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Modern chemical graph theory

Abstract Graph theory has a long history in chemistry. Yet as the breadth and variety of chemical data is rapidly changing, so too do graph encoding methods and analyses that yield qualitative and quantitative insights. Using illustrative cases within a basic mathematical framework, we showcase modern chemical graph theory's utility in Chemists' analysis and model development toolkit. The encoding of both experimental and simulation data is discussed at various levels of granularity of information. This is followed by a discussion of the two major classes of graph theoretical analyses: identifying connectivity patterns and partitioning methods. Measures, metrics, descriptors, and topological indices are then introduced with an emphasis upon enhancing interpretability and incorporation into physical models. Challenging data cases are described that include strategies for studying time dependence. Throughout, we incorporate recent advancements in computer science and applied mathematics that are propelling chemical graph theory into new domains of chemical study. This article is categorized under: Molecular and Statistical Mechanics > Molecular Dynamics and Monte‐Carlo Methods Structure and Mechanism > Computational Materials Science Structure and Mechanism > Molecular Structures

Leite, Leonardo S. G.

RWRtoolkit: multi-omic network analysis using random walks on multiplex networks in any species

Abstract We introduce RWRtoolkit, a multiplex generation, exploration, and statistical package built for R and command-line users. RWRtoolkit enables the efficient exploration of large and highly complex biological networks generated from custom experimental data and/or from publicly available datasets, and is species agnostic. A range of functions can be used to find topological distances between biological entities, determine relationships within sets of interest, search for topological context around sets of interest, and statistically evaluate the strength of relationships within and between sets. The command-line interface is designed for parallelization on high-performance cluster systems, which enables high-throughput analysis such as permutation testing. Several tools in the package have also been made available for use in reproducible workflows via the KBase web application.

Kainer, David (ORCID:0000000172714676)

An Integrated Vision-Based System for Spacecraft Attitude and Topology Determination for Formation Flight Missions

With the space industry's increasing focus upon multi-spacecraft formation flight missions, the ability to precisely determine system topology and the orientation of member spacecraft relative to both inertial space and each other is becoming a critical design requirement. Topology determination in satellite systems has traditionally made use of GPS or ground uplink position data for low Earth orbits, or, alternatively, inter-satellite ranging between all formation pairs. While these techniques work, they are not ideal for extension to interplanetary missions or to large fleets of decentralized, mixed-function spacecraft. The Vision-Based Attitude and Formation Determination System (VBAFDS) represents a novel solution to both the navigation and topology determination problems with an integrated approach that combines a miniature star tracker with a suite of robust processing algorithms. By combining a single range measurement with vision data to resolve complete system topology, the VBAFDS design represents a simple, resource-efficient solution that is not constrained to certain Earth orbits or formation geometries. In this paper, analysis and design of the VBAFDS integrated guidance, navigation and control (GN&C) technology will be discussed, including hardware requirements, algorithm development, and simulation results in the context of potential mission applications.

Rogers, Aaron

Users manual for AUTOMESH-2D: A program of automatic mesh generation for two-dimensional scattering analysis by the finite element method

AUTOMESH-2D is a computer program specifically designed as a preprocessor for the scattering analysis of two dimensional bodies by the finite element method. This program was developed due to a need for reproducing the effort required to define and check the geometry data, element topology, and material properties. There are six modules in the program: (1) Parameter Specification; (2) Data Input; (3) Node Generation; (4) Element Generation; (5) Mesh Smoothing; and (5) Data File Generation.

Hua, Chongyu

Nucleophilic Displacement Reactions of Silver-Based Metal–Organic Chalcogenolates

Here, we report nucleophilic displacement reactions that can increase the dimensionality or coordination number of silver-based metal–organic chalcogenolates (MOChas). MOChas are crystalline ensembles containing one-dimensional (1D) or two-dimensional (2D) inorganic topologies with structures and properties defined by the choice of metal, chalcogen, and ligand. MOChas can be readily prepared from a variety of small-molecule ligands and metals or metal ions. Although MOChas offer ligand diversity, most reported examples use relatively small ligands, typically involving short alkyl chains, aryl rings, or molecular cages. This is because larger, more complex molecules often yield poor product morphologies with indeterminate structures. In this study, we overcame this limitation by employing a ligand exchange strategy whereby a 1D MOCha, silver(I) methyl 2-mercaptobenzoate (2MMB), is used as a silver source for preparing 2D examples. The reaction proceeds generally toward products composed of the stronger nucleophile. We show that the reaction prefers displacing 1D topologies to yield 2D ones and replacing thiolates with selenolates. We performed a study to characterize the mechanism by which organic chalcogenols and dichalcogenides exchange with MOChas. The collected data and product analysis support a proposed mechanism of nucleophilic substitution, explaining how both organic chalcogenols and dichalcogenides can displace ligands in MOChas. This work provides a new synthetic route that will enable the preparation of more elaborate MOChas and heterostructures thereof. This approach enabled the preparation of previously inaccessible oligophenyl MOChas, which were successfully solved via small-molecule serial femtosecond crystallography (smSFX) at the SPring-8 Ångström Compact Free Electron LAser (SACLA) facility.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Representation and display of vector field topology in fluid flow data sets

The visualization of physical processes in general and of vector fields in particular is discussed. An approach to visualizing flow topology that is based on the physics and mathematics underlying the physical phenomenon is presented. It involves determining critical points in the flow where the velocity vector vanishes. The critical points, connected by principal lines or planes, determine the topology of the flow. The complexity of the data is reduced without sacrificing the quantitative nature of the data set. By reducing the original vector field to a set of critical points and their connections, a representation of the topology of a two-dimensional vector field that is much smaller than the original data set but retains with full precision the information pertinent to the flow topology is obtained. This representation can be displayed as a set of points and tangent curves or as a graph. Analysis (including algorithms), display, interaction, and implementation aspects are discussed.

Helman, James

Navier-Stokes calculation of transonic flow past the NTF 65 deg delta wing

Models of four delta wings were built and tested in the 8 x 8 ft Transonic Wind Tunnel at LaRC. The wings are identical in planform shape with a swept-back angle of 65 degrees, but bear different leading edge profiles. The models were tested under pressurized and cryogenic conditions to simulate true flight Reynolds numbers. Data on the aerodynamic forces and pressure distributions at various locations on the wings were taken at various flight Mach numbers and angles of attack. Effects of high Reynolds number and leading edge radius on the aerodynamic characteristics of the wings are being accessed. To thoroughly understand the turbulent, vortical flow around the wings, an effort to perform computational aerodynamic analysis is being made. The objective of the analysis is to supplement and validate the experimental data and explain the high Reynolds number and leading edge effects. GRIDGEN, a software developed by General Dynamics, is being used to generate the grid topology for the flow field around the wings. The flow solver to be used is CFL3D, a computation fluid dynamics code developed at LaRC. Based on the geometric description of the wings, a FORTRAN program called WINGSURF was written to generate the databases defining the surface geometry of the wings. To match the true geometry of the models in the wind tunnel for realistic comparison with experimental results, databases defining the sting support for the wing models were also created by two other FORTRAN programs, STINJOIN and STINREAR. Listing of the programs are attached and the geometry of a typical wing model with the sting support is shown. Other aspects of the investigation are discussed.

Wu, Chivey C.

[Development and Use of Hidrosig]

The NASA portion of this joint NSF-NASA grant consists of objective 2 and a part of objective 3. A major effort was made on objective 2, and it consisted of developing a numerical GIs environment called Hidrosig. This major research tool is being developed by the University of Colorado for conducting river-network-based scaling analyses of coupled water-energy-landform-vegetation interactions including water and energy balances, and floods and droughts, at multiple space-time scales.Objective 2: To analyze the relevant remotely sensed products from satellites, radars and ground measurements to compute the transported water mass for each complete Strahler stream using an 'assimilated water balance equation' at daily and other appropriate time scales. This objective requires analysis of concurrent data sets for Precipitation (PPT), Evapotranspiration (ET) and stream flows (Q) on river networks. To solve this major problem, our decision was to develop Hidrosig, a new Open-Source GIs software. A research group in Colombia, South America, developed the first version of Hidrosig, and Ricardo Mantilla was part of this effort as an undergraduate student before joining the graduate program at the University of Colorado in 2001. Hydrosig automatically extracts river networks from large DEMs and creates a "link-based" data structure, which is required to conduct a variety of analyses under objective 2. It is programmed in Java, which is a multi-platform programming language freely distributed by SUN under a GPL license. Some existent commercial tools like Arc-Info, RiverTools and others are not suitable for our purpose for two reasons. First, the source code is not available that is needed to build on the network data structure. Second, these tools use different programming languages that are not most versatile for our purposes. For example, RiverTools uses an IDL platform that is not very efficient for organizing diverse data sets on river networks. Hidrosig establishes a clear data organization framework that allows a simultaneous analysis of spatial fields along river network structures involving Horton- Strahler framework. Software tools for network extraction from DEMs and network-based analysis of geomorphologic and topologic variables were developed during the first year and a part of second year.

Gupta, Vijay K.

Discrete Data Transfer Technique for Fluid-Structure Interaction

This paper presents a general three-dimensional algorithm for data transfer between dissimilar meshes. The algorithm is suitable for applications of fluid-structure interaction and other high-fidelity multidisciplinary analysis and optimization. Because the algorithm is independent of the mesh topology, we can treat structured and unstructured meshes in the same manner. The algorithm is fast and accurate for transfer of scalar or vector fields between dissimilar surface meshes. The algorithm is also applicable for the integration of a scalar field (e.g., coefficients of pressure) on one mesh and injection of the resulting vectors (e.g., force vectors) onto another mesh. The author has implemented the algorithm in a C++ computer code. This paper contains a complete formulation of the algorithm with a few selected results.

Samareh, Jamshid A.

Search for triple Higgs boson production in the 6⁢𝑏 final state using 𝑝⁢𝑝 collisions at $\sqrt{s}$ = 13 TeV with the ATLAS detector

A search for the production of three Higgs bosons (𝐻⁡𝐻⁡𝐻) in the $b\bar{b}b\bar{b}b\bar{b}$ final state is presented. The search uses 126 fb −1 of proton-proton collision data at $\sqrt{s}$ =13 TeV collected with the ATLAS detector at the Large Hadron Collider. The analysis targets both nonresonant and resonant production of 𝐻⁡𝐻⁡𝐻. The resonant interpretations primarily consider a cascade decay topology of 𝑋 →𝑆⁢𝐻 → 𝐻⁡𝐻⁡𝐻 with masses of the new scalars 𝑋 and 𝑆 up to 1.5 and 1 TeV, respectively. In addition to scenarios where 𝑆 is off-shell, the nonresonant interpretation includes a search for Standard Model 𝐻⁡𝐻⁡𝐻 production, with limits on the trilinear and quartic Higgs self-coupling set. No evidence for 𝐻⁡𝐻⁡𝐻 production is observed. An upper limit of 59 fb is set, at the 95% confidence level, on the cross section for Standard Model 𝐻⁡𝐻⁡𝐻 production.

Artificial neural networks

Boundary Representation Tolerance Impacts on Mesh Generation and Adaptation

The control of discretization error is critical to obtaining reliable simulation results. Re-cent progress has matured anisotropic mesh adaptation, which automates discretization error control for complex geometries. However, the meshing process can fail when geometric model Boundary REPresentation (BREP) tolerances are larger than boundary layer surface nor-mal and tangential spacing requirements. Geometry sources are often created in Mechanical Computer-Aided Design (MCAD) systems, which are designed to produce models for manufacturing and not the stricter requirements of viscous flow analysis. BREP tolerances are strained by three factors: the inherent complexity of the model (e.g., large range of scales and complex topology), the numerical difficulties arising from surface/surface intersections, and the omission of crucial data during export and translation. Manual preparation of geometry is commonly employed to enable expert-guided mesh generation, which severely inhibits work-flow automation. Accommodation of loose BREP tolerances is required for automated mesh processes, because barrier issues may not be detected until well into the solution process. To raise awareness of this class of geometry issues and their impact on simulation, a survey of these barrier issues is presented with example mitigation techniques. This awareness may also impact geometry creation workflows to prevent the introduction of these artifacts.

CAD

Magnetic contribution of itinerant electrons to neutron diffraction in the topological antiferromagnet CeAlGe

We report a neutron diffraction study of the magnetic structure of CeAlGe, a candidate topological semimetal that hosts a noncollinear, multi-𝐤 magnetic phase. By measuring both low- and high-momentum-transfer magnetic Bragg peaks within a single experimental setup, we refine a magnetic structure model based solely on localized Ce moments. This model, which differs from that obtained using only high-𝑄 data, quantitatively reproduces the observed intensities, including the (000) zeroth-order magnetic satellites that are especially sensitive to subtle components of the modulation. While a contribution from itinerant electrons to the zeroth satellite cannot be definitively excluded, our analysis reveals no unambiguous evidence for such effects within experimental uncertainty. The refined magnetic structures exhibit topologically nontrivial winding patterns, derived from the fitted magnetic parameters, that support localized, particle-like spin textures with half-integer topological charges. These features provide a natural microscopic origin for the observed topological Hall effect, establishing CeAlGe as a model system where magnetism and topology are intimately linked.

Magnetic coupling

System-Level Efficiency Study of Modular DC/DC and Fuel Cell Stack Series–Parallel Configurations

This paper presents a system-level efficiency study of modular DC/DC converter and fuel cell stack configurations under series, parallel, and series–parallel connections. The investigation considers selected DC/DC converter topologies, including isolated and non-isolated architectures, boost, non-inverting buck-boost, and resonant converters, integrated with commercially available fuel cell stacks, including the Accelera FCE150, Ballard FCgen-HPS, and Toyota TFCM2. DC/DC converter modules are evaluated in modular configurations rated at 60 kW and 90 kW and two distinct output voltage ranges, specifically 580–730V and 780–930V, examining how different interconnection schemes impact overall system efficiency. The converters are evaluated under full load (100%), partial load (66%), and light load (33%) conditions, providing a comprehensive assessment of efficiency and operational characteristics across varying power demands. Approximately two-thousand efficiency data points are obtained from laboratory prototype–level component measurements and validated design evaluations across multiple converter topologies, modular configurations, voltage ranges, and load conditions, providing a robust dataset for comparative system-level efficiency analysis. The results highlight the effects of modularity and topology selection on system-level efficiency, offering a “playbook” framework for designers to select appropriate DC/DC converter arrangements and fuel cell stack connections for series, parallel, or hybrid configurations based on efficiency considerations.

DC/DC

Middleware Evaluation and Benchmarking for Use in Mission Operations Centers

Middleware technologies have been promoted as timesaving, cost-cutting alternatives to the point-to-point communication used in traditional mission operations systems. However, missions have been slow to adopt the new technology. The lack of existing middleware-based missions has given rise to uncertainty about middleware's ability to perform in an operational setting. Most mission architects are also unfamiliar with the technology and do not know the benefits and detriments to architectural choices - or even what choices are available. We will present the findings of a study that evaluated several middleware options specifically for use in a mission operations system. We will address some common misconceptions regarding the applicability of middleware-based architectures, and we will identify the design decisions and tradeoffs that must be made when choosing a middleware solution. The Middleware Comparison and Benchmark Study was conducted at NASA Goddard Space Flight Center to comprehensively evaluate candidate middleware products, compare and contrast the performance of middleware solutions with the traditional point- to-point socket approach, and assess data delivery and reliability strategies. The study focused on requirements of the Global Precipitation Measurement (GPM) mission, validating the potential use of middleware in the GPM mission ground system. The study was jointly funded by GPM and the Goddard Mission Services Evolution Center (GMSEC), a virtual organization for providing mission enabling solutions and promoting the use of appropriate new technologies for mission support. The study was broken into two phases. To perform the generic middleware benchmarking and performance analysis, a network was created with data producers and consumers passing data between themselves. The benchmark monitored the delay, throughput, and reliability of the data as the characteristics were changed. Measurements were taken under a variety of topologies, data demands, and data characteristics, using several middleware products. All results were compared to systems using traditional point-to-point socket communication. By comparing performance results under Merent settings, inferences could be made about each middleware's ability to meet certain requirements of the GPM mission. The second phase simulated a middleware-based mission operations center. Actual mission support tools were either used or simulated to create real world demands on the middleware. Network and computer demands were watched closely to verify that no specific idiosyncrasies of mission operations activities would prove unsupportable by the middleware. In our presentation, we will address some commonly accepted misconceptions concerning middleware in mission support architectures. Specifically, we will focus on the perception that middleware solutions are too slow or impose too much overhead for real-time mission operations, and that middleware solutions are too expensive for small

Antonucci, Rob

CFD analysis of turbopump volutes

An effort is underway to develop a procedure for the regular use of CFD analysis in the design of turbopump volutes. Airflow data to be taken at NASA Marshall will be used to validate the CFD code and overall procedure. Initial focus has been on preprocessing (geometry creation, translation, and grid generation). Volute geometries have been acquired electronically and imported into the CATIA CAD system and RAGGS (Rockwell Automated Grid Generation System) via the IGES standard. An initial grid topology has been identified and grids have been constructed for turbine inlet and discharge volutes. For CFD analysis of volutes to be used regularly, a procedure must be defined to meet engineering design needs in a timely manner. Thus, a compromise must be established between making geometric approximations, the selection of grid topologies, and possible CFD code enhancements. While the initial grid developed approximated the volute tongue with a zero thickness, final computations should more accurately account for the geometry in this region. Additionally, grid topologies will be explored to minimize skewness and high aspect ratio cells that can affect solution accuracy and slow code convergence. Finally, as appropriate, code modifications will be made to allow for new grid topologies in an effort to expedite the overall CFD analysis process.

Ascoli, Edward P.

Search for 𝛾⁢𝐻 production and constraints on the Yukawa couplings of light quarks to the Higgs boson

A search for 𝛾⁢𝐻 production is performed with data from the CMS experiment at the LHC corresponding to an integrated luminosity of 138 fb −1 at a proton-proton center-of-mass collision energy of 13 TeV. The analysis focuses on the topology of a boosted Higgs boson recoiling against a high-energy photon. The final states of 𝐻 → $b\bar{b}$ and 𝐻 → 4⁢ℓ are analyzed. This study examines effective 𝐻⁡𝑍⁢𝛾 and 𝐻⁡𝛾⁢𝛾 anomalous couplings within the context of an effective field theory. In this approach, the production cross section is constrained to be 𝜎 𝛾⁢𝐻 < 16.4 fb at 95% confidence level (CL). Simultaneous constraints on four anomalous couplings involving 𝐻⁡𝑍⁢𝛾 and 𝐻⁡𝛾⁢𝛾 are provided. Additionally, the production rate for 𝐻 → 4⁢ℓ is examined to assess potential enhancements in the Yukawa couplings between light quarks and the Higgs boson. Assuming the standard model values for the Yukawa couplings of the bottom and top quarks, the following simultaneous constraints are obtained: 𝜅 𝑢 =(0.0 ± 1.5) ×10 3 , 𝜅 𝑑 = (0.0$^{+6.7}_{−6.8}$) × 10 2 , 𝜅 𝑠 = 0$^{+30}_{−32}$, and 𝜅 𝑐 =0.0$^{+2.3}_{−2.8}$. This rules out the hypothesis that up- or down-type quarks in the first or second generation have the same Yukawa couplings as those in the third generation, with a CL greater than 95%.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS

Intermolecular Interactions in Direct Air Capture Materials: Insights from Charge Density Analysis

Direct air capture (DAC) materials enable the removal of CO 2 from the atmosphere, but improving their efficiency requires a detailed understanding of the intermolecular interactions that govern CO 2 sorption and release. Here, we present an experimental electron density study of methylglyoxal-bis(iminoguanidine) (MGBIG), a promising DAC material, using high-resolution X-ray and neutron diffraction data combined with quantum crystallographic analysis. This approach bridges theoretical and experimental data by quantifying electron density distributions and revealing how hydrogen bonds stabilize CO 2 -derived carbonate phases and may influence the desorption behavior. We identify distinct hydrogen-bonding environments in two crystalline carbonate phases: P1, a transient kinetic product, and P3, a thermodynamically stable phase. Multipolar refinement and electrostatic potential and multipole moment calculations precisely map electron density distributions, revealing key hydrogen bonds involved in CO 2 capture. Topological analysis of electron density highlights a cooperative hydrogen-bonding network in the thermodynamically favored P3 phase, where enhanced electron density delocalization and water-mediated interactions contribute to a more stable lattice. Energetic analyses confirm that stronger hydrogen bonding networks enhance the stability of P3 with a binding energy of −607.0 kJ/mol and greater lattice stability (−847.3 kJ/mol) compared to P1 (−302.5 and −571.0 kJ/mol, respectively). Electrostatic potential maps further illustrate polarization patterns that may influence the stability of the binding of CO 2 and release conditions. These findings establish a direct experimental framework for linking electron density distributions to intermolecular interactions in DAC materials, providing a rational design strategy for optimizing sorbents with improved CO 2 capture efficiency and reduced energy demands.

Electron density

A First Search for Argon-Bound Neutron-Antineutron Oscillation using the MicroBooNE LArTPC

The use of Liquid Argon Time Projection Chambers (LArTPCs) as a detector technology in neutrino experiments has grown considerably over the past two decades. The excellent spatial and calorimetric resolution offered by LArTPCs enable precise neutrino oscillation measurements as well as beyond-Standard Model searches. One such search, which is the focus of this note, is the search for nucleus-bound neutron-antineutron (n ₋ n̄) oscillation. The n ₋ n̄ oscillation process is a baryon number violating process that produces a unique, star-like topology as a result of multiple final state pions. This unique signature is a key feature that may be used to search for this signal process. This note describes a machine learning-based analysis of MicroBooNE data, making use of a sparse convolutional neural network to search for n ₋ n̄ oscillation-like signals in MicroBooNE. While the future DUNE LArTPC can search for this signature with high sensitivity, existing MicroBooNE data can be used to demonstrate and validate methodologies that can be used as part of the DUNE search. This document presents the first-ever search for n ₋ n̄ oscillation in a LArTPC, using MicroBooNE off-beam data (data collected when the neutrino beam was not running).

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS