experts are not available. The inverted pendulum system is employed as a test-bed to demonstrate the effectiveness of the proposed control scheme and the robustness of the acquired fuzzy controller.

Jang, Jyh-Shing R.↗

NASA NTRS2007

Improved Readout Scheme for SQUID-Based Thermometry

An improved readout scheme has been proposed for high-resolution thermometers, (HRTs) based on the use of superconducting quantum interference devices (SQUIDs) to measure temperature- dependent magnetic susceptibilities. The proposed scheme would eliminate counting ambiguities that arise in the conventional scheme, while maintaining the superior magnetic-flux sensitivity of the conventional scheme. The proposed scheme is expected to be especially beneficial for HRT-based temperature control of multiplexed SQUIDbased bolometer sensor arrays. SQUID-based HRTs have become standard for measuring and controlling temperatures in the sub-nano-Kelvin temperature range in a broad range of low-temperature scientific and engineering applications. A typical SQUIDbased HRT that utilizes the conventional scheme includes a coil wound on a core made of a material that has temperature- dependent magnetic susceptibility in the temperature range of interest. The core and the coil are placed in a DC magnetic field provided either by a permanent magnet or as magnetic flux inside a superconducting outer wall. The aforementioned coil is connected to an input coil of a SQUID. Changes in temperature lead to changes in the susceptibility of the core and to changes in the magnetic flux detected by the SQUID. The SQUID readout instrumentation is capable of measuring magnetic-flux changes that correspond to temperature changes down to a noise limit .0.1 nK/Hz1/2. When the flux exceeds a few fundamental flux units, which typically corresponds to a temperature of .100 nK, the SQUID is reset. The temperature range can be greatly expanded if the reset events are carefully tracked and counted, either by a computer running appropriate software or by a dedicated piece of hardware.

Penanen, Konstantin↗

DOE OSTI2020

Data-driven surrogates for high dimensional models using Gaussian process regression on the Grassmann manifold

This paper introduces a surrogate modeling scheme based on Grassmannian manifold learning to be used for cost-efficient predictions of high-dimensional stochastic systems. The method exploits subspace-structured features of each solution by projecting it onto a Grassmann manifold. This point-wise linear dimensionality reduction harnesses the structural information to assess the similarity between solutions at different points in the input parameter space. The method utilizes a solution clustering approach in order to identify regions of the parameter space over which solutions are sufficiently similarly such that they can be interpolated on the Grassmannian. In this clustering, the reduced-order solutions are partitioned into disjoint clusters on the Grassmann manifold using the eigen-structure of properly defined Grassmannian kernels and, the Karcher mean of each cluster is estimated. Then, the points in each cluster are projected onto the tangent space with origin at the corresponding Karcher mean using the exponential mapping. For each cluster, a Gaussian process regression model is trained that maps the input parameters of the system to the reduced solution points of the corresponding cluster projected onto the tangent space. Using this Gaussian process model, the full-field solution can be efficiently predicted at any new point in the parameter space. In certain cases, the solution clusters will span disjoint regions of the parameter space. In such cases, for each of the solution clusters we utilize a second, density-based spatial clustering to group their corresponding input parameter points in the Euclidean space. The proposed method is applied to two numerical examples. Here, the first is a nonlinear stochastic ordinary differential equation with uncertain initial conditions where the surrogate is used to predict the time history solution. The second involves modeling of plastic deformation in a model amorphous solid using the Shear Transformation Zone theory of plasticity, where the proposed surrogate is used to predict the full strain field of a material specimen under large shear strains.

42 ENGINEERING↗

DOE OSTI2022

Automatic Tuner for the Step Sizes of Gradient-Based RT-OPF DERMS Control Systems [SWR-22-50]

Gradient-based controllers have parameters called step sizes that determine how sensitive its control actions are to received inputs. Finding a practical setting for a step size is important. If it is too small, the controller is ineffective by not reacting in a significant manor to its received inputs. On the other hand, if it is too large, the actions implemented by the controller may be excessive and cause the controlled system to become unstable. The main objective of the Automatic Tuner for the Step Sizes of Gradient-Based RT-OPF DERMS Control Systems is to speed up the implementation of gradient-based control schemes by automatically tuning its step sizes instead of having a practitioner spend considerable time doing the task manually. Only simple adjustments need to be made to the code of each controller with a step size to allow the addition of an individual automatic tuner. This can be applied to any RT-OPF based control for DER management.

Comden, Joshua↗

NASA NTRS1994

Parameter estimation in a structural acoustic system with fully nonlinear coupling conditions

A methodology for estimating physical parameters in a class of structural acoustic systems is presented. The general model under consideration consists of an interior cavity which is separated from an exterior noise source by an enclosing elastic structure. Piezoceramic patches are bonded to or embedded in the structure; these can be used both as actuators and sensors in applications ranging from the control of interior noise levels to the determination of structural flaws through nondestructive evaluation techniques. The presence and excitation of patches, however, changes the geometry and material properties of the structure as well as involves unknown patch parameters, thus necessitating the development of parameter estimation techniques which are applicable in this coupled setting. In developing a framework for approximation, parameter estimation and implementation, strong consideration is given to the fact that the input operator is unbonded due to the discrete nature of the patches. Moreover, the model is weakly nonlinear. As a result of the coupling mechanism between the structural vibrations and the interior acoustic dynamics. Within this context, an illustrating model is given, well-posedness and approximations results are discussed and an applicable parameter estimation methodology is presented. The scheme is then illustrated through several numerical examples with simulations modeling a variety of commonly used structural acoustic techniques for systems excitations and data collection.

Banks, H. T.↗

NASA NTRS1999

Sampling Soil for Characterization and Site Description

The sampling scheme for soil characterization within the GLOBE program is uniquely different from the sampling methods of the other protocols. The strategy is based on an understanding of the 5 soil forming factors (parent material, climate, biota, topography, and time) at each study site, and how each of these interact to produce a soil profile with unique characteristics and unique input and control into the atmospheric, biological, and hydrological systems. Soil profile characteristics, as opposed to soil moisture and temperature, vegetative growth, and atmospheric and hydrologic conditions, change very slowly, depending on the parameter being measured, ranging from seasonally to many thousands of years. Thus, soil information, including profile description and lab analysis, is collected only one time for each profile at a site. These data serve two purposes: 1) to supplement existing spatial information about soil profile characteristics across the landscape at local, regional, and global scales, and 2) to provide specific information within a given area about the basic substrate to which elements within the other protocols are linked. Because of the intimate link between soil properties and these other environmental elements, the static soil properties at a given site are needed to accurately interpret and understand the continually changing dynamics of soil moisture and temperature, vegetation growth and phenology, atmospheric conditions, and chemistry and turbidity in surface waters. Both the spatial and specific soil information can be used for modeling purposes to assess and make predictions about global change.

Levine, Elissa↗

NASA NTRS2003

Computational and Experimental Flow Field Analyses of Separate Flow Chevron Nozzles and Pylon Interaction

A computational and experimental flow field analyses of separate flow chevron nozzles is presented. The goal of this study is to identify important flow physics and modeling issues required to provide highly accurate flow field data which will later serve as input to the Jet3D acoustic prediction code. Four configurations are considered: a baseline round nozzle with and without a pylon, and a chevron core nozzle with and without a pylon. The flow is simulated by solving the asymptotically steady, compressible, Reynolds-averaged Navier-Stokes equations using an implicit, up-wind, flux-difference splitting finite volume scheme and standard two-equation kappa-epsilon turbulence model with a linear stress representation and the addition of a eddy viscosity dependence on total temperature gradient normalized by local turbulence length scale. The current CFD results are seen to be in excellent agreement with Jet Noise Lab data and show great improvement over previous computations which did not compensate for enhanced mixing due to high temperature gradients.

Massey, Steven J.↗

DOE OSTI2024

Development of a Performance Portable Non-Equilibrium Plasma Fluid Solver on Adaptive Grids

This presentation will describe the numerical techniques, programming paradigms, verification, and performance of a non-equilibrium plasma fluid solver that can effectively utilize current and upcoming central processing and graphics processing unit (CPU+GPU) architectures. Our plasma fluid model solves the conservation equations for self-consistent electrostatic Poisson, electron and heavy species transport, and electron temperature on adaptive Cartesian grids. Our solver is written using performance portable adaptive mesh management library, AMReX (Zhang et al., JOSS, 4 (37) 1370, 2019), and can be built and run on widely available vendor specific GPU architectures (NVIDIA/AMD/Intel). We utilize a non-subcycled second order semi-implicit time-stepping method where all adaptive mesh refinement (AMR) levels are advanced with the same time step. The composite multi-level multigrid solver from within AMReX is used for each of the governing equations that are cast into a Helmholtz equation form. We have also developed a python based chemical mechanism parser framework that uses a similar format as CANTERA (Goodwin et al., Zenodo, 2018) yaml files as input. Our custom parser reads the yaml file and provides C++ files with transport and production rate functions that can be executed on both host (CPU) and device (GPU). We present verification of our solver using method of manufactured solutions that indicate formal second order accuracy with central diffusion and fifth order weighted-essentially-non-oscillatory (WENO) advection scheme. We also verify our solver with published literature on low-pressure capacitive and high-pressure streamer discharges. Our initial performance studies indicate 10X speed-up using 20 NVIDIA GPUs versus 200 CPUs for an atmospheric streamer discharge problem solved on a 512 x 1024 x 512 grid.

graphics processing units↗

NASA NTRS2012

Histogrammatic Method for Determining Relative Abundance of Input Gas Pulse

To satisfy the Major Constituents Analysis (MCA) requirements for the Vehicle Cabin Atmosphere Monitor (VCAM), this software analyzes the relative abundance ratios for N2, O2, Ar, and CO2 as a function of time and constructs their best-estimate mean. A histogram is first built of all abundance ratios for each of the species vs time. The abundance peaks corresponding to the intended measurement and any obfuscating background are then separated via standard peak-finding techniques in histogram space. A voting scheme is then used to include/exclude this particular time sample in the final average based on its membership to the intended measurement or the background population. This results in a robust and reasonable estimate of the abundance of trace components such as CO2 and Ar even in the presence of obfuscating backgrounds internal to the VCAM device. VCAM can provide a means for monitoring the air within the enclosed environments, such as the ISS (International Space Station), Crew Exploration Vehicle (CEV), a Lunar Habitat, or another vehicle traveling to Mars. Its miniature pre-concentrator, gas chromatograph (GC), and mass spectrometer can provide unbiased detection of a large number of organic species as well as MCA analysis. VCAM s software can identify the concentration of trace chemicals and whether the chemicals are on a targeted list of hazardous compounds. This innovation s performance and reliability on orbit, along with the ground team s assessment of its raw data and analysis results, will validate its technology for future use and development.

Mandrake, Lukas↗

DOE OSTI2020

Sub-Hertz resonance by weak measurement

Weak measurement (WM) with state pre- and post-selection can amplify otherwise undetectable small signals and thus has potential in precision measurement applications. Although frequency measurements offer the hitherto highest precision due to the stable narrow atomic transitions, it remains a long-standing interest to develop new schemes to further escalate their performance. Here, we demonstrate a WM-enhanced correlation spectroscopy technique capable of narrowing the resonance linewidth down to 0.1 Hz in a room-temperature atomic vapour cell. The potential of this technique for precision measurement is demonstrated through weak magnetic-field sensing. By judiciously pre- and post-selecting frequency-modulated input and output optical states in a nearly orthogonal manner, a sensitivity of 7 fT Hz -1/2 at a low frequency near DC is achieved using only one laser beam with 15 µW of power. Additionally, our results extend the WM framework to a non-Hermitian Hamiltonian and shed new light on metrology and bio-magnetic field sensing.

Science & Technology - Other Topics↗

NASA NTRS1994

Dual-Arm Generalized Compliant Motion With Shared Control

Dual-Arm Generalized Compliant Motion (DAGCM) primitive computer program implementing improved unified control scheme for two manipulator arms cooperating in task in which both grasp same object. Provides capabilities for autonomous, teleoperation, and shared control of two robot arms. Unifies cooperative dual-arm control with multi-sensor-based task control and makes complete task-control capability available to higher-level task-planning computer system via large set of input parameters used to describe desired force and position trajectories followed by manipulator arms. Some concepts discussed in "A Generalized-Compliant-Motion Primitive" (NPO-18134).

Backes, Paul G.↗

DOE OSTI2021

Towards Semantic Search in Building Sensor Data

This paper presents a search engine system for sensor time series data and metadata in the context of building management. It takes natural language queries as input, retrieves sensor time series data, ranks them with respect to their relevance to a given query, and visualizes the time series as search results. In addition, the system allows users to interact with the search results: they can define events of interest in the visualized results and search across sensor data for similar events, i.e., the search by example scheme. Quantitative evaluations and user studies demonstrate the value of this system for managing building sensor data.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2021

Creating heralded hyper-entangled photons using Rydberg atoms

Entangled photon pairs are a fundamental component for testing the foundations of quantum mechanics, and for modern quantum technologies such as teleportation and secured communication. Current state-of-the-art sources are based on nonlinear processes that are limited in their efficiency and wavelength tunability. This motivates the exploration of physical mechanisms for entangled photon generation, with a special interest in mechanisms that can be heralded, preferably at telecommunications wavelengths. Here we present a mechanism for the generation of heralded entangled photons from Rydberg atom cavity quantum electrodynamics (cavity QED). We propose a scheme to demonstrate the mechanism and quantify its expected performance. The heralding of the process enables non-destructive detection of the photon pairs. The entangled photons are produced by exciting a rubidium atom to a Rydberg state, from where the atom decays via two-photon emission (TPE). A Rydberg blockade helps to excite a single Rydberg excitation while the input light field is more efficiently collectively absorbed by all the atoms. The TPE rate is significantly enhanced by a designed photonic cavity, whose many resonances also translate into high-dimensional entanglement. The resulting high-dimensionally entangled photons are entangled in more than one degree of freedom: in all of their spectral components, in addition to the polarization—forming a hyper-entangled state, which is particularly interesting in high information capacity quantum communication. We characterize the photon comb states by analyzing the Hong-Ou-Mandel interference and propose proof-of-concept experiments.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2021

Examining Nuisance Aerosol Detections in Light of the Origin of the Screening Process (November 2021)

The evolution of philosophy and computations in the International Data Center (IDC) related to aerosol samples have had profound impacts on the number of recorded detections in the network since routine operations began in 2000. Key decisions from policymakers have been the list of triggering radionuclides, the scheme for categorizing these into interest levels 1-5, and an algorithm for determining when an anthropogenic isotope is seen so often that it is no longer interesting, known as the Exponential Weighted Moving Average (EWMA). These are described in the Operations Manual of the IDC. Key parameters that are controlled by the IDC but for which the IDC receives occasional input from policymakers include the constants in EWMA and the peak significance threshold for individual gamma rays, the latter of which directly leads to determination of the presence or absence of a radionuclide in a sample. There are also changes in computations which the IDC makes and informs policy makers about, such as changes in how background is computed, which could also affect the ease of detecting a peak – real or false. Rather than focus on the quantitative changes due to computation changes, this work records some thinking on how isotopes and peak significance levels were chosen, and the resulting detections seen over 18 years during the buildup of the International Monitoring System (IMS). These detections are considered on a global scale to try to determine the relative impact on monitoring, and in some cases, the nature of their existence. Repeated detections of 131I and 133I are the most troublesome, but they are not so frequent to be a major problem for the Verification Regime. These detections could probably be handled adequately using scientific methods currently under development for xenon backgrounds. It is also somewhat problematic that top-level analysis of aerosol backgrounds has not been reported previous to this. The steep increase in the rate of detections after 2016 are a concern, either in the actual backgrounds or from changes in the calculations methods used to generate the Reviewed Radionuclide Report (RRR.) Final conclusions of the authors are that the computational stability of the RRR is very important. With computational stability, changes can be usefully analyzed as being due to changes in radioactivity in Earth’s atmosphere This report is a distillation into text of a talk given in the Radionuclide Experts Group (RNEG) in Vienna during Working Group B (WGB) in February of 2019. This report does not directly contain any IDC data, only summaries by year, or by isotope, or by location. No specific IDC detection by time, location, or isotope is included.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

NASA NTRS2008

Application of the NASA A-Train to Evaluate Clouds Simulated by the Weather Research and Forecast Model

The CloudSat Mission, part of the NASA A-Train, is providing the first global survey of cloud profiles and cloud physical properties, observing seasonal and geographical variations that are pertinent to evaluating the way clouds are parameterized in weather and climate forecast models. CloudSat measures the vertical structure of clouds and precipitation from space through the Cloud Profiling Radar (CPR), a 94 GHz nadir-looking radar measuring the power backscattered by clouds as a function of distance from the radar. One of the goals of the CloudSat mission is to evaluate the representation of clouds in forecast models, thereby contributing to improved predictions of weather, climate and the cloud-climate feedback problem. This paper highlights potential limitations in cloud microphysical schemes currently employed in the Weather Research and Forecast (WRF) modeling system. The horizontal and vertical structure of explicitly simulated cloud fields produced by the WRF model at 4-km resolution are being evaluated using CloudSat observations in concert with products derived from MODIS and AIRS. A radiative transfer model is used to produce simulated profiles of radar reflectivity given WRF input profiles of hydrometeor mixing ratios and ambient atmospheric conditions. The preliminary results presented in the paper will compare simulated and observed reflectivity fields corresponding to horizontal and vertical cloud structures associated with midlatitude cyclone events.

Molthan, Andrew L.↗

DOE OSTI2024

RandONets: Shallow networks with random projections for learning linear and nonlinear operators

Deep neural networks have been extensively used for the solution of both the forward and the inverse problem for dynamical systems. However, their implementation necessitates optimizing a high-dimensional space of parameters and hyperparameters. This fact, along with the requirement of substantial computational resources, pose a barrier to achieving high numerical accuracy, but also interpretability. Here, to address the above challenges, we present Random Projection-based Operator Networks (RandONets): shallow networks with random projections and tailor-made numerical analysis methods that learn accurately and fast linear and nonlinear operators. Building on previous works, we prove that RandOnets are universal approximators of linear and nonlinear operators. Due to their simplicity, RandONets provide a one-step transformation of the input space, facilitating interpretability. For the evaluation of their performance, we focus on operators of PDEs. We show, that RandONets outperform by several orders of magnitude, both in terms of numerical approximation accuracy and computational cost, the “vanilla” DeepONets. Hence, we believe that our method will trigger further developments in the field of scientific machine learning, for the development of new ‘’light”schemes that will provide high accuracy while reducing dramatically the computational cost. A MATLAB toolbox for RandONets, including demos, is available on GitHub at https://github.com/GianlucaFabiani/RandONets.

Interpretable machine learning↗