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Experimenter's laboratory for visualized interactive science

The science activities of the 1990's will require the analysis of complex phenomena and large diverse sets of data. In order to meet these needs, we must take advantage of advanced user interaction techniques: modern user interface tools; visualization capabilities; affordable, high performance graphics workstations; and interoperable data standards and translator. To meet these needs, we propose to adopt and upgrade several existing tools and systems to create an experimenter's laboratory for visualized interactive science. Intuitive human-computer interaction techniques have already been developed and demonstrated at the University of Colorado. A Transportable Applications Executive (TAE+), developed at GSFC, is a powerful user interface tool for general purpose applications. A 3D visualization package developed by NCAR provides both color shaded surface displays and volumetric rendering in either index or true color. The Network Common Data Form (NetCDF) data access library developed by Unidata supports creation, access and sharing of scientific data in a form that is self-describing and network transparent. The combination and enhancement of these packages constitutes a powerful experimenter's laboratory capable of meeting key science needs of the 1990's. This proposal encompasses the work required to build and demonstrate this capability.

Hansen, Elaine R.↗

The Unit of Lightning

For the past century, scientists have made quantitative measurements of lightning discharges. In the process, they refined the definition of a lightning unit, or basic quantum of lightning, in order to base it on observable parameters. Although many components of a lightning discharge have been identified, lightning usually occur in groups of discharges or pulses that, although complex, can be organized into units of flashes. This unit definition is based mainly on measurements of lightning from electric field, video, and ground flash lightning locating networks. More recent instrumentation with various combinations of high sensitivity, high temporal, or high spatial resolution often measure signals produced by lightning that do not cleanly divide into flashes. The data from these systems indicate the need or a more fundamental unit for lightning. Such a unit would be of benefit for both basic understanding of lightning and comparing lightning information between instruments. Without a common lightning unit definition, intercomparisons are difficult. For an example, the Lightning Detection And Ranging system (LDAR) at Kennedy Space Center (KSC) have detected ,flash' rates as high as 600 per minute while analysis based on the Advanced Ground Based Field Mill network (AGBFM) detect only 33 "flashes" per minute in the same area and time periods. The satellite based Optical Transient Detector (OTD) and Lightning Imaging Sensor (LIS) sometimes see single "flashes" that last longer than 10 seconds. Such long duration flashes are not found in electric field records or ground strike location system data sets. The unit of lightning should be based on the fundamental components of the lightning discharge. This should make the unit as generally applicable as possible. For example, studies of NO(x) production by lightning depend on parameters of the individual lightning channels and not the summary flash characteristics. For such studies, the best unit of lightning may be closer to the classical stroke in the electric field data sets, flash in the LDAR data sets, and group in the OTD/LIS data sets. For this type of study, however, more than just the stroke count information is needed. In this paper, we will outline the current definitions of the unit of lightning and propose new basic definitions for the unit of lightning. Since different instruments detect lightning in different ways and different studies may need almost mutually exclusive aspects of the lightning discharge, there may not be a single definition of the unit of lightning that can be applied to all systems and all studies. However, common components can be found since all instrumentation are detecting aspects of the same phenomenon.

Mach, Douglas M.↗

An interactive machine learning platform for analyzing multi-particle coincidence data from cold target recoil ion momentum spectroscopy

We present SCULPT (Supervised Clustering and Uncovering Latent Patterns with Training), a comprehensive software platform for analyzing tabulated high-dimensional multi-particle coincidence data from Cold Target Recoil Ion Momentum Spectroscopy (COLTRIMS) experiments. The software addresses critical challenges in modern momentum spectroscopy by integrating advanced machine learning techniques with physics-informed analysis in an interactive web-based environment. SCULPT implements uniform manifold approximation and projection for non-linear dimensionality reduction to reveal correlations in high-dimensional data. We also discuss potential extensions to deep autoencoders for feature learning and genetic programming for automated discovery of physically meaningful observables. A novel adaptive confidence scoring system provides quantitative reliability assessments by evaluating user-selected clustering quality metrics with predefined weights that reflect each metric’s robustness. The platform features configurable molecular profiles for different experimental systems, interactive visualization with selection tools, and comprehensive data filtering capabilities. Utilizing a subset of SCULPT’s capabilities, we analyze photo-double-ionization data measured using the COLTRIMS method for three-body dissociation of the D 2 O molecule, revealing distinct fragmentation channels and their correlations with physics parameters. The software’s modular architecture and web-based implementation make it accessible to the broader atomic and molecular physics community, significantly reducing the time required for complex multi-dimensional analyses. This opens the door to finding and isolating rare events exhibiting non-linear correlations on the fly during experimental measurements, which can help steer exploration and improve the efficiency of experiments.

Artificial neural networks↗

Physics-guided dual implicit neural representations for source separation

Significant challenges exist in efficient data analysis of most advanced experimental and observational techniques because the collected signals often include unwanted contributions, such as background and signal distortions, that can obscure the physically relevant information of interest. To address this, we have developed a self-supervised machine-learning approach for source separation using a dual implicit neural representation framework that jointly trains two neural networks: one for approximating distortions of the physical signal of interest and the other for learning the effective background contribution. Our method learns directly from the raw data by minimizing a reconstruction-based loss function without requiring labeled data or pre-defined dictionaries. We demonstrate the effectiveness of our framework by considering a challenging case study involving large-scale simulated, as well as experimental, momentum-energy-dependent inelastic neutron scattering data in a four-dimensional parameter space, characterized by heterogeneous background contributions and unknown distortions to the target signal. The method is found to successfully separate physically meaningful signals from a complex or structured background even when the signal characteristics vary across all four dimensions of the parameter space. An analytical approach that informs the choice of the regularization parameter is presented. Our method offers a versatile framework for addressing source separation problems across diverse domains, ranging from superimposed signals in astronomical measurements to structural features in biomedical image reconstructions.

47 OTHER INSTRUMENTATION↗

Characterizing vertical upper ocean temperature structures in the European Arctic through unsupervised machine learning

In-situ observations of subsurface ocean temperatures are, in many regions, inconsistently distributed in time and space. These spatio-temporal inconsistencies in the observational network lead to difficulties in utilizing those observations effectively for ocean model evaluation or understanding larger-scale ocean characteristics. Model accuracy of subsurface ocean characteristics is especially important within regions that contain complex ocean structures. One such region is the European Arctic which not only contains several types of water masses with unique characteristics, but also wintertime sea ice coverage and complex bathymetry. This study presents an unsupervised neural networking technique that can be used in combination with traditional ocean model evaluation techniques to provide additional information on the accuracy of modeled vertical ocean temperature profiles. Self-organizing maps is an unsupervised machine learning technique that we apply to approximately twenty thousand Argo and CTD temperature profiles from 2012 to 2020 in the European Arctic to categorize the observed vertical ocean temperature structures in the top 150 m. The observed ocean profile categories, or neurons, defined by the self-organizing map show strong spatial and temporal dependencies. We then use the neuron weights, or the learned temperature profile structure of each neuron, to validate the spatial and temporal variability of modeled vertical temperature structures. This analysis gives us new insights about the model’s capabilities to reproduce specific vertical structures of the top-most ocean layer within different regions and seasons. Mapping modeled ocean temperature profiles onto the neuron-space of the observationally-defined self organized map highlights the potential of this method to advance our understanding of model deficiencies in that region.

54 ENVIRONMENTAL SCIENCES↗

Prediction of Distributed River Sediment Respiration Rates Using Community-Generated Data and Machine Learning

River sediment microbial respiration is a key indicator of ecosystem functioning and the biogeochemical fluxes across this critical zone link surface and subsurface waters. As such, there is tremendous interest in measuring and mapping these respiration rates. Respiration observations are expensive and labor intensive; there is limited data available to the community. An open science, collaborative initiative is collecting samples for respiration rate analysis and multi-scale metadata; this evolving data set is being used for making machine learning (ML) predictions at unsampled sites to help inform continued community engagement. However, it is a challenge to find an optimum configuration for ML models to work with this feature-rich (i.e., 100+ possible input variables) data set. Here, we present results from a two-tiered approach to managing the analysis of this complex data set: (a) a stacked ensemble of models that automatically optimizes hyperparameters and manages the training of many models and (b) feature permutation importance to detect the most important features in the models. The major elements of this workflow are modular, portable, open, and cloud-based thus making this implementation a potential template for other applications. The models developed here predict that sediment organic matter chemistry is one of the most important features for predicting sediment respiration rate. Other larger-scale, important features fall into the categories of climatic, ecological, geological, and fluvial settings. Leveraging these larger-scale features to generate data-driven estimates of river sediment respiration rates reveals spatially consistent but heterogeneous patterns across the river network of the Columbia River Basin.

54 ENVIRONMENTAL SCIENCES↗

Ligand-Induced Variations in Structural and Dynamical Properties Within an Enzyme Superfamily

Enzyme catalysis is a complex process involving several steps along the reaction coordinates, including substrate recognition and binding, chemical transformation, and product release. Evidence continues to emerge linking the functional and evolutionary role of conformational exchange processes in optimal catalytic activity. Ligand binding changes the conformational landscape of enzymes, inducing long-range conformational rearrangements. Using functionally distinct members of the pancreatic ribonuclease superfamily as a model system, we characterized the structural and conformational changes associated with the binding of two mononucleotide ligands. By combining NMR chemical shift titration experiments with the chemical shift projection analysis (CHESPA) and relaxation dispersion experiments, we show that biologically distinct members of the RNase superfamily display discrete chemical shift perturbations upon ligand binding that are not conserved even in structurally related members. Amino acid networks exhibiting coordinated chemical shift displacements upon binding of the two ligands are unique to each of the RNases analyzed. Our results reveal the contribution of conformational rearrangements to the observed chemical shift perturbations. These observations provide important insights into the contribution of the different ligand binding specificities and effects of conformational exchange on the observed perturbations associated with ligand binding for functionally diverse members of the pancreatic RNase superfamily.

Biochemistry & Molecular Biology↗

Experimenter's laboratory for visualized interactive science

The science activities of the 1990's will require the analysis of complex phenomena and large diverse sets of data. In order to meet these needs, we must take advantage of advanced user interaction techniques: modern user interface tools; visualization capabilities; affordable, high performance graphics workstations; and interoperatable data standards and translator. To meet these needs, we propose to adopt and upgrade several existing tools and systems to create an experimenter's laboratory for visualized interactive science. Intuitive human-computer interaction techniques have already been developed and demonstrated at the University of Colorado. A Transportable Applications Executive (TAE+), developed at GSFC, is a powerful user interface tool for general purpose applications. A 3D visualization package developed by NCAR provides both color-shaded surface displays and volumetric rendering in either index or true color. The Network Common Data Form (NetCDF) data access library developed by Unidata supports creation, access and sharing of scientific data in a form that is self-describing and network transparent. The combination and enhancement of these packages constitutes a powerful experimenter's laboratory capable of meeting key science needs of the 1990's. This proposal encompasses the work required to build and demonstrate this capability.

Hansen, Elaine R.↗

The Urban Fabric of the City as Its Affects Thermal Energy Responses Derived from Remote Sensing Data

The physical geography of the city affects numerous aspects of its interlinked biophysical, social, and land-atmosphere characteristics - those attributes that come together to form the total urban environment. One approach to studying the multitude of interactions that occur as a result of urbanization is to view the city from a systems ecology perspective, where energy and material cycle into and out of the urban milieu. Thus, the urban ecosystem is synergistic in linking land, air, water, and living organisms in a vast network of interrelated physical, human, and biological process. Given the number and the shear complexity of the exchanges and, ultimately, their effects, that occur within the urban environment, we are focusing our research on looking at how the morphology or urban fabric of the city, drives thermal energy exchanges across the urban landscape. The study of thermal energy attributes for different cities provides insight into how thermal fluxes and characteristics are partitioned across the city landscape in response to each city's morphology. We are using thermal infrared remote sensing data obtained at a high spatial resolution from aircraft, along with satellite data, to identify and quantify thermal energy characteristics for 4 U.S. cities: Atlanta, GA, Baton Rouge, LA, Salt Lake City, UT, and Sacramento, CA. Analysis of how thermal energy is spatially distributed across the urban landscapes for these cities provides a unique perspective for understanding how the differing morphology of cities forces land-atmosphere exchanges, such as the urban heat island effect, as well as related meteorological and air quality interactions. Keyword: urban ecosystems, remote sensing, urban heat island

Quattrochi, Dale A.↗

Control system optimization studies. Volume 2: High frequency cutoff filter analysis

The problem of digital implementation of a cutoff filter is approached with consideration to word length, sampling rate, accuracy requirements, computing time and hardware restrictions. Computing time and hardware requirements for four possible programming forms for the linear portions of the filter are determined. Upper bounds for the steady state system output error due to quantization for digital control systems containing a digital network programmed both in the direct form and in the canonical form are derived. This is accomplished by defining a set of error equations in the z domain and then applying the final value theorem to the solution. Quantization error was found to depend upon the digital word length, sampling rate, and system time constants. The error bound developed may be used to estimate the digital word length and sampling rate required to achieve a given system specification. From the quantization error accumulation, computing time and hardware point of view, and the fact that complex poles and zeros must be realized, the canonical form of programming seems preferable.

Fong, M. H.↗

DownScaleBench for developing and applying a deep learning based urban climate downscaling- first results for high-resolution urban precipitation climatology over Austin, Texas

Abstract Cities need climate information to develop resilient infrastructure and for adaptation decisions. The information desired is at the order of magnitudes finer scales relative to what is typically available from climate analysis and future projections. Urban downscaling refers to developing such climate information at the city (order of 1 – 10 km) and neighborhood (order of 0.1 – 1 km) resolutions from coarser climate products. Developing these higher resolution (finer grid spacing) data needed for assessments typically covering multiyear climatology of past data and future projections is complex and computationally expensive for traditional physics-based dynamical models. In this study, we develop and adopt a novel approach for urban downscaling by generating a general-purpose operator using deep learning. This ‘DownScaleBench’ tool can aid the process of downscaling to any location. The DownScaleBench has been generalized for both in situ (ground- based) and satellite or reanalysis gridded data. The algorithm employs an iterative super-resolution convolutional neural network (Iterative SRCNN) over the city. We apply this for the development of a high-resolution gridded precipitation product (300 m) from a relatively coarse (10 km) satellite-based product (JAXA GsMAP). The high-resolution gridded precipitation datasets is compared against insitu observations for past heavy rain events over Austin, Texas, and shows marked improvement relative to the coarser datasets relative to cubic interpolation as a baseline. The creation of this Downscaling Bench has implications for generating high-resolution gridded urban meteorological datasets and aiding the planning process for climate-ready cities.

Singh, Manmeet (ORCID:0000000233747149)↗

Reinterpreting π-stacking

The nature of π–π interactions has long been debated. The term “π-stacking” is considered by some to be a misnomer, in part because overlapping π-electron densities are thought to incur steric repulsion, and the physical origins of the widely-encountered “slip-stacked” motif have variously been attributed to either sterics or electrostatics, in competition with dispersion. Here, we use quantum-mechanical energy decomposition analysis to investigate π–π interactions in supramolecular complexes of polycyclic aromatic hydrocarbons, ranging in size up to realistic models of graphene, and for comparison we perform the same analysis on stacked complexes of polycyclic saturated hydrocarbons, which are cyclohexane-based analogues of graphane. Our results help to explain the short-range structure of liquid hydrocarbons that is inferred from neutron scattering, trends in melting-point data, the interlayer separation of graphene sheets, and finally band gaps and observation of molecular plasmons in graphene nanoribbons. Analysis of intermolecular forces demonstrates that aromatic π–π interactions constitute a unique and fundamentally quantum-mechanical form of non-bonded interaction. Not only do stacked π–π architectures enhance dispersion, but quadrupolar electrostatic interactions that may be repulsive at long range are rendered attractive at the intermolecular distances that characterize π-stacking, as a result of charge penetration effects. The planar geometries of aromatic sp 2 carbon networks lead to attractive interactions that are “served up on a molecular pizza peel”, and adoption of slip-stacked geometries minimizes steric (rather than electrostatic) repulsion. The slip-stacked motif therefore emerges not as a defect induced by electrostatic repulsion but rather as a natural outcome of a conformational landscape that is dominated by van der Waals interactions (dispersion plus Pauli repulsion), and is therefore fundamentally quantum-mechanical in its origins. This reinterpretation of the forces responsible for π-stacking has important implications for the manner in which non-bonded interactions are modeled using classical force fields, and for rationalizing the prevalence of the slip-stacked π–π motif in protein crystal structures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Syntgen: a system to generate temporal networks with user-specified topology

Abstract In the last few years, the study of temporal networks has progressed markedly. The evolution of clusters of nodes (or communities) is one of the major focus of these studies. However, the time dimension increases complexity, introducing new constructs and requiring novel and enhanced algorithms. In spite of recent improvements, the relative scarcity of timestamped representations of empiric networks, with known ground truth, hinders algorithm validation. A few approaches have been proposed to generate synthetic temporal networks that conform to static topological specifications while in general adopting an ad hoc approach to temporal evolution. We believe there is still a need for a principled synthetic network generator that conforms to problem domain topological specifications from a static as well as temporal perspective. Here, we present such a system. The unique attributes of our system include accepting arbitrary node degree and cluster size distributions and temporal evolution under user control, while supporting tunable joint distribution and temporal correlation of node degrees. Theoretical contributions include the analysis of conditions for graphic sequences of inter- and intracluster node degrees and cluster sizes and the development of a heuristic to search for the cluster membership of nodes that minimizes the shared information distance between clusterings. Our work shows that this system is capable of generating networks under user controlled topology with up to thousands of nodes and hundreds of clusters with strong topology adherence. Much larger networks are possible with relaxed requirements. The generated networks support algorithm validation as well as problem domain analysis.

Pereira, Luis Ramada↗

Scoreboard

Emerging HPC machines have given rise to enhanced compute power that far outstrips the machine's ability to save large scale results for post-processing. To combat this, in situ data analysis techniques are slowly being adopted. With in situ data management favoring workflows composed of multiple simulations and analyses connected in transit on heterogeneous machines, scientists and engineers need a tool that enables them to create data extracts, visualizations, and interactively monitor and steer their simulations. Scoreboard Phase II is a next generation analysis software that supports composite in transit workflows on heterogeneous architectures and restores interactivity to in situ data analysis through simulation monitoring and computational steering. Scoreboard provides a simulation dashboard with graphs of metrics over time, controls for setting custom simulation steering parameters, controls for managing the set of data extracts being produced in the simulation, as well as the ability to explore data extracts, all from a web browser. Realizing the vision outlined in this project required research into making a system that integrates end to end from simulations all the way to the user. In situ tools generally suffer from complexity and excessive software dependencies. Scoreboard, by contrast, is easy to build and integrate into simulation codes and it provides first class FORTRAN support. The Scoreboard library is capable of in situ and in transit data analysis that can produce data extracts commonly needed for Computational Fluid Dynamics (CFD) analysis. Simulations can transparently stage data in transit to a Scoreboard Endpoint program, which can accept their data and produce the requested data extracts. This lets simulations return to their work while the Endpoint works on the analysis. Efficiently staging the data at scale was a topic of this research. Scoreboard provides the means to let the user manage data extracts and monitor/steer many simulations from a web browser. This area of the research focused on discovery of in transit network components to expose and control their steering parameters within an interactive browser-based user interface that includes: system topology, gathered metrics, notifications, dynamically-generated steering controls, and exploration of visualization data products.

Whitlock, BradJoseph [Intelligent Light] (00000001↗

Performance Comparison of Wireless Sensor Network Standard Protocols in an Aerospace Environment: ISA100.11a and ZigBee Pro

Standards-based wireless sensor network (WSN) protocols are promising candidates for spacecraft avionics systems, offering unprecedented instrumentation flexibility and expandability. Ensuring reliable data transport is key, however, when migrating from wired to wireless data gathering systems. In this paper, we conduct a rigorous laboratory analysis of the relative performances of the ZigBee Pro and ISA100.11a protocols in a representative crewed aerospace environment. Since both operate in the 2.4 GHz radio frequency (RF) band shared by systems such as Wi-Fi, they are subject at times to potentially debilitating RF interference. We compare goodput (application-level throughput) achievable by both under varying levels of 802.11g Wi-Fi traffic. We conclude that while the simpler, more inexpensive ZigBee Pro protocol performs well under moderate levels of interference, the more complex and costly ISA100.11a protocol is needed to ensure reliable data delivery under heavier interference. This paper represents the first published, rigorous analysis of WSN protocols in an aerospace environment that we are aware of and the first published head-to-head comparison of ZigBee Pro and ISA100.11a.

Wagner, Raymond S.↗

COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms

We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, bioinformaticians and computational biologists. The diagrams of the C19DMap, curated from the literature, are integrated with relevant interaction and text mining databases. We demonstrate the application of network analysis and modelling approaches by concrete examples to highlight new testable hypotheses. This framework helps to find signatures of SARS-CoV-2 predisposition, treatment response or prioritisation of drug candidates. Such an approach may help deal with new waves of COVID-19 or similar pandemics in the long-term perspective.

59 BASIC BIOLOGICAL SCIENCES↗

Multi-Fidelity Stochastic Economic Dispatch for Operating Low Carbon Power Grids

Grid operators can address the inherently stochastic nature of renewables by solving a two-stage stochastic programming model that minimizes the cost of dispatch decisions while accounting for the complex grid dynamics. It is common to use a sample average approximation to estimate the expectation of the second stage costs in this model. However, the large sample count needed for numerical accuracy makes effective modeling large-scale electric grids computationally intractable. We introduce a control variate multi-fidelity estimator for the second-stage recourse that enables high quality dispatch decisions in real-time with a reduced computational burden. We obtain a hierarchy of model fidelities by linearizing the AC power flow system representation to DC power flow, and by relaxing transmission and voltage network constraints. We evaluate the performance of our proposed method on a synthetic grid with 73 buses against a deterministic baseline with persistence forecast and a high-fidelity reference. Our analysis shows a computational speed-up of 7.62x with a minimal loss in accuracy. The multi-fidelity method is well suited to fidelity combinations that use a simplified network topology in their lower fidelity model and is an attractive option for applications where accurate grid modeling needed on a limited computational budget.

24 POWER TRANSMISSION AND DISTRIBUTION↗

MDO and Cross-Disciplinary Practice in R&D: A Portrait of Principles and Current Practice

For several decades, Multidisciplinary Design Optimization (MDO) has served an important role in aerospace engineering by incorporating physics based disciplinary models into integrated system or sub-system models for use in research, development, (R&D) and design. This paper examines MDO's role in facilitating the integration of the researchers from different single disciplines during R&D and early design of large-scale complex engineered systems (LaCES) such as aerospace systems. The findings in this paper are summarized from a larger study on interdisciplinary practices and perspectives that included considerable empirical data from surveys, interviews, and ethnography. The synthesized findings were derived by integrating the data with theories from organization science and engineering. The over-arching finding is that issues related to cognition, organization, and social interrelations mostly dominate interactions across disciplines. Engineering issues, such as the integration of hardware or physics-based models, are not as significant. Correspondingly, the data showed that MDO is not the primary integrator of researchers working across disciplines during R&D and early design of LaCES. Cognitive focus such as analysis versus design, organizational challenges such as incentives, and social opportunities such as personal networks often drove the human interactive practices among researchers from different disciplines. Facilitation of the inherent confusion, argument, and learning in crossdisciplinary research was identified as one of several needed elements of enabling successful research across disciplines.

Rivas McGowan, Anna-Maria↗